bluuebunny/crossref_metadata_2025 huggingface dataset:
Interplay of BAF and MLL4 promotes cell type-specific enhancer activation
Authors: Park Young-Kwon , Lee Ji-Eun , O’Haren Tommy , McKernan Kaitlin , Yan Zhijiang , Wang Weidong , Peng Weiqun , Ge Kai
Published: June 2020

Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identified BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we showed that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.
A Simple Procedure for Bacterial Expression and Purification of the Fragile X Protein Family
Authors: Edwards Madison , Xu Mingzhi , Joseph Simpson
Published: June 2020

The fragile X protein family consists of three RNA-binding proteins involved in translational regulation. Fragile X mental retardation protein (FMRP) is well-studied, as its loss leads to fragile X syndrome, a neurodevelopmental disorder which is the most prevalent form of inherited mental retardation and the primary monogenetic cause of autism. Fragile X related proteins 1 and 2 (FXR1P & FXR2P) are autosomal paralogs of FMRP that are involved in promoting muscle development and neural development, respectively. There is great interest in studying this family of proteins, yet researchers have faced much difficulty in expressing and purifying the full-length versions of these proteins in sufficient quantities. We have developed a simple, rapid, and inexpensive procedure that allows for the recombinant expression and purification of full-length human FMRP, FXR1P, and FXR2P fromEscherichia coliin high yields, free of protein and nucleic acid contamination. In order to assess the proteins’ function after purification, we confirmed their binding to pseudoknot and G-quadruplex forming RNAs.
A low-cost platform suitable for sequencing-based recovery of natural variation in understudied plants
Authors: Howard-Till Rachel , Osorio Claudia E. , Till Bradley J.
Published: June 2020

Genetic characterization of wild and cultivated plants provides valuable knowledge for conservation and agriculture. DNA sequencing technologies are improving and costs are dropping. Yet, analysis of many species is hindered because they grow in regions that lack infrastructure for advanced molecular biology. We developed and adapted low-cost methods that address these issues. Tissue is collected and stored in silica-gel, avoiding the need for liquid nitrogen and freezers. We have optimized low-cost home-made DNA extraction to increase yields, reduce costs, and produce DNA suitable for next generation sequencing. We also describe how to build a gel documentation system for DNA quantification. As a proof of principle, we use these methods to evaluate wildBerberis darwinii, native to Southern Chile.

Method summary

We describe a suite of low-cost do-it-yourself methods for field collection of plant tissues, extraction of genomic DNA suitable for next generation sequencing, and home-made agarose gel documentation suitable for DNA quantification. These methods enable the collection and preparation of samples for genomic analysis in regions with limited infrastructure.
Rapid Single Cell Evaluation of Human Disease and Disorder Targets Using REVEAL: SingleCell™
Authors: Kumar Namit , Golhar Ryan , Sharma Kriti Sen , Holloway James L , Sarangi Srikant , Neuhaus Isaac , Walsh Alice M. , Pitluk Zachary W.
Published: June 2020

Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypothesis by querying extensive single-cell datasets.

Large single-cell datasets like human cell atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics and vaccine targets; as the world struggles to cope with the on-going spread of COVID-19 infections.

In this manuscript we describe, REVEAL: SingleCell which enables storage, retrieval and rapid query of single-cell datasets inclusive of millions of cells. The analytical database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypothesis. One such example includes identifying the most prevalent cell type annotation tag on returned cells.

We used REVEAL: SingleCell to evaluate expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in <60 seconds. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic.
Substrate Transport and Specificity in a Phospholipid Flippase
Authors: Wang Yong , Lyons Joseph A , Timcenko Milena , Kümmerer Felix , de Groot Bert L. , Nissen Poul , Gapsys Vytautas , Lindorff-Larsen Kresten
Published: June 2020

Type 4 P-type ATPases are lipid flippases which help maintain asymmetric phospholipid distribution in eukaryotic membranes by driving unidirectional translocation of phospholipid substrates. Recent cryo-EM and crystal structures have provided a detailed view of flippases, and we here use molecular dynamics simulations to study the first steps of phospholipid transport and lipid substrate specificity. Our simulations and new cryo-EM structure shows phospholipid binding to a groove and subsequent movement towards the centre of the membrane, and reveal a preference for phosphatidylserine lipids. We find that only the lipid head group stays in the groove while the lipid tails remain in the membrane, thus visualizing how flippases have evolved to transport large substrates. The flippase also induces deformation and thinning of the outer leaflet facilitating lipid recruitment. Our simulations provide insight into substrate binding to flippases and suggest that multiple sites and steps in the functional cycle contribute to substrate selectivity.
Three LysM effectors ofZymoseptoria triticicollectively disarm chitin-triggered plant immunity
Authors: Tian Hui , MacKenzie Craig I. , Rodriguez-Moreno Luis , van den Berg Grardy C.M. , Chen Hongxin , Rudd Jason J. , Mesters Jeroen R. , Thomma Bart P.H.J.
Published: June 2020

