bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrostatic Fields Have Strong Repellency Effects AgainstCulex pipiens
Authors: Tam Jonathan
Published: August 2020

Currently, the most effective mosquito repellents employ the use of the chemical N, N-Diethyl-meta-toluamide (DEET), often considered the gold standard of repellents. However, as DEET continues to be widely used, it is beginning to lose efficacy as mosquitoes gradually gain resistance to it. Additionally, DEET only protects the skin that it is applied on, and therefore, it is difficult to achieve 100% repellency for the entire body. As urbanization and climate change continue to increase the threat of widespread mosquito-borne illnesses, new forms of repellents must be developed to combat the possibility of an epidemic. Previous studies indicate that a multitude of insects, including spiders, flies, and mosquitoes, avoid electrostatic fields at sufficiently high voltages. In this study, I evaluate if electrostatic fields can be used as a potential personal repellent against mosquitoes and an alternative to chemical sprays. I found that by charging the surface of a person’s body with a high voltage (9800V) but minuscule current, I created a safe and effective method that repels mosquitoes from landing on the skin. This method has similar efficacy to DEET, with near 100% repellency after 20 minutes of charging. It also has the advantage of not needing to be reapplied and provides full-body protection, allowing greater protection to the user than DEET. These results introduce a promising method of repelling mosquitoes, that used together with present-day chemical repellents, can help provide greater protection to malaria-endemic countries.
Plasmodium falciparumincreases its investment in gametocytes in the wet season in asymptomatic individuals
Authors: Oduma Colins O. , Ogolla Sidney , Atieli Harrysone , Ondigo Bartholomew N. , Lee Ming-Chieh , Githeko Andrew K. , Dent Arlene E. , Kazura James W. , Yan Guiyun , Koepfli Cristian
Published: August 2020

In many regions, malaria transmission is seasonal, but it is not well understood whetherP. falciparummodulates its investment in transmission in response to seasonal vector abundance. In two sites in western Kenya (Chulaimbo and Homa Bay), we sampled 1116 asymptomatic individuals in the wet season, when vectors are abundant, and 1743 in the dry season. We screened forP. falciparumby qPCR, and gametocytes bypfs25RT-qPCR. Parasite prevalence in Chulaimbo and Homa Bay was 27.1% and 9.4% in the dry season, and 48.2% and 7.8% in the wet season respectively. Mean parasite densities did not differ between seasons (P=0.562). A contrasting pattern of gametocyte carriage was observed. In the wet season, fewer infections harbored gametocytes (22.3% vs. 33.8%,P=0.009), but densities were 3-fold higher (P<0.001). Thus, in the wet season, among gametocyte positive individuals, higher proportion of all parasites were gametocytes, reflecting an increased investment in transmission.
CRISPR Turbo Accelerated Knock Out (CRISPy TAKO) for rapidin vivoscreening of gene function
Authors: Plasil SL , Seth A , Homanics GE
Published: August 2020

The development of CRISPR/Cas9 technology has vastly sped up the process of genome editing by introducing a bacterial system that can be exploited for reverse genetics-based research. However, generating homozygous knockout (KO) animals using traditional CRISPR/Cas9-mediated techniques requires three generations of animals. A founder animal with a desired mutation is crossed to produce heterozygous F1 offspring which are subsequently interbred to generate homozygous F2 KO animals. This study describes a novel adaptation of the CRISPR/Cas9-mediated method to develop a homozygous gene-targeted KO animal cohort in one generation. A well-characterized ethanol-responsive gene,MyD88, was chosen as a candidate gene for generation ofMyD88-/-mice as proof of concept. Previous studies have reported changes in ethanol-related behavioral outcomes in MyD88 KO mice. Therefore, it was hypothesized that a successful one-generation KO of MyD88 should reproduce decreased responses to ethanols sedative effects, as well as increased ethanol consumption in males that were observed in previous studies. One-cell mouse embryos were simultaneously electroporated with four gRNAs targeting a critical Exon of MyD88 along with Cas9. DNA and RNA analysis of founder mice revealed a complex mix of genetic alterations, all of which were predicted to ablate MyD88 gene function. This study additionally compared responses of Mock treatment control mice generated through electroporation to controls purchased from a vendor. No substantial behavioral changes were noted between control cohorts. Overall, the CRISPR/Cas9 KO protocol reported here, which we callCRISPRTurboAcceleratedKnockOut (CRISPy TAKO), will be useful for reverse geneticin vivoscreens of gene function in whole animals.
Super-human cell death detection with biomarker-optimized neural networks
Authors: Linsley Jeremy W. , Linsley Drew A. , Lamstein Josh , Ryan Gennadi , Shah Kevan , Castello Nicholas A. , Oza Viral , Kalra Jaslin , Wang Shijie , Tokuno Zachary , Javaherian Ashkan , Serre Thomas , Finkbeiner Steven
Published: August 2020

