bluuebunny/crossref_metadata_2025 huggingface dataset:
Markers of brain and endothelial Injury and inflammation are acutely and sex specifically regulated in SARS-CoV-2 infection
Authors: Savarraj Jude , Park Eun S. , Copo Gabriela , Hinds Sarah , Morales Diego , Ahnstedt Hilda , Paz Atzhiry , Assing Andres , Juneja Shivanki , Kim Eunhee , Cho Sung-min , Gusdon Aaron , Dash Pramod , McCullough Louise , Choi H Alex
Published: May 2021

Objective

To investigate brain injury markers (BIM), endothelial injury markers (EIM) and cytokine/chemokine (CC) markers of systemic inflammation in coronavirus disease 2019 (COVID-19) and across sex.

Methods

Plasma samples from 57 subjects at <48 hours of COVID-19 hospitalization, 14 subjects at 3 months of COVID-19 hospitalization and 20 matched controls were interrogated for the levels of six BIMs - including GFAP, S100B, Syndecan-1, UCHLI, MAP2 and NSE, two EIMs – including sICAM1 and sVCAM1 and thirty-eight CCs. Statistical and bioinformatics methods were used to measure differences in the marker profiles across (a) COVID-19 vs controls and (b) men vs women.

Results

Three BIMs: MAP2, NSE and S100B, two EIMs: sICAM1 and sVCAM1 and seven CCs: GRO IL10, sCD40L, IP10, IL1Ra, MCP1 and TNFα were significantly (p<0.05) elevated in the COVID-19 cohort compared to controls. Two CCs: MDC and MIP1α were significantly lower in the COVID-19 cohort. Bioinformatics analysis reveal a stronger positive association between BIM/CC/EIMs in the COVID-19 cohort. Analysis across sex revealed that several BIMs and CCs including NSE, IL10, IL15 and IL8 were significantly (p<0.05) higher in men compared to women. Men also expressed a more robust BIM/ EIM/CC association profile compared to women. At 3 months, BIMs and CCs were not significantly different in the COVID-19 cohort compared to controls.

Conclusion

The acute elevation of BIMs, CCs, and EIMs and the robust associations among them at COVID-19 hospitalization suggest that brain injury is mediated by endotheliopathy and inflammation. Higher BIM and inflammatory markers in men additionally suggest that men are more susceptible to the risk compared to women.
Spread of endemic SARS-CoV-2 lineages in Russia
Authors: Klink Galya V. , Safina Ksenia R. , Garushyants Sofya K. , Moldovan Mikhail , Nabieva Elena ,   The CoRGI (Coronavirus Russian Genetic Initiative) Consortium, Komissarov Andrey B. , Lioznov Dmitry , Bazykin Georgii A
Published: May 2021

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in Russia before January 2021. Instead, since summer 2020, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). In February-March 2021, these lineages reached frequencies of 26.9% (95% C.I.: 23.1%-31.1%) and 32.8% (95% C.I.28.6%-37.2%) respectively in Russia. Their frequency has increased in different parts of Russia. Together with the fact that these lineages carry several spike mutations of interest, this suggests that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1, although there is no direct data on change in transmissibility. Comparison of frequency dynamics of lineages carrying subsets of characteristic mutations of B.1.1.317 and B.1.1.397+ suggests that, if indeed some of these mutations affect transmissibility, the transmission advantage of B.1.1.317 may be conferred by the (S:D138Y+S:S477N+S:A845S) combination; while the advantage of B.1.1.397+ may be conferred by the S:M153T change. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, and two lineages prospectively named B.1.1.v1 and B.1.1.v2, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.v1 and B.1.1.v2, 15.2% (95% C.I.: 7.6%-28.2%). The combinations of mutations observed in B.1.1.317, B.1.1.397+, AT.1, B.1.1.v1 and B.1.1.v2 together with frequency increase of these lineages make them candidate variants of interest.
Predictors for participation in DNA self-sampling of childhood cancer survivors in Switzerland
Authors: Waespe Nicolas , Strebel Sven , Marino Denis , Mattiello Veneranda , Muet Fanny , Nava Tiago , Schindera Christina , Belle Fabien N. , Mader Luzius , Spoerri Adrian , Kuehni Claudia E. , Ansari Marc
Published: May 2021

Research on germline genetic variants relies on a sufficient number of eligible participants which is difficult to achieve for rare diseases such as childhood cancer. With self-collection kits using saliva or buccal swabs, participants can contribute genetic samples conveniently from their home. We identified determinants of participation in DNA self-collection in this cross-sectional study.