Chitin is a major structural component of fungal cell walls and acts as a microbe-associated molecular pattern (MAMP) that, upon recognition by a plant host, triggers the activation of immune responses. In order to avoid the activation of these responses, the Septoria tritici blotch (STB) pathogen of wheat,Zymoseptoria tritici, secretes LysM effector proteins. Previously, the LysM effectors Mg1LysM and Mg3LysM were shown to protect fungal hyphae against host chitinases. Furthermore, Mg3LysM, but not Mg1LysM, was shown to suppress chitin-induced reactive oxygen species (ROS) production. Whereas initially a third LysM effector gene was disregarded as a presumed pseudogene, we now provide functional data to show that also this gene encodes a LysM effector, named Mgx1LysM, that is functional during wheat colonization. While Mg3LysM confers a major contribution toZ. triticivirulence, Mgx1LysM and Mg1LysM contribute toZ. triticivirulence with smaller effects. All three LysM effectors display partial functional redundancy. We furthermore demonstrate that Mgx1LysM binds chitin, suppresses the chitin-induced ROS burst and is able to protect fungal hyphae against chitinase hydrolysis. Finally, we demonstrate that Mgx1LysM is able to undergo chitin-induced polymerisation. Collectively, our data show thatZymoseptoria triticiutilizes three LysM effectors to disarm chitin-triggered wheat immunity.
Learning Mitigates Genetic Drift
Authors: Lenart Peter , Bienertová-Vašků Julie , Berec Luděk
Published: June 2020

Genetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species conservation efforts to speciation. The conventional approach assumes that genetic drift has the same effect on all populations undergoing the same change in size, regardless of different behaviors and history of the populations. However, here we reason that processes leading to a systematic increase of individuals’ chances of survival, such as learning or immunological memory, can mitigate the effects of genetic drift even if the overall mortality rate in the population does not change. We further test this notion in an agent-based model monitoring allele frequencies in a population of prey, either able or not able to learn. Importantly, both these populations start with the same effective size and have the same and constant overall mortality rates. Our results demonstrate that even under these conditions, learning can mitigate drift if generations overlap. Furthermore, this effect holds regardless if the population is haploid or diploid or whether it reproduces sexually or asexually. Therefore, our findings demonstrate that learning is an overlooked factor affecting the effective population size. These findings may be of importance not only for basic evolutionary theory but also for other fields using the concept of genetic drift.
Modelling movement and landscape connectivity of New Zealand native birds in highly structured agroecosystem networks
Authors: Zhang Jingjing , Pannell Jennifer L. , Case Bradley S. , Hinchliffe Graham , Stanley Margaret C. , Buckley Hannah L.
Published: June 2020

Understanding how spatial heterogeneity affects movement and dispersal is critical for maintaining functional connectivity in agroecosystems. Least-cost path models are popular conservation tools to quantify the cost of a species dispersing though the landscapes. However, the variability of species in life history traits and landscape configurations can affect their space-use patterns and should be considered in agroecosystem management aiming to improve functional biodiversity. In this study, we modelled the connectivity properties of native species on a real agroecosystem landscape dominated by sheep and beef farming in north Canterbury, New Zealand, where the recovery of native bird population is desired. We chose two species to act as case studies that were contrasting in their mobility: New Zealand pigeon/kererū (Hemiphaga novaeseelandiae; highly mobile) and southern brown kiwi/tokoeka (Apteryx australis; flightless). Networks of the least-cost paths of kererū and tokoeka were constructed based on their habitat preferences and movement capacities, and we compared and contrasted the connectivity properties and network topographies of their networks. We then compared the network metrics of western side (higher density of forest) with the eastern side (dominated by grazed grassland) of the study area where the vegetation composition was vastly different for both species. The results shown three variables were the most important contributors to the structure of the dispersal networks: the nature of the matrix, spatial structure of vegetation patches, and the gap-crossing ability of the study species. Tokoeka were able to utilise smaller habitat patches as stepping-stones for dispersal, while kererū can select more preferred habitat patches due to their high movement capacity. In contrast to the eastern side, we observed the western/forested side to have more, and stronger, links among habitat patches for both species, due to the presence of several large patches of native forest. Our work suggested that one size does not fit all, rather, conservation strategies that account for species’ life histories and movement traits are required to identify and preserve a connected ecological network.
Comparison of 12 molecular detection assays for SARS-CoV-2
Authors: Matsumura Yasufumi , Shimizu Tsunehiro , Noguchi Taro , Nakano Satoshi , Yamamoto Masaki , Nagao Miki
Published: June 2020

