bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracking the relation between gist and item memory over the course of long-term memory consolidation
Authors: Zeng Tima , Tompary Alexa , Schapiro Anna C. , Thompson-Schill Sharon L.
Published: January 2021

Our experiences in the world support memories not only of specific episodes but also of the generalities (the ‘gist’) across related experiences. It remains unclear how these two types of memories evolve and influence one another over time. 173 human participants encoded spatial locations from a distribution and reported both item memory (specific locations) and gist memory (center for the locations) across one to two months. After one month, gist memory was preserved relative to item memory, despite a persistent positive correlation between them. Critically, item memories were biased towards the gist over time; however, with a spatial outlier item, the local center excluding the outlier became the source of bias, instead of the reported center overweighting the outlier. Our results suggest that the extraction of gist is sensitive to the regularities of items, and that the gist starts to guide item memories over longer durations as their relative strengths change.
Aberration correction in STED microscopy to increase imaging depth in living brain tissue
Authors: Bancelin Stéphane , Mercier Luc , Murana Emanuele , Nägerl Valentin
Published: January 2021

We demonstrate an approach based on adaptive optics to improve the spatial resolution of STED microscopy inside thick biological tissue by a priori correction of spherical aberrations as a function of imaging depth. We first measured the aberrations in a phantom sample of gold and fluorescent nanoparticles suspended in an agarose gel with a refractive index closely matching living brain tissue. Using a spatial light modulator to apply corrective phase shifts, we imaged neurons in living brain slices and show that the corrections can substantially increase image quality. Specifically, we could measure structures as small as 80 nm at a depth of 90μm inside the biological tissue, and obtain a 60% signal increase after correction.
Seeing the World Like Never Before: Human stereovision through perfect optics
Authors: Ng Cherlyn J , Blake Randolph , Banks Martin S , Tadin Duje , Yoon Geunyoung
Published: January 2021

Stereovision is the ability to perceive fine depth variations from small differences in the two eyes’ images. Using adaptive optics, we show that even minute optical aberrations that are not clinically correctable, and go unnoticed in everyday vision, can affect stereo acuity. Hence, the human binocular system is capable of using unnaturally fine details that are not encountered in everyday vision. More importantly, stereoacuity was still considerably variable even with perfect optics. This variability can be attributed to neural adaptation. Our visual system tries to compensate for these aberrations through neural adaptation that optimizes stereovision when viewing stimuli through one’s habitual optics. However, the same adaptation becomes ineffective when the optics are changed, even if improved. Beyond optical imperfections, we show that stereovision is limited by neural adaptation to one’s own optics.

Significance statement

Humans, and animals with front-facing eyes, view the world from slightly different vantage points. This creates small differences in the left and right images that can be utilized for fine depth perception (stereovision). Retinal images are also subject to imperfections that are often different in the optics of the two eyes. Using advanced optical correction techniques, we show that even the smallest imperfections that escape clinical detection affect stereovision. We also find that neural processes become adapted to a person’s own optics. Hence, stereovision is directly impacted by the optics of the eyes, and indirectly via neural adaptation. Since the optics change over the lifespan, our results imply that the adult binocular system is adaptable with possibilities for binocular rehabilitation.
Fission yeast Rad8/HLTF facilitates Rad52-dependent chromosomal rearrangements through PCNA lysine 107 ubiquitination
Authors: Su Jie , Toyofuku Naoko , Nakagawa Takuro
Published: January 2021

Rad52 recombinase can cause gross chromosomal rearrangements (GCRs). However, the mechanism of Rad52-dependent GCRs remains unclear. Here, we show that fission yeast Rad8/HLTF facilitates Rad52-dependent GCRs through the ubiquitination of lysine 107 (K107) of PCNA, a DNA sliding clamp. Loss of Rad8 reduced isochromosomes resulting from centromere inverted repeat recombination. Rad8 HIRAN and RING finger mutations reduced GCRs, suggesting that Rad8 facilitates GCRs through 3’ DNA-end binding and ubiquitin ligase activity. Mms2 and Ubc4 but not Ubc13 ubiquitin-conjugating proteins were required for GCRs. Consistent with this, PCNA K107R but not K164R mutation greatly reduced GCRs. Rad8-dependent PCNA K107 ubiquitination facilitates Rad52-dependent GCRs, as PCNA K107R, rad8, and rad52 mutations epistatically reduced GCRs. Remarkably, K107 is located at the interface between PCNA subunits, and an interface mutation D150E bypassed the requirement of PCNA K107 ubiquitination for GCRs. This study uncovers the role of Rad8-dependent PCNA K107 ubiquitination in Rad52-dependent GCRs.
The elevational ascent and spread of invasive annual grass dominance in the Great Basin, USA
Authors: Smith Joseph T. , Allred Brady W. , Boyd Chad S. , Davies Kirk W. , Jones Matthew O. , Kleinhesselink Andrew R. , Maestas Jeremy D. , Morford Scott L. , Naugle David E.
Published: January 2021

Aim

In the western US, sagebrush (Artemisiaspp.) and salt desert shrublands are rapidly transitioning to communities dominated by exotic annual grasses, a novel and often self-reinforcing state that threatens the economic sustainability and conservation value of rangelands. Climate change is predicted to directly and indirectly favor annual grasses, potentially pushing transitions to annual grass dominance into higher elevations and north-facing aspects. We sought to quantify the expansion of annual grass-dominated vegetation communities along topographic gradients over the past several decades.