Cell death is an essential process in biology that must be accounted for in live microscopy experiments. Nevertheless, cell death is difficult to detect without perturbing experiments with stains, dyes or biosensors that can bias experimental outcomes, lead to inconsistent results, and reduce the number of processes that can be simultaneously labelled. These additional steps also make live microscopy difficult to scale for high-throughput screening because of the cost, labor, and analysis they entail. We address this fundamental limitation of live microscopy with biomarker-optimized convolutional neural networks (BO-CNN): computer vision models trained with a ground truth biosensor that detect live cells with superhuman, 96% accuracy more than 100 times faster than previous methods. Our models learn to identify important morphological characteristics associated with cell vitality without human input or additional perturbations, and to generalize to other imaging modalities and cell types for which they have no specialized training. We demonstrate that we can interpret decisions from BO-CNN models to gain biological insight into the patterns they use to achieve superhuman accuracy. The BO-CNN approach is broadly useful for live microscopy, and affords a powerful new paradigm for advancing the state of high-throughput imaging in a variety of contexts.
Optimal policy for attention-modulated decisions explains human fixation behavior
Authors: Jang Anthony , Sharma Ravi , Drugowitsch Jan
Published: August 2020

Traditional accumulation-to-bound decision-making models assume that all choice options are processed simultaneously with equal attention. In real life decisions, however, humans tend to alternate their visual fixation between individual items in order to efficiently gather relevant information [46, 23, 21, 12, 15]. These fixations also causally affect one’s choices, biasing them toward the longer-fixated item [38, 2, 25]. We derive a normative decision-making model in which fixating a choice item boosts information about that item. In contrast to previous models [25, 39], we assume that attention enhances the reliability of information rather than its magnitude, consistent with neurophysiological findings [3, 13, 29, 45]. Furthermore, our model actively controls fixation changes to optimize information gathering. We show that the optimal model reproduces fixation patterns and fixation-related choice biases seen in human decision-makers, and provides a Bayesian computational rationale for the fixation bias. This insight led to additional behavioral predictions that we confirmed in human behavioral data. Finally, we explore the consequences of changing the relative allocation of cognitive resources to the attended versus the unattended item, and show that decision performance is benefited by a more balanced spread of cognitive resources.
Japanese encephalitis virus capsid protein interacts with non-lipidated MAP1LC3 on replication membranes and lipid droplets
Authors: Sarkar Riya , Sharma Kiran Bala , Kumari Anita , Asthana Shailendra , Kalia Manjula
Published: August 2020

Studies have shown that Japanese encephalitis virus (JEV), replicates on ER derived membranes that are marked by autophagosome negative non-lipidated MAP1LC3 (LC3-I). Depletion of LC3 exerts a profound inhibition on virus replication and egress. Here, we further characterize the role of LC3 in JEV replication, and through immunofluorescence and immunoprecipitation show that LC3-I interacts with the virus capsid protein in infected cells. This association was observed on capsid localized to both the replication complex and lipid droplets (LDs). JEV infection decreased the number of LDs per cell indicating a link between lipid metabolism and virus replication. This capsid-LC3 interaction was independent of the autophagy adaptor protein p62/SQSTM1. Further, no association of capsid was seen with the GABARAP protein family, suggesting that this interaction was specific for LC3. High resolution protein-protein docking studies identified a putative LC3-interacting region (LIR) in capsid,56FTAL59, and other key residues that could mediate a direct interaction between the two proteins.
Susceptibility to Residual Inhibition is Associated with Hearing Loss and Tinnitus Chronicity
Authors: Hu Suyi , Anschuetz Lukas , Hall Deborah A. , Caversaccio Marco , Wimmer Wilhelm
Published: August 2020

Residual inhibition, i.e. the temporary suppression of tinnitus loudness after acoustic stimulation, is a frequently observed phenomenon that may have prognostic value for clinical applications. However, it is unclear in which subjects residual inhibition is more likely and how stable the suppression can be induced repeatedly. The primary aim of this work was to evaluate the effect of hearing loss and tinnitus chronicity on residual inhibition susceptibility. The secondary aim was to investigate the short-term repeatability of residual inhibition. Residual inhibition was assessed in 74 tinnitus subjects with 60-second narrowband noise stimuli in 10 consecutive trials. The subjects were assigned to groups according to their depth of suppression (substantial residual inhibition vs. comparator group). In addition, a categorization in normal hearing and hearing loss groups, related to the degree of hearing loss at the frequency corresponding to the tinnitus pitch, was made. Logistic regression was used to identify factors associated with susceptibility to residual inhibition. Repeatability of residual inhibition was assessed using mixed-effects ordinal regression including post-stimulus time and repetitions as factors. Tinnitus chronicity was not associated with residual inhibition for subjects with hearing loss, while a statistically significant negative association between tinnitus chronicity and residual inhibition susceptibility was observed in normal hearing subjects (odds ratio: 0.63; CI: 0.41 to 0.83; p = 0.0076). Moreover, repeated states of suppression can be stably induced. Our results suggest that long chronicity and residual inhibition susceptibility could be indicators for hidden lesions along the auditory pathway in subjects with normal hearing thresholds at their tinnitus frequency.
First-in-Human Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine
Authors: Keech Cheryl , Glenn Gregory M. , Albert Gary , Cho Iksung , Robertson Andreana , Reed Patricia , Neal Susan , Plested Joyce S. , Zhu Mingzhu , Cloney-Clark Shane , Zhou Haixia , Smith Gale , Patel Nita , Frieman Matthew B. , Haupt Robert E. , Logue James , McGrath Marisa , Weston Stuart , Piedra Pedro A. , Desai Chinar , Callahan Kathleen , Lewis Maggie , Price-Abbott Patricia , Formica Neil , Shinde Vivek , Fries Louis , Lickliter Jason D. , Griffin Paul , Wilkinson Bethanie
Published: August 2020

Background

NVX-CoV2373 is a recombinant nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins. We present the Day 35 primary analysis of our trial of NVX-CoV2373 with or without the saponin-based Matrix-M1 adjuvant in healthy adults.

