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Physics
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Experimental Condensed Matter Physics
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MCQ
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Ionization and temperature measurements in warm dense copper using x-ray absorption spectroscopy.
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https://arxiv.org/abs/2509.13272
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September 16, 2025
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Researchers investigated the ionization and temperature of warm dense copper (Cu) using X-ray absorption spectroscopy (XAS) at the OMEGA Laser Facility to characterize plasmas at several times solid density. The experimental configuration consists of a planar target and a separate backlighter positioned 3 mm away. A series of 60 laser beams, delivering 3.4–5.4 kJ per side of 351 nm light, and the achieved laser intensity is 161 - 770 TW/cm2 over the three pulse length configurations, was symmetrically focused onto a planar buried-layer target composed of 125 μm CH ablators enclosing a 10 μm-thick Cu foil (8.96 g/cm3 solid density) with a 500 µm diameter, surrounded by an Au washer. The laser spot (≈approximately 880 μm diameter) was smoothed with distributed phase plates and spectral dispersion to generate uniform counter-propagating shocks. A 6 μm Ge backlighter foil, coated on graphite and irradiated with six additional beams (≈1.2 kJ, 500 ps pulse), is produced at a spot diameter of 140 μm. The transmitted x-rays were recorded using the EFX flat-crystal spectrometer (Si 111) over the 6.3–11.4 keV range on an image plate with Mn, Fe, and W filters serving as fiducial markers. Shock timing and planarity, as well as shock break-in and break-out of the Cu layer, were verified through a line-imaging VISAR system and a streaked optical pyrometer (SOP) on one-sided targets, ensuring symmetric compression and precise backlighter synchronization. 3 VISAR measurement is done with 1 ns, 2 ns, or 3 ns square pulses using 14 beams per side, respectively. Each measurement has two VISAR channels with different sensitivities; one leg was set with 33.66 µm/ns/fringe, and the second with 13.538 µm/ns/fringe.
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- Shock breakout times (in ns) and planarity were measured with the VISAR system.
- Shock velocity time history as a function of position across the target measured with the VISAR system.
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An investigation into shock breakout times and shock velocity time histories as a function of position across the target of warm dense copper (Cu) plasma is conducted using a VISAR system. The experimental configuration consists of a planar target and a separate backlighter positioned 3 mm away. A series of 60 laser beams was symmetrically focused onto a planar buried-layer target surrounded by an Au washer. The laser spot was smoothed with distributed phase plates and spectral dispersion to generate uniform counter-propagating shocks, compressing the Cu layer. A Ge backlighter foil, coated on graphite and irradiated with six additional beams, is produced. The transmitted X-rays were also recorded using the EFX flat-crystal spectrometer. Which behavior is most likely observed?
a) Shocks were non-planar over the target region, and warm dense copper shows Ionization Potential Depression (IPD).
b) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
c) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features red shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
d) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of the K-edge relative to the cold edge, but no shift for the bound-bound resonance 1s→3p absorption.
|
b) Shocks were highly planar over the target region, and the absorption spectra of warm dense copper features blue shift of both the K-edge and the bound-bound resonance 1s→3p absorption relative to the cold edge.
|
- Generating warm dense matter in the laboratory often involves significant temporal and spatial gradients that complicate the analysis of experimental observables. Incorporating gradients in the analysis of experimental data, while possible, increases the uncertainties in the inferred plasma conditions.
- At these high-density conditions, the measured Cu K-edge exhibits sensitivity to the electron temperature, allowing for a direct inference of the temperature from the slope of the Cu K-edge.
- Temperature sensitivity of the K-edge can still be the dominant edge effect, in general, as the temperature nears the Fermi energy, the K-edge shape of the non-degenerate material becomes unsuitable as a temperature inference.
|
[{"label":"RBK Item","value":"Generating WDM in the laboratory often involves significant temporal and spatial gradients that complicate the analysis of experimental observables. Incorporating gradients in the analysis of experimental data, while possible, increases the uncertainties in the inferred plasma conditions. "},{"label":"Title","value":"Quantifying electron temperature distributions from time-integrated x-ray emission spectra"},{"label":"URL","value":"https://pubs.aip.org/aip/rsi/article-abstract/93/9/093517/2849062/Quantifying-electron-temperature-distributions?redirectedFrom=fulltext"},{"label":"Date","value":"Sep 26, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 7 in the paper"},{"label":"RBK Item","value":"Temperature sensitivity of the K-edge can still be the dominant edge effect, in general, as the temperature nears the Fermi energy, the K-edge shape of the non-degenerate material becomes unsuitable as a temperature inference."},{"label":"Title","value":"X-ray absorption 𝐾 edge as a diagnostic of the electronic temperature in warm dense aluminum"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.92.085117"},{"label":"Date","value":"Aug 10, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled, but this is cited as reference 10 in the paper"}]
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Biology
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Neurobiology, Animal Behavior and Cognition.
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Free-Format Question
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Dopamine induces fear extinction by activating the reward-responding amygdala neurons
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12067255/
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April 28, 2025.
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Researchers tested whether ventral tegmental area (VTA) dopamine signaling in the basolateral amygdala (BLA) drives fear extinction by acting on reward-responding posterior BLA (pBLA) neurons versus fear-coding anterior BLA (aBLA) neurons, using adult mice (DAT-IRES-Cre; EYFP controls; subtype mapping with Rspo2-Cre for aBLA and Ppp1r1b/Cartpt-Cre for pBLA). DAT-Cre mice received bilateral VTA injections of Cre-dependent ChR2-EYFP (activation) or eNpHR3.0-EYFP (inhibition); controls received EYFP; optic fibers were implanted over pBLA or aBLA to manipulate VTA→BLA terminals. Training: Day 1 contextual fear conditioning (baseline ~3 min, then 3 footshocks, 0.60 mA, 2 s); Day 2 45-min extinction (no shocks); Day 3 10-min retrieval. Intervention (extinction only): starting 5 min into extinction, deliver 8 cycles of 3-min light separated by 2-min no-light (activation: blue 450–470 nm, 8–12 mW, 20 Hz pulses; inhibition: green 520–550 nm, 8–12 mW, continuous) with fibers targeted to pBLA or aBLA. Behavior videos were recorded with VideoFreeze software and freezing level was scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68). Freezing was quantified in 5-min bins across extinction and again during retrieval.
|
- Extinction learning: Percent freezing per 5-min bin across the 45-min Day 2 session (9 bins). Scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68).
- Extinction memory: Percent freezing during the Day 3 retrieval test (10 min). Scored manually by experimenters who were blinded to conditions or automatically with DeepLabCut behavior analysis toolbox and custom Python code (68).
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Mice underwent contextual fear conditioning (Day 1: context + three 0.60 mA, 2 s shocks), 45-min extinction (Day 2, no shocks), and 10-min retrieval (Day 3). During extinction, VTA dopamine terminals in pBLA (Ppp1r1b⁺) or aBLA (Rspo2⁺) were optogenetically manipulated beginning 5 min into the session using 8 cycles of 3 min light separated by 2 min: activation (blue 450–470 nm, 8–12 mW, 20 Hz) or inhibition (green 520–550 nm, 8–12 mW, constant). Freezing was binned in 5-min windows across extinction and measured again at retrieval. How do these projection-specific manipulations (activation and inhibition of VTA dopamine terminals in the pBLA and in aBLA) affect fear extinction and retrieval compared with EYFP controls?
|
Activation of VTA dopamine terminals in the pBLA promotes faster extinction and improved retrieval, indicating an enhancement of extinction learning. In contrast, inhibition of pBLA dopamine input impairs both extinction and retrieval. Activation of VTA terminals in the aBLA leads to increased freezing later in extinction and poorer retrieval performance, suggesting interference with extinction memory formation, while inhibition of aBLA terminals produces no reliable behavioral change.
|
- Fear extinction is a form of new learning that allows for the adaptive control of fear behaviors and is commonly studied using Pavlovian conditioning tasks.
- aBLA Rspo+ neurons encode negative valence and drive aversive behaviors whereas pBLA Ppp1r1b+ neurons encode positive valence and drive appetitive behaviors.
- VTA dopamine as a teaching signal: DA activity to shock omission can initiate extinction learning and is required for extinction.
- Terminal activation (ChR2, blue, pulsed) vs inhibition (eNpHR3.0, green, constant) at BLA terminals tests sufficiency/necessity of VTA→BLA pathways.
- Freezing is the behavioral measure; decreases across 5-minute bins and at retrieval indicate successful extinction.
|
[{"label":"RBK Item","value":"Fear extinction is a form of new learning that allows for the adaptive control of fear behaviors and is commonly studied using Pavlovian conditioning tasks."},{"label":"Title","value":"Conditioned reflexes: An investigation of the physiological activity of the cerebral cortex"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC4116985/"},{"label":"Date","value":"Jul, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"aBLA Rspo+ neurons encode negative valence and drive aversive behaviors whereas pBLA Ppp1r1b+ neurons encode positive valence and drive appetitive behaviors."},{"label":"Title","value":"Antagonistic negative and positive neurons of the basolateral amygdala"},{"label":"URL","value":"https://www.nature.com/articles/nn.4414"},{"label":"Date","value":"Oct 17, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"VTA dopamine as a teaching signal: DA activity to shock omission can initiate extinction learning and is required for extinction."},{"label":"Title","value":"A dopaminergic switch for fear to safety transitions"},{"label":"URL","value":"https://www.nature.com/articles/s41467-018-04784-7"},{"label":"Date","value":"Jun 27, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Biology
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Physiology
|
Free-Format Question
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Effect of combined Respiratory Muscle Training on Sleep and
Cardiovascular Biometrics in a non-clinical cohort
|
https://www.biorxiv.org/content/10.1101/2025.06.27.661934v1
|
July 1, 2025
|
This prospective study investigated the effects of combined inspiratory and expiratory RMT (cRMT) on sleep parameters and cardiovascular biometrics, specifically heart rate variability (HRV), in a non-clinical adult cohort. Utilizing a wearable device for remote data collection, this randomized controlled trial included 67 participants divided into good and poor sleeper groups based on historical sleep data. Participants were selected from existing users of the Biostrap EVO (Biostrap LLC) wearable device. Participants were selected into two sub-samples based on their historical sleep characteristics.
Participants who met the following criteria based on historical Biostrap data were considered good sleepers (n = 44): less than five awakenings per night, an average sleep score >70 out of 100, and an average sleep SpO2 of >96 24. The sleep score was determined from factors including total sleep duration,
minutes of deep sleep (estimated), number of involuntary awakenings, relative HR compared to an individual's rolling 30 day average, and absolute number of low SpO2 readings with bins of 90-95, 80 to 89, and below 80 representing specific penalties. This gives a gross sleep score that is then corrected
based on sleep efficiency, calculated as the total time asleep relative to the time in bed with a 5% buffer (no penalty). The remaining participants who did not meet these criteria were considered poor sleepers (n= 23). Within each subsample, participants were randomized into control and intervention groups. All participants signed a written informed consent form prior to participating in the study.
All participants completed a one-week baseline phase, during which participants were required to wear their wrist-worn Biostrap wearable device each night while sleeping. Following the baseline phase, all participants completed a five-week experimental phase including combined inspiratory and expiratory combined RMT (cRMT). Participants randomized to the intervention group (n = 29) were required to use the Breather Fit (PN Medical, FL, USA), an cRMT device. The device provides adjustable resistance during inhale and exhale for strengthening the inspiratory and expiratory muscle groups. The training protocol included three sets of 10 breaths, twice per day on six days of the week. The target intensity of cRMT was 70% of maximum effort and those in the intervention group were supplied with an instructional
video on cRMT and device care. Participants of the control group (n = 38) received no respiratory exercise. All participants were required to continue wearing the Biostrap EVO device throughout the experimental phase. Lastly, all participants completed a one-week washout phase, during which they
continued wearing the Biostrap device but ceased using the RMT device.
|
-Measurement of sleep parameters and cardiovascular biometrics of the participants.
- Heart rate variability (HRV) in participants in the intervention and control groups.
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During a five-week intervention period, participants in the intervention group underwent cRMT using a Breather Fit device, while control group participants did not receive the intervention. What would you expect to happen in terms of heart rate variability and sleep parameters between the participants in intervention and control groups?
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Study findings demonstrated a significant increase in overnight HRV metrics during the intervention period compared to the baseline, indicating improved autonomic cardiac function. However, no significant changes were observed in any parameters of sleep quality.
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-Insufficient sleep has various short- and long-term consequences, including an elevated risk of cardiovascular and metabolic diseases.
-Previous research has demonstrated that resistive respiratory muscle training (RMT) can enhance both sleep quality and cardiovascular health in individuals diagnosed with obstructive sleep apnea, underscoring its efficacy as a non-pharmacological
therapeutic strategy for this patient group.
-Sleep-breathing disorders such as obstructive sleep apnea (OSA) increase the incidence of major adverse events in patients with
cardiovascular disease.
-Given the intricate relationship between sleep-breathing disorders and cardiovascular health, heart rate variability (HRV) emerges as a critical non-invasive biomarker for assessing the autonomic nervous
system’s response to these conditions.
-HRV is the variation or irregularity in duration of beat-to-beat or interbeat intervals.
|
[{"label":"RBK Item","value":"-Insufficient sleep has various short- and long-term consequences, including an elevated risk of cardiovascular and metabolic diseases. "},{"label":"Title","value":"Short- and long-term health consequences of sleep disruption"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/28579842/"},{"label":"Date","value":"May 19, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Previous research has demonstrated that resistive respiratory muscle training (RMT) can enhance both sleep quality and cardiovascular health in individuals diagnosed with obstructive sleep apnea, underscoring its efficacy as a non-pharmacological therapeutic strategy for this patient group. "},{"label":"Title","value":"Effects of inspiratory muscle training in patients with obstructive sleep apnoea syndrome: a systematic review and meta-analysis"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/36419804/"},{"label":"Date","value":"Dec 1, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Sleep-breathing disorders such as obstructive sleep apnea (OSA) increase the incidence of major adverse events in patients with cardiovascular disease."},{"label":"Title","value":"A systematic review on the association of sleep-disordered breathing with cardiovascular pathology in adults"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/36253378/\n"},{"label":"Date","value":"Oct 17, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-Given the intricate relationship between sleep-breathing disorders and cardiovascular health, heart rate variability (HRV) emerges as a critical non-invasive biomarker for assessing the autonomic nervous system’s response to these conditions. "},{"label":"Title","value":"An Overview of Heart Rate Variability Metrics and Norms"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/29034226/ "},{"label":"Date","value":"Sep 28, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"-HRV is the variation or irregularity in duration of beat-to-beat or interbeat intervals."},{"label":"Title","value":"A healthy heart is not a metronome: an integrative review of the heart's anatomy and heart rate variability"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25324790/"},{"label":"Date","value":"Sep 30, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Organic Chemistry
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Free-Format Question
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Total Synthesis of Eudesmanolides Alantolactone, Isoalantodiene, Alloalantolactone, and 5α,6α-Epoxyalantolactone
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https://chemrxiv.org/engage/chemrxiv/article-details/68a9905d23be8e43d6a01501
|
August 29, 2025
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To a flamed dried round-bottomed flask was added thiourea Jacobsen's organocatalyst (40.0 mg, 0.104 mmol, 5 mol%), 1-(4-Bromofuran-2-yl)-5-methylhex-5-en-1-one
(0.535 g, 2.08 mmol, 1 equiv) and CH₂Cl₂ (4.2 mL, 0.5 M). The reaction flask was cooled to –78 °C in an acetone/dry ice bath, and TMSCN (0.57 mL, 4.56 mmol, 2.22 equiv) was added dropwise. The reaction was stirred for 15 min at the same temperature and 2,2,2-trifluoroethanol (0.16 mL, 2.12 mmol, 1 equiv) was then added to the reaction flask. The mixture was stirred for 4 days at –78 °C using a cryocooler. After warming to rt the reaction was concentrated in vacuo, and the yellow oil obtained in this manner was purified by silica gel flash column chromatography (eluting with 5% Et₂O/hexanes) to yield the title compound (22, 0.50 g, 67%) as a clear, colorless oil.
The enantiomers of the product could not be resolved by chiral GC or SFC analyses. Consequently, the researchers advanced the material to stereoselective IMDAF and desilylation, where these products were resolvable by chiral SFC analysis.
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- Yield of the enantiomeric mixture using NMR.
- Enantiomeric excess determined by chiral SFC analysis
|
1-(4-bromofuran-2-yl)-5-methylhex-5-en-1-one was reacted with TMSCN (excess) and Jacobsen's thiourea catalyst (5 mol%) in CH₂Cl₂ at -78 °C for 4 d. What is the name of the product obtained?
|
2-(4-bromofuran-2-yl)-6-methyl-2-((trimethylsilyl)oxy)hept-6-enenitrile
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- Ketones can be enantioselectively cyanosilylated in the presence of Jacobsen's thiourea catalyst and TMSCN
-Alantolactone and isoalantolactone, members of the eudesmanolide class of
sesquiterpenoid lactones, have been extensively investigated for their pharmacological function
|
[{"label":"RBK Item","value":"Ketones can be enantioselectively cyanosilylated in the presence of Jacobsen's thiourea catalyst and TMSCN."},{"label":"Title","value":"Thiourea-Catalyzed Enantioselective Cyanosilylation of Ketones"},{"label":"URL","value":"https://pubs.acs.org/doi/10.1021/ja052511x"},{"label":"Date","value":"June 4, 2005"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled "},{"label":"RBK Item","value":"Alantolactone and isoalantolactone, members of the eudesmanolide class of\nsesquiterpenoid lactones, have been extensively investigated for their pharmacological function"},{"label":"Title","value":"Alantolactone: A Natural Plant Extract as a Potential Therapeutic Agent for Cancer"},{"label":"URL","value":"https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2021.781033/full"},{"label":"Date","value":"November 25, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Alantolactone and isoalantolactone, members of the eudesmanolide class of\nsesquiterpenoid lactones, have been extensively investigated for their pharmacological function"},{"label":"Title","value":"Isoalantolactone: a review on its pharmacological effects"},{"label":"URL","value":"https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1453205/full"},{"label":"Date","value":"September 22, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
Physics
|
Spintronics
|
MCQ
|
Enhanced Spin Pumping and Magnetization dynamics in Ni_80Fe_20/MoS_2 stack via interface modification
|
https://arxiv.org/abs/2505.09248
|
May 14, 2025
|
An experiment is conducted to investigate the magnetization dynamics at the interface of a spintronic heterostructure. A thin film of Permalloy ($Ni_{80}Fe_{20}$, or Py) with a thickness of 5 nm is deposited via DC magnetron sputtering onto a silicon substrate ($Si/SiO_{2}$) that is covered by a monolayer of molybdenum disulfide ($ML-MoS_{2}$). For comparison, a reference sample of 5 nm Py is also deposited directly onto a bare $Si/SiO_{2}$ substrate. The quality and thickness of the deposited layers are confirmed via X-ray reflectivity (XRR) using a Rigaku X-ray diffractometer. The dynamic magnetic properties of the samples are then characterized at room temperature using broadband ferromagnetic resonance (FMR) spectroscopy, where the derivative of the microwave absorption is measured as a function of an in-plane applied DC magnetic field. These measurements were conducted at room temperature using a lock-in-based broadband FMR setup (NanOsc). The spectra were recorded at a microwave frequency of 11 GHz.
|
- Ferromagnetic resonance (FMR) spectra showing the derivative of microwave absorption (dI/dH) as a function of the in-plane DC magnetic field ($H_{DC}$) for the reference Py (5 nm) and ML-MoS_{2}/Py (5 nm) sample.
|
An experiment compares the ferromagnetic resonance (FMR) spectrum of a 5 nm Permalloy (Py) film deposited on a bare silicon substrate with an identical Py film deposited on a silicon substrate covered by a monolayer of $MoS_{2}$. Based on the principles of magnetization dynamics, what is the most likely shape of the FMR spectrum for the Py film deposited on the monolayer $MoS_{2}$?
