bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of cannabis use on immune cell populations and the viral reservoir in people with HIV on suppressive antiretroviral therapy
Authors: Falcinelli Shane D. , Cooper-Volkheimer Alicia D , Semenova Lesia , Wu Ethan , Richardson Alexander , Ashokkumar Manickam , Margolis David M , Archin Nancie M. , Rudin Cynthia D , Murdoch David , Browne Edward P 
Published: December 2022

AbstractHIV infection remains incurable due to the persistence of a viral reservoir during antiretroviral therapy. Cannabis (CB) use is prevalent amongst people with HIV (PWH), but the impact of CB on the latent HIV reservoir has not been investigated. Peripheral CD4 and CD8 T cells from a cohort of CB-using PWH and a matched cohort of non-users on antiretroviral therapy were evaluated for expression of maturation/activation markers, HIV-specific T cell responses, and the frequency of intact proviral DNA. CB use was associated with increased abundance of naïve T cells, reduced effector T cells, and reduced expression of activation markers. CB users also exhibited reduced levels of exhausted and senescent T cells compared to non-using controls. HIV-specific CD8 T cell responses were unaffected by CB use. While the abundance of intact proviruses was not significantly affected by CB use across the whole cohort, we observed that, for participants with high frequency of NKG2A or CD16 expression in NK cells, CB use was associated with a smaller intact HIV reservoir. This analysis is consistent with the hypothesis that CB use reduces activation, exhaustion and senescence in the T cells of PWH and may influence the size of the HIV reservoir.
Guided-topic modelling of single-cell transcriptomes enables sub-cell-type and disease-subtype deconvolution of bulk transcriptomes
Authors: Swapna Lakshmipuram Seshadri , Huang Michael , Li Yue 
Published: December 2022

AbstractCell-type composition is an important indicator of health. We present Guided Topic Model for deconvolution (GTM-decon) to automatically infer cell-type-specific gene topic distributions from single-cell RNA-seq data for deconvolving bulk transcriptomes. GTM-decon performs competitively on deconvolving simulated and real bulk data compared with the state-of-the-art methods. Moreover, as demonstrated in deconvolving disease transcriptomes, GTM-decon can infer multiple cell-type-specific gene topic distributions per cell type, which captures sub-cell-type variations. GTM-decon can also use phenotype labels from single-cell or bulk data as a guide to infer phenotype-specific gene distributions. In a nested-guided design, GTM-decon identified cell-type-specific differentially expressed genes from bulk breast cancer transcriptomes.
Uncovering Changes in Microbiome Profiles Across Commercial and Backyard Poultry Farming Systems
Authors: Muyyarikkandy Muhammed Shafeekh , Parzygnat Jessica , Thakur Siddhartha 
Published: December 2022

AbstractEnvironmental health and microbiome can affect poultry production in a variety of ways. Poor environmental conditions can lead to increased stress, disease, and mortality in poultry, resulting in reduced production. Poor environmental conditions can also reduce the diversity of microbial populations in the poultry microbiome, which can lead to an increased risk of disease and reduced production. Finally, microorganisms in the environment can be introduced to the poultry microbiome, which can increase the risk of disease and reduce production. Additionally, poultry production can have significant impacts on the environmental microbiome. Poultry farming can alter soil and water microbiomes through pollution from manure and other agricultural runoff. These changes can lead to increased concentrations of certain microbes as well as an altered balance between beneficial microorganisms. In this study, we investigated the changes in the microbiome profiles of commercial and backyard broiler farming systems at different time points. To explore the microbiome profiles, fecal, soil, litter samples, and swabs from feeders and waterers were collected three times over the production period from a single flock. Each backyard farm was sampled at three time points: 10, 31, and 52 days of production and days 10, 24, and 38 of production in commercial farms. Statistical and network analyses were performed using DADA2 and MicrobiomeAnalyst platforms. Our results show marked differences in alpha diversity, beta diversity, and relative abundance of taxa between commercial and backyard farms over time. The observed species index significantly differed between the backyard and commercial farms for the soil, litter, and waterer samples. In addition, the fecal samples from backyard farms were found to have more Firmicutes, Bacteriodota, Desulfobacteria, Synergitota, Fusobacteriota, and Campilobacterota. Moreover, clustering showed different patterns in commercial and backyard farms with distinct marker taxa for each production system. Furthermore, the microbiome profiles of commercial and backyard farms evolved differently over time.
Context-dependent effects of temperature and community complexity on trophic interaction strength in a mite community
Authors: Torres-Campos Inmaculada , Magalhães Sara , Moya-Laraño Jordi , Montserrat Marta 
Published: December 2022