Molecular testing for SARS-CoV-2 is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. All the assays showed a specificity of 100% (95% confidence interval, 95.8 to 100). The N2 assay kit of the US Centers for Disease Control and Prevention (CDC) and the N2 assay of the Japanese National Institute of Infectious Disease (NIID) were the most sensitive assays with 100% sensitivity (95% confidence interval, 94.7 to 100), followed by the CDC N1 kit, E assay by Corman, and NIID N2 assay multiplex with internal control reactions. These assays are reliable as first-line molecular assays in laboratories when combined with appropriate internal control reactions.
COVID-19 Antibody in Thai Community Hospitals
Authors: Nopsopon Tanawin , Pongpirul Krit , Chotirosniramit Korn , Hiransuthikul Narin
Published: June 2020

Background

COVID-19 seroprevalence data has been scarce, especially in less developed countries with a relatively low infection rate.

Methods

A locally developed rapid IgM/IgG test kit was used for screening hospital staff and patients who required procedural treatment or surgery in 52 hospitals in Thailand from April 8 to June 26, 2020. A total of 857 participants were tested—675 were hospital staff and 182 were pre-procedural patients. (Thai Clinical Trials Registry: TCTR20200426002)

Results

Overall, 5.5% of the participants (47 of 857) had positive immunoglobulin M (IgM), 0.2% (2 of 857) had positive immunoglobulin G (IgG) and IgM. Hospitals located in the Central part of Thailand had the highest IgM seroprevalence (11.9%). Preprocedural patients had a higher rate of positive IgM than the hospital staff (12.1% vs. 3.7%). Participants with present upper respiratory tract symptoms had a higher rate of positive IgM than those without (9.6% vs. 4.5%). Three quarters (80.5%, 690 of 857) of the participants were asymptomatic, of which, 31 had positive IgM (4.5%) which consisted of 20 of 566 healthcare workers (3.5%) and 11 of 124 preprocedural patients (8.9%).

Conclusions

COVID-19 antibody test could detect a substantial number of potential silent spreaders in Thai community hospitals. Antibody testing should be encouraged for mass screening, especially in asymptomatic individuals.
Contact Tracing Evaluation for COVID-19 Transmission during the Reopening Phase in a Rural College Town
Authors: Moon Sifat Afroj , Scoglio Caterina
Published: June 2020

Contact tracing can play a vital role in controlling human-to-human transmission of a highly contagious disease such as COVID-19. To investigate the benefits and costs of contact tracing, we develop an individual-based contact-network model and a susceptible-exposed-infected-confirmed (SEIC) epidemic model for the stochastic simulations of COVID-19 transmission. We estimate the unknown parameters (reproductive ratio R0 and confirmed rate δ2) by using observed confirmed case data. After a two month-lockdown, states in the USA have started the reopening process. We investigate for four different reopening situations: under “stay-at-home” order or no reopening, 25 % reopening, 50 % reopening, and 75 % reopening. We model contact tracing in a two-layer network by modifying the basic SEIC epidemic model. The two-layer network is composed by the contact network in the first layer and the tracing network in the second layer. Since the full contact list of an infected individual patient can be hard to obtain, then we consider different fractions of contacts from 60% to 5%. The goal of this paper is to assess the effectiveness of contact tracing to control the COVID-19 spreading during the initial phase of the reopening process of a rural college town.

In this research, we assess the benefits and cost of contact tracing as a key mitigation strategy to control the spreading of COVID-19. In terms of benefits, our simulation results show that increasing the fraction of traced contacts decreases the size of the epidemic. For example, tracing 20% of the contacts is enough for all four reopening scenarios to reduce the epidemic size by half. Considering the act of quarantining susceptible households as the contact tracing cost, we have observed an interesting phenomenon. When we increase the fraction of traced contacts from 5% to 20%, the number of quarantined susceptible people increases because each individual confirmed case is mentioning more contacts. However, when we increase the fraction of traced contacts from 20% to 60%, the number of quarantined susceptible people decreases because the increment of the mentioned contacts is balanced by a reduced number of confirmed cases. The outcomes of this research are valuable in the reopening process of the USA. Furthermore, the framework is generic enough to use any locations and for other diseases as well.
Epidemiological model with anomalous kinetics - The Covid-19 pandemics
Authors: Tirnakli Ugur , Tsallis Constantino
Published: June 2020