Methods

This is a randomized, observer-blinded, placebo-controlled, phase 1 trial in 131 healthy adults. Trial vaccination comprised two intramuscular injections, 21 days apart. Primary outcomes were reactogenicity, safety labs, and immunoglobulin G (IgG) anti-spike protein response. Secondary outcomes included adverse events, wild-type virus neutralizing antibody, and T-cell responses.

Results

Participants received NVX-CoV2373 with or without Matrix-M1 (n=106) or placebo (n=25). There were no serious adverse events. Reactogenicity was mainly mild in severity and of short duration (mean ≤2 days), with second vaccinations inducing greater local and systemic reactogenicity. The adjuvant significantly enhanced immune responses and was antigen dose-sparing, and the two-dose 5μg NVX-CoV2373/Matrix-M1 vaccine induced mean anti-spike IgG and neutralizing antibody responses that exceeded the mean responses in convalescent sera from COVID-19 patients with clinically significant illnesses. The vaccine also induced antigen-specific T cells with a largely T helper 1 (Th1) phenotype.

Conclusions

NVX-CoV2373/Matrix-M1 was well tolerated and elicited robust immune responses (IgG and neutralization) four-fold higher than the mean observed in COVID-19 convalescent serum from participants with clinical symptoms requiring medical care and induced CD4+ T-cell responses biased toward a Th1 phenotype. These findings suggest that the vaccine may confer protection and support transition to efficacy evaluations to test this hypothesis. (Funded by the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number, NCT04368988).
Insights into the first wave of the COVID-19 pandemic in Bangladesh: Lessons learned from a high-risk country
Authors: Siam Md. Hasanul Banna , Hasan Md. Mahbub , Raheem Md. Enayetur , Khan Hasinur Rahaman , Siddiqee Mahbubul H. , Hossain Mohammad Sorowar
Published: August 2020

Background

South Asian countries including Bangladesh have been struggling to control the COVID-19 pandemic despite imposing months of lockdown and other public health measures (as of June 30, 2020). In-depth epidemiological information from these countries is lacking. From the perspective of Bangladesh, this study aims to understand the epidemiological features and gaps in public health preparedness.

Method

This study used publicly available data (8 March-30 June 2020) from the respective health departments of Bangladesh and Johns Hopkins University Coronavirus Resource Centre. Descriptive statistics was used to report the incidence, case fatality rates (CFR), and trend analysis. Spatial distribution maps were created using ArcGIS Desktop. Infection dynamics were analyzed via SIR models.

Findings

In 66 days of nationwide lockdown and other public health efforts, a total of 47,153 cases and 650 deaths were reported. However, the incidence was increased by around 50% within a week after relaxing the lockdown. Males were disproportionately affected in terms of infections (71%) and deaths (77%) than females. The CFR for males was higher than females (1.38% vs 1.01%). Over 50% of infected cases were reported among young adults (20-40-year age group). Geospatial analysis between 7 June 2020 and 20 June 2020 showed that the incidences increased 4 to 10-fold in 12 administrative districts while it decreased in the epicenter. As compared to the EU and USA, trends of the cumulative incidence were slower in South Asia with lower mortality.

Conclusion

Our findings on gaps in public health preparedness and epidemiological characteristics would contribute to facilitating better public health decisions for managing current and future pandemics like COVID-19 in the settings of developing countries.
Changes in health and functioning of care home residents over two decades: what can we learn from population based studies?
Authors: Barker Robert O , Hanratty Barbara , Kingston Andrew , Ramsay Sheena , Matthews Fiona E
Published: August 2020

Background

Care home residents have complex care and support needs, as demonstrated by their vulnerability during the COVID-19 pandemic. There is a perception that the needs of residents have increased, but evidence is limited. We investigated changes in health and functioning of care home residents over two decades in England and Wales.

Methods

We conducted a repeated cross-sectional analysis over a 24-year period (1992-2016), using data from three longitudinal studies, the Cognitive Function and Ageing Studies (CFAS) I and II and English Longitudinal Study of Ageing (ELSA). To adjust for ageing of respondents over time results are presented for the 75-84 age group.

Results

Analysis of 2,280 observations from 1,745 care home residents demonstrated increases in severe disability (difficulty in at least two from washing, dressing and toileting). The prevalence of severe disability increased from 63% in 1992 to 87% in 2014 (subsequent fall in 2016 although wide confidence intervals). The prevalence of complex multimorbidity (problems in at least three out of six body systems) increased within studies over time, from 33% to 54% in CFAS I/II between 1992 and 2012, and 26% to 54% in ELSA between 2006 and 2016.

