bluuebunny/crossref_metadata_2025 huggingface dataset:
An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation
Authors: Schoof Michael , Faust Bryan , Saunders Reuben A. , Sangwan Smriti , Rezelj Veronica , Hoppe Nick , Boone Morgane , Billesbølle Christian B. , Puchades Cristina , Azumaya Caleigh M. , Kratochvil Huong T. , Zimanyi Marcell , Deshpande Ishan , Liang Jiahao , Dickinson Sasha , Nguyen Henry C. , Chio Cynthia M. , Merz Gregory E. , Thompson Michael C. , Diwanji Devan , Schaefer Kaitlin , Anand Aditya A. , Dobzinski Niv , Zha Beth Shoshana , Simoneau Camille R. , Leon Kristoffer , White Kris M. , Chio Un Seng , Gupta Meghna , Jin Mingliang , Li Fei , Liu Yanxin , Zhang Kaihua , Bulkley David , Sun Ming , Smith Amber M. , Rizo Alexandrea N. , Moss Frank , Brilot Axel F. , Pourmal Sergei , Trenker Raphael , Pospiech Thomas , Gupta Sayan , Barsi-Rhyne Benjamin , Belyy Vladislav , Barile-Hill Andrew W. , Nock Silke , Liu Yuwei , Krogan Nevan J. , Ralston Corie Y. , Swaney Danielle L. , García-Sastre Adolfo , Ott Melanie , Vignuzzi Marco ,   QCRG Structural Biology Consortium, Walter Peter , Manglik Aashish
Published: August 2020

Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains stability and function after aerosolization, lyophilization, and heat treatment. These properties may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century.
Contrasting selection at multiple life stages maintains divergent adaptation between sunflower ecotypes
Authors: Goebl April M. , Kane Nolan C. , Doak Daniel F. , Rieseberg Loren H. , Ostevik Kate L.
Published: August 2020

Conspecific populations living in adjacent, but contrasting, microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow maintains genetic homogeneity except at loci experiencing strong, divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and persistence of divergent populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness components, absolute fitness, and allele frequency change at multiple life stages. This framework allows us to demonstrate that only local ecotypes experience positive population growth (lambda>1) and that the maintenance of divergent adaptation is mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and contribute to the persistence of each ecotype in its respective habitat.
Bi-paratopic and multivalent human VH domains neutralize SARS-CoV-2 by targeting distinct epitopes within the ACE2 binding interface of Spike
Authors: Bracken Colton J. , Lim Shion A. , Solomon Paige , Rettko Nicholas J. , Nguyen Duy P. , Zha Beth Shoshana , Schaefer Kaitlin , Byrnes James R. , Zhou Jie , Lui Irene , Liu Jia , Pance Katarina ,   QCRG Structural Biology Consortium, Zhou Xin X. , Leung Kevin K. , Wells James A.
Published: August 2020

Neutralizing agents against SARS-CoV-2 are urgently needed for treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domain binders with high affinity toward neutralizing epitopes without the need for high-resolution structural information. We constructed a VH-phage library and targeted a known neutralizing site, the angiotensin-converting enzyme 2 (ACE2) binding interface of the trimeric SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified 85 unique VH binders to two non-overlapping epitopes within the ACE2 binding site on Spike-RBD. This enabled us to systematically link these VH domains into multivalent and bi-paratopic formats. These multivalent and bi-paratopic VH constructs showed a marked increase in affinity to Spike (up to 600-fold) and neutralization potency (up to 1400-fold) on pseudotyped SARS-CoV-2 virus when compared to the standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with half-minimal inhibitory concentration (IC50) of 4.0 nM (180 ng/mL). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain bound an RBD at the ACE2 binding site, explaining its increased neutralization potency and confirming our original design strategy. Our results demonstrate that targeted selection and engineering campaigns using a VH-phage library can enable rapid assembly of highly avid and potent molecules towards therapeutically important protein interfaces.
Markedly heterogeneous COVID-19 testing plans among US colleges and universities
Authors: Booeshaghi A. Sina , Tan Fayth , Renton Benjamin , Berger Zackary , Pachter Lior
Published: August 2020

As the COVID-19 pandemic worsens in the United States [1], colleges that have invited students back for the fall are finalizing mitigation plans to lessen the spread of SARS-CoV-2. Even though students have largely been away from campuses over the summer, several outbreaks associated with colleges have already occurred [2], foreshadowing the scale of infection that could result from hundreds of thousands of students returning to college towns and cities. While many institutions have released return-to-campus plans designed to reduce viral spread and to rapidly identify outbreaks should they occur, in many cases communications by college administrators have been opaque. To contribute to an evaluation of university preparedness for the COVID-19 pandemic, we assessed a crucial element: COVID-19 on-campus testing. We examined testing plans at more than 500 colleges and universities throughout the US, and collated statistics, as well as narratives from publicly facing websites. We discovered a highly variable and muddled state of COVID-19 testing plans among US institutions of higher education that has been shaped by discrepancies between scientific studies and federal guidelines. We highlight cases of divergence between university testing plans and public health best practices, as well as potential bioethical issues.
Alcohol boosts pheromone production in male flies and makes them sexier
Authors: Keesey Ian W. , Doll Georg , Chakraborty Sudeshna Das , Baschwitz Amelie , Lemoine Marion , Kaltenpoth Martin , Svatoš Aleš , Sachse Silke , Knaden Markus , Hansson Bill S.
Published: August 2020

