bluuebunny/crossref_metadata_2025 huggingface dataset:
Field evaluation of specificity and sensitivity of a standard SARS-CoV-2 antigen rapid diagnostic test: A prospective study at a teaching hospital in Northern Ghana
Authors: Abdul-Mumin Alhassan , Abubakari Abdulai , Agbozo Faith , Abdul-Karim Abass , Nuertey Benjamin Demah , Mumuni Kareem , Heuschen Anna-Katharina , Hennig Lisa , Denkinger Claudia M. , Müller Olaf , Jahn Albrecht
Published: June 2021

Background

The testing capacity for SARS-CoV-2 in Africa is rather limited. Antigen-detection rapid diagnostic tests (Ag-RDTs) are a cheap and rapid alternative to reverse transcriptase-polymerase chain reaction (RT-PCR) tests, but there is little data about their performance under real life conditions in tropical countries.

Objective

To evaluate the performance of a standard Ag-RDT in a population of a major hospital in northern Ghana.

Methods

Prospective, cross-sectional, blinded verification of the performance of the SD Biosensor Standard Q SARS-CoV-2 Ag-RDT under real life conditions in 135 symptomatic patients and 58 contacts of RT-PCR positives at Tamale Teaching Hospital in February 2021. Nasopharyngeal samples were taken under standard conditions and tested against RT-PCR in the hospital laboratory.

Results

193 participants (median age 35 years, 109 male) were included into the study for which both RT-PCR test and Ag-RDT results were available. A total of 42 (22%) were RT-PCR positive. Of the 42 RT-PCR positives, 27 were Ag-RDT positive, resulting in a sensitivity of 64% (95% CI 49-79). Sensitivity among symptomatic patients was 58% (95% CI 38-78). 123 were identified Ag-RDT negatives of the 151 RT-PCR negatives, resulting in a specificity of 81% (95% CI 75-87).

Conclusions

SARS-CoV-2 Ag-RDTs appear to have a rather low sensitivity and particularly a low specificity under real life conditions in Africa. The role of existing Ag-RDTs in countries with high-temperature climates and limited resources still needs more data and discussion.
Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data
Authors: Ellmen Isaac , Lynch Michael D.J. , Nash Delaney , Cheng Jiujun , Nissimov Jozef I. , Charles Trevor C.
Published: June 2021

Detection of SARS-CoV-2 in wastewater is an important strategy for community level surveillance. Variants of concern (VOCs) can be detected in the wastewater samples using next generation sequencing, however it can be challenging to determine the relative abundance of different VOCs since the reads cannot be assembled into complete genomes. Here, we present Alcov (abundance learning of SARS-CoV-2 variants), a tool that uses mutation frequencies in SARS-CoV-2 sequencing data to predict the distribution of VOC lineages in the sample. We used Alcov to predict the distributions of lineages from three wastewater samples which agreed well with clinical data. By predicting not just which VOCs are present, but their relative abundances in the population, Alcov extracts a more complete snapshot of the variants which are circulating in a community.
Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity
Authors: Riou Catherine , Keeton Roanne , Moyo-Gwete Thandeka , Hermanus Tandile , Kgagudi Prudence , Baguma Richard , Tegally Houriiyah , Doolabh Deelan , Iranzadeh Arash , Tyers Lynn , Mutavhatsindi Hygon , Tincho Marius B. , Benede Ntombi , Marais Gert , Chinhoyi Lionel R. , Mennen Mathilda , Skelem Sango , du Bruyn Elsa , Stek Cari ,   SA-CIN, de Oliveira Tulio , Williamson Carolyn , Moore Penny L. , Wilkinson Robert J. , Ntusi Ntobeko A. B. , Burgers Wendy A.
Published: June 2021

SARS-CoV-2 variants have emerged that escape neutralization and potentially impact vaccine efficacy. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is poorly studied. We assessed both neutralizing antibody and T cell responses in 44 South African COVID-19 patients infected either with B.1.351, now dominant in South Africa, or infected prior to its emergence (‘first wave’), to provide an overall measure of immune evasion. We show for the first time that robust spike-specific CD4 and CD8 T cell responses were detectable in B.1.351-infected patients, similar to first wave patients. Using peptides spanning only the B.1.351 mutated regions, we identified CD4 T cell responses targeting the wild type peptides in 12/22 (54.5%) first wave patients, all of whom failed to recognize corresponding B.1.351-mutated peptides (p=0.0005). However, responses to the mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3/44) mounted CD8 responses that targeted the mutated regions. First wave patients showed a 12.7 fold reduction in plasma neutralization of B.1.351. This study shows that despite loss of recognition of immunodominant CD4 epitope(s), overall CD4 and CD8 T cell responses to B.1.351 are preserved. These observations may explain why, despite substantial loss of neutralizing antibody activity against B.1.351, several vaccines have retained the ability to protect against severe COVID-19 disease.

