bluuebunny/crossref_metadata_2025 huggingface dataset:
Disability-adjusted life years (DALYs) due to the direct health impact of COVID-19 in India, 2020
Authors: Singh Balbir B , Devleesschauwer Brecht , Khatkar Mehar S , Lowerison Mark , Singh Baljit , Dhand Navneet K , Barkema Herman W
Published: August 2021

COVID-19 has affected all countries. Its containment represents a unique challenge for India due to a large population (>1.38 billion) across a wide range of population densities. Assessment of the COVID-19 disease burden is required to put the disease impact into context and support future pandemic policy development. Here, we present the national-level burden of COVID-19 in India in 2020 that accounts for differences across urban and rural regions and across age groups. Disability-adjusted life years (DALY) due to COVID-19 were estimated in the Indian population in 2020, comprised of years of life lost (YLL) and years lived with disability (YLD). Scenario analyses were conducted to account for excess deaths not recorded in the official data and for reported COVID-19 deaths. The direct impact of COVID-19 in 2020 in India was responsible for 14,106,060 (95% uncertainty interval [UI] 14,030,129–14,213,231) DALYs, consisting of 99.2% (95% UI 98.47–99.64%) YLLs and 0.80% (95% UI 0.36–1.53) YLDs. DALYs were higher in urban (56%; 95% UI 56–57%) than rural areas (44%; 95% UI 43.4–43.6) and in males (64%) than females (36%). In absolute terms, the highest DALYs occurred in the 51–60-year-old age group (28%) but the highest DALYs per 100,000 persons were estimated for the 71-80 year old age group (5,481; 95% UI 5,464–5,500 years). There were 4,823,791 (95% UI 4,760,908–4,924,307) DALYs after considering reported COVID-19 deaths only. The DALY estimations have direct and immediate implications not only for public policy in India, but also internationally given that India represents one sixth of the world’s population.
COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants
Authors: Junker Daniel , Dulovic Alex , Becker Matthias , Wagner Teresa R. , Kaiser Philipp D. , Traenkle Bjoern , Kienzle Katharina , Bunk Stefanie , Struemper Carlotta , Haeberle Helene , Schmauder Kristina , Ruetalo Natalia , Malek Nisar , Althaus Karina , Koeppen Michael , Rothbauer Ulrich , Walz Juliane S. , Schindler Michael , Bitzer Michael , Göpel Siri , Schneiderhan-Marra Nicole
Published: August 2021

As global vaccination campaigns against SARS-CoV-2 proceed, there is particular interest in the longevity of immune protection, especially with regard to increasingly infectious virus variants. Neutralizing antibodies (Nabs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are promising correlates of protective immunity and have been successfully used for prevention and therapy. As SARS-CoV-2 variants of concern (VOCs) are known to affect binding to the ACE2 receptor and by extension neutralizing activity, we developed a bead-based multiplex ACE2-RBD inhibition assay (RBDCoV-ACE2) as a highly scalable, time-, cost-, and material-saving alternative to infectious live-virus neutralization tests. By mimicking the interaction between ACE2 and the RBD, this serological multiplex assay allows the simultaneous analysis of ACE2 binding inhibition to the RBDs of all SARS-CoV-2 VOCs and variants of interest (VOIs) in a single well. Following validation against a classical virus neutralization test and comparison of performance against a commercially available assay, we analyzed 266 serum samples from 168 COVID-19 patients of varying severity. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. ACE2 binding inhibition, while highly individualistic, positively correlated with IgG levels. ACE2 binding inhibition also correlated with disease severity up to WHO grade 7, after which it reduced.
A composite endpoint for acceptability evaluation of oral drug formulations in the pediatric population
Authors: Wargenau Manfred , Reidemeister Sibylle , Klingmann Ingrid , Klingmann Viviane
Published: August 2021

Introduction

A medicine’s acceptability is likely to have significant impact on pediatric compliance. EMA and FDA guidance on this topic ask for investigation of acceptability. Although palatability and deglutition are denoted as elements of acceptability, the impact of both on acceptability remains unclear as an unambiguous definition of acceptability is lacking. Actually, globally applied standards for acceptability definition, testing methodology and assessment criteria do not exist. A definition of acceptability establishing a composite endpoint that combines deglutition and palatability in different age groups is presented here.

Methods

This composite acceptability endpoint is based on validated assessment methods for deglutition and palatability in children of different age groups with different galenic placebo formulations, in line with criteria EMA proposed for assessing acceptability in children from newborn to 18 years. Data from two studies investigating mini-tablets, oblong tablets, orodispersible films and syrup were used to investigate the validity, expediency and applicability of the suggested composite acceptability assessment tool.

Results

The new composite endpoint is highly suitable and efficient to distinguish preferences of oral formulations: Mini-tablets and oblong tablets were significantly better accepted than syrup and orodispersible film.