The attraction ofDrosophila melanogastertowards byproducts of alcoholic fermentation, especially ethanol, has been extensively studied1–4. However, the adaptive value of this behavior has not been elucidated. Previous studies have suggested anthropomorphic interpretations ofD. melanogasterbehavior towards alcohols5,6. Here, we instead assert that there exists a simple yet vital biological rationale for alcohol contact and consumption by these insects. We show that exposure to alcohols, especially methanol, results in an immediate amplification of fatty acid ester pheromone levels, which in turn elevates the probability that a male will successfully compete for a female during courtship. We proceed to identify three types of olfactory sensory neurons that detect ethanol and methanol. Moreover, we trace the ensuing neural circuits and reveal their role in controlling both attraction and aversion, where valence is balanced around mating status. Based on our results, we deduce that male flies associate with sources of alcohol as a biological imperative related to reproduction, and we provide an assessment of how and whyD. melanogasteris associated with alcohol using a sound ecological and natural history approach to this previously enigmatic biological phenomenon.

One sentence summary

Flies gain pheromone and courtship advantages with alcohol, but methanol is toxic, thus flies must balance risk versus reward.
Characterisation of 22446 patients attending UK emergency departments with suspected COVID-19 infection: Observational cohort study
Authors:   The PRIEST Research Group (details in Appendix 1), Goodacre Steve , Thomas Ben , Lee Ellen , Sutton Laura , Loban Amanda , Waterhouse Simon , Simmonds Richard , Biggs Katie , Marincowitz Carl , Schutter Jose , Connelly Sarah , Sheldon Elena , Hall Jamie , Young Emma , Bentley Andrew , Challen Kirsty , Fitzimmons Chris , Harris Tim , Lecky Fiona , Lee Andrew , Maconochie Ian , Walter Darren
Published: August 2020

Background

Hospital emergency departments play a crucial role in the Initial management of suspected COVID-19 infection. We aimed to characterise patients attending emergency departments with suspected COVID-19, including subgroups based on sex, ethnicity and COVID-19 test results.

Methods

We undertook a mixed prospective and retrospective observational cohort study in 70 emergency departments across the United Kingdom (UK). We collected presenting data from 22446 people attending with suspected COVID-19 between 26 March 2020 and 28 May 2020. Outcomes were admission to hospital, COVID-19 result, organ support (respiratory, cardiovascular or renal), and death, by record review at 30 days.

Results

Adults were acutely unwell (median NEWS2 score 4) and had high rates of admission (67.1%), COVID-19 positivity (31.2%), organ support (9.8%) and death (15.9%). Children had much lower rates of admission (27.4%), COVID-19 positivity (1.2%), organ support (1.4%) and death (0.3%). Adult men and women presented in similar numbers (10210 versus 10506), but men were more likely to be admitted (72.9% v 61.4%), require organ support (12.2% v 7.7%) and die (18.7% v 13.3%). Black or Asian adults tended to be younger than White adults (median age 54, 50 and 67 years), were less likely to be admitted (60.8%, 57.3%, 69.6%) or die (11.9%, 11.2%, 16.8%), but were more likely to require organ support (15.9%, 14.3%, 8.9%) or have a positive COVID-19 test (40.8%, 42.1%, 30.0%). Adults admitted with confirmed COVID-19 had similar age and comorbidities (except chronic lung disease) to those who did not have COVID-19 confirmed, but were much more likely to need organ support (22.2% v 8.9%) or die (32.7% v 15.9%).

Conclusions

Important differences exist between patient groups presenting to the emergency department with suspected COVID-19. People with confirmed COVID-19 have a poor prognosis, compared with similar emergency admissions without confirmed COVID-19.

Registration

ISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533
Contextualising Single-Arm Ophthalmology Trials With Real-World Data: An Emulated Target Trial Comparing The Efficacy of Interventions For Neovascular Age-Related Macular Degeneration
Authors: Thomas Darren S. , Lee Aaron Y. , Müller Philipp L. , Schwartz Roy , Olvera-Barrios Abraham , Warwick Alasdair N. , Patel Praveen J. , Heeren Tjebo F.C. , Egan Catherine , Taylor Paul , Tufail Adnan
Published: August 2020