A) The spectrum exhibits two distinct resonance peaks, as the discontinuous, island-like MoS_{2} underlayer creates two different magnetic environments.
B) The spectrum shows a single resonance peak that is significantly broadened compared to the reference sample, due to increased Gilbert damping from spin pumping into the $MoS_{2}$ layer.
C) The spectrum shows a single resonance peak that is shifted to a lower magnetic field compared to the reference sample, caused by a change in the interfacial anisotropy.
D) The spectrum shows a single resonance peak that is significantly sharper and narrower than the reference sample, as the two-dimensional nature of the $MoS_{2}$ interface reduces magnetic inhomogeneities.
|
A) The spectrum exhibits two distinct resonance peaks, as the discontinuous, island-like MoS_{2} underlayer creates two different magnetic environments.
|
- Pure spin currents can be generated via spin pumping on material interfaces.
- Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena.
- Gilbert damping can be enhanced at material interfaces.
- The intrinsic FMR linewidth for conduction electrons arises from spin-orbit coupling.
|
[{"label":"RBK Item","value":"Pure spin currents can be generated via spin pumping on material interfaces.\n"},{"label":"Title","value":"Spin pumping and magnetization dynamics in metallic multilayers"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.66.224403"},{"label":"Date","value":"December 5, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 7)."},{"label":"RBK Item","value":"Pure spin currents can be generated via spin pumping on material interfaces."},{"label":"Title","value":"Nonlocal magnetization dynamics in ferromagnetic heterostructures"},{"label":"URL","value":"https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.77.1375"},{"label":"Date","value":"December 1, 2005"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 6)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Atomically Thin MoS₂: A New Direct-Gap Semiconductor"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.105.136805"},{"label":"Date","value":"September 24, 2010 "},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 12)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Giant spin-orbit-induced spin splitting in two-dimensional transition-metal dichalcogenide semiconductors"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevB.84.153402"},{"label":"Date","value":"October 14, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 13)."},{"label":"RBK Item","value":"Two dimensional (2D) semiconducting layered transition metal dichalcogenides (TMDs) have unique electronic band structures, valley effects, strong spin orbit coupling, and broken inversion symmetry, which enable distinct charge and spin transport phenomena."},{"label":"Title","value":"Control of valley polarization in monolayer MoS2 by optical helicity"},{"label":"URL","value":" https://doi.org/10.1038/nnano.2012.96"},{"label":"Date","value":"June 17, 2012 "},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 14)."},{"label":"RBK Item","value":"Gilbert damping can be enhanced at material interfaces."},{"label":"Title","value":"Study of fully epitaxial Fe/Pt bilayers for spin pumping by ferromagnetic resonance spectroscopy"},{"label":"URL","value":"https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.134405"},{"label":"Date","value":"April 5, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 41)."},{"label":"RBK Item","value":"The intrinsic FMR linewidth for conduction electrons arises from spin-orbit coupling."},{"label":"Title","value":"Origin of Intrinsic Gilbert Damping"},{"label":"URL","value":"https://doi.org/10.1103/PhysRevLett.102.137601"},{"label":"Date","value":"March 31, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"No OA version available; paywalled source is the canonical reference for this RBK item. This paper is used as a reference in the main paper (Reference 38)."}]
|
Chemistry
|
Archaeological chemistry
|
MCQ
|
Adjacent radiocarbon dating of Iron Age site foundation
|
https://chemrxiv.org/engage/chemrxiv/article-details/682ec5413ba0887c3332b980
|
May 28, 2025
|
Researchers have developed a chemical procedure for radiocarbon dating metal archaeological samples. A total of six samples from the iconic Iron Age site Creney-le-Paradis were analysed, all consisting of fibres extracted from mineralised textiles still in contact with a bronze substrate. The conversion of the samples to CO2 took place in sealed quartz tubes under vacuum (l = 16 cm, 0.8 cm diameter; Möller, Switzerland) and heated to 643 K for 30 min in a muffle furnace (SOLO Industrieöfen GmbH, Biel, Switzerland). After the combustion process, CO2 is purified in a dedicated vacuum line for cryo-trapping. Water is trapped in a Peltier module cooled to 248 K, while carbon dioxide is trapped in a calibrated volume cold finger fitted with a pressure sensor and cooled to 78 K with liquid nitrogen. The latter is finally transferred, frozen, and flame-sealed in a borosilicate tube cooled with a liquid nitrogen trap. 14C measurement of the purified CO2 fraction, corresponding to the mineral carbon in the carbonates, is carried out via a gas interface system (GIS) coupled to the accelerator mass spectrometer (AMS). The black solid residue left in the broken glass ampoule is treated with 1-M HCl, ensuring the removal of other carbonate contamination. The dried solid residue is packed in an aluminum boat and its 14C content is measured by direct combustion in an elemental analyzer (EA) coupled to the AMS. All radiocarbon measurements were performed on the compact Mini Carbon Dating System (MICADAS) at the Laboratory of Ion Beam Physics, ETH Zurich, Switzerland.
|
• Stable isotope ratios expressed as δ13C in ‰ units.
• Radiocarbon ages expressed in BP years units.
• Calendar ages expressed in BC years units.
|
Researchers have developed a chemical procedure for radiocarbon dating metallic archaeological samples. A total of six samples from the iconic Iron Age site Creney-le-Paradis were analysed, all consisting of fibres extracted from mineralised textiles still in contact with the bronze substrate. Two CO2 fractions were obtained by both thermal decomposition of copper carbonates and combustion of the remaining solid organic residue, if any. Then, the CO2 fractions were assessed by AMS, and their respective 13C/12C ratios were measured by IRMS. Radiocarbon ages were calibrated using Oxcal v.4.4 software with the Intcal20 atmospheric curve. Mark all the correct options.
A. The mean radiocarbon age is 2619 ± 11 yr BP, and the calendar age is 808-790 BC.
B. The calendar age is 2619 ± 11 yr BC, and the mean radiocarbon age is 808-790 BP.
C. δ13C values range from −27 to -22‰.
D. δ13C values range from −22 to −17‰.
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A. The mean radiocarbon age is 2619 ± 11 yr BP, and the calendar age is 808-790 BC.
D. δ13C values range from −22 to −17‰.
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• The advent of accelerator mass spectrometers (AMS) allows the number of 14C atoms to be measured relative to the number of 12C atoms.
• 13C/12C isotope ratio can be expressed as a δ13C value, which indicates the possible origin of the dated carbon fraction.
|
[{"label":"RBK Item","value":"The advent of accelerator mass spectrometers (AMS) allows the number of 14C atoms to be measured relative to the number of 12C atoms."},{"label":"Title","value":"Carbon-14: Direct Detection at Natural Concentrations"},{"label":"URL","value":"https://www.science.org/doi/10.1126/science.198.4316.507"},{"label":"Date","value":"November 4, 1977"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"13C/12C isotope ratio can be expressed as a δ13C value, which indicates the possible origin of the dated carbon fraction. "},{"label":"Title","value":"STABLE ISOTOPES IN ECOSYSTEM STUDIES"},{"label":"URL","value":"https://www.annualreviews.org/content/journals/10.1146/annurev.es.18.110187.001453"},{"label":"Date","value":"November 1, 1987"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Physics
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Applied physics, thermodynamics, mechanical engineering, energy and transport.
|
MCQ
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Reducing Temperature Swing and Rectifying Radiative Heat Transfer for Passive Dynamic Space Thermal Control with Variable-Emittance Coatings
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https://arxiv.org/abs/2509.13794
|
Sep 17, 2025
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Tunable VO2-based Fabry-Pérot (VO2FP) variable-emittance coating made of 55-nm VO2, 500-nm silicon, and 200-nm aluminum thin films was fabricated on a double-side polished silicon wafer via thin film sputtering. Black Actar and highly reflective tungsten mirrors are used to calibrate the parasitic head load and heat flux sensor sensitivity. With the cold finger at 80 K to mimic external radiative scenarios in space. A tungsten mirror was fabricated by sputtering 200-nm-thick tungsten at a rate of 0.15 nm/s onto a polished silicon wafer. Double-sided, polished silicon wafers, 280 µm thick, with various doping levels, were commercially purchased with different resistivities. A freshly deposited aluminum mirror was used as the reference. A commercial black Actar sample was attached to a polished silicon wafer with thermal paste. The spectral reflectance of these static-emittance samples was measured at a temperature of 25°C. The radiative thermal tests were conducted under high vacuum (<10^ (-3) Pa) inside a cryostat (Janis VPF-800) equipped with a cold finger and a custom-made sample mount. A test sample, along with a heat flux sensor (FluxTeq, PHFS-01) of ±5% accuracy and a polyimide thin-film heater (OMEGA Engineering, KHLVA-101/10-P), was first attached to a 5-mm-thick acrylic carrier plate of 1-inch square size. After the acrylic carrier plate was pinned onto the brackets with approximately 2 mm spacing between the sample and the cold finger, the cryostat was then brought down to high vacuum, followed by the filling of liquid nitrogen (LN2) to cool the cold finger to 80 K, which simulates the cold space thermal environment. A Fourier transform infrared spectrometer (Thermo Fisher Scientific, iS50) along with a variable-angle reflection accessory (Harrick Scientific, Seagull) was used to measure the spectral specular reflectance at 10° incidence angle in the wavelength range from 2 µm to 22 µm at a resolution of 4 cm-1 with each spectrum averaged over 32 scans. Spectral measurements were taken twice, once during the heating cycle and once during the cooling cycle, over the range of 27 °C to 91 °C. After each temperature reached the set point for 5 minutes, with a fluctuation of less than 1 °C, measurements were taken.
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- Spectral infrared reflectance (in %) measured against wavelength from 2 μm to 22 μm on a tunable VO₂FP variable-emittance coating in the heating cycle from 27 °C to 91 °C.
- Spectral infrared reflectance (in %) measured against wavelength from 2 μm to 22 μm on a tunable VO₂FP variable-emittance coating in the cooling cycle from 27 °C to 91 °C.
|
A tunable VO2-based Fabry-Pérot (VO2FP) variable-emittance coating, composed of VO2 and aluminum thin films, was fabricated on a double-sided polished silicon wafer via thin-film sputtering. A Fourier transform infrared spectrometer, along with a variable-angle reflection accessory (Harrick Scientific, Seagull), was used to measure the spectral specular reflectance at 10° incidence angle in the wavelength range from 2 μm to 22 μm. Predict which statements accurately describe the behavior of spectral infrared reflectance and emittance for the tunable VO₂FP emitter across heating and cooling cycles?
a) A high reflection dip around 19 - 21 μm wavelength and reflectance increases as the temperature decreases.
b) A high reflection dip around 19 - 21 μm wavelength and reflectance decreases as the temperature decreases.
c) A law reflecting a dip around 6 - 9 μm wavelength and reflectance decreases as the temperature decreases.
d) A law reflecting a dip around 6 - 9 μm wavelength and reflectance increases as the temperature decreases.
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d) A law reflecting a dip around 6 - 9 μm wavelength and reflectance increases as the temperature decreases.
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-Slight angular dependence of the total emittance for the VO2FP emitter at the metallic phase due to the nature of wave interference when FP resonance is excited; therefore, the total hemispherical emittance of the VO2FP emitter in the metallic phase is reduced by 10% from the total normal emittance, while it remains the same in the insulating phase without excitation of FP resonance.
- The undoped and medium-doped silicon samples have almost the same total hemispherical emittance with the tunable VO2FP emitter in its insulating and metallic phase, respectively.
|
[{"label":"RBK Item","value":"Slight angular dependence of the total emittance for the VO2FP emitter at the metallic phase due to the nature of wave interference when FP resonance is excited; therefore, the total hemispherical emittance of the VO2FP emitter in the metallic phase is reduced by 10% from the total normal emittance, while it remains the same in the insulating phase without excitation of FP resonance. "},{"label":"Title","value":"Vanadium dioxide based Fabry-Perot emitter for dynamic radiative cooling applications"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/pii/S002240731630574X?casa_token=Txf3yLnmKmQAAAAA:55GKPd5JdT7D7ILEzEajIolvZqK_C8PY5yy89APKv-c-DVpbM_TW7gQLTo6fwz_pKZ5uoj09z1kt"},{"label":"Date","value":"Aug, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Open-access, this is cited as reference 13 in the paper"}]
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Biology
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Biology/ Microbiology
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Free-Format Question
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Early Pregnancy Marks Significant Shifts in the Oral Microbiome
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https://www.biorxiv.org/content/10.1101/2025.09.29.679276v2
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November 5, 2025
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To analyze the development of the oral microbiome during pregnancy, the researchers recruited an Israeli cohort of pregnant women sampled during T1, T2, and T3. A total of 346 Israeli women were recruited, and 467 oral microbiome samples were processed: 235 from T1 (11-14 gestational weeks), 144 from T2 (24-28 gestational weeks), and 88 from T3 (32-38 gestational weeks). At recruitment, the height and current weight of the study participants were recorded, and participants were interviewed by a dietitian for stress level, working hours, sleeping hours, smoking, education, and a 24-hour recall for food intake, categorizing food remarks in 4: Normal, Vegan or Vegetarian, High Carb, and Gluten Free. Participants then provided a saliva sample, collected in 1.5 ml tubes and stored at 125 -80°C until processing. Similar procedures were repeated in the study population in T2 (24-28 gestational weeks) and T3 (32-38 gestational weeks) of pregnancy. DNA was extracted from all collected samples using the PowerSoil DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to the manufacturer’s instructions and following a 2˜min bead beating step (BioSpec, Bartlesville, OK, USA). The variable V4 region of the 16S rRNA gene was PCR-amplified using the 515F and 806R barcoded primers following the Earth Microbiome Project protocol. Each PCR reaction contained 25 µl with ∼40 ng/µl of DNA, 2 µl 515F (forward, 10 µM) primer, 2 µl 806R (reverse, 10 µM) primer, and 25 µl PrimeSTAR Max PCR Readymix (Takara, Mountain View, CA, USA). PCR conditions were as follows: 30 cycles of denaturation at 98°C for 10 s, annealing at 55°C for 5 s, and extension at 72° C for 20 s, followed by a final elongation at 72° C for 1 min. Amplicons were purified using AMPure magnetic beads(Beckman Coulter, Indianapolis, IN, USA) and quantified using the Picogreen dsDNA quantitation kit (ThermoFisher, Waltham, MA, USA). Equimolar amounts of DNA from individual samples were pooled and sequenced using the Illumina MiSeq platform at the Azrieli Faculty of Medicine’s Genome Center. Microbiome associations were obtained from analyzing DNA samples.
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-Microbiome associations obtained from processing of DNA samples collected from saliva of women at 3 stages of pregnancy (T1, T2, T3).
-Categories of food intake per women: normal, vegetarian or vegan, high carb, and gluten-free, registered from interviews with a dietary.
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Researchers analyzed the development of the oral microbiome during pregnancy by collecting saliva samples from 346 Israeli women at different pregnancy stages (T1, T2, and T3). Saliva samples were processed to extract DNA and obtain microbiome associations. Besides the sample collection, the 346 women were interviewed regarding their food intake habits, categorizing them in 4 different types of diet: normal, vegetarian or vegan, high carb, and gluten-free. Which of those types of diet would show the strongest and most consistent associations with oral microbiome composition?
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Gluten-free diet showed the strongest and most consistent associations with oral microbiome composition across all trimesters
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-The oral microbiome undergoes distinct compositional changes throughout pregnancy, influenced by hormonal, immunologic, and metabolic shifts.
- Pregnancy associated changes can increase susceptibility to oral disease and have been associated with adverse pregnancy outcomes.
-Conversely, diets rich in fiber, plant polyphenols, and micronutrients, such as vitamin D and calcium, are associated with greater oral microbial diversity, resilience, and anti-inflammatory properties.
|
[{"label":"RBK Item","value":"The oral microbiome undergoes distinct compositional changes throughout pregnancy, influenced by hormonal, immunologic, and metabolic shifts."},{"label":"Title","value":"Metabarcoding analysis of oral microbiome during pregnancy"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/39742335/"},{"label":"Date","value":"December 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Pregnancy associated changes can increase susceptibility to oral disease and have been associated with adverse pregnancy outcomes."},{"label":"Title","value":"Microbiome and Pregnancy Dysbiosis: A Narrative Review on Offspring Health"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/40292452/"},{"label":"Date","value":"March 15, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Conversely, diets rich in fiber, plant polyphenols, and micronutrients, such as vitamin D and calcium, are associated with greater oral microbial diversity, resilience, and anti-inflammatory properties."},{"label":"Title","value":"Acquiring and maintaining a normal oral microbiome: current perspective"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25019064/"},{"label":"Date","value":"June 26, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant Biology
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Free-Format Question
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Role of AtCPK5 and AtCPK6 in the regulation of the plant immune response triggered by rhamnolipids in Arabidopsis
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https://www.biorxiv.org/content/10.1101/2025.10.22.683368v1
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October 23, 2025
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Researchers examined the RL (Rhamnolipid)-induced resistance to Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000). To do this, the strain was grown at 28 °C under stirring in King’s B (KB) liquid medium supplemented with antibiotic: 50 μg/mL rifampicin. Arabidopsis plants (WT, cpk5, cpk6, and cpk5/6 double mutant) were grown individually for 4 weeks in soil. For each experiment, six pots per condition were used (biological replicates, n = 6). Two days before infection, plants were sprayed with RLs (0.6mg/mL) or water as a control and were placed in a high-humidity atmosphere. The plants were then infiltrated with bacterial suspension at a concentration of 10^7 CFU/mL (in 10 mM MgCl2) using a needleless syringe. Bacterial quantification in planta (colony-forming units;CFU) was performed 3 days post-infection (dpi). To this end, all plant leaves from the same pot were harvested, weighed, and crushed in a mortar with 10 mL of 10 mM MgCl2, and serial dilutions were performed. For each dilution, 10 μL were dropped on KB plate supplemented with appropriate antibiotics. CFU were counted after 2 days of incubation at 28 °C. The number of bacteria per milligram of plant fresh mass was obtained with the following formula: CFU.mg^-1 = ((N × Vd/Vi × 10^𝑛−1 × 100)/M) where N= CFU number, Vi= volume depot on plate, Vd= total volume, n=dilution number, and M=plant fresh mass).
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- Bacterial load (CFU/mg fresh weight;P. syringae) in Arabidopsis plants (WT, cpk5, cpk6, and cpk5/6 double mutant) pretreated with vs. without rhamnolipids.
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Researchers investigated how RL (rhamnolipid) treatment affects resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis wild-type and mutant plants (cpk5, cpk6, and cpk5/6). Two days before infection, plants were sprayed with RLs (0.6mg/mL) or water as a control and were placed in a high-humidity atmosphere. The plants were then infiltrated with bacterial suspension at a concentration of 10^7 CFU/mL (in 10 mM MgCl2) using a needleless syringe. Bacterial quantification in planta (colony-forming units;CFU) was performed 3 days post-infection (dpi). Plant leaves from the same pot were harvested, weighed, and crushed in a mortar with 10 mL of 10 mM MgCl2, and serial dilutions were performed. For each dilution, 10 μL were dropped on KB plate supplemented with appropriate antibiotics. CFU were counted after 2 days of incubation at 28 °C. The number of bacteria per milligram of plant fresh mass was obtained with the following formula: CFU.mg^-1 = ((N × Vd/Vi × 10^𝑛−1 × 100)/M) where N= CFU number, Vi= volume depot on plate, Vd= total volume, n=dilution number, and M=plant fresh mass).
