bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells
Authors: Rangan Ramya , Khavnekar Sagar , Lerer Adam , Johnston Jake , Kelley Ron , Obr Martin , Kotecha Abhay , Zhong Ellen D. 
Published: August 2023

ABSTRACTAdvances in cryo-electron tomography (cryo-ET) have produced new opportunities to visualize the structures of dynamic macromolecular machinery in native cellular environments. Here, we describe a machine learning approach that can reconstruct the structural landscape and dynamics of biomolecular complexes present in cryo-ET subtomograms. This method, cryoDRGN-ET, learns a deep generative model of 3D density maps directly from subtomogram tilt series images and can capture states diverse in both composition and conformation. We use this approach to reconstruct thein situtranslation dynamics of prokaryotic ribosomes, and we reveal the distribution of functional states during translation elongation populated byS. cerevisiaeribosomes inside cells.
Targeting host deoxycytidine kinase mitigatesStaphylococcus aureusabscess formation
Authors: Winstel Volker , Abt Evan R. , Le Thuc M. , Radu Caius G. 
Published: August 2023

AbstractHost-directed therapy (HDT) is an emerging approach to overcome antimicrobial resistance in pathogenic microorganisms. Specifically, HDT targets host-encoded factors required for pathogen replication and survival without interfering with microbial growth or metabolism, thereby eliminating the risk of resistance development. By applying HDT and a drug repurposing approach, we demonstrate that (R)-DI-87, a clinical-stage anti-cancer drug and potent inhibitor of mammalian deoxycytidine kinase (dCK), mitigatesStaphylococcus aureusabscess formation in organ tissues upon invasive bloodstream infection. Mechanistically, (R)-DI-87 shields phagocytes from staphylococcal death-effector deoxyribonucleosides that target dCK and the mammalian purine salvage pathway-apoptosis axis. In this manner, (R)-DI-87-mediated protection of immune cells amplifies macrophage infiltration into deep-seated abscesses, a phenomenon coupled with enhanced pathogen control, ameliorated immunopathology, and reduced disease severity. Thus, pharmaceutical blockade of dCK represents an advanced anti-infective intervention strategy against which staphylococci cannot develop resistance and may help to fight fatal infectious diseases in hospitalized patients.
Temporal regularities shape perceptual decisions and striatal dopamine signals
Authors: Fritsche Matthias , Majumdar Antara , Strickland Lauren , Liebana Garcia Samuel , Bogacz Rafal , Lak Armin 
Published: August 2023

AbstractPerceptual decisions should depend on sensory evidence. However, such decisions are also influenced by past choices and outcomes. These choice history biases may reflect advantageous strategies to exploit temporal regularities of natural environments. However, it is unclear whether and how observers can adapt their choice history biases to different temporal regularities, to exploit the multitude of temporal correlations that exist in nature. Here, we show that mice adapt their perceptual choice history biases to different temporal regularities. This adaptation is well captured by a normative reinforcement learning algorithm with multi-trial belief states, comprising both current trial sensory and previous trial memory states. We demonstrate that striatal dopamine tracks predictions of the model and behavior, pointing towards the involvement of dopamine in forming adaptive history biases. Our results reveal the adaptive nature of perceptual choice history biases, and shed light on their underlying computational principles and neural implementation.
Hyperactivity of mTORC1 and mTORC2-dependent signaling mediate epilepsy downstream of somatic PTEN loss
Authors: Cullen Erin R. , Safari Mona , Mittelstadt Isabelle , Weston Matthew C. 
Published: August 2023

AbstractGene variants that hyperactivate PI3K-mTOR signaling in the brain lead to epilepsy and cortical malformations in humans. Some gene variants associated with these pathologies only hyperactivate mTORC1, but others, such asPTEN,PIK3CA, andAKT, hyperactivate both mTORC1- and mTORC2-dependent signaling. Previous work established a key role for mTORC1 hyperactivity in mTORopathies, however, whether mTORC2 hyperactivity contributes is not clear. To test this, we inactivated mTORC1 and/or mTORC2 downstream of earlyPtendeletion in a new model of somaticPtenloss-of-function (LOF) in the cortex and hippocampus. Spontaneous seizures and epileptiform activity persisted despite mTORC1 or mTORC2 inactivation alone, but inactivating both mTORC1 and mTORC2 simultaneously normalized brain activity. These results suggest that hyperactivity of both mTORC1 and mTORC2 can cause epilepsy, and that targeted therapies should aim to reduce activity of both complexes.
Local translation is engaged to sustain synaptic function in impaired Wallerian degeneration
Authors: Paglione Maria , Restivo Leonardo , Zakhia Sarah , Rosell Arnau Llobet , Terenzio Marco , Neukomm Lukas J. 
Published: August 2023