Methods of causal inference have shown promise in replicating randomised trials using real-world data recorded by Electronic Health Records (EHRs). We herein emulated a target trial on the intention-to-treat efficacy of off-label bevacizumab (q6w) pro re nata relative to fixed-interval aflibercept (q8w) for improving week-54 visual acuity of eyes affected by neovascular age-related macular degeneration. The bevacizumab arm (n 65) was taken from the ABC randomised controlled trial. A total of 4,471 aflibercept-treated eyes aligning with the ABC trial eligibility were identified from EHRs and synthetic control arms were created by emulating randomisation conditional on age, sex, and baseline visual read via exact matching and propensity score methods. We undertook an inferiority analysis on mean difference at 54 weeks; outcomes regression on achieving a change in visual acuity of ≥ 15, ≥ 10, and ≤ −15 Early Treatment Diabetic Retinopathy Letters (ETDRS) letters at week 54; and a time-to-event analysis on achieving a change in visual acuity of ≥ 15, ≥ 10, and ≤ −15 ETDRS letters by week 54. Our findings suggest off-label bevacizumab to be neither non-inferior nor superior to licensed aflibercept. While being no substitute for randomised controlled trials, emulated target trials could aid the interpretation of single-armed trials.
Revisiting a null hypothesis: exploring the parameters of oligometastasis treatment
Authors: Scaborough Jessica A. , Tom Martin C. , Scott Jacob G.
Published: August 2020

In the treatment of patients with metastatic cancer, the current paradigm states that metastasis-directed therapy does not prolong life. This paradigm forms the basis of clinical trial null hypotheses, where trials are built to test the null hypothesis: patients garner no overall survival benefit from targeting metastatic lesions. However, with advancing imaging technology and increasingly precise techniques for targeting lesions, a much larger proportion of metastatic disease can be treated. As a result, the life-extending benefit of targeting metastatic disease is becoming increasingly clear. In this work, we suggest shifting this qualitative null hypothesis, and describe a mathematical model which can be used to frame a new, quantitative null. We begin with a very simple formulation of tumor growth, an exponential function, and use it to show that while any amount of cell kill will extend survival, in many cases the extent is so small as to be unnoticeable in a clinical context or out-weighed by factors related to toxicity and treatment time. Recasting the null in these quantitative terms will allow trialists to design trials specifically to increase understanding of what circumstances (patient selection, disease burden, tumor growth kinetics) can lead to improved OS when targeting metastatic lesions, rather than whether or not targeting metastases extends survival for patients with (oligo-)metastatic disease.
Mass molecular testing for COVID19 using NGS-based technology and a highly scalable workflow
Authors: de Mello Malta Fernanda , Amgarten Deyvid , Val Felipe Camilo , Santana Rubia Anita Ferraz , Cervato Murilo Castro , de Azevedo Bruna Mascaro Cordeiro , de Souza Basqueira Marcela , Alves Camila Oliveira dos Santos , Nobrega Maria Soares , Pinho João Renato Rebello
Published: August 2020

Since first reported case of the new coronavirus infection in Wuhan, China, researchers and governments have witnessed an unseen rise in the number of cases. Thanks to the rapid work of Chinese scientists, the pathogen now called SARS-CoV-2 has been identified and its whole genome has been deposited in public databases by early January 2020. The availability of the genome has allowed researchers to develop Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assays, which are now the gold-standard for molecular diagnosis of the respiratory syndrome COVID19. Because of the rising number of cases and rapid spreading, the world has been facing a shortage of RT-PCR supplies, especially the ones involved in RNA extraction. This has been a major bottleneck to increase testing capacity in many countries that do not significantly manufacture these supplies (Brazil included). Additionally, RT-PCR scalability is highly dependent on equipment that usually perform testing of 96 samples at a time. In this work, we describe a cost-effective molecular NGS-based test for diagnosis of COVID19, which uses a single-step RNA extraction and presents high scalability and accuracy when compared to the gold-standard RT-PCR. A single run of the NGS-based test using the Illumina NextSeq 550 mid-end sequencing equipment is able to multiplex 1,536 patient’s samples, providing individual semi-qualitative results (detected, not detected). Detected results are provided with fragments per million (FPM) values, which was demonstrated to correlate with RT-PCR Cycle Threshold (CT) values. Besides, usage of the high-end Illumina Novaseq platform may yield diagnostic for up to 6,144 samples in a single run. Performance results when compared with RT-PCR show general accuracy of 96% (or 98% when only samples with CT values for gene N lower than 30 are considered). We have also developed an online platform, called VarsVID®, a Varstation® feature, to help test executors to easily scale testing numbers. Sample registering, wet-lab worksheets, sample sheet for sequencing and results’ display are all features provided by VarsVID® on Varstation®. Altogether, these results will contribute to control COVID19 pandemics.
Application of a generalized SEIR model for covid-19 in Algeria
Authors: Lounis Mohamed , Azevedo Juarez dos Santos
Published: August 2020