AbstractBoth temperature and community complexity are known to affect trophic interaction strength (TIS), but whether their effect is additive or not is as yet an open question. Here we used a 2-predator/3-prey system consistently occurring in avocado orchards to explore the effects of increasing warming and community complexity on the strength of predator:prey trophic interactions. The two predator species differed in their diet breath (acarnivoreand anomnivore) and the prey types included a herbivore, heterospecific juvenile predators, and/or pollen. Overall, analyses revealed multiplicative effects of community complexity and both temperature and predator diet breath on the net predator:prey(s) TIS. Indeed, warming led to increased TIS in the community with omnivore as top predator, but only in absence of its preferred food source. When the carnivore was the top predator, in contrast, higher temperatures led to TIS being more negative, but only for the IGprey. We conclude that sources of context dependence in specific systems need to be identified to unveil effects of warming on communities.
Effects of food supplementation and helminth removal on space use and spatial overlap in wild rodent populations
Authors: Mistrick Janine , Veitch Jasmine S.M. , Kitchen Shannon M. , Clague Samuel , Newman Brent C. , Hall Richard J. , Budischak Sarah A. , Forbes Kristian M. , Craft Meggan E. 
Published: December 2022

ABSTRACT1. Animal space use and spatial overlap can have important consequences for population-level processes such as social interactions and pathogen transmission. Identifying how environmental variability and inter-individual variation affect spatial patterns and in turn influence interactions in animal populations is a priority for the study of animal behavior and disease ecology. Environmental food availability and macroparasite infection are common drivers of variation, but there are few experimental studies investigating how they affect spatial patterns of wildlife.2. Bank voles (Clethrionomys glareolus) are a tractable study system to investigate spatial patterns of wildlife and are amenable to experimental manipulations. We conducted a replicated, factorial field experiment in which we provided supplementary food and removed helminths in vole populations in natural forest habitat and monitored vole space use and spatial overlap using capture-mark-recapture methods.3. Using network analysis, we quantified vole space use and spatial overlap. We compared the effects of food supplementation and helminth removal and investigated the impact of season, sex, and reproductive status on space use and spatial overlap.4. We found that food supplementation decreased vole space use while helminth removal increased space use. Space use also varied by sex, reproductive status, and season. Spatial overlap was similar between treatments despite up to three-fold differences in population size.5. By quantifying the spatial effects of food availability and macroparasite infection on wildlife populations, we demonstrate the potential for space use and population density to trade off and maintain consistent spatial overlap in wildlife populations. This has important implications for spatial processes in wildlife including pathogen transmission.
Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models
Authors: Strober Benjamin J. , Tayeb Karl , Popp Joshua , Qi Guanghao , Gordon M. Grace , Perez Richard , Ye Chun Jimmie , Battle Alexis 
Published: December 2022

AbstractGenetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-specific expression quantitative trait loci (eQTLs) from single-cell transcriptomic data. This allows discovery of the contexts or cell types modulating genetic regulation without prior knowledge. Applied to peripheral blood single-cell eQTL data, SURGE contexts capture continuous representations of distinct cell types and groupings of biologically related cell types. We demonstrate the disease-relevance of SURGE context-specific eQTLs using colocalization analysis and stratified LD-score regression.
voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues
Authors: Schneider Arthur L. , Martins-Silva Rita , Kaizeler Alexandre , Saraiva-Agostinho Nuno , Barbosa-Morais Nuno L. 
Published: December 2022