One Sentence Summary

T cell immunity to SARS-CoV-2 B.1.351 is preserved despite some loss of variant epitope recognition by CD4 T cells.
The zinc transporter ZnuABC is critical for the virulence of Chromobacterium violaceum and contributes to diverse zinc-dependent physiological processes
Authors: Santos Renato E. R. S. , da Silva Júnior Waldir P. , Harrison Simone , Skaar Eric P. , Chazin Walter J. , da Silva Neto José F.
Published: June 2021

Chromobacterium violaceum is a ubiquitous environmental bacterium that causes sporadic life-threatening infections in humans. How C. violaceum acquires zinc to colonize environmental and host niches is unknown. In this work, we demonstrated that C. violaceum employs the zinc uptake system ZnuABC to overcome zinc limitation in the host, ensuring the zinc supply for several physiological demands. Our data indicated that the C. violaceum ZnuABC transporter is encoded in a zur-CV_RS15045-CV_RS15040-znuCBA operon. This operon was repressed by the zinc uptake regulator Zur and derepressed in the presence of the host protein calprotectin (CP) and the synthetic metal chelator EDTA. A ΔznuCBA mutant strain showed impaired growth under these zinc-chelated conditions. Moreover, the deletion of znuCBA provoked a reduction in violacein production, swimming motility, biofilm formation, and bacterial competition. Remarkably, the ΔznuCBA mutant strain was highly attenuated for virulence in an in vivo mouse infection model and showed a low capacity to colonize the liver, grow in the presence of CP, and resist neutrophil killing. Overall, our findings demonstrate that ZnuABC is essential for C. violaceum virulence, contributing to subvert the zinc-based host nutritional immunity.
Prevalence of laboratory-related musculoskeletal disorders among biomedical scientists
Authors: Alwahaibi Nasar , Al Sadairi Mallak , Al Abri Ibrahim , Al Rawahi Samira
Published: June 2021

Background

Laboratory–related musculoskeletal disorders (LMSDs) are injuries resulted from working in the laboratory. Biomedical scientists (BMSs) play an important role in any health care system. However, they are at high risk of exposure to LMSDs. This study aimed to estimate the prevalence and the associated risk factors of LMSDs among this group of healthcare professionals.

Methods

A cross-sectional survey (Nordic musculoskeletal) was used to estimate the prevalence of LMSDs among BMSs. Data were analyzed using Statistical Package for Social Science software version 25. Chi-square was performed to find the significant association between LMSDs and different risk factors.

Results

The study included 83 BMSs. Females represented 63.9% and 36.1% were in the age group of 35–44. The overall prevalence of LMSDs was 77.1%. The most prevalent LMSDs were neck, shoulders, and lower back with 50.6%, 49.4%, and 43.4%, respectively. Neck complaints and upper back complaints were found statistically significant with the female gender. Shoulders complaints were associated with pipetting and microscopy. Lower back complaints were associated with pipetting and heavy work at home. A total of 65.57% of BMSs had irregular symptoms of LMSDs, 54.10% experienced moderate pain due to these symptoms, and 44.26% had symptoms that persisted from hours to days.

Conclusion

The study found that the prevalence of LMSDs among BMSs was high. Good knowledge, attitude, practice, and training of ergonomics may minimize the prevalence of LMSDs among BMSs.
Limits and potential of combined folding and docking using PconsDock
Authors: Pozzati Gabriele , Zhu Wensi , Bassot Claudio , Lamb John , Kundrotas Petras , Elofsson Arne
Published: June 2021

In the last decade, de novo protein structure prediction accuracy for individual proteins has improved significantly by utilising deep learning (DL) methods for harvesting the co-evolution information from large multiple sequence alignments (MSA). In CASP14, the best groups predicted the structure of most proteins with impressive accuracy. The same approach can, in principle, also be used to extract information about evolutionary-based contacts across protein-protein interfaces. However, most of the earlier studies have not used the latest DL methods for inter-chain contact distance prediction. This paper introduces a fold-and-dock method, PconsDock, based on predicted residue-residue distances with trRosetta. PconsDock can simultaneously predict the tertiary and quaternary structure of a protein pair, even when the structures of the monomers are not known. The straightforward application of this method to a standard dataset for protein-protein docking yielded limited success. However, using alternative methods for MSA generating allowed us to dock accurately significantly more proteins. We also introduced a novel scoring function, PconsDock, that accurately separates 98% of correctly and incorrectly folded and docked proteins. The average performance of the method is comparable to the use of traditional, template-based or ab initio shape-complementarity-only docking methods. However, no a priori structural information for the individual proteins is needed. Moreover, the results of conventional and fold-and-dock approaches are complementary, and thus a combined docking pipeline could increase overall docking success significantly. PconsDocck contributed to the best model for one of the CASP14 oligomeric targets, H1065.
Automated Generation of Cerebral Blood Flow Maps Using Deep Learning and Multiple Delay Arterial Spin-Labelled MRI
Authors: Luciw Nicholas J. , Shirzadi Zahra , Black Sandra E. , Goubran Maged , MacIntosh Bradley J.
Published: June 2021