Conclusion

Over two decades, there has been an increase in disability and the complexity of health problems amongst care home residents in England and Wales. A rise in support needs for residents places increasing demands on care home staff and health professionals. This is an important concern for policymakers when considering the impact of COVID-19 infection in care homes.

Key points

Care home residents have complex care and support needs, which has contributed to their vulnerability during the COVID-19 pandemic.

Despite a perception that the needs of care home residents have increased over time, the epidemiological evidence is limited.

This study demonstrates an increase in the level of disability and the complexity of health problems amongst care home residents in England and Wales over two decades.

The rise in support needs for care home residents places increasing demands on care home staff and health professionals, and should be an important consideration for policymakers and service commissioners when considering the impact of current and future waves of COVID-19 infection in this setting.
COVID-19 Test & Trace Success Determinants: Modeling On A Network
Authors: Reich Ofir
Published: August 2020

What determines the success of a COVID-19 Test & Trace policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing, we find that important determinants of successful containment are: (i) the time from symptom onset until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced. Comparatively less important is (iii) the time of test analysis and contact tracing. When the share of contacts successfully traced is higher, the Test & Trace Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace systems and policies could affect all three parameters, Symptom Onset to Test Time should be considered, alongside test turnaround time and contact tracing coverage, as a key determinant of Test & Trace success.
Inflammasome activation in COVID-19 patients
Authors: Rodrigues Tamara S. , de Sá Keyla S.G. , Ishimoto Adriene Y. , Becerra Amanda , Oliveira Samuel , Almeida Leticia , Gonçalves Augusto V. , Perucello Debora B. , Andrade Warrison A. , Castro Ricardo , Veras Flavio P. , Toller-Kawahisa Juliana E. , Nascimento Daniele C. , de Lima Mikhael H.F. , Silva Camila M. S. , Caetite Diego B. , Martins Ronaldo B. , Castro Italo A. , Pontelli Marjorie C. , de Barros Fabio C. , do Amaral Natália B. , Giannini Marcela C. , Bonjorno Letícia P. , Lopes Maria Isabel F. , Benatti Maíra N. , Santana Rodrigo C. , Vilar Fernando C. , Auxiliadora-Martins Maria , Luppino-Assad Rodrigo , de Almeida Sergio C.L. , de Oliveira Fabiola R. , Batah Sabrina S. , Siyuan Li , Benatti Maira N. , Cunha Thiago M. , Alves-Filho José C. , Cunha Fernando Q. , Cunha Larissa D. , Frantz Fabiani G. , Kohlsdorf Tiana , Fabro Alexandre T. , Arruda Eurico , de Oliveira Renê D.R. , Louzada-Junior Paulo , Zamboni Dario S.
Published: August 2020

Severe cases of COVID-19 are characterized by a strong inflammatory process that may ultimately lead to organ failure and patient death. The NLRP3 inflammasome is a molecular platform that promotes inflammation via cleavage and activation of key inflammatory molecules including active caspase-1 (Casp1p20), IL-1β and IL-18. Although the participation of the inflammasome in COVID-19 has been highly speculated, the inflammasome activation and participation in the outcome of the disease is unknown. Here we demonstrate that the NLRP3 inflammasome is activated in response to SARS-CoV-2 infection and it is active in COVID-19, influencing the clinical outcome of the disease. Studying moderate and severe COVID-19 patients, we found active NLRP3 inflammasome in PBMCs and tissues of post-mortem patients upon autopsy. Inflammasome-derived products such as Casp1p20 and IL-18 in the sera correlated with the markers of COVID-19 severity, including IL-6 and LDH. Moreover, higher levels of IL-18 and Casp1p20 are associated with disease severity and poor clinical outcome. Our results suggest that the inflammasome is key in the pathophysiology of the disease, indicating this platform as a marker of disease severity and a potential therapeutic target for COVID-19.
Unique monocyte transcriptomic profiles are associated with preclinical atherosclerosis in women with systemic lupus erythematosus (SLE)
Authors: Woodridge Laurel , Chocano Elvira C , Ashford Paul , Robinson George , Waddington Kirsty , Rahman Anisur , Orengo Christine , Jury Elizabeth C , Torra Inés Pineda
Published: August 2020