We generalize the phenomenological, law of mass action-like, SIR and SEIR epidemiological models to situations with anomalous kinetics. Specifically, the contagion and removal terms, normally linear in the fractionIof infecteds, are taken to depend onand, respectively. These dependencies can be understood as highly reduced effective descriptions of contagion via anomalous diffusion of susceptibles and infecteds in fractal geometries, and removal (i.e., recovery or death) via complex mechanisms leading to slowly decaying removal-time distributions. We obtain rather convincing fits to time series for both active cases and mortality with the same values of (qup,qdown) for a given country, suggesting that such aspects may in fact be present in the evolution of the Covid-19 pandemic. We also obtain approximate values for the effective populationNeff, which turns out to be a small percentage of the entire populationNfor each country.
COVID-19-associated ARDS treated with DEXamethasone (CoDEX): Study design and rationale for a randomized trial
Authors: Tomazini Bruno M. , Maia Israel S. , Bueno Flavia R. , Silva Maria Vitoria A.O. , Baldassare Franca Pellison , Costa Eduardo Leite V. , Moura Ricardo A.B. , Honorato Michele , Costa André N. , Cavalcanti Alexandre B. , Rosa Regis , Avezum Álvaro , Veiga Viviane C. , Lopes Renato D. , Damiani Lucas P. , Machado Flávia R. , Berwanger Otavio , Azevedo Luciano C.P. ,   for the COALITION COVID-19 Brazil III Investigators
Published: June 2020

OBJECTIVES

The infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) spreads worldwide and is considered a pandemic. The most common manifestation of SARS-CoV2 infection (Coronavirus disease 2019 - COVID-19) is viral pneumonia with varying degrees of respiratory compromise and up to 40% of hospitalized patients might develop Acute Respiratory Distress Syndrome (ARDS). Several clinical trials evaluated the role of corticosteroids in non-COVID-19 ARDS with conflicting results. We designed a trial to evaluate the effectiveness of early intravenous dexamethasone administration on the number of days alive and free of mechanical ventilation within 28 days after randomization in adult patients with moderate or severe ARDS due to confirmed or probable COVID-19.

METHODS

This is a pragmatic, prospective, randomized, stratified, multicenter, open-label, controlled trial including 350 patients with early-onset (less than 48h before randomization) moderate or severe ARDS, defined by the Berlin criteria, due to COVID-19. Eligible patients will be randomly allocated to either standard treatment plus dexamethasone (intervention group) or standard treatment without dexamethasone (control group). Patients in the intervention group will receive dexamethasone 20mg IV once daily for 5 days, followed by dexamethasone 10mg IV once daily for additional 5 days or until Intensive Care Unit (ICU) discharge, whichever occurs first. The primary outcome is ventilator-free days within 28 days after randomization, defined as days alive and free from invasive mechanical ventilation. Secondary outcomes are all-cause mortality rates at day 28, evaluation of the clinical status at day 15 assessed with a 6-level ordinal scale, mechanical ventilation duration from randomization to day 28, Sequential Organ Failure Assessment (SOFA) Score evaluation at 48h, 72h and 7 days and ICU-free days within 28.

ETHICS AND DISSEMINATION

This trial was approved by the Brazilian National Committee of Ethics in Research (Comissão Nacional de Ética em Pesquisa - CONEP) and National Health Surveillance Agency (ANVISA). An independent data monitoring committee will perform interim analyses and evaluate adverse events throughout the trial. Results will be submitted for publication after enrolment and follow-up are complete.

ClinicalTrials.gov identifier

NCT04327401
A cross-sectional study of immune seroconversion to SARS-CoV-2 in front-line maternity health professionals
Authors: Bampoe Sohail , Lucas Dominique Nuala , Neall Georgina , Sceales Penny , Aggarwal Reena , Caulfield Kim , Siassakos Dimitrios , Odor Peter Mark
Published: June 2020

COVID-19, the respiratory disease caused by the SARS-CoV-2, is thought to cause a milder illness in pregnancy with a greater proportion of asymptomatic carriers. This has important implications for the risk of patient-to-staff, staff-to-staff and staff-to patient transmission among health professionals in maternity. The aim of this study was to investigate the prevalence of previously undiagnosed SARS-CoV-2 infection in health professionals from two tertiary-level maternity units in London, UK and to determine associations between HCW characteristics, reported symptoms and serological evidence of prior SARS-CoV-2 infection.

200 anaesthetists, midwives and obstetricians with no previously confirmed diagnosis of COVID-19 were tested for immune seroconversion using laboratory IgG assays. Comprehensive symptom and medical histories were also collected. 5/40 (12.5%; 95% CI: 4.2-26.8) anaesthetists, 7/52 (13.5%; 95% CI: 5.6-25.8%) obstetricians and 17/108 (15.7%; 95% CI: 9.5-24.0%) midwives were seropositive, with an overall total of 29/200 (14.5%; 95% CI: 9.9-20.1%) of maternity healthcare workers testing positive for IgG antibodies against SARS-CoV-2. Of those who had seroconverted, 10/29 (35.5%) were completely asymptomatic. Fever or cough were only present in 6/29 (20.7%) and (10/29 (34.5%) respectively. Anosmia was the most common symptom occurring in 15/29 (51.7%) seropositive participants and was the only symptom that was predictive of positive seroconversion (OR 18; 95% CI 6 – 55). 58.6% of those who were seropositive had not self-isolated at any point and continued to provide patient care in the hospital setting.

