bluuebunny/crossref_metadata_2025_split huggingface dataset:
N-myc Downstream Regulated Gene 1 (NDRG1) functions as a molecular switch for cellular adaptation to hypoxia
Authors: Park Jong S. , Gabel Austin M. , Kassir Polina , Kang Lois , Chowdhary Prableen K. , Osei-Ntansah Afia , Tran Neil D. , Viswanathan Soujanya , Canales Bryanna , Ding Pengfei , Lee Young-Sam , Brewster Rachel 
Published: September 2021

ABSTRACTLack of oxygen (hypoxia and anoxia) is detrimental to cell function and survival and underlies many disease conditions. Hence, metazoans have evolved mechanisms to adapt to low oxygen. One such mechanism, metabolic suppression, decreases the cellular demand for oxygen by downregulating ATP-demanding processes. However, the molecular mechanisms underlying this adaptation are poorly understood. Here, we report on the role of ndrg1a in hypoxia adaptation of the anoxia-tolerant zebrafish embryo. ndrg1a is expressed in the kidney and ionocytes, cell types that use large amounts of ATP to maintain ion homeostasis. ndrg1a mutants are viable and develop normally when raised under normal oxygen. However, their survival and kidney function is reduced relative to WT embryos following exposure to prolonged anoxia. We further demonstrate that Ndrg1a binds to the energy-demanding sodium-potassium ATPase (NKA) pump under anoxia and is required for its degradation, which may preserve ATP in the kidney and ionocytes and contribute to energy homeostasis. Lastly, we show that sodium azide treatment, which increased lactate levels, was sufficient to trigger NKA degradation in an Ndrg1a-dependent manner. These findings support a model whereby Ndrg1a is essential for hypoxia adaptation and functions downstream of lactate signaling to induce NKA degradation, a process known to conserve cellular energy.
Cytosolic aspartate aminotransferase moonlights as a ribosome binding modulator of Gcn2 activity during oxidative stress
Authors: Crawford Robert A. , Ashe Mark P. , Hubbard Simon J. , Pavitt Graham D. 
Published: September 2021

AbstractRegulation of translation is a fundamental facet of the cellular response to rapidly changing external conditions. Specific RNA-binding proteins (RBPs) co-ordinate the translational regulation of distinct mRNA cohorts during stress. To identify RBPs with previously under-appreciated roles in translational control, we used polysome profiling and mass spectrometry to identify and quantify proteins associated with translating ribosomes in unstressed yeast cells and during oxidative stress and amino acid starvation, which both induce the integrated stress response (ISR). Over 800 proteins were identified across polysome gradient fractions, including ribosomal proteins, translation factors and many others without previously described translation-related roles, including numerous metabolic enzymes. We identified variations in patterns of polysome enrichment in both unstressed and stressed cells and identified proteins enriched in heavy polysomes during stress. Genetic screening of polysome-enriched RBPs identified the cytosolic aspartate aminotransferase, Aat2, as a ribosome-associated protein whose deletion conferred growth sensitivity to oxidative stress. Loss of Aat2 caused aberrantly high activation of the ISR via enhanced eIF2α phosphorylation andGCN4activation. Importantly, non-catalyticAAT2mutants retained polysome association and did not show heightened stress sensitivity. Aat2 therefore has a separate ribosome-associated translational regulatory or ‘moonlighting’ function that modulates the ISR independent of its aspartate aminotransferase activity.
A transcriptome atlas of the mouse iris at single cell resolution defines cell types and the genomic response to pupil dilation
Authors: Wang Jie , Rattner Amir , Nathans Jeremy 
Published: September 2021

