Miracle-dz/UniFAR-FTUs huggingface dataset:
Heavy-tailed neuronal connectivity arises from Hebbian self-organization

The strengths of connections in networks of neurons are heavy-tailed, with some neurons connected much more strongly than most. Now a simple network model can explain how this heavy-tailed connectivity emerges across four different species. The connections in networks of neurons are heavy-tailed, with a small number of neurons connected much more strongly than the vast majority of pairs. However, it remains unclear whether this heavy-tailed connectivity emerges from simple underlying mechanisms. Here we propose a minimal model of synaptic self-organization: connections are pruned at random, and the synaptic strength rearranges under a mixture of preferential and random dynamics. Under these generic rules, networks evolve to produce distributions of connectivity strength that are asymptotically scale-free, with a power-law exponent that depends only on the probability of preferential (rather than random) growth. Extending our model to include neuronal activity and Hebbian plasticity, we find that clustering in the network also emerges naturally. We confirm these predictions in the connectomes of several animals, suggesting that heavy-tailed and clustered connectivity may arise from general principles of network self-organization rather than mechanisms specific to individual species or systems.
Affinity-optimizing variants within cardiac enhancers disrupt heart development and contribute to cardiac traits

Enhancers direct precise gene expression patterns during development and harbor the majority of variants associated with disease. We find that suboptimal affinity ETS transcription factor binding sites are prevalent within Ciona and human developmental heart enhancers. Here we demonstrate in two diverse systems, Ciona intestinalis and human iPSC-derived cardiomyocytes (iPSC-CMs), that single nucleotide changes can optimize the affinity of ETS binding sites, leading to gain-of-function gene expression associated with heart phenotypes. In Ciona, ETS affinity-optimizing SNVs lead to ectopic expression and phenotypic changes including two beating hearts. In human iPSC-CMs, an affinity-optimizing SNV associated with QRS duration occurs within an SCN5A enhancer and leads to increased enhancer activity. Our mechanistic approach provides a much-needed systematic framework that works across different enhancers, cell types and species to pinpoint causal enhancer variants contributing to enhanceropathies, phenotypic diversity and evolutionary changes. In Brief The prevalent use of low-affinity ETS sites within developmental heart enhancers creates vulnerability within genomes whereby single nucleotide changes can dramatically increase binding affinity, causing gain-of-function enhancer activity that impacts heart development. Highlights ETS affinity-optimizing SNVs can lead to migration defects and a multi-chambered heart. An ETS affinity-optimizing human SNV within an SCN5A enhancer increases expression and is associated with QRS duration. Searching for ETS affinity-optimizing variants is a systematic and generalizable approach to pinpoint causal enhancer variants.
Ablation of SYK kinase from primary human Natural Killer cells via CRISPR/Cas9 enhances cytotoxicity and cytokine production

Cytomegalovirus (CMV) infection alters natural killer (NK) cell phenotype and function toward a more memory-like immune state. These cells, termed adaptive NK cells, typically express CD57 and NKG2C but lack expression of the Fc receptor γ chain (Gene: FCER1G, FcRγ), PLZF, and SYK. Functionally, adaptive NK cells display enhanced antibody-dependent cellular cytotoxicity (ADCC) and cytokine production. However, the mechanism behind this enhanced function is unknown. To understand what drives cytotoxicity and cytokine production in adaptive NK cells, we optimized a CRISPR/Cas9 system to ablate genes from primary human NK cells. ADCC by human NK cells is exclusively mediated by the CD16A (FcγRIIIA) signaling apparatus, which includes FcRγ, CD3ζ, SYK, SHP-1, ZAP-70, and the transcription factor PLZF. We ablated the genes encoding these molecules and tested subsequent ADCC and cytokine production. We found that ablating the FcRγ chain caused a modest increase in TNFα production. Ablation of PLZF did not enhance ADCC or cytokine production. Importantly, SYK kinase ablation significantly enhanced both cytotoxicity and cytokine production, while ZAP-70 kinase ablation diminished function. Ablation of the phosphatase SHP-1 resulted in mixed effects on function, with NK cells demonstrating enhanced cytotoxicity but reduced cytokine production. These results indicate that the enhanced cytotoxicity and cytokine production of CMV-induced adaptive NK cells is more likely due to the loss of SYK than the lack of FcRγ or PLZF. The lack of SYK expression may limit SHP-1-mediated inhibition of CD16A signaling, leading to enhanced cytotoxicity and cytokine production. In addition to providing mechanistic answers about CMV-induced adaptive NK cell functionality, our results indicate that NK chimeric antigen receptor (CAR) therapeutics that invoke ADCC signaling molecules (e.g., CD3ζ chain) may benefit from ablating SYK, while maintaining ZAP-70, to increase functionality.
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its ∼30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages as: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein. Our data suggest that the nsp7- 10/11 structure in complex with Mpro strongly resembles the unbound polyprotein, and that both polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we used limited proteolysis assays to characterize the effect of a series of inhibitors/binders on Mpro processing of nsp7-11 and Mpro inhibition using a polyprotein substrate. Teaser We elucidated the structural basis of order of cleavage of SARS-CoV-2 nsp7-11 polyprotein, with implications for Mpro inhibition.
Impact of the aryl hydrocarbon receptor on Aurora A kinase and the G2/M phase pathway in hematopoietic stem and progenitor cells