Predict the relative disease sensitivity (bacterial susceptibility) of all Arabidopsis plant genotypes after RL pretreatment and infection with P. syringae pv. tomato DC3000.
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After pretreatment with RL, plant backgrounds will display similarly low disease senstivity.
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-Rhamnolipids (RLs) are natural, highly biodegradable molecules produced by some bacteria that can induce disease resistance to phytopathogens in various plant species, therefore activating the immune response.
- CPKs are involved in plant development and plant response to biotic and abiotic stress.
|
[{"label":"RBK Item","value":"Rhamnolipids (RLs) are natural, highly biodegradable molecules produced by some bacteria that can induce disease resistance to phytopathogens in various plant species, therefore activating the immune response."},{"label":"Title","value":"Biosurfactants in Plant Protection Against Diseases: Rhamnolipids and Lipopeptides Case Study"},{"label":"URL","value":"https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2020.01014/full"},{"label":"Date","value":"September 7, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"CPKs are involved in plant development and plant response to biotic and abiotic stress."},{"label":"Title","value":"The role of CDPKs in plant development, nutrient and stress signaling"},{"label":"URL","value":"https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.996203/full"},{"label":"Date","value":"September 29, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Behavioral ecology / Primatology
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MCQ
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Social Tolerance and Innovation in Capuchins: socially more tolerant brown capuchins are better problem-solvers than less tolerant white-faced capuchins
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https://www.biorxiv.org/content/10.1101/2025.09.05.674457v1.full
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September 7, 2025
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Researchers tested three groups of white-faced capuchins (Cebus capucinus)(n = 23 individuals in total) and three groups of brown capuchins (Sapajus apella) (n = 20 individuals in total) to explore and compare the relationship between social tolerance and problem-solving propensities. To measure social tolerance, they prepared an area of 1 m2 per five animals in the group, in which they distributed apple pieces and measured the proportion of individuals within the co-feeding area at each scan sample. To measure problem-solving propensities, they designed three versions of novel extractive foraging devices requiring one to three steps to acquire the food reward. For the first puzzle, animals had to rotate a door to either the left or right to access a hidden reward (1/24 of an apple) by reaching into a box. For the second puzzle, animals had to pull on a chain reaching out of a box, which moved a blockade out of the way so that they could push in a door and reach into the box. For the third puzzle, animals had to pull a metal rod blocking a slider that had to be pulled upwards and held in position to reach into the box and then pull on a chain to access the hidden reward. Researchers analyzed the approaching, exploring, and solving behaviour separately.
|
- Proportion of individuals within the co-feeding area at each scan sample (social tolerance)
- Proportion of individuals within the puzzle area at each scan sample (social tolerance)
- Number of approaches to a food puzzle area.
- Approaching a food puzzle area duration.
- Approaches to a food puzzle area latency
- Number of exploration events (touch, sniff, interact) during the approaches to a food puzzle area
- Number of times the capuchins successfully solved the puzzles
- Exploration of food puzzle events latency.
- Time to solve a puzzle
|
Researchers tested three groups of white-faced capuchins (Cebus capucinus) and three groups of brown capuchins (Sapajus apella) to explore and compare the relationship between social tolerance and problem-solving propensities. To measure social tolerance, they prepared an area of 1 m2 per five animals in the group, in which they distributed apple pieces and measured the proportion of individuals within the co-feeding area at each scan sample. To measure problem-solving propensities, they designed three versions of novel extractive foraging devices requiring one to three steps to acquire the food reward. Which of the following outcomes is most likely?
A. Both species should show the same levels of social tolerance and problem-solving propensities.
B. White-faced capuchins should show the highest level of social tolerance and problem-solving propensities.
C. White-faced capuchins should show the lowest level of social tolerance and problem-solving propensities.
D. White-faced capuchins should show the highest level of social tolerance and the lowest level of problem-solving propensities.
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C. White-faced capuchins should show the lowest level of social tolerance and problem-solving propensities.
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- Social tolerance has increasingly been linked to the facilitation of social learning across a variety of species, including chimpanzees, orangutans, macaques, capuchin monkeys, lemurs, and birds.
- White-faced capuchins (Cebus capucinus) and brown capuchins (Sapajus apella) exhibit a diverse array of traditions
- White-faced capuchins (Cebus capucinus) are less known for using tools (but see Barrett et al., 2018), but they regularly engage in object use (Boinski, 1988).
- Robust capuchins (Sapajus spp.) have fewer documented social traditions but exhibit a wide range of foraging traditions, including tool-use, and show notable social tolerance in these contexts, tolerating close proximity of conspecifics
|
[{"label":"RBK Item","value":"Social tolerance has increasingly been linked to the facilitation of social learning across a variety of species, including chimpanzees, orangutans, macaques, capuchin monkeys, lemurs, and birds. "},{"label":"Title","value":"Social tolerance and role model diversity increase tool use learning opportunities across chimpanzee ontogeny"},{"label":"URL","value":"https://www.nature.com/articles/s42003-025-07885-4"},{"label":"Date","value":"March 28, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"White-faced capuchins (Cebus capucinus) and brown capuchins (Sapajus apella) exhibit a diverse array of traditions."},{"label":"Title","value":"The Complete Capuchin: The Biology of the Genus Cebus"},{"label":"URL","value":"https://www.cambridge.org/br/universitypress/subjects/life-sciences/biological-anthropology-and-primatology/complete-capuchin-biology-genus-icebusi?format=PB&isbn=9780521667685#contents"},{"label":"Date","value":"June 21, 2004"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Reference book (the URL provided is for reference only)"},{"label":"RBK Item","value":"White-faced capuchins (Cebus capucinus) are less known for using tools (but see Barrett et al., 2018), but they regularly engage in object use"},{"label":"Title","value":"Habitual stone-tool-aided extractive foraging in white-faced capuchins, Cebus capucinus"},{"label":"URL","value":"https://royalsocietypublishing.org/doi/10.1098/rsos.181002"},{"label":"Date","value":"July 25, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Robust capuchins (Sapajus spp.) have fewer documented social traditions but exhibit a wide range of foraging traditions, including tool-use, and show notable social tolerance in these contexts, tolerating close proximity of conspecifics"},{"label":"Title","value":"Wild capuchin monkeys use stones and sticks to access underground food"},{"label":"URL","value":"https://www.nature.com/articles/s41598-024-61243-8"},{"label":"Date","value":"May 06, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Neuroscience
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Free-Format Question
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Developmental and Stress-Induced Effects on 5-HT3R-Expressing Interneurons within Auditory Cortex
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https://www.biorxiv.org/content/10.1101/2025.09.08.675013v1
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Sep 09, 2025
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Researchers characterized the cell type-specific expression profiles of 5-HT3R within two major subpopulations of 5-HT3R cells, NDNF⁺ and VIP⁺, in A1, to analyze their developmental trajectories under normal conditions and the influence of early life stress (ELS). Brain sections containing A1 were obtained from mixed-sex groups of Mongolian gerbils (Meriones unguiculatus) to study the development of cell populations. Two control groups, CTR10 and CTR15, were sacrificed at postnatal days 10 and 15, respectively, to characterize the timeline of normal development in A1 during the auditory cortex (ACx) critical period. A third control group, CTR30, was sacrificed at postnatal day 30 to assess the closure of the critical period. Two additional groups, “Restraint” ELS (ELSR) and “Open field” (ELSO), were subjected to a separate form of stress induction during the ACx critical period, and sacrificed at postnatal day 30. For each sample, coronal sections containing A1 were collected on a cryostat microtome, and adhered to SuperFrost Plus slides. RNA fluorescent in situ hybridization (FISH) was performed using RNAscope probes, which were hybridized at 40°C for 2 hours, followed by of signal amplification, and fluorescent labeling using channel-specific horseradish peroxidases and TSA vivid fluorophores All slides were counterstained with DAPI for 30s prior to coverslipping. NDNF⁺ and VIP⁺ cells were quantified through the neocortical layers 1-4 (L1, L2/3, and L4), which were visually identified based on packing densities illuminated by DAPI. Tiled images of A1 containing L1-L4 were taken at 40x in four channels to generate A1 “maps” which were used to identify all cells that expressed NDNF⁺ and VIP⁺ mRNA within the region of interest. The RNAscope assay was used to quantify the levels of Htr3a mRNA expression through the count of discrete fluorescent puncta of each NDNF⁺ and VIP⁺ cell within A1 image at 150x in three channels.
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- Comparison of NDNF⁺ and VIP⁺ cell densities across layers under normal development and the influence of ELS.
- Quantification of fluorescent puncta in NDNF⁺ and VIP⁺ cells under normal development and the influence of ELS.
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Two subpopulations of cells, NDNF⁺ and VIP⁺, contribute to 5-HT3R expression, which may play a role in regulating critical period plasticity in ACx. Quantification of cells and mRNA expression for each cell subpopulation was performed by manual counting of images obtained through RNA fluorescent in situ hybridization (FISH) to evaluate the effect of ELS. Results were compared between the A1 sections of L1-L4 from: a) control groups, sacrificed at postnatal days 10, 15, and 30; b) the ELSR group, sacrificed at postnatal day 30; c) the ELSO group, sacrificed at postnatal day 30. In NDNF⁺ Layer 1, what is the comparison of cell density between ELSR and CTR30?
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NDNF⁺ cell density is significantly higher in ELSR compared to CTR30
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- Early life stress (ELS) contributes to neuropsychiatric disease in both humans and animal models.
- The auditory cortex (ACx) is a brain region where exposure to ELS during a critical period impairs both neural and behavioral responses to a variety of auditory stimuli that rely on temporal processing.
- Serotonin (5-HT) is a neurotransmitter linked to stress, developmental plasticity, and the auditory system.
- 5-HT3 receptors (5-HT3R) are serotonin receptors that may have a role in regulating critical period plasticity in ACx. 5-HT3R gene expression can be affected by ELS.
- Vasoactive intestinal peptide (VIP) are cells that are densely populated in superficial cortical layers that express 5-HT3R.
- Neuron derived neurotrophic factor (NDNF) are cells that are mostly confined to L1, and that express 5-HT3R
|
[{"label":"RBK Item","value":"Early life stress (ELS) contributes to neuropsychiatric disease in both humans and animal models"},{"label":"Title","value":"Childhood adversities and adult psychopathology in the WHO World Mental Health Surveys"},{"label":"URL","value":"https://doi.org/10.1192/bjp.bp.110.080499"},{"label":"Date","value":"Nov, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"The auditory cortex (ACx) is a brain region where exposure to ELS during a critical period impairs both neural and behavioral responses to a variety of auditory stimuli that rely on temporal processing."},{"label":"Title","value":"Early-Life Stress Impairs Perception and Neural Encoding of Rapid Signals in the Auditory Pathway\n"},{"label":"URL","value":"https://doi.org/10.1523/JNEUROSCI.1787-22.2023."},{"label":"Date","value":"May 3, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Serotonin (5-HT) is a neurotransmitter linked to stress, developmental plasticity, and the auditory system."},{"label":"Title","value":"Context-dependent modulation of auditory processing by serotonin"},{"label":"URL","value":"https://doi.org/10.1016/j.heares.2010.12.015"},{"label":"Date","value":"Sep, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Vasoactive intestinal peptide (VIP) are cells that are densely populated in superficial cortical layers that express 5-HT3R."},{"label":"Title","value":"Primary auditory thalamus relays directly to cortical layer 1 interneurons"},{"label":"URL","value":"https://doi.org/10.1101/2024.07.16.603741"},{"label":"Date","value":"Jul 18, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Neuron derived neurotrophic factor (NDNF) are cells that are mostly confined to L1, and that express 5-HT3R"},{"label":"Title","value":"Primary auditory thalamus relays directly to cortical layer 1 interneurons"},{"label":"URL","value":"https://doi.org/10.1101/2024.07.16.603741"},{"label":"Date","value":"Jul 18, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Chemistry
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Analytical Chemistry
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Numerical Values
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Towards enhanced selection of antibiotics in a hospital laboratory – development of a rapid electrochemical-based antimicrobial sensitivity test for Urinary Tract Infections.
|
https://chemrxiv.org/engage/chemrxiv/article-details/68839d31728bf9025e354df8
|
July 29, 2025
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Clinical midstream urine samples received for culture and antibiotic susceptibility testing (AST) were collected across three external hospital laboratories: Glasgow Royal Infirmary (GRI, UK), the North-East Innovation Lab at the Newcastle upon Tyne Hospitals NHS Foundation Trust (NuTH, UK), and Breach Candy Hospital Trust (BCHT, India). A total of 89 clinically derived urine samples were screened, with site-specific inclusion criteria used to preferentially select UTI-positive specimens (e.g., leukocyte or nitrite positivity on urinalysis at GRI, predefined microscopy-based screening at NuTH, and pus cell count plus leucocyte esterase positivity at BCHT). For RapidPlate™ testing, 20 μL of each selected urine sample was directly inoculated into wells of a disposable electrochemical cartridge containing agar gels with nutrients, redox mediator, and a panel of six UTI-relevant antibiotics—amoxicillin, cefalexin, ciprofloxacin, fosfomycin, nitrofurantoin, and trimethoprim—each present at a single concentration corresponding to the EUCAST breakpoint and arranged in triplicate wells alongside positive and negative control wells. Cartridges were inserted into RapidPlate™ reader units, which performed electrochemical impedance spectroscopy–based monitoring of bacterial growth in the presence and absence of each antibiotic. In parallel, standard clinical AST was carried out on the same urine samples at each site using the routine reference methods: VITEK 2 automated broth microdilution (N445 card) at GRI and Kirby–Bauer disk diffusion (KBDD) at NuTH and BCHT, with species-specific breakpoints applied according to local clinical guidelines. For each clinical sample and antibiotic combination across all three clinical sites, the categorical AST result reported by the RapidPlate™ system (susceptible, resistant or, where applicable, intermediate/susceptible–increased exposure) was later compared with the corresponding categorical AST result from the site-specific reference method.
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- For each included clinical urine sample at each hospital site (Glasgow Royal Infirmary, Newcastle upon Tyne Hospitals, Breach Candy Hospital Trust) and for each antibiotic on the RapidPlate™ panel (amoxicillin, cefalexin, ciprofloxacin, fosfomycin, nitrofurantoin, trimethoprim), researchers recorded the categorical antibiotic susceptibility result reported by the RapidPlate™ system (e.g. susceptible, resistant or, where applicable, intermediate/susceptible–increased exposure) based on electrochemical impedance measurements collected during the cartridge run time.
- For the same clinical urine samples and antibiotics, at each site, researchers recorded the categorical antibiotic susceptibility result reported by the local routine reference method (VITEK 2 automated broth microdilution at Glasgow Royal Infirmary; Kirby–Bauer disk diffusion at Newcastle upon Tyne Hospitals and Breach Candy Hospital Trust), using site-specific species–antibiotic clinical breakpoints.
- For all sample–antibiotic pairs that had valid categorical results from both RapidPlate™ and the corresponding reference method, researchers counted the number of pairs in which RapidPlate™ and the reference method reported the same susceptibility category, as well as the total number of such pairs across all three clinical sites.
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Researchers used a RapidPlate electrochemical impedance–based antibiotic susceptibility test on clinical midstream urine samples at three hospital laboratories and compared its antibiotic susceptibility predictions to conventional reference methods (VITEK 2 broth microdilution and Kirby–Bauer disk diffusion). Considering all three clinical sites together, what was the overall categorical agreement (in percent) between RapidPlate™ and the reference methods?
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94% [89% - 99%]
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-Current standard methods for antibiotic susceptibility testing (AST) include automated systems such as VITEK 2 (bioMérieux, France), in addition to traditional techniques like Kirby-Bauer disk diffusion and broth microdilution
- Electrochemical impedance spectroscopy (EIS) is amongst the most sensitive electrochemical techniques for evaluating interfacial and bulk solution changes in a system. EIS can monitor differences in the electrical properties of the system over time by applying an alternating current at a range of frequencies.
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[{"label":"RBK Item","value":"Current standard methods for antibiotic susceptibility testing (AST) include automated systems such as VITEK 2 (bioMérieux, France), in addition to traditional techniques like Kirby-Bauer disk diffusion and broth microdilution"},{"label":"Title","value":"Current and Emerging Methods of Antibiotic Susceptibility Testing\n"},{"label":"URL","value":"https://www.mdpi.com/2075-4418/9/2/49"},{"label":"Date","value":"May 3, 2019"},{"label":"RBK Item","value":"- Electrochemical impedance spectroscopy (EIS) is amongst the most sensitive electrochemical techniques for evaluating interfacial and bulk solution changes in a system. EIS can monitor differences in the electrical properties of the system over time by applying an alternating current at a range of frequencies."},{"label":"Title","value":"10 - Impedance biosensors"},{"label":"URL","value":"https://www.sciencedirect.com/science/chapter/edited-volume/abs/pii/B9780323884310000041"},{"label":"Date","value":"May 8, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Chemistry
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Catalysis
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Free-Format Question
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An investigation of the physical and chemical changes of Pd nanoparticles on carbon supports in response to the release of hydrogen from aqueous formate solutions
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https://chemrxiv.org/engage/chemrxiv/article-details/68d16d29f2aff16770fa93bd
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September 25, 2025
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Researchers prepared and analyzed Pd nanoparticles supported on carbon materials to examine their structural and chemical evolution during hydrogen release from aqueous sodium formate. Three supports were used: carbon black (Vulcan XC-72), nitrogen-doped carbon (NC), and graphitic carbon nitride (g-C₃N₄). Nitrogen-doped carbon was obtained by heating a melamine–carbon black mixture at 700 °C under nitrogen, while g-C₃N₄ was synthesized by heating urea at 500 °C in air. Pd catalysts were produced by reducing H₂PdCl₄ with NaBH₄ in trisodium citrate solution at 25 °C, yielding a 1 wt% Pd loading. The product was filtered, washed, and dried at 85 °C for 24 h, and selected samples were calcined at 250 °C for 3 h in air. Structural and compositional analyses included inductively coupled plasma–optical emission spectrometry (PerkinElmer 7300 DV) to determine Pd content, X-ray diffraction (Rigaku SmartLab SE, Cu Kα, 2θ = 2–100°) to assess crystallinity, and nitrogen physisorption (Micromeritics ASAP 2020) using BET and BJH models to measure surface area and pore volume. Pd dispersion was quantified by CO chemisorption (Micromeritics ASAP 2020C, 30 °C, pre-reduced at 100 °C for 0.5 h), and nanoparticle morphology was examined by aberration-corrected scanning transmission electron microscopy (Thermo Fisher Themis Z, 300 kV). Catalytic performance was tested in a 50 mL batch reactor containing 250 mg of catalyst and 10 mL of 1 M sodium formate at 65 °C under N₂ with stirring at 500 rpm for 2 h, where gas evolution was monitored by pressure change and analyzed using a micro-gas chromatograph. In-situ X-ray absorption spectroscopy was performed at the Stanford Synchrotron Radiation Lightsource beamline 4-1 to monitor Pd oxidation states during reaction using Pd K-edge XANES and EXAFS scans (24126–25238 eV, 0.5 × 4 mm beam). Catalyst reuse tests were carried out by recovering the solid after reaction, washing with deionized water, drying at 80 °C, and re-calcining at 180 or 250 °C for 3 h when required. All synthesis, characterization, and catalytic experiments were conducted under controlled temperature and atmospheric conditions to ensure reproducibility.
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- Pd oxidation state and local atomic structure characterized by in-situ X-ray Absorption Spectroscopy (XAS, SSRL beamline 4-1) with Pd K-edge XANES and EXAFS scans (24126–25238 eV, beam size 0.5 × 4 mm) under reaction conditions.