Location

Our analysis focused on rangelands among three ecoregions in the Great Basin of the western US, where several species of exotic annual grasses are widespread among shrub and perennial grass-dominated vegetation communities.

Methods

We used recently developed remote sensing-based rangeland vegetation data to produce yearly maps of annual grass-dominated vegetation communities spanning the period 1990–2020. With these maps, we quantified the rate of spread and characterized changes in the topographic distribution (i.e., elevation and aspect) of areas transitioning to annual grass dominance.

Results

We documented more than an eight-fold increase in annual grass-dominated area (to >77,000 km2) occurring at an average rate of >2,300 km2yr-1. In 2020, annual grasses dominated one fifth (19.8%) of Great Basin rangelands. This rapid expansion is associated with a broadening of the topographic niche, with widespread movement into higher elevations and north-facing aspects.

Main conclusions

Accelerated, strategic intervention is critically needed to conserve the fragile band of rangelands being compressed between annual grassland transitions at lower elevations and woodland expansion at higher elevations.
Association between breastfeeding during infancy and white matter microstructure in early childhood
Authors: Kar Preeti , Reynolds Jess E. , Grohs Melody N. , Bell Rhonda C. , Jarman Megan , Dewey Deborah , Lebel Catherine
Published: January 2021

Introduction

Associations between breastfeeding and brain development, in the context of child, perinatal, and sociodemographic variables, remain unclear. This study investigates whether exclusive breastfeeding for the first 6 months and total duration of any breastfeeding are associated with brain white matter microstructure in young children.

Methods

This study included a sample of 83 mothers and 85 typically developing children (42 males). Children underwent their first diffusion tensor imaging scan between ages 2.34-6.97 years; some children returned multiple times, providing a total of 331 datasets. Feeding information was collected from the mothers at 3, 6, and 12 months postpartum and at their child’s scan to calculate breastfeeding status at 6 months (exclusive or not) as well as total duration of any breastfeeding. Linear regression was used to investigate associations between breastfeeding exclusivity/duration and fractional anisotropy (FA, a measure sensitive to myelination/axonal packing/fibre coherence) for the whole brain and 10 individual white matter tracts.

Results

Breastfeeding exclusivity and duration were associated with global and regional white matter microstructure, even after controlling for perinatal and sociodemographic factors. Greater exclusivity was associated with higher FA in females and lower FA in males.

Conclusions

These findings suggest white matter differences associated with breastfeeding that differ by sex. These may stem from different trajectories in white matter development between males and females in early childhood and suggest possible long-term white matter differences associated with breastfeeding.
Computational exploration of treadmilling and protrusion growth observed in fire ant rafts
Authors: Wagner Robert J. , Vernerey Franck J.
Published: January 2021

Condensed active matter systems regularly achieve cooperative emergent functions that individual constituents could not accomplish alone. The rafts of fire ants (Solenopsis invicta) are often studied in this context for their ability to create structures comprised entirely of their own bodies, including tether-like protrusions that facilitate exploration of flooded environments. While similar protrusions are observed in cytoskeletons and cellular aggregates, they are generally dependent on morphogens or external gradients leaving the isolated role of local interactions poorly understood. Here we demonstrate through an ant-inspired, agent-based numerical model how protrusions in ant rafts may emerge spontaneously due to local interactions and how phases of exploratory protrusion growth may be induced by increased ant activity. These results provide an example in which functional morphogenesis of condensed active matter may emerge purely from locally-driven collective motion and may provide a source of inspiration for the development of autonomous active matter and swarm robotics.
Epidemiological and Clinical Characteristics, and Virologic Features of COVID-19 Patients in Kazakhstan: a Nation-Wide, Retrospective, Cohort Study
Authors: Yegorov Sergey , Goremykina Maiya , Ivanova Raifa , Good Sara V. , Babenko Dmitriy , Shevtsov Alexandr , MacDonald Kelly S. , Zhunussov Yersin
Published: January 2021

Background

The earliest coronavirus disease-2019 (COVID-19) cases in Central Asia were announced in March 2020 by Kazakhstan. Despite the implementation of aggressive measures to curb infection spread, gaps remain in the understanding of the clinical and epidemiologic features of the regional pandemic.

Methods

We did a retrospective, observational cohort study of patients with laboratory-confirmed COVID-19 in Kazakhstan between February and April 2020. We compared demographic, clinical, laboratory and radiological data of patients with different COVID-19 severities on admission. Univariable and multivariable logistic regression was used to assess factors associated with disease severity and death. Whole-genome SARS-CoV-2 analysis was performed in 53 patients without a recent history of international travel.