Recent evidence suggests that the environment-sensing transcription factor aryl hydrocarbon receptor (AHR) is an important regulator of hematopoiesis. Yet, the mechanisms and extent of AHR-mediated regulation within the most primitive hematopoietic cells, hematopoietic stem and progenitor cells (HSPCs), are poorly understood. Through a combination of transcriptomic and flow cytometric approaches, this study provides new insight into how the AHR influences HSPCs. Comparative analysis of intraphenotypic transcriptomes of hematopoietic stem cells (HSCs) and multipotent progenitor (MPP) cells from AHR knockout (AHR KO) and wild-type (WT) mice revealed significant differences in gene expression patterns. Notable among these were differences in expression of cell cycle regulators, specifically an enrichment of G2/M checkpoint genes when Ahr was absent. This included the regulator Aurora A kinase (Aurka, AurA). Interrogation of AurA protein levels in HSPC subsets using flow cytometry, in combination with inducible AHR KO or in vivo AHR antagonism showed that attenuation of AHR increased levels of AurA in HSCs and lineage-biased MPP cells. Overall, these data highlight a potential novel mechanism by which AHR controls HSC homeostasis and HSPC differentiation. These findings advance the understanding of how AHR influences and regulates primitive hematopoiesis. Highlights (max 85 characters) AHR alters gene expression during HSC-MPP transition. Transcriptomic analysis shows AHR regulation of key G2/M phase regulators Inducible AHR KO mice show increased AurA levels in HSPC populations Acute antagonism of AHR increased AurA levels across multiple HSPC populations
Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery

Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP- dependent non-specific DNA binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParBpSM of the ribbon-helix-helix (RHH) family. We show that parSpSM with four or more contiguous ParBpSM-binding sequence repeats is required to assemble a stable ParApSM-ParBpSM complex and efficiently activate the ParApSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parSpSM sequence array destabilizes the ParApSM-ParBpSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParApSM-ATP.
The U.S. faculty job market survives the SARS-CoV-2 global pandemic

Purpose This paper aims to identify the extent to which the COVID-19 pandemic disrupted the academic job market and the ways in which faculty job applicants altered their applications in response to a changing academia. Design/methodology/approach The data presented here is the portion relevant to COVID-19 collected in a survey of faculty job applicants at the end of the 2019-2020 job cycle in North America (spring 2020). An additional “mid-pandemic” survey was used in fall 2020 for applicants participating in the following job search cycle to inquire about how they were adapting their application materials. A portion of data from the 2020-2022 job cycle surveys was used to represent the “late-pandemic”. Job posting data from the Higher Education Recruitment Consortium (HERC) is also used to study job availability. Findings Examination of faculty job postings from 2018 through 2022 found that while they decreased in 2020, the market recovered in 2021 and beyond. While the market recovered, approximately 10% of the faculty job offers reported by 2019–20 survey respondents were rescinded. Respondents also reported altering their application documents in response to the pandemic as well as delaying or even abandoning their faculty job search. Originality This paper provides a longitudinal perspective with quantitative data on how the academic job market changed through the major events of the COVID-19 pandemic in North America, a subject of intense discussion and stress, particularly amongst early career researchers.
DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery

We present here a bi-modal CNN based deep-learning system, DeepPlnc, to identify plant lncRNAs with high accuracy while using sequence and structural properties. Unlike most of the existing software, it works accurately even in conditions with ambiguity of boundaries and incomplete sequences. It scored consistently high for performance metrics while breaching accuracy of >98% when tested across a large number of validated instances. During benchmarking it consistently outperformed all the compared tools and maintained a highly significant lead in the range of 4.6%-10.3% from the second best performing tool (p-value << 0.01). DeepPlnc was used to annotate a de novo assembled transcriptome of a himalayan species where again it suggested its much better suitability for genome and transcriptome annotation purposes than the existing tools. DeepPlnc has been made freely available as a web-server and stand-alone program at https://scbb.ihbt. res.in/DeepPlnc/.
Historical forest disturbance results in variation in functional resilience of seed dispersal mutualisms

Mutualistic interactions provide essential ecosystem functions, such as promoting and maintaining diversity. Understanding if functionally important mutualisms are resilient (able to resist and recover) to anthropogenic disturbance is important to understand the capacity for diversity to recover. Animal-mediated seed dispersal supports plant population growth and community structure, and disturbance of this function can threaten plant diversity and contribute to low resiliency. Ant-mediated seed dispersal mutualisms are particularly sensitive to anthropogenic disturbance, as they rely on one to a few high-quality dispersal partners. In North American eastern deciduous forests (NAEDF), ants in the genus Aphaenogaster are “keystone dispersers” of 30-40% of understory forbs adapted to dispersal by ants (myrmecochores). The majority of present day NAEDF have regenerated from previous disturbance in the form of historical land use change (HLUC), due to clearing for agriculture. Previous studies have revealed that myrmecochore diversity is not resilient to HLUC. Here, we ask if seed dispersal mutualisms are resilient to HLUC and if decreases in mutualistic interactions with partners, Aphaenogaster sp. , or increases in antagonistic interactions cause degradation of function. In a large-scale natural experiment (20 sites), we measured seed removal, the abundance of mutualistic partners and other invertebrates interacting with seeds, myrmecochore cover and diversity, along with ant habitat and forest structure. We found lower and more variable seed removal in secondary forests compared to remnant forests. A path analysis of all forests revealed that abundance of mutualists was the primary determinant of variation in seed removal, and that seed damage by antagonists (invasive slugs) negatively affected dispersal and was higher in secondary forests. In a path analysis of remnant forests, the link between mutualist abundance and seed removal was absent, but present in the secondary forest path, suggesting that seed dispersal is more variable and dependent on mutualist abundance in secondary forests and is stable and high in remnant forests. Here we show that functional resilience to HLUC is variable and may impede recovery of understory plant communities. This work provides key insights on the effects of anthropogenic disturbance on mutualistic interactions and how the resilience of critical ecosystem functions impacts diversity resiliency.
Type I interferon and MAVS signaling restricts chikungunya virus heart infection and cardiac tissue damage

Chikungunya virus (CHIKV) infection has been associated with severe cardiac manifestations. However, how CHIKV infection leads to heart disease remains unknown. Using C57BL/6 mice, we show that cardiac fibroblasts are the main target of CHIKV infection in the heart, and that cardiac tissue infection induces a local and robust type I interferon (IFN-I) response in both infected and non-infected cardiac cells. The loss of IFN-I signaling results in increased CHIKV infection, virus spreading, and apoptosis in cardiac tissue. Importantly, signaling through the mitochondrial antiviral-signaling protein (MAVS) is essential for efficient CHIKV clearance from the heart. Indeed, persistent infection in cardiac tissue of MAVS-deficient mice leads to cardiac damage characterized by focal myocarditis and major vessel vasculitis. This study provides a new mouse model of CHIKV cardiac infection and mechanistic insight on how CHIKV can lead to cardiac damage, underscoring the importance of monitoring cardiac function in patients with CHIKV infections. mice were returned to their cages, mosquitoes were killed and homogenized, and viral titers of the infected mosquitoes were determined by plaque assay. Infected experimental mice were euthanized at different timepoints post infection by CO 2 inhalation. Blood was collected by cardiac puncture, and mice were immediately dissected for transcardiac perfusion. Mice were perfused with 30 ml of cold PBS with a 21G to 23G needle. Quality of cardiac perfusion was assessed by confirming full blood removal in liver and kidneys. Then, hearts were extracted and placed in a 12-well plate with 1 ml PBS. Each heart was opened in four chambers and confirmed free of any blood clot. All the mice in this study were perfused with the exception of those used for histopathology and immunostaining. Heart, calf muscle and pancreas were collected in 500 μl of PBS containing one (heart and pancreas) or two (calf muscle) 5 mm stainless steel beads (QIAGEN), homogenized with TissueLyser II (QIAGEN) at 30 1/s for 2 min (heart and pancreas) or 4 min (calf muscle). Debris was removed by centrifugation at 8,000 rpm for 8 min. Blood was collected in 1.5 ml tubes containing 20 ml of 0.5 M EDTA and centrifuged at 8,000 rpm for 8 min. Viral titers were quantified by plaque assay in cells or TCID 50 in BHK-21 cells.
Suction feeding of West African lungfish (Protopterus annectens): An XROMM analysis of jaw mechanics, cranial kinesis, and hyoid mobility