This study was the largest study of baseline immune seroconversion in maternity healthcare workers conducted to date and reveals that 1 in 6 were seropositive, of whom 1 in 3 were asymptomatic. This has significant implications for the risk of occupational transmission of SARS-CoV-2 for both staff and patients in maternity and regular testing of staff, including asymptomatic staff should be considered to reduce transmission risk.
A Systematic Review and Meta-analysis of D-Dimer Levels in Patients Hospitalized with Coronavirus Disease 2019 (COVID-19)
Authors: Bansal Agam , Singh Achintya D , Jain Vardhmaan , Aggarwal Manik , Gupta Samiksha , Padappayil Rana P , Gupta Mohak , Mian Agrima
Published: June 2020

Aim

To determine if the d-dimer levels are elevated in individuals with COVID 19 having worse clinical outcomes including all-cause mortality, ICU admission or ARDS

Methods

We conducted a systematic review and meta-analysis of published literature in Pubmed, Embase and Cochrane database through April 9, 2020 for studies evaluating the d-dimer levels in patients with and without a worse clinical outcome (all-cause mortality, ICU admission and ARDS). A total of 6 studies included in the meta-analysis.

Results

The values of d-dimer were found to be significantly increased in patients with the composite clinical end point than in those without (SMD, 1.67 ug/ml (95% CI, 0.72-2.62 ug/ml). The SMD of the studies (Tang et al, Zhou et al, Chen et al), which used only mortality as an outcome measure was 2.5 ug/mL (95% CI, 0.62-4.41).

Conclusion

The results of this concise meta-analysis suggest that d-dimer is significantly increased in patients having a worse clinical outcome (all-cause mortality, ICU admission or ARDS).
Uncertainty stress, and its impact on disease fear and prevention behaviors during the COVID-19 epidemic in China: A panel study
Authors: Yang Xiaozhao Yousef , Peng Sihui , Yang Tingzhong , Zhang Weifang , Wang Huihui , Cottrell Randall R
Published: June 2020

Objective

To examine changing trends of uncertainty stress, and its impact on disease fear and prevention behaviors during the Chinese COVID-19 epidemic using a prospective observational study.

Methods

The study employed a longitudinal design. Participants were recruited for an online panel survey from chat groups on social media platforms. There were 5 waves of interviews. Information on uncertainty stress and related variables were collected via the online survey. Descriptive statistics and the GIM program were used for data analysis.

Results

Participants numbered 150 for the linkable baseline survey and 102 (68%) for the final survey. Uncertainty stress(β: -0.047, S.E: 0.118, p>0.05) did not show a statistically significant temporal change trend over the observation period. Disease fear manifested a statistically significant downwards trend (β: -0.342, S.E: 0.157, p<0.05), and prevention behaviors indicated an upwards trend (β: 0.048, S.E: 0.021, p<0.05) during the observation period. Uncertainty stress was positively associated with disease fear (β: 0.45046, S.E: 0.05964, p<0.0001), and negatively associated with self-efficacy (β: -0.6698, S.E: 0.01035, p<0.0001), and prevention behaviors (β:-0.02029, S.E: 0.00876, p: 0.0209).

Conclusion

This study yielded new information about uncertainty stress among Chinese people during the COVID-19 epidemic. Policy changes and public education are essential for minimizing the negative effects of uncertainty stress in disease prevention.
Human papillomavirus type 16 sub-lineages and integration in cancer
Authors: Jackson Robert , Ortigas-Vásquez Alejandro , Zehbe Ingeborg
Published: June 2020

Our lab has been intrigued by the fact that viral genomes often take on the role of mobile elements to perpetuate their existence in a complex organism’s genome. Multiple DNA viruses such as Epstein-Barr virus, hepatitis B virus, and human papillomavirus (HPV) can invade their host genome, as “genomic parasites”. We have been investigating HPV type 16 (HPV16), which is a prominent human tumour virus. In our recentin vitrowork using 3D organoids, a common variant of HPV16’s coding region elicited early integration into the host genome compared to the HPV16 prototype sequence. Next-generation sequencing (NGS) data confirmed a transcriptomic profile of increased proliferation and chromosomal instability—both hallmarks of cancer. Epidemiologically, this variant is associated with a high cervical cancer incidence. To take inquiries a step further, we investigated variant-specific integration across HPV16-related cancers using NGS data from population-derived clinical samples in The Cancer Genome Atlas (TCGA)-curated database. Data were analyzed for HPV16 positivity, sub-lineage, and viral-host integration using a bioinformatic pipeline of open-source tools, including HPVDetector. Here, we report the analysis of 120 cervical cancer cases comprising HPV16 positive and negative samples as well as their different sub-lineage and integration status. The integration signature between variant and prototype did not differ quantitatively but qualitatively: that of the variant being related to hypoxia/energetics (Warburg effect) and that of the prototype being much more varied to include host immune abrogation and cancer pathways activation. We conclude by discussing challenges and future directions for expanding these analyses.
S-IRFindeR: stable and accurate measurement of intron retention
Authors: Broseus Lucile , Ritchie William
Published: June 2020