The purpose of this work was to develop and evaluate a deep learning approach for estimation of cerebral blood flow (CBF) and arterial transit time (ATT) from multiple post-label delay (PLD) arterial spin-labelled (ASL) MRI. Six-PLD ASL MRI was acquired on a 1.5T or 3T system among 99 older males and females with and without cognitive impairment. We trained and compared two network architectures: standard feed-forward convolutional neural network (CNN) and U-Net. Mean absolute error (MAE) was evaluated between model estimates and ground truth obtained through conventional processing. The best-performing model was re-trained on inputs with missing PLDs to investigate generalizability to different PLD schedules. Relative to the CNN, the U-Net yielded lower MAE on training data. On test data, the U-Net MAE was 8.4±1.4 ml/100g/min for CBF and 0.22±0.09 s for ATT. Model uncertainty, estimated with Monte Carlo dropout, was associated with model error. Network estimates remained stable when tested on inputs with up to three missing PLD images. Mean processing times were: U-Net pipeline = 10.77s; ground truth pipeline = 10min 41s. These results suggest hemodynamic parameter estimation from 1.5T and 3T multi-PLD ASL MRI is feasible and fast with a deep learning image-generation approach.
OrtSuite – from genomes to prediction of microbial interactions within targeted ecosystem processes
Authors: Saraiva João Pedro , Bartholomäus Alexandre , Kallies René , Gomes Marta , Bicalho Marcos , Vogt Carsten , Chatzinotas Antonis , Stadler Peter , Dias Oscar , da Rocha Ulisses Nunes
Published: June 2021

The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96 % of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. Identification of putative synergistic species interactions was evaluated using the sequenced genomes of an independent study which had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy to use workflow that allows for rapid functional annotation based on a user curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.
The biaxial mechanics of thermally denaturing skin - Part I: Experiments
Authors: Meador William D. , Sugerman Gabriella P. , Tepole Adrian Buganza , Rausch Manuel K.
Published: June 2021

The mechanics of collageneous soft tissues, such as skin, are sensitive to heat. Thus, quantifying and modeling thermo-mechanical coupling of skin is critical to our understanding of skin’s physiology, pathophysiology, as well as its treatment. However, key gaps persist in our knowledge about skin’s coupled thermo-mechanics. Among them, we haven’t quantified the role of skin’s microstructural organization in its response to superphysiological loading. To fill this gap, we conducted a comprehensive set of experiments in which we combined biaxial mechanical testing with histology and two-photon imaging under liquid heat treatment. Among other observations, we found that unconstrained skin, when exposed to high temperatures, shrinks anisotropically with the principle direction of shrinkage being aligned with collagen’s principle orientation. Additionally, we found that when skin is isometrically constrained, it produces significant forces during denaturing that are also anisotropic. Finally, we found that denaturation significantly alters the mechanical behavior of skin. For short exposure times, this alteration is reflected in a reduction of stiffness at high strains. At long exposure times, the tissue softened to a point where it became untestable. We supplemented our findings with confirmation of collagen denaturation in skin via loss of birefringence and second harmonic generation. Finally, we captured all time-, temperature-, and direction-dependent experimental findings in a hypothetical model. Thus, this work fills a fundamental gap in our current understanding of skin thermo-mechanics and will support future developments in thermal injury prevention, thermal injury management, and thermal therapeutics of skin.
A Xeno-free Media for the In Vitro Expansion of Human Spermatogonial Stem Cells
Authors: Robinson Meghan , Witherspoon Luke , Willerth Stephanie , Flannigan Ryan
Published: June 2021

In vitro expansion of spermatogonial stem cells (SSCs) has been established using animal-derived fetal bovine serum (FBS) and bovine serum albumin (BSA). However, the use of animal components during cell culture introduces the risk of contaminating cells with pathogens, and leads to animal epitope expression, rendering them unsuitable for medical use. Therefore, this study set out to develop a xeno-free, fully defined media for the expansion of human SSCs. We show that the molecules Prostaglandin D2 (PGD-2) and Insulin-Like Growth Factor 1 (IGF-1) can replace FBS and BSA in cell culture media without loss of viability or expansion capability, and that Rho-Associated, Coiled-Coil Containing Protein Kinase (ROCK) inhibitor Y-27632 supplementation improves viability after cryopreservation. Long-term SSC cultures expanded in xeno-free, defined culture conditions shared identical protein expression profiles for well-known SSC markers, while gene expression analyses revealed a significant improvement in quiescent SSC and pan-germ markers. This xeno-free, defined formulation allows for standardized SSC culture free of animal pathogens.
Common Permutation Methods in Animal Social Network Analysis Do Not Control for Non-independence
Authors: Hart Jordan D. A. , Weiss Michael N. , Brent Lauren J. N. , Franks Daniel W.
Published: June 2021