The novel coronavirus diseases 2019 (COVID-19) in Wuhan is continuing to impress the world by its fast spread and the number of affected persons attracting an unprecedented attention. In this article, we used the classical SEIR model and a generalized SEIR model called SEIRDP model inspired in a model previously used during the outbreak in China to predict the evolution of COVID-19 in Algeria for a future period of 100 days using official reported data from early April to early August, 2020. Initial evaluation showed that thetwo models had a net correspondence with the reported data during this period for cumulative infected cases but the number of cumulative deaths was underestimated with the classical SEIR model. Model prediction with the SEIRDP concluded that the number of cumulative infected cases will increase in the next days reaching a number of about 60 k in middle November with a median of about 300 daily cases. Also, the number of estimated deaths will be around 2k. These results suggest that the COVID-19 is ongoing to infect more persons which may push national authorities to carefully act in the probable leaving of containment.
Effective reproduction number for COVID-19 in Aotearoa New Zealand
Authors: Binny Rachelle N. , Lustig Audrey , Brower Ann , Hendy Shaun C. , James Alex , Parry Matthew , Plank Michael J. , Steyn Nicholas
Published: August 2020

The effective reproduction number, Reff, is the average number of secondary cases infected by a primary case, a key measure of the transmission potential for a disease. Compared to many countries, New Zealand has had relatively few COVID-19 cases, many of which were caused by infections acquired overseas. This makes it difficult to use standard methods to estimate Reff. In this work, we use a stochastic model to simulate COVID-19 spread in New Zealand and report the values of Reff from simulations that gave best fit to case data. We estimate that New Zealand had an effective reproduction number Reff = 1.8 for COVID-19 transmission prior to moving into Alert Level 4 on March 25 2020 and that after moving into Alert level 4 this was reduced to Reff = 0.35. Our estimate Reff = 1.8 for reproduction number before Alert Level 4, is relatively low compared to other countries. This could be due, in part, to measures put in place in early-to mid-March, including: the cancellation of mass gatherings, the isolation of international arrivals, and employees being encouraged to work from home.
Hypersensitivity reactions to IL-1 and IL-6 inhibitors are linked to common HLA-DRB1*15 alleles
Authors: Hollenbach Jill , Ombrello Michael J. , Tremoulet Adriana , Duque Jaime S. Rosa , Chua Gilbert T. , Montero-Martin Gonzalo , Burns Jane C. , Shimizu Chisato , Deutsch Gail , Monos Dimitri , Mallajosyula Vamsee , Xu Jianpeng , Ghosh Debopam , Tan Serena , Remmers Elaine , Canna Scott , Szymanski Ann Marie , Rubin Danielle , Fernandez-Vina Marcelo A. , Saper Vivian E. , Mellins Elizabeth D. ,   Drug Hypersensitivity in sJIA Consortium investigators
Published: August 2020

In Saper et al (2019), we described systemic JIA patients who developed a high-fatality diffuse lung disease (DLD) while on IL-1 or IL-6 inhibitors. We observed severe delayed drug hypersensitivity reactions (DHR) in a significant subset. Because alleles of the human leukocyte antigen (HLA) loci can mediate DHR, we investigated HLA genotype association with these DHR. We typed subjects treated with these inhibitors: 34 sJIA/DHR/DLD, 11 sJIA/DHR without DLD, 18 drug-tolerant sJIA, and 19 Kawasaki disease (KD) patients in an anti-IL-1(anakinra) trial. We also accessed genotypes from a large sJIA case/control cohort.

We first compared White subjects with sJIA/DHR to 550 ancestry-matched sJIA subjects. We found striking enrichments of HLA-DRB1*15:01, HLA-DQA1*01:02, and DQB1*06:02, alleles in near-complete linkage (White individuals). HLA-DRB 1*15:01 (as haplotype proxy) was increased in White sJIA subjects with DHR/DLD versus sJIA drug-tolerant controls and was observed upon inclusion of sJIA+DHR-only and KD+DHR White subjects. In our entire cohort regardless of ancestry, 75% carried HLA-DRB 1*15:01 or the structurally related DRB1*15:03 and DRB1*15:06, which were absent among drug-tolerant subjects (p=5 x 10-13; Odds Ratio lower bound=20.11).

Patients who harbor HLA-DRB1*15 alleles are at high risk of developing DHR to anti-IL-1/IL-6. Our data also suggest DHR maybe a trigger/enhancer of DLD in sJIA patients and support performing prospective HLA screening in sJIA, its adult-onset counterpart, and other inflammatory conditions where these drugs are used, such as KD.
A system-level gene regulatory network model forPlasmodium falciparum
Authors: Neal ML , Wei L , Peterson E , Arrieta-Ortiz ML , Danziger SA , Baliga NS , Kaushansky A , Aitchison JD
Published: August 2020