AbstractWe herein introduce voyAGEr, an online graphical interface to explore age-related gene expression alterations in 49 human tissues. voyAGEr offers a visualisation and statistical toolkit for the finding and functional exploration of sex– and tissue-specific transcriptomic changes with age. In its conception, we developed a novel bioinformatics pipeline leveraging RNA sequencing data, from the GTEx project, encompassing more than 900 individuals. voyAGEr reveals transcriptomic signatures of the known asynchronous ageing between tissues, allowing the observation of tissue-specific age-periods of major transcriptional changes, associated with alterations in different biological pathways, cellular composition, and disease conditions.Notably, voyAGEr was created to assist researchers with no expertise in bioinformatics, providing a supportive framework for elaborating, testing and refining their hypotheses on the molecular nature of human ageing and its association with pathologies, thereby also aiding in the discovery of novel therapeutic targets. voyAGEr is freely available athttps://compbio.imm.medicina.ulisboa.pt/app/voyAGEr.
A cornichon protein controls polar localization of the PINA auxin transporter inPhyscomitrium patens
Authors: Yáñez-Domínguez C. , Lagunas-Gómez D. , Torres-Cifuentes D.M. , Bezanilla M. , Pantoja O. 
Published: December 2022

AbstractNewly synthesized membrane proteins pass through the secretory pathway starting at the endoplasmic reticulum and packaged into COPII vesicles to continue to the Golgi apparatus before reaching their membrane of residence. It is known that cargo receptor proteins form part of the COPII complex and play a role in the recruitment of cargo proteins for their subsequent transport through the secretory pathway. The role of cornichon proteins is conserved from yeast to vertebrates, but it is poorly characterized in plants. To study the role of this protein in cellular traffic mechanisms in plants, the mossPhyscomitrium patenshas been selected since it can be studied at the single-cell level. Here, we studied the role of the two moss cornichon homologs in the secretory pathway. Mutant analyzes revealed that cornichon genes regulate different growth processes during the moss life cycle, by controlling auxin transport; with CNIH2 functioning as a specific cargo receptor for the auxin efflux carrier PINA, with the C-terminus of the receptor regulating the interaction and trafficking of PINA.
Gap-free nuclear and mitochondrial genomes ofFusarium verticillioidesstrain HN2
Authors: Yang Wei , Zhai Haoyu , Yang Lei , Yang Qun , Song Le , Wu Jianyu , Lai Zhibing , Li Guotian 
Published: December 2022

AbstractFusarium ear rot (FER) and Fusarium stalk rot (FSR) caused by the filamentous fungusFusarium verticillioideshave become increasingly serious around the world. Additionally, fumonisins produced byF. verticillioidesthreaten food and feed security. By adding the contribution of genomic resources to better understand the pathosystem including the mechanisms ofF. verticillioides–maize interactions, and further improving the quality of theF. verticillioidesgenome, the gap-free nuclear genome and mitochondrial genome ofF. verticillioidesstrain HN2 were sequenced and assembled. Using Oxford Nanopore long reads and next-generation sequencing short reads, the final 42.81-Mb genome was assembled into 12 contigs (N50 = 4.16-Mb). A total of 13,466 protein-coding genes were annotated, including 1,076 secreted proteins that contain 342 candidate effectors. In addition, we assembled the complete 53,764 bp mitochondrial genome.F. verticillioidesstrain 7600 genome assemblies are fragmented and high-quality reference genomes were needed. The genomes presented here will serve as an important resource forF. verticillioidesresearch.
Neural substrates in Parkinson’s Disease psychosis: A systematic review
Authors: Pisani Sara , Gunasekera Brandon , Lu Yining , Vignando Miriam , ffytche Dominic , Aarsland Dag , Chaudhuri K. Ray , Ballard Clive , Lee Jee-Young , Kim Yu Kyeong , Velayudhan Latha , Bhattacharyya Sagnik 
Published: December 2022