Women with Systemic Lupus Erythematosus (SLE) show significantly increased cardiovascular risk compared to the general population. However, despite CVD being a major cause of morbidity and mortality for these women, this increased risk is not managed clinically and tools to dissect and predict their cardiovascular risk are lacking. Notably, this elevated CVD risk is not captured by traditional risk factors. To explore molecular programs underlying asymptomatic atherosclerosis in SLE we used a well-characterised cohort of CVD-free women with SLE, scanned for asymptomatic atherosclerotic plaques using non-invasive ultrasound imaging of the carotid and femoral arteries. We investigated the transcriptomic profiles of CD14+ circulating monocytes in women with SLE with or without preclinical atherosclerosis. We identified unique monocytic gene expression profiles that distinguished the presence of preclinical plaques in women with SLE. In addition, advanced bioinformatic analysis revealed functional pathways and interactions between the genes identified that could explain mechanistic differences in plaque formation. We propose that these molecular signatures could help understand why a subset of women with SLE are predisposed to develop atherosclerosis and at higher risk of developing clinical CVD. Collectively with other efforts, these molecular insights will help to better define atherosclerosis in the context of SLE which will be critical for future patient stratification and identification of anti-atherosclerotic therapies.
Cas9-induced large deletions and small indels are controlled in a convergent fashion
Authors: Kosicki Michael , Allen Felicity , Bradley Allan
Published: August 2020

Repair of Cas9-induced double-stranded breaks results primarily in formation of small indels, but can also cause potentially harmful large deletions. While mechanisms leading to the creation of small indels are relatively well understood, very little is known about the origins of large deletions. Using a novel library of clonal mouse embryonic stem cellsbona fidedeficient for 32 DNA repair genes, we have shown that large deletion frequency increases in cells impaired for non-homologous end joining and decreases in cells deficient for the central resection geneNbnand the microhomology-mediated end joining genePolq. Across deficient clones, increase in large deletion frequency was closely correlated with the increase in the extent of microhomology and the size of small indels, implying a continuity of repair processes across different genomic scales. Furthermore, by targeting diverse genomic sites, we identified examples of repair processes that were highly locus-specific, discovering a novel role for exonuclease Trex1. Finally, we present evidence that indel sizes increase with the overall efficiency of Cas9 mutagenesis. These findings may have impact on both basic research and clinical use of CRISPR-Cas9, in particular in conjunction with repair pathway modulation.
Physioxia stimulates extra-cellular matrix deposition and increases mechanical properties of human chondrocyte-derived tissue-engineered cartilage
Authors: Dennis J E , Whitney G A , Rai J , Fernandes R J , Kean T J
Published: August 2020

Cartilage tissue has been recalcitrant to tissue engineering approaches. In this study, human chondrocytes were formed into self-assembled cartilage sheets, cultured in physiologic (5%) and atmospheric (20%) oxygen conditions and underwent biochemical, histological and biomechanical analysis at one- and two-months. The results indicated that sheets formed at physiological oxygen tension were thicker, contained greater amounts of glycosaminoglycans (GAGs) and type II collagen, and had greater compressive and tensile properties than those cultured in atmospheric oxygen. In all cases, cartilage sheets stained throughout for extracellular matrix components. Type II-IX-XI collagen heteropolymer formed in the neo-cartilage and fibrils were stabilized by trivalent pyridinoline cross-links. Collagen cross-links were not significantly affected by oxygen tension but increased with time in culture. Physiological oxygen tension and longer culture periods both served to increase extracellular matrix components. The foremost correlation was found between compressive stiffness and the GAG to collagen ratio.

Tissue-engineered cartilage formed from human articular chondrocytes produces thicker, stiffer, more extracellular-matrix rich cartilage tissue when grown under physiological (5%) vs. atmospheric oxygen (20%) tension.
vCOMBAT: a Novel Tool to Create and Visualize a COmputational Model of Bacterial Antibiotic Target-binding
Authors: Tran Vi Ngoc-Nha , Shams Alireza , Ascioglu Sinan , Martinecz Antal , Liang Jingyi , Clarelli Fabrizio , Mostowy Rafal , Cohen Ted , zur Wiesch Pia Abel
Published: August 2020

Motivation

As antibiotic resistance creates a significant global health threat, we need not only to accelerate the development of novel antibiotics but also to develop better treatment strategies using existing drugs to improve their efficacy and prevent the selection of further resistance. We require new tools to rationally design dosing regimens to from data collected in early phases of antibiotic and dosing development. Mathematical models such as mechanistic pharmacodynamic drug-target binding explain mechanistic details of how the given drug concentration affects its targeted bacteria. However, there are no available tools in the literature that allows non-quantitative scientists to develop computational models to simulate antibiotic-target binding and its effects on bacteria.

Results

In this work, we have devised an extension of a mechanistic binding-kinetic model to incorporate clinical drug concentration data. Based on the extended model, we develop a novel and interactive web-based tool that allows non-quantitative scientists to create and visualize their own computational models of bacterial antibiotic target-binding based on their considered drugs and bacteria. We also demonstrate how Rifampicin affects bacterial populations of Tuberculosis (TB) bacteria using our vCOMBAT tool.

