bluuebunny/crossref_metadata_2025 huggingface dataset:
Nature calls: intelligence and natural foraging style predict poor welfare in captive parrots
Authors: Mellor Emma L. , McDonald Kinkaid Heather K. , Mendl Michael T. , Cuthill Innes C. , van Zeeland Yvonne R. A. , Mason Georgia J.
Published: October 2021

Understanding why some species thrive in captivity, while others struggle to adjust, can suggest new ways to improve animal care. Approximately half of all Psittaciformes, a highly threatened order, live in zoos, breeding centres and private homes. Here, some species are prone to behavioural and reproductive problems that raise conservation and ethical concerns. To identify risk factors, we analysed data on hatching rates in breeding centres (115 species, 10 255 pairs) and stereotypic behaviour (SB) in private homes (50 species, 1378 individuals), using phylogenetic comparative methods (PCMs). Small captive population sizes predicted low hatch rates, potentially due to genetic bottlenecks, inbreeding and low availability of compatible mates. Species naturally reliant on diets requiring substantial handling were most prone to feather-damaging behaviours (e.g. self-plucking), indicating inadequacies in the composition or presentation of feed (often highly processed). Parrot species with relatively large brains were most prone to oral and whole-body SB: the first empirical evidence that intelligence can confer poor captive welfare. Together, results suggest that more naturalistic diets would improve welfare, and that intelligent psittacines need increased cognitive stimulation. These findings should help improve captive parrot care and inspire further PCM research to understand species differences in responses to captivity.
Oral and intranasal Ad5 SARS-CoV-2 vaccines decrease disease and viral transmission in a golden hamster model
Authors: Langel Stephanie N. , Johnson Susan , Martinez Clarissa I. , Tedjakusuma Sarah N. , Peinovich Nadine , Dora Emery G. , Kuehl Philip J. , Irshad Hammad , Barrett Edward G. , Werts Adam , Tucker Sean N
Published: October 2021

Transmission-blocking strategies that slow the spread of SARS-CoV-2 and protect against COVID-19 are needed. We have developed a shelf-stable, orally-delivered Ad5-vectored SARS-CoV-2 vaccine candidate that expresses the spike protein. Here we demonstrated that oral and intranasal SARS-CoV-2 vaccination of this candidate protected against disease in index hamsters, and decreased aerosol transmission to unvaccinated, naïve hamsters. We confirmed that mucosally-vaccinated hamsters had robust antibody responses. We then induced a post-vaccination infection by inoculating vaccinated index hamsters with SARS-CoV-2. Oral and IN-vaccinated hamsters had decreased viral RNA and infectious virus in the nose and lungs and experienced less lung pathology compared to mock-vaccinated hamsters post challenge. Naive hamsters exposed in a unidirectional air flow chamber to mucosally-vaccinated, SARS-CoV-2-infected hamsters had lower nasal swab viral RNA and exhibited less clinical symptoms of disease than control animals. Our data demonstrate that oral immunization is a viable strategy to decrease SARS-CoV-2 disease and aerosol transmission.
Circulating proteins to predict adverse COVID-19 outcomes
Authors: Su Chen-Yang , Zhou Sirui , Gonzalez-Kozlova Edgar , Butler-Laporte Guillaume , Brunet-Ratnasingham Elsa , Nakanishi Tomoko , Jeon Wonseok , Morrison David , Laurent Laetitia , Afilalo Jonathan , Afilalo Marc , Henry Danielle , Chen Yiheng , Carrasco-Zanini Julia , Farjoun Yossi , Pietzner Maik , Kimchi Nofar , Afrasiabi Zaman , Rezk Nardin , Bouab Meriem , Petitjean Louis , Guzman Charlotte , Xue Xiaoqing , Tselios Chris , Vulesevic Branka , Adeleye Olumide , Abdullah Tala , Almamlouk Noor , Moussa Yara , DeLuca Chantal , Duggan Naomi , Schurr Erwin , Brassard Nathalie , Durand Madeleine , Del Valle Diane Marie , Thompson Ryan , Cedillo Mario A. , Schadt Eric , Nie Kai , Simons Nicole W , Mouskas Konstantinos , Zaki Nicolas , Patel Manishkumar , Xie Hui , Harris Jocelyn , Marvin Robert , Cheng Esther , Tuballes Kevin , Argueta Kimberly , Scott Ieisha ,   The Mount Sinai COVID-19 Biobank Team, Greenwood Celia M T , Paterson Clare , Hinterberg Michael A. , Langenberg Claudia , Forgetta Vincenzo , Pineau Joelle , Mooser Vincent , Marron Thomas , Beckmann Noam , Kenigsberg Ephraim , Kim-schulze Seunghee , Charney Alexander W. , Gnjatic Sacha , Kaufmann Daniel E. , Merad Miriam , Richards J Brent
Published: October 2021