AbstractNeural underpinnings of Parkinson’s Disease psychosis (PDP) remain unclear to this day with relatively few studies and reviews available. Using a systematic review approach, here we aimed to qualitatively synthesize evidence from studies investigating PD psychosis-specific alterations in brain structure, function or chemistry using different neuroimaging modalities. PubMed, Web of Science and Embase databases were searched for fMRI, rsfMRI, DTI, PET, and SPECT studies comparing PDP patients with PD patients without psychosis (PDnP). We report findings from 18 studies (291 PDP patients, mean age ± SD = 68.65 ± 3.76 years; 48.5% males; 433 PDnP patients, mean age ± SD = 66.97 ± 3.80 years; 52% males). Qualitative synthesis revealed widespread patterns of altered brain function across task-based and resting-state fMRI studies in PDP compared to PDnP patients. Similarly, white matter abnormalities were reported in parietal, temporal, and occipital regions. Hypometabolism and reduced dopamine transporter binding were also reported whole brain and in subcortical areas. This suggests extensive alterations affecting regions involved in high order visual processing and attentional networks.
A combined DTI-fMRI approach for optimizing the delineation of posteromedial vs. anterolateral entorhinal cortex
Authors: Syversen Ingrid Framås , Reznik Daniel , Witter Menno P. , Kobro-Flatmoen Asgeir , Schröder Tobias Navarro , Doeller Christian F. 
Published: December 2022

AbstractIn the entorhinal cortex (EC), attempts have been made to identify the human homologue regions of the medial (MEC) and lateral (LEC) subdivision using either functional magnetic resonance imaging (fMRI) or diffusion tensor imaging (DTI). However, there are still discrepancies between entorhinal subdivisions depending on the choice of connectivity seed regions and the imaging modality used. While DTI can be used to follow the white matter tracts of the brain, fMRI can identify functionally connected brain regions. In this study, we used both DTI and resting-state fMRI in 103 healthy adults to investigate both structural and functional connectivity between the EC and associated cortical brain regions. Differential connectivity with these regions was then used to predict the locations of the human homologues of MEC and LEC. Our results from combining DTI and fMRI support a subdivision into posteromedial (pmEC) and anterolateral (alEC) EC and reveal a confined border between the pmEC and alEC. Furthermore, the EC subregions obtained by either imaging modality showed similar distinct connectivity patterns: While pmEC showed increased connectivity preferentially with the default mode network, the alEC exhibited increased connectivity with regions in the dorsal attention and salience networks. Optimizing the delineation of the human homologues of MEC and LEC with a combined, cross-validated DTI-fMRI approach allows to define a likely border between the two subdivisions and has implications for both cognitive and translational neuroscience research.
Intracellular fraction of zona pellucida protein 3 is required for the oocyte to embryo transition in mice
Authors: Israel Steffen , Seyfarth Julia , Nolte Thomas , Drexler Hannes C.A. , Fuellen Georg , Boiani Michele 
Published: December 2022

AbstractIn oocyte biology the zona pellucida has long been known to operate three extracellular functions, namely, encasing the oocytes in ovarian follicles, mediating sperm-oocyte interaction and preventing premature embryo contact with maternal epithelia. The present study uncovers a fourth function that is fundamentally distinct from the other three, being critical for embryonic cell survival. Intriguingly, the three proteins of the mouse zona pellucida (ZP1, ZP2, ZP3) were found abundantly present also inside the embryo four days after fertilization, as shown by mass spectrometry, immunoblotting and immunofluorescence.Trim-away-mediated knockdown of ZPs in fertilized oocytes resulted in various grades of embryopathy: knockdown of ZP1 impeded blastocyst expansion, knockdown of ZP2 hampered the 2ndzygotic cleavage, while knockdown of ZP3 hampered the 1stzygotic cleavage - unlike the overexpression. Transcriptome analysis of ZP3-knockdown embryos pointed at defects of cytoplasmic translation in the context of embryonic genome activation. This conclusion was supported by reduced protein synthesis in the ZP3-knockdown and by the lack of cleavage arrest when knockdown was postponed from the 1-cell to the late 2-cell stage. These data place constraints on the long-standing notion that the zona pellucida proteins only operate in the extracellular space. We postulate that such noncanonical localization of ZP3 reflect novel roles in the embryo’s interior during the oocyte-to-embryo transition in mice.Graphical abstract
ROS signaling-induced mitochondrial Sgk1 regulates epithelial cell plasticity
Authors: Li Yingxiang , Liu Chengdong , Rolling Luke , Sikora Veronica , Chen Zhimin , Gurwin Jack , Barabell Caroline , Lin Jiandie , Duan Cunming 
Published: December 2022

