bluuebunny/crossref_metadata_2025 huggingface dataset:
The state of oligomerization of Rubisco controls the rate of LSU translation inChlamydomonas reinhardtii
Authors: Wietrzynski Wojciech , Traverso Eleonora , Wollman Francis-André , Wostrikoff Katia
Published: October 2020

Ribulose 1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) is a key enzyme for photosynthesis-driven life on Earth. While present in all photosynthetic organisms, its most prominent form is a hetero-oligomer in which a Small Subunit (SSU) stabilizes the core of the enzyme built from Large Subunits (LSU), yielding, after a chaperone-assisted multistep assembly, a LSU8SSU8hexadecameric holoenzyme. Here we useChlamydomonas reinhardtii, and a combination of site-directed mutants, to dissect the multistep biogenesis pathway of Rubiscoin vivo. We identify assembly intermediates, in two of which LSU is associated with the RAF1 chaperone. Using genetic and biochemical approaches we further unravel a major regulation process during Rubisco biogenesis which places translation of its large subunit under the control of its ability to assemble with the small subunit, by a mechanism of Control by Epistasy of Synthesis (CES). Altogether this leads us to propose a model where the last assembly intermediate, an octameric LSU8-RAF1 complex which delivers LSU to SSU to form the Rubisco enzyme, converts to a key regulator form able to exert a negative feed-back on the initiation of translation of LSU, when SSU is not available.
Ultrasound neuromodulation through nanobubble-actuated sonogenetics
Authors: Hou Xuandi , Qiu Zhihai , Kala Shashwati , Guo Jinghui , Wong Kin Fung , Zhu Ting , Zhu Jiejun , Xian Quanxiang , Yang Minyi , Sun Lei
Published: October 2020

Ultrasound neuromodulation is a promising new method to manipulate brain activity noninvasively. Here, we detail a neurostimulation scheme using gas-filled nanostructures, gas vesicles (GVs), as actuators for improving the efficacy and precision of ultrasound stimuli. Sonicated primary neurons displayed dose-dependent, repeatable Ca2+responses, closely synced to stimuli, and increased nuclear expression of the activation marker c-Fos only in the presence of GVs but not without. We identified mechanosensitive ion channels as important mediators of this effect, and neurons heterologously expressing the mechanosensitive MscL-G22S channel showed greater activation at lower acoustic pressure. This treatment scheme was also found not to induce significant cytotoxicity, apoptosis or membrane poration in treated cells. Altogether, we demonstrate a simple and effective method to achieve enhanced and more selective ultrasound neurostimulation.

Graphical abstract
Genetic effects on brain traits impact cell-type specific gene regulation during neurogenesis
Authors: Aygün Nil , Elwell Angela L. , Liang Dan , Lafferty Michael J. , Cheek Kerry E. , Courtney Kenan P. , Mory Jessica , Hadden-Ford Ellie , Krupa Oleh , de la Torre-Ubieta Luis , Geschwind Daniel H. , Love Michael I. , Stein Jason L.
Published: October 2020

Interpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing is generally performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements active during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map expression quantitative trait loci (eQTLs), splicing QTLs (sQTLs), and allele specific expression in primary human neural progenitors (n=85) and their sorted neuronal progeny (n=74), identifying numerous loci not detected in either bulk developing cortical wall or adult cortex. Using colocalization and genetic imputation via transcriptome wide association, we uncover cell-type specific regulatory mechanisms underlying risk for brain-relevant traits that are active during neocortical differentiation. Specifically, we identified a progenitor-specific eQTL forCENPWco-localized with common variant associations of cortical area and educational attainment.
Restriction of SARS-CoV-2 Replication by Targeting Programmed −1 Ribosomal Frameshifting In Vitro
Authors: Sun Yu , Abriola Laura , Surovtseva Yulia V. , Lindenbach Brett D. , Guo Junjie U.
Published: October 2020

Translation of open reading frame 1b (ORF1b) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires programmed −1 ribosomal frameshifting (−1 PRF) promoted by an RNA pseudoknot. The extent to which SARS-CoV-2 replication may be sensitive to changes in −1 PRF efficiency is currently unknown. Through an unbiased, reporter-based high-throughput compound screen, we identified merafloxacin, a fluoroquinolone antibacterial, as a −1 PRF inhibitor of SARS-CoV-2. Frameshift inhibition by merafloxacin is robust to mutations within the pseudoknot region and is similarly effective on −1 PRF of other beta coronaviruses. Importantly, frameshift inhibition by merafloxacin substantially impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing the proof of principle of targeting −1 PRF as an effective antiviral strategy for SARS-CoV-2.
Undaria pinnatifidaexudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts
Authors: Lozada Mariana , Diéguez María C. , García Patricia E. , Bigatti Gregorio , Livore Juan Pablo , Giarratano Erica , Gil Mónica N. , Dionisi Hebe M.
Published: October 2020