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4,701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict adverse COVID-19 outcomes in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4,701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different adverse COVID-19 outcomes were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of adverse COVID-19 outcomes. Further research is needed to understand how to incorporate protein measurement into clinical care.
Impact of Diabetes Status on Immunogenicity of Trivalent Inactivated Influenza Vaccine in Older Adults
Authors: Spencer Sarah , Chung Jessie R. , Belongia Edward A. , Sundaram Maria , Meece Jennifer , Coleman Laura A. , Zimmerman Richard , Nowalk Mary Patricia , Moehling Krissy K. , Ross Ted , Carter Chalise E. , Shay David , Levine Min , Liepkalns Justine , Kim Jin Hyang , Sambhara Suryaprakash , Thompson Mark , Flannery Brendan
Published: October 2021

Individuals with type 2 diabetes mellitus experience high rates of influenza virus infection and complications. We compared the magnitude and duration of serologic response to trivalent influenza vaccine in adults aged 50-80 with and without type 2 diabetes mellitus. Serologic response to influenza vaccination was similar in both groups: greater fold-increases in antibody titer occurred among individuals with lower pre-vaccination antibody titers. Waning of antibody titers was not influenced by diabetes status.
Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae
Authors: Thompson Ryan C. , Simons Nicole W. , Wilkins Lillian , Cheng Esther , Del Valle Diane Marie , Hoffman Gabriel E. , Fennessy Brian , Mouskas Konstantinos , Francoeur Nancy J. , Johnson Jessica S. , Lepow Lauren , Berichel Jessica Le , Chang Christie , Beckmann Aviva G. , Wang Ying-chih , Nie Kai , Zaki Nicholas , Tuballes Kevin , Barcessat Vanessa , Cedillo Mario A. , Huckins Laura , Roussos Panagiotis , Marron Thomas U. ,   The Mount Sinai COVID-19 Biobank Team, Glicksberg Benjamin S. , Nadkarni Girish , Gonzalez-Kozlova Edgar , Kim-Schulze Seunghee , Sebra Robert , Merad Miriam , Gnjatic Sacha , Schadt Eric E. , Charney Alexander W. , Beckmann Noam D.
Published: October 2021

Summary Paragraph

Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.
Reactivating Memories from a Mathematical Task over a Period of Sleep
Authors: Bassard Adrianna M. , Paller Ken A.
Published: October 2021

Sleep, especially slow-wave sleep (SWS), has been found to facilitate memory consolidation for many types of learning. Mathematical learning, however, has seldom been examined in this context. Solving multiplication problems involves multiple steps before problems can be mastered or answers memorized, and thus it can depend on both skill learning and fact learning. Here we aimed to test the hypothesis that memory reactivation during sleep contributes to multiplication learning. To do so, we used a technique known as targeted memory reactivation (TMR), or the pairing of newly learned information with specific stimuli that are later presented during sleep. With TMR, specific memories can be reactivated over a period of sleep without disrupting ongoing sleep. We applied TMR during an afternoon nap to reactivate half of the multiplication problems that had previously been practiced. Results showed no effect of TMR on response time or accuracy of multiplication problem solving. Because these results were unexpected, we also used a variation of this paradigm to examine results in subjects who remained awake. Comparisons between the wake and sleep groups showed no difference in response time or accuracy in either the initial test or the final test. Although neither TMR nor sleep differentially influenced multiplication performance, correlational analysis provided some clues about mathematical problem solving and sleep. On the basis of these findings, even though they did not provide convincing support for our hypotheses, we suggest future experiments that could help produce a better understanding of the relevance of sleep and memory reactivation for this type of learning.
Proteoglycan Clusters as a Site of Coordinated, Multi-Dendritic Plasticity
Authors: Chelini Gabriele , Durning Peter , O’Donovan Sinead , Klengel Torsten , Balasco Luigi , Berciu Cristina , Boyer-Boiteau Anne , Bozzi Yuri , McCullumsmith Robert , Ressler Kerry J. , Berretta Sabina
Published: October 2021

Experience-dependent learning depends on synaptic plasticity. While plasticity in individual synapses has been extensively investigated, the mechanisms underlying coordinated changes across sets of synapses on multiple dendrites, likely needed to encode effective adaptations to a salient stimulus, are not well understood. The extracellular matrix is uniquely well suited to fulfill this function, as rapid glia-driven remodeling of its local composition powerfully impact synaptic plasticity. We show that extracellular matrix microenvironments, named CS6 clusters, dynamically form around several dendrites in response to sensory stimuli in coincidence to stimulus-driven synaptic plasticity. CS6 clusters, formed by glia-dependent secretion of extracellular matrix components surrounding sets of adjacent dendrites, may represent a novel structure supporting coordinated synaptic plasticity.