Accurate quantification of intron retention levels is currently the crux for detecting and interpreting the function of retained introns. Using both simulated and real RNA-seq datasets, we show that current methods suffer from several biases and artefacts, which impair the analysis of intron retention. We designed a new approach to measure intron retention levels called the Stable Intron Retention ratio that we have implemented in a novel algorithm to detect and measure intron retention called S-IRFindeR. We demonstrate that it provides a significant improvement in accuracy, higher consistency between replicates and agreement with IR-levels computed from long-read sequencing data.

S-IRFindeR is freely available at:https://github.com/lbroseus/SIRFindeR/.
Novel PE and APC Tandems: Additional Near-Infrared Fluorochromes for Use in Spectral Flow Cytometry
Authors: Seong Yekyung , Wu Yian , Nguyen Denny , Thakur Archana , Nguyen Tuan Andrew , Harding Fiona
Published: June 2020

Recent advances in flow cytometry instrumentation and fluorochrome chemistries have greatly increased fluorescent conjugated antibody combinations that can be used reliably and easily in routine experiments. The Cytek Aurora flow cytometer has three excitation lasers (405nm, 488nm, and 640nm) and incorporates the latest Avalanche Photodiode (APD) technology, demonstrating significant improvement in sensitivity for fluorescent emission signals longer than 800nm. However, there are limited commercially available fluorochromes capable of excitation with peak emission signals beyond 800nm. To address this gap, we engineered 6 new fluorochromes: PE-750, PE-800, PE-830 for the 488nm laser and APC-750, APC-800, APC-830 for the 640nm laser. Utilizing the principal of fluorescence resonance energy transfer (FRET), these novel structures were created by covalently linking a protein donor dye with an organic small molecule acceptor dye. Additionally, each of these fluorochrome conjugates were shown to be compatible with Fixation/Permeabilization buffer reagents, and demonstrated acceptable brightness and stability when conjugated to antigen-specific monoclonal antibodies. These six novel fluorochrome reagents can increase the numbers of fluorochromes that can be used on a 3-laser spectral flow cytometer.
NRF-1 and HIF-1α modulate activity of human VDAC1 gene promoter during starvation and hypoxia in HeLa cells
Authors: Guarino Francesca , Zinghirino Federica , Mela Lia , Pappalardo Xena , Messina Angela , De Pinto Vito
Published: June 2020

VDAC (Voltage Dependent Anion Channel) is a family of pore forming protein located in the outer mitochondrial membrane. Its channel property ensures metabolites exchange between mitochondria and the rest of the cell resulting in metabolism and bioenergetics regulation, and in cell death and life switch. VDAC1 is the best characterized and most abundant isoform, and is involved in many pathologies, as cancer or neurodegenerative diseases. However, little information is available about its gene expression regulation in normal and/or pathological conditions. In this work, we explored VDAC1 gene expression regulation in normal conditions and in the contest of metabolic and energetic mitochondrial dysfunction and cell stress. The most active area of the putative promoter region was characterized in terms of transcription factors responsive elements both by bioinformatic studies and promoter activity experiments. In particular, we found a predominant presence of NRF-1 together with other transcription factors binding sites, involved in cell growth, proliferation, development and we studied their prevalence in gene activity. Furthermore, upon depletion of nutrients or controlled hypoxia, as reported in various pathologies, we found that VDAC1 transcripts levels were significantly increased in a time related manner. VDAC1 promoter activity was also validated by gene reporter assays. According to PCR real-time data, it was confirmed that VDAC1 promoter activity is further stimulated when are exposed to stress. A bioinformatic survey suggested NRF-1 e HIF-1α as the most active TFBS. Their validation was obtained by mutagenesis and overexpression experiments. In conclusion, we demonstrated experimentally the involvement of both NRF-1 and HIF-1α in the regulation of VDAC1 promoter activation at basal level and in cell stress conditions.
Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Authors: Audain E , Wilsdon A , Breckpot J , Izarzugaza JMG , Fitzgerald TW , Kahlert AK , Sifrim A , Wünnemann F , Perez-Riverol Y , Abdul-Khaliq H , Bak M , Bassett AS , Belmont JW , Benson DW , Berger F , Daehnert I , Devriendt K , Dittrich S , Daubeney P , Garg V , Hackmann K , Hoff K , Hofmann P , Dombrowsky G , Pickardt T , Bauer U , Keavney BD , Klaassen S , Kramer HH , Marshall CR , Milewicz DM , Lemaire SA , Coselli J , Mitchell ME , Tomita-Mitchell A , Prakash SK , Stamm K , Stewart AFR , Silversides CK , Siebert R , Stiller B , Rosenfeld JA , Vater I , Postma AV , Caliebe A , Brook JD , Andelfinger G , Hurles ME , Thienpont B , Larsen LA , Hitz MP
Published: June 2020