Many of the gene regulatory processes ofPlasmodium falciparum, the deadliest malaria parasite, remain poorly understood. To develop a comprehensive guide for exploring this organism’s gene regulatory network, we generated a system-level model ofPlasmodium falciparumgene regulation using a well-validated, machine-learning approach for predicting interactions between transcription regulators and their targets. The resulting network accurately predicts expression levels of transcriptionally coherent gene regulatory programs in independent transcriptomic data sets from parasites collected by different research groups in diverse laboratory and field settings. Thus, our results indicate that our gene regulatory model has predictive power and utility as a hypothesis-generating tool for illuminating clinically relevant gene regulatory mechanisms withinPlasmodium falciparum. Using the set of regulatory programs we identified, we also investigated correlates of artemisinin resistance based on gene expression coherence. We report that resistance is associated with incoherent expression across many regulatory programs, including those controlling genes associated with erythrocyte-host engagement. These results suggest that parasite populations with reduced artemisinin sensitivity are more transcriptionally heterogenous. This pattern is consistent with a model where the parasite utilizes bet-hedging strategies to diversify the population, rendering a subpopulation more able to navigate drug treatment.
Decision Support Systems based on Scientific Evidence: Bibliometric Networks of InvasiveLantana camara
Authors: Mishra Preet , Prasad Abhishek , Babu Suresh , Yadav Gitanjali
Published: August 2020

Extraction and analysis of useful knowledge from the vast amount of relevant published literature can add valuable insights to any research theme or area of interest. We introduce a simplified bibliometric data analysis protocol for gaining substantial insights into research thematics, which can also serve as a handy practical skill for researchers, while working from home. In this paper, we provide ways of developing a holistic research strategy using bibliometric-data driven approaches that integrate network analysis and information management, without the need of full paper access. This protocol is a comprehensive multi-modular pathway for analysis of metadata obtained from major scientific publishing houses by use of a Decision Support System (DSS). A simple case study on the invasive speciesLantana camarahas been presented as a proof-of-concept to show how one can implement this DSS based protocol. Some perspectives are also provided on how the outcomes can be used directly or scaled up for long term research interventions. We hope that this work will simplify exploratory literature review, and enable rational design of research objectives for scholars, as well as development of comprehensive grant proposals that address gaps in research.
TRPV2 interaction with small molecules and lipids revealed by cryo-EM
Authors: Protopopova Anna D. , Pumroy Ruth A. , de la Roche Jeanne , Haug Ferdinand M. , Sousa Bárbara B. , Gallo Pamela N. , Bernardes Gonçalo J.L. , Leffler Andreas , Moiseenkova-Bell Vera Y.
Published: August 2020

Transient receptor potential vanilloid 2 (TRPV2) plays a critical role in a variety of physiological and pathophysiological processes, putting TRPV2 on the list of important drug targets. Yet, specific TRPV2 agonists and antagonists are currently unavailable. Their development requires a precise knowledge of how the currently known non-specific small molecules interact with TRPV2 at the molecular level. Here we present TRPV2 structures in ligand-bound states resolved by cryo-electron microscopy in the presence of 2-aminoethoxydiphenyl borate (2-ABP), 2-APB with doxorubicin (DOXO), and ruthenium red (RR). We identified a novel 2-APB drug binding site between the S5 helix and S4-S5 linker on two adjacent TRPV2 monomers and determined the mechanism of TRPV2 pore block by RR. We also showed that a large organic molecule like DOXO can enter the TRPV2 pore in the presence of 2-APB. Additionally, we discovered a structural lipid bound in a unique position in the “vanilloid pocket”, which is absent in the 2-APB-bound state of the channel, allowing us to propose a model for TRPV2 channel gating. Together, this work provides a further understanding of TRPV2 function and a structural framework for the development of TRPV2-specific modulators.
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing
Authors: Bhoyar Rahul C. , Jain Abhinav , Sehgal Paras , Divakar Mohit Kumar , Sharma Disha , Imran Mohamed , Jolly Bani , Ranjan Gyan , Rophina Mercy , Sharma Sumit , Siwach Sanjay , Pandhare Kavita , Sahoo Swayamprabha , Sahoo Maheswata , Nayak Ananya , Mohanty Jatindra Nath , Das Jayashankar , Bhandari Sudhir , Mathur Sandeep K , Kumar Anshul , Sahlot Rahul , Rojarani Pallavali , Lakshmi Juturu Vijaya , Surekha Araveti , Sekhar Pulala Chandra , Mahajan Shelly , Masih Shet , Singh Pawan , Kumar Vipin , Jose Blessy , Mahajan Vidur , Gupta Vivek , Gupta Rakesh , Arumugam Prabhakar , Singh Anjali , Nandy Ananya , Raghavendran P.V. , Jha Rakesh Mohan , Kumari Anupama , Gandotra Sheetal , Rao Vivek , Faruq Mohammed , Kumar Sanjeev , Betsy Reshma G , Narendra Varma G , Roy Shuvra Shekhar , Sengupta Antara , Chattopadhyay Sabyasachi , Singhal Khushboo , Pradhan Shalini , Jha Diksha , Naushin Salwa , Wadhwa Saruchi , Tyagi Nishu , Poojary Mukta , Scaria Vinod , Sivasubbu Sridhar
Published: August 2020

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
Predictive coding of natural images by V1 activity revealed by self-supervised deep neural networks
Authors: Uran Cem , Peter Alina , Lazar Andreea , Barnes William , Klon-Lipok Johanna , Shapcott Katharine A , Roese Rasmus , Fries Pascal , Singer Wolf , Vinck Martin
Published: August 2020