One Sentence Summary

Extracellular matrix clusters form microenvironments for coordinated multi-dendrite synaptic plasticity.
Cooperative breeding and the emergence of multilevel societies in birds
Authors: Camerlenghi Ettore , McQueen Alexandra , Delhey Kaspar , Cook Carly N. , Kingma Sjouke A. , Farine Damien R. , Peters Anne
Published: October 2021

Multilevel societies (MLSs), where social levels are hierarchically nested within each other, are considered one of the most complex forms of animal societies. Although thought to mainly occur in mammals, it is suggested that MLSs could be under-detected in birds. Here we propose that the emergence of MLSs could be common in cooperatively breeding birds, as both systems are favoured by similar ecological and social drivers. We first investigate this proposition by systematically comparing evidence for multilevel social structure in cooperative and non-cooperative birds in Australia and New Zealand, global hotspots for cooperative breeding. We then analyse non-breeding social networks of cooperatively breeding superb fairy-wrens (Malurus cyaneus) to reveal their structured multilevel society, with three hierarchical social levels that are stable across years. Our results confirm recent predictions that MLSs are likely to be widespread in birds and suggest that these societies could be particularly common in cooperatively breeding birds.
Novel microRNAs targeting NMDA receptor subunits in animal models of schizophrenia
Authors: Gunasekaran Sowmya , Jacob Reena S. , Omkumar Ramakrishnapillai V.
Published: October 2021

N-methyl-D-aspartate receptors (NMDAR) are downregulated in schizophrenia possibly through microRNAs (miRNAs) that are differentially expressed in this condition. We screened the miRNAs that are altered in schizophrenia against the targets, Grin2A and Grin2B subunits of NMDAR using bioinformatic tools. Among the predicted miRNAs some interacted with the 3’-UTR sequences of Grin2A (miR-296, miR-148b, miR-129-2, miR-137) and Grin2B (miR-296, miR-148b, miR-129-2, miR-223) in dual luciferase assays. This was supported by downregulation of the GluN2B protein in primary hippocampal neurons upon overexpressing Grin2B targeting miRNAs. In two models of schizophrenia-pharmacological MK-801 model and neurodevelopmental methylazoxymethanol acetate (MAM) model which showed cognitive deficits - protein levels of GluN2A and GluN2B were downregulated but their transcript levels were upregulated. MiR-296-3p, miR-148b-5p and miR-137 levels showed upregulation in both models which could have interacted with Grin2A/Grin2B transcripts resulting in translational arrest. In MAM model, reciprocal changes in the expression of the 3p and 5p forms of miR-148b and miR-137 were observed. Expression of neuregulin 1 (NRG1), BDNF and CaMKIIα, genes implicated in schizophrenia, were also altered in these models. This is the first report of downregulation of GluN2A and GluN2B by miR-296, miR-148b and miR-129-2. Mining miRNAs regulating NMDA receptors might give insights into the pathophysiology of this disorder, providing avenues in therapeutics.
B.1.617.3 SARS CoV-2 spike E156G/Δ157-158 mutations contribute to reduced neutralization sensitivity and increased infectivity
Authors: Mishra Tarun , Joshi Garima , Kumar Atul , Dalavi Rishikesh , Pandey Pankaj , Shukla Sanjeev , Mishra Ram Kumar , Chande Ajit
Published: October 2021

SARS CoV-2 variants raise significant concerns due to their ability to cause vaccine breakthrough infections. Here, we sequence-characterized the spike gene, isolated from a breakthrough infection, that corresponded to B.1.617.3 lineage. Delineating the functional impact of spike mutations using reporter pseudoviruses (PV) revealed that N-terminal domain (NTD)-specific E156G/Δ157-158 contributed to increased infectivity and reduced sensitivity to ChAdOx1 nCoV-19 vaccine (Covishield™)-elicited neutralizing antibodies. A six-nucleotide deletion (467-472) in the spike coding region introduced this change in the NTD. We confirmed the presence of E156G/Δ157-158 in the RT-PCR-positive cases concurrently screened, in addition to other circulating spike (S1) mutations like T19R, T95I, L452R, E484Q, and D614G. Notably, E156G/Δ157-158 was present in more than 85% of the sequences reported from the USA, UK, and India in August 2021. The spike PV bearing combination of E156G/Δ157-158 and L452R further promoted infectivity and conferred immune evasion. Additionally, increased cell-to-cell fusion was observed when spike harbored E156G/Δ157-158, L452R, and E484Q, suggesting a combinatorial effect of these mutations. Notwithstanding, the plasma from a recovered individual robustly inhibited mutant spike PV, indicating the increased breadth of neutralization post-recovery. Our data highlights the importance of spike NTD-specific changes in determining infectivity and immune escape of variants.
DLPFC controls the rapid neural response to visual threat: An ERP and rTMS study
Authors: Cinq-Mars Justine , Blumenthal Anna , Grund Alessa , Hétu Sébastien , Blanchette Isabelle
Published: October 2021