The invasive kelpUndaria pinnatifidahas spread from northeastern Asia to temperate coastal environments worldwide, with profound effects on colonized ecosystems. In this work, we analyzed the effect of exudates fromU. pinnatifidaon the chemical and microbial properties of seawater from a semi-enclosed gulf from Atlantic Patagonia. Exudates ofU. pinnatifida,consisting mainly of carbohydrates, were released at a rate of 1.6 ± 0.8 mg C g−1algae day−1, affecting the quality and optical properties of seawater in experimental incubations. Parallel factor analysis based on excitation-emission matrices collected from exudates revealed the presence of two humic-like and one non-humic fluorescent components. Exudate release stimulated microbial growth and polysaccharide degrading activity in seawater. After a 7-day incubation of fresh seawater with the exudates, changes in microbial community structure were analyzed by large-scale 16S rRNA gene amplicon sequencing. Copiotrophic and fermentative genera such asSpirochaeta(Spirochaetes) andPropionigenium(Fusobacteria) increased in the incubations with algal exudates. Genomic potential prediction revealed that the selected bacterial community could have higher ribosome content - an indicator of the potential for reaching higher metabolic rates - and genes for the degradation of complex organic compounds such as polysaccharides and other carbohydrates present in the exudates. Nutrient addition triggered the emergence of other microbial populations with different ecophysiological niches: unclassified Flavobacteriales, unclassified bacteria related to the recently described Phylum Kiritimatiellaeota, as well as potential pathogens such asVibrio(Gammaproteobacteria) andArcobacter(Epsilonproteobacteria), suggesting potential synergistic effects between invasive macroalgae and human activities.
Recurrent Switching Dynamical Systems Models for Multiple Interacting Neural Populations
Authors: Glaser Joshua I. , Whiteway Matthew , Cunningham John P. , Paninski Liam , Linderman Scott W.
Published: October 2020

Modern recording techniques can generate large-scale measurements of multiple neural populations over extended time periods. However, it remains a challenge to model non-stationary interactions between high-dimensional populations of neurons. To tackle this challenge, we develop recurrent switching linear dynamical systems models for multiple populations. Here, each high-dimensional neural population is represented by a unique set of latent variables, which evolve dynamically in time. Populations interact with each other through this low-dimensional space. We allow the nature of these interactions to change over time by using a discrete set of dynamical states. Additionally, we parameterize these discrete state transition rules to capture which neural populations are responsible for switching between interaction states. To fit the model, we use variational expectation-maximization with a structured mean-field approximation. After validating the model on simulations, we apply it to two different neural datasets: spiking activity from motor areas in a non-human primate, and calcium imaging from neurons in the nematodeC. elegans. In both datasets, the model reveals behaviorally-relevant discrete states with unique inter-population interactions and different populations that predict transitioning between these states.
Selective participation of single cortical neurons in neuronal avalanches
Authors: Bellay Timothy , Shew Woodrow L. , Yu Shan , Falco-Walter Jessica J. , Plenz Dietmar
Published: October 2020

Neuronal avalanches are scale-invariant neuronal population activity patterns in cortex that emergein vivoin the awake state andin vitroduring balanced excitation and inhibition. Theory and experiments suggest that avalanches indicate a state of cortex that improves numerous aspects of information processing by allowing for the transient and selective formation of local as well as system-wide spanning neuronal groups. If avalanches are indeed involved with information processing, one might expect that particular single neurons would participate in particular avalanche patterns selectively. Alternatively, all neurons could participate with equal likelihood in each avalanche as would be expected for a population rate code. Distinguishing these hypotheses, however, has been difficult as robust avalanche analysis requires technically challenging measures of their intricate organization in space and time at the population level, while also recording sub- or suprathreshold activity from individual neurons with high temporal resolution. Here we identify repeated avalanches in the ongoing local field potential (LFP) measured with high-density microelectrode arrays in the cortex of awake nonhuman primates and in acute cortex slices from rats. We studied extracellular unit firingin vivoand intracellular responses of pyramidal neuronsin vitro. We found that single neurons participate selectively in specific LFP-based avalanche patterns. Furthermore, we showin vitrothat manipulating the balance of excitation and inhibition abolishes this selectivity. Our results support the view that avalanches represent the selective, scale-invariant formation of neuronal groups in line with the idea of Hebbian cell assemblies underlying cortical information processing.
Structure of the light harvesting 2 complex reveals two carotenoid energy transfer pathways in a photosynthetic bacterium
Authors: Gardiner Alastair T. , Naydenova Katerina , Castro-Hartmann Pablo , Nguyen-Phan Tu C. , Russo Christopher J. , Sader Kasim , Hunter C. Neil , Cogdell Richard J. , Qian Pu
Published: October 2020

We report the 2.4 Å resolution structure of the light harvesting 2 complex (LH2) fromMarichromatium (Mch.) purpuratumdetermined by electron cryo-microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. Two sets of distinct carotenoids are identified in the structure, and a network of energy transfer pathways from the carotenoids to bacteriochlorophyllamolecules is shown. The geometry imposed by the heptameric ring controls the resonant coupling of the long wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.

