bluuebunny/crossref_metadata_2025 huggingface dataset:
Protection of apigenin against acrylonitrile-induced sperm and testis injury in rats: involvement of activation of ASK1-JNK/p38 signaling pathway
Authors: Shi Ying , Bai Jin , Dang Yuhui , Bai Qingli , Zheng Rong , Chen Jia , Li Zhilan
Published: February 2021

This study aims to clarify if apigenin (AP) could play a pivotal role in attenuating acrylonitrile (ACN)-induced sperm and testis injury by inhibiting ASK1-JNK/p38 signaling pathway. Male Sprague–Dawley rats were randomly divided into five groups: a control group (corn oil), an ACN group (ACN 46 mg kg−1), an ACN + AP1 group (ACN + AP 117 mg kg−1), an ACN + AP2 group (ACN + AP 234 mg kg−1) and an ACN + AP3 group (ACN + AP 351 mg kg−1). The ACN + AP groups were given ACN by gavage after a pretreatment with different dosages of AP for 30 min, whereas the rats in the control group received an equivalent volume of corn oil. The gavage was conducted for 6 days per week in 4 weeks. The results showed that AP reduced sperm deformity rate and DNA fragment index and attenuated the testicular injury induced by ACN. AP could also alleviate oxidative stress, downregulate ASK1-JNK/p38 signaling pathway and eventually inhibit mitochondria-mediated testicular apoptosis. In brief, AP could dampen oxidative stress thereby inhibiting testicular apoptosis mediated by ASK1-JNK/p38 signaling pathway, alleviating ACN-induced sperm and testis injury and exerting a protective effect on male reproductive system.
Don't Hold Your Breath—A Video-Based Study of Procedural Intervals During Pediatric Rapid Sequence Intubation
Authors: Shah Ashish , Edmunds Katherine , Dean Preston , Frey Mary , Boyd Stephanie , Ahaus Karen , Zhang Yin , Varadarajan Kartik , Kerrey Benjamin T.
Published: February 2021

Objective

Develop a framework for data collection to determine the contributions of both laryngoscopy and tube delivery intervals to the apneic period in unsuccessful and successful attempts among patients undergoing rapid sequence intubation (RSI) in a pediatric emergency department (PED).

Design

This was a retrospective, observational study of RSI.

Setting

An academic PED.

Patients

A consecutive sample of all intubations attempts of first provider physicians performing RSI in the shock trauma suite over a 10-month period in 2018–2019.

Measurement and Main Results

Data were collected by structured video review. The main outcome was the duration of the laryngoscopy and tube delivery intervals per attempt. We compared interval duration between successful and unsuccessful attempts, adjusting for age, accounting for repeated measures, and clustering by provider. There were 69 patients with 89 total intubation attempts. Sixty-three patients were successfully intubated by the first provider (91%). Pediatric emergency medicine fellows performed 54% of the attempts. The median duration of the apneic period per attempt was longer in unsuccessful attempts (57 vs 44 seconds; median of difference, −10.5; 95% confidence interval [CI], −17.0 to −4.0). The duration of laryngoscopy was similar (18 vs 13 seconds; median of difference, −3.5; 95% CI, −8.0 to 1.0), but tube delivery was longer in unsuccessful attempts (25.5 vs. 11 seconds; median of difference, −12.5; 95% CI, −17.0 to −4.0). These results did not change when adjusting for age or clustering by provider.

Conclusions

We successfully developed a specific, time-based framework for the contributors to prolonged apnea in RSI. Prolonged tube delivery accounted for more of the apneic period. Future studies and improvement should focus on problems during tube delivery in the PED.
Modelling and predicting the effect of social distancing and travel restrictions on COVID-19 spreading
Authors: Parino Francesco , Zino Lorenzo , Porfiri Maurizio , Rizzo Alessandro
Published: February 2021

To date, the only effective means to respond to the spreading of the COVID-19 pandemic are non-pharmaceutical interventions (NPIs), which entail policies to reduce social activity and mobility restrictions. Quantifying their effect is difficult, but it is key to reducing their social and economic consequences. Here, we introduce a meta-population model based on temporal networks, calibrated on the COVID-19 outbreak data in Italy and applied to evaluate the outcomes of these two types of NPIs. Our approach combines the advantages of granular spatial modelling of meta-population models with the ability to realistically describe social contacts via activity-driven networks. We focus on disentangling the impact of these two different types of NPIs: those aiming at reducing individuals’ social activity, for instance through lockdowns, and those that enforce mobility restrictions. We provide a valuable framework to assess the effectiveness of different NPIs, varying with respect to their timing and severity. Results suggest that the effects of mobility restrictions largely depend on the possibility of implementing timely NPIs in the early phases of the outbreak, whereas activity reduction policies should be prioritized afterwards.
A centriole's subdistal appendages: contributions to cell division, ciliogenesis and differentiation
Authors: Hall Nicole A. , Hehnly Heidi
Published: February 2021