Conclusion

Since the suggested acceptability criterion takes both deglutition and palatability into account as composite endpoint, it is highly sensitive to detect acceptability differences between oral formulations. It is a well-defined, valid approach, which particularly meets regulatory requirements in an appropriate and comprehensive manner and may in future serve as an easy, standardized method to assess and compare acceptability of pediatric formulations with active substances.
Predictors of Adolescent Engagement and Outcomes – a cross-sectional study using the Togetherall (formerly Big White Wall) digital mental health platform
Authors: Marinova Nushka , Rogers Tim , MacBeth Angus
Published: August 2021

Online mental health platforms can improve access to, and use of, mental health support for young people who may find it difficult to engage with face-to-face delivery.

We modelled engagement and change in anxiety and depression symptoms in adolescent users of the Togetherall (formerly “Big White Wall”) anonymous digital mental health peer-support platform.

A cross-sectional study assessed online activity data from members of Togetherall in UK adolescents referred from mental health services (N=606). Baseline demographics, depression, anxiety, and usage statistics were assessed. Symptom levels among participants who chose to take validated anxiety and depression measures were measured. And participant characteristics were used to predict engagement.

Mean number of logins for adolescent members was higher for older adolescents, and for a longer duration than younger adolescents. Mean number of logins and usage time was higher in female adolescents than males. For the total sample, 47.9% of users accessed more than one course, and 27% accessed at least one self-help resource. Gender and age predicted number of joined courses. Greater accessed self-help materials predicted reduced anxiety symptoms. Members’ mean baseline symptom levels were: GAD-7 between 13.63 and 14.79; PHQ-9 between 16.8 and 18.58.

Data were derived from a naturalistic design and modelling of multiple symptom scores should be interpreted with caution.

Findings show that adolescents readily engage with an anonymous online platform for common mental disorder, with scope for tailored pathways for different symptom profiles. Members benefit from engagement with Togetherall materials and courses.
Effect of COVID-19 infection related experiences on outing behaviors when a state of emergency is declared: a cohort study
Authors: Mori Takahiro , Nagata Tomohisa , Ikegami Kazunori , Hino Ayako , Tateishi Seiichiro , Tsuji Mayumi , Matsuda Shinya , Fujino Yoshihisa , Mori Koji ,   the CORoNaWork project
Published: August 2021

Background

Restricting the movement of the public to gathering places and limiting close physical contact are effective measures against COVID-19 infection. In Japan, states of emergency have been declared in specific prefectures to reduce public movement and control COVID-19 transmission. We investigated how COVID-19 infection related experiences including people with a history of infection, people with a history of close contact, and people whose acquaintances have been infected, affected self-restraint related to outing behaviors during the second state of emergency in Japan.

Methods

A prospective cohort study was conducted among workers aged 20–65 years using data from an internet survey. The baseline survey was conducted on December 22–25, 2020, and a follow-up survey was on February 18–19, 2021. There were 19,941 participants who completed both surveys and were included in the final analysis. We identified eight outing behaviors: (1) eating out (4 people or fewer); (2) eating out (5 people or more); (3) gathering with friends and colleagues; (4) day trip; (5) overnight trip (excluding visiting home); (6) visiting home; (7) shopping for daily necessities; and (8) shopping for other than daily necessities. We set self-restraint regarding each outing behavior after the second state of emergency was declared in January 2021 as the dependent variable, and COVID-19 infection related experiences as independent variables. Odds ratios were estimated using multilevel logistic regression analyses.

Results

Significant differences by COVID-19 infection related experiences were identified: compared to people without COVID-19 related experiences, people with a history of COVID-19 were less likely self-restraint from most outing behaviors. People whose acquaintance had been diagnosed with COVID-19 were significantly more likely to refrain from most outing behaviors. There was no significant difference in any outing behaviors for people with a history of close contact only.

Conclusions

To maximize the effect of a state of emergency, health authorities should disseminate information for each person in the target population, taking into account potential differences related to the COVID-19 infection related experiences.
Predictors of bovineSchistosoma japonicuminfection in rural Sichuan, China
Authors: Grover Elise , Paull Sara , Kechris Katerina , Buchwald Andrea , James Katherine , Liu Yang , Carlton Elizabeth J.
Published: August 2021

In China, bovines are believed to be the most common animal source of human schistosomiasis infections, though little is known about what factors promote bovine infections. The current body of literature features inconsistent, and sometimes contradictory results, and to date, few studies have looked beyond physical characteristics to identify the broader environmental conditions that predict bovine schistosomiasis. Because schistosomiasis is a sanitation-related, water-borne disease transmitted by many animals, we hypothesized that several environmental factors − such as the lack of improved sanitation systems, or participation in agricultural production that is water-intensive − could promote schistosomiasis infection in bovines. Using data collected as a part of a repeat cross-sectional study conducted in rural villages in Sichuan, China from 2007 to 2016, we used a Random Forests, machine learning approach to identify the best physical and environmental predictors of bovineS. japonicuminfection. Candidate predictors included: 1) physical/biological characteristics of bovines, 2) human sources of environmental schistosomes, 3) socio-economic indicators, 4) animal reservoirs, and 5) agricultural practices. The density of bovines in a village and agricultural practices such as the area of rice and dry summer crops planted and the use of night soil as an agricultural fertilizer, were among the top predictors of bovineS. japonicuminfection in all collection years. Additionally, human infection prevalence, pig ownership and bovine age were found to be strong predictors of bovine infection in at least one year. Our findings highlight that presumptively treating bovines in villages with high bovine density or human infection prevalence may help to interrupt transmission. Furthermore, village-level predictors were stronger predictors of bovine infection than household-level predictors, suggesting future investigations may need to apply a broad ecological lens to identify potential underlying sources of persistent transmission.
Dynamics of gut microbiome – mediated bile acid metabolism in progression to islet autoimmunity
Authors: Lamichhane Santosh , Sen Partho , Dickens Alex M. , Alves Marina Amaral , Härkönen Taina , Honkanen Jarno , Vatanen Tommi , Xavier Ramnik J. , Hyötyläinen Tuulia , Knip Mikael , Orešič Matej
Published: August 2021