Individuals are faster at detecting threatening stimuli than neutral stimuli. While generally considered a rapid bottom-up response, this threat superiority effect is also modulated by top-down mechanisms known to rely on the dorsolateral prefrontal cortex (DLPFC). What remains unclear is whether the response is modulated only at later stages of processing, or whether rapid attention to threat itself is controlled in a top-down manner. To test this, we used repetitive transcranial magnetic stimulation (rTMS) to inhibit activity in the DLPFC, and measured EEG to index the immediate neural response to threat. Participants attended two sessions where they performed a visual search task with threatening or neutral targets. Prior to this, they received 15 minutes of 1 Hz inhibitory or sham rTMS targeting the right DLPFC. We measured the impact of rTMS on the P1, a rapid visually-evoked potential that is modulated by attention. We found that threatening targets increased the amplitude of the P1 in the sham condition, but inhibition of the DLPFC abolished this increase. These results suggest that the neural signature of rapid attentional detection of threat, even at its earliest stage, is influenced in a top-down fashion by the right DLPFC.
Automatic Metadata Generation for Fish Specimen Image Collections
Authors: Pepper Joel , Greenberg Jane , Bakiş Yasin , Wang Xiaojun , Bart Henry , Breen David
Published: October 2021

Metadata are key descriptors of research data, particularly for researchers seeking to apply machine learning (ML) to the vast collections of digitized specimens. Unfortunately, the available metadata is often sparse and, at times, erroneous. Additionally, it is prohibitively expensive to address these limitations through traditional, manual means. This paper reports on research that applies machine-driven approaches to analyzing digitized fish images and extracting various important features from them. The digitized fish specimens are being analyzed as part of the Biology Guided Neural Networks (BGNN) initiative, which is developing a novel class of artificial neural networks using phylogenies and anatomy ontologies. Automatically generated metadata is crucial for identifying the high-quality images needed for the neural network’s predictive analytics. Methods that combine ML and image informatics techniques allow us to rapidly enrich the existing metadata associated with the 7,244 images from the Illinois Natural History Survey (INHS) used in our study. Results show we can accurately generate many key metadata properties relevant to the BGNN project, as well as general image quality metrics (e.g. brightness and contrast). Results also show that we can accurately generate bounding boxes and segmentation masks for fish, which are needed for subsequent machine learning analyses. The automatic process outperforms humans in terms of time and accuracy, and provides a novel solution for leveraging digitized specimens in ML. This research demonstrates the ability of computational methods to enhance the digital library services associated with the tens of thousands of digitized specimens stored in open-access repositories world-wide.
Event-driven acquisition for content-enriched microscopy
Authors: Mahecic Dora , Stepp Willi L. , Zhang Chen , Griffié Juliette , Weigert Martin , Manley Suliana
Published: October 2021

A common goal of fluorescence microscopy is to collect data on specific biological events. Yet, the event-specific content that can be collected from a sample is limited, especially for rare or stochastic processes. This is due in part to photobleaching and phototoxicity, which constrain imaging speed and duration. We developed an event-driven acquisition (EDA) framework, in which neural network-based recognition of specific biological events triggers real-time control in an instant structured illumination microscope (iSIM). Our setup adapts acquisitions on-the-fly by switching between a slow imaging rate while detecting the onset of events, and a fast imaging rate during their progression. Thus, we capture mitochondrial and bacterial divisions at imaging rates that match their dynamic timescales, while extending overall imaging durations. Because EDA allows the microscope to respond specifically to complex biologi-cal events, it acquires data enriched in relevant content.
A high throughput screening assay for inhibitors of SARS-CoV-2 pseudotyped particle entry
Authors: Xu Miao , Pradhan Manisha , Gorshkov Kirill , Petersen Jennifer D. , Shen Min , Guo Hui , Zhu Wei , Klumpp-Thomas Carleen , Michael Sam , Itkin Misha , Itkin Zina , Straus Marco R. , Zimmerberg Joshua , Zheng Wei , Whittaker Gary R. , Chen Catherine Z.
Published: October 2021

Effective small molecule therapies to combat the SARS-CoV-2 infection are still lacking as the COVID-19 pandemic continues globally. High throughput screening assays are needed for lead discovery and optimization of small molecule SARS-CoV-2 inhibitors. In this work, we have applied viral pseudotyping to establish a cell-based SARS-CoV-2 entry assay. Here, the pseudotyped particles (PP) contain SARS-CoV-2 spike in a membrane enveloping both the murine leukemia virus (MLV) gag-pol polyprotein and luciferase reporter RNA. Upon addition of PP to HEK293-ACE2 cells, the SARS-CoV-2 spike protein binds to the ACE2 receptor on the cell surface, resulting in priming by host proteases to trigger endocytosis of these particles, and membrane fusion between the particle envelope and the cell membrane. The internalized luciferase reporter gene is then expressed in cells, resulting in a luminescent readout as a surrogate for spike-mediated entry into cells. This SARS-CoV-2 PP entry assay can be executed in a biosafety level 2 containment lab for high throughput screening. From a collection of 5,158 approved drugs and drug candidates, our screening efforts identified 7 active compounds that inhibited the SARS-CoV-2-S PP entry. Of these seven, six compounds were active against live replicating SARS-CoV-2 virus in a cytopathic effect assay. Our results demonstrated the utility of this assay in the discovery and development of SARS-CoV-2 entry inhibitors as well as the mechanistic study of anti-SARS-CoV-2 compounds. Additionally, particles pseudotyped with spike proteins from SARS-CoV-2 B.1.1.7 and B.1.351 variants were prepared and used to evaluate the therapeutic effects of viral entry inhibitors.
ORPER: a workflow for constrained SSU rRNA phylogenies
Authors: Cornet Luc , Ahn Anne-Catherine , Wilmotte Annick , Baurain Denis
Published: October 2021