AbstractThe iris controls the level of retinal illumination by controlling pupil diameter. It is a site of diverse ophthalmological diseases and it is a potential source of cells for ocular auto-transplantation. The present study provides foundational data on the mouse iris based on single nucleus RNA sequencing. More specifically, this work has (1) defined all of the major cell types in the mouse iris and ciliary body, (2) led to the discovery of two types of iris stromal cells and two types of iris sphincter cells, (3) revealed the differences in cell type-specific transcriptomes in the resting, constricted, and dilated states, and (4) identified and validated antibody and in situ hybridization probes that can be used to visualize the major iris cell types. By immunostaining for specific iris cell-types, we have observed and quantified distortions in nuclear morphology associated with iris dilation and clarified the neural crest contribution to the iris by showing thatWnt1-Cre-expressing progenitors contribute to nearly all iris cell types, whereasSox10-Cre-expressing progenitors contribute only to stromal cells. This work should be useful as a point of reference for investigations of iris development, disease, and pharmacology, for the isolation and propagation of defined iris cell types, and for iris cell engineering and transplantation.
Multi-omic Characterization of Pancreatic Cancer-Associated Macrophage Polarization Reveals Deregulated Metabolic Programs Driven by the GMCSF-PI3K Pathway
Authors: Boyer Seth M. , Lee Ho-Joon , Steele Nina G. , Zhang Li , Sajjakulnukit Peter , Andren Anthony , Ward Matthew H. , Basrur Venkatesha , Zhang Yaqing , Nesvizhskii Alexey I. , di Magliano Marina Pasca , Halbrook Christopher J. , Lyssiotis Costas A. 
Published: September 2021

AbstractThe pancreatic ductal adenocarcinoma (PDA) microenvironment is composed of a variety of cell types and marked by extensive fibrosis and inflammation. Tumor-associated macrophages (TAM) are abundant, and they are important mediators of disease progression and invasion. TAMs are polarized in situ to a tumor promoting and immunosuppressive phenotype via cytokine signaling and metabolic crosstalk from malignant epithelial cells and other components of the tumor microenvironment (TME). However, the specific distinguishing features and functions of TAMs remain poorly defined. Here, we generated tumor-educated macrophages (TEM)in vitroand performed detailed, multi-omic characterization (i.e. transcriptomics, proteomics, metabolomics). Our results reveal unique genetic and metabolic signatures of TEMs, the veracity of which were queried against our in-house single cell RNA sequencing (scRNA-seq) dataset of human pancreatic tumors. This analysis identified expression of novel, metabolic TEM markers in human pancreatic TAMs, including ARG1, ACLY, and TXNIP. We then utilized our TEM model system to study the role of mutant Kras signaling in cancer cells on TEM polarization. This revealed an important role for GM-CSF and lactate on TEM polarization, molecules released from cancer cells in a mutant Kras-dependent manner. Lastly, we demonstrate that GM-CSF dysregulates TEM gene expression and metabolism through PI3K-AKT pathway signaling. Collectively, our results define new markers and programs to classify pancreatic TAMs, how these are engaged by cancer cells, and the precise signaling pathways mediating polarization.
AgRP neurons coordinate the mitigation of activity-based anorexia
Authors: Sutton Ames K. , Duane Sean C. , Shamma Ahmed M. , Skillings Anna , Krashes Michael J. 
Published: September 2021

AbstractAnorexia nervosa (AN) is a debilitating and deadly disease characterized by low body mass index due to diminished food intake, and oftentimes concurrent hyperactivity. A high percentage of AN behavioral and metabolic phenotypes can be replicated in rodents given access to a voluntary running wheel and subject to food restriction, termed activity-based anorexia (ABA). Despite the well-documented body weight loss observed in AN human patients and ABA rodents, much less is understood regarding the neurobiological underpinnings of these maladaptive behaviors. Moreover, while exercise has been shown to diminish the activity of hunger-promoting hypothalamic agouti-related peptide (AgRP) neurons, much less is known regarding their activity and function in the mediation of food intake during ABA. Here, feeding microstructure analysis revealed ABA mice decreased food intake due to increased interpellet interval retrieval and diminished meal number. Longitudinal activity recordings of AgRP neurons in ABA animals revealed a maladaptive inhibitory response to food. We then demonstrated that ABA development or progression can be mitigated by chemogenetic AgRP activation through the reprioritization of food intake (increased meal number) over hyperactivity. These results elucidate a potential neural target for the amelioration of behavioral maladaptations present in AN patients.
Combining CRISPR/Cas9 and brain imaging: from genes to molecules to networks
Authors: Marciano Sabina , Ionescu Tudor Mihai , Saw Ran Sing , Cheong Rachel Y. , Kirik Deniz , Maurer Andreas , Pichler Bernd , Herfert Kristina 
Published: September 2021