Previous studies suggest that the human gut microbiome is dysregulated in islet autoimmunity, preceding the clinical onset of type 1 diabetes (T1D). The microbiota of the gut plays an important role in the regulation of bile acid (BA) metabolism. However, not much is known about the regulation of BAs during progression to T1D. Here, we analyzed BAs in a longitudinal series of serum (n= 333) and stool (n= 304) samples, collected at 3, 6, 12, 18, 24 and 36 months of age, from children who developed a single islet autoantibody (P1Ab), multiple islet autoantibodies (P2Ab), and controls (CTRs) who remained autoantibody (AAb) negative during the follow-up. In addition, we analyzed the stool microbiome by shotgun metagenomics in a subgroup of these children (n=111). Factor analysis showed that age had the strongest impact on BA and microbiome profiles. We found that, at an early age, the systemic BA (including taurine and glycine conjugates) and microbial secondary BA pathways were altered in the P2Ab group as compared to the P1Ab or CTR groups. Our findings thus suggest that dysregulated BA metabolism in early life may contribute to the risk and pathogenesis of T1D.
Disruption ofBrachypodiumLichenase Alters Metabolism of Mixed-linkage Glucan and Starch
Authors: Fan Mingzhu , Jensen Jacob K. , Zemelis-Durfee Starla , Kim Sang-Jin , Chan Jia-Yi , Beaudry Claudia M. , Brandizzi Federica , Wilkerson Curtis G.
Published: August 2021

Mixed-linkage glucan (MLG), which is widely distributed in grasses, is a polysaccharide highly abundant in cell walls of grass endosperm and young vegetative tissues. Lichenases are enzymes that hydrolyze MLG first identified in MLG-rich lichens. In this study, we identify a gene encoding a lichenase we nameBrachypodium distachyon LICHENASE 1(BdLCH1), which is highly expressed in the endosperm of germinating seeds and coleoptiles and at lower amounts in mature shoots. RNA in situ hybridization showed thatBdLCH1is primarily expressed in chlorenchyma cells of mature leaves and internodes. Disruption of BdLCH1 resulted in an eight-fold increase in MLG content in senesced leaves. Consistent with the in situ hybridization data, immunolocalization results showed that MLG was not removed in chlorenchyma cells oflch1mutants as it was in wild type and implicate the BdLCH1 enzyme in removing MLG in chlorenchyma cells in mature vegetative tissues. We also show that MLG accumulation inlch1mutants was resistant to dark induced degradation, and eight-week-oldlch1plants showed a faster rate of starch breakdown than wild type in darkness. Our results suggest a role for BdLCH1 in modifying the cell wall to support highly metabolically active cells.
Genome-wide in vivo screen of circulating tumor cells identifies SLIT2 as a regulator of metastasis
Authors: Xia Fan , Ma Yuan , Chen Kangfu , Duong Bill , Ahmed Sharif , Atwal Randy , Philpott David , Ketela Troy , Pantea Jennifer , Lin Sichun , Angers Stephane , Kelley Shana O.
Published: August 2021

Circulating tumor cells (CTCs) break free from primary tumors and travel through the bloodstream and lymphatic system to seed metastatic tumors, which are the major cause of death from cancer. The identification of the major genetic factors that enhance production and persistence of CTCs in the bloodstream at a whole genome level would enable more comprehensive molecular mechanisms of metastasis to be elucidated and the identification of novel therapeutic targets, but this remains a challenging task due to the heterogeneity and extreme rarity of CTCs. Here, we describe the firstin vivogenome-wide CRISPR KO screen using CTCs directly isolated from a mouse xenograft. This screen elucidatedSLIT2– a gene encoding a secreted protein acting as a cellular migration cue – as the most significantly represented gene knockout in the CTC population.SLIT2knockout cells are highly metastatic with hypermigratory and mesenchymal phenotype. Reduced expression ofSLIT2is observed in human tumors, indicating its role as a negative modulator of tumor progression and metastasis.
Habitat fragmentation induces rapid divergence of migratory and isolated sticklebacks
Authors: Ramesh A. , Groothuis A.G.G. , Weissing F.J. , Nicolaus M.
Published: August 2021