We invited 928 childhood cancer survivors in Switzerland with a median age of 26.5 years (interquartile range 18.8-36.5), of which 463 (50%) participated. Foreign nationality (odds ratio [OR] 0.5, 95%-confidence interval [CI] 0.4-0.7), survivors aged 30-39 years at study versus other age groups (OR 0.5, CI 0.4-0.8), and those with a known cancer predisposition syndrome (OR 0.5, CI 0.3-1.0) participated less. Survivors with a second primary neoplasm (OR 1.9, CI 1.0-3.8) or those living in a French or Italian speaking region (OR 1.3, 1.0-1.8) tended to participate more.

We showed that half of survivors participate in germline DNA self-sampling relying completely on mailing of sample kits. Foreign nationality, age 30-39 years, and cancer predisposition syndromes were associated with less participation. More targeted recruitment strategies may be advocated for these subgroups. To increase participation in DNA self-sampling, understanding and perceptions of survivors need to be better understood.
Sex Differences in Functional Topography of Association Networks
Authors: Shanmugan Sheila , Seidlitz Jakob , Cui Zaixu , Adebimpe Azeez , Bassett Danielle S. , Bertolero Maxwell A. , Davatzikos Christos , Fair Damien A. , Gur Raquel E. , Gur Ruben C. , Larsen Bart , Li Hongming , Pines Adam , Raznahan Armin , Roalf David R. , Shinohara Russell T. , Vogel Jacob , Wolf Daniel H. , Fan Yong , Alexander-Bloch Aaron , Satterthwaite Theodore D.
Published: May 2021

Prior work has shown that there is substantial interindividual variation in the spatial distribution of functional networks across the cerebral cortex, orfunctional topography. However, it remains unknown whether there are sex differences in the topography of individualized networks in youth. Here we leveraged an advanced machine learning method (sparsity-regularized nonnegative matrix factorization) to define individualized functional networks in 693 youth (ages 8-23 years) who underwent functional magnetic resonance imaging as part of the Philadelphia Neurodevelopmental Cohort. Multivariate pattern analysis using support vector machines classified participant sex based on functional topography with 83% accuracy (p<0.0001). Brain regions most effective in classifying participant sex belonged to association networks, including the ventral attention and default mode networks. Mass-univariate analyses using generalized additive models with penalized splines provided convergent results. Comparative analysis using transcriptomic data from the Allen Human Brain Atlas revealed that sex differences in multivariate patterns of functional topography correlated with the expression of genes on the X-chromosome. These results identify normative developmental sex differences in the functional topography of association networks and highlight the role of sex as a biological variable in shaping brain development in youth.

SIGNIFICANCE STATEMENT

We identify normative developmental sex differences in the functional topography of personalized association networks including the ventral attention network and default mode network. Furthermore, chromosomal enrichment analyses revealed that sex differences in multivariate patterns of functional topography were spatially coupled to the expression of X-linked genes as well as astrocytic and excitatory neuronal cell-type signatures. These results highlight the role of sex as a biological variable in shaping functional brain development in youth.
Neural Activation in the Olfactory Epithelium of the East African Cichlid (Haplochromis chilotes) in Response to Odorant Exposure
Authors: Kawamura Riki , Nikaido Masato
Published: May 2021

Fishes use olfaction to gain various information vital for survival and communication. To understand biodiversity in fishes, it is important to identify what receptors individual fish use to detect specific chemical compounds. However, studies of fish olfactory receptors and their ligands are still limited to a few model organisms represented primarily by zebrafish. Here, we tested the neural activation of olfactory sensory neurons (OSNs) in East African cichlids, the most diversified teleost lineage, by in situ hybridization with a c-fos riboprobe. We confirmed that microvillous neurons contributed the most to the detection of amino acids, as in other fishes. Conversely, we found that ciliated neurons contributed the most to detection of conjugated steroids, known as pheromone candidates. We also found that V2Rs, the major expressed receptor in microvillous neurons exhibited differential responsiveness to amino acids, and further suggested that the cichlid-specific duplication of V2R led to ligand differentiation in cichlids by demonstrating a differential response to arginine. Finally, we established a nonlethal method to collect cichlid urine and showed how various OSNs, including V1R+ neurons, respond to male urine. This study provides an experimental basis for understanding how cichlids encode natural odors and illuminates how olfaction has contributed to the diversification of cichlids by combining with phylogenetic studies of olfactory receptors gene evolutions.
A technical pipeline for screening microbial communities as a function of substrate specificity through single cell fluorescent imaging
Authors: Leivers Shaun , Lagos Leidy , La Rosa Sabina Leanti , Westereng Bjørge
Published: May 2021

The study of specific glycan uptake and metabolism has been shown to be an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards target. In this study, we successfully used the fluorescent label 2-aminobenzamide (2-AB), most commonly employed for enhancing the detection of protein anchored glycans, to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, were able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it was possible to comprehensively track the metabolism of the labelled glycans in both supernatants and at a single cell level. We envisage this combination of complimentary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities.