Predictive coding is an important candidate theory of self-supervised learning in the brain. Its central idea is that neural activity results from an integration and comparison of bottom-up inputs with contextual predictions, a process in which firing rates and synchronization may play distinct roles. Here, we quantified stimulus predictability for natural images based on self-supervised, generative neural networks. When the precise pixel structure of a stimulus falling into the V1 receptive field (RF) was predicted by the spatial context, V1 exhibited characteristic γ-synchronization (30-80Hz), despite no detectable modulation of firing rates. In contrast to γ, β-synchronization emerged exclusively for unpredictable stimuli. Natural images with high structural predictability were characterized by high compressibility and low dimensionality. Yet, perceptual similarity was mainly determined by higher-level features of natural stimuli, not by the precise pixel structure. When higher-level features of the stimulus in the receptive field were predicted by the context, neurons showed a strong reduction in firing rates and an increase in surround suppression that was dissociated from synchronization patterns. These findings reveal distinct roles of synchronization and firing rates in the predictive coding of natural images.
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Authors: Alqassem Israa , Sonthalia Yash , Klitzke-Feser Erika , Shim Heejung , Canzar Stefan
Published: August 2020

Alternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular condition or developmental stage. In addition, a large fraction of human disease mutations affect splicing and lead to aberrant mRNA and protein products. Current methods that interrogate the transcriptome based on RNA-seq either suffer from short read length when trying to infer full-length transcripts, or are restricted to predefined units of alternative splicing that they quantify from local read evidence. Instead of attempting to quantify individual outcomes of the splicing process such as local splicing events or full-length transcripts, we propose to quantify alternative splicing using a simplified probabilistic model of the underlying splicing process. Our model is based on the usage of individual splice sites and can generate arbitrarily complex types of splicing patterns. In our method, McSplicer, we estimate the parameters of our model using all read data at once and we demonstrate in our experiments that this yields more accurate estimates compared to competing methods. Our model is able to describe multiple effects of splicing mutations using few, easy to interpret parameters, as we illustrate in an experiment on RNA-seq data from autism spectrum disorder patients. McSplicer is implemented in Python and available as open-source athttps://github.com/canzarlab/McSplicer.
Capturing Neonatal Cardiomyocyte – Endothelial interactions on-a-Chip
Authors: Tavassoli Hossein , Kang Young Chan , Rorimpandey Prunella , Pimanda John E , Chandrakanthan Vashe , Chan Peggy P.Y.
Published: August 2020

The neonatal heart has been the focus of numerous investigations due to its inherent regenerative potential. However, the interactions between neonatal cardiomyocytes (CMs) and endothelial cells (ECs) have been difficult to model and study due to the lack of an appropriate device. Here, we developed a method to culture primary neonatal CMs and ECs in a microchip and characterise their behavioural properties over a 14-day period. By implementing cell migration analyses coupled with immunostaining and confocal microscopy, we were able to identify and quantify sub-populations of migratory and non-migratory ECs. In CM–EC co-cultures, migrating ECs were found to move in higher numbers and longer distances compared to migrating CMs. In the presence of CMs, non-migrating ECs established connexin gap junctions and formed CM–EC cell aggregates, which were likely a priming event for endothelial organoid formation. This microfluidic device also enabled us to visualise the temporal sequence organoid formation and phenomena such as collective cell migration, CM–EC trans-differentiation and synchronisation of CM beating. This microchip based culture system has potential applications for tissue engineering and drug discovery.
Dissecting the microenvironment around biosynthetic scaffolds in murine skin wound healing
Authors: Hu Chen , Chu Chenyu , Liu Li , Jin Shue , Yang Renli , Rung Shengan , Li Jidong , Qu Yili , Man Yi
Published: August 2020

Structural properties of biomaterials play critical roles in guiding cell behaviors and influence the immune response against them. We fabricated electrospun membranes with three types of surface topography (Random, Aligned, and Latticed). The aligned membranes showed immunomodulatory ability, and led to faster wound healing, reduced fibrotic response and enhanced regeneration of cutaneous appendages when used in skin wound repair. Based on that, we performed single-cell RNA sequencing analysis on cells from wounded mouse skin in the presence or absence of the Aligned scaffold. Keratinocytes, fibroblasts, and immune cells including neutrophils, monocytes, macrophages, dendritic cells, and T cells showed diverse cellular heterogeneity. More hair follicle progenitor cells, inner root sheath cells (anagen-related) and fibroblast subsets were found in the Aligned group, which corresponded to the improved regeneration of hair follicles and faster wound closure in the presence of scaffold. Immune responses towards the biomaterial differed from that of control group. In aligned samples, infiltrated macrophages and neutrophils were reduced, whereas more effector T cells were recruited. The time course of immune response was possibly advanced towards an adaptive immunity-dominant stage by the scaffold. The microenvironment around scaffold involved intricate interplay of immune cells and cutaneous cells, and wound healing was the comprehensive results of numerous influencing factors working together.
Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)
Authors: Marla Soma , Mishra Pallavi , Maurya Ranjeet , Singh Mohar , Wankhede D. P. , Gupta Anil. K. , Rao N. S. , Singh S. K. , Kumar Rajesh
Published: August 2020