Availability

vCOMBAT online tool is publicly available athttps://combat-bacteria.org/.
Estimating SNP heritability in presence of population substructure in biobank-scale datasets
Authors: Lin Zhaotong , Seal Souvik , Basu Saonli
Published: August 2020

SNP heritability of a trait is measured by the proportion of total variance explained by the additive effects of genome-wide single nucleotide polymorphisms (SNPs). Linear mixed models are routinely used to estimate SNP heritability for many complex traits. The basic concept behind this approach is to model genetic contribution as a random effect, where the variance of this genetic contribution attributes to the heritability of the trait. This linear mixed model approach requires estimation of ‘relatedness’ among individuals in the sample, which is usually captured by estimating a genetic relationship matrix (GRM). Heritability is estimated by the restricted maximum likelihood (REML) or method of moments (MOM) approaches, and this estimation relies heavily on the GRM computed from the genetic data on individuals. Presence of population substructure in the data could significantly impact the GRM estimation and may introduce bias in heritability estimation. The common practice of accounting for such population substructure is to adjust for the top few principal components of the GRM as covariates in the linear mixed model. Here we propose an alternative way of estimating heritability in multi-ethnic studies. Our proposed approach is a MOM estimator derived from the Haseman-Elston regression and gives an asymptotically unbiased estimate of heritability in presence of population stratification. It introduces adjustments for the population stratification in a second-order estimating equation and allows for the total phenotypic variance vary by ethnicity. We study the performance of different MOM and REML approaches in presence of population stratification through extensive simulation studies. We estimate the heritability of height, weight and other anthropometric traits in the UK Biobank cohort to investigate the impact of subtle population substructure on SNP heritability estimation.
Molecular details of protein condensates probed by microsecond-long atomistic simulations
Authors: Zheng Wenwei , Dignon Gregory L. , Xu Xichen , Regy Roshan M. , Fawzi Nicolas L. , Kim Young C. , Best Robert B. , Mittal Jeetain
Published: August 2020

The formation of membraneless organelles in cells commonly occurs via liquid-liquid phase separation (LLPS), and is in many cases driven by multivalent interactions between intrinsically disordered proteins (IDPs). Molecular simulations can reveal the specific amino acid interactions driving LLPS, which is hard to obtain from experiment. Coarse-grained simulations have been used to directly observe the sequence determinants of phase separation but have limited spatial resolution, while all-atom simulations have yet to be applied to LLPS due to the challenges of large system sizes and long time scales relevant to phase separation. We present a novel multiscale computational framework by obtaining initial molecular configurations of a condensed protein-rich phase from equilibrium coarse-grained simulations, and back mapping to an all-atom representation. Using the specialized Anton 2 supercomputer, we resolve microscopic structural and dynamical details of protein condensates through microsecond-scale all-atom explicit-solvent simulations. We have studied two IDPs which phase separatein vitro: the low complexity domain of FUS and the N-terminal disordered domain of LAF-1. Using this approach, we explain the partitioning of ions between phases with low and high protein density, demonstrate that the proteins are remarkably dynamic within the condensed phase, identify the key residue-residue interaction modes stabilizing the dense phase, all while showing good agreement with experimental observations. Our approach is generally applicable to all-atom studies of other single and multi-component systems of proteins and nucleic acids involved in the formation of membraneless organelles.
Spontaneous replication fork collapse regulates telomere length homeostasis in wild type cells
Authors: Paschini Margherita , Reyes Cynthia M. , Gillespie Abigail E. , Lewis Karen A. , Glustrom Leslie W. , Sharpee Tatyana O. , Wuttke Deborah S. , Lundblad Victoria
Published: August 2020

Telomeres present unique challenges for genomes with linear chromosomes, including the inability of the semi-conservative DNA replication machinery to fully duplicate the ends of linear molecules. This is solved in virtually all eukaryotes by the enzyme telomerase, through the addition of telomeric repeats onto chromosome ends. It is widely assumed that the primary site of action for telomerase is the single-stranded G-rich overhang at the ends of chromosomes, formed after DNA replication is complete. We show here that the preferred substrate for telomerase in wild type yeast is instead a collapsed fork generated during replication of duplex telomeric DNA. Furthermore, newly collapsed forks are extensively elongated by telomerase by as much as ∼200 nucleotides in a single cell division, indicating that a major source of newly synthesized telomeric repeats in wild type cells occurs at collapsed forks. Fork collapse and the subsequent response by telomerase are coordinated by the dual activities of a telomere-dedicated RPA-like complex, which facilitates replication of duplex telomeric DNA and also recruits telomerase to the fork, thereby ensuring a high probability of re-elongation if DNA replication fails. We further show that the ability of telomerase to elongate newly collapsed forks is dependent on the Rad51 protein, indicating that telomerase activity in response to fork collapse proceeds through a regulatory pathway distinct from how telomerase engages fully replicated chromosome termini. We propose a new model in which spontaneous replication fork collapse and the subsequent response by telomerase is a major determinant of telomere length homeostasis.
Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein (N protein) and its consequences
Authors: Rahman M. Shaminur , Islam M. Rafiul , Ul Alam A. S. M. Rubayet , Islam Israt , Hoque M. Nazmul , Akter Salma , Rahaman Md. Mizanur , Sultana Munawar , Hossain M. Anwar
Published: August 2020