The centrosome is a highly conserved structure composed of two centrioles surrounded by pericentriolar material. The mother, and inherently older, centriole has distal and subdistal appendages, whereas the daughter centriole is devoid of these appendage structures. Both appendages have been primarily linked to functions in cilia formation. However, subdistal appendages present with a variety of potential functions that include spindle placement, chromosome alignment, the final stage of cell division (abscission) and potentially cell differentiation. Subdistal appendages are particularly interesting in that they do not always display a conserved ninefold symmetry in appendage organization on the mother centriole across eukaryotic species, unlike distal appendages. In this review, we aim to differentiate both the morphology and role of the distal and subdistal appendages, with a particular focus on subdistal appendages.
Interactions between auditory statistics processing and visual experience emerge only in late development
Authors: Berto Martina , Pietrini Pietro , Ricciardi Emiliano , Bottari Davide
Published: February 2021

The human auditory system relies on both detailed and summarized representations to recognize different sounds. As local features can exceed the storage capacity, average statistics are computed over time to generate more compact representations at the expense of temporal details availability. This study aimed to identify whether these fundamental sound analyses develop and function exclusively under the influence of the auditory system or interact with other modalities, such as vision. We employed a validated computational synthesis approach allowing to control directly statistical properties embedded in sounds. To address whether the two modes of auditory representation (local features processing and statistical averaging) are influenced by the availability of visual input in different phases of development, we tested samples of sighted controls (SC), congenitally blind (CB), and late-onset (> 10 years of age) blind (LB) individuals in two separate experiments which uncovered auditory statistics computations from behavioral performances. In experiment 1, performance relied on the availability of local features at specific time points; in experiment 2, performance benefited from computing average statistics over longer durations. As expected, when sound duration increased, detailed representation gave way to summary statistics in SC. In both experiments, the sample of CB individuals displayed a remarkably similar performance revealing that both local and global auditory processes are not altered by blindness since birth. Conversely, LB individuals performed poorly compared to the other groups when relying on local features, with no impact on statistical averaging. The dampening in the performance was not associated with the onset and duration of visual deprivation. Results provide clear evidence that vision is not necessary for the development of the auditory computations tested here. Remarkably, a functional interplay between acoustic details processing and vision emerges at later developmental phases. Findings are consistent with a model in which the efficiency of local auditory processing is vulnerable in case sight becomes unavailable. Ultimately results are in favor of a shared computational framework for auditory and visual processing of local features, which emerges in late development.
In vitroevolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2
Authors: Szemiel Agnieszka M. , Merits Andres , Orton Richard J. , MacLean Oscar , Pinto Rute Maria , Wickenhagen Arthur , Lieber Gauthier , Turnbull Matthew L. , Wang Sainan , Mair Daniel , da Silva Filipe Ana , Willett Brian J. , Wilson Sam J. , Patel Arvind H. , Thomson Emma C. , Palmarini Massimo , Kohl Alain , Stewart Meredith E.
Published: February 2021

Remdesivir (RDV) is used widely for COVID-19 patients despite varying results in recent clinical trials. Here, we show how serially passaging SARS-CoV-2in vitroin the presence of RDV selected for drug-resistant viral populations. We determined that the E802D mutation in the RNA-dependent RNA polymerase was sufficient to confer decreased RDV sensitivity without affecting viral fitness. Analysis of more than 200,000 sequences of globally circulating SARS-CoV-2 variants show no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we also observed changes in the Spike (i.e., H69 E484, N501, H655) corresponding to mutations identified in emerging SARS-CoV-2 variants indicating that they can arisein vitroin the absence of immune selection. This study illustrates SARS-CoV-2 genome plasticity and offers new perspectives on surveillance of viral variants.