- Palladium loading (wt%) measured using Inductively Coupled Plasma–Optical Emission Spectroscopy (ICP-OES, PerkinElmer 7300 DV) to quantify Pd content on carbon supports.
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Palladium nanoparticles supported on carbon materials were assessed as catalysts for hydrogen release from aqueous sodium formate. Three supports- carbon black (Vulcan XC-72), nitrogen-doped carbon (NC), and graphitic carbon nitride (g-C₃N₄)- were employed, with NC synthesized by heating a melamine-carbon black mixture at 700 °C under N₂ and g-C₃N₄ prepared by urea pyrolysis at 500 °C in air. Pd catalysts (1 wt%) were obtained by reducing H₂PdCl₄ with NaBH₄ in trisodium citrate at 25 °C, followed by drying and optional calcination at 250 °C. Structural and chemical characterization included ICP–OES for Pd content, XRD for crystallinity, N₂ physisorption for surface area, CO chemisorption for Pd dispersion, and STEM for nanoparticle morphology. Catalytic performance was evaluated in a batch reactor (65 °C, 1 M sodium formate) by monitoring gas evolution and composition via micro-GC. In-situ XANES/EXAFS at the Pd K-edge tracked oxidation-state changes during reaction, and reuse tests examined catalyst stability following washing and re-calcination. What will in-situ XANES analysis reveal about the role of palladium oxide (PdO) as an active catalyst for formate dehydrogenation?
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In-situ XANES experiments unambiguously demonstrate that PdO is rapidly reduced to metallic Pd and then forms Pd hydride upon exposure to a formate solution, showing that PdO does not play a direct role in the mechanism of H2 formation.
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- Palladium nanoparticles on carbon supports (Pd/C) are effective for catalyzing hydrogen release from aqueous formate solutions but typically suffer from a gradual decrease of activity.
- Nitrogen doping of carbon supports is observed to enhance the rates of hydrogen release from aqueous formate solutions
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[{"label":"RBK Item","value":"Shin and cowrokers argued that desorption of hydrogen from the Pd metal is rate\nlimiting and the presence of nitrogen on a graphene sheet decreases the binding energy of hydrogen\nresulting in a lower barrier for the reaction. These results suggest that the benefits of N-containing\nsupports are twofold: retaining active Pd sites through an increased stability of Pd nanoparticles."},{"label":"Title","value":"Novel nanoporous N-doped\ncarbon-supported ultrasmall Pd nanoparticles: Efficient catalysts for hydrogen storage and\nrelease"},{"label":"URL","value":".\nhttps://doi.org/10.1016/j.apcatb.2016.10.080."},{"label":"Date","value":"29 October 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Koh and Jeon found that the electron-rich pyridinic and pyrrolic\nnitrogen groups could donate electrons to Pd, resulting in electron-enriched Pd through strong\ninteractions between Pd and nitrogen. Our XPS results show that although Pd/NC has only 2 at.%\nN, the large majority of this is pyridinic and pyrrolic. The N in the Pd/g-C₃N₄ catalyst\nis mostly pyridinic, and therefore the enhanced activity observed for both N-containing catalysts\nis likely derive from an electronic effect similar to that proposed by Koh and Jeon."},{"label":"Title","value":". Electronically modified Pd\ncatalysts supported on N-doped carbon for the dehydrogenation of formic acid."},{"label":"URL","value":"https://doi.org/10.1016/j.ijhydene.2016.04.102."},{"label":"Date","value":"August 20, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Biomaterials / Bone tissue engineering
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MCQ
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Tenascin-c functionalised self-assembling peptide hydrogels for critical-sized bone defect reconstruction
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https://www.sciencedirect.com/science/article/pii/S0142961225004727
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July 11, 2025
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Researchers aimed to explore the influence of functionalizing a self-assembling peptide hydrogel with Tenascin-c for bone defect reconstructions. The encoding nucleotide sequence of the tenascin-c monomer was collected from the NCBI public database (GeneID: 3371) and trimmed down to the 3rd to 5th units of the TNCIII domains, from G2725 to C3534 (transcript variant 1; NM_002160.4); the sequence was cross-referenced against the Uniprot database (P24821). The F3 (3rd TNCIII domain), F5 (5th TNCIII domain), and F35 (3rd, 4th, and 5th TNCIII domains) fragments had the peptide sequence 5′-GGGGFEFKFEFK-3′ added at the C-terminal to make them competent for self-functionalisation; a tetraglycine spacer was installed between the tenascin and peptide block units for flexibility. The inserts were capped with restriction sites at the 5’ (BamHI) and 3’ (XhoI) ends and submitted to the Genscript Gene Synthesis service for cloning into a pGEX-6P-1 vector harbouring a GST tag. Rosetta 2 pLysS/BL21-DE3 E. Coli were transformed with the different plasmids to produce the different Tenascin-c fragments, which were purified with a 1 mL sepharose column, dialysed for 45 min against PBS at pH 11.5 using a Slide-A-Lyser column (Thermo Fischer Scientific), and concentrated to 9 - 10 mg/mL by liquid evaporation. The Polymers & Peptides research group from the University of Manchester and Cell Guidance Systems Ltd provided the Delta1 peptide hydrogel. It was received as a ready-to-use peptide solution concentrated at 20 mg/mL. 0.5 μL of 5 M NaOH per 100 μL hydrogel was added to decrease fibre stability and facilitate the subsequent fragment incorporation. Hydrogel functionalisation consisted of adding the concentrated fragment stock to the Delta1 peptide solution, followed by rigorous vortexing. The fragment concentration in the hydrogels was kept consistent with the molarity of the F35 hydrogel group, functionalised at 1 mg/mL; accordingly, the F3 and F5 hydrogel groups were prepared at 0.66 mg/mL. The dilution factor was kept consistent across all hydrogel groups by supplementation of PBS at pH 11.5, where appropriate. Bone marrow-derived human mesenchymal stem cells (MSC) were harvested from a donor femoral head and supplied at passage 0 (P0) by PromoCell. The MSCs were expanded and sustained in basal media (DMEM) with 4.5 g/L glucose (Gibco), 11 mg/mL sodium pyruvate (Gibco), 1 % MEM non-essential amino acids (Gibco), 10 % fetal bovine serum (FBS) (Cytiva), 1 % penicillin/streptomycin (76 Units/mL and 76 μg/mL respectively) (Gibco), 2.3 mM L-glutamine (Sigma), and 0.25 μg/ mL Amphotericin B (Gibco)). Basal media was replenished every 72 h, and cells were passaged at 80 % confluency. Bone marrow-derived human mesenchymal stem cells (MSC), were consistently seeded at 1.000.000 cells/mL in the previously prepared hydrogel groups and rigorously vortexed; 50 μl of the cell/hydrogel mixture was formed in a non-tissue culture treated 48 well plate. The loaded gels were promptly submerged with 500 μL of basal media and left to incubate for 1 h in cell culture conditions, after which the media was replenished; the media was again replenished after 24 h and from there every 72 h. For the osteogenic differentiation of MSCs in vitro, hydrogel groups were prepared and supplemented with recombinant human BMP-2 to a 5 μg/mL concentration. The hydrogels were seeded, loaded in 50 μl volumes, and maintained over three weeks as previously described. Conditions were replicated thrice for the time points day 7, 14, and 21. The hydrogels were digested in pronase (5 mg/mL) (Merck) for 10 min at 37 °C, the RNA was subsequently extracted using the TriZol method. Recovered RNA was reverse-translated to a cDNA library using the QuantiTect Reverse Transcription Kit (Qiagen), as per the manufacturer's instructions. Samples were then used in the qPCR assay to quantify the expression of RPL13A (housekeeping gene), bone alkaline phosphatase (ALP), osteopontin (OPN), osterix (OSX), and osteocalcin (OCN) using the ΔΔCt method. Mineralisation was evaluated by Alizarin Red staining to visualise and compare calcium deposition across the hydrogel groups.
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- RT-qPCR: MSCs in Delta 1, F3, F5, and F35 hydrogel groups supplemented with recombinant human BMP-2 to 5 μg/mL, for genes RPL13A (housekeeping gene), ALP, OPN, OSX, and OCN using the ΔΔCt method (Day 7, Day 14, Day 21).
- Mineralisation (calcium deposit patterns) by Alizarin Red staining on day 21: Delta1 + BMP-2 vs functionalised hydrogels + BMP-2.
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Researchers aimed to investigate the impact of functionalizing a self-assembling peptide hydrogel with Tenascin-C for bone defect reconstructions. Three different fragments of the Tenascin-c protein ( i.e. F3: 3rd TNCIII domain; F5: 5th TNCIII domain; F35: 3rd, 4th, and 5th TNCIII domains) were generated in E. coli with the peptide sequence 5′-GGGGFEFKFEFK-3′ added at the C-terminal to make them competent for self-functionalisation and a tetraglycine spacer in-between the tenascin and peptide block units for flexibility. These were mixed with the Delta1 peptide hydrogel (Polymers & Peptides research group, University of Manchester), keeping the concentration in the hydrogels consistent with the molarity of the F35 hydrogel group (1 mg/mL); accordingly, the F3 and F5 hydrogel groups were prepared at 0.66 mg/mL. Bone marrow-derived human mesenchymal stem cells (MSC) were seeded at 1.000.000 cells/mL in the previously prepared hydrogel groups, and 50 μl of the cell/hydrogel mixture was formed in a non-tissue culture-treated 48-well plate. For the osteogenic differentiation of MSCs in vitro, the hydrogel groups were supplemented with recombinant human BMP-2 at a concentration of 5 μg/mL and cultured for 7, 14, and 21 days. At each time point, RT-qPCR was performed to assess the expression of osteogenic genes. To evaluate functional osteogenic outcomes, Alizarin Red staining was also performed to detect calcium deposition within the hydrogels. Which of the following outcomes is most likely?
A) Gene expression in F35 was comparable between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, while mineralisation was comparable across all groups
B) Gene expression of osteogenic markers showed modest upregulation in functionalised hydrogels compared to Delta1 + BMP-2, with F35 trending highest, and mineralisation was comparable across all groups.
C) Functionalised hydrogels and Delta1 + BMP-2 showed similar gene expression overall, but F3 and F5 exhibited slightly higher early marker expression, while mineralisation was minimal in Delta1 and more robust in the functionalised groups
D) Gene expression was largely similar between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, but mineralisation was stronger in the functionalised groups
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D) Gene expression was largely similar between Delta1 + BMP-2 and functionalised hydrogels + BMP-2, but mineralisation was stronger in the functionalised groups
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- The tenascin-c monomer contains ‘fibronectin type III-like’ domain type (TNCIII), containing the 3rd and 5th TNCIII domains an RGD integrin-binding motif and an heparin-binding domain.
- Self-assembling peptide hydrogels arise in an aqueous environment from the spontaneous assembly of customised peptide building blocks to form a supramolecular fibre network.
- Self-assembling peptide hydrogels can be functionalised through ‘self-functionalisation’: a bioactive molecule of interest conjugated with the peptide building block to allow its incorporation in the fibre architecture.
|
[{"label":"RBK Item","value":"- The tenascin-c monomer contains ‘fibronectin type III-like’ domain type (TNCIII), containing the 3rd and 5th TNCIII domains an RGD integrin-binding motif and an heparin-binding domain."},{"label":"Title","value":"The tenascin family of ECM glycoproteins: Structure, function, and regulation during embryonic development and tissue remodeling"},{"label":"URL","value":"https://doi.org/10.1002/(SICI)1097-0177(200006)218:2<235::AID-DVDY2>3.0.CO;2-G"},{"label":"Date","value":"May 24, 2000"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Self-assembling peptide hydrogels arise in an aqueous environment from the spontaneous assembly of customised peptide building blocks to form a supramolecular fibre network"},{"label":"Title","value":" Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers;"},{"label":"URL","value":"https://doi.org/10.1073/pnas.191250198"},{"label":"Date","value":"October 09, 2001\n"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"- Self-assembling peptide hydrogels can be functionalised through ‘self-functionalisation’: a bioactive molecule of interest conjugated with the peptide building block to allow its incorporation in the fibre architecture"},{"label":"Title","value":"Nanofibrillar Peptide Hydrogels for the Immobilization of Biocatalysts for Chemical Transformations"},{"label":"URL","value":"https://doi.org/10.1002/marc.201400027"},{"label":"Date","value":"March 07, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Microbiology
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MCQ
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ICP1 bacteriophage treatment antagonizes colonization of the zebrafish larval intestine by Vibrio cholerae
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https://www.biorxiv.org/content/10.1101/2025.09.01.673471v1
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Sep 01, 2025
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Researchers evaluated the influence of the aquatic environment on phage infection by performing in vitro bacteria-bacteriophage predation experiments. At a concentration of 10⁹ cells per mL,Vibrio cholerae was added to two different medias: Lysogeny broth (LB), used as a control, and artificial fresh water (AFW), used as the experimental condition. The bacteria concentration was diluted 1:1000. Bacteriophage ICP 1 was added to the bacterial culture at a Multiplicity of Infection (MOI) value of 2. A separate experiment was performed in Rhine water following the protocol described in Silva-Valenzuela, et al. (2018), where overnight grown V. cholerae were diluted 1:1000 and grown for 8 hours at 37° C in LB. A 20 μL inoculum of V. cholerae was added into 2.5 mL of Rhine water. After overnight growth in Rhine water, Bacteriophage ICP 1 was added to the culture at a MOI of 2. At 0, 1, 2, 4, 7 and 24 hours serial dilutions, Colony Forming Units (CFU), and Plaque Forming Units (PFU) counts were performed for each media.
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- CFU of V. cholerae in LB at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in LB at 0, 1, 2, 4, 7, and 24 hours.
- CFU of V. cholerae in AFW at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in AFW at 0, 1, 2, 4, 7, and 24 hours.
- CFU of V. cholerae in Rhine water at 0, 1, 2, 4, 7, and 24 hours.
- PFU of ICP1 in Rhine water at 0, 1, 2, 4, 7, and 24 hours.
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The interaction between Vibrio cholerae and the bacteriophage ICP1 was evaluated in-vitro through predation experiments in two different aquatic environments: artificial fresh water (AFW), and Rhine water; and a control environment: Lysogeny broth (LB). Counts of CFU, and PFU were performed for each experiment at 0, 1, 2, 4, 7, and 24 hours. Which of the following outcomes is most likely?
a) Only Rhine water will show an increase in bacteriophage propagation activity.
b) Only AFW will show an increase in bacteriophage propagation activity.
c) None of the aquatic environments will show an increase in bacteriophage propagation activity.
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a) Only Rhine water will show an increase in bacteriophage propagation activity.
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- Vibrio cholerae is the causative agent of the diarrheal disease cholera.
- Vibrio cholerae has shown antimicrobial resistant strains, which necessitates the need for alternative
approaches to treat cholera.
- Bacteriophages are viruses that specifically infect bacteria, and offer a promising therapeutic strategy against bacteria due to their host specificity and self-limiting life cycles.
- ICP1 is a bacteriophage that has been previously oral administered to V. cholerae in a phage cocktail, and has shown to reduce disease severity of V. cholerae, marked by decreased diarrhea, and lower bacterial loads in feces.
- Zebrafish larvae (Danio rerio) naturally ingest V. cholerae from their surrounding aquatic environment.
- The protocol Silva-Valenzuela, et al. (2018) describes a method in the section Predation Assay in Aquatic Microcosms to culture V. cholerae in autoclaved filter sterilized fresh water or 0.7% Instant Ocean.
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[{"label":"RBK Item","value":"Bacteriophages are viruses that specifically infect bacteria, and offer a promising therapeutic strategy against bacteria due to their host specificity and self-limiting life cycles."},{"label":"Title","value":"Insights into Bacteriophage Application in Controlling Vibrio Species"},{"label":"URL","value":"https://doi.org/10.3389/fmicb.2016.01114"},{"label":"Date","value":"Jul 18, 2016 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"ICP1 is a bacteriophage that has been previously oral administered to V. cholerae in a phage cocktail, and has shown to reduce disease severity of V. cholerae, marked by decreased diarrhea, and lower bacterial loads in feces."},{"label":"Title","value":"A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models"},{"label":"URL","value":"https://doi.org/10.1038/ncomms14187"},{"label":"Date","value":"Feb 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Zebrafish larvae (Danio rerio) naturally ingest V. cholerae from their surrounding aquatic environment."},{"label":"Title","value":"Zebrafish as a Natural Host Model for Vibrio cholerae Colonization and Transmission"},{"label":"URL","value":"https://doi.org/10.1128/AEM.03580-13"},{"label":"Date","value":"Feb 14, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"The protocol Silva-Valenzuela, et al. (2018) describes a method in the section Predation Assay in Aquatic Microcosms to culture V. cholerae in autoclaved filter sterilized fresh water or 0.7% Instant Ocean. "},{"label":"Title","value":"Niche adaptation limits bacteriophage predation of Vibrio cholerae in a nutrient-poor aquatic environment"},{"label":"URL","value":"https://doi.org/10.1073/pnas.1810138116"},{"label":"Date","value":"Jan 11, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Neuroscience
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MCQ
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Modeling neurodegenerative diseases in Drosophila is conditioned by stress resistance and gut microbiome composition of the reference line
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https://www.biorxiv.org/content/10.1101/2025.09.03.673979v1
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Sep 8, 2025
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Researchers tested whether acute oxidative stress induced by ingestion of paraquat in two apparently identical but independent Drosophila lines of the w1118 strain, wlineA and wlineB, would show a comparable response. The w1118 lines were cultured under conventionally reared (CR) and germ-free (GF) conditions. Under CR conditions, flies were maintained at 25°C on standard cornmeal-yeast (CMY) agar medium supplemented with an antifungal agent, under a 12:12 light-dark cycle. Under GF conditions, female adults emerging from eggs deposited on autoclaved standard culture medium (supplemented with an antibiotic cocktail) were maintained on antibiotic-supplemented standard medium. Axenicity was confirmed by incubating whole-body lysates. To measure Drosophila oxidative stress resistance, 7-day-old non-virgin female flies reared under CR and GF conditions were starved, anesthetized, and transferred to Petri dishes containing two layers of Whatman filter paper soaked with 400 µl of 20 mM paraquat in 2% (w/v) sucrose, and incubated under saturated humidity. Fly survival was scored at multiple time points over a 4-day period.
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- Survival percentage after acute oxidative stress.
- Survival time after acute oxidative stress.
- Median survival time after acute oxidative stress.
- Resistance to oxidative stress curves.
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Acute oxidative stress induced by ingestion of paraquat was evaluated in two apparently identical but independent Drosophila lines of the w1118 strain, wlineA and wlineB, that were cultured conventionally reared (CR) and germ-free (GF) conditions. Fly survival was scored at several time points over a 4-days period following paraquat induction. Which of the following outcomes best describes the paraquat resistance on the w1118 lines under the different growth conditions?
a) wlineA showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
b) wlineA paraquat resistance increased when cultured under GF condition compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
c) wlineA showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR. wlineB paraquat resistance increased when cultured under GF condition compared to CR.
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b) wlineA paraquat resistance increased when cultured under GF condition compared to CR. wlineB showed no significant difference in paraquat resistance when cultured under GF conditions compared to CR.
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- Drosophila is a genus of fly that is currently one of the major model organisms to study human diseases and progress in their treatments.
- Paraquat is a pro-oxidant herbicide commonly used to model drug-induced Parkinson Disease in Drosophila.