The non-independence of social network data is a cause for concern among behavioural ecologists conducting social network analysis. This has led to the adoption of several permutation-based methods for testing common hypotheses. One of the most common types of analysis is nodal regression, where the relationships between node-level network metrics and nodal covariates are analysed using a permutation technique known as node-label permutations. We show that, contrary to accepted wisdom, node-label permutations do not automatically account for the non-independences assumed to exist in network data, because regression-based permutation tests still assume exchangeability of residuals. The same assumption also applies to the quadratic assignment procedure (QAP), a permutation-based method often used for conducting dyadic regression. We highlight that node-label permutations produce the same p-values as equivalent parametric regression models, but that in the presence of non-independence, parametric regression models can also produce accurate effect size estimates. We also note that QAP only controls for a specific type of non-independence between edges that are connected to the same nodes, and that appropriate parametric regression models are also able to account for this type of non-independence. Based on this, we suggest that standard parametric models could be used in the place of permutation-based methods. Moving away from permutation-based methods could have several benefits, including reducing over-reliance on p-values, generating more reliable effect size estimates, and facilitating the adoption of alternative types of statistical analysis.
Influence of the metallized coils on human leg blood circulation
Authors: Dehtjars Jurijs , Jašina Ksenija , Larins Viesturs , Okss Aleksandrs , Pudovskis Konstantins , Tolmača Nelli , Vadhiraj Vijay Vyas
Published: June 2021

The aim of the study was to find out if magnetic field generated by the human body affects a human blood flow. The idea is based on Lenz’s law where the blood flow induces an opposing alternating magnetic field (OAMF). In the experiment the OAMF will be modulated by repeating heart contractions (pulses). In an experiment with metallized coils it was found that wearing metal coils affects blood flow and it differs from when coils were not worn.
Combustible and electronic cigarette exposures increase ACE2 activity and SARS-CoV-2 Spike binding
Authors: Ghosh Arunava , Girish Vishruth , Yuan Monet Lou , Coakley Raymond D. , Alexis Neil E. , Sausville Erin L. , Vasudevan Anand , Chait Alexander R. , Sheltzer Jason M. , Tarran Robert
Published: June 2021

The outbreak of coronavirus disease 2019 (COVID-19) has extensively impacted global health. The causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to the angiotensin-converting enzyme 2 (ACE2) receptor, a transmembrane metallo-carboxypeptidase that is expressed in both membrane-anchored (mACE2) and soluble (sACE2) forms in the lung. Tobacco use has been speculated as a vulnerability factor for contracting SARS-CoV-2 infection and subsequent disease severity, whilst electronic cigarettes (e-cigarettes) have been shown to induce harmful proteomic and immune changes in the lungs of vapers. We therefore tested the hypothesis that combustible tobacco (e.g. cigarettes) and non-combustible e-cigarettes could affect ACE2 activity and subsequent SARS-CoV-2 infection. We observed that sACE2 activity was significantly higher in bronchoalveolar lavage fluid from both smokers and vapers compared to age-matched non-smokers. Exposure to cigarette smoke increased ACE2 levels, mACE2 activity, and sACE2 in primary bronchial epithelial cultures. Finally, treatment with either cigarette smoke condensate or JUUL e-liquid increased infections with a spike-coated SARS-CoV-2 pseudovirus. Overall, these observations suggest that tobacco product use elevates ACE2 activity and increases the potential for SARS-CoV-2 infection through enhanced spike protein binding.
Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep
Authors: Chen Ping , Zhou Hui , Huang Yanyan , Xie Zhe , Zhang Mengjie , Wei Yuli , Li Jia , Ma Yuewei , Luo Min , Ding Wenmian , Cao Junwei , Jiang Tao , Nan Peng , Fang Jiasong , Li Xuan
Published: June 2021

Background

The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.

Results

We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts’ nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.

Conclusion

Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.
Repurposing diphenylbutylpiperidine-class antipsychotic drugs for host-directed therapy ofMycobacterium tuberculosisandSalmonella entericainfections
Authors: Heemskerk MT , Korbee CJ , Esselink J , Carvalho dos Santos C , van Veen S , Gordijn IF , Vrieling F , Walburg KV , Engele CG , Dijkman K , Wilson L , Verreck FAW , Ottenhoff THM , Haks MC
Published: June 2021

The persistent increase of multidrug-resistant (MDR)Mycobacterium tuberculosis(Mtb) infections negatively impacts Tuberculosis (TB) treatment outcomes. Host-directed therapies (HDT) pose an complementing strategy, particularly sinceMtbis highly successful in evading host-defense by manipulating host-signaling pathways. Here, we screened a library containing autophagy-modulating compounds for their ability to inhibit intracellularMtb-bacteria. Several active compounds were identified, including two drugs of the diphenylbutylpiperidine-class, Fluspirilene and Pimozide, commonly used as antipsychotics. Both molecules inhibited intracellularMtbin pro- as well as anti-inflammatory primary human macrophages in a host-directed manner and synergized with conventional anti-bacterials. Importantly, these inhibitory effects extended to MDR-Mtbstrains and the unrelated intracellular pathogen,Salmonella entericaserovar Typhimurium (Stm). Mechanistically Fluspirilene and Pimozide were shown to regulate autophagy and alter the lysosomal response, partly correlating with increased bacterial localization to autophago(lyso)somes. Pimozide’s and Fluspirilene’s efficacy was inhibited by antioxidants, suggesting involvement of the oxidative-stress response inMtbgrowth control. Furthermore, Fluspirilene and especially Pimozide counteractedMtb-induced STAT5 phosphorylation, thereby reducingMtbphagosome-localized CISH that promotes phagosomal acidification.