One Sentence Summary

SARS-CoV-2 drug resistance & genome plasticity
Detection Of Genomic Variants Of SARS-CoV-2 Circulating In Wastewater By High-Throughput Sequencing
Authors: Pérez-Cataluña Alba , Chiner-Oms Álvaro , Cuevas-Ferrando Enric , Díaz-Reolid Azahara , Falcó Irene , Randazzo Walter , Girón-Guzmán Inés , Allende Ana , Bracho María A. , Comas Iñaki , Sánchez Gloria
Published: February 2021

The use of SARS-CoV-2 metagenomics in wastewater can allow the detection of variants circulating at community level. After comparing with clinical databases, we identified three novel variants in the spike gene, and six new variants in the spike detected for the first time in Spain. We finally support the hypothesis that this approach allows the identification of unknown SARS-CoV-2 variants or detected at only low frequencies in clinical genomes.

Abstract Figure
Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period
Authors: Weber Nicholas D. , Goñi-Salaverri Ainhoa , Rodríguez Jose A. , Unfried Juan Pablo , Alameda Daniel , Fernández-Alonso Mirian , Sáez Elena , Maestro-Galilea Sheila , Alegre Felix , Carmona-Torre Francisco , Marin-Oto Marta , Olagüe Cristina , Odriozola Leticia , Navarro-Alonso Mar , Sanchez-Ostiz Rafael , Argemi Josepmaria , Pozo Jose Luis del , Lara-Astiaso David
Published: February 2021

Background

Spain is one of the countries most heavily affected by the COVID-19 pandemic. As in other countries such as UK and USA, nursing homes have been an important human reservoir for the virus and the population with the highest mortality worldwide. The presence of asymptomatic carriers within nursing homes is one of the factors that could provoke new outbreaks during the relaxing of lockdown measures.

Methods

We developed a high-throughput protocol for RNA extraction of patient samples based on silane magnetic beads in multi-well plates. The sensitivity, specificity and reproducibility rates were assessed using positive and negative clinical samples from the Clinica Universidad de Navarra, Spain. We utilized the protocol to test a pilot cohort of 138 residents and 87 staff from a nursing home in Northern Navarre, Spain.

Findings

Our protocol showed high sensitivity (100%), specificity (96·0%) and linear correlation with PCR cycle threshold values obtained with a standard testing kit (R2 = 0·807, p=3E-05). Testing of 225 individuals from the nursing home revealed 63 residents (46%) and 14 staff (16%) positive for SARS-CoV-2. Only 18 of the positive residents (28·6%) were symptomatic at time of testing. During follow-up, 6 PCR-negative symptomatic residents were retested and resulted positive. One-month mortality among positive residents was higher than in negative residents (15·9% vs 1·3%), regardless of age or comorbidities.

Interpretation

Rapid silane bead-based RNA extraction expanded the testing capabilities and COVID-19 patients were promptly identified. Personal and public health measures were enacted to avoid spreading and tighten clinical surveillance. The ability to easily adapt the technical capabilities of academic research centers to large-scale testing for SARS-CoV-2 could provide an invaluable tool for ensuring a safe lifting of lockdown in countries with high numbers of cases.

Funding

European Molecular Biology Organization and Genomics Unit, Cima Universidad de Navarra.
Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species
Authors: Le Luyer J. , Milhade L. , Reisser C. , Soyez C. , Monaco C. J. , Belliard C. , Le Moullac G. , Ky C.-L. , Pernet F.
Published: February 2021

Ocean warming is a particularly challenging threat for tropical marine bivalves’ species because many live already near their upper thermal limits. The thermal sensitivity of organisms is a strong contributor to the biogeographic boundaries of populations and species. The potential of thermal plastic response (range of thermal breadth) is typically reduced for marine populations living in stable thermal environments, e.g., in extreme latitudes organisms as traduced in the climatic variability hypothesis. However, regional-scale heterogeneity among tropical environments, such as archipelagos in French Polynesia, might also serve in modulating this plastic potential. The questions remain now, how tropical organisms are able to cope with abnormally elevated temperature on long-term (several weeks) and how environmental-variability might drive the potential of resilience? To answer these questions, we benefit from two ecologically divergent populations of a marine tropical mollusc species,Pinctada margaritifera, that usually experience either large diurnal variations (tide-pools, Marquesas archipelago) or lower temperature with stable to moderate variations (Gambier archipelago). Individuals were maintained in common garden experiment at several controlled temperature conditions (23°C, 28°C, 32°C and 34°C) over a 48 days period. We explored genetic divergence as well as thermal plastic responses by combining lipidomic and transcriptomic approaches. We show thatP. margaritiferahave capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Furthermore, we identified genetic variation between populations that overlapped with genes expression variations, including genes involved in the respiration machinery, a central process delimiting critical temperatures in marine invertebrates. This study is the first of a series looking at the global adaptation and acclimation mechanisms in response to climate change inPinctadaspecies.
AnLRframework incorporating sensitivity analysis to model multiple direct and secondary transfer events on skin surface
Authors: Gill Peter , Bleka Øyvind , Roseth Arne , Fonneløp Ane Elida
Published: February 2021