The adaptive capacity of many organisms is seriously challenged by human-imposed environmental change, which currently happens at unprecedented rates and magnitudes. For migratory fish, habitat fragmentation is a major challenge that can compromise their survival and reproduction. Therefore, it is important to study if fish populations can adapt to such modifications of their habitat. Here, we study whether originally anadromous three-spined stickleback populations (Gasterosteus aculeatus;‘migrants’) changed in behavior and morphology in response to human-induced isolation. We made use of a natural field-experiment, where the construction of pumping stations and sluices in the 1970s unintendedly created replicates of land-locked stickleback populations (‘resident’) in the Netherlands. For two years, we systematically tested populations of residents and migrants for differences in morphology and behavioral traits (activity, aggressiveness, exploration, boldness and shoaling) in lab-based assays. We detected differences between migrant and resident populations in virtually all phenotypic traits studied: compared to the ancestral migrants, residents were smaller in size, had fewer and smaller plates and were significantly more active, aggressive, exploratory and bolder and shoaled less. Despite large ecological differences between 2018 and 2019, results were largely consistent across the two years. Our study shows that human-induced environmental change has led to the rapid and consistent morphological and behavioral divergence of stickleback populations in about 50 generations. Such changes may be adaptive but this remains to be tested.

Lay summary

The adaptive capacity of many organisms is seriously challenged by human-imposed environmental changes. For example, migratory fish encounter man-made barriers that impede their movements and force them to adopt a resident lifecycle. Here we study whether and how populations of three-spined sticklebacks diverged in response to human-induced isolation. We show that about 50 generations of isolation were sufficient to induce substantial morphological and behavioral differentiation between land-locked populations (‘residents’) and their migratory ancestors (‘migrants’).
brca2-mutant zebrafish exhibit context- and tissue-dependent alterations in cell phenotypes and response to injury
Authors: Kouprianov Vassili A. , Selmek Aubrie A. , Ferguson Jordan L. , Mo Xiaokui , Shive Heather R.
Published: August 2021

Cancer cells frequently co-opt molecular programs that are normally activated in specific contexts, such as embryonic development and the response to injury. Determining the impact of cancer-associated mutations on cellular phenotypes within these discrete contexts can provide new insight into how such mutations lead to dysregulated cell behaviors and subsequent cancer onset. Here we assess the impact of heritable BRCA2 mutation on embryonic development and the injury response using a zebrafish model (Danio rerio). Unlike most mouse models for BRCA2 mutation, brca2-mutant zebrafish are fully viable and thus provide a unique tool for assessing both embryonic and adult phenotypes. We find that maternally provided brca2 is critical for normal oocyte development and embryonic survival in zebrafish, suggesting that embryonic lethality associated with BRCA2 mutation is likely to reflect defects in both meiotic and embryonic developmental programs. On the other hand, we find that adult brca2-mutant zebrafish exhibit aberrant proliferation of several cell types under basal conditions and in response to injury in tissues at high risk for cancer development. These divergent effects exemplify the often-paradoxical outcomes that occur in embryos (embryonic lethality) versus adult animals (cancer predisposition) with mutations in cancer susceptibility genes such as BRCA2. The altered cell behaviors identified in brca2-mutant embryonic and adult tissues, particularly in adult tissues at high risk for cancer, indicate that the effects of BRCA2 mutation on cellular phenotypes are both context- and tissue-dependent.
Distinct neural codes in primate Hippocampus and Lateral Prefrontal Cortex during associative learning in virtual environments
Authors: Corrigan B. W. , Gulli R. A. , Doucet G. , Roussy M. , Luna R. , Sachs A.J. , Martinez-Trujillo J. C.
Published: August 2021

The hippocampus (HPC) and the lateral prefrontal cortex (LPFC) are two cortical areas of the primate brain deemed essential to cognition. Here we hypothesize that the codes mediating neuronal communication in HPC and LPFC microcircuits have distinctively evolved to serve plasticity and memory function at different spatiotemporal scales. We used a virtual reality task in which animals navigated through a maze using a joystick and selected one of two targets in the arms of the maze according to a learned context-color rule. We found that neurons and neuronal populations in both regions encode similar information about the task. Moreover, we demonstrate that many HPC neurons concentrate spikes into bursts, whereas most layer II/III LPFC neurons sparsely distribute spikes over time. As the animals learned the task HPC neurons, but not LPFC neurons, increased their burst rate as a function of performance. When integrating spike rates over short intervals, HPC neuronal ensembles reached maximum decoded information with fewer neurons than LPFC ensembles. Our results show that during associative learning HPC principal cells concentrate spikes in bursts enabling temporal summation and fast synaptic plasticity in small populations of neurons and ultimately facilitating rapid encoding of associative memories. On the other hand, layers II/III LPFC pyramidal cells fire spikes more sparsely distributed in time and over a larger number of neurons. The latter would facilitate broadcasting of signals loaded in short term memory across neuronal populations without necessarily triggering fast synaptic plasticity.
Mechano-arrhythmogenicity is enhanced during late repolarisation in ischemia and driven by a TRPA1-, calcium-, and reactive oxygen species-dependent mechanism
Authors: Cameron Breanne A , Quinn T Alexander
Published: August 2021

Background

Cardiac dyskinesis in regional ischemia results in arrhythmias through mechanically-induced changes in electrophysiology (‘mechano-arrhythmogenicity’) that involve ischemic alterations in voltage-calcium (Ca2+) dynamics, creating a vulnerable period (VP) in late repolarisation.

Objective

To determine cellular mechanisms of mechano-arrhythmogenicity in ischemia and define the importance of the VP.