In conclusion, two approved antipsychotic drugs, Pimozide and Fluspirilene, constitute highly promising and rapidly translatable candidates for HDT againstMtbandStmand act by modulating the autophagic/lysosomal response by multiple mechanisms.
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA
Authors: Shi Honglue , Kimsey Issac J. , Liu Hsuan-Fu , Pham Uyen , Schumacher Maria A. , Al-Hashimi Hashim M.
Published: June 2021

Watson-Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative ‘Hoogsteen’ bps, expanding the functional complexity of DNA. We developed ‘Hoog-finder’, which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson-Crick in crystal structures of protein-DNA complexes. We uncovered seventeen Hoogsteen bps, seven of which were in complex with six proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks, and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
Lack of Age-related Respiratory Changes in Daphnia
Authors: Anderson Cora E. , Ekwudo Millicent N. , Jonas-Closs Rachael A , Cho Yongmin , Peshkin Leonid , Kirschner Marc W. , Yampolsky Lev Y.
Published: June 2021

Aging is a multifaceted process of accumulation of damages and waste in cells and tissues; age-related changes in mitochondria and in respiratory metabolism have been in the focus of aging research for decades. Here we investigated age-related changes in respiration rates, lactate/pyruvate ratio, a commonly used proxy for NAD+/NADH balance, and mitochondrial membrane potential in 4 genotypes of an emerging model organism for aging research, a cyclic parthenogen Daphnia magna. We show that total body weight-adjusted respiration rate decreases with age, although this decrease is small in magnitude and not observed in anaesthetized animals, thus likely to be accounted for by decrease in locomotion and feeding activity. Lactate/pyruvate ratio and mitochondrial membrane potential (Ψmt) showed no age-related changes, with a possible exception of Ψmt measured in the optical lobe and in epipodites (excretory organs) in which Ψmt showed a maximum at middle age. We conclude that actuarial senescence in Daphnia is not caused by a decline in respiratory metabolism and discuss possible mechanisms of maintaining mitochondrial healthspan throughout the lifespan.
Adaptable and Automated Rodent Behavior Maze System
Authors: Olson Jacob M , Leppla Christopher A , Bladon John H , Jadhav Shantanu P
Published: June 2021

Mazes are a fundamental and widespread tool in behavior and systems neuroscience research in rodents. However, their form and inflexibility often restrict potential experimental paradigms that involve multiple or adaptive maze designs. Unique layouts often cost substantial engineering and time investments from trainee scientists. To alleviate these issues, we have developed an automated modular maze system that is flexible and scalable. This system will allow for experiments with multiple track configurations in rapid succession. Additionally, the flexibility can expedite prototyping of behaviors. Finally, the standardized componentry enhances experimental reproducibility and repeatability. This maze system presents advantages over current maze options and can facilitate novel behavior and systems neuroscience research.

Highlights

Modular maze system enables same-day behavior recordings from multiple flexibly-configured maze environments.

High degree of experimental reproducibility and repeatability.

Automated lick-detection, liquid reward delivery, and movable barriers.

Electronics interface with SpikeGadgets hardware for plug-and-play automated control.

Flexibility enables rapid experimental piloting.
Long-COVID following mild SARS CoV-2 infection: characteristic T cell alterations and response to antihistamines
Authors: Glynne Paul , Tahmasebi Natasha , Gant Vanya , Gupta Rajeev
Published: June 2021

Background

Long-COVID is characterised by the emergence of multiple debilitating symptoms following SARS CoV2 infection. Its aetiology is unclear, and it often follows a mild acute illness. Anecdotal reports of gradual clinical responses to histamine receptor antagonists (HRA) suggest a histamine-dependent mechanism distinct from anaphylaxis. Histamine is a paracrine regulator of T-cells: although T-cell perturbations are reported in acute COVID-19, the T-cell landscape in recovered patients and its relationship to long-COVID remains under-explored.

Objective

To survey T-cell populations in patients recovered from mild COVID-19, comparing those with long-COVID and asymptomatic individuals, and to analyse these data in light of symptoms and response to HRA.

Design

Prospective observational cohort study.

Setting

Single-site outpatient clinic

Participants

65 (87 to 408 days post mild COVID-19). None had sought treatment for acute COVID-19. 16 recovered uneventfully (asymptomatic group), 49 presented with long-COVID (symptomatic group), of whom 25 received HRA.