Bayesian logistic regression is used to model the probability of DNA recovery following direct and secondary transfer and persistence over a 24 hour period between deposition and sample collection. Sub-source level likelihood ratios provided the raw data for activity-level analysis. Probabilities of secondary transfer are typically low, and there are challenges with small data-sets with low numbers of positive observations. However, the persistence of DNA over time can be modelled by a single logistic regression for both direct and secondary transfer, except that the time since deposition must be compensated by anoffsetvalue for the latter. This simplifies the analysis. Probabilities are used to inform an activity-level Bayesian Network that takes account of alternative propositions e.g. time of assault and time of social activities. The model is extended in order to take account of multiple contacts between person of interest and ‘ victim’. Variables taken into account include probabilities of direct and secondary transfer, along with background DNA from unknown individuals. The logistic regression analysis is Bayesian -for each analysis, 4000 separate simulations were carried out. Quantile assignments enable calculation of a plausible range of probabilities and sensitivity analysis is used to describe the corresponding variation ofLRs that occur when modelled by the Bayesian network. It is noted that there is need for consistent experimental design, and analysis, to facilitate inter-laboratory comparisons. Appropriate recommendations are made. The open-source program written in R-code ALTRaP (Activity Level, Transfer, Recovery and Persistence) enables analysis of complex multiple transfer propositions that are commonplace in cases-work e.g. between those who cohabit. A number of case examples are provided. ALTRaP can be used to replicate the results and can easily be modified to incorporate different sets of data and variables.
Evolution of lower levels of inter-locus sexual conflict inD. melanogasterpopulations under strong selection for rapid development
Authors: Mital Avani , Sarangi Manaswini , Dey Snigdhadip , Joshi Amitabh
Published: February 2021

D. melanogasterlaboratory populations subjected to selection for rapid development and early reproduction have been found to have evolved reduced adult body size and lower levels of inter-locus sexual conflict compared to their ancestral controls. We tested the contribution of a smaller body to the evolution of reduced sexual conflict in these populations, since body size differences are known to affect sexual conflict levels in this species. We cultured larvae from the control populations at high density to obtain flies as small as those from the selected populations. The effect of body size reduction on sexual conflict was asymmetric, with smaller body size resulting in reduced male manipulative ability but not female resistance to mating-induced harm. These results were not due to differences in behavioural patterns of smaller flies, such as differences in overall mating exposure of females to different types of males. We hypothesize that evolution for rapid development and the correlated reduction in body size has resulted in lower male manipulative ability, and sexually antagonistic co-evolution has lowered female resistance to such manipulations. These populations have also evolved incipient reproductive isolation from their controls, likely through sexual conflict (reported earlier), and our results support the view that this is an outcome of strong, directional selection for rapid development.
No evidence for somatosensory attenuation during action observation of self-touch
Authors: Kilteni Konstantina , Engeler Patrick , Boberg Ida , Maurex Linnea , Ehrsson H. Henrik
Published: February 2021

The discovery of mirror neurons in the macaque brain in the 1990s triggered investigations on putative human mirror neurons and their potential functionality. The leading proposed function has been action understanding: accordingly, we understand the actions of others by ‘simulating’ them in our own motor system through a direct matching of the visual information to our own motor programs. Furthermore, it has been proposed that this simulation involves the prediction of the sensory consequences of the observed action, similar to the prediction of the sensory consequences of our executed actions. Here, we tested this proposal by quantifying somatosensory attenuation behaviorally during action observation. Somatosensory attenuation manifests during voluntary action and refers to the perception of self-generated touches as less intense than identical externally generated touches because the self-generated touches are predicted from the motor command. Therefore, we reasoned that if an observer simulates the observed action and, thus, he/she predicts its somatosensory consequences, then he/she should attenuate tactile stimuli simultaneously delivered to his/her corresponding body part. In three separate experiments, we found a systematic attenuation of touches during executed self-touch actions, but we found no evidence for attenuation when such actions were observed. Failure to observe somatosensory attenuation during observation of self-touch is not compatible with the hypothesis that the putative human mirror neuron system automatically simulates the observed action. In contrast, our findings emphasize a sharp distinction between the motor representations of self and others.
Evolution of gene-rich germline restricted chromosomes in black-winged fungus gnats through introgression (Diptera: Sciaridae)
Authors: Hodson Christina N. , Jaron Kamil S. , Gerbi Susan , Ross Laura
Published: February 2021