Congenital Heart Disease (CHD) affects approximately 7-9 children per 1000 live births. Numerous genetic studies have established a role for rare genomic variants at the copy number variation (CNV) and single nucleotide variant level. In particular, the role ofde novomutations (DNM) has been highlighted in syndromic and non-syndromic CHD. To identify novel haploinsufficient CHD disease genes we performed an integrative analysis of CNVs and DNMs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm (TAA). We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed mutation rate testing for DNMs identified in 2,489 parent-offspring trios. Our combined analysis revealed 21 genes which were significantly affected by rare genomic deletions and/or constrained non-synonymousde novomutations in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5BandWHSC1) have only been associated in singletons and small cases series, or show new associations with CHD. In addition, a systems level analysis revealed shared contribution of CNV deletions and DNMs in CHD probands, affecting protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes.
Sex-linked gene expression and the reversion to hermaphroditism inCarica papayaL. (Caricaceae)
Authors: Chae T , Harkess A , Moore RC
Published: June 2020

One evolutionary path from hermaphroditism to dioecy is via a gynodioecious intermediate. The evolution of dioecy may also coincide with the formation of sex chromosomes that possess sex-determining loci that are physically linked in a region of suppressed recombination. Dioecious papaya (Carica papaya) has an XY chromosome system, where the presence of a Y chromosome determines males. However, in cultivation, papaya is gynodioecious, due to the conversion of the male Y chromosome to a hermaphroditic Yhchromosome during its domestication. We investigated gene expression linked to the X, Y, and Yhchromosomes at different floral developmental stages in order to identify differentially expressed genes (DEGs) that may be involved in the sexual reversion of males to hermaphrodites. We identified 309 sex-biased genes found on the sex chromosomes, most of which are found in the pseudoautosomal regions (PARs). Female (XX) expression in the sex determining region (SDR) was almost double that of X-linked expression in males (XY) and hermaphrodites (XYh), which rules out dosage compensation for most sex-linked gene; although, an analysis of hemizygous X-linked loci found evidence of partial dosage compensation. Furthermore, we identified a potential candidate gene associated with both sex determination and the transition to hermaphroditism, a homolog of the MADS-box proteinSHORT VEGETATIVE PHASE(SVG).
A new method for counting reproductive structures in digitized herbarium specimens using Mask R-CNN
Authors: Davis Charles , Champ Julien , Park Daniel S. , Breckheimer Ian , Lyra Goia M. , Xie Junxi , Joly Alexis , Tarapore Dharmesh , Ellison Aaron M. , Bonnet Pierre
Published: June 2020

Phenology–the timing of life-history events–is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from>3000 specimens of six common wildflower species of the eastern United States (Anemone canadensisL.,A. hepaticaL.,A. quinquefoliaL.,Trillium erectumL.,T. grandiflorum(Michx.) Salisb., andT. undulatumWild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with>87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥ 90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the threeTrilliumspecies, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant response to ongoing climatic change.
The causal role of three frontal cortical areas in grasping
Authors: Caprara I , Janssen P
Published: June 2020

Efficient object grasping requires the continuous control of arm and hand movements based on visual information. Previous studies have identified a network of parietal and frontal areas that is crucial for the visual control of prehension movements. Electrical microstimulation of 3D shape-selective clusters in AIP during fMRI activates areas F5a and 45B, suggesting that these frontal areas may represent important downstream areas for object processing during grasping, but the role of area F5a and 45B in grasping is unknown. To assess their causal role in the frontal grasping network, we reversibly inactivated 45B, F5a and F5p during visually-guided grasping in macaque monkeys. First, we recorded single neuron activity in 45B, F5a and F5p to identify sites with object responses during grasping. Then, we injected muscimol or saline to measure the grasping deficit induced by the temporary disruption of each of these three nodes in the grasping network. The inactivation of all three areas resulted in a significant increase in the grasping time in both animals, with the strongest effect observed in area F5p. These results not only confirm a clear involvement of F5p, but also indicate causal contributions of area F5a and 45B in visually-guided object grasping.
Whole genomes reveal severe bottleneck among Asian hunter-gatherers following the invention of agriculture
Authors: Chakraborty Saikat , Basu Analabha ,   the GenomeAsia 100K Consortium
Published: June 2020