The continuous increase of sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects evermore complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER” (containerized in Singularity), which allows determining the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.
GEF Cytohesin-2/ARNO: a novel bridge between cell migration and immunoregulation in synovial fibroblasts
Authors: Wang Yilin , Çil Çağlar , Harnett Margaret M. , Pineda Miguel A.
Published: October 2021

The guanine nucleotide exchange factor cytohesin-2 (ARNO) is a major activator of the small GTPase ARF6, and has been shown to play an important role(s) in cell adhesion, migration and cytoskeleton reorganization in various cell types and models of disease. Interestingly, dysregulated cell migration, in tandem with hyper-inflammatory responses, is one of the hallmarks associated with activated synovial fibroblasts (SFs) during chronic inflammatory joint diseases, like rheumatoid arthritis. The role of ARNO in this process was unknown but we hypothesized that the pro-inflammatory milieu of inflamed joints induces local activation of ARNO-mediated pathways in SFs, promoting an invasive cell phenotype that ultimately leads to bone and cartilage damage. Thus, we used small interference RNA to investigate the impact of ARNO on the pathological migration and inflammatory responses of murine SFs, revealing a fully functional ARNO-ARF6 pathway in SFs, which can be rapidly activated by IL-1β. Such activation promotes cell migration and formation of focal adhesions. Unexpectedly, ARNO was also shown to modulate SF-inflammatory responses, dictating the precise cytokine and chemokine expression profile. Our results uncover a novel role for ARNO in SF-dependent inflammation, that potentially links pathogenic migration with initiation of local joint inflammation, offering new approaches for targeting the fibroblast compartment in chronic arthritis and joint disease.
Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis
Authors: Peters Jessica K. , Tibble Ryan W. , Warminski Marcin , Jemielity Jacek , Gross John D.
Published: October 2021

Poxviruses encode decapping enzymes that remove the protective 5’ cap from both host and viral mRNAs to commit transcripts for decay by the cellular exonuclease Xrn1. Decapping by these enzymes is critical for poxvirus pathogenicity by means of simultaneously suppressing host protein synthesis and limiting the accumulation of viral dsRNA, a trigger for antiviral responses. Here we present the first high resolution structural view of the vaccinia virus decapping enzyme D9. This Nudix enzyme contains a novel domain organization in which a three-helix bundle is inserted into the catalytic Nudix domain. The 5’ mRNA cap is positioned in a bipartite active site at the interface of the two domains. Specificity for the methylated guanosine cap is achieved by stacking between conserved aromatic residues in a manner similar to that observed in canonical cap binding proteins VP39, eIF4E, and CBP20 and distinct from eukaryotic decapping enzyme Dcp2.
Novel elasticity measurement techniques reveal that the C. elegans cuticle is required for physical integrity with age
Authors: Rahimi Mohammad , Sohrabi Salman , Murphy Coleen T.
Published: October 2021

Changes in biomechanical properties have profound impacts on human health. C. elegans might serve as a model for studying the molecular genetics of mammalian tissue decline. Previously, we found that collagens are required for insulin signaling mutants’ long lifespan and that overexpression of specific collagens extends wild-type lifespan. However, whether these effects on lifespan are due to mechanical changes during aging has not yet been established. Here, we have developed two novel methods to study the cuticle: we measure mechanical properties of live animals using osmotic shock (OS), and we directly perform the tensile test (TT) on isolated cuticles using microfluidic technology. Using these tools, we find that cuticle, not the muscle, is responsible for changes in ‘stretchiness’ of C. elegans, and that cuticle stiffness is highly non-linear and anisotropic. We also found that collagen mutations alter integrity of the cuticle by significantly altering elasticity. Additionally, aging stiffens the cuticle under mechanical loads beyond the cuticle’s healthy stretched state. Measurements of elasticity showed that long-lived daf-2 mutants were considerably better at preventing progressive mechanical changes with age. These tests of C. elegans biophysical properties suggest that the cuticle is responsible for their resilience.
Linking individual differences in human primary visual cortex to contrast sensitivity around the visual field
Authors: Himmelberg Marc M. , Winawer Jonathan , Carrasco Marisa
Published: October 2021