Genome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in Next Generation sequencing. Of late multiple draft assemblies of plant genomes are reported in many organisms. The draft assemblies ofCajanus cajanare with different levels of genome completeness; contain large number of repeats, gaps and segmental duplications. Draft assemblies with portions of genome missing, are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and prediction of gene component as desired by crop researchers. Genome coveragei.e.number of sequenced raw reads mapped on to certain locations of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. Present work was aimed at improvement of coverage in reportedde novosequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of Pigeonpea, a legume widely cultivated in India. The two assemblies comprised 72% and 75% of estimated coverage of genome respectively. We employed assembly reconciliation approach to compare draft assemblies and merged them to generate a high quality near complete assembly with enhanced contiguity. Finished assembly has reduced number of gaps than reported in draft assemblies and improved genome coverage of 82.4%. Quality of the finished assembly was evaluated using various quality metrics and for presence of specific trait related functional genes. Employed pair-end and mate-pair local library data sets enabled to resolve gaps, repeats and other sequence errors yielding lengthier scaffolds compared to two draft assemblies. We report prediction of putative host resistance genes from improved sequence againstFusariumwilt disease and evaluated them in both wet laboratory and field phenotypic conditions.
The influence of heart rate variability biofeedback on cardiac regulation and functional brain connectivity
Authors: Schumann Andy , Cruz Feliberto de la , Köhler Stefanie , Brotte Lisa , Bär Karl-Jürgen
Published: August 2020

Background

Heart rate variability (HRV) biofeedback has a beneficial impact on perceived stress and emotion regulation. However, its impact on brain function is still unclear. In this study, we aimed to investigate the effect of an 8-week HRV-biofeedback intervention on functional brain connectivity in healthy subjects.

Methods

HRV biofeedback was carried out in five sessions per week, including four at home and one in our lab. A control group playedjump‘n’run gamesinstead of the training. Functional magnetic resonance imaging was conducted before and after the intervention in both groups. To compute resting state functional connectivity (RSFC), we defined regions of interest in the ventral medial prefrontal cortex (VMPFC) and a total of 260 independent anatomical regions for network-based analysis. Changes of RSFC of the VMPFC to other brain regions were compared between groups. Temporal changes of HRV during the resting state recording were correlated to dynamic functional connectivity of the VMPFC.

Results

First, we corroborated the role of the VMPFC in cardiac autonomic regulation. We found that temporal changes of HRV were correlated to dynamic changes of prefrontal connectivity, especially to the middle cingulate cortex, left anterior insula, right amygdala, supplementary motor area, dorsal and ventral lateral prefrontal regions. The biofeedback group showed a drop in heart rate by 5.5 beats/min and an increased RMSSD as a measure of HRV by 10.1ms (33%) after the intervention. Functional connectivity of the VMPFC increased mainly to the right anterior insula, the dorsal anterior cingulate cortex and the dorsolateral prefrontal cortex after biofeedback intervention when compared to changes in the control group. Network-based statistic showed that biofeedback had an influence on a broad functional network of brain regions.

Conclusion

Our results show that increased vagal modulation induced by HRV-biofeedback is accompanied by changes in functional brain connectivity during resting state.
High-Resolution Satellite Imagery to AssessSargassumInundation Impacts to Coastal Areas
Authors: Hernandez William J. , Morell Julio M. , Armstrong Roy A.
Published: August 2020

A change detection analysis utilizing Very High-resolution (VHR) satellite imagery was performed to evaluate the changes in benthic composition and coastal vegetation in La Parguera, southwestern Puerto Rico, attributable to the increased influx of pelagicSargassum sppand its accumulations in cays, bays, inlets and near-shore environments. Satellite imagery was co-registered, corrected for atmospheric effects, and masked for water and land. A Normalized Difference Vegetation Index (NDVI) and an unsupervised classification scheme were applied to the imagery to evaluate the changes in coastal vegetation and benthic composition. These products were used to calculate the differences from 2010 baseline imagery, to potential hurricane impacts (2018 image), and potentialSargassumimpacts (2020 image). Results show a negative trend in Normalized Difference Vegetation Index (NDVI) from 2010 to 2020 for the total pixel area of 24%, or 546,446 m2. These changes were also observed in true color images from 2010 to 2020. Changes in the NDVI negative values from 2018 to 2020 were higher, especially for the Isla Cueva site (97%) and were consistent with the field observations and drone surveys conducted since 2018 in the area. The major changes from 2018 and 2020 occurred mainly in unconsolidated sediments (e.g.sand, mud) and submerged aquatic vegetation (e.g.seagrass, algae), which can have similar spectra limiting the differentiation from multi-spectral imagery. Areas prone toSargassumaccumulation were identified using a combination of 2018 and 2020 true color VHR imagery and drone observations. This approach provides a quantifiable method to evaluateSargassumimpacts to the coastal vegetation and benthic composition using change detection of VHR images, and to separate these effects from other extreme events.
Development of photosynthetic carbon fixation model using multi-excitation wavelength fast repetition rate fluorometry in Lake Biwa
Authors: Kazama Takehiro , Hayakawa Kazuhide , Kuwahara Victor S. , Shimotori Koichi , Imai Akio , Komatsu Kazuhiro
Published: August 2020