Germline restricted DNA has evolved in diverse animal taxa, and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline restricted DNA has evolved, especially in flies, in which three diverse families, Chironomidae, Cecidomyiidae, and Sciaridae exhibit germline restricted chromosomes (GRCs). We conducted a genomic analysis of germline restricted chromosomes in the fungus gnatBradysia(Sciara)coprophila(Diptera: Sciaridae), which carries two large germline restricted “L” chromosomes. We sequenced and assembled the genome ofB. coprophila, and used differences in sequence coverage and k-mer frequency between somatic and germ tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs inB. coprophilaare large, gene-rich, and have many genes with paralogs on other chromosomes in the genome. We also found that the GRC genes are extraordinarily divergent from their paralogs, and have sequence similarity to another Dipteran family (Cecidomyiidae) in phylogenetic analyses, suggesting that these chromosomes have arisen in Sciaridae through introgression from a related lineage. These results suggest that the GRCs may have evolved through an ancient hybridization event, raising questions about how this may have occurred, how these chromosomes became restricted to the germline after introgression, and why they were retained over time.
Resting-state brain activity can predict target-independent aptitude in fMRI-neurofeedback training
Authors: Nakano Takashi , Takamura Masahiro , Nishimura Haruki , Machizawa Maro , Ichikawa Naho , Yoshino Atsuo , Okada Go , Okamoto Yasumasa , Yamawaki Shigeto , Yamada Makiko , Suhara Tetsuya , Yoshimoto Junichiro
Published: February 2021

Neurofeedback (NF) aptitude, which refers to an individual’s ability to change its brain activity through NF training, has been reported to vary significantly from person to person. The prediction of individual NF aptitudes is critical in clinical NF applications. In the present study, we extracted the resting-state functional brain connectivity (FC) markers of NF aptitude independent of NF-targeting brain regions. We combined the data in fMRI-NF studies targeting four different brain regions at two independent sites (obtained from 59 healthy adults and six patients with major depressive disorder) to collect the resting-state fMRI data associated with aptitude scores in subsequent fMRI-NF training. We then trained the regression models to predict the individual NF aptitude scores from the resting-state fMRI data using a discovery dataset from one site and identified six resting-state FCs that predicted NF aptitude. Next we validated the prediction model using independent test data from another site. The result showed that the posterior cingulate cortex was the functional hub among the brain regions and formed predictive resting-state FCs, suggesting NF aptitude may be involved in the attentional mode-orientation modulation system’s characteristics in task-free resting-state brain activity.
homeRNA: A self-sampling kit for the collection of peripheral blood and stabilization of RNA
Authors: Haack Amanda J. , Lim Fang Yun , Kennedy Dakota S. , Day John H. , Adams Karen N. , Lee Jing J. , Berthier Erwin , Theberge Ashleigh B.
Published: February 2021

Gene expression analysis (e.g., targeted gene panels, transcriptomics) from whole blood can elucidate mechanisms of immune function and aid in the discovery of biomarkers. Conventional venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developedhomeRNA: a kit for self-collection of peripheral blood (∼0.5 mL) and immediate stabilization of cellular RNA, using the Tasso- SST™ blood collection device with a specially designed stabilizer tube containing RNAlater™. To assess the feasibility ofhomeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 47 participants) where we senthomeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 61/65). Among participants who successfully collected blood, 93% reported no or minimal pain/discomfort using the kit (n = 39/42), and 79% reported very easy/somewhat easy stabilization protocol (n = 33/42). Total RNA yield from the stabilized samples ranged between 0.20 µg and 5.99 µg (mean = 1.51 µg), and all but one RNA Integrity Number (RIN) values were above 7.0 (mean = 8.1), indicating limited RNA degradation. Results from this study demonstrate the self-collection and RNA stabilization of whole blood withhomeRNA by participants themselves, in their own home.
Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels
Authors: Peng Junhui , Svetec Nicolas , Zhao Li
Published: February 2021

Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host-pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis ofDrosophilaprotein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions may play a role in the co-adaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected in evolution, in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and co-adaptation in the adaptive evolution of proteins both at the species and population levels.
Effects of treatment with three antibiotics, vancomycin, neomycin, and AVNM on gut microbiome in C57BL/6 mice
Authors: Ray Pratikshya , Chakraborty Subhayan , Ghosh Arindam , Aich Palok
Published: February 2021