Findings

Of the 1072 patients with laboratory-confirmed COVID-19 in March-April 2020, the median age was 36 years (IQR 24–50) and 484 (45%) were male. On admission, 683 (64%) participants had mild, 341 (32%) moderate, and 47 (4%) severe-to-critical COVID-19 manifestation; 20 deaths (1.87%) were reported at study exit. Multivariable regression indicated increasing odds of severe disease associated with older age (odds ratio 1.05, 95% CI 1.03-1.07, per year increase; p<0.001), the presence of comorbidities (2.13, 95% CI 1.07-4.23; p<0.031) and elevated white blood cell count (WBC, 1.14, 95% CI 1.01-1.28; p<0.032) on admission, while older age (1.09, 95% CI 1.06-1.12, per year increase; p<0.001) and male sex (5.97, 95% CI 1.95-18.32; p<0.002) were associated with increased odds of death. The Kazakhstan SARS-CoV-2 isolates grouped into seven distinct lineages O/B.4.1, S/A.2, S/B.1.1, G/B.1, GH/B.1.255, GH/B.1.3 and GR/B.1.1.10.

Interpretation

Older age, comorbidities, increased WBC count, and male sex were risk factors for COVID-19 disease severity and mortality in Kazakhstan. The broad SARS-CoV-2 diversity suggests multiple importations and community-level amplification, likely predating the declaration of state emergency. Continuous epidemiologic and genomic surveillance may be critical for a better understanding of the regional COVID-19 dynamics.
Current state of COVID-19 knowledge, attitude, practices, and associated factors among Bangladeshi food handlers from various food industries
Authors: Jubayer Md. Fahad , Kayshar Md. Shahidullah , Kabir Md. Faizul , Arifin Md. Shoaib , Islam Limon Md. Tariqul , Uddin Md. Nasir , Al-Emran Md.
Published: January 2021

While people around the world are terrified of the global pandemic coronavirus disease 2019 (COVID-19) and are dying for a permanent solution, undertaking preventive safety measures are said to be the most effective way to stay away from it. People’s adherences to these measures are broadly dependent on their knowledge, attitude, and practices (KAP). People working in the food industries must be extra cautious during this time because they are in close proximity to consumable items. The present study was designed to evaluate food handlers’ knowledge, attitude, and practices regarding COVID-19 in different food industries in Bangladesh. A number of 400 food handlers from 15 food industries took part in this online-based study. The information was collected from the participants through a questionnaire prepared in Google form. With a correct response rate of about 90% on average (knowledge 89.7%, attitude 93%, practices 88.2%), the participants showed an acceptable of KAP regarding COVID-19. Education and working experiences had a significant association with the total KAP scores (p < 0.05). The findings may assist public health professionals and practitioners in developing targeted strategies for implementing such studies in other industrial sectors and taking appropriate measures based on the KAP studies.
Integrated Vaccination and Non-Pharmaceutical Interventions based Strategies in Ontario, Canada, as a Case Study: a Mathematical Modeling Study
Authors: Betti Matthew , Bragazzi Nicola Luigi , Heffernan Jane , Kong Jude , Raad Angie
Published: January 2021

Background

Recently, two “Coronavirus disease 2019” (COVID-19) vaccine products have been authorized in Canada. It is of crucial importance to model an integrated/combined package of non-pharmaceutical (physical/social distancing) and pharmaceutical (immunization) public health control measures.

Methods

A modified epidemiological, compartmental SIR model was utilized and fit to the cumulative COVID-19 case data for the province of Ontario, Canada, from September 8, 2020 to December 8, 2020. Different vaccine roll-out strategies were simulated until 75 percent of the population is vaccinated, including a no-vaccination scenario. We compete these vaccination strategies with relaxation of non-pharmaceutical interventions. Non-pharmaceutical interventions were supposed to remain enforced and began to be relaxed on either January 31, March 31, or May 1, 2021.

Results

Based on projections from the data and long-term extrapolation of scenarios, relaxing the public health measures implemented by re-opening too early would cause any benefits of vaccination to be lost by increasing case numbers, increasing the effective reproduction number above 1 and thus increasing the risk of localized outbreaks. If relaxation is, instead, delayed and 75 percent of the Ontarian population gets vaccinated by the end of the year, re-opening can occur with very little risk.

Interpretation

Relaxing non-pharmaceutical interventions by re-opening and vaccine deployment is a careful balancing act. Our combination of model projections from data and simulation of different strategies and scenarios, can equip local public health decision- and policy-makers with projections concerning the COVID-19 epidemiological trend, helping them in the decision-making process.
Socioeconomic Disparities in the Effects of Pollution on Spread of Covid-19: Evidence from US Counties
Authors: Allen Osvaldo , Brown Ava , Wang Ersong
Published: January 2021

This paper explores disparities in the effect of pollution on confirmed cases of Covid-19 based on counties’ socioeconomic and demographic characteristics. Using data on all US counties on a daily basis over the year 2020 and applying a rich panel data fixed effect model, we document that: 1) there are discernible social and demographic disparities in the spread of Covid-19. Blacks, low educated, and poorer people are at higher risks of being infected by the new disease. 2) The criteria pollutants including Ozone, CO, PM10, and PM2.5 have the potential to accelerate the outbreak of the novel coronavirus. 3) The disadvantaged population is more vulnerable to the effects of pollution on the spread of coronavirus. Specifically, the effects of pollution on confirmed cases become larger for blacks, low educated, and counties with lower average wages in 2019.
An Electronic Health Record Compatible Model to Predict Personalized Treatment Effects from the Diabetes Prevention Program: A Cross-Evidence Synthesis Approach Using Clinical Trial and Real World Data
Authors: Kent David M , Nelson Jason , Pittas Anastassios , Colangelo Francis , Koenig Carolyn , van Klaveren David , Ciemins Elizabeth , Cuddeback John
Published: January 2021

Background

An intensive lifestyle modification program or metformin pharmacotherapy reduced the risk of developing diabetes in patients at high risk, but are not widely used in the 88 million American adults with prediabetes.