IMPORTANCE

Information on how bacterial consortia utilize polysaccharides at strain level, whilst progressing rapidly in recent years still lacks a suitable way to study the vast range of ornamentations and structural motifs found in the natural glycans we consume in everyday life. As multi-omic approaches commonly require complex and costly analysis, a screening platform, as described in our work, could be seen as both a complementary and essential new tool in the understanding of microbial polysaccharide metabolism. Our study demonstrates a fast and efficient glycan labelling technique composed of several integrated procedures and advanced analytical methodologies. Chromatography and mass spectrometry are applied in the tracking of metabolized labelled glycans whilst microscopy and flow cytometry are used in the visualization of labelled bacteria at a single cell level.
The globular C1q receptor is required for epidermal growth factor receptor signaling during Candida albicans infection
Authors: Phan Quynh T. , Lin Jianfeng , Solis Norma V. , Eng Michael , Swidergall Marc , Wang Feng , Li Shan , Gaffen Sarah L. , Chou Tsui-Fen , Filler Scott G.
Published: May 2021

During oropharyngeal candidiasis, Candida albicans activates the epidermal growth factor receptor (EGFR), which induces oral epithelial cells to both endocytose the fungus and synthesize proinflammatory mediators that orchestrate the host immune response. To elucidate the signaling pathways that are stimulated when C. albicans interacts with EGFR, we analyzed the proteins that associate with EGFR when C. albicans infects human oral epithelial cells. We identified 1214 proteins that were associated with EGFR in C. albicans-infected cells. We investigated the function of seven of these proteins that either showed increased association with EGFR in response to C. albicans or that mediated the interaction of other microbial pathogens with epithelial cells. Among these proteins, EGFR was found to associate with WW domain-binding protein 2, toll-interacting protein, interferon-induced transmembrane protein 3, and the globular C1q receptor (gC1qR) in viable epithelial cells. Each of these proteins was required for maximal endocytosis of C. albicans and they all regulated fungal-induced production of IL-1β and/or IL-8, either positively or negatively. gC1qR functioned as a key coreceptor with EGFR. Interacting with the C. albicans Als3 invasin, gC1qR was required for the fungus to stimulate both EGFR and the ephrin type-A receptor 2. The combination of gC1qR and EGFR was necessary for maximal endocytosis of C. albicans and secretion of IL-1β, IL-8, and GM-CSF. Thus, this work provides an atlas of proteins that associate with EGFR and identifies several that play a central role in the response of human oral epithelial cells to C. albicans infection.

IMPORTANCE

Oral epithelial cells play a key role in the pathogenesis of oropharyngeal candidiasis. In addition to being target host cells for C. albicans adherence and invasion, they secrete proinflammatory cytokines and chemokines that recruit T cells and activated phagocytes to foci of infection. It is known that C. albicans activates EGFR on oral epithelial cells, which induces these cells to endocytose the organism and stimulates them to secrete proinflammatory mediators. To elucidate the EGFR signaling pathways that govern these responses, we analyzed the epithelial cell proteins that associate with EGFR in C. albicans-infected epithelial cells. We identified four proteins that physically associate with EGFR and that regulate different aspects of the epithelial response to C. albicans. One of these is gC1qR, which is required for C. albicans to activate EGFR, induce endocytosis, and stimulate the secretion of proinflammatory mediators, indicating that gC1qR functions as a key co-receptor with EGFR.
Recovery from the COVID-19 pandemic by mass vaccination: emergent lessons from the United States and India
Authors: Michael Edwin , Newcomb Ken , Mubayi Anuj , Mahmood Imran
Published: May 2021

The advent of vaccinations has heightened global optimism that the end of the SARS-CoV-2 pandemic could be in sight. However, concerns, including the impact of variations in the rates of vaccination between countries, raise questions about the use of mass vaccination for accomplishing a quick recovery from the contagion. Here, we used a SEIR-based model calibrated to data on the pandemic and vaccinations reported for the United States (US) and India to gain strategic insights into using mass vaccinations for ending COVID-19. We estimate that while up to 65% of the US population is already immune to the virus due to the recent rapid mass vaccinations carried out, only 13% of the Indian population may be immune currently owing to a slow rate of vaccination and the effect of a stricter lockdown imposed to curb the first wave of the pandemic. We project that due to the higher immune to susceptible ratio already achieved in the US, the pandemic will only decline if the present rates of vaccinations and social mitigations are continued and remain effective. By contrast, the recent loosening of social measures coupled with a slow rate of vaccination is the chief reason for the virus resurgence in India, with only immediate lockdowns coupled with ramping up of vaccinations providing the means to control the present wave. These results highlight that using mass vaccination to achieve a speedy recovery from the SARS-CoV-2 pandemic will depend crucially on the ability to carry out national vaccinations as rapidly as possible.
Epigenetic Patterns in a Complete Human Genome
Authors: Gershman Ariel , Sauria Michael E.G. , Hook Paul W. , Hoyt Savannah J. , Razaghi Roham , Koren Sergey , Altemose Nicolas , Caldas Gina V. , Vollger Mitchell R. , Logsdon Glennis A. , Rhie Arang , Eichler Evan E. , Schatz Michael C. , O’Neill Rachel J. , Phillippy Adam M. , Miga Karen H. , Timp Winston
Published: May 2021

The completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existing epigenetic studies omit unassembled and unmappable genomic regions (e.g. centromeres, pericentromeres, acrocentric chromosome arms, subtelomeres, segmental duplications, tandem repeats). Leveraging the new assembly, we were able to measure enrichment of epigenetic marks with short reads using k-mer assisted mapping methods. This granted array-level enrichment information to characterize the epigenetic regulation of these satellite repeats. Using nanopore sequencing data, we generated base level maps of the most complete human methylome ever produced. We examined methylation patterns in satellite DNA and revealed organized patterns of methylation along individual molecules. When exploring the centromeric epigenome, we discovered a distinctive dip in centromere methylation consistent with active sites of kinetochore assembly. Through long-read chromatin accessibility measurements (nanoNOMe) paired to CUT&RUN data, we found the hypomethylated region was extremely inaccessible and paired to CENP-A/B binding. With long-reads we interrogated allele-specific, longrange epigenetic patterns in complex macro-satellite arrays such as those involved in X chromosome inactivation. Using the single molecule measurements we can clustered reads based on methylation status alone distinguishing epigenetically heterogeneous and homogeneous areas. The analysis provides a framework to investigate the most elusive regions of the human genome, applying both long and short-read technology to grant new insights into epigenetic regulation.
Quadratic and adaptive computations yield an efficient representation of song in Drosophila auditory receptor neurons
Authors: Clemens Jan , Murthy Mala
Published: May 2021

Sensory neurons encode information using multiple nonlinear and dynamical transformations. For instance, auditory receptor neurons in Drosophila adapt to the mean and the intensity of the stimulus, change their frequency tuning with sound intensity, and employ a quadratic nonlinearity. While these computations are considered advantageous in isolation, their combination can lead to a highly ambiguous and complex code that is hard to decode. Combining electrophysiological recordings and computational modelling, we investigate how the different computations found in auditory receptor neurons in Drosophila combine to encode behaviorally-relevant acoustic signals like the courtship song.

The computational model consists of a quadratic filter followed by a divisive normalization stage and reproduces population neural responses to artificial and natural sounds. For general classes of sounds, like band-limited noise, the representation resulting from these highly nonlinear computations is highly ambiguous and does not allow for a recovery of information about the frequency content and amplitude pattern. However, for courtship song, the code is simple and efficient: The quadratic filter improves the representation of the song envelope while preserving information about the song’s fine structure across intensities. Divisive normalization renders the presentation of the song envelope robust to the relatively slow fluctuations in intensity that arise during social interactions, while preserving information about the species-specific fast fluctuations of the envelope.

Overall, we demonstrate how a sensory system can benefit from adaptive and nonlinear computations while minimizing concomitant costs arising from ambiguity and complexity of readouts by adapting the code for behaviorally-relevant signals.
TIGER: The gene expression regulatory variation landscape of human pancreatic islets
Authors: Alonso Lorena , Piron Anthony , Morán Ignasi , Guindo-Martínez Marta , Bonàs-Guarch Sílvia , Atla Goutham , Miguel-Escalada Irene , Royo Romina , Puiggròs Montserrat , Garcia-Hurtado Xavier , Suleiman Mara , Marselli Lorella , Esguerra Jonathan L.S. , Turatsinze Jean-Valéry , Torres Jason M. , Nylander Vibe , Chen Ji , Eliasson Lena , Defrance Matthieu , Amela Ramon ,   MAGIC, Mulder Hindrik , Gloyn Anna L. , Groop Leif , Marchetti Piero , Eizirik Decio L. , Ferrer Jorge , Mercader Josep M. , Cnop Miriam , Torrents David
Published: May 2021

GWAS have identified more than 700 genetic signals associated with type 2 diabetes (T2D). To gain insight into the underlying molecular mechanisms, we created the Translational human pancreatic Islet Genotype tissue-Expression Resource (TIGER), aggregating >500 human islet RNA-seq and genotyping datasets. We imputed genotypes using 4 reference panels and meta-analyzed cohorts to improve coverage of expression quantitative trait loci (eQTL) and developed a method to combine allele-specific expression across samples (cASE). We identified >1 million islet eQTLs (56% novel), of which 53 colocalize with T2D signals (60% novel). Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identified 8 novel cASE colocalizations, among which an SLC30A8 T2D associated variant. We make all the data available through the open-access TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translate this into therapeutic insight and precision medicine for T2D.
Desmin intermediate filaments and tubulin detyrosination stabilize growing microtubules in the cardiomyocyte
Authors: Salomon Alexander K. , Phyo Sai Aung , Okami Naima , Heffler Julie , Robison Patrick , Bogush Alexey I. , Prosser Benjamin L.
Published: May 2021