One Sentence Summary

The structure of a heptameric LH2 antenna complex reveals new energy transfer pathways and the basis for assembling LH rings.
Thermally tolerant symbionts may explain Caribbean octocoral resilience to heat stress
Authors: Pelosi Jessie , Eaton Katherine M. , Mychajliw Samantha , terHorst Casey P. , Coffroth Mary Alice
Published: October 2020

Coral reef ecosystems are under threat from the frequent and severe impacts of anthropogenic climate change, particularly rising sea surface temperatures. The effects of thermal stress may be ameliorated by adaptation and/or acclimation of the host, symbiont, or holobiont (host + symbiont) to increased temperatures. We examined the role of the symbiont in promoting thermal tolerance of the holobiont, usingAntillogorgia bipinnata(octocoral host) andBreviolum antillogorgium(symbiont) as a model system. We identified five distinct genotypes ofB. antillogorgiumfrom symbiont populations isolated fromAntillogorgiacolonies in the Florida Keys. Three symbiont genotypes were cultured and maintained at 26°C (ambient historical temperature) and two were cultured and maintained at 30°C (elevated historical temperature) for two years. Following culturing, we analyzed the growth rate and carrying capacity of each symbiont genotype at both ambient and elevated temperatures in culture (in vitro). All genotypes grew well at both temperatures, indicating thermal tolerance among theseB. antillogorgiumcultures. Prior culturing at the elevated temperature, however, did not result in increased thermal tolerance. We then inoculated juvenileA. bipinnatapolyps with each of the five symbiont genotypes, and reared these polyps at both ambient and elevated temperatures (in hospiteexperiment). All genotypes were able to establish symbioses with polyps in both temperature treatments. Survivorship of polyps at 30°C was significantly lower than survivorship at 26°C, but all treatments had surviving polyps at 56 days post-infection, suggestive of broad thermal tolerance inB. antillogorgium, which may play a part in the increased resilience of Caribbean octocorals during heat stress events.
Role of Udd protein and heterochromatin in transcriptional selection of individual rRNA genes in theDrosophilagermline
Authors: Fefelova Elena A. , Pleshakova Irina M. , Pirogov Sergei A. , Mikhaleva Elena A. , Poltorachenko Valentin A. , Blokh Roman S. , Abramov Yuri A. , Romashin Daniil D. , Gvozdev Vladimir A. , Klenov Mikhail S.
Published: October 2020

Eukaryotic genomes contain hundreds of nearly identical rRNA genes, many of which are transcriptionally silent. However, the mechanisms of selective regulation of individual rDNA units remain poorly understood. InDrosophila melanogaster, rDNA repeats containing insertions of R1/R2 retrotransposons within the 28S rRNA sequence undergo inactivation. Here we found that rRNA genes with insertions are specifically enriched with H3K9me3 and HP1a repressive marks, but disruption of heterochromatin components only slightly affects their silencing. Intriguingly, the loss of Udd (Under-developed) protein interacting with Pol I transcription initiation complex, causes an upregulation of R2-inserted rDNA copies in germ cells by two orders of magnitude that is accompanied by the reduction of heterochromatin marks. Thus, for the first time we revealed a factor required for distinguishing between active and silent rDNA units to such a large extent. To clarify a relationship between the rDNA transcriptional status and heterochromatin establishment, we showed that inhibition of transcription by actinomycin D increases the level of H3K9me3 mark erasing the epigenetic differences between inserted and uninserted rRNA genes. Altogether, we suggest that Udd coupled with Pol I transcription initiation machinery defines activation or silencing of individual rDNA units, whereas their transcription level consequently dictates their chromatin state.
In vitrogut modeling as a tool for adaptive evolutionary engineering ofLactiplantibacillus plantarum
Authors: Isenring Julia , Geirnaert Annelies , Hall Alex R. , Jans Christoph , Lacroix Christophe , Stevens Marc J.A.
Published: October 2020

Research and marketing of probiotics demand for holistic strain improvement considering both, the biotic and abiotic gut environment. Here we aim to establish the continuousIn vitrocolonic fermentation model PolyFermS as a tool for adaptive evolutionary engineering. Immobilized fecal microbiota from adult donors were steadily cultivated up to 72 days in PolyFermS reactors, providing a long-term compositional and functional stable ecosystem akin to the donor’s gut. Inoculation of the gut microbiota with immobilized or planktonicLactiplantibacillus plantarumNZ3400, a derivative of the probiotic model strain WCFS1, led to successful colonization. Whole genome sequencing of 45 recovered strains revealed mutations in 16 genes involved in signaling, metabolism, transport, and cell surface. Remarkably, mutations in LP_RS14990, LP_RS15205, and intergenic region LP_RS05100<LP_RS05095 were found in recovered strains from different adaptation experiments. Combined addition of the reference strain NZ3400 and each of those mutants to the gut microbiota resulted in increased abundance of the corresponding mutant in PolyFermS microbiota after 10 days, showing the beneficial nature of these mutations. Our data show that the PolyFermS system is a suitable technology to generate adapted mutants for colonization in colonic conditions. Analysis thereof will provide knowledge about factors involved in gut microbiota colonization and persistence.