Measurements

Structured long-COVID symptom questionnaire; quantification of T-cell subsets using a standard diagnostic assay.

Results

HRA significantly reduced mean symptom burden. T-cell profiles distinguished asymptomatic and long-COVID groups, but did not predict response to HRA. Long-COVID patients had reduced CD4+ and CD8+ effector memory (EM) cells and increased PD-1 expression on central memory (CM) cells. Asymptomatic controls had reduced CD8+ EM cells and increased CD28 expression on CM cells.

Conclusion

HRA reduce long-COVID symptoms. T-cell perturbations persist for up to 400 days following mild acute COVID-19 irrespective of long-COVID symptoms.

Limitations

Preliminary, single health system study.

Primary Funding Source

Philanthropic donations from The Dominvs Group and Sir Peter Wood
Immunogenicity of the ChAdOx1 nCoV-19 and the BBV152 Vaccines in Patients with Autoimmune Rheumatic Diseases
Authors: Shenoy Padmanabha , Ahmed Sakir , Cherian Somy , Paul Aby , Shenoy Veena , Vijayan Anuroopa , Reji Reshma , Thampi Arya , Sageer Babu AS , Mohan Manju
Published: June 2021

Introduction

There is limited information on the effectiveness of COVID-19 vaccination in patients with autoimmune rheumatic diseases (AIRD).

Methods

136 consecutive patients with rheumatic diseases who never had a diagnosis of COVID-19 previously, and had completed vaccination with either the ChAdOx1 or BBV152 vaccines were recruited. Their IgG antibody titres to the Spike protein were estimated 1 month after the second dose.

Results

102 patients had AIRD while the 34 had non-AIRD. Lesser patients with AIRD (92/102) had positive antibodies titres than ones with non-AIRD(33/34) [p<0.001]. Amongst patients who received the ChAdOX1 vaccine, the AIRD group had lower antibody titres. Although the AIRD patients receiving BBV152 had similarly lower titres numerically, this did not attain statistical significance probably due to lesser numbers. Comparing the two vaccines, 114(95%) of those who received ChAdOx1 (n=120) and 11(68.7%) of those who received BBV152(n=16) had detectable antibodies [p=0.004]. Antibody titres also were higher in ChAdOx1 recipients when compared to BBV152.

To validate the findings, we estimated antibody titres in 30 healthy people each who had received either vaccine. All 30 who had received ChAdOX1 and only 23/30 of those who had received BBV152 had positive antibodies (p=0.011).

Conclusion

In this preliminary analysis, patients with AIRD had lower seroconversion rates as well as lower antibody titres as compared to patients with non-AIRD. Also,the humoral immunogenicity of the BBV152 vaccine appears to be less than that of the ChAdOX1 vaccine. Validation using larger numbers and testing of cellular immunity is urgently required.
Estimating body segment parameters from three-dimensional human body scans
Authors: Kudzia Pawel , Jackson Erika , Dumas Genevieve
Published: June 2021

Body segment parameters are inputs for a range of applications. The estimation of body segment parameters that are participant-specific is desirable as it requires fewer prior assumptions and can reduce outcome measurement errors. Commonly used methods for estimating participant-specific body segment parameters are either expensive and out of reach (medical imaging), have many underlying assumptions (geometrical modelling) or are based on a specific subset of a population (regression models). Our objective was to develop a participant-specific 3D scanning and body segmentation method that estimates body segment parameters without any assumptions about the geometry of the body, ethnic background, and gender, is low-cost, fast, and can be readily available. Using a Microsoft Kinect camera, we developed a 3D surface scanning protocol that estimated participant-specific body segment parameters. To evaluate our system, we performed repeated 3D scans of 21 healthy participants (10 male, 11 female). We used open-source software to segment each body scan into 16 segments (head, torso, abdomen, pelvis, left and right hand, forearm, upper arm, foot, shank and thigh) and wrote custom software to estimate each segment’s mass, mass moment of inertia in the three principal orthogonal axes relevant to the center of the segment, longitudinal length, and center of mass. We compared our body segment parameter estimates to those obtained using two comparison methods and found that our system was consistent in estimating total body volume between repeated scans (male p=0.1194, female p = 0.2240), estimated total body mass without significant differences when compared to our comparison method and a medical scale (male p=0.8529, female p = 0.6339), and generated consistent and comparable estimates across all of the body segment parameters of interest. The work here outlines an inexpensive 3D surface scanning approach for estimating a range of participant-specific body segment parameters.
A cross-biomes bacterial diversity shed light on ocean-atmosphere microbial transmission
Authors: Lang-Yona Naama , Flores J. Michel , Haviv Rotem , Alberti Adriana , Poulain Julie , Belser Caroline , Trainic Miri , Gat Daniella , Ruscheweyh Hans-Joachim , Wincker Patrick , Sunagawa Shinichi , Rudich Yinon , Koren Ilan , Vardi Assaf
Published: June 2021