AbstractReceptors, transporters and ion channels are important targets for therapy development in neurological diseases including Alzheimeŕs disease, Parkinsońs disease, epilepsy, schizophrenia and major depression. Several receptors and ion channels identified by next generation sequencing may be involved in disease initiation and progression but their mechanistic role in pathogenesis is often poorly understood. Gene editing andin vivoimaging approaches will help to identify the molecular and functional role of these targets and the consequence of their regional dysfunction on whole brain level. Here, we combine CRISPR/Cas9 gene-editing within vivopositron emission tomography (PET) and functional magnetic resonance imaging (fMRI) to investigate the direct link between genes, molecules, and the brain connectome. The extensive knowledge of theSlc18a2gene encoding the vesicular monoamine transporter (VMAT2), involved in the storage and release of dopamine, makes it an excellent target for studying the gene networks relationships while structurally preserving neuronal integrity and function. We edited theSlc18a2in the substantia nigra pars compacta of adult rats and usedin vivomolecular imaging besides behavioral, histological, and biochemical assessments to characterize the CRISPR/Cas9-mediated VMAT2 knockdown. Simultaneous PET/fMRI was performed to investigate molecular and functional brain alterations. We found that stage-specific adaptations of brain functional connectivity follow the selective impairment of presynaptic dopamine storage and release. Our study reveals that recruiting different brain networks is an early response to the dopaminergic dysfunction preceding neuronal cell loss. Our combinatorial approach is a novel tool to investigate the impact of specific genes on brain molecular and functional dynamics which will help to develop tailored therapies for normalizing brain function. The method can easily be transferred to higher-order species allowing for a direct comparison of the molecular imaging findings.
Bacterial supergroup specific “Cost” of Wolbachia infections in Nasonia vitripennis
Authors: Tiwary Alok , Babu Rahul , Sen Ruchira , Raychoudhury Rhitoban 
Published: September 2021

AbstractThe maternally-inherited endosymbiont, Wolbachia, is known to alter the reproductive biology of its arthropod hosts for its benefit and can induce both positive and negative fitness effects in many hosts. Here we describe the effects of the maintenance of two distinct Wolbachia infections, one each from supergroups A and B, on the parasitoid host Nasonia vitripennis. We compare the effect of Wolbachia infections on various traits between the uninfected, single A infected, single B infected, and the double infected strains with their cured versions. Contrary to the previous reports, our results suggest that there is a significant cost associated with the maintenance of Wolbachia infections where traits like family size, fecundity, longevity, and rates of male copulation are compromised in Wolbachia infected strains. The double infected and supergroup B infection strains show higher Wolbachia titer than supergroup A. The double infected Wolbachia strain has the most detrimental impact on the host as compared to single infections. Moreover, there is a supergroup-specific negative impact on these wasps as the supergroup B infections elicit the most pronounced negative effects. These findings raise important questions on the mechanism of survival and maintenance of these reproductive parasites in arthropod hosts.
Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome
Authors: Lin Changfan , Schneps Connor M. , Chandrasekaran Siddarth , Ganguly Abir , Crane Brian R. 
Published: September 2021

SUMMARYCryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light and triggering its degradation. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM binding. A generally-applicable Select Western-blot-Free Tagged-protein Interaction (SWFTI) assay enables quantification of CRY binding to TIM in dark and light. The assay is utilized to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bind TIM constitutively, whereas those incapable of photoreduction bind TIM weakly. In response to flavin redox state, two conserved histidine residues contribute to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify protein-protein interactions and photoreceptor targeting.
The influence of age and sex on the pre-treatment immune microenvironment of a carcinogen induced murine model of bladder cancer
Authors: Hamade Ali , Li Deyang , Tyryshkin Kathrin , Xu Minqi , Chenard Stephen , Conseil Gwenaelle , Yolmo Priyanka , Siemens D. Robert , Koti Madhuri 
Published: September 2021