Importance

Improvement of bacterial strains to specific abiotic environmental factors is broadly used to enhance strain characteristics for processing and product quality. However, there is currently no multidimensional probiotic strain improvement approach for both, abiotic and biotic factors of a colon microbiota. The continuous PolyFermS fermentation model allows stable and reproducible continuous cultivation of colonic microbiota and provides conditions akin to the host gut with high control and easy sampling. This study investigated the suitability of PolyFermS for adaptive evolutionary engineering of a probiotic model organism for lactobacilli,Lactiplantibacillus plantarum, to an adult human colonic microbiota. The application of PolyFermS controlled gut microbiota environment led to adaptive evolution ofL. plantarumstrains for enhanced gut colonization characteristics. This novel tool for strain improvement can be used to reveal relevant factors involved in gut microbiota colonization and develop adapted probiotic strains with enhanced functionality in the gut.
TET2 drives 5hmc marking ofGATA6and epigenetically defines pancreatic ductal adenocarcinoma transcriptional subtypes
Authors: Eyres Michael , Landfredini Simone , Burns Adam , Blake Andrew , Willenbrock Frances , Goldin Robert , hughes Daniel , Hughes Sophie , Thapa Asmita , Vavoulis Dimitris , Hubert Aline , D’Costa Zenobia , Sabbagh Ahmad , Abraham Aswin G. , Blancher Christine , Jones Stephanie , Verrill Clare , Silva Michael , Soonawalla Zahir , Maughan Timothy , Schuh Anna , Mukherjee Somnath , O’Neill Eric
Published: October 2020

Background and Aims

Pancreatic ductal adenocarcinoma (PDAC) is characterised by advanced disease stage at presentation, aggressive disease biology and resistance to therapy resulting in extremely poor five-year survival <10%. PDAC is classified into transcriptional subtypes with distinct survival characteristics, although how these arise is not known. Epigenetic deregulation, rather than genetics, has been proposed to underpin progression but exactly why is unclear and hindered by analysis of clinical samples.

Methods

Genome-wide epigenetic mapping of DNA modifications 5-hydroxymethylcytosine (5mc) and 5-hydroxymethylcytosine (5hmc) using oxidative bisulphite sequencing (oxBS). Bioinformatics using iCluster and mutational profiling to identify overlap with transcriptional signatures in FFPE from resected patients and confirmation in vivo.

Results

We find that more aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci including GATA6 that promote differentiated classical-pancreatic subtypes. We show that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5mc-hydroxylase TET2. Furthermore, we find that SMAD4 directly supports TET2 levels in the pancreas and classical-pancreatic tumors and loss of SMAD4 expression is associated reduced 5hmc, GATA6 and squamous-like tumors. Importantly, enhancing TET2 stability using Metformin and VitaminC/ascorbic acid (AA) restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependencein vitroandin vivo.

Conclusions

We identify epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data shows that restoring epigenetic control increases biomarkers of classical-pancreatic tumors and raises the possibility that combination of Vitamin C and Metformin may prolong survival in patients with squamous-like pancreatic cancer.
Bird size with dinosaur-level cancer defences: can evolutionary lags during miniaturisation explain cancer robustness in birds?
Authors: Erten E. Yagmur , Tollis Marc , Kokko Hanna
Published: October 2020

An increased appreciation of the ubiquity of cancer risk across the tree of life means we also need to understand the more robust cancer defences some species seem to have. Peto’s paradox, the finding that large-bodied species do not suffer from more cancer even if their lives require far more cell divisions than those of small species, can be explained if large size selects for better cancer defences. Since birds live longer than non-flying mammals of an equivalent body size, and birds are descendants of moderate-sized dinosaurs, we ask whether ancestral cancer defence innovations are retained if body size shrinks in an evolutionary lineage. Our model derives selection coefficients and fixation events for gains and losses of cancer defence innovations over macroevolutionary time, based on known relationships between body size, intrinsic cancer risk, extrinsic mortality (modulated by flight ability) and effective population size. We show that evolutionary lags can, under certain assumptions, explain why birds, descendants of relatively large bodied dinosaurs, retain low cancer risk. Counterintuitively, it is possible for a bird to be ‘too robust’ for its own good: excessive cancer suppression can take away from reproductive success. On the other hand, an evolutionary history of good cancer defences may also enable birds to reap the lifespan-increasing benefits of other innovations such as flight.
Fast 3D printing of large-scale biocompatible hydrogel models
Authors: Anandakrishnan Nanditha , Ye Hang , Guo Zipeng , Chen Zhaowei , Mentkowski Kyle I. , Lang Jennifer K. , Rajabian Nika , Andreadis Stelios T. , Ma Zhen , Spernyak Joseph A. , Lovell Jonathan F. , Wang Depeng , Xia Jun , Zhou Chi , Zhao Ruogang
Published: October 2020