In heart failure, an increased abundance of post-translationally detyrosinated microtubules stiffens the cardiomyocyte and impedes its contractile function. Detyrosination promotes interactions between microtubules, desmin intermediate filaments and the sarcomere to increase cytoskeletal stiffness, yet the mechanism by which this occurs is unknown. We hypothesized that detyrosination may regulate the growth and shrinkage of dynamic microtubules to facilitate interactions with desmin and the sarcomere. Through a combination of biochemical assays and direct observation of growing microtubule plus-ends in adult cardiomyocytes, we find that desmin is required to stabilize growing microtubules at the sarcomere Z-disk, where desmin also rescue shrinking microtubules from continued depolymerization. Further, reducing detyrosination (tyrosination) promotes frequent depolymerization and inefficient growth of microtubules. This is concomitant with tyrosination promoting the interaction of microtubules with the depolymerizing protein complex of end-binding protein 1 (EB1) and CAP-Gly domain containing linker protein 1 (CLIP1/CLIP170). The futile growth of tyrosinated microtubules reduces their opportunity for stabilizing interactions at the Z-disk, coincident with tyrosination globally reducing microtubule lifetimes and stability. These data provide a model for how intermediate filaments and tubulin detyrosination establish long-lived and physically reinforced microtubules in the cardiomyocyte, and inform on the mechanism of action for therapies that target microtubules for the treatment of cardiac disease.
Engineering improved Cas13 effectors for targeted post-transcriptional regulation of gene expression
Authors: Charles Emeric J , Kim Shin Eui , Knott Gavin J. , Smock Dylan , Doudna Jennifer , Savage David F.
Published: May 2021

Cas13 is a family of unique RNA-targeting CRISPR-Cas effectors, making it an appealing tool for probing and perturbing RNA function. However only a few Cas13 homologs have been shown to mediate robust RNA targeting in human cells, suggesting that unknown elements may be limiting their efficacy. Furthermore, many Cas13 enzymes show high degrees of toxicity upon targeting and have not been shown to mediate specific knockdown in other cell types such as E. coli. Here, we show that catalytically inactive Cas13 enzymes can be repurposed for efficient translational repression in bacteria with no associated growth defects. To achieve this advance, we carried out a directed evolution screen to engineer functional Cas13a variants, and identified a number of stabilizing mutations, which enabled efficient post transcriptional knockdown of gene expression. In vitro characterization of the resulting engineered Lbu Cas13a mutant, termed eLbu, revealed both stabilization and altered cleavage kinetics. Finally, we show that eLbu can be used for efficient exon skipping in human cells. This work represents the first demonstration of targeted translational repression in E. coli using a CRISPR enzyme, as well as the first directed evolution of a Cas13 enzyme. Such a platform could allow for engineering other aspects of this protein family to obtain more robust RNA targeting tools.
Single-cell phenotypic characteristics of phenotypic resistance under recurring antibiotic exposure inEscherichia coli
Authors: Kollerová Silvia , Jouvet Lionel , Smelková Julia , Zunk-Parras Sara , Rodríguez-Rojas Alexandro , Steiner Ulrich K.
Published: May 2021

Despite increasing interest, non-heritable, phenotypic drug resistance, such as tolerance and persistence towards antibiotics, remains less characterized compared to genetic resistance. Non-heritable drug resistance challenges antibiotic treatment and have implications towards heritable resistance evolution. Phenotypically resistant cells have commonly been characterized as growth arrested cells prior and during antibiotic application that quickly resume growth post-application. Here, we add novel combinations of characteristics of phenotypic resistantE. colisingle cells—that are of particular interest towards genetically fixed resistance—, and contrast those to susceptible cells of the isoclonal initial population by exposure to different levels of recurrent antibiotic. We find that phenotypic resistant cells reduced their growth rate by about 50% compared to growth rates prior to antibiotic exposure, but cells do not go into near growth arrest. The growth reduction is induced by antibiotic exposure and not caused by a stochastic switch or predetermined state as frequently described. Cells exhibiting constant intermediate growth survived best under antibiotic exposure and, contrary to expectations, selection did not primarily act on fast growing cells. Our findings support diverse modes of phenotypic resistance, and we revealed resistant cell characteristics that supports acclaims of an underappreciated role of phenotypic resistant cells towards resistance evolution.
Environment, rather thanHematodiniumparasitization, determines collateral disease contraction in a crustacean host
Authors: Davies Charlotte E. , Thomas Jessica E. , Malkin Sophie H. , Batista Frederico M. , Rowley Andrew F. , Coates Christopher J.
Published: May 2021