- w1118 is a mutant Drosophila strain which carries a null mutation in a gene (white) encoding an ABC-type guanine transporter involved in eye pigmentation.
|
[{"label":"RBK Item","value":"Drosophila is a genus of fly that is currently one of the major model organisms to study human diseases and progress in their treatments"},{"label":"Title","value":"Human Disease Models in Drosophila melanogaster and the Role of the Fly in Therapeutic Drug Discovery"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3082451/"},{"label":"Date","value":"Jun, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Paraquat is a pro-oxidant herbicide commonly used to model drug-induced Parkinson Disease in Drosophila"},{"label":"Title","value":"Interaction of Genetic and Environmental Factors in a Drosophila Parkinsonism Model\n"},{"label":"URL","value":"https://www.jneurosci.org/content/jneuro/27/10/2457.full.pdf"},{"label":"Date","value":"Mar 7, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"w1118 is a mutant Drosophila strain which carries a null mutation in a gene (white) encoding an ABC-type guanine transporter involved in eye pigmentation"},{"label":"Title","value":"Transformation of white locus DNA in Drosophila: Dosage compensation, zeste interaction, and position effects"},{"label":"URL","value":"https://doi.org/10.1016/0092-8674(84)90240-X"},{"label":"Date","value":"Feb, 1984"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
|
Biology
|
Biochemistry / Molecular Biology
|
Free-Format Question
|
Vitamin B12 supports skeletal muscle oxidative phosphorylation capacity in male mice
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https://www.biorxiv.org/content/10.1101/2025.05.19.654973v2
|
May 19, 2025
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Researchers measured the oxygen consumption rate (OCR) from mitochondrial homogenates of tibialis anterior (TA), and red muscle (cumulation of the soleus, and red portions from the quadriceps, and gastrocnemius) samples harvested from Male Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻ mice to evaluate the effects of Mtr expression, and B12 content in the mitochondrial electron transport chain complexes (Complex I, Complex II and Complex IV). These mice had been previously weaned onto one of two defined diets for 7 weeks: a control AIN93G-based diet (C) containing 25 μg/kg vitamin B12, and a vitamin B12-deficient AIN93G-based diet (-B12) containing 0 μg/kg vitamin B12. Both diets included 1% succinyl sufathiazole antibiotics. Mice were sacrificed by cervical dislocation following CO2 euthanasia, and mitochondria were isolated from both skeletal muscle tissues. Quadricep, TA, gastrocnemius, and soleus wet wights were normalized to tibia length (mm), and stored at -80° C. In each sample, the OCR of each oxidative phosphorylation complex was determined. Mitochondria from frozen muscle were isolated in ice-cold MAS buffer using a Potter–Elvehjem (Teflon-glass) homogenizer with 25 strokes followed by centrifugation. Pierce BCA Protein Assay was performed to evaluate the protein concentration. Mitochondrial homogenates were loaded into the assay plates in the following conditions: a) TA in the Seahorse XFe24 microplate (150 µg of homogenate in 100 µl of MAS), and b) Red muscle in the Seahorse XFe96 (30 µg of homogenate in 70 µl of MAS), and then centrifuged (2,000 x g, 5 min., 4°C). The OCR was evaluated using Wave software (Agilent), and was defined by the highest respiratory capacity value following the injection of the corresponding complex-stimulating substrate: Complex I (1 mM NADH); Complex II (5 mM succinate + 2 µM rotenone); and Complex IV (0.5 mM N,N,N′,N′-Tetramethyl-pphenylenediamine dihydrochloride (TMPD) + 1 mM ascorbic acid).
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- Protein concentration in mitochondria isolated from skeletal muscle groups (tibialis anterior (TA) and red muscle) of male mice (Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻) following different diets (control diet and vitamin B12-deficient diet).
- Oxygen consumption rate (OCR) (pmol O2/min/µg protein) across oxidative phosphorylation complexes (Complex I, II, and IV) in mitochondria isolated from skeletal muscle groups (tibialis anterior (TA) and red muscle) of male mice (Mtr⁺ᐟ⁺, and Mtr⁺ᐟ⁻) following different diets (control diet and vitamin B12-deficient diet).
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Levels of Mtr expression and dietary vitamin B12 content can influence the oxygen consumption rate (OCR) across oxidative phosphorylation complexes in mitochondria from skeletal muscle. These conditions were evaluated by measuring OCR in tibialis anterior (TA) and red muscle samples from male Mtr⁺/⁺ and Mtr⁺/⁻ mice exposed to two diets: a control diet (C; 25 μg/kg vitamin B12) and a vitamin B12-deficient diet (−B12; 0 μg/kg vitamin B12). Both diets included 1% succinyl sulfathiazole antibiotics. After 7 weeks, skeletal muscle tissues were collected and normalized to tibia length following mouse sacrifice. Mitochondria were isolated from the tissue in an ice-cold MAS buffer using a Potter–Elvehjem homogenizer and centrifugation. Protein concentration was determined using the Pierce BCA Protein Assay. Mitochondrial homogenates were loaded into assay plates (TA in Seahorse XFe24 and red muscle in Seahorse XFe96) before centrifugation. OCR was measured in the mitochondria using Wave software for each complex (Complex I, Complex II, and Complex IV). When evaluating Complex II from mitochondria isolated from TA, which conditions (mouse group and diet) would show the highest OCR?
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Mtr⁺/⁺ mice in a vitamin B-12 deficient diet
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- Vitamin B12 is an essential cofactor of the methionine synthase enzyme.
- Impaired FOCM, either by dietary or genetic means, leads to decreased dTMP synthesis and uracil misincorporation in mitochondrial DNA (mtDNA) as well as nDNA.
- mtDNA encodes proteins that are components of the electron transport chain complexes, which drive cellular energy production via oxidative phosphorylation in the mitochondria.
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[{"label":"RBK Item","value":"Vitamin B12 is an essential cofactor of the methionine synthase enzyme which is part of the folate-mediated one-carbon metabolism."},{"label":"Title","value":"Vitamin B12 deficiency"},{"label":"URL","value":"https://bevital.no/pdf_files/literature/green_2017%20_nrdp_3_17040.pdf"},{"label":"Date","value":"Jun 29, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Impaired FOCM, either by dietary or genetic means, leads to decreased dTMP synthesis and uracil misincorporation in mitochondrial DNA (mtDNA) as well as nDNA."},{"label":"Title","value":"Nuclear Folate Metabolism"},{"label":"URL","value":"https://doi.org/10.1146/annurev-nutr-071714-034441"},{"label":"Date","value":"Aug, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"mtDNA encodes proteins that are components of the electron transport chain complexes, which drive cellular energy production via oxidative phosphorylation in the mitochondria."},{"label":"Title","value":"The little big genome: the organization of mitochondrial DNA"},{"label":"URL","value":"https://doi.org/10.2741/4511"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Jan 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular oncology
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MCQ
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Loss of the Y chromosome in bladder cancer drives metabolic reprogramming
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https://www.biorxiv.org/content/10.1101/2025.08.26.672471v1
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Aug 31, 2025
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Researchers evaluated whether the absence of the DDR2 gene in Loss of Y chromosome (LOY) tumour cells affected glucose fluctuations in the culture medium or within the clarified cell lysate, as well as its effects on L-lactate abundance. Two cell lines were used and cultured under DMEM medium: CON_YnegN as the control and DDR2KO_YnegN as the experimental cells. Culture medium was harvested, and cell lysates were prepared. Glucose and L-lactate levels were analyzed using a RayBiotech colorimetric assay kit and measured according to the manufacturer’s protocol. Approximately 1 × 10⁵ cells were seeded in each well of a 6-well plate for 72 hours before collecting culture media or cell lysates for analysis.
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- Optical density of Glucose in culture media and cell lysate.
- Optical density of Lactate in culture media.
- Relative glucose comparison between the culture media and the cell lysate for CON_YnegN and DDR2KO_YnegN.
- Relative lactate comparison in the culture media between CON_YnegN and DDR2KO_YnegN.
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A mutation in the DDR2 gene in LOY tumour cells may affect glucose levels and L-lactate abundance. The mutant cell line DDR2KO_YnegN and a control line were cultured in DMEM medium. The culture medium was then harvested, and cell lysates were prepared to measure glucose and L-lactate levels. For glucose, which of the following outcomes explains the DDR2KO_YnegN cells' metabolism in the culture medium and the cell lysates?
a) In both the culture medium and the cell lysates, glucose levels remained stable.
b) In the culture medium, glucose levels indicate increased consumption, while in the cell lysates, they suggest a decrease in intracellular glucose levels.
c) In the culture medium, glucose levels indicate reduced consumption, while in the cell lysates, they suggest an increase in intracellular glucose levels.
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c) In the culture medium, glucose levels indicate reduced consumption, while in the cell lysates, they suggest an increase in intracellular glucose levels.
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- Loss of the Y chromosome (LOY) contributes to both phenotypes in bladder cancer (BC), where metabolic reprogramming may provide a potential explanation.
- Metabolic reprogramming allows tumor cells to adapt their energy production and biosynthetic pathways, such as by shifting to aerobic glycolysis and lactate production even in the presence of oxygen.
- DDR2 is a collagen receptor that influences BC aggressiveness and tumor response to immune checkpoint inhibitors, and is known to influence cancer cell metabolism, particularly glycolysis.
- YnegN is a cell line in which cells naturally lack Y chromosome genes, also known as LOY.
- DDR2KO_YnegN are YnegN cells in which the DDR2 gene is knocked out using CRISPR-Cas9.
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[{"label":"RBK Item","value":"Loss of the Y chromosome (LOY) contributes to both phenotypes in bladder cancer (BC), where metabolic reprogramming may provide a potential explanation"},{"label":"Title","value":"Immunosurveillance encounters cancer metabolism"},{"label":"URL","value":"https://doi.org/10.1038/s44319-023-00038-w"},{"label":"Date","value":"Jan 12, 2024"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Metabolic reprogramming allows tumor cells to adapt their energy production and biosynthetic pathways, such as by shifting to aerobic glycolysis and lactate production even in the presence of oxygen."},{"label":"Title","value":"Understanding the Warburg effect: the metabolic requirements of cell proliferation"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2849637/"},{"label":"Date","value":"May 22, 2009"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"DDR2 is a collagen receptor that influences BC aggressiveness and tumor response to immune checkpoint inhibitors, and is known to influence cancer cell metabolism, particularly glycolysis."},{"label":"Title","value":"DDR2 coordinates EMT and metabolic reprogramming as a shared effector of FOXQ1 and SNAI1"},{"label":"URL","value":"https://doi.org/10.1158/2767-9764.crc-22-0013"},{"label":"Date","value":"Nov 09, 2022"},{"label":"Justification (“Paywalled”, “OA”, “No OA exists”, \"Other (justify)\")","value":"OA"}]
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Biology
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Plant Biology
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MCQ
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The Arabidopsis UMAMIT30 transporter contributes to amino acid root exudation
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https://www.biorxiv.org/content/10.1101/2025.08.23.671809v1
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Aug 27, 2025
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Researchers evaluated whether the loss of UMAMIT30 function, an amino acid transporter, affects Arabidopsis thaliana growth. Seeds from wild-type Arabidopsis thaliana Col-0 plants and UMAMIT30 mutants (umamit30-1 and umamit30-2) were surface sterilized three times in 10% bleach for two minutes each, followed by three washes with sterile water. The seeds were then resuspended in 0.1% phytoagar and stratified in the dark at 4°C for two days. Seeds were plated onto 1x MS agar plates (4.4 g/L Murashige and Skoog Basal Medium with vitamins, 0.5% sucrose, 0.5 g/L MES, and 0.7% PhytoAgar, pH 5.7). Plates were sealed and incubated vertically in a reach-in growth chamber at 25 ± 2°C, 75% RH, under a 16 h light/8 h dark cycle, and 100 µmoles/m²/s light intensity for two weeks. Fresh and dry biomass of whole plants, shoots, and roots was measured. For dry weight analysis, samples were freeze-dried overnight using a lyophilizer.
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- Biomass dry weight of the whole plant, shoots, and roots.
- Biomass fresh weight of the whole plant, shoots, and roots.
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Mutations in UMAMIT30, an amino acid transporter from Arabidopsis thaliana, may alter amino acids homeostasis and impact growth phenotypes. To evaluate the effect on growth, two seed mutants, umamit30-1 and umamit30-2, were grown in MS agar plates for two weeks after which fresh and dry biomass of the whole plant, shoots, and roots were measured. Which of the following outcomes is most likely?
a) Neither of the umamit30 mutants alters amino acid homeostasis and impacts growth phenotypes.
b) Only umamit30-1 mutants alter amino acid homeostasis and impact growth phenotypes.
c) Only umamit30-2 mutants alter amino acid homeostasis and impact growth phenotypes.
d) Both umamit30 mutants alter amino acids homeostasis and impact growth phenotypes.
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a) Neither of the UMAMIT30 mutants alters amino acid homeostasis and impacts growth phenotypes.
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- Arabidopsis thaliana is a plant species in which plant–environment interactions are influenced by root exudation.
- Plant root exudates typically consist of primary metabolites such as sugars, amino acids, and organic acids, as well as secondary metabolites.
- The amino acid composition of root exudates modulates bacterial metabolism, affecting the beneficial interaction between Arabidopsis roots and plant growth-promoting bacteria.
- UMAMIT transporters (Usually Multiple Amino acids Move In and out Transporters) are facilitator proteins that exhibit amino acid export activity in root-to-soil secretion.
- UMAMIT30 is a member of the UMAMIT transporter family.
- umamit30-1 is an Arabidopsis thaliana mutant in which UMAMIT30 expression is knocked out.
- umamit30-2 is an Arabidopsis thaliana mutant in which UMAMIT30 expression is knocked out.
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[{"label":"RBK Item","value":"Arabidopsis thaliana is a plant species in which plant–environment interactions are influenced by root exudation"},{"label":"Title","value":"Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?"},{"label":"URL","value":"https://escholarship.org/content/qt69z6h6mx/qt69z6h6mx.pdf "},{"label":"Date","value":"Jan, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Plant root exudates typically consist of primary metabolites such as sugars, amino acids, and organic acids, as well as secondary metabolites."},{"label":"Title","value":"Substrate flow in the rhizosphere"},{"label":"URL","value":"https://doi.org/10.1007/BF00011685\n"},{"label":"Date","value":"Dec, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"The amino acid composition of root exudates modulates bacterial metabolism, affecting the beneficial interaction between Arabidopsis roots and plant growth-promoting bacteria."},{"label":"Title","value":"The Arabidopsis LHT1 Amino Acid Transporter Contributes to Pseudomonas simiae-Mediated Plant Growth Promotion by Modulating Bacterial Metabolism in the Rhizosphere"},{"label":"URL","value":"https://doi.org/10.3390/plants12020371"},{"label":"Date","value":"Jan 12, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"UMAMIT transporters (Usually Multiple Amino acids Move In and out Transporters) are facilitator proteins that exhibit amino acid export activity in root-to-soil secretion."},{"label":"Title","value":"Amino Acid Export in Developing Arabidopsis Seeds Depends on UmamiT Facilitators"},{"label":"URL","value":"https://doi.org/10.1016/j.cub.2015.10.038"},{"label":"Date","value":"Dec 07, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular oncology / Immunotherapy
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Free-Format Question
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Demonstration of SLU7 as a new pan-cancer target
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https://www.biorxiv.org/content/10.1101/2025.08.25.672085v1
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Aug 29, 2025
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To evaluate SLU7 as a potential cancer therapy target, two Pm299L-derived cell lines were generated: Pm299L-iCas9-sgSLU7 and Pm299L-iCas9-sgNTC. First, Pm299L cells were transduced with lentiviral vectors encoding a DOX-inducible Cas9, and a single clone with strong inducible expression (Pm299L-iCas9) was selected. This clone was then transduced with sgRNAs targeting SLU7 exon 3 or a non-targeting control (sgNTC). Cells were selected using neomycin and puromycin, and expanded. SLU7 knockdown in the cell lines after DOX treatment was confirmed by Western blot, using antibodies against SLU7, Cas9, and other relevant markers (PARP1, ACTIN, γ-H2AX).
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- Band intensity of each protein evaluated
- Comparison of protein expression levels of SLU7, Cas9, PARP1, ACTIN, and γ-H2AX, in the cell lines (Pm299L-iCas9-sgSLU7 and Pm299L-iCas9-sgNTC)
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The target protein SLU7, the effector protein Cas9, the marker proteins PARP1 and γ-H2AX, and the control proteins ACTIN and GAPDH were evaluated by Western blot to assess the potential of SLU7 as a cancer therapy target. These proteins were extracted from two generated cell lines: Pm299L-iCas9-sgSLU7, a transducted cell line in which SLU7 gene is knocked down after DOX administration, and Pm299L-iCas9-sgNTC, a non-targeting control. After DOX administration in Pm299L-iCas9-sgSLU7 cells, which protein bands would be expected to show increased intensity on the Western blot compared to the control?
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Cas9, PARP1, and γ-H2AX
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- SLU7 is an essential splicing factor required for the survival of cancer cells.
- SLU7 knockdown induces apoptosis across different cancer types, preceded by a cascade of molecular events including oxidative stress, R-loop accumulation, transcription-dependent genomic instability, DNA damage, replicative catastrophe, inhibition of DNA methylation, and disruption of NMD.
- sgRNA are single-guide RNAs.
- Pm299L is a mouse hepatocellular carcinoma (HCC) cell line.
- Doxycycline (DOX) induces high expression of Cas9 in an inducible manner in this system, while the cells constitutively express either a sgRNA directed against the SLU7 gene (sgSLU7) or a non-targeting control sgRNA (sgNTC).
- Pm299L-iCas9-sgSLU7 is a mouse Pm299L cell line that was first transduced with lentiviral particles encoding a (DOX)-inducible Cas9, along with a sgRNA targeting exon 3 of the SLU7 gene.
- Pm299L-iCas9-sgNTC is a mouse Pm299L cell line first transduced with lentiviral particles encoding a doxycycline (DOX)-inducible Cas9 and a non-targeting (NTC) sgRNA.
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[{"label":"RBK Item","value":"SLU7 is an essential splicing factor for the survival of cancer cells."},{"label":"Title","value":"Splicing regulator SLU7 preserves survival of hepatocellular carcinoma cells and other solid tumors via oncogenic miR-17-92 cluster expression"},{"label":"URL","value":"https://doi.org/10.1038/onc.2015.517"},{"label":"Date","value":"Jan 25, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"SLU7 knockdown induces apoptosis across different cancer types, preceded by a cascade of molecular events: oxidative stress, R-loop accumulation, transcription-dependent genomic instability, DNA damage, replicative catastrophe, inhibition of DNA methylation, and disruption of NMD."},{"label":"Title","value":"Splicing Factor SLU7 Prevents Oxidative Stress-Mediated Hepatocyte Nuclear Factor 4α Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage"},{"label":"URL","value":"https://doi.org/10.1002/hep.32029"},{"label":"Date","value":"Nov, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Zoology / Cryobiology
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MCQ
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Cryopreservation of Platynereis dumerilii larvae
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https://www.biorxiv.org/content/10.1101/2025.07.31.667934v2
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Aug 2, 2025
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Researchers tested different individuals and combinations of cryoprotectant agents (CPAs), such as dimethyl sulfoxide (Me₂SO), ethylene glycol (EG), propylene glycol (PG), glycerol (Gly), and sucrose (SUC), to develop a cryopreservation protocol that ensures long-term viability and supports proper post-thaw growth and development of Platynereis dumerilii. Platynereis dumerilii were kept in a 50/50 mix of natural seawater and artificial sea water, adjusted to a salinity of 35 ppt, a pH between 7.9 and 8.2, a general culture temperature at 18-20 °C for optimum growth rate, and a 16:8 light/dark cycle. To assess the cryoprotectant toxicity, eight-days old larvae were exposed to CPA solutions in two phases. In the first phase, larvaes exposure to each permeating CPA had a duration of 3 minutes. The individual CPA analyzed were the following: Me₂SO, 1.4M; EG, 1.4M; PG, 1.4M. In the second phase, the exposure was of 30 minutes to a combination of CPAs that were tested by reducing Me₂O content and supplementing it with glycerol and/or sucrose. The combination of CPAs analyzed were the following: Me₂SO, 0.8M; Me₂SO 0.8M + 0.1% SUC (w/v); Me₂SO 0.8M + Gly 0.68M; Me₂SO 0.8M + Gly 0.68M + 0.1% SUC (w/v). After the exposure, the larvae were filtered, and transferred to clean sea water for observation.