Objective

Develop an electronic health record (EHR)-based risk tool that provides point-of-care estimates of diabetes risk to support targeting interventions to patients most likely to benefit.

Design

Cross-design synthesis: risk prediction model developed and validated in large observational database, treatment effect estimates from risk-based reanalysis of clinical trial data.

Setting

Outpatient clinics in US.

Patients

Risk model development cohort: 1.1 million patients with prediabetes from the OptumLabs Data Warehouse (OLDW); validation cohort: distinct sample of 1.1 million patients in OLDW. Randomized clinical trial cohort: 3081 people from the Diabetes Prevention Program (DPP) study.

Interventions

Randomization in the DPP: 1) an intensive program of lifestyle modification; 2) standard lifestyle recommendations plus 850 mg metformin twice daily; or 3) standard lifestyle recommendations plus placebo twice daily.

Results

Eleven variables reliably obtainable from the EHR were used to predict diabetes risk. This model validated well in the OLDW (c-statistic = 0.76; observed 3-year diabetes rate was 1.8% in lowest-risk quarter and 19.6% in highest-risk quarter). In the DPP, the hazard ratio for lifestyle modification was constant across all levels of risk (HR = 0.43, 95% CI 0.35 – 0.53); while the HR for metformin was highly risk-dependent (HR HR = 1.1 [95% CI: 0.61 - 2.0] in the lowest-risk quarter vs. HR=0.45 [95% CI: 0.35 0.59] in the highest risk quarter). Fifty-three percent of the benefits of population-wide dissemination of the DPP lifestyle modification, and 76% of the benefits of population-wide metformin therapy can be obtained targeting the highest risk quarter of patients.

Limitations

Differences in variable definitions and in missingness across observational and trial settings may introduce estimation error in risk-based treatment effects.

Conclusion

An EHR-compatible risk model might support targeted diabetes prevention to more efficiently realize the benefits of the DPP interventions.
Blood omega-3 fatty acids and death from COVID-19: A Pilot Study
Authors: Asher Arash , Tintle Nathan L. , Myers Michael , Lockshon Laura , Bacareza Heribert , Harris William S.
Published: January 2021

Very-long chain omega-3 fatty acids (EPA and DHA) have anti-inflammatory properties that may help reduce morbidity and mortality from COVID-19 infection. We conducted a pilot study in 100 patients to test the hypothesis that RBC EPA+DHA levels (the Omega-3 Index, O3I) would be inversely associated with risk for death by analyzing the O3I in banked blood samples drawn at hospital admission. To have adequate power (>80%) in this pilot study, we pre-specified a significance level of 0.10. Fourteen patients died, one of 25 in quartile 4 (Q4) (O3I ≥5.7%) and 13 of 75 in Q1-3. After adjusting for age and sex, the odds ratio for death in patients with an O3I in Q4 vs Q1-3 was 0.25, p=0.07. Thus, we have suggestive evidence that the risk for death from COVID-19 was lower in those with the highest O3I levels. These preliminary findings need to be confirmed in larger studies.
Early Vocal Development in Tuberous Sclerosis Complex
Authors: Gipson Tanjala T. , Ramsay Gordon , Ellison Ellen , Bene Edina , Long Helen L. , Oller D. Kimbrough
Published: January 2021

Objective

To determine whether entry into the canonical stage, canonical babbling ratios (CBR) and the level of volubility (vocal measures) are delayed in infants with Tuberous Sclerosis Complex (TSC), we completed human coding of their vocalizations at 12 months and compared the results to typically developing infants with no clinical features (TD/NCF).

Methods

We randomly selected videos from 40 infants with TSC from the TACERN database. All 78 videos were coded in real-time in AACT (Action Analysis, Coding and Training).

Results

Entry into thecanonical stagewas delayed in the great majority of the infants with TSC. TheCBRfor the TD/NCF infants was significantly higher than for the infants with TSC (TD/NCF mean = .346, SE = .19; TSC mean = .117, SE = .023).Volubilitylevel in infants with TSC was less than half that of TD/NCF infants (TD/NCF mean = 9.82, SE = 5.78; TSC mean = 3.99, SE = 2.16). CBR and volubility were also lower in TSC infants than in TD/NCF infants recorded all-day at home.