The emerging novel coronavirus SARS-CoV-2 has created a global confusing pandemic health crisis that warrants an accurate and detailed characterization of the rapidly evolving viral genome for understanding its epidemiology, pathogenesis and containment. We explored 61,485 sequences of the Nucleocapsid (N) protein, a potent diagnostic and prophylactic target, for identifying the mutations to review their roles in RT-PCR based diagnosis and observe consequent impacts. Compared to the Wuhan reference strain, a total of 1034 unique nucleotide mutations were identified in the mutant strains (49.15%, n=30,221) globally. Of these mutations, 367 occupy primer binding sites including 3’-end mismatch to primer-pair of 11 well characterized primer sets. Noteworthy, CDC (USA) recommended N2 primer set contained lower mismatch than the other primer sets. Moreover, 684 amino acid (aa) substitutions located across 317 (75.66% of total aa) unique positions including 82, 21, and 83 of those in RNA binding N-terminal domain (NTD), SR-rich region, and C-terminal dimerization domain (CTD), respectively. Moreover, 11 in-frame deletions were revealed, mostly (n =10) within the highly flexible linker region, and the rest within the NTD region. Furthermore, we predicted the possible consequences of high-frequency mutations (≥ 20) and deletions on the tertiary structure of the N protein. Remarkably, we observed that high frequency (67.94% of mutated sequences) coevolving mutations (R203K and G204R) destabilized and decreased overall structural flexibility. Despite being proposed as the alternate target to spike protein for vaccine and therapeutics, ongoing nonsynonymous evolution of the N protein may challenge the endeavors, thus need further immunoinformatics analyses. Therefore, continuous monitoring is required for tracing the ongoing evolution of the SARS-CoV-2 N protein in prophylactic and diagnostic interventions.
Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage
Authors: Gupta Suruchi , Singh Ravail , Paul Prosenjit
Published: August 2020

The spread of COVID-19 is a global concern that has taken a toll on entire human health. Researchers across the globe has been working in devising the strategies to combat this dreadful disease. Studies focused on genetic variability helps design effective drugs and vaccines. Considering this, the present study entails the information regarding the genome-wide mutations detected in the 108 SARS CoV-2 genomes worldwide. We identified a few hypervariable regions localized in orf1ab, spike, and nucleocapsid gene. These nucleotide polymorphisms demonstrated their effect on both codon usage as well as amino acid usage pattern. Altogether the present study provides valuable information that would be helpful to ongoing research on 2019-nCoV vaccine development.
Phasic oxygen dynamics underlies fast choline-sensitive biosensor signals in the brain of behaving rodents
Authors: Santos Ricardo M. , Sirota Anton
Published: August 2020

Fast time-scale modulation of synaptic and cellular physiology by acetylcholine is critical for many cognitive functions, but direct local measurement of neuromodulator dynamics in freely-moving behaving animals is technically challenging. Recentin vivobrain measurements using choline oxidase (ChOx)-based electrochemical biosensors have reported surprising fast cholinergic transients associated with reward-related behavioral events. However,in vivorecordings with conventional ChOx biosensors could be biased by phasic local field potential and O2-evoked enzymatic responses. Here, we have developed a Tetrode-based Amperometric ChOx (TACO) sensor enabling minimally invasive artifact-free simultaneous measurement of cholinergic activity and O2. Strikingly, the TACO sensor revealed highly-correlated O2and ChOx transients following spontaneous locomotion and sharp-wave/ripples fluctuations in the hippocampus of behaving rodents. Quantitative analysis of spontaneous activity,in vivoandin vitroexogenous O2perturbations revealed a directional effect of O2on ChOx phasic signals. Mathematical modeling of biosensors identified O2-evoked non-steadystate ChOx kinetics as a mechanism underlying artifactual biosensor phasic transients. This phasic O2-dependence of ChOx-based biosensor measurements confounds phasic cholinergic dynamics readoutin vivo,challenging previously proposed ACh role in reward-related learning. The discovered mechanism and quantitative modeling is generalizable to any oxidase-based biosensor, entailing rigorous controls and new biosensor designs.
Correlative Light Electron Ion Microscopy revealin vivolocalisation of bedaquiline inMycobacterium tuberculosisinfected lungs
Authors: Fearns Antony , Greenwood Daniel J. , Rodgers Angela , Jiang Haibo , Gutierrez Maximiliano G.
Published: August 2020

Correlative light, electron and ion microscopy (CLEIM) offers huge potential to track the intracellular fate of antibiotics, with organelle-level resolution. However, a correlative approach that enables subcellular antibiotic visualisation in pathogen-infected tissue is lacking. Here, we developed CLEIM in tissue (CLEIMiT), and used it to identify the cell-type specific accumulation of an antibiotic in lung lesions of mice infected withMycobacterium tuberculosis.Using CLEIMiT, we found that the anti-TB drug bedaquiline is localised not only in foamy macrophages in the lungs during infection but also accumulate in polymorphonuclear (PMN) cells.
Frontoparietal dynamics and value accumulation in intertemporal choice
Authors: Liu Qingfang , Yi Woojong , Rodriguez Christian A. , McClure Samuel M. , Turner Brandon M.
Published: August 2020

Intertemporal choice requires choosing between a smaller reward available after a shorter time delay and a larger reward available after a longer time delay. Previous studies suggest that intertemporal preferences are formed by generating a subjective value of the monetary rewards that depends on reward amount and the associated time delay. Neuroimaging results indicate that this subjective value is tracked by ventral medial prefrontal cortex (vmPFC) and ventral striatum. Subsequently, an accumulation process, subserved by a network including dorsal medial frontal cortex (dmFC), dorsal lateral prefrontal cortex (dlPFC) and posterior parietal cortex (pPC), selects a choice based on the subjective values. The mechanisms of how value accumulation interacts with subjective valuation to make a choice, and how brain regions communicate during decision making are undetermined. We developed and performed an EEG experiment that parametrically manipulated the probability of preferring delayed larger rewards. A computational model equipped with time and reward information transformation, selective attention, and stochastic value accumulation mechanisms was constructed and fit to choice and response time data using a hierarchical Bayesian approach.