Large scale cell-laden hydrogel models hold great promise for tissue repair and organ transplantation, but their fabrication is faced with challenges in achieving clinically-relevant size and hierarchical structures. 3D bioprinting is an emerging technology, but its application in large, solid hydrogel fabrication has been limited by the slow printing speed that can affect the part quality and the biological activity of the encapsulated cells. Here we present a Fast hydrogeL prOjection stereolithogrAphy Technology (FLOAT) that allows the creation of a centimeter-sized, multiscale solid hydrogel model within minutes. Through precisely controlling the photopolymerization condition, we established low suction force-driven, high-velocity flow of the hydrogel prepolymer that supports the continuous replenishment of the prepolymer solution below the curing part and the nonstop part growth. We showed that this process is unique to the hydrogel prepolymer without externally supplemented oxygen. The rapid printing of centimeter-sized hydrogel models using FLOAT was shown to significantly reduce the part deformation and cellular injury caused by the prolonged exposure to the environmental stresses in layer-by-layer based printing methods. Media perfusion in the printed vessel network was shown to promote cell survival and metabolic function in the deep core of the large-sized hydrogel model over long term. The FLOAT is compatible with multiple photocurable hydrogel materials and the printed scaffold supports the endothelialization of prefabricated vascular channels. Together, these studies demonstrate a rapid 3D hydrogel printing method and highlight the potential of this method in the fabrication of large-sized engineered tissue models.
Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19
Authors: Yang Andrew C. , Kern Fabian , Losada Patricia M. , Maat Christina A. , Schmartz Georges , Fehlmann Tobias , Schaum Nicholas , Lee Davis P. , Calcuttawala Kruti , Vest Ryan T. , Gate David , Berdnik Daniela , McNerney M. Windy , Channappa Divya , Cobos Inma , Ludwig Nicole , Schulz-Schaeffer Walter J. , Keller Andreas , Wyss-Coray Tony
Published: October 2020

Though SARS-CoV-2 primarily targets the respiratory system, it is increasingly appreciated that patients may suffer neurological symptoms of varied severity1–3. However, an unbiased understanding of the molecular processes across brain cell types that could contribute to these symptoms in COVID-19 patients is still missing. Here, we profile 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and 1 influenza patient. We complement transcriptomic data with immunohistochemical staining for the presence of SARS-CoV-2. We find that all major cortex parenchymal and choroid plexus cell types are affected transcriptionally with COVID-19. This arises, in part, from SARS-CoV-2 infection of the cortical brain vasculature, meninges, and choroid plexus, stimulating increased inflammatory signaling into the brain. In parallel, peripheral immune cells infiltrate the brain, microglia activate programs mediating the phagocytosis of live neurons, and astrocytes dysregulate genes involved in neurotransmitter homeostasis. Among neurons, layer 2/3 excitatory neurons—evolutionarily expanded in humans4—show a specific downregulation of genes encoding major SNARE and synaptic vesicle components, predicting compromised synaptic transmission. These perturbations are not observed in terminal influenza. Many COVID-19 gene expression changes are shared with those in chronic brain disorders and reside in genetic variants associated with cognitive function, schizophrenia, and depression. Our findings and public dataset provide a molecular framework and new opportunities to understand COVID-19 related neurological disease.
Human bronchial epithelial cell-derived extracellular vesicle therapy for pulmonary fibrosis via inhibition of TGF-β-WNT crosstalk
Authors: Kadota Tsukasa , Fujita Yu , Araya Jun , Watanabe Naoaki , Fujimoto Shota , Kawamoto Hironori , Minagawa Shunsuke , Hara Hiromichi , Ohtsuka Takashi , Yamamoto Yusuke , Kuwano Kazuyoshi , Ochiya Takahiro
Published: October 2020