Methods and Results

Voltage-Ca2+ dynamics were simultaneously monitored in rabbit ventricular myocytes by dual-fluorescence imaging to assess the VP in control and simulated ischemia (SI). The VP was longer in SI than in control (146±7 vs 54±8ms; p<0.0001) and was reduced by blocking KATP channels with glibenclamide (109±6ms; p<0.0001). Cells were rapidly stretched (10-18% increase in sarcomere length over 110-170ms) with carbon fibres during diastole or the VP. Mechano-arrhythmogenicity, associated with stretch and release in the VP, was greater in SI than control (7 vs 1% of stretches induced arrhythmias; p<0.005) but was similar in diastole. Arrhythmias during the VP were more complex than in diastole (100 vs 69% had sustained activity; p<0.05). In the VP, incidence was reduced with glibenclamide (2%; p<0.05), by chelating intracellular Ca2+ (BAPTA; 2%; p<0.05), blocking mechano-sensitive TRPA1 (HC-030031; 1%; p<0.005), or by scavenging (NAC; 1%; p<0.005) or blocking reactive oxygen species (ROS) production (DPI; 2%; p<0.05). Ratiometric Ca2+ imaging revealed that SI increased diastolic Ca2± (+9±1%, p<0.0001), which was not prevented by HC-030031 or NAC.

Conclusion

In ischemia, mechano-arrhythmogenicity is enhanced specifically during the VP and is mediated by ROS, TRPA1, and Ca2+.
Engineering large-scale perfused tissues via synthetic 3D soft microfluidics
Authors: Grebenyuk Sergei , Abdel Fattah Abdel Rahman , Rustandi Gregorius , Kumar Manoj , Toprakhisar Burak , Salmon Idris , Verfaillie Catherine , Ranga Adrian
Published: August 2021

The vascularization of engineered tissues and organoids has remained a major unresolved challenge in regenerative medicine. While multiple approaches have been developed to vascularize in vitro tissues, it has thus far not been possible to generate sufficiently dense networks of small-scale vessels to perfuse large de novo tissues. Here, we achieve the perfusion of multi-mm3 tissue constructs by generating networks of synthetic capillary-scale 3D vessels. Our 3D soft microfluidic strategy is uniquely enabled by a 3D-printable 2-photon-polymerizable hydrogel formulation, which allows for precise microvessel printing at scales below the diffusion limit of living tissues. We demonstrate that these large-scale engineered tissues are viable, proliferative and exhibit complex morphogenesis during long-term in-vitro culture, while avoiding hypoxia and necrosis. We show by scRNAseq and immunohistochemistry that neural differentiation is significantly accelerated in perfused neural constructs. Additionally, we illustrate the versatility of this platform by demonstrating long-term perfusion of developing liver tissue. This fully synthetic vascularization platform opens the door to the generation of human tissue models at unprecedented scale and complexity.
Genomic characterization of a pathogenic isolate of Saccharomyces cerevisiae reveals an extensive and dynamic landscape of structural variation
Authors: Heasley Lydia R. , Argueso Juan Lucas
Published: August 2021

The budding yeast Saccharomyces cerevisiae has been extensively characterized for many decades and is a critical resource for the study of numerous facets of eukaryotic biology. Recently, the analysis of whole genome sequencing data from over 1000 natural isolates of S. cerevisiae has provided critical insights into the evolutionary landscape of this species by revealing a population structure comprised of numerous genomically diverse lineages. These survey-level analyses have been largely devoid of structural genomic information, mainly because short read sequencing is not suitable for detailed characterization of genomic architecture. Consequently, we still lack a complete perspective of the genomic variation the exists within the species. Single molecule long read sequencing technologies, such as Oxford Nanopore and PacBio, provide sequencing-based approaches with which to rigorously define the structure of a genome, and have empowered yeast geneticists to explore this poorly described realm of eukaryotic genomics. Here, we present the comprehensive genomic structural analysis of a pathogenic isolate of S. cerevisiae, YJM311. We used long read sequence analysis to construct a haplotype-phased, telomere-to-telomere length assembly of the YJM311 diploid genome and characterized the structural variations (SVs) therein. We discovered that the genome of YJM311 contains significant intragenomic structural variation, some of which imparts notable consequences to the genomic stability and developmental biology of the strain. Collectively, we outline a new methodology for creating accurate haplotype-phased genome assemblies and highlight how such genomic analyses can define the structural architectures of S. cerevisiae isolates. It is our hope that through continued structural characterization of S. cerevisiae genomes, such as we have reported here for YJM311, we will comprehensively advance our understanding of eukaryotic genome structure-function relationships, structural diversity, and evolution.
A small molecule drug screening identifies colistin sulfate as an enhancer of Natural Killer cell cytotoxicity
Authors: Cortés-Kaplan Serena , Hasim Mohammed S. , Kaczmarek Shelby , Taha Zaid , Maznyi Glib , McComb Scott , Lee Seung-Hwan , Diallo Jean-Simon , Ardolino Michele
Published: August 2021