AbstractThe incidence of urothelial carcinoma of the bladder is four times higher in males than females; however, females tend to present with a more aggressive disease, a poorer response to immunotherapy and suffer worse clinical outcomes. Recent findings have demonstrated sexual dimorphism in the tumor immune microenvironment of non-muscle invasive bladder cancer and associated clinical outcomes. However, a significant gap in knowledge remains with respect to the current pre-clinical modeling approaches and more precisely recapitulating these differences towards improved therapeutic design. Based on the similarities in mucosal immune physiology between humans and mice, we evaluated the sex and age-related immune alterations in healthy murine bladders. Bulk-RNA sequencing and multiplex immunofluorescence based spatial immune profiling of healthy murine bladders from male and female mice of age groups spanning young to old showed a highly altered immune landscape that exhibited sex and age associated differences, particularly in the context of B cell associated responses. Spatial profiling using markers specific to macrophages, T lymphocytes, B lymphocytes, activated dendritic cells, high endothelial venules, myeloid cells and the PD-L1 immune checkpoint showed sex and age associated differences. Bladders from healthy older female mice showed a higher number of tertiary lymphoid structures (TLSs) compared to both young female and male equivalents. Spatial immune profiling of N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN) carcinogen exposed male and female bladders from young and old mice revealed a similar frequency of TLS formation, sex differences in the bladder immune microenvironment and, age differences in latency of tumor induction. These findings support the incorporation of sex and age as factors in pre-clinical modeling of NMIBC and will potentially advance the field of immunotherapeutic drug development to improve clinical outcomes in NMIBC.
HOIL-1-catalysed ubiquitylation of unbranched glucosaccharides and its activation by ubiquitin oligomers
Authors: Kelsall Ian R. , McCrory Elisha H. , Xu Yingqi , Scudamore Cheryl L. , Nanda Sambit K. , Mancebo-Gamella Paula , Wood Nicola T. , Knebel Axel , Matthews Stephen J. , Cohen Philip 
Published: September 2021

AbstractHOIL-1, a component of the Linear Ubiquitin Assembly Complex (LUBAC), ubiquitylates serine and threonine residues in proteins, forming ester bonds (Kelsall et al, 2019, PNAS 116, 13293-13298). Here we report that mice expressing the E3 ligase-inactive HOIL-1[C458S] mutant accumulate polyglucosan in brain, cardiac muscle and other organs, indicating that HOIL-1’s E3 ligase activity is essential to prevent these toxic polysaccharide deposits from accumulating. We found that HOIL-1 monoubiquitylates glycogen and α1:4-linked maltoheptaose in vitro and identify the C6 hydroxyl moiety of glucose as the site of ester-linked ubiquitylation. The HOIL-1-catalysed monoubiquitylation of maltoheptaose was accelerated >100-fold by Met1-linked or Lys63-linked ubiquitin oligomers, which interact with the catalytic RBR domain of HOIL-1. HOIL-1 also transferred preformed ubiquitin oligomers to maltoheptaose en bloc, producing polyubiquitylated maltoheptaose in one catalytic step. The Sharpin and HOIP components of LUBAC, but not HOIL-1, bound to amylose resin in vitro, suggesting a potential function in targeting HOIL-1 to unbranched glucosaccharides in cells. We suggest that monoubiquitylation of unbranched glucosaccharides may initiate their removal by glycophagy to prevent precipitation as polyglucosan.
Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family
Authors: Stogios Peter J. , Bordeleau Emily , Xu Zhiyu , Skarina Tatiana , Evdokimova Elena , Chou Sommer , Diorio-Toth Luke , D’Souza Alaric W. , Patel Sanket , Dantas Gautam , Wright Gerard D. , Savchenko Alexei 
Published: September 2021