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- Exposure time in minutes after exposure to individual and combined CPAs.
- Survival post-thaw percentage after exposure to individual and combined CPAs.
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The cryoprotectant toxicity of individual and combined cryoprotectant agents (CPAs) were evaluated in eight day old Platynereis dumerilii to develop a cryopreservation protocol. Larvae were observed after being exposed to CPAs in two phases. The first phase consisted of a 3 minute exposure to individual CPAs: Me₂SO, 1.4M; EG, 1.4M; PG, 1.4M. The second phase involved a 30 minute exposure to combined CPAs: Me₂SO, 0.8M; Me₂SO 0.8M + 0.1% SUC (w/v); Me₂SO 0.8M + Gly 0.68M; Me₂SO 0.8M + Gly 0.68M + 0.1% SUC (w/v). Which of the CPAs would you expect to result in the highest post-thaw survival percentage after the 3-minute exposure?
a) All individual CPAs tested will result in the same post-thaw survival percentage.
b) Only Me₂SO 1.4M will result in the highest post-thaw survival percentage.
c) Only EG 1.4M will result in the highest post-thaw survival percentage.
d) Only PG 1.4M will result in the highest post-thaw survival percentage.
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a) All individual CPAs tested will result in the same post-thaw survival percentage.
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- Platynereis dumerilii is a marine annelid that has emerged as a significant model organism in chronobiological, neurobiological, developmental and evolutionary biology research.
- Cryopreservation offers a means to store and preserve biological materials for future use enabling long-term storage, facilitating sample transportation, and ensuring the availability of biological specimens.
- Cryoprotectant agents (CPAs) are substances used to preserve the biological samples in cryobiology with different modes of action, some penetrating the tissue while others protecting the surface.
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[{"label":"RBK Item","value":"Platynereis dumerilii is a marine annelid that has emerged as a significant model organism in chronobiological, neurobiological, developmental and evolutionary biology research."},{"label":"Title","value":"Seasonal variation in UVA light drives hormonal and behavioral changes in a marine annelid via a ciliary opsin"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7611595/"},{"label":"Date","value":"Jan 11, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Cryopreservation offers a means to store and preserve biological materials for future use enabling long-term storage, facilitating sample transportation, and ensuring the availability of biological specimens."},{"label":"Title","value":"Cryopreservation of Marine Invertebrates: From Sperm to Complex Larval Stages"},{"label":"URL","value":"https://doi.org/10.1007/978-1-0716-0783-1_18"},{"label":"Date","value":"Aug 15, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"}]
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Biology
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Animal Behavior and Cognition
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MCQ
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Nighttime Caffeine Intake Increases Motor Impulsivity
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https://www.biorxiv.org/content/10.1101/2025.06.09.658656v1
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Jun 13, 2025
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Researchers examined whether nighttime caffeine consumption affected inhibitory control in female and male Drosophila melanogaster of the Canton-S (CS) wild-type strain. Flies were raised on a standard cornmeal/sucrose/yeast/agar medium at 25° C with 50 % relative humidity under a 12:12h light-dark cycle. For the experiment, flies were collected under carbon dioxide within two days after eclosion and housed in same-sex groups. For nighttime caffeine exposure, groups of female or male flies were transferred to vials containing caffeine-laced food 30 min before lights-off and remained on this food throughout the dark cycle. Caffeine concentrations used were 1, 5, 7.5, and 10 mg/ml. At the end of the dark cycle, the Go/No-Go assay was performed by placing individual flies into a clear rectangular plexiglass chamber connected to a filtered air source. After a 1-minute acclimation period, a continuous airflow of 10 L/min was applied for 10 minutes. Fly behavior was video recorded to monitor and analyze movements before and during airflow exposure. Movements exceeding 60 mm/sec were classified as loss of inhibition events (LIEs), which were scored per fly per min.
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- Number of movements exceeding 60 mm/sec following nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml).
- Number of loss of inhibition events (LIEs) following nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml).
- Comparison of the number of LIEs following consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml) between female and male flies.
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Nighttime consumption of different caffeine concentrations (1, 5, 7.5, and 10 mg/ml) in male and female Drosophila melanogaster of the Canton-S (CS) wild-type strain was evaluated to determine its effect on inhibitory control by loss of inhibition events (LIEs). Movements exceeding 60 mm/sec were counted as LIEs after nighttime caffeine exposure. These values were obtained through a Go/No-Go assay that was performed at the end of the dark cycle in flies by monitoring and analyzing movements before and during a continuous 10 L/min airflow exposure. Which of the following outcomes is most likely?
a) After nighttime caffeine consumption, male flies exhibited more LIEs than female flies at all concentrations tested.
b) After nighttime caffeine consumption, female flies exhibited more LIEs than male flies at all concentrations tested.
c) After nighttime caffeine consumption, there was no significant difference in LIEs between male and female flies at all concentrations tested.
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b) After nighttime caffeine consumption, female flies exhibited more LIEs than male flies at all concentrations tested.
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- Caffeine is a psychoactive substance that increases alertness, reduces fatigue, and improves performance, especially under conditions of sleep deprivation.
- Drosophila melanogaster is a fly species used as a model system to investigate how nighttime caffeine intake affects inhibitory control.
- Inhibitory control is a fundamental executive function responsible for suppressing inappropriate actions, such as impulsive flying in flies.
- Loss of inhibition event (LIEs) is a measure of impulsivity that in flies is quantified by rapid movements at speeds exceeding 60 mm/sec.
- Go/No-Go test measures the ability to suppress movement in response to adverse conditions such as strong airflow or predator sounds.
|
[{"label":"RBK Item","value":"Caffeine is a psychoactive substance that increases alertness, reduces fatigue, and improves performance, especially under conditions of sleep deprivation."},{"label":"Title","value":"Trends in intake and sources of caffeine in the diets of US adults: 2001–2010"},{"label":"URL","value":"https://doi.org/10.3945/ajcn.113.080077"},{"label":"Date","value":"May, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Loss of inhibition event (LIEs) is a measure of impulsivity that in flies is quantified by rapid movements at speeds exceeding 60 mm/sec."},{"label":"Title","value":"Social context and dopamine signaling converge in the mushroom body to drive impulsivity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11870619/"},{"label":"Date","value":"Feb 22, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Go/No-Go test measures the ability to suppress movement in response to adverse conditions such as strong airflow or predator sounds."},{"label":"Title","value":"Social context and dopamine signaling converge in the mushroom body to drive impulsivity"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11870619/"},{"label":"Date","value":"Feb 22, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Microbiology
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MCQ
|
Streptococcus pneumoniae accessory capsular genes modulate fitness, pathogenicity and immune evasion
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https://www.biorxiv.org/content/10.1101/2025.09.11.675585v1.full
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September 15, 2025
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Researchers deleted all six acl (accessory capsular locus) genes from the Streptococcus pneumoniae serotype 3 GPSC9-ST5435 strain BVY11Z and reintroduced the genes into the capsular locus of serotype 3 GPSC10-ST700 strain BVY23H, using an allelic replacement strategy. To evaluate the role of the serotype 3 acl in modulating susceptibility to opsonophagocytic killing (OPK), they subjected WT ST700 and its acl reintroduction mutant (ST700 acl+ -cat), as well as WT5435 and its acl deletion mutant (ST5435 acl::cat), to an OPK assay. To determine if the bacterial tyrosine kinase (BYK) capsule regulation system plays a role in OPK susceptibility, they additionally tested the ST5435 cpsB deletion mutant (ST5435 cpsB::spec) and ST5435 cpsD deletion mutant (ST5435 cpsD::cat) in the OPK assay.
Genetic manipulation of S. pneumoniae was carried out using a competence-stimulating peptide (CSP)-mediated transformation assay. Strains were grown in 12 mL of THY pH 6.8 supplemented with 1 mM CaCl2 and 0.2% BSA at 37°C with 5% CO2 to an OD600 of 0.01-0.03. Cultures were then harvested and resuspended in 1 mL of pre-warmed THY pH 8.0, supplemented with 1 mM CaCl2 and 0.2% BSA. 400 ng/ml CSP was added to the bacterial suspension (CSP-1 for ST5435, CSP-2 for ST700; Cambridge Biosciences). Suspensions were incubated at room temperature (RT) for 5 minutes, mixed with 300-500 ng transforming DNA, and further incubated at 37°C with 5% CO2 for 2 hours. The entire suspension was then plated on blood agar plates supplemented with relevant antibiotics. To construct the transforming DNA for making the unencapsulated (cps::cat) mutants, the areas flanking the capsular locus were amplified using primer pairs 001/002 and 003/004 from WT ST700 genomic DNA and primer pairs 001/002 and 005/006 from WT ST5435 genomic DNA. The chloramphenicol resistance cassette (cat) was amplified from pEMcat using primer pairs 007/008. PCR products corresponding to the upstream and downstream regions and cat were joined using overlap extension PCR (OE-PCR) with primer pairs 001/004 or 001/006, respectively. The purified OE-PCR product was used in transformation assays. Transforming DNA for making the acl-mutant (acl::cat) was constructed as described above using primer pairs 001/002 and 009/010 to amplify the up/downstream region of acl from ST5435 and primer pair 001/010 to generate the OE-PCR product. Transforming DNA for making the cpsD mutant (cpsD::cat) was constructed similarly using primer pairs 011/012 and 013/014 for the initial PCR and primer pair 011/014 for the OE-PCR product. Transforming DNA for making the cpsB mutant (cpsB::spec) utilized primer pairs 015/016 and 017/018 to amplify the flanking region, and primer pair 015/018 for the OE-PCR. Instead of cat, a spectinomycin resistance cassette (spec) was amplified from pR412 using primer pair 019/020 and used in OE-PCR. To reintroduce acl into ST700 (acl+), the entire acl region was amplified in 3kb fragments from WT ST5435 genomic DNA using primer pairs 021/022 and 023/024. The downstream region, which encompasses part of the coding region for Ugd, was amplified from WT ST700 genomic DNA using primer pairs 025/010. The three PCR pieces and the cat cassette were assembled using NEB Gibson Assembly master mix to obtain the transforming DNA.
OPK analysis was performed using a WHO-approved standardized assay. The strains were compared to assess the reduction in killing against a reference serotype 3 strain (an optochin-resistant variant of the ST180 strain Wu2) using pooled serum samples from adults vaccinated with PCV13. THY and 4% filtered fetal bovine serum were used for the assay. Strains were incubated with serial dilutions of pooled human serum prior to treatment with HL-60 cells, baby rabbit complement, and plating onto agar plates. The opsonic index was calculated as the reciprocal of the serum dilution, reducing the bacterial colony forming units (CFU) to 50% of the no serum control.
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- Opsonic index (OI) for each tested strain
- Bacterial colony forming units (CFU).
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Researchers tested whether the absence of acl genes contributes to increased opsonophagocytic resistance in Streptococcus pneumoniae. To test this hypothesis, they deleted all six acl (accessory capsular locus) genes from the Streptococcus pneumoniae serotype 3 GPSC9-ST5435 strain BVY11Z (hereafter WT ST5435) and reintroduced the genes into the capsular locus of serotype 3 GPSC10-ST700 strain BVY23H (hereafter WT ST700). Then, they subjected these strains to a WHO standard OPK assay using pooled serum from PCV-immunised adults. Additionally, they tested the ST5435 cpsB deletion mutant (ST5435 cpsB::spec) and ST5435 cpsD deletion mutant (ST5435 cpsD::cat) in the OPK assay. Which of the following outcomes are most likely?
A. Reintroducing the acl region into GPSC10-ST700 would reduce its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would reduce its resistance to opsonophagocytic killing.
B. Reintroducing the acl region into GPSC10-ST700 would increase its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would increase its resistance to opsonophagocytic killing
C. Reintroducing the acl region into GPSC10-ST700 would increase its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would decrease its resistance to opsonophagocytic killing
D. Reintroducing the acl region into GPSC10-ST700 would decrease its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would increase its resistance to opsonophagocytic killing.
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A. Reintroducing the acl region into GPSC10-ST700 would reduce its resistance to opsonophagocytic killing, and mutating acl in a serotype 3 ST5435 background would reduce its resistance to opsonophagocytic killing.
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1. Pneumococcal polysaccharide-conjugate vaccines (PCV) target the polysaccharide capsule (CPS)
2. Current PCVs induce suboptimal protection against serotype 3 strains
3. (ST) 700–GPSC10 serotype 3 lineage is characterized by the absence of at least 6 acl genes and a distinct antimicrobial resistance (AMR) profile compared to other serotype 3 strains.
4. Accessory capsular genes (acl) regulate capsule production and shedding.
5. cpsB and cpsD are truncated homologs of acl genes, and are part of a bacterial tyrosine kinase (BYK) system that regulates capsule expression and chain length
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[{"label":"RBK Item","value":"(ST) 700–GPSC10 serotype 3 lineage is characterized by the absence of at least 6 acl genes and a distinct antimicrobial resistance (AMR) profile compared to other serotype 3 strains."},{"label":"Title","value":"Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction"},{"label":"URL","value":"https://academic.oup.com/jid/article/230/1/e189/7633460?login=false"},{"label":"Date","value":"March 26, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"cpsB and cpsD are truncated homologs of acl genes, and are part of a bacterial tyrosine kinase (BYK) system that regulates capsule expression and chain length "},{"label":"Title","value":"The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers"},{"label":"URL","value":"https://www.pnas.org/doi/full/10.1073/pnas.2103377118"},{"label":"Date","value":"November 3, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Pneumococcal polysaccharide-conjugate vaccines (PCV) target the polysaccharide capsule (CPS)"},{"label":"Title","value":"Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis"},{"label":"URL","value":"https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00665-0/fulltext"},{"label":"Date","value":"Dec 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Current PCVs induce suboptimal protection against serotype 3 strains"},{"label":"Title","value":"Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis"},{"label":"URL","value":"https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(24)00665-0/fulltext"},{"label":"Date","value":"Dec 17, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Pathology
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Free-Format Question
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A hierarchy of causes of death in senescent C. elegans
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https://www.biorxiv.org/content/10.1101/2025.08.21.671442v1
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Aug 25, 2025
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Researchers tested whether uterine tumors contribute to late-life mortality in Caenorhabditis elegans in the absence of bacterial infection. Worms were grown at 20˚C on agar plates containing nematode growth media, seeded with E. coli OP50 as a food source. Nematodes at two developmental stages, L4 and D2 (defined as day 0 and day 2 of adulthood, respectively), were evaluated under the following conditions of substance administration: 50 μM floxuridine (FUDR); 50 μM FUDR + 4mM carbenicillin (Carb). Mortality was assessed every 1 - 2 days, with individuals considered as alive if any movement was observed.
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- Lifespan in days under substance administration (50 μM FUDR; 50 μM FUDR + 4mM Carb).
- Survival percentage under substance administration (50 μM FUDR; 50 μM FUDR + 4mM Carb).
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Mortality scoring was performed in Caenorhabditis elegans at two stages, L4 and D2, following administration of 50 μM floxuridine (FUDR), and 50 μM FUDR + 4mM carbenicillin (Carb), to evaluate whether uterine tumors contribute to late-life mortality when bacterial infection is inhibited. What would you expect to happen to the lifespan of C. elegans at each stage when FUDR + Carb are administered?
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In the presence of Carb and FUDR, L4 had a slightly shortened lifespan, but D2 had a significantly increased lifespan.
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- Caenorhabditis elegans is a short-lived nematode whose death results from a combination of extrinsic and intrinsic factors, with infection by its bacterial food source being one of the major extrinsic causes.
- Escherichia coli is a bacteria used as a food source for C. elegans and is the major cause of infection to which all individuals succumb in later life.
- Uterine tumors are among the most striking pathologies observed in senescent C. elegans hermaphrodites.
- 5-fluoro-2’-deoxyuridine or floxuridine (FUDR) is a drug used in the treatment of colorectal cancer that can prevent uterine tumor development.
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[{"label":"RBK Item","value":"Caenorhabditis elegans is a short-lived nematode whose death results from a combination of extrinsic and intrinsic factors, with infection by its bacterial food source being one of the major extrinsic causes."},{"label":"Title","value":"Run-on of germline apoptosis promotes gonad senescence in C. elegans"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5129915/"},{"label":"Date","value":"May 31, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Escherichia coli is a bacteria used as a food source for C. elegans and is the major cause of infection to which all individuals succumb in later life."},{"label":"Title","value":"Genetic analysis of tissue aging in Caenorhabditis elegans: a role for heat-shock factor and bacterial proliferation."},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC1462187/"},{"label":"Date","value":"Jul 01, 2002"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"Uterine tumors are among the most striking pathologies observed in senescent C. elegans hermaphrodites."},{"label":"Title","value":"TGF-β and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2955983/"},{"label":"Date","value":"Oct 15, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"5-fluoro-2’-deoxyuridine or floxuridine (FUDR) is a drug used in the treatment of colorectal cancer that can prevent uterine tumor development."},{"label":"Title","value":"MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC3969279/"},{"label":"Date","value":"Feb 16, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Plant genetics
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MCQ
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DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana
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https://www.biorxiv.org/content/10.1101/2025.08.21.671646v1.full
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August 26, 2025.
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Researchers investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana wild-type accessions Columbia-0 (Col-0) and C24 as parental lines. Two heterozygous mutants were generated: (a) C24 (DDM1/ddm1-9), resulting from a cross between wild-type C24 and the ddm1-9 mutant line (C24 background); and (b) Col (DDM1/ddm1-1), resulting from a cross between wild-type Col-0 and the ddm1-1 mutant line (Col-0 background). The F1 generation was obtained by crossing the two heterozygous mutants, C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1). Plants were grown under controlled environmental conditions with a 16-h light / 8-h dark photoperiod at 22 °C. Seeds were sown on plastic dishes containing Murashige and Skoog (MS) agar medium supplemented with 1.0% sucrose (pH 5.7), and seedlings were transferred to soil 14 days after sowing (DAS). Rosette diameter and leaf area were measured to evaluate plant size and heterosis in F1 plants at 14, 21, and 28 DAS. Rosette diameter was defined as the maximum diameter of the rosette, measured between the two largest leaves at a given developmental stage. It depends on both the leaf blade and petiole lengths. Leaf area was calculated from photographs using image analysis with ImageJ software.
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- Rosette diameter (mm) at 14, 21, and 28 days after sowing in heterozygous and homozygous F1 lines after the cross of heterozygous mutants (C24 (DDM1/ddm1-9) x Col (DDM1/ddm1-1)).
- Leaf area at 14, 21, and 28 days after sowing in heterozygous and homozygous F1 lines after the cross of heterozygous mutants (C24 (DDM1/ddm1-9) x Col (DDM1/ddm1-1)).
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Researchers investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana wild-type accessions Columbia-0 and C24. To determine the effect of the DDM1 mutation, two heterozygous mutants, C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1), obtained from crosses with the respective wild-type accessions, were crossed to evaluate rosette diameter (mm) at 14, 21, and 28 days after sowing (DAS). At which time point after sowing is it most likely that the cross between C24 (DDM1/ddm1-9) and Col (DDM1/ddm1-1) will show the smallest statistical differences in rosette diameter among genotypes?