A central question in neuroscience is how the organization of cortical maps relates to perception, for which human primary visual cortex (V1) is an ideal model system. V1 nonuniformly samples the retinal image, with greater cortical magnification (surface area per degree of visual field) at the fovea than periphery and at the horizontal than vertical meridian. Moreover, the size and cortical magnification of V1 varies greatly across individuals. Here, we used fMRI and psychophysics in the same observers to quantify individual differences in V1 cortical magnification and contrast sensitivity at the four polar angle meridians. Across observers, the overall size of V1 and localized cortical magnification positively correlated with contrast sensitivity. Moreover, greater cortical magnification and higher contrast sensitivity at the horizontal than the vertical meridian were strongly correlated. These data reveal a link between cortical anatomy and visual perception at the level of individual observer and stimulus location.
A high-carbohydrate diet prolongs dysbiosis and Clostridioides difficile carriage and increases late-onset CDI and mortality in a hamster model of infection
Authors: Bhute Shrikant S. , Mefferd Chrisabelle C. , Phan Jacqueline R. , Ahmed Muneeba , Fox-King Amelia E. , Alarcia Stephanie , Villarama Jacob V. , Abel-Santos Ernesto , Hedlund Brian P.
Published: October 2021

Studies using mouse models of Clostridioides difficile infection (CDI) have demonstrated a variety of relationships between dietary macronutrients on antibiotic-associated CDI; however, few of these effects have been examined in hamster models of CDI. In this study, we investigated the effect of a high-carbohydrate diet previously shown to protect mice from CDI on the progression and resolution of CDI in a hamster disease model. Hamsters fed the high-carbohydrate diet developed distinct diet-specific microbiomes during antibiotic treatment and CDI, with lower diversity, persistent C. difficile carriage, and delayed microbiome restoration. In contrast to 0% mortality in mice, 80% of hamsters fed the high-carbohydrate diet developed fulminant CDI and died, including several cases of late-onset CDI, whereas only 33% of hamsters fed a standard lab diet developed CDI only during the acute phase. We speculate that prolonged dysbiosis in these animals allowed C. difficile to proliferate following a three-day vancomycin course administered as part of this model system, leading to secondary CDI and eventual mortality. This study, along with similar studies in mouse models of CDI, suggests high-carbohydrate diets promote antibiotic-associated dysbiosis and long-term C. difficile carriage, which may convert to symptomatic CDI when conditions change.

Importance

The effects of diet on CDI are not completely known, although most studies in mouse CDI models show that dietary carbohydrates ameliorate CDI. Here, we used a high-carbohydrate diet previously shown to protect mice against CDI to assess its effect on a hamster model of CDI and paradoxically found that it promoted dysbiosis, C. difficile carriage, and higher mortality. A common thread in both mouse and hamster experimental models was that the high-carbohydrate diet promoted long-term carriage of C. difficile, which may have converted to fulminant CDI only in the highly susceptible hamster model system. If diets high in carbohydrates also promote dysbiosis and C. difficile carriage in humans, then these diets might paradoxically increase chances of CDI relapse despite their protective effects against primary CDI.
A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics
Authors: Burclaff Joseph , Bliton R. Jarrett , Breau Keith A , Ok Meryem T , Gomez-Martinez Ismael , Ranek Jolene S , Bhatt Aadra P , Purvis Jeremy E , Woosley John T , Magness Scott T
Published: October 2021

Background and Aims

Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 humans.

Methods

12,590 single epithelial cells from three independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and capacity for response to extrinsic signals along the gut axis across different humans.

Result

Cells were assigned to 25 epithelial lineage clusters. Human intestinal stem cells (ISCs) are not specifically marked by many murine ISC markers. Lysozyme expression is not unique to human Paneth cells (PCs), and PCs lack expression of expected niche-factors. BEST4+cells express NPY and show maturational differences between SI and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell-junction, and nutrient absorption genes show unappreciated regional expression differences across lineages. Differential expression of receptors and drug targets across lineages reveals biological variation and potential for variegated responses.

Conclusions

Our study identifies novel lineage marker genes; covers regional differences; shows important differences between mouse and human gut epithelium; and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomical regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.
LGG-1/GABARAP lipidation is dispensable for autophagy and development inC .elegans
Authors: Leboutet Romane , Largeau Céline , Prigent Magali , Quinet Grégoire , Rodriguez Manuel S. , Cuif Marie-Hélène , Culetto Emmanuel , Lefebvre Christophe , Legouis Renaud
Published: October 2021

The ubiquitin-like proteins Atg8/LC3/GABARAP are required for multiple steps of autophagy such as initiation, cargo recognition and engulfment, vesicle closure and degradation. Most of LC3/GABARAP functions are considered dependent on their post-translational modifications and addressing to membranes through a conjugation to a lipid, the phosphatidylethanolamine. Contrarily to mammals,C. eleganspossesses single homologs of LC3 and GABARAP families, named LGG-2 and LGG-1. Using site directed mutagenesis, we inhibited the conjugation of LGG-1 to the autophagosomal membrane and generated mutants that express only cytosolic forms, either the precursor or the cleaved protein. LGG-1 is an essential gene for autophagy and development inC. elegans, but we discovered that its functions could be fully achieved independently of its localization to the membrane. This study reveals an essential role for the cleaved form of LGG-1 in autophagy but also in an autophagy independent embryonic function. Our data question the use of the lipidated GABARAP/LC3 as the main marker of autophagic flux and highlight the high plasticity of autophagy.
Time-Dependent Image Restoration of Low-SNR Live Cell Ca2+ Fluorescence Microscopy Data
Authors: Woelk Lena-Marie , Kannabiran Sukanya A. , Brock Valerie , Gee Christine E. , Lohr Christian , Guse Andreas H. , Diercks Björn-Philipp , Werner René
Published: October 2021