Higher organisms, especially mammals, harbor diverse microbiota in the gut that plays a major role in maintaining health and physiological homeostasis. Perturbation of gut flora helps identifying their roles. Antibiotics are potent perturbing agents of microbiome. Select antibiotics like vancomycin, neomycin, and AVNM (an antibiotic cocktail containing ampicillin, vancomycin, neomycin, and metronidazole) were used to perturb the gut microbiota of C57BL/6 male mice to understand their roles in host immunity and metabolism. The current study revealed that the resulting gut microbial composition was different, and diversity (at the phylum and genus level) was reduced differentially following each antibiotic treatment. Vancomycin treatment caused a significant increase in Verrucomicrobia and Proteobacteria phyla. The treatment with neomycin yielded an increase in the Bacteroidetes phylum, while the treatment with AVNM led to an increase in Proteobacteria phylum with lowest diversity of microbiome in the gut. The current results also revealed that the different antibiotics treatment caused variation in the cecal index, expression of immune genes (TNF-α, IL-10, IFN-γ) in the colon, and short-chain fatty acids (SCFA) level in the blood of mice. A strong correlation was observed for antibiotic-induced differential dysbiosis patterns of gut microbiota and the altered immune and SCFA profile of the host. The outcome of the present study could be clinically important.
Assessing evolutionary and developmental transcriptome dynamics in homologous cell types
Authors: Feregrino Christian , Tschopp Patrick
Published: February 2021

Background

During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built – largely – by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear.

Results

Here, using a paradigm of morphological diversification, the tetrapod limb, and singlecell RNA-sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. We developed a user-friendly bioinformatics workflow to detect gene co-expression modules and test for their conservation across developmental stages and species boundaries. Using mouse limb data as reference, we identified 19 gene co-expression modules with varying tissue or cell type-restricted activities. Testing for co-expression conservation revealed modules with high evolutionary turnover, while others seemed maintained – to different degrees, in module make-up, density or connectivity – over developmental and evolutionary timescales.

Conclusions

We present an approach to identify evolutionary and developmental dynamics in gene co-expression modules during patterning-relevant stages of homologous cell type specification.
Novel gut pathobionts confound results in a widely used mouse model of human inflammatory disease
Authors: Forster Samuel C. , Clare Simon , Beresford-Jones Benjamin S. , Harcourt Katherine , Notley George , Stares Mark , Kumar Nitin , Soderholm Amelia T. , Adoum Anne , Wong Hannah , Morón Bélen , Brandt Cordelia , Dougan Gordon , Adams David J. , Maloy Kevin J. , Pedicord Virginia A. , Lawley Trevor D.
Published: February 2021

The mammalian gut microbiota consists of hundreds of anaerobic bacterial species that shape intestinal homeostasis and influence host immune responses. Although the causal roles of specific human gut bacterial species in health and disease are emerging, the role of indigenous gut bacteria in driving immunophenotypic variability in mouse models of human disease remains poorly understood. We performed a large-scale experiment using 579 laboratory mice designed to identify and validate the causes of disease variability in the widely used dextran sulphate sodium (DSS) mouse model of inflammatory bowel disease. Using microbiome analysis, coupled with machine learning and targeted anaerobic culturing, we identified and isolated the novel gut pathobiont speciesDuncaniella muricoliticaandAlistipes okayasuensisand fulfilled Koch’s postulates in mice to show that each pathobiont exerts dominant effects in the DSS model leading to variable treatment responses. We show these pathobiont species are common, but not ubiquitous, in mouse facilities around the world, raising experimental design opportunities for improved mouse models of human intestinal diseases.
A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
Authors: Staneva Desislava P. , Carloni Roberta , Auchynnikava Tatsiana , Tong Pin , Rappsilber Juri , Jeyaprakash A. Arockia , Matthews Keith R. , Allshire Robin C.
Published: February 2021

Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by ‘writer’ and ‘eraser’ enzymes, respectively. Nucleosomal PTMs are recognised by a variety of ‘reader’ proteins which alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 68 predicted readers, writers and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 63 of them in the parasite’s bloodstream form. ChIP-seq demonstrated that fifteen candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins exhibit a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identified distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET-domain and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcriptional start regions. The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.
High expression of CD38 and MHC class II on CD8+T cells during severe influenza disease reflects bystander activation and trogocytosis
Authors: Jia Xiaoxiao , Chua Brendon Y , Loh Liyen , Koutsakos Marios , Kedzierski Lukasz , Olshanski Moshe , Heath William R , Xu Jianqing , Wang Zhongfang , Kedzierska Katherine
Published: February 2021