AbstractAfter injury, the severed axon separated from the soma activates programmed axon degeneration, an evolutionarily conserved pathway to initiate its degeneration within a day. Conversely, severed projections deficient in programmed axon degeneration remain morphologically preserved with functional synapses for weeks to months after injury. How this synaptic function is sustained remains currently unknown. Here, we demonstrate that dNmnat-mediated over-expression attenuates programmed axon degeneration in distinct neuronal populations. Severed projections remain morphologically preserved for weeks after injury. When evoked, they elicit a postsynaptic behavior which is a readout for preserved synaptic function. We used ribosomal pulldown to isolate translatomes from these projections. Transcriptional profiling revealed several enriched biological classes. Identified candidates were validated in a screen using a novel system to automatically quantify evoked antennal grooming behavior as a proxy for preserved synaptic function. We used RNAi-mediated knockdown to identify mTOR as a mediator of local protein synthesis, and specifically candidates involved in protein ubiquitination and calcium homeostasis, required for preserved synaptic function. Our dataset uncovered several uncharacterized genes linked to human diseases. It may therefore offer insights into novel avenues for therapeutic treatments.
Retinal origin of orientation but not direction selective maps in the superior colliculus
Authors: de Malmazet Daniel , Kühn Norma K. , Li Chen , Farrow Karl 
Published: August 2023

AbstractNeurons in the mouse superior colliculus (“colliculus”) are arranged in ordered spatial maps. While orientationselective (OS) neurons form a concentric map aligned to the center of vision, direction-selective (DS) neurons are arranged in patches with changing preferences across the visual field. It remains unclear if these maps are a consequence of feed-forward input from the retina or local computations in the colliculus. To determine whether these maps originate in the retina, we mapped the local and global distribution of orientation- and direction-selective retinal ganglion cell boutons using in-vivo two-photon calcium imaging. We found that OS boutons formed patches that matched the distribution of OS neurons within the colliculus. DS boutons displayed less regional specializations, better reflecting the organization of DS neurons in the retina. Both eyes convey similar orientation but different DS inputs to the colliculus, as shown in recordings from retinal explants. These data demonstrate that orientation and direction maps within the colliculus are independent, implying that orientation maps are inherited from the retina, but direction maps require local circuits.
The role of heterochronic gene expression and regulatory architecture in early developmental divergence
Authors: Harry Nathan D. , Zakas Christina 
Published: August 2023

ABSTRACTNew developmental programs can evolve through adaptive changes to gene expression. The annelidStreblospio benedictihas a developmental dimorphism, which provides a unique intraspecific framework for understanding the earliest genetic changes that take place during developmental divergence. Using comparative RNAseq through ontogeny, we find that only a small proportion of genes are differentially expressed at any time, despite major differences in larval development and life-history. These genes shift expression profiles across morphs by either turning off any expression in one morph or changing the timing or amount of gene expression. We directly connect the contributions of these mechanisms to differences in developmental processes. We examine F1offspring— using reciprocal crosses— to determine maternal mRNA inheritance and the regulatory architecture of gene expression. These results highlight the importance of both novel gene expression and heterochronic shifts in developmental evolution, as well as thetrans-acting regulatory factors in initiating divergence.
Cell-Free Protein Expression in Polymer Materials
Authors: Lee Marilyn S. , Lee Jennifer A. , Biondo John R. , Lux Jeffrey E. , Raig Rebecca M. , Berger Pierce N. , Bernhards Casey B. , Kuhn Danielle L. , Gupta Maneesh K. , Lux Matthew W. 
Published: August 2023

ABSTRACTWhile synthetic biology has advanced complex capabilities like sensing and molecule synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics makes incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over cellular viability or release of genetically modified organisms. Here we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobialsin situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable bio-functionality in a ubiquitous class of synthetic materials.
Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity ofStaphylococcus saprophyticus
Authors: Youngblom Madison A. , Imhoff Madeline R. , Smyth Lilia M. , Mohamed Mohamed A. , Pepperell Caitlin S. 
Published: August 2023