Idiopathic pulmonary fibrosis (IPF) is characterized by devastating and progressive lung parenchymal fibrosis, resulting in poor patient prognosis. An aberrant recapitulation of developmental lung gene expression, including genes for transforming growth factor (TGF)-β and WNT, has been widely implicated in the pathogenic IPF wound healing process that results from repetitive alveolar epithelial injury. Extracellular vesicles (EVs) have been shown to carry bioactive molecules and to be involved in various physiological and pathological processes. Here, we demonstrate that, by attenuating WNT signaling, human bronchial epithelial cell-derived EVs (HBEC EVs) inhibit TGF-β mediated induction of both myofibroblast differentiation and lung epithelial cellular senescence. This effect of HBEC EVs is more pronounced than that observed with mesenchymal stem cell-derived EVs. Mechanistically, the HBEC EV microRNA (miRNA) cargo is primarily responsible for attenuating both myofibroblast differentiation and cellular senescence. This attenuation occurs via inhibition of canonical and non-canonical WNT signaling pathways. Among enriched miRNA species present in HBEC EVs, miR-16, miR-26a, miR-26b, miR-141, miR-148a, and miR-200a are mechanistically involved in reducing WNT5A and WNT10B expression in LFs, and in reducing WNT3A, WNT5A, and WNT10B expression in HBECs. Mouse models utilizing intratracheal administration of EVs demonstrate efficient attenuation of bleomycin-induced lung fibrosis development accompanied by reduced expression of both β-catenin and markers of cellular senescence. These findings indicate that EVs derived from normal resident lung HBECs may possess anti-fibrotic properties. They further suggest that, via miRNA-mediated inhibition of TGF-β-WNT crosstalk, HBEC EVs administration can be a promising anti-fibrotic modality of treatment for IPF.
Reverse-transcription recombinase-aided amplification assay for H5 subtype avian influenza virus
Authors: Wang Suchun , Li Yang , Jiang Nan , Zhang Fuyou , Zhuang Qingye , Hou Guangyu , Jiang Lijian , Yu Jianmin , Yu Xiaohui , Liu Hualei , Zhao Chenglong , Yuan Liping , Huang Baoxu , Wang Kaicheng
Published: October 2020

The H5 subtype Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse-transcription recombinase-aided amplification assay for the detection of H5 subtype avian influenza virus. Assays were performed at a single temperature (39°C), and the results were obtained within 20 min. The assay showed no cross-detection with Newcastle disease virus or infectious bronchitis virus. The analytical sensitivity was 103RNA copies per reaction at a 95% confidence interval according to probit regression analysis, with 100% specificity. Compared with published reverse-transcription quantitative real-time polymerase chain reaction assays, the κ value of the reverse transcription recombinase-aided amplification assay in 365 avian clinical samples was 0.970 (p < 0.001). The sensitivity for avian clinical sample detection was 94.44% (95%CI, 70.63% - 99.71%), and the specificity was 100% (95%CI, 98.64% - 100%). These results indicated that our reverse-transcription recombinase-aided amplification assay may be a valuable tool for detecting H5 subtype avian influenza virus.
Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle
Authors: Balart-García Pau , Cieslak Alexandra , Escuer Paula , Rozas Julio , Ribera Ignacio , Fernández Rosa
Published: October 2020

The chemosensory system has experienced relevant changes in subterranean animals, facilitating the orientation into darkness via the perception of specific chemical signals critical to survive in this particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna is largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to the deep subterranean) in order to interrogate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odorant and gustatory gene repertoires compared to polyphagous epigean beetles. Moreover, S. longicornis showed a large diversity of odorant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication in the ionotropic co-receptor I R25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may have been reshaped by the low complexity of chemical signals of this particular environment, and that gene duplication and loss may have played an important role in the evolution of genes involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level.
Multivariate genome-wide association study identifies 780 unique genetic loci associated with cortical morphology
Authors: Shadrin Alexey A. , Kaufmann Tobias , van der Meer Dennis , Palmer Clare E. , Makowski Carolina , Loughnan Robert , Jernigan Terry L. , Seibert Tyler M. , Hagler Donald J , Smeland Olav B. , Chu Yunhan , Lin Aihua , Cheng Weiqiu , Hindley Guy , Thompson Wesley K. , Fan Chun C. , Holland Dominic , Westlye Lars T. , Frei Oleksandr , Andreassen Ole A. , Dale Anders M.
Published: October 2020

Brain morphology has been shown to be highly heritable, yet only a small portion of the heritability is explained by the genetic variants discovered so far. Here we exploit the distributed nature of genetic effects across the brain and apply the Multivariate Omnibus Statistical Test (MOSTest) to genome-wide association studies (GWAS) of vertex-wise structural magnetic resonance imaging (MRI) cortical measures from N=35,657 participants in the UK Biobank. We identified 695 loci for cortical surface area and 539 for cortical thickness, in total 780 unique genetic loci associated with cortical morphology. This reflects an approximate 10-fold increase compared to the commonly applied univariate GWAS methods. Power analysis indicates that applying MOSTest to vertex-wise structural MRI data triples the effective sample size compared to conventional univariate GWAS approaches. Functional follow up including gene-based analyses implicate 10% of all protein-coding genes and point towards pathways involved in neurogenesis and cell differentiation.
Contributions of Implicit and Explicit Memories to Sensorimotor Adaptation of Movement Extent During Goal-Directed Reaching
Authors: Lantagne Devon D , Mrotek Leigh Ann , Slick Rebecca A , Beardsley Scott A , Thomas Danny G , Scheidt Robert A
Published: October 2020