Direct measurements of gross primary productivity (GPP) in the water column are essential, but can be spatially and temporally restrictive. Fast repetition rate fluorometry (FRRf) is a bio-optical technique based on chlorophylla(Chl-a) fluorescence that can estimate the electron transport rate (ETRPSII) at photosystem II (PSII) of phytoplankton in real time. However, derivation of phytoplankton GPP in carbon units from ETRPSIIremains challenging because the electron requirement for carbon fixation (Фe,C) can vary depending on multiple factors. Also, the FRRf is still relatively novel, especially in freshwater ecosystems where phosphorus limitation and cyanobacterial blooms are common. The goal of the present study is to construct a robust Фe,Cmodel for freshwater ecosystems using simultaneous measurements of ETRPSIIby FRRf with multi-excitation wavelengths coupled with traditional carbon fixation rate by the13C method. The study was conducted in oligotrophic and mesotrophic areas in Lake Biwa from July 2018 to May 2019. The combination of excitation light at 444, 512 and 633 nm correctly estimated ETRPSIIof cyanobacteria. The range of Фe,Cin the phytoplankton community varied from 1.1 to 31.0 mol e−mol C−1during the study period. Generalized liner model showed the best model including 12 physicochemical and biological factors explained 67% of the variance in Фe,C. Among all factors, water temperature was the most significant, while PAR intensity was not. The GPP values estimated by FRRf (GPPf) with the best Фe,Cmodel relative to13C (GPP13C) varied 0.5–1.5. Further,GPPfestimated with more parsimonious Фe,Cmodels were also comparable toGPP13C. This study quantifies the applicability of thein situFRRf methodology, and supports continuous monitoring of GPP by FRRf in lakes with large spatio-temporal variability of environmental conditions and phytoplankton assemblages.
Aerobic glycolysis supports hepatitis B virus biosynthesis through interaction between viral surface antigen and pyruvate kinase isoform M2
Authors: Wu Yi-Hsuan , Yang Yi , Chen Ching-Hung , Hsiao Chia-Jen , Li Tian-Neng , Liao Kuan-Ju , Chen Bor-Sen , Wang Lily Hui-Ching
Published: August 2020

As an intracellular pathogen, the reproduction of hepatitis B virus (HBV) depends on the occupancy of host metabolism machinery. Here we test a hypothesis if HBV may govern intracellular biosynthesis to achieve a productive reproduction. To test this hypothesis, we set up an affinity purification screen for host factors that interact with viral large surface antigen (LHBS). This identified pyruvate kinase isoform M2 (PKM2), a key regulator of glucose metabolism, as a binding partner of LHBS. We showed that the expression of LHBS affected oligomerization of PKM2 in hepatocytes, and thereby increased glucose consumption and lactate production, a phenomenon known as aerobic glycolysis. Interestingly, recovering PKM2 activity in hepatocytes by chemical activators, TEPP-46 or DASA-58, reduced biosynthesis of viral surface and core antigens. In addition, reduction of glycolysis by culturing in low-glucose condition or treatment with 2-deoxyglucose also decreased biosynthesis of viral surface antigen, without affecting general host proteins. Finally, TEPP-46 largely suppressed proliferation of LHBS-positive cells on 3-dimensional agarose plates, but showed no effect on the traditional 2-dimensional cell culture. Taken together, these results indicate that virus-induced metabolic switch may supportde novobiosynthesis of HBV in hepatocytes. In addition, aerobic glycolysis is likely essential for LHBS-mediated oncogenesis. Accordingly, restriction of glucose metabolism may be considered as a novel strategy to restrain viral mediated biosynthesis and oncogenesis during chronic HBV infection.

Author summary

Chronic HBV infection is a life-long threat of patients, with a 25~40% increased risk of developing liver cirrhosis and cancer. Persistent expression of oncogenic viral products in the liver, especially LHBS, is an oncogenic caveat and resistant to current antiviral agents. Here we show that viral LHBS binds to host PKM2 and diminishes its kinase activity. This virus-host interaction induces metabolic switch from oxidative phosphorylation to aerobic glycolysis, with increased glucose consumption and lactate production. We show that such metabolic switch not only favors biosynthesis of HBV but also provokes hepatocarcinogenesis. Notably, restoration of PKM2 activity by chemical activators decreases expressions of viral products and largely suppresses virus-mediated hepatocarcinogenesis. This study highlights the importance of host metabolism in supporting viral biosynthesis and indicates a novel therapeutic approach to control chronic HBV infection via modulating host metabolic switch.