Microbes are ubiquitous in the oceans and the atmosphere, playing essential roles in biogeochemical processes. The bio-exchanges between the two environments can provide important insights into microbial distribution and diversity but are still not well understood. We simultaneously surveyed the genomic diversity of airborne and marine bacterial communities across 15 000 kilometers in the Atlantic and Pacific oceans. Higher variability of microbial community composition was observed in the atmosphere than in the ocean surface waters. In addition, a greater similarity was observed between oceans than their overlaying atmosphere, and between atmospheric samples than with the ocean beneath. We additionally detected a higher coverage rate and relative abundance of marine bacteria in the Pacific atmosphere as compared to the Atlantic, while the dominant fraction in the Atlantic atmosphere was annotated as soil-associated bacteria. This study advances our understanding of microbial dispersion in the ocean, the atmosphere, and the exchange between them, as well as their potential impact on microbial composition, ecology, and biogeochemistry.
Expression of extracellular Hsp90 is a molecular signature of T cell activation, providing a means to image and target T Cell activation in autoimmune disease
Authors: Scarneo Scott A. , Smith Aaron P. , Favret Jacob , O’Connell Robert , Pickeral Joy , Yang Kelly W. , Ferrari Guido , Loiselle David R. , Hughes Philip F. , Kulkarni Manjusha M , Gargesha Madhusudhana , Scott Bryan , Roy Debashish , Haynes Barton F. , Kwiek Jesse J. , Haystead Timothy A. J.
Published: June 2021

Heat shock protein 90 (Hsp90) maintains cellular proteostasis during stress and has been under investigation as a therapeutic target in cancer for over two decades. We and others have identified an extracellularly expressed form of Hsp90, eHsp90, that previously appeared to be restricted to rapidly proliferating cells exhibiting a metastatic phenotype. Here, we used HS-131, a fluor-tethered eHsp90 inhibitor, to quantify the effect of T cell activation on the expression of eHsp90 in human and mouse T cells. In cell based assays, stimulation of human T cells induced a 20-fold increase in eHsp90 expression at the plasma membrane, suggesting trafficking of eHsp90 is acutely regulated by TCR and inflammatory mediated signaling. Following injection of HS-131 in mouse models of human rheumatoid arthritis and inflammatory bowel disease, we detected localization of the probe at sites of active disease, consistent with immune cell invasion. Moreover, despite rapid hepatobiliary clearance, HS-131 demonstrated efficacy in delaying the onset and progression of disease in the arthritis model. Our results suggest eHsp90 expression at the plasma membrane of T cells is a molecular marker of autoimmune induced activation and potentially a therapeutic target for chronic diseases such as rheumatoid arthritis and inflammatory bowel disease.

Perspective

T cells mediate many maladaptive disease pathologies such as autoimmune disorders. Many immunosuppressants in clinical use act by preventing the activation of T cells. However, this approach can lead to increased rates of opportunistic infection and malignancy. Here, we show for the first time that eHsp90 is upregulated during T cell activation in response to exogenous ligands. Therefore, pharmacological inhibition of eHsp90 may provide a means to target only activated T cells for immunosuppression. Selective targeting of only activated T cells could be efficacious against autoimmune disease without increasing the incidence of undesirable outcomes. Additionally, the presence of eHsp90 on the surface of activated T cells could be diagnostically useful to track the status and progression of autoimmune disease in patients.
Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
Authors: Thorne Lucy G , Bouhaddou Mehdi , Reuschl Ann-Kathrin , Zuliani-Alvarez Lorena , Polacco Ben , Pelin Adrian , Batra Jyoti , Whelan Matthew V.X. , Ummadi Manisha , Rojc Ajda , Turner Jane , Obernier Kirsten , Braberg Hannes , Soucheray Margaret , Richards Alicia , Chen Kuei-Ho , Harjai Bhavya , Memon Danish , Hosmillo Myra , Hiatt Joseph , Jahun Aminu , Goodfellow Ian G. , Fabius Jacqueline M. , Shokat Kevan , Jura Natalia , Verba Klim , Noursadeghi Mahdad , Beltrao Pedro , Swaney Danielle L. , Garcia-Sastre Adolfo , Jolly Clare , Towers Greg J. , Krogan Nevan J.
Published: June 2021

Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more effectively suppress host innate immune responses in airway epithelial cells. We found that B.1.1.7 isolates have dramatically increased subgenomic RNA and protein levels of Orf9b and Orf6, both known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation, and Orf9b binding and activity was regulated via phosphorylation. We conclude that B.1.1.7 has evolved beyond the Spike coding region to more effectively antagonise host innate immune responses through upregulation of specific subgenomic RNA synthesis and increased protein expression of key innate immune antagonists. We propose that more effective innate immune antagonism increases the likelihood of successful B.1.1.7 transmission, and may increase in vivo replication and duration of infection.
Microglial CX3CR1I249/M280 variant limits neurogenesis and remyelination in cuprizone-induced multiple sclerosis model
Authors: Mendiola Andrew S. , Church Kaira A. , Cardona Sandra M. , Vanegas Difernando , Garcia Shannon A. , Macklin Wendy , Lira Sergio A. , Ransohoff Richard M. , Kokovay Erzsebet , Lin Chin-Hsing Annie , Cardona Astrid E.
Published: June 2021