A. At 14 DAS.
B. At 21 DAS.
C. At 28 DAS.
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B. At 21 DAS.
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- Heterosis, also known as hybrid vigor, refers to the superior performance of the first filial generation (F1) plants compared to their parental lines.
- Epigenetics refers to mechanisms that influence gene regulatory networks without altering the underlying DNA sequence.
- Epigenetic regulation is important in the control of heterosis.
- DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeling factor that has been shown to diminish heterosis in A. thaliana.
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[{"label":"RBK Item","value":"Epigenetics refers to mechanisms that influence gene regulatory networks without altering the underlying DNA sequence."},{"label":"Title","value":"SHeterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity"},{"label":"URL","value":"https://www.pnas.org/doi/10.1073/pnas.1204464109"},{"label":"Date","value":"April 09, 2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Epigenetic regulation is important in the control of heterosis"},{"label":"Title","value":"Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids"},{"label":"URL","value":"https://academic.oup.com/plphys/article/176/2/1627/6117228"},{"label":"Date","value":"Dec 01, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"DECREASE IN DNA METHYLATION 1 (DDM1) is a chromatin remodeling factor that has been shown to diminish heterosis in A. thaliana."},{"label":"Title","value":"Role of DNA methylation in hybrid vigor in Arabidopsis thaliana"},{"label":"URL","value":"https://www.pnas.org/doi/10.1073/pnas.1613372113?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed"},{"label":"Date","value":"Oct 7, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Entomology
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MCQ
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Effects of Three Natural Dietary Compounds on Insect Pests
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https://www.biorxiv.org/content/10.1101/2025.05.23.655814v2
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May 28, 2025
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Researchers evaluated the relative efficacy of three natural compounds —neem oil, boric acid, and gallotannin acid— against larvae of three pest species: Rhynchophorus ferrugineus (red palm weevil), Plodia interpunctella (Indian meal moth), and Spodoptera exigua (beet armyworm). The larvae were reared on an optimal artificial semi‒diet composed of agar (20 g), distilled water (880 ml), brewer’s yeast (50 g), wheat germ (50 g), corn meal (50 g), ascorbic acid (4.5 g), coconut fiber (8 g), and a vitamin/amino acid additive (50 ml). The diet provided 15.0% crude protein (as a percentage of dry weight). The rearing of R. ferrugineus was conducted following the protocol established by Martin & Cabello (2006), whereas that of P. interpunctella and S. exigua followed the method of Cabello et al. (1984). The three compounds tested were boric acid (99.5%, Panreac Quimica S.L.U., Barcelona, Spain), gallotannin acid (tannic acid 99.5%, Panreac Quimica S.L.U., Barcelona, Spain), and neem oil (azadirachtin, 3.2% LS, Sipcam, Valencia, Spain). Each II-instar larva in a 20 ml Coulter vial (20 ml) was an experimental unit. Treatments included five neem oil concentrations (0, 6.3, 12.5, 25.0, 50.0 ppm), six boric acid concentrations (0, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm), and seven gallotannin acid concentrations (0, 156.3, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm). There were 20 repetitions per treatment (concentration), totaling 100 experimental units for neem oil trial, 120 for boric acid trial, and 140 for gallotannin acid trial. Larval survival was tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species. Trials were conducted at 25±2 °C, 65±10% R.H. and photo period of 0:24 hours light: dark on R. ferrugineus and P. interpunctella species, and 16:9 hours on S. exigua species. Larval survival was analyzed by the Kaplan-Meier method with subsequent comparisons between treatments carried out via the long-rank test in each trial. These analyses were performed via IBM SPSS software, version 28. Effective median lethal concentrations (LC50) were calculated via probit analysis. If there is natural mortality in the controls, adjusted mortality is used according to Abbott’s formula.
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- Larval survival (tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species)
- Effective median lethal concentrations (LC50) of the tested compounds (neem oil, boric acid, and gallotannin acid)
- Corrected mortality (%) across species (Rhynchophorus ferrugineus, Plodia interpunctella and Spodoptera exigua) after compound treatment (neem oil, boric acid, and gallotannin acid)
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Researchers evaluated the relative efficacy of three natural compounds —neem oil, boric acid, and gallotannin acid— against larvae of three pest species: Rhynchophorus ferrugineus, Plodia interpunctella, and Spodoptera exigua. The larvae were reared on an optimal artificial semi‒diet composed of agar (20 g), distilled water (880 ml), brewer’s yeast (50 g), wheat germ (50 g), corn meal (50 g), ascorbic acid (4.5 g), coconut fiber (8 g), and a vitamin/amino acid additive (50 ml). The diet provided 15.0% crude protein (as a percentage of dry weight). The three compounds tested were boric acid (99.5%), gallotannin acid (tannic acid 99.5%), and neem oil (azadirachtin, 3.2% LS). Each II-instar larva in a 20 ml Coulter vial (20 ml) was an experimental unit. Treatments included five neem oil concentrations (0, 6.3, 12.5, 25.0, 50.0 ppm), six boric acid concentrations (0, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm), and seven gallotannin acid concentrations (0, 156.3, 312.5, 625.0, 1,250.0, 2,500.0, 5,000.0 ppm). There were 20 repetitions per treatment (concentration), totaling 100 experimental units for neem oil trial, 120 for boric acid trial, and 140 for gallotannin acid trial. Larval survival was tracked at intervals: 3, 6, 9, 12, 15, and 20 days for R. ferrugineus, and 3, 6, 9, 12, and 15 days for the other species. Trials were conducted at 25±2 °C, 65±10% R.H. and photo period of 0:24 hours light: dark on R. ferrugineus and P. interpunctella species, and 16:9 hours on S. exigua species. Larval survival was analyzed by the Kaplan-Meier method. Effective median lethal concentrations (LC50) were calculated via probit analysis. If there is natural mortality in the controls, adjusted mortality is used according to Abbott’s formula. Which of the following outcomes is most likely?
A. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for all species
B. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for Rhynchophorus ferrugineus and Plodia interpunctella, but not for Spodoptera exigua.
C At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 12 days for Rhynchophorus ferrugineus only
D. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 15 days for all species
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A. At the highest concentration tested (5000 ppm), boric acid resulted in an effectiveness (corrected mortalities) of 100% at 9 or 12 days for all species
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- The red palm weevil Rhynchophorus ferrugineus is a pest species that affects various palm and coconut trees
- The Indian meal moth Plodia interpunctella is a species that affects mainly stored plant products
- The beet armyworm Spodoptera exigua is a pest affecting herbaceous and horticultural crops
- Boric acid and borate salts serve as active ingredients in pesticides, effectively targeting insects, spiders, mites, algae, molds, fungi, and weeds.
- Gallotannin acid, also known as tannic acid, is the most well known hydrolysable tannin.
- Azadirachtin, which is a tetranortriterpenoid, is an active ingredient of neem (Azadirachta indica A. Juss.) seed oil. It controls two hundred species of insects, including locusts, gypsy moths, cockroaches, and fall armyworms
|
[{"label":"RBK Item","value":"The red palm weevil Rhynchophorus ferrugineus is a pest species that affects various palm and coconut trees"},{"label":"Title","value":"Biología y ecología del Curculiónido rojo de la palmera, Rhynchophorus ferrugineus"},{"label":"URL","value":"https://www.researchgate.net/publication/256445857_Biologia_y_ecologia_del_Curculionido_rojo_de_la_palmera_Rhynchophorus_ferrugineus_Olivier_1790_Col_Dryophthoridae"},{"label":"Date","value":"January, 2005 "},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The Indian meal moth Plodia interpunctella is a species that affects mainly stored plant products"},{"label":"Title","value":"Biology and management of Plodia interpunctella (Lepidoptera: Pyralidae) in stored products"},{"label":"URL","value":"https://www.sciencedirect.com/science/article/abs/pii/S0022474X06000671?via%3Dihub"},{"label":"Date","value":"December, 2007"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"The beet armyworm Spodoptera exigua is a pest affecting herbaceous and horticultural crops"},{"label":"Title","value":"Biología, ecología y control de Spodoptera exigua (Hübner, 1808) (Lep., Noctuidae) en cultivo de pimiento en invernadero"},{"label":"URL","value":"https://digibug.ugr.es/handle/10481/55815"},{"label":"Date","value":"1994"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA, pdf available for download."},{"label":"RBK Item","value":"Boric acid and borate salts serve as active ingredients in pesticides, effectively targeting insects, spiders, mites, algae, molds, fungi, and weeds."},{"label":"Title","value":"Boric Acid Technical Fact Sheet"},{"label":"URL","value":"https://www.npic.orst.edu/factsheets/archive/borictech.html"},{"label":"Date","value":"2012"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Gallotannin acid, also known as tannic acid, is the most well known hydrolysable tannin."},{"label":"Title","value":"The Multifunctional Roles of Polyphenols in Plant-Herbivore Interactions"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/33535511/"},{"label":"Date","value":"Feb 01, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Azadirachtin, which is a tetranortriterpenoid, is an active ingredient of neem (Azadirachta indica A. Juss.) seed oil. It controls two hundred species of insects, including locusts, gypsy moths, cockroaches, and fall armyworms"},{"label":"Title","value":"The Toxicology and Biochemistry of Insects, 1st Edition"},{"label":"URL","value":"https://www.taylorfrancis.com/books/mono/10.1201/9781420059762/toxicology-biochemistry-insecticides-simon-yu"},{"label":"Date","value":"March 04, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"}]
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Biology
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Molecular Biology
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Free-Format Question
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A novel expression system enabling scalable production of glycosylated flavonoids in Escherichia coli W using a plant-derived toxic gene
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https://www.biorxiv.org/content/10.1101/2025.09.09.674713v1
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Sep 13, 2025
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Researchers compared prunin production in the SBG2339 strain, which contains the synthetic phosphate (Pi)-depletion promoter system known as Pliar, with conventional strains SBG1818 and SBG2303, which use the RhaR/Prha and XylS/Pm promoters, respectively. To evaluate the performance of this regulatory system, the E. coli platform SBG1888 was first constructed to optimize efficient UDPG biosynthesis. This strain combined the parental chassis SBG1869 with the pUDG plasmid. For consistent expression analysis and fair comparison with conventional systems, all transcriptional units were standardized using the same ribosome binding site (RBS; STD) and a low-copy origin of replication (RK2). The SbaiC7OGT gene was then expressed in SBG1888 under the control of three different regulatory systems: 1) The phosphate-responsive Pliar53 promoter, resulting in strain SBG2339; 2) The RhaR/Prha promoter, resulting in strain SBG1818; 3) The XylS/Pm promoter, resulting in strain SBG2303. All media used with the Pliar53 system were supplemented with 5 mM phosphate. Gene expression was induced only during the production phase, using phosphate-depleted M3 medium supplemented with yeast extract (YE). A concentration of 3 mM naringenin was administered as the substrate for the production of naringenin-7-O-glucoside (prunin). Flavonoid quantification was carried out using high-performance liquid chromatography (HPLC) coupled with a diode array detector (DAD).
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- Prunin concentration in different E. coli strains (SBG2339, SBG1818, and SBG2303)
- Comparison of prunin production driven by different promoter systems (Pliar53, RhaR/Prha, and XylS/Pm)
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Prunin production regulated by three different systems (Pliar53, RhaR/Prha, and XylS/Pm)was evaluated using E. coli strains SBG2339, SBG1818, and SBG2303, respectively. These strains were derived from the engineered platform SBG1888, which expresses the SbaiC7OGT gene. Prunin concentrations were measured in each strain after 24 hours of naringenin administration to enhance flavonoid production, and quantified using high-performance liquid chromatography (HPLC). What would you expect to happen to prunin production in strain SBG2303 compared to the other two strains evaluated?
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The SBG2303 strain will yield a lower prunin production than both the SBG2339 and SBG1818 strains.
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- Prunin, or naringenin-7-O-glucoside, is a flavonoid biosynthesized in plants.
- Naringenin is a substrate used for the production of prunin.
- SbaiC7OGT is a UDP-glycosyltransferase gene from Scutellaria baicalensis that catalyzes the 7-O-glycosylation of flavonoids.
- Escherichia coli is a microbial host commonly used for the heterologous expression of plant-derived molecules.
- Pliar53 is a synthetic phosphate (Pi)-depletion promoter system inspired by the bacterial phosphate (PHO) starvation response, in which low Pi concentrations activate the PHO regulon.
- XylS/Pm is a regulatory system inducible by m-toluic acid, whose derivatives are toxic and may interfere with enzymatic reactions.
- RhaR/Prha is a regulatory system inducible by L-rhamnose, whose high cost limits its application in large-scale processes.
|
[{"label":"RBK Item","value":"Naringenin is a substrate used for the production of prunin."},{"label":"Title","value":"Flavonoids naringenin chalcone, naringenin, dihydrotricin, and tricin are lignin monomers in papyrus"},{"label":"URL","value":"https://academic.oup.com/plphys/article/188/1/208/6400262"},{"label":"Date","value":"Oct 18, 2021"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"SbaiC7OGT is a UDP-glycosyltransferase gene from Scutellaria baicalensis that catalyzes the 7-O-glycosylation of flavonoids."},{"label":"Title","value":"Cloning and expression of UDP-glucose: flavonoid 7-O-glucosyltransferase from hairy root cultures of Scutellaria baicalensis"},{"label":"URL","value":"https://link.springer.com/article/10.1007/PL00008158"},{"label":"Date","value":"May, 2000"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"Escherichia coli is a microbial host commonly used for the heterologous expression of plant-derived molecules."},{"label":"Title","value":"Flavonoids, terpenoids, and polyketide antibiotics: Role of glycosylation and biocatalytic tactics in engineering glycosylation"},{"label":"URL","value":"https://doi.org/10.1016/j.biotechadv.2020.107550"},{"label":"Date","value":"May, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"Pliar53 is a synthetic phosphate (Pi)-depletion promoter system inspired by the bacterial phosphate (PHO) starvation response, in which low Pi concentrations activate the PHO regulon."},{"label":"Title","value":"Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli"},{"label":"URL","value":"https://doi.org/10.1016/j.biotechadv.2023.108154"},{"label":"Date","value":"Sep, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"Paywalled"},{"label":"RBK Item","value":"XylS/Pm is a regulatory system inducible by m-toluic acid, whose derivatives are toxic and may interfere with enzymatic reactions."},{"label":"Title","value":"Modular plasmid design for autonomous multi-protein expression in Escherichia coli"},{"label":"URL","value":"https://jbioleng.biomedcentral.com/articles/10.1186/s13036-025-00483-2"},{"label":"Date","value":"Feb 10, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"},{"label":"RBK Item","value":"RhaR/Prha is a regulatory system inducible by L-rhamnose, whose high cost limits its application in large-scale processes."},{"label":"Title","value":"Modular plasmid design for autonomous multi-protein expression in Escherichia coli"},{"label":"URL","value":"https://jbioleng.biomedcentral.com/articles/10.1186/s13036-025-00483-2"},{"label":"Date","value":"Feb 10, 2025"},{"label":"Justification (\"Paywalled\", \"OA\", \"No OA Exists\")","value":"OA"}]
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Biology
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Molecular Biology / Genetics
|
Free-Format Question
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Loss-of-function mutations in PLD4 lead to systemic lupus erythematosus
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https://www.nature.com/articles/s41586-025-09513-x
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September 10, 2025
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Researchers tested whether six mutations (P181L, D189E, R201Q, Y248C, A323V, G457D) in phospholipase D family member 4 (PLD4) from patients with systemic lupus erythematosus (SLE) had any effect on exonuclease activity. To evaluate the mutation, an assay was performed using lysates from reconstituted HEK293T PLD3-KO with wild-type PLD4 cells that were maintained in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% penicillin-streptomycin. Protein lysates were collected and purified using Flag-tag magnetic beads, then subjected to a PLD4 enzymatic activity assay (50 mM MES, pH 5.5, 150 mM NaCl, 2.5 μM substrate, 10 nM or 20 nM purified PLD4). The incubation was performed at 37 ° C for various time points (16, 35, and 50 h) and analyzed by TBE–PAGE, with nucleic acid staining conducted for 15 minutes prior to imaging.
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- Intensity of ssDNA band fragmentation across mutants (P181L, D189E, R201Q, Y248C, A323V, G457D) at 16, 35 and 50 hours.
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Six mutations (P181L, D189E, R201Q, Y248C, A323V, G457D) in phospholipase D family member 4 (PLD4) from patients with systemic lupus erythematosus (SLE) were evaluated in cell lysates from reconstituted HEK293T PLD3-KO with wild-type PLD4 cells to evaluate the effect on exonuclease activity. Previously, cells were in Dulbecco's modified Eagle’s medium supplemented with 10% FBS and 1% penicillin-streptomycin. Protein lysates, collected and purified using Flag-tag magnetic beads, were subjected to a PLD4 enzymatic activity assay (50 mM MES, pH 5.5, 150 mM NaCl, 2.5 μM substrate, 10 nM or 20 nM purified PLD4) and incubated at 37 ° C (16, 35, and 50 h). Analysis was performed through TBE–PAGE, with nucleic acid staining conducted for 15 minutes prior to imaging. Which of the evaluated mutations are expected to show ssDNA fragmentation?
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None of the mutants are expected to show ssDNA fragmentation
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- Systemic lupus erythematosus (SLE) is a complex multiorgan condition of variable severity.
- Phospholipase D family member 4 (PLD4) is a 5′ exonuclease that localizes in the endolysosomes and can cleave single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), thereby restricting the overactivation of TLR7 and TLR9.
|
[{"label":"RBK Item","value":"Systemic lupus erythematosus (SLE) is a complex multiorgan condition of variable severity."},{"label":"Title","value":"Genetics and pathogenesis of systemic lupus erythematosus and lupus nephritis"},{"label":"URL","value":"https://pubmed.ncbi.nlm.nih.gov/25825084/"},{"label":"Date","value":"Jun, 2015"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"Paywalled"},{"label":"RBK Item","value":"Phospholipase D family member 4 (PLD4) is a 5′ exonuclease that localizes in the endolysosomes and can cleave single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), thereby restricting the overactivation of TLR7 and TLR9."},{"label":"Title","value":"PLD3 and PLD4 are single stranded acid exonucleases that regulate endosomal nucleic acid sensing"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6105523/"},{"label":"Date","value":"Feb 13, 2019"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics
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Free-Format Question
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ARABIDOPSIS Bsister and SEEDSTICK MADS-box transcription factors modulate maternal nutrient flow for seed development in Arabidopsis
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https://www.biorxiv.org/content/10.1101/2025.07.21.665905v1
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July 24, 2025
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Researchers evaluated whether mutation of abs (tt16-6) and stk (stk-2) in Arabidopsis thaliana had any effect in the development of ovules and seeds by monitoring scratch accumulation. A wild-type seed (wt), and mutant seeds (abs, stk, and abs stk) were sown either directly on soil or on Murashige and Skoog (MS) medium and then moved to soil. Before sowing in germination medium, seeds were surface-sterilized with 70% ethanol for 2 minutes (min), 1% bleach for 5 min, and then washed three times with sterile water. After 10 days, the seedlings were moved to soil and grown in a growth chamber under long-day conditions (22°C, 16 h light/8 h dark).To visualize starch accumulation, pistils were isolated from flowers before anthesis. Starch staining was performed with Lugol's solution and the pistils were dissected in water to isolate the ovules. The signal was observed using a Zeiss Axiophot D1 microscope equipped with DIC optics. Images were recorded with an Axiocam MRc5 camera (Zeiss) using the Axiovision program.
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- Lugol staining intensity in mature ovules of Arabidopsis thaliana to assess starch accumulation across wild-type (WT) and mutant lines (abs, stk, and abs stk).