AbstractStaphylococcus saprophyticusis a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods.S. saprophyticusis also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample ofS. saprophyticusisolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations ofS. saprophyticus. We found that divergence of the two major clades ofS. saprophyticusis likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described inS. saprophyticusand its association with bovine mastitis. Finally, we found that in general, strains ofS. saprophyticusfrom different niches are genetically similar with the exception of built environments, which function as a ‘sink’ forS. saprophyticuspopulations. This work increases our understanding of the ecology ofS. saprophyticusand of the genomics of bacterial generalists.Data summaryRaw sequencing data for newly sequencedS. saprophyticusisolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here:https://github.com/myoungblom/sapro_genomics.Impact statementIt is not known whether human and cattle diseases caused byS. saprophyticusrepresent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles ofS. saprophyticusUTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found thatS. saprophyticusappears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.
Transcriptional Profiles of Non-neuronal and Immune Cells in Mouse Trigeminal Ganglia
Authors: Mecklenburg Jennifer , Shein Sergey A. , Hovhannisyan Anahit H. , Zou Yi , Lai Zhao , Ruparel Shivani , Tumanov Alexei V. , Akopian Armen N. 
Published: August 2023

AbstractNon-neuronal cells constitute 90-95% of sensory ganglia. These cells play critical roles in modulation of nociceptive signal transmissions by sensory neurons. Accordingly, the aim of this review-study was to identify, profile and summarize TG non-neuronal cell types in naïve male mice using published and our own data generated by single-cell RNA sequencing (scRNA-seq), flow cytometry (FC) and immunohistochemistry (IHC). TG contains 5 types of non-neuronal cells: glial, fibroblasts, smooth muscle, endothelial and immune cells. There is agreement among publications for glial, fibroblasts, smooth muscle and endothelial cells. Based on gene profiles, glial cells were classified as Schwann cells and satellite glial cells (SGC).Mpzhad dominant expression in Schwann cells, andFabp7is specific for SCG. Two types of Col1a2+fibroblasts located throughout TG were distinguished using gene profiles. TG smooth muscle and endothelial cells representing blood vessels were detected with well recognized markers. Our study split reported single TG immune cell group into 3 types of macrophages and 4 types of neutrophils. Macrophages were located among neuronal bodies and nerve fibers, and were sub-grouped by unique transcriptomic profiles and usingCcr2,Cx3cr1andIba1as markers. S100a8+neutrophils were located in dura surrounding TG and were sub-grouped by clustering and expressions ofCsf3r,Ly6G, Ngp, ElaneandMpo. Overall, generated and summarized here dataset on non-neuronal TG cells could provide essential and fundamental information for studies on cell plasticity, interactomic network between neurons and non-neuronal cells and function during variety of pain conditions in the head and neck region.
Development of Polarity-Reversed Endometrial Epithelial Organoids
Authors: Ahmad Vakil , Yeddula Sai Goutham Reddy , Telugu Bhanu P. , Spencer Thomas E. , Kelleher Andrew M. 
Published: August 2023

AbstractThe uterine epithelium is composed of a single layer of hormone responsive polarized epithelial cells that line the lumen and form tubular glands. Endometrial epithelial organoids (EEO) can be generated from uterine epithelia and recapitulate cell composition and hormone responsesin vitro. As such, the development of EEO represents a major advance for facilitating mechanistic studiesin vitro. However, a major limitation for the use of EEO cultured in basement membrane extract and other hydrogels is the inner location of apical membrane, thereby hindering direct access to the apical surface of the epithelium to study interactions with the embryo or infectious agents such as viruses and bacteria. Here, a straightforward strategy was developed that successfully reverses the polarity of EEO. The result is an apical-out organoid that preserves a distinct apical-basolateral orientation and remains responsive to ovarian steroid hormones. Our investigations highlight the utility of polarity-reversed EEO to study interactions withE. coliand blastocysts. This method of generating apical-out EEO lays the foundation for developing newin vitrofunctional assays, particularly regarding epithelial interactions with embryos during pregnancy or other luminal constituents in a pathological or diseased state.
Protein Kinase A is a Functional Component of Focal Adhesions
Authors: Kang Mingu , Senatore Amanda J. , Naughton Hannah , McTigue Madeline , Beltman Rachel J. , Herppich Andrew A. , Pflum Mary Kay H. , Howe Alan K. 
Published: August 2023