Although co-expression of CD38 and HLA-DR on CD8+T cells reflects activation during influenza, SARS-CoV-2, Dengue, Ebola and HIV-1 viral infections, high and prolonged CD38+HLA-DR+expression can be associated with severe and fatal disease outcomes. As the expression of CD38+HLA-DR+is poorly understood, we used mouse models of influenza A/H7N9, A/H3N2 and A/H1N1 infection to investigate the mechanisms underpinning CD38+MHC-II+phenotype on CD8+T-cells. Our analysis of influenza-specific immunodominant DbNP366+CD8+T-cell responses showed that CD38+MHC-II+co-expression was detected on both virus-specific and bystander CD8+T-cells, with increased numbers of both CD38+MHC-II+CD8+T-cell populations observed in the respiratory tract during severe infection. To understand the mechanisms underlying CD38 and MHC-II expression, we also used adoptively-transferred transgenic OT-I CD8+T-cells recognising the ovalbumin-derived KbSIINFEKL epitope and A/H1N1-SIINKEKL infection. Strikingly, we found that OT-I cells adoptively-transferred into MHC-II−/−mice did not display MHC-II after influenza virus infection, suggesting that MHC-II was acquired via trogocytosis in wild-type mice. Additionally, detection of CD19 on CD38+MHC II+OT-I cells further supports that MHC-II was acquired by trogocytosis, at least partially, sourced from B-cells. Our results also revealed that co-expression of CD38+MHC II+on CD8+T-cells was needed for the optimal recall ability following secondary viral challenge. Overall, our study provides evidence that both virus-specific and bystander CD38+MHC-II+CD8+T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38+MHC II+phenotype for CD8+T-cell memory establishment and recall.

Co-expression of CD38 and MHC-II on CD8+T cells is recognized as a classical hallmark of activation during viral infections. High and prolonged CD38+HLA-DR+expression, however, can be associated with severe disease outcomes and the mechanisms are unclear. Using our established influenza wild-type and transgenic mouse models, we determined how disease severity affected the activation of influenza-specific CD38+MHC-II+CD8+T cell responsesin vivoand the antigenic determinants that drive their activation and expansion. Overall, our study provides evidence that both virus-specific and bystander CD38+MHC-II+CD8+T-cells are recruited to the site of infection during severe disease, and that MHC-II expression occurs, at least in part, via trogocytosis from antigen-presenting cells. Our findings also highlight the importance of the CD38+MHC II+phenotype for CD8+T-cell memory establishment and recall.
Elucidating the patterns of seed-to-seedling transmission ofXanthomonas citripv.malvacearum, the causal agent of cotton bacterial blight
Authors: Mijatović Jovana , Severns Paul M. , Kemerait Robert C. , Walcott Ron R. , Kvitko Brian H.
Published: February 2021

Cotton bacterial blight (CBB) was a major disease of cotton in the United States in the early part of the 20thcentury. The recent reemergence of CBB, caused byXanthomonas citripv.malvacearum(Xcm) revealed many gaps in our understanding of this important disease. In this study, we employed a field isolate ofXcmfrom Georgia USA (WT) to generate a non- pathogenic,hrcVmutant lacking a functional Type III Secretion System (T3SS-). We tagged the WT and T3SS- strains with an auto-bioluminescent Tn7reporter and compared colonization patterns of susceptible and resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. Wildtype and T3SS-Xcmstrains colonized cotton cotyledons of resistant and susceptible cotton cultivars. However,Xcmpopulations were significantly higher in susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS-Xcmstrains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission ofXcmmay involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potentialXcmreservoirs for CBB outbreaks.
Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression
Authors: Maulding Nathan D , Seiler Spencer , Pearson Alex , Kreusser Nick , Stuart Josh
Published: February 2021