Host, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genusHematodiniumis detrimental to crustaceans globally – considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune-suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), whereHematodiniumsp. is endemic, to determine the extent of collateral infections across two distinct environments (open water, semi- closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162Hematodinium-positive crabs and size/sex-matched these to 162Hematodinium-free crabs out of 1,191 analysed. Crabs were interrogated for additional disease-causing agents; haplosporidians, microsporidians, mikrocytids,Vibriospp., fungi,Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity or composition of collateral infections betweenHematodinium-positive andHematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity towardHematodiniumin the presence or absence of other pathogens. We contendHematodiniumsp. is an immune-evader rather than immune-suppressor, which suggests an evolutionary drive toward latency in this environmentally plastic host.
Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals
Authors: Planas Delphine , Veyer David , Baidaliuk Artem , Staropoli Isabelle , Guivel-Benhassine Florence , Rajah Maaran Michael , Planchais Cyril , Porrot Françoise , Robillard Nicolas , Puech Julien , Prot Matthieu , Gallais Floriane , Gantner Pierre , Velay Aurélie , Le Guen Julien , Kassis-Chikhani Najibi , Edriss Dhiaeddine , Belec Laurent , Seve Aymeric , Péré Hélène , Courtellemont Laura , Hocqueloux Laurent , Fafi-Kremer Samira , Prazuck Thierry , Mouquet Hugo , Bruel Timothée , Simon-Lorière Etienne , Rey Felix A. , Schwartz Olivier
Published: May 2021

The SARS-CoV-2 B.1.617 lineage emerged in October 2020 in India1–6. It has since then become dominant in some indian regions and further spread to many countries. The lineage includes three main subtypes (B1.617.1, B.1617.2 and B.1.617.3), which harbour diverse Spike mutations in the N-terminal domain (NTD) and the receptor binding domain (RBD) which may increase their immune evasion potential. B.1.617.2 is believed to spread faster than the other versions. Here, we isolated infectious B.1.617.2 from a traveller returning from India. We examined its sensitivity to monoclonal antibodies (mAbs) and to antibodies present in sera from COVID-19 convalescent individuals or vaccine recipients, in comparison to other viral lineages. B.1.617.2 was resistant to neutralization by some anti-NTD and anti-RBD mAbs, including Bamlanivimab, which were impaired in binding to the B.1.617.2 Spike. Sera from convalescent patients collected up to 12 months post symptoms and from Pfizer Comirnaty vaccine recipients were 3 to 6 fold less potent against B.1.617.2, relative to B.1.1.7. Sera from individuals having received one dose of AstraZeneca Vaxzevria barely inhibited B.1.617.2. Thus, B.1.617.2 spread is associated with an escape to antibodies targeting non-RBD and RBD Spike epitopes.
Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain
Authors: Stoeber Jonathan , Williams Jonathan K. , Moghe Prabhas V. , Baum Jean
Published: May 2021

α-Synuclein (αS) is an intrinsically disordered protein (IDP) that aggregates into amyloid fibrils during the progression of Parkinson’s Disease and other synucleinopathies. The N-terminal domain (residues 1-60) is now understood to play a critical role in the initial nucleation of aggregation, as well as a pivotal role in the monomer-fibril interaction underlying amyloid seeding. Here we report on the interaction between αS and the polyphenol tannic acid (TA), where a combination of solution NMR, atomic force microscopy (AFM), and ThT assays have identified that TA targets the αS N-terminal domain to inhibit amyloid fibril formation in a pH dependent manner. This work highlights the importance of targeting the N-terminus of αS to arrest fibril formation, and suggests the importance of including polyphenolic moieties in future amyloid inhibitors.
Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau
Authors: Ren Ze , Zhang Cheng , Li Xia , Ma Kang , Cui Baoshan
Published: May 2021

Thermokarst lakes are forming from permafrost thaw and severely affected by accelerating climate change. Sediment and water in these lakes are distinct habitats but closely connected. However, our understanding of the differences and linkages between sediment and water in thermokarst lakes remain largely unknow, especially from the perspective of community assembly mechanisms. Here, we examined bacterial communities in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau. Bacterial taxa were divided to abundant and rare according to their relative abundance, and the Sorensen dissimilarity (βsor) was partitioned into turnover (βturn) and nestedness (βnest). The whole bacterial communities as well as the abundant and rare subcommunities differed substantially between sediment and water, in terms of taxonomical composition, α-diversity, and β-diversity. Sediment had significantly lower α-diversity indexes but higher β-diversity than water. Abundant taxa had significantly higher relative abundances but lower α-diversity and β-diversity than rare taxa. Moreover, bacterial communities are predominantly governed by strong turnover processes (βturn/βsorratio of 0.925). Abundant subcommunities were significantly lower in βturn/βsorratio compared to rare subcommunities. Bacterial communities in sediment had a significantly higher βturn/βsorratio than in water. The results suggest that the bacterial communities of thermokarst lakes, especially rare subcommunities or particularly in sediment, might be strongly structured by environmental filtering and geographical isolation, leading to compositional distinct. This integral study increased our current knowledge of thermokarst lakes, enhancing our understanding of the community assembly rules and ecosystem structures and processes of these rapid changing and vulnerable ecosystems.
Distinct REV-ERBα Conformational State Predicted by GaMD Simulations Leads to the Structure-Based Discovery of Novel REV-ERBα Antagonist
Authors: Hegazy Lamees , Valfort Aurore-Cecile , Burris Thomas P. , Elgendy Bahaa
Published: May 2021