Conclusions

Entry into the canonical stage was delayed, while canonical babbling ratios and volubility were low in infants with TSC. Assessing prediction of neurodevelopmental outcome using these vocal measures in combination with non-vocal measures will be the focus of planned studies in this high-risk population.
Characterising SARS-CoV-2 viral clearance kinetics to improve the design of antiviral pharmacometric studies
Authors: Watson James A , Kissler Stephen , Day Nicholas PJ , Grad Yonatan , White Nicholas J
Published: January 2021

A consensus methodology for pharmacometric assessment of candidate SARS-CoV-2 antiviral drugs would be useful for comparing trial results and improving trial design. The time to viral clearance, assessed by serial qPCR of nasopharyngeal swab samples, has been the most widely reported measure of virological response in clinical trials, but it has not been compared formally with other metrics, notably model-based estimates of the rate of viral clearance. We analysed prospectively gathered viral clearance profiles from 280 infection episodes in vaccinated and unvaccinated individuals. We fitted different phenomenological pharmacodynamic models (single exponential decay, bi-exponential, penalised splines) and found that the clearance rate, estimated from a mixed effects single exponential decay model, is a robust pharmacodynamic summary of viral clearance. The rate of viral clearance, estimated from viral densities during the first week following peak viral load, provides increased statistical power (reduced type 2 error) compared with time to clearance. We recommend that pharmacometric antiviral assessments should be conducted in early illness with serial qPCR samples taken over one week.
Enhancing cancer targeting of γ9δ2TCR through modified NKG2D co-stimulation
Authors: Hernández-López Patricia , van Diest Eline , Johanna Inez , Heijhuurs Sabine , Straetemans Trudy , Sebestyén Zsolt , Beringer Dennis X. , Kuball Jürgen
Published: January 2021

Despite the ability of γδT cells to mediate tumor killing independently of MHC recognition, all the clinical trials that have been carried out using these cells showed low response rate in patients, in part due to its poor proliferation ability. Recently, a new generation of CAR-T cells called αβT cells engineered to express a defined γδTCR (TEG) has been developed. TEGs are αβT cells engineered to express a defined γδTCR. These cells are able to mediate effective antitumor reactivity without showing any reactivity towards healthy tissue, and combine the best qualities of both αβT and γδT cells. In fact, the high affinity γ9δ2TCR clone 5 has recently been selected within the TEG format as a clinical candidate (TEG001). Here we present a strategy to improve the antitumor activity of TEG001 by co-expressing an activating chimeric co-receptor together with γδTCR-Cl5.Therefore, we developed three different co-receptors by fusing the extracellular domain of the activating cell surface receptor NKG2D, that is able to bind stress induced ligands typically expressed on tumor cells, to the cytoplasmic signaling domains of the T cell costimulatory proteins ICOS, CD28 and 4-1BB. We determined that introduction of the chimeric co-receptors NKG2D-CD28wtand NKG2D-4-1BBCD28TMimproved the activity of TEG001 against tumors that were recognized by γδTCR-Cl5 and expressed NKG2D ligands, but did not affect tumors that either were not recognized by γδTCR-Cl5 or did not express NKG2D ligands. This ‘chimeric co-receptors’ approach open a wide range of opportunities that lead to a next generation of TEGs.
Hydraulic diversity stabilizes productivity in a large-scale subtropical tree biodiversity experiment
Authors: Schnabel Florian , Liu Xiaojuan , Kunz Matthias , Barry Kathryn E. , Bongers Franca J. , Bruelheide Helge , Fichtner Andreas , Härdtle Werner , Li Shan , Pfaff Claas-Thido , Schmid Bernhard , Schwarz Julia A. , Tang Zhiyao , Yang Bo , Bauhus Jürgen , von Oheimb Goddert , Ma Keping , Wirth Christian
Published: January 2021

Extreme climatic events threaten forests and their climate mitigation potential globally. Understanding the drivers promoting ecosystem stability is therefore considered crucial to mitigate adverse climate change effects on forests. Here, we use structural equation models to explain how tree species richness, asynchronous species dynamics and diversity in hydraulic traits affect the stability of forest productivity along an experimentally manipulated biodiversity gradient ranging from 1 to 24 tree species. Tree species richness improved stability by increasing species asynchrony. That is, at higher species richness, inter-annual variation in productivity among tree species buffered the community against stress-related productivity declines. This effect was mediated by the diversity of species’ hydraulic traits regarding drought tolerance and stomatal control, but not by the community-weighted means of these traits. The identified mechanisms by which tree species richness stabilizes forest productivity emphasize the importance of hydraulically diverse, mixed-species forests to adapt to climate change.
Structural and Functional Analyses Explain Pea KAI2 Receptor Diversity and Reveal Stereoselective Catalysis During Signal Perception
Authors: Guercio Angelica M. , Torabi Salar , Cornu David , Dalmais Marion , Bendahmane Abdelhafid , Signor Christine Le , Pillot Jean-Paul , Bris Philippe Le , Boyer François-Didier , Rameau Catherine , Gutjahr Caroline , de Saint Germain Alexandre , Shabek Nitzan
Published: January 2021