ABSTRACTThe environmental microbiome harbors a vast repertoire of antibiotic resistance genes (ARGs) which can serve as evolutionary predecessors for ARGs found in pathogenic bacteria, or can be directly mobilized to pathogens in the presence of selection pressures. Thus, ARGs from benign environmental bacteria are an important resource for understanding clinically relevant resistance. Here, we conduct a comprehensive functional analysis of the Antibiotic_NAT family of aminoglycoside acetyltransferases. We determined a pan-family antibiogram of 21 Antibiotic_NAT enzymes, including 8 derived from clinical isolates and 13 from environmental metagenomic samples. We find that environment-derived representatives confer high-level, broad-spectrum resistance, including against the atypical aminoglycoside apramycin, and that a metagenome-derived gene likely is ancestral to an AAC(3) gene found in clinical isolates. Through crystallographic analysis, we rationalize the molecular basis for diversification of substrate specificity across the family. This work provides critical data on the molecular mechanism underpinning resistance to established and emergent aminoglycoside antibiotics and broadens our understanding of ARGs in the environment.
Elongated sample plot shapes produce higher measurement precision in clustering populations
Authors: McGarvey Richard , Burch Paul , Matthews Janet M. 
Published: September 2021

AbstractMonitoring the density of natural populations is crucial for ecosystem management decision making and natural resource management. The most widely used method to measure the population density of animal and plant species in natural habitats is to count organisms in sample plots. Yet evaluation of survey performance by different sample plot shapes, e.g. quadrats compared with transects, has been largely neglected since the 1990s and has not been undertaken using simulation. Simulating populations and surveys, we evaluated population density measurement precision for 900 cases, testing 30 sample plot survey designs in each of 30 spatially clustered populations. We varied three design options: elongation of plot shape while keeping sample area constant, systematic or random plot allocation, and sample size. Survey design performance varied markedly: elongating the plot shape always improved survey precision; allocating plots systematically sometimes did. (i) Averaged across all tested populations, elongated (1:100) transect plot shapes were 2-to-3 times more precise than square (10:10) quadrats. (ii) The precision of systematic surveys accelerated with sample plot number, increasing faster than the (known) linear increase under simple random sampling. This non-linear, concave upward, dependence of systematic precision on sample size has not previously been reported. (iii) The most precise design we evaluated used long narrow transects allocated systematically. Averaging among all 30 tested populations, a researcher would need 600 random square (10:10) quadrats to equal the precision achieved by 100 systematic (1:100) transects. Finding this average efficiency difference of 600% for a survey sample size of 100 plots, these simulation results imply that field trips requiring five sampling days using random quadrats could achieve equal precision in one or two days using systematic elongated transects. For all clustered populations we tested, long narrow transects resulted in a more efficient design for sample plot survey.
Population differentiation of polygenic score predictions under stabilizing selection
Authors: Yair Sivan , Coop Graham 
Published: September 2021

1AbstractGiven the many small-effect loci uncovered by genome-wide association studies (GWAS), polygenic scores have become central to the drive for genomic medicine and have spread into various areas including evolutionary studies of adaptation. While promising, these scores are fraught with issues of portability across populations, due to mis-estimated effect sizes and missing causal loci across populations unrepresented in large-scale GWAS. The poor portability of polygenic scores at first seems at odds with the view that much of common genetic variation is shared among populations. Here we investigate one potential cause of this discrepancy, stabilizing selection on complex traits. Somewhat counter-intuitively, while stabilizing selection to the same optimum phenotype leads to lower phenotypic differentiation among populations, it increases genetic differentiation at GWAS loci because it accelerates the turnover of polymorphisms underlying trait variation within populations. We develop theory to show how stabilizing selection impacts the utility of polygenic scores when applied to unrepresented populations. Specifically, we quantify their reduced prediction accuracy and find they can substantially overstate average genetic differences of phenotypes among populations. Our work emphasizes stabilizing selection to the same optimum as a useful null evolutionary model to draw connections between patterns of allele frequency and polygenic score differentiation.