Live cell Ca2+ fluorescence microscopy is a cornerstone of cellular signaling analysis and imaging. The demand for high spatial and temporal imaging resolution is, however, intrinsically linked to a low signal-to-noise ratio (SNR) of the acquired spatio-temporal image data, which impedes subsequent image analysis. Advanced deconvolution and image restoration algorithms can partly mitigate the corresponding problems, but are usually defined only for static images. Frame-by-frame application to spatio-temporal image data neglects inter-frame contextual relationships and temporal consistency of the imaged biological processes. Here, we propose a variational approach to time-dependent image restoration built on entropy-based regularization specifically suited to process low- and lowest-SNR fluorescence microscopy data. The advantage of the presented approach is demonstrated by means of four data sets: synthetic data for in-depth evaluation of the algorithm behavior; two data sets acquired for analysis of initial Ca2+ microdomains in T cells; and, to illustrate transferability of the methodical concept to different applications, one dataset depicting spontaneous Ca2+ signaling in jGCaMP7b-expressing astrocytes. To foster re-use and reproducibility, the source code is made publicly available.
How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations
Authors: Rath Soumya Lipsa , Tripathy Madhusmita , Mandal Nabanita
Published: October 2021

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unravelling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature induced fluctuations should be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low temperature behaviour. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~30 to 40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.
Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria
Authors: Brewer Tess E. , Wagner Andreas
Published: October 2021

Rapid bacterial growth depends on the speed at which ribosomes can translate mRNA into proteins. mRNAs that encode successive stretches of proline can cause ribosomes to stall, substantially reducing translation speed. Such stalling is especially detrimental for species that must grow and divide rapidly. Here we focus on di-prolyl motifs (XXPPX) and ask whether their incidence varies with growth rate. To find out we conducted a broad survey of such motifs in >3000 bacterial genomes across 36 phyla. Indeed, fast-growing species encode fewer motifs than slow-growing species, especially in highly expressed proteins. We also found many di-prolyl motifs within thermophiles, where prolines can help maintain proteome stability. Moreover, bacteria with complex, multicellular lifecycles also encode many di-prolyl motifs. This is especially evident in the slow-growing phylum Myxococcota. Bacteria in this phylum encode many serine-threonine kinases, and many di-prolyl motifs at potential phosphorylation sites within these kinases. Serine-threonine kinases are involved in cell signaling and help regulate developmental processes linked to multicellularity in the Myxococcota. Altogether, our observations suggest that weakened selection on translational rate, whether due to slow or thermophilic growth, may allow di-prolyl motifs to take on new roles in biological processes that are unrelated to translational rate.
Ubr1-induced selective endo-phagy/autophagy protects against the endosomal and Ca2+-induced proteostasis disease stress
Authors: Wang Ben B. , Xu Haijin , Isenmann Sandra , Huang Cheng , Elorza-Vidal Xabier , Rychkov Grigori Y , Estévez Raúl , Schittenhelm Ralf B. , Lukacs Gergely L. , Apaja Pirjo M.
Published: October 2021

The defence mechanisms against endo-lysosomal homeostasis stress remain incompletely understood. Here, we identify Ubr1 as a protein quality control (QC) ubiquitin ligase that counteracts proteostasis stress by enhancing cargo selective autophagy for lysosomal degradation. Astrocyte regulatory cluster membrane protein MLC1 mutations increased intracellular Ca2+and caused endosomal compartment stress by fusion and enlargement. Endosomal protein QC pathway using ubiquitin QC ligases CHIP and Ubr1 with ESCRT-machinery was able to target only a fraction of MLC1-mutants for lysosomal degradation. As a consequence of the endosomal stress, we found an alternative QC route dependent on Ubr1, SQSTM1/p62 and arginylation to bypass MLC1-mutants to endosomal autophagy (endo-phagy). Significantly, this unfolded a general biological endo-lysosomal QC pathway for arginylated Ubr1-SQSTM1/p62 autophagy targets during Ca2+-assault. Conversely, the loss of Ubr1 with the absence of arginylation elicited endosomal compartment stress. These findings underscore the critical housekeeping role of Ubr1-dependent endo-phagy/autophagy in constitutive and provoked endo-lysosomal proteostasis stress, and link Ubr1 to Ca2+-homeostasis and proteins implicated in various diseases including cancers and brain disorders.
A Deep Learning Proteomic Scale Approach for Drug Design
Authors: Overhoff Brennan , Falls Zackary , Mangione William , Samudrala Ram
Published: October 2021