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Starch accumulation was determined by Lugol staining intensity in isolated ovules from dissected pistils of Arabidopsis thaliana wild-type (WT) and mutant lines (abs, stk, and abs stk). Pistils were collected from flowers prior to anthesis, from plants grown from seeds previously sown either directly in soil or initially on Murashige and Skoog (MS) medium and later transferred to soil. Before sowing on germination medium, seeds were surface-sterilized with 70% ethanol for 2 minutes, followed by 1% bleach for 5 minutes, and rinsed with sterile water. After 10 days, seedlings were transferred to soil and grown under long-day conditions in a growth chamber. Starch staining was performed using Lugol's solution, and signal detection was carried out with a Zeiss Axiophot D1 microscope equipped with DIC optics. At the final stages of ovule development in the abs mutant, based on Lugol staining intensity, which ovules sections would be expected to show higher starch accumulation?
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Higher starch accumulation is expected within the embryo sac, at the boundary between the nucellus and the chalaza, between the chalaza and the funiculus, and in the micropylar integuments.
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- Starch accumulation occurs in gamethophytic and sporophytic tissues when arabidopsis ovules behave as sink organs.
- ARABIDOPSIS Bsister/TRANSPARENT TESTA 16 (ABS/TT16) sporophytically expresses MADS-box genes that regulates the differentiation and pigmentation of the endothelium, as well as nucellus degeneration.
- Abs mutants exhibit abnormal cell morphology in the endothelium, and after fertilization, fails to accumulate proanthocyanidins (PAs) that give the typical pigmentation to the Arabidopsis seeds.
- SEEDSTICK (STK) sporophytically expresses MADS-box genes that are required for seed coat differentiation, seed size and seed abscission.
- Stk mutants are characterized by ectopic accumulation of PAs in the seed coat.
- Abs stk double mutants have ovules that are characterized by an increased accumulation of starch, lack of endothelium differentiation and division, and severe fertility defects.
|
[{"label":"RBK Item","value":"Starch accumulation occurs in gamethophytic and sporophytic tissues when arabidopsis ovules behave as sink organs."},{"label":"Title","value":"Starch Turnover and Metabolism during Flower and Early Embryo Development"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5129708/"},{"label":"Date","value":"Oct 28, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"ARABIDOPSIS Bsister/TRANSPARENT TESTA 16 (ABS/TT16) sporophytically expresses MADS-box genes that regulates the differentiation and pigmentation of the endothelium, as well as nucellus degeneration."},{"label":"Title","value":"Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5399669/"},{"label":"Date","value":"Apr 15, 2017"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Abs mutants exhibit abnormal cell morphology in the endothelium, and after fertilization, fails to accumulate proanthocyanidins (PAs) that give the typical pigmentation to the Arabidopsis seeds."},{"label":"Title","value":"Proanthocyanidin-Accumulating Cells in Arabidopsis Testa: Regulation of Differentiation and Role in Seed Development"},{"label":"URL","value":"https://pmc.ncbi.nlm.nih.gov/articles/PMC280558/"},{"label":"Date","value":"Nov, 2003"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"SEEDSTICK (STK) sporophytically expresses MADS-box genes that are required for seed coat differentiation, seed size and seed abscission."},{"label":"Title","value":"SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004856"},{"label":"Date","value":"Dec 18, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Stk mutants are characterized by ectopic accumulation of PAs in the seed coat."},{"label":"Title","value":"SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004856"},{"label":"Date","value":"Dec 18, 2014"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Abs stk double mutants have ovules that are characterized by an increased accumulation of starch, lack of endothelium differentiation and division, and severe fertility defects. "},{"label":"Title","value":"The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2011.04878.x"},{"label":"Date","value":"Dec 16, 2011"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant genetics / Plant biotechnology
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Free-Format Question
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Diploid gametes in maize by mutation of A-Type cyclins: a step towards apomeiosis and synthetic apomixis
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https://www.biorxiv.org/content/10.1101/2025.05.16.654085v1
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May 19, 2025
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Researchers tested whether the maize genome contains A-type cyclins similar to those found in Arabidopsis thaliana. They identified eight A-type cyclins and tested their ability to produce diploid gametes in the B104 maize variety. To determine whether the loss of function of maize A-type cyclins results in diploid gamete formation, the researchers used CRISPR-Cas9 technology to create single and multiplexed gRNAs that targeted three A-type cyclins: CYC2, CYC6, and CYC27, because those genes were more abundant in Meiosis I than the others. Edits on the target genes were confirmed by DNA sequencing (single and multiplexed (CYC2-CYC6 and CYC2-CYC27)). Diploid gamete formation was evaluated by Flow Cytometry, using WT B104 pollen grains and leaves to determine the haploid-diploid controls. To assess the penetrance of diploid gamete formation, they performed crosses using the knock-out mutants as mother or father when crossing to wild-type plants.
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- Ploidy of male gametes and somatic cells, determined by measuring DNA content of nuclei from pollen and leaves using flow cytometry.
- Penetrance of the diploid gamete phenotype, inferred by calculating the percentage of filled, viable kernels resulting from reciprocal crosses between mutant and wild-type plants.
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Diploid gamete formation regulated by A-type cyclins in maize was evaluated by targeting three genes using CRISPR-Cas9 in a single or multiplexed fashion. Diploid gamete formation was measured by performing flow cytometry on pollen grains or leaves of edited plants. What ploidy would you expect to find in an individual derived from a self-pollinated plant edited in CYC6?
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Progeny are diploid because the single mutant produces normal haploid gametes, showing that neither male nor female meiosis was disrupted to a detectable level.
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1. A-type cyclins are required for meiosis II.
2. Unreduced gametes are gametes that did not undergo a meiotic division, resulting in 2n gametes.
3. Multiplexed gRNAs refer to constructs containing gRNAs that target more than one gene.
4. Wild-type Maize is a diploid species
|
[{"label":"RBK Item","value":"A-type cyclins are required for meiosis II."},{"label":"Title","value":"The CYCLIN-A CYCA1;2/TAM Is Required for the Meiosis I to Meiosis II Transition and Cooperates with OSD1 for the Prophase to First Meiotic Division Transition"},{"label":"URL","value":"https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000989"},{"label":"Date","value":"Jun 17, 2010"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Unreduced gametes are gametes that did not undergo a meiotic division, resulting in 2n gametes."},{"label":"Title","value":"Turning Meiosis into Mitosis"},{"label":"URL","value":"https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000124"},{"label":"Date","value":"Jun 9, 2009"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Biology
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Plant Biotechnology, Developmental Genetics
|
Free-Format Question
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Gene regulatory network analysis of somatic embryogenesis identifies morphogenic genes that increase maize transformation frequency
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https://www.biorxiv.org/content/10.1101/2025.06.22.659756v1
|
June 23, 2025
|
An experiment was conducted to identify new morphogenic regulator genes that could improve maize transformation efficiency.
Researchers induced somatic embryogenesis by transforming immature maize embryos with Agrobacterium carrying vectors expressing BABY BOOM and WUSCHEL2. 1 week after transformation, transformed cells were isolated and sorted using fluorescence-activated cell sorting, yielding approx 100,000 cells for single-cell RNA sequencing (10x Genomics). After quality filtering, 6,830 cells were analyzed. Gene regulatory network inference using MINI-EX identified regulons in clusters associated with somatic embryogenesis, which were prioritized using text mining of relevant literature, yielding 60 candidate genes. These were screened by expressing each under a maize ubiquitin promoter in vectors containing a RUBY reporter (producing visible red pigment for visual confirmation). Immature B104 maize embryos were transformed via Agrobacterium, and morphogenic responses were monitored by light microscopy. Four candidates (bHLH48, EREB152, GRF4, and HB77) showed the strongest responses and were selected for validation.
For validation, each candidate was cloned into vector pG3K-Cre-AG-RUBY with a Cre/loxP auto-excision system. Immature zygotic embryos from B104 maize (11-12 days after pollination, from at least three ears) were transformed using Agrobacterium, with approximately 189-194 explants per treatment. Five treatments were tested: the four candidates plus tdTomato (negative control). At 43 days after transformation, explants with RUBY-expressing shoots were imaged using a Canon EOS 1200D camera and counted, and transformation frequency was calculated as the percentage of explants producing transgenic shoots (number of embryos with RUBY-positive shoots at 43 DAT / total embryos infected) × 100 %).
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- Transformation frequency: percentage of total explants transformed (as indicated by RUBY expression), measured using a Canon EOS 1200D camera for visual observation, across five experimental treatments: (1) tdTomato (negative control); (2) bHLH48; (3) EREB152; (4) GRF4; and (5) HB77
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An experiment was carried out to identify new genes that could improve maize transformation efficiency. Using single-cell RNA sequencing and gene regulatory network analysis, researchers identified 60 candidate transcription factors. The four most promising candidates were validated in transformation experiments using immature B104 maize embryos transformed with vectors containing each candidate, along with a Cre/loxP auto-excision system and RUBY reporter. Transformation frequency was measured at 43 days after transformation as the percentage of explants producing transgenic shoots. Among the four newly identified candidate morphogenic regulators (bHLH48, EREB152, GRF4, and HB77), which one produced the greatest improvement in transformation efficiency compared to the negative control?
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EREB152 produced the greatest improvement.
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- Somatic embryogenesis is the process by which a somatic plant cell develops into an embryo and potentially a fertile plant. It's a critical step in generating transgenic plants, through Agrobacterium-mediated transformation and gene editing.
- Low transformation frequencies in maize pose problems for maize crop improvement, with only a fraction of transgenic events being high quality single-copy insertions.
- Expression of morphogenic regulator transcription factors such as BABY BOOM and WUSCHEL2 can induce direct somatic embryogenesis in maize explants, substantially increasing transformation efficiency.
- Although BABY BOOM and WUSCHEL2 are useful in promoting transformation efficiency, they can cause infertility and excessive callus formation, necessitating onerous interventions involving Cre/loxP auto-excision to remove them after embryo induction.
- Alternative morphogenic regulators from different transcription factor families (such as GRF-GIF fusions in wheat and maize, or WOX2A in maize) have shown promise for improving transformation while overcoming the problems with BABY BOOM and WUSCHEL2.
- Single-cell RNA sequencing enables the identification of cell-type-specific gene regulatory networks during developmental processes, pinpointing master regulator transcription factors that potentially enhance somatic embryogenesis.
|
[{"label":"RBK Item","value":"Somatic embryogenesis is the process by which a somatic plant cell develops into an embryo and potentially a fertile plant. It's a critical step in generating transgenic plants, through Agrobacterium-mediated transformation and gene editing."},{"label":"Title","value":"Rapid genotype “independent” Zea mays L. (maize) transformation via direct somatic embryogenesis"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s11627-018-9905-2"},{"label":"Date","value":"April 30, 2018"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Low transformation frequencies in maize pose problems for maize crop improvement, with only a fraction of transgenic events being high quality single-copy insertions."},{"label":"Title","value":"Use of GRF‐GIF chimeras and a ternary vector system to improve maize (Zea mays L.) transformation frequency\n"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.16880"},{"label":"Date","value":"June 23, 2024"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Expression of morphogenic regulator transcription factors such as BABY BOOM and WUSCHEL2 can induce direct somatic embryogenesis in maize explants, substantially increasing transformation efficiency."},{"label":"Title","value":"Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation"},{"label":"URL","value":"https://academic.oup.com/plcell/article/28/9/1998/6098336"},{"label":"Date","value":"September 6, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Although BABY BOOM and WUSCHEL2 are useful in promoting transformation efficiency, they can cause infertility and excessive callus formation, necessitating onerous interventions involving Cre/loxP auto-excision to remove them after embryo induction."},{"label":"Title","value":"Use of non-integrating Zm-Wus2 vectors to enhance maize transformation: Non-integrating WUS2 enhances\ntransformation"},{"label":"URL","value":"https://link.springer.com/article/10.1007/s11627-019-10042-2"},{"label":"Date","value":"January 2, 2020"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Alternative morphogenic regulators from different transcription factor families (such as GRF-GIF fusions in wheat and maize, or WOX2A in maize) have shown promise for improving transformation while overcoming the problems with BABY BOOM and WUSCHEL2."},{"label":"Title","value":"A key to totipotency: Wuschel‐like homeobox 2a unlocks embryogenic culture response in maize ( Zea mays L.)"},{"label":"URL","value":"https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.14098"},{"label":"Date","value":"June 26, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Single-cell RNA sequencing enables the identification of cell-type-specific gene regulatory networks during developmental processes, pinpointing master regulator transcription factors that potentially enhance somatic embryogenesis."},{"label":"Title","value":"MINI-EX: Integrative inference of single-cell gene regulatory networks in plants"},{"label":"URL","value":"https://www.cell.com/molecular-plant/fulltext/S1674-2052(22)00368-9"},{"label":"Date","value":"November 7, 2022"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
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Chemistry
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Chemistry
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MCQ
|
Lab-Scale Thermal Decomposition of Hydrogen Peroxide as
Green Propellant over Low-Cost Catalysts Based on Copper
Deposited on Different Supports
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https://www.mdpi.com/2226-4310/12/5/440
|
May 15, 2025
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Researchers investigate the thermal degradation of the H2O2 green monopropellant. Three distinct catalysts—copper supported on γ-alumina, graphite, and MNC clay—were used. Conversely, a LABSYS evo-gasorption apparatus (Category: DTA/TG/DSC, Model: Setaram Instrumentation) was used to perform differential thermal analysis– thermogravimetry (DTA–TG) measurements in order to investigate the thermal breakdown of H2O2 at constant atmospheric pressure (p = 1 atm). A syringe was used to inject a 30% (w/w) H2O2 microdroplet into the metallic sample cell. It was investigated how the three different catalysts affected the H2O2 thermogram. A microdroplet of liquid H2O2 was combined with a modest amount (a few micrograms) of powdered catalyst in the
aluminum sample cell for each thermal study. Before each run, the following experimental conditions were maintained:
(i) Carrier gas: argon, with a flow rate of 50 mL·min⁻1;
(ii) Heating rate: 10 °C·min⁻1, from room temperature up to 250 °C;
(iii) The H2O2 droplet was added directly to the catalyst particles already placed in the aluminum cell.
After sealing the apparatus, a stabilization period of approximately 2 min was allowed for the system (carrier gas and sample) to equilibrate. The thermal run was then initiated to record the DTA–TG thermograms.
Experiments were run at two constant temperatures: 0 °C and 36 °C
|
- Differential pressure (ΔP, in kPa) vs time (minutes) was recorded.
- ΔP for each catalyst (Cu/γ-alumina, Cu/graphite, Cu/clay) compared to the uncatalyzed control.
- ΔP at 0 °C and 36 °C to assess temperature effects on decomposition rate.
|
Which of the following statements best describes the observed catalytic activity (as measured by differential pressure, ΔP, vs time) for the decomposition of 30 % H₂O₂ over the three copper-supported catalysts (Cu/γ-alumina, Cu/graphite, Cu/clay) compared to the uncatalyzed decomposition, at 36 °C and 0 °C?
A. At both temperatures all three catalysts produce rates almost identical to each other; the rates follow a similar trend, with 0°C just being slower than 36 °C, each gives a large increase over the uncatalyzed reaction at both temperatures.
B. At 0°C all three catalysts give a similar rate, none of them is clearly faster than another, but at 36 °C Cu/γ-alumina gives the highest rate (largest ΔP increase), followed by Cu/graphite, then Cu/clay, each significantly faster than uncatalyzed at both temperatures.
C. At 0 °C, Cu/clay a rate that is slower than the uncatalyzed reaction at the beginning, then becomes faster than the uncatalyzed reaction, while Cu/graphite, and Cu/γ-alumina have a similar rate and are higher than the uncatalyzed reaction. At 36 °C all three are faster than uncatalyzed reaction, Cu/γ-alumina is the fastest, closely followed by Cu/graphite, then Cu/clay.
D. At 0 °C all three catalysts begin slightly faster than the uncatalyzed reaction then all three become much faster, the variability being larger than the difference between the catalysts. At 36 °C the reaction with all three catalysts is much faster than the uncatalyzed reaction, with Cu/γ-alumina being much faster than Cu/graphite, then Cu/clay lags because the copper particles came off the support particles.
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C. At 0 °C, Cu/clay a rate that is slower than the uncatalyzed reaction at the beginning, then becomes faster than the uncatalyzed reaction, while Cu/graphite, and Cu/γ-alumina have a similar rate and are higher than the uncatalyzed reaction. At 36 °C all three are faster than uncatalyzed reaction, Cu/γ-alumina is the fastest, closely followed by Cu/graphite, then Cu/clay.
|
-As the world increasingly focuses on sustainable and environmentally friendly solutions, there is a growing interest in exploring greener alternative propellants that offer comparable performance while mitigating the drawbacks associated with hydrazine and its derivatives.
-The thermal decomposition of hydrogen peroxide (H2O2) as a promising green
propellant was performed over free-noble metallic-based catalysts deposited on abundant supports.
-Green monopropellants have the potential for long-term cost savings due to reduced safety measures, disposal costs, and regulatory compliance requirements associated with hazardous materials such as hydrazine
|
[{"label":"RBK Item","value":"As the world increasingly focuses on sustainable and environmentally friendly solutions, there is a growing interest in exploring greener alternative propellants that offer comparable performance while mitigating the drawbacks associated with hydrazine and its derivatives."},{"label":"Title","value":"Propulsion Systems, Propellants, Green Propulsion Subsystems and their Applications: A Review"},{"label":"URL","value":"https://ect-journal.kz/index.php/ectj/article/view/1491"},{"label":"Date","value":"March 20, 2023"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"},{"label":"RBK Item","value":"Green monopropellants have the potential for long-term cost savings due to reduced safety measures, disposal costs, and regulatory compliance requirements associated with hazardous materials such as hydrazine"},{"label":"Title","value":"Development of green propellants for future space applications"},{"label":"URL","value":"https://www.jes.or.jp/mag/stem/Vol.77/documents/Vol.77,No.5,p.105-110.pdf"},{"label":"Date","value":"June 14, 2016"},{"label":"Justification (\"Paywalled\", \"OA\", \"Other (justify)\")","value":"OA"}]
|
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in Data Studio
SciPredict: Can LLMs Predict the Outcomes of Research Experiments?
Paper: SciPredict: Can LLMs Predict the Outcomes of Research Experiments in Natural Sciences?
Overview
SciPredict is a benchmark evaluating whether AI systems can predict experimental outcomes in physics, biology, and chemistry. The dataset comprises 405 questions derived from recently published empirical studies (post-March 2025), spanning 33 subdomains.
Dataset Structure
- Total Questions: 405 (5,716 rows including model responses)
- Domains: Physics (9 subdomains), Chemistry (10 subdomains), Biology (14 subdomains)
- Question Formats: Multiple-choice (MCQ), Free-format, Numerical
Key Fields
DOMAIN: Scientific domain (Physics, Biology, Chemistry)FIELD: Specific field within the domainPQ_FORMAT: Question format (MCQ, Free-Format, Numerical)TITLE: Paper titleURL: Paper URLPUBLISHING_DATE: Publication dateEXPERIMENTAL_SETUP: Description of the experimental configurationMEASUREMENT_TAKEN: What was measured in the experimentOUTCOME_PREDICTION_QUESTION: The prediction taskGTA: Ground truth answerBACKGROUND_KNOWLEDGE: Expert-curated background knowledgeRELATED_PAPERS_DATA: Related papers information
Key Findings
- Model accuracy: 14-26% (vs. ~20% human expert accuracy)
- Poor calibration: Models cannot distinguish reliable from unreliable predictions
- Background knowledge helps: Providing expert-curated context improves performance
- Format matters: Performance degrades from MCQ → Free-form → Numerical
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