Phase-based functional connectivity between putative dmFC and pPC was found to be associated with stimulus processing and to resemble the reconstructed accumulation dynamics from the best performing computational model across experimental conditions. By combining computational modeling and phase-based functional connectivity, our results suggest an association between value accumulation, choice competition, and frontoparietal connectivity in intertemporal choice.

Author summary

Intertemporal choice is a prominent experimental assay for impulsivity. Behavior in the task involves several cognitive functions including valuation, action selection and self-control. It is unknown how these different functions are temporally implemented during the course of decision making. In the current study, we combined formal computational models of intertemporal choice with a phase-based EEG measure of activity across brain regions to show that functional connectivity between dmFC and pPC reflects cognitive mechanisms of both visual stimulus processing and choice value accumulation. The result supports the notion that dynamic interaction between frontopatietal regions instantiates the critical value accumulation process in intertemporal choice.
Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity
Authors: Hoffmann Markus , Hofmann-Winkler Heike , Smith Joan C. , Krüger Nadine , Sørensen Lambert K. , Søgaard Ole S. , Hasselstrøm Jørgen Bo , Winkler Michael , Hempel Tim , Raich Lluís , Olsson Simon , Yamazoe Takashi , Yamatsuta Katsura , Mizuno Hirotaka , Ludwig Stephan , Noé Frank , Sheltzer Jason M. , Kjolby Mads , Pöhlmann Stefan
Published: August 2020

Antiviral therapy is urgently needed to combat the coronavirus disease 2019 (COVID-19) pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The protease inhibitor camostat mesylate inhibits SARS-CoV-2 infection of lung cells by blocking the virus-activating host cell protease TMPRSS2. Camostat mesylate has been approved for treatment of pancreatitis in Japan and is currently being repurposed for COVID-19 treatment. However, potential mechanisms of viral resistance as well as camostat mesylate metabolization and antiviral activity of metabolites are unclear. Here, we show that SARS-CoV-2 can employ TMPRSS2-related host cell proteases for activation and that several of them are expressed in viral target cells. However, entry mediated by these proteases was blocked by camostat mesylate. The camostat metabolite GBPA inhibited the activity of recombinant TMPRSS2 with reduced efficiency as compared to camostat mesylate and was rapidly generated in the presence of serum. Importantly, the infection experiments in which camostat mesylate was identified as a SARS-CoV-2 inhibitor involved preincubation of target cells with camostat mesylate in the presence of serum for 2 h and thus allowed conversion of camostat mesylate into GBPA. Indeed, when the antiviral activities of GBPA and camostat mesylate were compared in this setting, no major differences were identified. Our results indicate that use of TMPRSS2-related proteases for entry into target cells will not render SARS-CoV-2 camostat mesylate resistant. Moreover, the present and previous findings suggest that the peak concentrations of GBPA established after the clinically approved camostat mesylate dose (600 mg/day) will result in antiviral activity.
Common and distinct roles of frontal midline theta and occipital alpha oscillations in coding temporal intervals and spatial distances
Authors: Liang Mingli , Zheng Jingyi , Isham Eve , Ekstrom Arne
Published: August 2020

Judging how far something is and how long it takes to get there are critical to memory and navigation. Yet, the neural codes for spatial and temporal information remain unclear, particularly the involvement of neural oscillations in maintaining such codes. To address these issues, we designed an immersive virtual reality environment containing teleporters that displace participants to a different location after entry. Upon exiting the teleporters, participants made judgements from two given options regarding either the distance they had travelled (spatial distance condition) or the duration they had spent inside the teleporters (temporal duration condition). We wirelessly recorded scalp EEG while participants navigated in the virtual environment by physically walking on an omnidirectional treadmill and traveling through teleporters. An exploratory analysis revealed significantly higher alpha and beta power for short distance versus long distance traversals, while the contrast also revealed significantly higher frontal midline delta-theta-alpha power, and global beta power increases for short versus long temporal duration teleportation. Analyses of occipital alpha instantaneous frequencies revealed their sensitivity for both spatial distances and temporal durations, suggesting a novel and common mechanism for both spatial and temporal coding. We further examined the resolution of distance and temporal coding by classifying discretized distance bins and 250ms time bins based on multivariate patterns of 2-30 Hz power spectra, finding evidence that oscillations code fine-scale time and distance information. Together, these findings support partially independent coding schemes for spatial and temporal information, suggesting that low-frequency oscillations play important roles in coding both space and time.