ABSTRACTFocal adhesions (FAs) form the junction between extracellular matrix (ECM)-bound integrins and the actin cytoskeleton and also transmit signals that regulate cell adhesion, cytoskeletal dynamics, and cell migration. While many of these signals are rooted in reversible tyrosine phosphorylation, phosphorylation of FA proteins on Ser/Thr residues is far more abundant yet its mechanisms and consequences are far less understood. The cAMP-dependent protein kinase (protein kinase A; PKA) has important roles in cell adhesion and cell migration and is both an effector and regulator of integrin-mediated adhesion to the ECM. Importantly, subcellular localization plays a critically important role in specifying PKA function. Here, we show that PKA is present in isolated FA-cytoskeleton complexes and active within FAs in live cells. Furthermore, using kinase-catalyzed biotinylation of isolated FA-cytoskeleton complexes, we identify fifty-three high-stringency candidate PKA substrates within FAs. From this list, we validate tensin-3 (Tns3) – a well-established molecular scaffold, regulator of cell migration, and component of focal and fibrillar adhesions – as a novel direct substrate for PKA. These observations identify a new pathway for phospho-regulation of Tns3 and, importantly, establish a new and important niche for localized PKA signaling and thus provide a foundation for further investigation of the role of PKA in the regulation of FA dynamics and signaling.
Clonal and Scalable Endothelial Progenitor Cell Lines from Human Pluripotent Stem Cells
Authors: Lee Jieun , Sternberg Hal , Bignone Paola A. , Murai James , Malik Nafees N. , West Michael D. , Larocca Dana 
Published: August 2023

AbstractHuman pluripotent stem cells (hPSCs) can be used as a renewable source of endothelial cells for treating cardiovascular disease and other ischemic conditions. Here, we present the derivation and characterization of a panel of distinct clonal embryonic endothelial progenitor cell (eEPC) lines that were differentiated from human embryonic stem cells (hESCs). The hESC line, ESI-017, was first partially differentiated to produce candidate cultures from which eEPC were cloned. Endothelial cell identity was assessed by transcriptomic analysis, cell surface marker expression, immunocytochemical marker analysis, and functional analysis using a vascular network forming assay. The transcriptome of the eEPC lines was compared to various adult endothelial lines as well as various non-endothelial cells including both adult and embryonic origins. This resulted in a variety of distinct cell lines with functional properties of endothelial cells and strong transcriptomic similarity to adult endothelial primary cell lines. The eEPC lines, however, were distinguished from adult endothelium by a novel pattern of embryonic gene expression. We demonstrated scalability of up to 80 population doublings and stable with long-term expansion over 50 passages and stable angiogenic properties at late passage in the EPC line. Taken together, these data support the finding that hESC-derived clonal eEPC lines are useful as a source of scalable therapeutic cells and cell products for treating cardiovascular disease. These eEPC lines offer a highly promising resource for preclinical studies and therapeutic interventions.
Emerging Threat of Ranavirus: Prevalence, Genetic Diversity, and Climatic Drivers ofRanavirus(Family Iridoviridae) in ectothermic vertebrates of Asia
Authors: Herath Jayampathi , Dan Sun , Ellepola Gajaba , Subramaniam Kuttichantran , Meegaskumbura Madhava 
Published: August 2023

ABSTRACTRanavirus disease, caused by viruses within the genusRanavirus(familyIridoviridae), is considered a globally emerging infectious disease linked to mass mortality events in both wild and cultured ectothermic vertebrates. Surveillance work is however limited in Asia hence prevalence and the dynamics of the disease remains poorly understood. To understand disease burden and the potential biotic and abiotic drivers in southern China region, we conducted a systematic surveillance of the ranavirus across Guangxi Zhuang Autonomous region (GAR). For this, we used a multifaceted approach involving screening of amphibians and other potential reservoirs, diagnostic tests, phylogenetic analyses, prevalence estimation, co-infection assessments, and climatic niche analyses. Over one thousand individuals were sampled across 25 sampling sites. We found ninety-two individuals from 18 species of ectothermic vertebrates to be infected with ranavirus. Two lineages were responsible – Rana nigromaculata ranavirus and Tiger frog virus were identified using phylogenetic analysis based on the major capsid protein (MCP) gene fragment. We also found evidence of a co-infection with ranavirus andBdthat can be highly detrimental to host populations; possibly the first such documentation in Asia. Our niche modelling analysis suggests that precipitation and seasonality play an important role in ranavirus prevalence in Guangxi region – southwestern, southeastern, central and northeastern regions of GAR can be considered to be optimum habitats for ranaviruses. Infection rates in wild frog species have reached 100% in some areas, even in nature reserves. Our research also indicates that culture facilities and pet farms are frequently infected, serving as likely vectors for the regional and global spread of ranaviruses. The knowledge generated suggests the need for systematic surveillance, stringent biosecurity measures, and control of international animal trade to prevent further transmission and protection of biodiversity and aquaculture industries across Asia.