Because of their crucial role in tumor immunity, NK cells have quickly become a prime target for immunotherapies, with adoptive transfer of NK cells and the use of NK cell engagers quickly moving to clinical stage. On the other hand, only few studies have focused on small molecule drugs capable of unleashing NK cell against cancer. In this context, repurposing small molecule is an attractive strategy to identify new immunotherapies from already approved drugs. Here, we screened 1,200 FDA-approved drugs from the Prestwick Chemical Library, to identify compounds that increase NK cell cytotoxic potential. Using a high-throughput luciferase-release cytotoxicity assay, we found that the antibiotic colistin sulfate increased cytotoxicity of human NK cells towards cancer cells. The effect of colistin was short lived and was not observed when NK cells were pretreated with the drug, showing how NK cell activity was potentiated only when the compound was present at the time of recognition of cancer cells. Further studies are needed to uncover the mechanism of action and the pre-clinical efficacy of colistin sulfate in mouse cancer models.
Camera trap based niche partitioning model of medium size ungulates and its implications on tiger’s prey availability in SE Asian rainforest
Authors: Wibowo Andri
Published: August 2021

The presence and survival of the Sumatran tiger were determined by the presence, density, and activity of its prey. Several medium size mammal belongs to the ungulate were known as the potential prey for the tiger. While, the information on the temporal availability of this prey in the rainforest is still limited. In here this study aimed to aims to model the niche partitioning of several mammalian species that was potential prey for tiger. The studied species were including barking deer (Muntiacus muntjak), bearded pig (Sus barbatus), and wild boar (Sus scrofa). The method was using camera trap with data analyses including the calculation of Kernel density, diel activity, and niche partitioning determined using overlap index. . Based on the results, barking deer and wild boar showed only singular activity peak while bearded pig has several activity peaks. Only wild boar showed a strict diurnal activity pattern between 06:00 h and 12:00 h. Barking deer showed a crepuscular behavior with several activities observed at 18:00 h. While bearded pig showed a nocturnal behavior and showed at least two peaks of activity, one between 09:00 to 13:00 and another between 18:00 to 24:00 h. Barking deer and bearded pig uses almost similar niches since those species have the highest overlap indices value equals 0.504(95%CI:0.193-0.824). The lowest overlap indices value was observed for barking deer and wild boar with overlap indice values of 0.032(95%CI:0.0-0.162). Considering the diurnal activity pattern of the tiger that is mostly active at day, then the available preys were either barking deer or bearded pigs. While since barking deer and bearded pigs were using the same niche, then there will be potential competition.
Chromosomal rearrangements preserve adaptive divergence in ecological speciation
Authors: Jackson Craig E. , Xu Sen , Ye Zhiqiang , Pfrender Michael E. , Lynch Michael , Colbourne John K. , Shaw Joseph R.
Published: August 2021

Despite increasing empirical evidence that chromosomal rearrangements may play an important role in adaptive divergence and speciation, the degree to which divergent genomic regions are associated with chromosomal rearrangements remains unclear. In this study, we provide the first whole-genome analyses of ecological speciation and chromosomal evolution in a Daphnia species complex, using chromosome-scale assemblies and natural-population sequencing of the recently diverged species pair, Daphnia pulicaria and Daphnia pulex, which occupy distinct yet overlapping habitats in North America, and the outgroup species Daphnia obtusa. Our results describe a mixed mode of geographic divergence (isolation with secondary contact) resulting in a heterogeneous landscape of genomic divergence. Large contiguous “continents of divergence” encompass over one third of the genome (36%) and contain nearly all the fixed differences (94%) between the species, while the background genome has been homogenized. Chromosomal rearrangements between species, including inversions and intrachromosomal translocations, are associated with the continents of divergence and capture multiple adaptive alleles in genes and pathways thought to contribute to the species’ phenotypic differences.
Super-enhancer signature reveals key mechanisms associated with resistance to non-alcoholic steatohepatitis in humans with obesity
Authors: Hung Yu-Han , Sritharan Ramja , Vohl Marie-Claude , Ilkayeva Olga , Biertho Laurent , Tchernof André , White Phillip J. , Sethupathy Praveen
Published: August 2021

The molecular underpinnings of non-alcoholic steatohepatitis (NASH) development in patients are poorly understood. Active enhancer landscapes are known to determine cell states and behaviors. Super-enhancers, in particular, have helped reveal key disease drivers in several cancer types; however, they remain unexplored in human NASH. To define the enhancer signature of NASH-prone (NP) and NASH-resistant (NR) phenotypes in humans with obesity, we performed chromatin run-on sequencing (ChRO-seq) analysis on liver biopsies of individuals with obesity who were stratified into either NP or NR. We first demonstrated that NP and NR groups exhibit distinct active enhancer signatures. The subsequent identification of NP- and NR-specific super-enhancers revealed the specific genes that are likely the most critical for each of the phenotypes, including HES1 for NP and GATM for NR. Integrative analysis with results from genome-wide association studies of NAFLD and related traits identified disease/trait-loci specific to NP or NR enhancers. Further analysis of the ChRO-seq data pointed to critical roles for serine/glycine metabolism in NASH resistance, which was corroborate by profiling of circulating amino acids in the same patients. Overall, the distinct enhancer signatures of human NP and NR phenotypes revealed key genes, pathways, and transcription factor networks that promote NASH development.
NeuralDock: Rapid and conformation-agnostic docking of small molecules
Authors: Sha Congzhou M. , Wang Jian , Dokholyan Nikolay V.
Published: August 2021