AbstractMany types of differentiated cells can reenter the cell cycle upon injury or stress. The mechanisms underlying this cell plasticity are still poorly understood. Here we investigated cell plasticity regulation using a zebrafish model, in which a population of differentiated epithelial cells are reactivated under a physiological context. We observed a robust and sustained increase in mitochondrial membrane potential in reactivated cells. Genetic and pharmacological perturbations show that elevated mitochondrial metabolism and ATP synthesis are critical for cell reactivation. Elevated mitochondrial metabolism increases mitochondrial ROS levels, which induces Sgk1 expression in the mitochondria. Deletion and inhibition of Sgk1 in zebrafish abolished cell reactivation. Similarly, ROS-dependent mitochondrial expression of SGK1 promotes S phase entry in human breast cancer cells. Mechanistically, Sgk1 coordinates mitochondrial activity with ATP synthesis by modulating F1Fo-ATP synthase phosphorylation. These findings suggest a conserved intramitochondrial signaling loop regulating epithelial cell renewal.One sentence highlightThis study reports a new intramitochondrial signaling loop regulating epithelial cell renewal.
CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin
Authors: van Schie Janne J.M. , de Lint Klaas , Molenaar Thom M. , Gines Macarena Moronta , Balk Jesper A. , Rooimans Martin A. , Roohollahi Khashayar , Pai Govind M. , Borghuis Lauri , Ramadhin Anisha R. , Dorsman Josephine C. , Wendt Kerstin S. , Wolthuis Rob M.F. , de Lange Job 
Published: December 2022

ABSTRACTThe cohesin complex regulates higher order chromosome architecture through maintaining sister chromatid cohesion and folding chromatin by active DNA loop extrusion. Impaired cohesin function underlies a heterogeneous group of genetic syndromes and is associated with cancer. Here, by using synthetic lethality CRISPR screens in isogenic human cell lines defective of specific cohesion regulators, we mapped the genetic dependencies induced by absence of DDX11 or ESCO2. The obtained high confidence synthetic lethality networks are strongly enriched for genes involved in DNA replication and mitosis and support the existence of parallel sister chromatid cohesion establishment pathways. Among the hits, we identified the chromatin binding, BRCT-domain containing protein PAXIP1 as a novel cohesin regulator. Depletion of PAXIP1 severely aggravated cohesion defects in ESCO2 defective cells, leading to mitotic cell death. PAXIP1 promoted the global chromatin association of cohesin, independent of DNA replication, a function that could not be explained by indirect effects of PAXIP1 on transcription or the DNA damage response. Cohesin regulation by PAXIP1 required its binding partner PAGR1 and a conserved FDF motif in PAGR1. Similar motifs were previously found in multiple cohesin regulators, including CTCF, to mediate physical interactions with cohesin. PAXIP1 co-localizes with cohesin on multiple genomic loci, including at active gene promoters and enhancers. Together, this study identifies the PAXIP1-PAGR1 complex as a novel regulator of cohesin occupancy on chromatin. Possibly, this role in cohesin regulation is also relevant for previously described functions of PAXIP1 in transcription, immune cell maturation and DNA repair.