The SARS-CoV-2 pandemic has challenged humankind’s ability to quickly determine the cascade of health effects caused by a novel infection. Even with the unprecedented speed at which vaccines were developed and introduced into society, identifying therapeutic interventions and drug targets for patients infected with the virus remains important as new strains of the virus may evolve, or future coronaviruses may emerge, that are resistant to current vaccines. The application of transcriptomic RNA sequencing of infected samples may shed new light on the pathways involved in viral mechanisms and host responses. We describe the application of “dual RNA-seq” analysis to consider both the host and pathogen transcriptomes simultaneously, to investigate for the first time theco-regulation of human and SARS-CoV-2 genes. Together with differential expression analysis, we describe the tissue specificity of SARS-CoV-2 expression, an inferred lipopolysaccharide response, and co-regulation ofCXCL’s, SPRR’s, S100’swith SARS-CoV-2 expression. Lipopolysaccharide response pathways in particular offer promise for future therapeutic research and the prospect of subgrouping patients based on chemokine expression that may help explain the vastly different reactions patients have to infection. Taken together these findings illuminate previously unappreciated SARS-CoV-2 expression signatures, identify new therapeutic considerations, and contribute a pipeline for studying multi-transcriptome systems.
Testing for parallel genomic and epigenomic footprints of adaptation to urban life in a passerine bird
Authors: Caizergues Aude E. , Luyer Jeremy Le , Grégoire Arnaud , Szulkin Marta , Senar Juan-Carlos , Charmantier Anne , Perrier Charles
Published: February 2021

Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in Evolutionary Biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.eparallel) or involves mostly non-parallel molecular processes among cities, we analysed three distinct pairs of city and forest Great tit populations across Europe. Results reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in the modulation gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to nervous system, immunity, behaviour, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely non-parallel mechanisms of rapid adaptation in new environments such as urbanized areas.
The lncRNAEPB41L4A-AS1regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression
Authors: Samdal Helle , Hegre Siv Anita , Chawla Konika , Liabakk Nina-Beate , Aas Per Arne , Sporsheim Bjørnar , Sætrom Pål
Published: February 2021

The long non-coding RNA (lncRNA)EPB41L4A-AS1is aberrantly expressed in various cancers and has been reported to be involved in metabolic reprogramming and as a repressor of the Warburg effect. Although the biological relevance ofEPB41L4A-AS1is evident, its functional role seems to vary depending on cell type and state of disease. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we previously identifiedEPB41L4A-AS1to be one of 59 lncRNAs with potential cell cycle functions. Here, we demonstrate thatEPB41L4A-AS1exists as bright foci and regulates gene expression in the nucleus in bothcisandtrans. Specifically, we find thatEPB41L4A-AS1positively regulates its sense overlapping geneEPB41L4Aand influences expression of hundreds of other genes, including genes involved in cell proliferation. Finally, we show thatEPB41L4A-AS1affects cell cycle phase distribution, though these effects vary between cell types.
Sustained Interleukin-1β overexpression exacerbates Tau pathology in a murine tauopathy model via cyclooxygenase-1
Authors: Ghosh Simantini , Shaftel Solomon S. , Kyrkanides Stephanos , Olschowka John A. , O’Banion M. Kerry
Published: February 2021

Pathologic accumulation of abnormally phosphorylated tau in neurofibrillary tangles is a hallmark feature of Alzheimer’s disease and other tauopathies. Interleukin-1β ◻◻◻ −1β◻ is a major proinflammatory cytokine in the central nervous system that has been implicated in the pathogenesis of tauopathies as well as Alzheimer’s disease. To explore the role of chronic IL-1β overexpression in tauopathiesin vivowe used an inducible model of IL-1β overexpression developed in our laboratory. The IL-1β (IL-1) mice bear a transcriptional stop flanked by LoxP elements upstream of a human IL-1β gene. Upon delivery of Cre, the IL-1 transgene is locally activated by excision of the stop sequence. The IL-1 mice were bred to JNPL3 (Tau) mice, which overexpress human tau with the P301L mutation. Expression of IL-1β was induced in the dentate gyrus of 8 to 8.5 month old progeny by stereotaxic injection of FIV-Cre. One and three months later, Tau/IL-1 mice demonstrated 2-4 fold increases in phospho-tau and glial activation. To attenuate IL-1β mediated inflammation, we reduced PGE2production via pharmacological inhibition of cyclooxygenase-1 (COX-1) with SC560 in Tau/IL-1 mice, and observed significant reductions in phospho-tau pathology and microglial activation. Further, we found upregulation in active forms of p38MAPK, which was significantly reduced in mice receiving SC560 treatment. Our results demonstrate that IL-1β has a direct exacerbating effect on tau pathologyin vivo, and inhibiting COX-1 can reverse this. COX-1 inhibition can therefore serve as a valuable therapeutic strategy for tauopathies with an advanced inflammatory component.