Virtual screening is a cost- and time-effective alternative to traditional high-throughput screening in the drug discovery process. Both virtual screening approaches, structure-based molecular docking and ligand-based cheminformatics, suffer from computational cost, low accuracy, and/or reliance on prior knowledge of a ligand that binds to a given target. Here, we propose a neural network framework, NeuralDock which accelerates the process of high-quality computational docking by a factor of 106, and does not require prior knowledge of a ligand that binds to a given target. By approximating both protein-small molecule conformational sampling and energy-based scoring, NeuralDock accurately predicts the binding energy and affinity of a protein-small molecule pair, based on protein pocket 3D structure and small molecule topology. We use NeuralDock and 25 GPUs to dock 937 million molecules from the ZINC database against superoxide dismutase-1 in 21 hours, which we validate with physical docking using MedusaDock. Due to its speed and accuracy, NeuralDock may be useful in brute-force virtual screening of massive chemical libraries and training of generative drug models.
Evolving a generalist biosensor for bicyclic monoterpenes
Authors: d’Oelsnitz Simon , Nguyen Vylan , Alper Hal S. , Ellington Andrew D.
Published: August 2021

Prokaryotic transcription factors can be repurposed as analytical and synthetic tools for precise chemical measurement and regulation. Monoterpenes encompass a broad chemical family that are commercially valuable as flavors, cosmetics, and fragrances, but have proven difficult to measure, especially in cells. Herein, we develop genetically-encoded, generalist monoterpene biosensors by using directed evolution to expand the effector specificity of the camphor-responsive TetR-family regulator CamR from Pseudomonas putida. Using a novel negative selection coupled with a high-throughput positive screen (Seamless Enrichment of Ligand-Inducible Sensors, SELIS), we evolve CamR biosensors that can recognize four distinct monoterpenes: borneol, fenchol, eucalyptol, and camphene. Different evolutionary trajectories surprisingly yielded common mutations, emphasizing the utility of CamR as a platform for creating generalist biosensors. Systematic promoter optimization driving the reporter increased the system’s signal-to-noise ratio to 150-fold. These sensors can serve as a starting point for the high-throughput screening and dynamic regulation of bicyclic monoterpene production strains.
Monitoring the Antimicrobial Resistance Dynamics of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing
Authors: Carroll Laura M. , Buehler Ariel J. , Gaballa Ahmed , Siler Julie D. , Cummings Kevin J. , Cheng Rachel A. , Wiedmann Martin
Published: August 2021

Livestock represent a possible reservoir for facilitating the transmission of the zoonotic foodborne pathogen Salmonella enterica to humans; there is also concern that strains can acquire resistance to antimicrobials in the farm environment. Here, we use whole-genome sequencing (WGS) to characterize Salmonella strains (n = 128) isolated from healthy dairy cattle and their associated environments on 13 New York State farms to assess the diversity and microevolution of this important pathogen at the level of the individual herd. Additionally, the accuracy and concordance of multiple in silico tools are assessed, including: (i) two in silico serotyping tools, (ii) combinations of five antimicrobial resistance (AMR) determinant detection tools and one to five AMR determinant databases, and (iii) one antimicrobial minimum inhibitory concentration (MIC) prediction tool. For the isolates sequenced here, in silico serotyping methods outperformed traditional serotyping and resolved all un-typable and/or ambiguous serotype assignments. Serotypes assigned in silico showed greater congruency with the Salmonella whole-genome phylogeny than traditional serotype assignments, and in silico methods showed high concordance (99% agreement). In silico AMR determinant detection methods additionally showed a high degree of concordance, regardless of the pipeline or database used (≥98% agreement between susceptible/resistant assignments for all pipeline/database combinations). For AMR detection methods that relied exclusively on nucleotide BLAST, accuracy could be maximized by using a range of minimum nucleotide identity and coverage thresholds, with thresholds of 75% nucleotide identity and 50-60% coverage adequate for most pipeline/database combinations. In silico characterization of the microevolution and AMR dynamics of each of six serotype groups (S. Anatum, Cerro, Kentucky, Meleagridis, Newport, Typhimurium/Typhimurium variant Copenhagen) revealed that some lineages were strongly associated with individual farms, while others were distributed across multiple farms. Numerous AMR determinant acquisition and loss events were identified, including the recent acquisition of cephalosporin resistance-conferring blaCMY- and blaCTX-M-type beta-lactamases. The results presented here provide high-resolution insight into the temporal dynamics of AMR Salmonella at the scale of the individual farm and highlight both the strengths and limitations of WGS in tracking zoonotic pathogens and their associated AMR determinants at the livestock-human interface.
Ecological dynamics of the gut microbiome in response to dietary fiber
Authors: Liu Hongbin , Liao Chen , Tang Jinhui , Chen Junyu , Lei Chaobi , Zheng Linggang , Wu Lu , Zhang Chenhong , Liu Yang-Yu , Xavier Joao , Dai Lei
Published: August 2021