The invention of agriculture (IOA) by anatomically modern humans (AMH) around 10,000 years before present (ybp) is known to have led to an increase in AMH’s carrying capacity and hence its population size. Reconstruction of historical demography using high coverage (~30X) whole genome sequences (WGS) from >700 individuals from different South Asian (SAS) and Southeast Asian (SEA) populations reveals that although several present day populous groups did indeed experience a positive Neolithic Demographic Transition (NDT), most hunter-gatherers (HGs) experienced a demographic decrease. Differential fertility between HGs and non-HGs, exposure of HGs to novel pathogens from non-HGs could have resulted in such contrasting patterns. However, we think the most parsimonious explanation of the drastic decrease in population size of HGs is their displacement/enslavement by non-HGs.

Significance Statement

The invention of agriculture, around 10000 years ago, facilitated more food production which could feed larger populations. This had far-reaching socio-political and demographic impacts, including a ~10,000 fold increase in global population-size in the last 10,000 years. However, this increase in population size is not a universal truth and present day hunter-gatherer populations, in contrast, have dwindled in size, often drastically. The signatures of this rise in population size are discernible from the genomes of present-day individuals. Using genomic data, we show that for the majority of Asian hunter-gatherers, population-sizes drastically decreased following the invention of agriculture. We argue that a combination of displacement, enslavement and disease resulted in the decimation of hunter-gatherer societies.
Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumour immunity
Authors: Manczinger Máté , Balogh Gergő , Tamás Papp Benjamin , Koncz Balázs , Asztalos Leó , Kemény Lajos , Papp Balázs , Pál Csaba
Published: June 2020

The human leukocyte antigen class I (HLA-I) genes shape our immune response against pathogens and cancer. Certain HLA-I variants can bind a much wider range of peptides than others, a feature that could be favorable against a range of viral diseases. However, the implications of this phenomenon on cancer immune response is unknown. In this paper, we quantified peptide repertoire breadth (or promiscuity) of a representative set of HLA-I alleles, and found that cancer patients that carry HLA-I alleles with high peptide binding promiscuity are characterized by significantly worse prognosis after immune checkpoint inhibitor treatment. This trend can be explained by a reduced capacity of promiscuous HLA-I molecules to discriminate between human self and tumour peptides, yielding a shift in regulation of T-cells in the tumour microenvironment from activation to tolerance. In summary, HLA-I peptide binding specificity shapes neopeptide immunogenicity and the self-immunopeptidome repertoire in an antagonistic manner. It could also underlie a negative trade-off between antitumour immunity and the genetic susceptibility to viral infections.
Development of a Finite Element Model to Predict the Cellular Micromechanical Environment in Tissue Engineering Scaffolds
Authors: Page Mitchell I , Linde Peter E , Puttlitz Christian M
Published: June 2020

Cell fate in tissue engineering (TE) strategies is paramount to regenerate healthy, functional organs. The mechanical loads experienced by cells play an important role in cell fate. However, in TE scaffolds with a cell-laden hydrogel matrix, it is prohibitively complex to prescribe and measure this cellular micromechanical environment (CME). Accordingly, this study aimed to develop a finite element (FE) model of a TE scaffold unit cell that can be subsequently implemented to predict the CME and cell fates under prescribed loading. The compressible hyperelastic mechanics of a fibrin hydrogel were characterized by fitting unconfined compression and confined compression experimental data. This material model was implemented in a unit cell FE model of a TE scaffold. The FE mesh and boundary conditions were evaluated with respect to the mechanical response of a region of interest (ROI). A compressible second-order reduced polynomial hyperelastic model gave the best fit to the experimental data (C10= 1.72×10-4, C20= 3.83×10-4, D1= 3.41, D2= 8.06×10-2). A mesh with seed sizes of 40 μm and 60 μm in the ROI and non-ROI regions, respectively, yielded a converged model in 54 minutes. The in-plane boundary conditions demonstrated minimal influence on ROI mechanics for a 2-by-2 unit cell. However, the out-of-plane boundary conditions did exhibit an appreciable influence on ROI mechanics for a two bilayer unit cell. Overall, the developed unit cell model facilitates the modeling of the mechanical state of a cell-laden hydrogel within a TE scaffold under prescribed loading. This model will be utilized to characterize the CME in future studies, and 3D micromechanical criteria may be applied to predict cell fate in these scaffolds.