Microglia have been implicated in multiple sclerosis (MS) pathogenesis. The fractalkine receptor CX3CR1 regulates the activation of pathogenic microglia in models of MS and the human polymorphic CX3CR1I249/M280 (hCX3CR1I249/M280) variant increases MS disease progression. However, the role of hCX3CR1I249/M280 on microglial activation and central nervous system repair and regenerative mechanisms remain unknown. Therefore, using transgenic mice expressing the hCX3CR1I249/M280 variant, we aimed to determine the contribution of defective CX3CR1 signaling to remyelination and neurogenesis in the cuprizone model of focal demyelination. Here, we report that mice expressing hCX3CR1I249/M280 exhibit marked demyelination and microgliosis follow acute cuprizone treatment. Cuprizone-treated CX3CR1-deficient and fractalkine-deficient mice displayed a comparable phenotype. Nanostring gene expression analysis in demyelinated lesions showed that hCX3CR1I249/M280 upregulates genes associated with inflammation, oxidative stress and disease-associated microglia. In addition, gene expression analysis in the subgranular zone (SGZ) of the hippocampus in hCX3CR1I249/M280 mice was associated with a significant downregulation of gene networks linked to neurogenesis following acute demyelination. Confocal microscopy showed that hCX3CR1I249/M280 or loss of CX3CR1 signaling inhibits the generation of progeny from the neurogenic niche, including cells involved in myelin repair. These results provide evidence for the pathogenic capacity of hCX3CR1I249/M280 on microglia dysfunction and therapeutic targeting of CX3CR1 to promote CNS repair in MS.
Quantitative examination of five stochastic cell-cycle and cell-size control models forEscherichia coliandBacillus subtilis
Authors: Treut Guillaume Le , Si Fangwei , Li Dongyang , Jun Suckjoon
Published: June 2021

We examine five quantitative models of the cell-cycle and cell-size control inEscherichia coliandBacillus subtilisthat have been proposed over the last decade to explain single-cell experimental data generated with high-throughput methods. After presenting the statistical properties of these models, we test their predictions against experimental data. Based on simple calculations of the defining correlations in each model, we first dismiss the stochastic Helmstetter-Cooper model and the Initiation Adder model, and show that both the Replication Double Adder and the Independent Double Adder model are more consistent with the data than the other models. We then apply a recently proposed statistical analysis method and obtain that the Independent Double Adder model is the most likely model of the cell cycle. By showing that the Replication Double Adder model is fundamentally inconsistent with size convergence by the adder principle, we conclude that the Independent Double Adder model is most consistent with the data and the biology of bacterial cell-cycle and cell-size control. Mechanistically, the Independent Adder Model is equivalent to two biological principles: (i) balanced biosynthesis of the cell-cycle proteins, and (ii) their accumulation to a respective threshold number to trigger initiation and division.
5-methylcytosine modification byPlasmodiumNSUN2 stabilizes mRNA and mediates the development of gametocytes
Authors: Liu Meng , Guo Gangqiang , Qian Pengge , Mu Jianbing , Lu Binbin , He Xiaoqin , Shang Xiaomin , Yang Guang , Shen Shijun , Liu Wenju , Wang Liping , Gu Liang , Mu Quankai , Yu Xinyu , Zhao Yuemeng , Culleton Richard , Cao Jun , Jiang Lubin , Wellems Thomas E. , Yuan Jing , Jiang Cizhong , Zhang Qingfeng
Published: June 2021

5-methylcytosine (m5C) is an important epitranscriptomic modification involved in mRNA stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles ofPlasmodiumparasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (P. yoelii) and human (P. falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to thePlasmodiumtranscripts and that aPlasmodiumortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knock-out ofP. yoelii nsun2(pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in rodent and human malaria parasites. Restoration of thensun2gene in the knock-out parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species ofPlasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites.

Significance

Modifications of RNA including methylations of cytosine (m5C) and adenosine (m6A) have important roles in RNA metabolism, cellular responses to stress, and biological processes of differentiation and development. Here, we report on the profiles of m5C mRNA modifications in malaria parasites that infect rodents (Plasmodium yoelii) and humans (Plasmodium falciparum). These parasites have genes that encode homologs of human and plant NSUN2 methyltransferases (m5C “writers”). We show that one of these homologs, termed PyNSUN2, stabilizes mRNA transcripts inP. yoeliiand mediates m5C-associated development of the parasite sexual stages (gametocytes). Further research on m5C and other epitranscriptomic modifications may yield new insights into molecular pathways of gametocyte development and mosquito infectivity that can be exploited to interrupt malaria transmission.