Suction feeding in fishes is characterized by rapid movement of cranial elements, but extant lungfishes (Sarcopterygii: Dipnoi) exhibit a reduced number and mobility of cranial bones relative to actinopterygian fishes. Despite fusion of cranial elements, lungfishes are proficient at suction feeding, though the impacts of novel cranial morphology and reduced cranial kinesis on feeding remain poorly understood. We used X-ray Reconstruction of Moving Morphology (XROMM) to study the kinematics of six mobile skeletal elements (neurocranium, upper jaw, lower jaw, ceratohyal, clavicle, and cranial rib) and two muscles (costoclavicular portion of the hypaxialis and rectus cervicis) during the feeding strikes of West African lungfish (Protopterus annectens). We found that feeding by P. annectens on non-evasive prey is relatively slow, with a mean time to peak gape of 264 ms. Lower jaw depression and clavicular rotation were hinge-like, with one degree of freedom, but the ceratohyals rotated in a complex motion involving depression and long-axis rotation. We quantified the relative contributions to oral cavity volume change (RCVC) and found that oral cavity expansion is driven primarily by ceratohyal and clavicle motion. P. annectens suction feeds relatively slowly but successfully through muscle shortening of hypaxial and rectus cervicis muscles driving extreme hyoid mobility.
Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics

Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived bile acids capable of inhibiting its growth, which are thought to be a mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. difficile remain unknown. In this study, we sought to use chemical proteomics to identify bile acid-interacting proteins in C. difficile. Using photoaffinity bile acid probes and chemical proteomics, we identified a previously uncharacterized MerR family protein, CD3583 (now BapR), as a putative bile acid-sensing transcription regulator. Our data indicate that BapR binds and is stabilized by lithocholic acid (LCA) in C. difficile. Although loss of BapR did not affect C. difficile’s sensitivity to LCA, ΔbapR cells elongated more in the presence of LCA compared to wild-type cells. Transcriptomics revealed that BapR regulates the expression of the gene clusters mdeA-cd3573 and cd0618-cd0616, and cwpV, with the expression of the mdeA-cd3573 locus being specifically de-repressed in the presence of LCA in a BapR-dependent manner. Electrophoretic mobility shift assays revealed that BapR directly binds to the mdeA promoter region. Since mdeA is involved in amino acid-related sulfur metabolism and the mdeA-cd3573 locus encodes putative transporters, we propose that BapR senses a gastrointestinal tract-specific small molecule, LCA, as an environmental cue for metabolic adaptation.
Genomic Signatures Associated with Transitions to Viviparity in Cyprinodontiformes

The transition from oviparity to viviparity has occurred independently over a hundred times across vertebrates, presenting a compelling case of phenotypic convergence. However, whether repeated, independent evolution of viviparity is driven by redeployment of similar genetic mechanisms and whether these leave a common genetic signature in genomic divergence remains unknown. Whilst investigations into the evolution of viviparity have demonstrated striking similarity among the genes and pathways involved across vertebrate groups, quantitative tests for genome-wide convergence provide ambivalent answers. Here, we investigate molecular convergence during independent transitions to viviparity across an order of ray-finned freshwater fish (Cyprinodontiformes). We assembled de novo and publicly-available genomes of viviparous and oviparous species to quantify molecular convergence across coding and non-coding regions. We found no evidence for an excess of molecular convergence in amino acid substitutions and rates of sequence divergence, implying independent genetic changes are associated with these transitions. However, statistical power and biological confounds (hemiplasy and introgression) could constrain our ability to detect correlated evolution. We therefore also identified candidate genes with potential signatures of molecular convergence in viviparous Cyprinodontiformes lineages. While we detected no evidence of positive or relaxed selection for these genes in branches associated with the evolution of viviparity in Cyprinodontiformes, motif-enrichment and gene ontology analyses suggest transcriptional changes associated with early morphogenesis, brain development and immunity occurred alongside the evolution of viviparity. Overall, our findings indicate that an excess of molecular convergence, at any level, is not strongly associated with independent transitions to viviparity in these fish.