Computational approaches have accelerated novel therapeutic discovery in recent decades. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multi-target therapeutic discovery, repurposing, and design aims to improve their efficacy and safety by employing a holistic approach by computing interaction signatures between every drug/compound and a large library of non-redundant protein structures corresponding to the human proteome fold space. These signatures are compared and analyzed to determine if a given drug/compound is efficacious and safe for a given indication/disease. In this study, we used a deep learning based autoencoder to first reduce the dimensionality of CANDO computed drug-proteome interaction signatures. We then employed a reduced conditional variational autoencoder to generate novel drug-like compounds when given a target encoded “objective” signature. Using this model, we designed compounds to recreate the interaction signatures for twenty approved and experimental drugs and showed that 16/20 designed compounds are predicted to be significantly (p-value ≤ .05) more behaviorally similar relative to all corresponding controls, and 20/20 are predicted to be more behaviorally similar relative to a random control. We further observed that redesigns of objectives developed via rational drug design perform significantly better than those derived from natural sources (p-value ≤.05), suggesting that the model has learned an abstraction of rational drug design. We also show that designed compounds are structurally diverse and synthetically feasible when compared to their respective objective drugs despite consistently high predicted behavioral similarity. Finally, we generated new designs that enhance thirteen drugs/compounds associated with non-small cell lung cancer and anti-aging properties using their predicted proteomic interaction signatures. This work represents a significant step forward in automating holistic therapeutic design with machine learning, and subsequently offers a reduction in the time needed to generate novel, effective, and safe drug leads for any indication.
The reovirus σ3 protein inhibits NF-κB-dependent antiviral signaling
Authors: McNamara Andrew J. , Brooks Austin D. , Danthi Pranav
Published: October 2021

Viral antagonism of innate immune pathways is a common mechanism by which viruses evade immune surveillance. Infection of host cells with reovirus leads to the blockade of NF-κB, a key transcriptional regulator of the hosts’ innate immune response. One mechanism by which reovirus infection results in inhibition of NF-κB is through a diminishment in levels of upstream activators, IKKβ and NEMO. Here, we demonstrate a second, distinct mechanism by which reovirus blocks NF-κB. We report that expression of a single viral protein, σ3, is sufficient to inhibit expression of NF-κB target genes. Further, σ3-mediated blockade of NF-κB occurs without changes to IKK levels or activity. Expression of only a subset of NF-κB target genes is reduced. Among NF-κB targets, the expression of type I interferon is significantly diminished by σ3 expression. Correspondingly, ectopic expression of σ3 enhances viral replication. Expression of NF-κB target genes varies following infection with closely related reovirus strains. Our genetic analysis identifies that these differences are controlled by polymorphisms in the amino acid sequence of σ3. This work identifies a new role for reovirus σ3 as a viral antagonist of the NF-κB-dependent antiviral pathways.

IMPORTANCE

Host cells mount a response to curb virus replication in infected cells and prevent spread of virus to neighboring, as yet uninfected cells. The NF-κB family of proteins is important for the cell to mediate this response. In this study, we show that a single protein, σ3, produced by mammalian reovirus, impairs the function of NF-κB. We demonstrate that by blocking NF-κB, σ3 diminishes the hosts’ response to infection and promotes viral replication. This work identifies a second, previously unknown mechanism by which reovirus blocks this aspect of the host cell response.
Performance Comparison of Computational Prediction Methods for the Function and Pathogenicity of Non-coding Variants
Authors: Wang Zheng , Zhao Guihu , Li Bin , Fang Zhenghuan , Chen Qian , Wang Xiaomeng , Luo Tengfei , Wang Yijing , Zhou Qiao , Li Kuokuo , Xia Lu , Zhang Yi , Zhou Xun , Pan Hongxu , Zhao Yuwen , Wang Yige , Wang Lin , Guo Jifeng , Tang Beisha , Xia Kun , Li Jinchen
Published: October 2021

Non-coding variants in the human genome greatly influence some traits and complex diseases by their own regulation and modification effects. Hence, an increasing number of computational methods are developed to predict the effects of variants in the human non-coding sequences. However, it is difficult for users with insufficient knowledge about the performances of computational methods to select appropriate computational methods from dozens of methods. In order to solve this problem, we assessed 12 performance measures of 24 methods on four independent non-coding variant benchmark datasets: (I) rare germline variant from ClinVar, (II) rare somatic variant from COSMIC, (III) common regulatory variant dataset, and (IV) disease associated common variant dataset. All 24 tested methods performed differently under various conditions, indicating that these methods have varying strengths and weaknesses under different scenarios. Importantly, the performance of existing methods was acceptable in the rare germline variant from ClinVar with area under curves (AUCs) of 0.4481 - 0.8033 and poor in the rare somatic variant from COSMIC (AUCs: 0.4984 - 0.7131), common regulatory variant dataset (AUCs: 0.4837 - 0.6472), and disease associated common variant dataset (AUCs: 0.4766 -0.5188). We also compared the prediction performance among 24 methods for non-codingde novomutations in autism spectrum disorder and found that the CADD and CDTS methods showed better performance. Summarily, we assessed the performances of 24 computational methods under diverse scenarios, providing preliminary advice for proper tool selection and new method development in interpreting non-coding variants.