KAI2 are plant α/β hydrolase receptors, which perceive smoke-derived butenolide signals (karrikins) and putative endogenous, yet unidentified phytohormones (KAI2-ligands, KLs). The number of functional KAI2 receptors varies among plant species. It has been suggested thatKAI2gene duplication and sub-functionalization plays an adaptative role for diverse environments or ligand diversification by altering the receptor responsiveness to specific KLs. Legumes represent one of the largest families of flowering plants and contain many essential agronomic crops. Prior to legume diversification,KAI2underwent duplication, resulting inKAI2AandKAI2B. Integrating plant genetics, ligand perception and enzymatic assays, and protein crystallography, we demonstrate thatPisum sativumKAI2A and KAI2B act as receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a stronger affinity than KAI2A towards the KAI2-ligand (-)-GR24 and remarkably hydrolyses a broader range of substrates including the strigolactone-like isomer (+)-GR24. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical and structural analyses as well as recorded mass spectra of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, further illuminating the role of KAI2 not only as receptors but also asbona fideenzymes. Our work uncovers the stereoselectivity of ligand perception and catalysis by evolutionarily diverged KAI2 receptors in KAR/KL signaling pathways and proposes adaptive sensitivity to KAR/KL and strigolactone phytohormones by KAI2B.
Loss of cGMP-dependent protein kinase II alters ultrasonic vocalizations in mice, a model for speech impairment in human microdeletion 4q21 syndrome
Authors: Tran Tiffany M. , Sherwood Jessica K. , Sathler Matheus F. , Hofmann Franz , Stone-Roy Leslie M. , Kim Seonil
Published: January 2021

Chromosome 4q21 microdeletion leads to a human syndrome that exhibits restricted growth, facial dysmorphisms, mental retardation, and absent or delayed speech. One of the key genes in the affected region of the chromosome isPRKG2, which encodes cGMP-dependent protein kinase II (cGKII). Mice lacking cGKII exhibit restricted growth and deficits in learning and memory, as seen in the human syndrome. However, speech/vocalization impairments in these mice have not been determined. Moreover, the molecular pathway underlying speech impairment in humans is not fully understood. Here, we employed cGKII knockout (KO) mice as a model for the human microdeletion syndrome to test whether vocalizations are affected by loss of thePRKG2gene. Mice emit ultrasonic vocalizations (USVs) to communicate in social situations, stress, and isolation. We thus recorded ultrasonic vocalizations as a model for speech in humans. We isolated postnatal day 5-7 pups from the nest to record and analyze USVs and found significant differences in vocalizations of KO mice relative to wild-type and heterozygous mutant mice. KO mice produced fewer calls that were shorter duration, higher frequency, and lower intensity. Because neuronal activity in the hypothalamus is important for the production of animal USVs following isolation from the nest, we assessed hypothalamic activity in KO pups following isolation. Indeed, we found abnormal hyperactivation of hypothalamic neurons in cGKII KO pups after isolation. Taken together, our studies indicate that cGKII is important for neuronal activation in the hypothalamus, which is required for the production of USVs in neonatal mice. We further suggest cGKII KO mice can be a valuable animal model for human microdeletion 4q21 syndrome.

Highlights

Chromosome 4q21 microdeletion leads to a human syndrome that exhibits restricted growth, mental retardation, and absent or delayed speech.

ThecGMP-dependent protein kinase II (cGKII)gene is one of the genes located in the affected region of the chromosome.

cGKII knockout mice show restricted growth and deficits in learning and memory.

Altered ultrasonic vocalizations and abnormal activation in hypothalamic neurons are found when infant cGKII knockout pups are isolated from the nest.

cGKII knockout mice can be a valuable animal model for human microdeletion 4q21 syndrome.
Guanosine tetraphosphate (ppGpp) accumulation inhibits chloroplast gene expression and promotes super grana formation in the mossPhyscomitrium(Physcomitrella)patens
Authors: Harchouni Seddik , England Samantha , Vieu Julien , Aouane Aicha , Citerne Sylvie , Legeret Bertrand , Li-Beisson Yonghua , Menand Benoît , Field Ben
Published: January 2021

The nucleotides guanosine tetraphosphate and pentaphosphate (or ppGpp) are implicated in the regulation of chloroplast function in plants. ppGpp signalling is best understood in the model vascular plantArabidopsis thalianawhere it acts to regulate plastid gene expression to influence photosynthesis, plant development and immunity. However, little is known about the conservation or diversity of ppGpp signaling in other land plants. Here, we studied the function of ppGpp in the mossPhyscomitrium(previouslyPhyscomitrella)patensusing an inducible system for triggering ppGpp accumulation. We used this approach to investigate the effects of ppGpp on chloroplast function, photosynthesis and growth. We demonstrate that ppGpp accumulation causes a dramatic drop in photosynthetic capacity by inhibiting chloroplast gene expression. This was accompanied by the unexpected reorganisation of the thylakoid system into super grana. Surprisingly, these changes did not affect gametophore growth, suggesting that bryophytes and vascular plants may have different tolerances to defects in photosynthesis. Our findings point to the existence of both highly conserved and more specific targets of ppGpp signalling in the land plants that may reflect different growth strategies.
INPP5E regulates CD3ζ enrichment at the immune synapse by phosphoinositide distribution control
Authors: Chiu Tzu-Yuan , Yang Fu-Hua , Chong Weng Man , Tsai Hsing-Chen , Wang Won-Jing , Liao Jung-Chi
Published: January 2021