REV-ERBα is a nuclear hormone receptor that plays important role in the regulation of many physiological processes such as circadian clock regulation, inflammation, and metabolism. Despite its importance, few chemical tools are available to study this receptor. In addition, there is no available X-ray crystal structures of REV-ERB bound with synthetic ligands, hampering the development of targeted therapeutics. SR8278 is the only identified synthetic antagonist of REV-ERB. We have performed Gaussian accelerated molecular dynamics (GaMD) simulations to sample the binding pathway of SR8278 and associated conformational changes to REV-ERBα. The simulations revealed a novel and more energetically favorable conformational state than the starting conformation. The new conformation allows ligand binding to the orthosteric binding site in a specific orientation. This state is reached after a tryptophan (Trp436) rotameric switch coupled with H3-H6 distance change. We used the newly identified GaMD conformational state in structure-based virtual screening of one million compounds library which led to the identification of novel REV-ERBα antagonist. This study is the first that demonstrates a synthetic ligand binding pathway to REV-ERBα, which provided important insights into the REV-ERBα functional mechanism and lead to the discovery of novel REV-ERBα antagonists. This study further emphasizes the power of computational chemistry methods in advancing drug discovery research.
Age and infectious dose significantly affect disease progression after RHDV2 infection in naïve domestic rabbits
Authors: Hall Robyn N. , King Tegan , O’Connor Tiffany , Read Andrew J. , Arrow Jane , Trought Katherine , Duckworth Janine , Piper Melissa , Strive Tanja
Published: May 2021

Rabbit haemorrhagic disease virus 2 (RHDV2 or GI.2, referring to any virus with lagovirus GI.2 structural genes) is a recently emerged calicivirus that causes generalised hepatic necrosis and disseminated intravascular coagulation leading to death in susceptible lagomorphs (rabbits and hares). Previous studies investigating the virulence of RHDV2 have reported conflicting results, with case fatality rates ranging from 0% to 100% even within a single study. Lagoviruses are of particular importance in Australia and New Zealand where they are used as biocontrol agents to manage wild rabbit populations; wild rabbits threaten over 300 native species and result in economic impacts in excess of $200 million AUD to Australian agricultural industries. It is critically important that any pest control method is both highly effective (i.e., virulent, in the context of viral biocontrols) and has minimal animal welfare impacts. To determine whether RHDV2 might be a suitable candidate biocontrol agent, we investigated the virulence and disease progression of a naturally occurring Australian recombinant RHDV2 in both 5-week-old and 11-week-old New Zealand White laboratory rabbits after either high or low dose oral infection. Objective measures of disease progression were recorded through continuous body temperature monitoring collars, continuous activity monitors, and twice daily observations. We observed a 100% case fatality rate in both infected kittens and adult rabbits after either high dose or low dose infection. Clinical signs of disease, such as pyrexia, weight loss, and reduced activity, were evident in the late stages of infection. Clinical disease, i.e., welfare impacts, were limited to the period after the onset of pyrexia, lasting on average 12 hours and increasing in severity as disease progressed. These findings confirm the high virulence of this RHDV2 variant in naïve rabbits. While age and infectious dose significantly affected disease progression, the case fatality rate was consistently 100% under all conditions tested.
The Hox gene Antennapedia regulates wing development through 20-hydroxyecdysone in insect
Authors: Fang Chunyan , Xin Yaqun , Sun Tao , Monteiro Antónia , Ye Zhanfeng , Dai Fangyin , Lu Cheng , Tong Xiaoling
Published: May 2021