We examined how explicit memory of kinematic performance contributes to motor adaptation during goal-directed reaching. Twenty subjects grasped the handle of a horizontal planar robot that rendered spring-like resistance to movement. Subjects made rapid “out-and-back” reaches to capture a remembered visual target at the point of maximal reach extent. The robot’s resistance changed unpredictably between reaches, inducing target capture errors that subjects attempted to correct from one trial to the next. The subjects performed four sets of trials. Three were performed without concurrent visual cursor feedback of hand motion. Two of these required self-assessment of performance between trials, whereby subjects reported peak reach extent on the most recent trial. This was done by either moving a cursor on a horizontal display (visual self-assessment), or by moving the robot’s handle back to the recalled location (proprioceptive self-assessment). Two control conditions were performed either without or with concurrent visual cursor feedback of hand motion. We analyzed movement kinematics and used regression analyses to quantify the extent to which prior reach errors and explicit memories of prior performance contribute to subsequent reach performance. Consistent with prior reports, providing concurrent visual feedback of hand motion increased reach accuracy and reduced the impact of past performance errors on future performance, relative to the no-vision control condition. By contrast, we found no impact of interposed self-assessment on reach kinematics or on how prior target capture errors influence subsequent reach performance. Self-assessments were biased toward the remembered target location, differing markedly from actual reach performances. Including self-assessments as explicit memory of performance in the regression analyses did not improve model predictive accuracy. Therefore, we conclude that explicit memories of prior kinematic performance do not contribute to implicit sensorimotor adaptation of movement extent.
Altered food habits? Understanding the feeding preference of free-ranging Grey langur (Semnopithecus entellus) within an urban settlement
Authors: Dasgupta Dishari , Banerjee Arnab , Karar Rikita , Banerjee Debolina , Mitra Shohini , Sardar Purnendu , Karmakar Srijita , Bhattacharya Aparajita , Ghosh Swastika , Bhattacharjee Pritha , Paul Manabi
Published: October 2020

Urbanization affects concurrent human-animal movements as a result of altered resource availability and land use pattern, which leads to considerable ecological consequences. While some animals find themselves adrift, homeless with the uncertainty of resources resulting from the urban encroachment, few of them manage to survive by altering their natural behavioural patterns, and co-exist with humans. Folivorous colobines, such as grey langur, whose feeding repertoire largely consists of plant parts, tend to be more attuned to the urban high-calorie food sources to attain maximum fitness benefits within the concrete jungle having an insignificant green cover. However, such a mismatch between their generalized feeding behaviour and specialized gut physiology reminds us of the Liem’s paradox and demands considerable scientific attention which could tell us the story behind colobines’ successful co-existence within human settlements. Besides understanding their population dynamics, the effective management of these urbanized, free-ranging, non-human primate populations also depends on their altered feeding preferences, altogether which could lead us to the development of an ecologically sound urban ecosystem. Here, we have used a field-based experimental set up which allows langurs to choose between natural and urban food options, being independent of any inter-specific conflicts over resources due to food scarcity. The multinomial logit model reveals the choice-based decision making of these free-ranging grey langurs in an urban settlement of West Bengal, India, where they have not only learned to approach the human-provisioned urban food items but also shown a keen interest in it. While urbanization imposes tremendous survival challenges to these animals, it also opens up for various alternative options for human-animal co-existence which is reflected in this study, and could guide us for the establishment of a sustainable urban ecosystem in the future.

HIGHLIGHTS

The feeding repertoire of free-ranging grey langurs at Dakshineswar largely consists of urban food items in contrast to the langurs of Nangi, and Nalpur who mostly depend on natural food sources.

High human-langur interactions together with the scarcity of natural plant-based food sources could be considered as an intriguing driving force behind langurs’ altered feeding habits in Dakhineswar.

The field-based experimental set up allows free-ranging langurs to choose between natural and urban food options in an urban settlement like Dakhineswar.

Urban food items outperformed natural food items as the most chosen one, indicating langurs’ altered feeding preferences which facilitate their successful co-existence within an urban ecosystem.
The PRC2-dependent epigenetic reprograming of the bladder epithelium exacerbates urinary tract infections
Authors: Guo Chunming , Zhao Mingyi , Sui Xinbing , Balsara Zarine , Zhai Songhui , Zhu Ping , Li Xue
Published: October 2020

Mucosal imprint sensitizes recurrent urinary tract infections (UTIs), a significant health and quality of life burden worldwide, which are associated with heightened inflammatory host response, severe basal cell hyperplasia and impaired superficial cell differentiation. Here, we show that bladder infections induce expression ofEzh2, the methyltransferase of polycomb repressor complex 2 (PRC2)-dependent epigenetic gene silencing program. In mouse models of UTIs, urothelium-specific inactivation of PRC2 reduces the urine bacteria burden. The mutants exhibit a blunted inflammatory response likely due to the diminished activity ofNF-κBsignaling pathway. PRC2 inactivation also improves urothelial differentiation and attenuates basal cell hyperplasia phenotype. Moreover, the Ezh2-specific small molecule inhibitors markedly improve disease outcomes of bladder superinfection and chronic cystitis. Taken together, these findings suggest that the UTI-induced epigenetic reprograming in the bladder urothelium likely contributes to the mucosal imprint, and further suggest that targeting PRC2 methyltransferase offers a non-antibiotic strategy to mitigate UTIs.
Small-MoleculeIn VitroInhibitors of the Coronavirus Spike – ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2
Authors: Bojadzic Damir , Alcazar Oscar , Chen Jinshui , Buchwald Peter
Published: October 2020

Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and ACE2, which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable / less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound-library that is focused on the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel drug-like compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50s of 0.2-3.0 μM); whereas, control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs identified here bind SARS-CoV-2-S and not ACE2. Selected promising compounds inhibited the entry of a SARS-CoV-2-S expressing pseudovirus into ACE2-expressing cells in concentration-dependent manner with low micromolar IC50s (6-30 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for coronavirus attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.
Glycolysis Inhibition Regulates Endothelial Junctions by Perturbing Actin and Focal Adhesions
Authors: Schwarz G. , Gajwani P. , Rehman J. , Leckband D.
Published: October 2020

One of the central functions of the endothelium is to maintain a vascular barrier that prevents fluid leakiness and immune cell influx from the circulating blood into the tissue. The barrier integrity of the endothelium is largely controlled by adherens junctions (AJs) and the key AJ molecule VE-cadherin, which maintains cell cohesion via homotypic trans-interaction with VE-cadherin molecules on neighboring endothelial cells. Tension is required to maintain junction homeostasis, but little is known about the role of endothelial metabolism and bioenergetics in regulating junctional forces. Because glycolysis is the main source of ATP generation in endothelial cells, we examined the bioenergetic control of the mechanics of VE-cadherin junctions, by focusing on the glycolysis regulatory enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Results from traction force imbalance measurements and a VE-cadherin tension sensor revealed that inhibiting PFKFB3 significantly reduced the average junctional tension and the force on VE-cadherin complexes. The decrease in tension was largely due to mechanical changes distal from the cell-cell contacts. Specifically, inhibiting glycolysis perturbs focal adhesions and disrupts actin organization, directly impacting the net force on intercellular contacts. These findings identify a critical role of cellular metabolism for the mechanics and integrity of vascular endothelial junctions, by maintaining global cell mechanics.

Statement of Significance

This study examines how forces at intercellular junctions are bioenergetically regulated. Results reveal altered mechanical force generation and transmission due to the breakdown of stress-transmitting fibers during lung injury. These junctions control the barrier function of the vascular endothelium, which requires tight inter cellular adhesions to prevent fluid and macromolecules from passing through the endothelial barrier. We determined how the availability of ATP affects the tension between human endothelial cells, by regulating forces produced remotely from the junctions. These global changes alter both the force at the junctions themselves, and the force transmitted across the entire cell through actin fibers.
Training-induced prefrontal neuronal changes transfer between tasks
Authors: Tang Hua , Riley Mitchell R. , Singh Balbir , Qi Xue-Lian , Blake David T. , Constantinidis Christos
Published: October 2020

Training to improve working memory is associated with changes in prefrontal activation and confers lasting benefits, some of which generalize to untrained tasks, though the issue remains contentious and the neural substrate underlying such transfer are unknown. To assess how neural activity changes induced by training transfer across tasks, we recorded single units, multi-unit activity (MUA) and local field potentials (LFP) with chronic electrode arrays implanted in the prefrontal cortex of two monkeys, as they were trained to perform cognitive tasks. Mastering different tasks was associated with distinct changes in neural activity, which included redistribution of power across frequency bands in the LFP, recruitment of larger numbers of MUA sites, and increase or decrease of mean neural activity across single units. In every training phase, changes induced by the actively learned task transferred to an untrained control task, which remained the same across the training period. The results explicate the neural basis through which training can transfer across cognitive tasks.
A Bacterial Signaling Network Controls Antibiotic Resistance by Regulating Anaplerosis of 2-oxoglutarate
Authors: Hurst M. N. , Beebout C. J. , Mersfelder R. , Hollingsworth A. , Guckes K. R. , Bermudez T. , Floyd K. A. , Reasoner S. A. , Williams D. , Hadjifrangiskou M.
Published: October 2020

Antibiotic resistance has become a global threat. In addition to acquiring resistance via horizontal gene transfer, bacteria can evade killing by temporarily modifying their cell envelope to prevent antibiotic-bacterial interactions. A critical gap in knowledge is how bacteria balance the metabolic needs of altering the cell envelope with the constant need to generate energy. Cross-regulation between two signaling networks inEscherichia coliincreases resistance to positively charged antibiotics. We show that increased resistance is supported by metabolic re-wiring controlled by the QseB transcription factor. QseB controls the increase in 2-oxoglutarate required for lipid A modification, by upregulating three anaplerotic pathways that feed acetyl Co-A, succinate and fumarate into the TCA cycle. Exogenous addition of 2-oxoglutarate restores antibiotic resistance in theqseBdeletion mutant. Antibiotic resistant clinical isolates bear mutations within QseB-mediated anaplerotic pathways. These findings are significant, because they uncover a previously unknown mechanism of metabolic control of antibiotic resistance.