The immune synapse, a specialized interface formed between T lymphocytes and antigen-presenting cells (APCs) after antigen recognition, is essential for T cell activation and the adaptive immune response. It has been shown that this interface shares similarities with the primary cilium, a sensory organelle in eukaryotic cells, although roles of ciliary proteins on the immune synapse remain elusive. In this study, we find that inositol polyphosphate-5-phosphatase E (INPP5E), a cilium-enriched protein responsible for regulating phosphoinositide localization, accumulated at the immune synapse during antigen-specific conjugation or antibody capping, and formed a complex with CD3ζ, ZAP-70, and Lck. Silencing INPP5E in T-cells impaired polarized distribution of CD3ζ at the immune synapse, and correlated with a failure of PI(4,5)P2clearance at the center of the synapse. Moreover, INPP5E silencing decreased proximal TCR signaling, including phosphorylation of CD3ζ and ZAP-70, and finally, attenuated IL-2 secretion. Our results suggest that INPP5E is a new player in phosphoinositide manipulation at the synapse, controlling the TCR signaling cascade.
Altered A-type potassium channel function impairs dendritic spike initiation and temporammonic long-term potentiation in Fragile X syndrome
Authors: Ordemann Gregory J. , Apgar Christopher J. , Chitwood Raymond A. , Brager Darrin H.
Published: January 2021

Fragile X syndrome (FXS) is the leading monogenetic cause of cognitive impairment and autism spectrum disorder. Area CA1 of the hippocampus receives current information about the external world from the entorhinal cortex via the temporoammonic (TA) pathway. Given its role in learning and memory, it is surprising that little is known about TA long-term potentiation (TA-LTP) in FXS. We found that TA-LTP was impaired infmr1KO mice. Furthermore, dendritic Ca2+influx was smaller and dendritic spike threshold was depolarized infmr1KO mice. Dendritic spike threshold and TA-LTP were restored by block of A-type K+channels. The impairment of TA-LTP coupled with enhanced Schaffer collateral LTP may contribute to spatial memory alterations in FXS. Furthermore, as both of these LTP phenotypes are attributed to changes in A-type K+channels in FXS, our findings provide a potential therapeutic target to treat cognitive impairments in FXS.
Consistent Force Field Captures Homolog Resolved HP1 Phase Separation
Authors: Latham Andrew P. , Zhang Bin
Published: January 2021

Many proteins have been shown to function via liquid-liquid phase separation. Computational modeling could offer much needed structural details of protein condensates and reveal the set of molecular interactions that dictate their stability. However, the presence of both ordered and disordered domains in these proteins places a high demand on the model accuracy. Here, we present an algorithm to derive a coarse-grained force field, MOFF, that can model both ordered and disordered proteins with consistent accuracy. It combines maximum entropy biasing, least-squares fitting, and basic principles of energy landscape theory to ensure that MOFF recreates experimental radii of gyration while predicting the folded structures for globular proteins with lower energy. The theta temperature determined from MOFF separates ordered and disordered proteins at 300 K and exhibits a strikingly linear relationship with amino acid sequence composition. We further applied MOFF to study the phase behavior of HP1, an essential protein for posttranslational modification and spatial organization of chromatin. The force field successfully resolved the structural difference of two HP1 homologs, despite their high sequence similarity. We carried out large scale simulations with hundreds of proteins to determine the critical temperature of phase separation and uncover multivalent interactions that stabilize higher-order assemblies. In all, our work makes significant methodological strides to connect theories of ordered and disordered proteins and provides a powerful tool for studying liquid-liquid phase separation with near-atomistic details.
Determining the pathogenicity of variants of uncertain significance and identification of a founder variant in the epilepsy-associated gene,SZT2
Authors: Calhoun Jeffrey D , Aziz Miriam C , Happ Hannah C , Gunti Jonathan , Gleason Colleen , Mohamed Najma , Zeng Kristy , Hiller Meredith , Bryant Emily , Mithal Divakar , Bellinski Irena , Kinsley Lisa , Grimmel Mona , Schwaibold Eva MC , Smith-Hicks Constance , Chassevent Anna , Scala Marcello , Accogli Andrea , Torella Annalaura , Striano Pasquale , Capra Valeria , Bird Lynne M. , Ben-Sahra Issam , Ekhilevich Nina , Hershkovitz Tova , Weiss Karin , Millichap John , Gerard Elizabeth E , Carvill Gemma L
Published: January 2021

Biallelic pathogenic variants inSZT2result in a neurodevelopmental disorder with shared features, including early-onset epilepsy, developmental delay, macrocephaly, and corpus callosum abnormalities. SZT2 is as a critical scaffolding protein in the amino acid sensing arm of the mTOR signaling pathway. Due to its large size (3432 amino acids), lack of crystal structure, and absence of functional domains, it is difficult to determine the pathogenicity ofSZT2missense and in-frame deletions. We report a cohort of twelve individuals with biallelicSZT2variants and phenotypes consistent withSZT2-related neurodevelopmental disorder. The majority of this cohort contained one or moreSZT2variants of uncertain significance (VUS). We developed a novel individualized platform to functionally characterizeSZT2VUSs. We identified a recurrent in-frame deletion (SZT2 p.Val1984del) which was determined to be a loss-of-function variant and therefore likely pathogenic. Haplotype analysis determined this single in-frame deletion is a founder variant in those of Ashkenazi Jewish ancestry. Overall, we present a FACS-based rapid assay to distinguish pathogenic variants from VUSs inSZT2, using an approach that is widely applicable to other mTORopathies including the most common causes of the focal genetic epilepsies,DEPDC5, TSC1/2, MTORandNPRL2/3.
Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2
Authors: Li Zhen-lu , Buck Matthias
Published: January 2021