A long-standing view in the field of evo-devo is that insect forewings develop without any Hox gene input. The Hox gene Antennapedia (Antp), despite being expressed in the thoracic segments of insects, has no effect on wing development. This view has been obtained from studies in two main model species, Drosophila and Tribolium. Here, we show that partial loss of function of Antp resulted in reduced and malformed adult wings in Bombyx, Drosophila, and Tribolium. Antp mediates wing growth in Bombyx by directly regulating the ecdysteriod biosynthesis enzyme gene (shade) in the wing tissue, which leads to local production of the growth hormone 20E. In turn, 20E signaling also up-regulates Antp. Additional targets of Antp are wing cuticular protein genes CPG24, CPH28, and CPG9, essential for wing development. We propose, thus, that insect wing development occurs in an Antp-dependent manner.
Notch controls the cell cycle to define leader versus follower identities during collective cell migration
Authors: Alhashem Zain , Feldner-Busztin Dylan , Revell Christopher , Portillo Macarena Alvarez-Garcillan , Richardson Joanna , Rocha Manuel , Gauert Anton , Corbeaux Tatianna , Prince Victoria E , Bentley Katie , Linker Claudia
Published: May 2021

Coordination of cell proliferation and migration is fundamental for life, and its dysregulation has catastrophic consequences, as cancer. How cell cycle progression affects migration, and vice-versa, remains largely unknown. We address these questions by combining in silico modelling and in vivo experimentation in the zebrafish Trunk Neural Crest (TNC). TNC migrate collectively, forming chains with a leader cell directing the movement of trailing followers. We show that the acquisition of migratory identity is autonomously controlled by Notch signalling in TNC. High Notch activity defines leaders, while low Notch determines followers. Moreover, cell cycle progression is required for TNC migration and is regulated by Notch. Cells with low Notch activity stay longer in G1 and become followers, while leaders with high Notch activity quickly undergo G1/S transition and remain in S-phase longer. We propose that migratory behaviours are defined through the interaction of Notch signalling and cell cycle progression.
Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction
Authors: Turzo SM Bargeen Alam , Seffernick Justin T. , Rolland Amber D. , Donor Micah T. , Heinze Sten , Prell James S. , Wysocki Vicki , Lindert Steffen
Published: May 2021

Among a wide variety of mass spectrometry (MS) methodologies available for structural characterizations of proteins, ion mobility (IM) provides structural information about protein shape and size in the form of an orientationally averaged collision cross-section (CCS). While IM data have been predominantly employed for the structural assessment of protein complexes, CCS data from IM experiments have not yet been used to predict tertiary structure from sequence. Here, we are showing that IM data can significantly improve protein structure determination using the modeling suite Rosetta. The Rosetta Projection Approximation using Rough Circular Shapes (PARCS) algorithm was developed that allows for fast and accurate prediction of CCS from structure. Following successful rigorous testing for accuracy, speed, and convergence of PARCS, an integrative modelling approach was developed in Rosetta to use CCS data from IM experiments. Using this method, we predicted protein structures from sequence for a benchmark set of 23 proteins. When using IM data, the predicted structure improved or remained unchanged for all 23 proteins, compared to the predicted models in the absence of CCS data. For 15/23 proteins, the RMSD (root-mean-square deviation) of the predicted model was less than 5.50 Å, compared to only 10/23 without IM data. We also developed a confidence metric that successfully identified near-native models in the absence of a native structure. These results demonstrate the ability of IM data inde novostructure determination.
MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula
Authors: Carrère Sébastien , Verdier Jérôme , Gamas Pascal
Published: May 2021

Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs.

Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers.

Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.
Anin vivoapproach to characterize novel variants associated with musculoskeletal disorders
Authors: McAdow Jennifer , Yang Shuo , Ou Tiffany , Huang Gary , Dobbs Matthew B. , Gurnett Christina A. , Johnson Aaron N.
Published: May 2021

Nemaline Myopathy (NM) is the most common congenital myopathy, characterized by extreme weakness of the respiratory, limb, and facial muscles. Pathogenic variants inTropomyosin 2(TPM2), which encodes a skeletal muscle specific actin binding protein essential for sarcomere function, cause a spectrum of musculoskeletal disorders that include NM as well as Cap Myopathy, congenital fiber type disproportion, and distal arthrogrypsosis (DA).TPM2-related disorders have not been modeledin vivo, so we expressed a series of dominant, pathogenicTPM2variants inDrosophilaembryos and found two variants, K49Del and E122K, significantly affected muscle morphogenesis and muscle function, in part by disrupting myotube guidance. Transient overexpression of K49Del and E122K also disrupted the morphogenesis of immortalized mouse myoblastsin vitro, and negatively affected zebrafish muscle development and functionin vivo. We used our transient overexpression assays in zebrafish to characterize two novelTPM2variants that we identified in DA patients (V129A and E139K), and found these variants caused musculoskeletal defects similar to those of the known pathogenic variants. In addition, the severity of musculoskeletal phenotypes in zebrafish expressingTPM2variants correlated with the severity of clinical phenotypes observed in DA patients. Our study establishes transient overexpression in zebrafish as an efficient platform to characterize variants of uncertain significance inTPM2 in vivo, and suggests that this method can be used to predict the clinical severity of variants associated with DA and congenital myopathies.