Dietary fibers are generally thought to benefit intestinal health. Their impacts on the composition and metabolic function of the gut microbiome, however, vary greatly across individuals. Previous research showed that each individual’s response to fibers depends on their baseline gut microbiome, but the ecology driving microbiota remodeling during fiber intake remained unclear. Here, we studied the long-term dynamics of gut microbiome and short-chain fatty acids (SCFAs) in isogenic mice with distinct microbiota baselines fed with the fermentable fiber inulin compared to the non-fermentable fiber cellulose. We found that inulin produced generally rapid response followed by gradual stabilization to new equilibria, and those dynamics were baseline-dependent. We parameterized an ecology model from the timeseries data, which revealed a group of bacteria whose growth significantly increases in response to inulin. and whose baseline abundance and interspecies competition explains the baseline-dependence of microbiome density and community composition dynamics. Fecal levels of of SCFAs, such as propionate, is associated with the abundance of inulin responders, yet inter-individual variation of gut microbiome impedes the prediction of SCFAs by machine learning models. Finally, we showed that our methods and major findings are generalizable to dietary resistant starch. This study emphasizes the importance of ecological modeling to understand microbiome responses to dietary changes and the need for personalized interventions.
Lytic Replication and Reactivation from B Cells Is Not Required for Maintaining Gammaherpesvirus Latency in vivo
Authors: Gupta Arundhati , Owens Shana M. , Oldenburg Darby G. , White Douglas W. , Forrest J. Craig
Published: August 2021

Gammaherpesviruses (GHVs) are lymphotropic tumor viruses with a biphasic infectious cycle. Lytic replication at the primary site of infection is necessary for GHVs to spread throughout the host and establish latency in distal sites. Dissemination is mediated by infected B cells that traffic hematogenously from draining lymph nodes to peripheral lymphoid organs, such as the spleen. B cells serve as the major reservoir for viral latency, and it is hypothesized that periodic reactivation from latently infected B cells contributes to maintaining long-term chronic infection. While fundamentally important to an understanding of GHV biology, aspects of B cell infection in latency establishment and maintenance are incompletely defined, especially roles for lytic replication and reactivation in this cell type. To address this knowledge gap and overcome limitations of replication-defective viruses, we generated a recombinant murine gammaherpesvirus 68 (MHV68) in which ORF50, the gene that encodes the essential immediate-early replication and transcription activator protein (RTA), was flanked by loxP sites to enable conditional ablation of lytic replication by ORF50 deletion in cells that express Cre recombinase. Following infection of mice that encode Cre in B cells with this virus, splenomegaly and viral reactivation from splenocytes were significantly reduced, however the number of latently infected splenocytes was equivalent to WT MHV68. Despite ORF50 deletion, MHV68 latency was maintained over time in spleens of mice at levels approximating WT, reactivation-competent MHV68. Stimulation of polyclonal B cell activation and proliferation by treating mice with lipopolysaccharide (LPS), which promotes MHV68 reactivation ex vivo, yielded equivalent increases in the number of latently infected cells for both ORF50-deleted and WT MHV68, even when mice were simultaneously treated with the antiviral drug cidofovir. Together, these data demonstrate that lytic replication in B cells is not required for MHV68 latency establishment and maintenance and further indicate that B cell proliferation, and not reactivation per se, is a major mechanism for maintaining latent viral genomes in the host.

IMPORTANCE

Gammaherpesviruses establish lifelong chronic infections in cells of the immune system and place infected hosts at risk for developing lymphomas and other diseases. It is hypothesized that gammaherpesviruses must initiate acute infection in these cells to establish and maintain long-term infection, but this has not been directly tested. We report here the use of a viral genetic system that allows for cell-type-specific deletion of a viral gene that is essential for replication and reactivation. We employ this system in an in vivo model to reveal that viral replication is not required to initiate or maintain infection within immune cells.
OsSWEET11b, a sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility
Authors: Wu Lin-Bo , Eom Joon-Seob , Isoda Reika , Li Chenhao , Char Si Nian , Luo Dangping , Luu Van Thi , Nakamura Masayoshi , Yang Bing , Frommer Wolf B.
Published: August 2021

SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by transcription activator-like effectors (TALe) ofXanthomonasssp. is a key factor for bacterial leaf blight (BLB) infection of rice, cassava and cotton. Here, we identified the so far unknown OsSWEET11b with roles in male fertility and BLB susceptibility in rice. While singleossweet11aorbmutants were fertile, double mutants were sterile. Since clade III SWEETs can transport gibberellin (GA), a key hormone for rice spikelet fertility, sterility and BLB susceptibility might be explained by GA transport deficiencies. However, in contrast to the Arabidopsis homologs, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility must therefore depend on SWEET11b-mediated sucrose transport. Ectopic induction ofOsSWEET11bby designer TALe enables TALe-freeXanthomonas oryzaepv.oryzae(Xoo) to cause disease, identifyingOsSWEET11bas a BLB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence ofXoo. Notably, only three of now six clade III SWEETs are targeted by knownXoostrains from Asia and Africa. The identification of OsSWEET11b has relevance in the context of fertility and for protecting rice against emergingXoostrains that evolve TALes to exploitOsSWEET11b.