The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.
Hypertrophied human adipocyte spheroids asin vitromodel of weight gain and adipose tissue dysfunction
Authors: Ioannidou Anna , Alatar Shemim , Åhlander Matilda , Hornell Amanda , Fisher Rachel M. , Hagberg Carolina E
Published: January 2021

The rise in obesity prevalence has created an urgent need for new and improved methods to study human adipocytes and the pathogenic effects of weight gainin vitro. Despite numerous studies showing the advantages of culturing adipocyte progenitors as 3D structures, the majority continue using traditional 2D cultures which result in small, multilocular adipocytes with poor representability. We hypothesized that providing differentiating pre-adipocytes with a vascular growth niche would mimicin vivoadipogenesis and improve the differentiation process. Here we present a simple, easily applicable culture protocol that allows for the differentiation and culturing of human adipocytes with a more unilocular morphology and larger lipid droplets than previous protocols. We moreover offer a protocol for inducing adipocyte enlargementin vitro, resulting in larger lipid droplets and development of several key features of adipocyte dysfunction, including altered adipokine secretions and impaired lipolysis. Taken together, our hypertrophied human adipocyte spheroids offer an improved culture system for studying the cellular and molecular mechanisms causing metabolic dysfunction and inflammation during weight gain.
Noncanonical Electromechanical Coupling Mechanism of an HCN Channel
Authors: Dai Gucan , Aman Teresa K. , DiMaio Frank , Zagotta William N.
Published: January 2021

Pacemaker hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels exhibit a reversed voltage-dependent gating, activating by membrane hyperpolarization instead of depolarization. Sea urchin HCN (spHCN) channels also undergo an inactivation with hyperpolarization which occurs only in the absence of cyclic nucleotide. Here we applied transition metal ion FRET and Rosetta modeling to measure differences in the structural rearrangements between activation and inactivation of spHCN channels. We found that removal of cAMP produced a largely rigid-body rotation of the C-linker relative to transmembrane domain, bringing the A’ helix in close proximity to the voltage-sensing S4 helix. In addition, rotation of the C-linker was elicited by hyperpolarization in the absence but not in the presence of cAMP. These results suggest the A’ helix functions like a mechanical clutch to engage inactivation. cAMP binding disengages the clutch, permitting the hyperpolarization-dependent activation mediated by the S5 helix. Furthermore, rearrangement of A’ helix during recovery from inactivation of spHCN channels was similar to that for the activation of KCNH channels, suggesting a conserved mechanism for this noncanonical electromechanical coupling in the CNBD channel family.
Evidence for a hydrogen sulfide-sensing E3 ligase in yeast
Authors: Johnson Zane M. , Wang Yun , Sutter Benjamin M. , Tu Benjamin P.
Published: January 2021

In yeast, control of sulfur amino acid metabolism relies upon Met4, a transcription factor which activates the expression of a network of enzymes responsible for the biosynthesis of cysteine and methionine. In times of sulfur abundance, the activity of Met4 is repressed via ubiquitination by the SCFMet30E3 ubiquitin ligase, but the mechanism by which the F-box protein Met30 senses sulfur status to tune its E3 ligase activity remains unresolved. Herein, we show that Met30 responds to flux through the transsulfuration pathway to regulate theMETgene transcriptional program. In particular, Met30 is responsive to the biological gas hydrogen sulfide, which is sufficient to induce ubiquitination of Met4in vivo. Additionally, we identify important cysteine residues in Met30’s WD-40 repeat region that sense the availability of sulfur in the cell. Our findings reveal how SCFMet30dynamically senses the flow of sulfur metabolites through the transsulfuration pathway to regulate synthesis of these special amino acids.
Compensating complete loss of signal recognition particle during co-translational protein targeting by the translation speed and accuracy
Authors: Zhao Liuqun , Fu Gang , Cui Yanyan , Xu Zixiang , Cai Tao , Zhang Dawei
Published: January 2021

Signal recognition particle (SRP) is critical for delivering co-translational proteins to the bacterial inner membrane. Previously, we identified SRP suppressors inEscherichia colithat inhibit translation initiation and elongation, which provided insights into the mechanism of bypassing the requirement of SRP. Suppressor mutations tended to be located in regions that govern protein translation under evolutionary pressure. To test this hypothesis, we re-executed the suppressor screening of SRP. Here we isolated a novel SRP suppressor mutation located in the Shine-Dalgarno sequence of the S10 operon, which partially offset the targeting defects of SRP-dependent proteins. We found that the suppressor mutation decreased the protein translation rate, which extended the time window of protein targeting. This increased the possibility of the correct localization of inner membrane proteins. Furthermore, the fidelity of translation was decreased in suppressor cells, suggesting that the quality control of translation was inactivated to provide an advantage in tolerating toxicity caused by the loss of SRP. Our results demonstrated that the inefficient protein targeting due to SRP deletion can be rescued through modulating translational speed and accuracy.