bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early-childhood inflammation blunts the transcriptional maturation of cerebellar neurons
Authors: Ament Seth A. , Cortes-Gutierrez Marcia , Herb Brian R. , Mocci Evelina , Colantuoni Carlo , McCarthy Margaret M. 
Published: July 2022

AbstractInflammation early in life is a clinically established risk factor for autism spectrum disorders and schizophrenia, yet the impact of inflammation on human brain development is poorly understood. The cerebellum undergoes protracted postnatal maturation, making it especially susceptible to perturbations contributing to risk of neurodevelopmental disorders. Here, using single-cell genomics, we characterize the postnatal development of cerebellar neurons and glia in 1-5-year-old children, comparing those who died while experiencing inflammation vs. non-inflamed controls. Our analyses reveal that inflammation and postnatal maturation are associated with extensive, overlapping transcriptional changes primarily in two subtypes of inhibitory neurons: Purkinje neurons and Golgi neurons. Immunohistochemical analysis of a subset of these brains revealed no change to Purkinje neuron soma size but evidence for increased activation of microglia in those subjects experiencing inflammation. Maturation- and inflammation-associated genes were strongly enriched for those implicated in neurodevelopmental disorders. A gene regulatory network model integrating cell type-specific gene expression and chromatin accessibility identified seven temporally specific gene networks in Purkinje neurons and suggested that the effects of inflammation correspond to blunted cellular maturation.One Sentence SummaryPost-mortem cerebelli from children who perished under conditions that included inflammation exhibit transcriptomic changes consistent with blunted maturation of Purkinje neurons compared to those who succumbed to sudden accidental death.
Contributions of Ccr4 and Gcn2 to the translational response of C. neoformans to host-relevant stressors and Integrated Stress Response induction
Authors: Knowles Corey M. , Goich David , Bloom Amanda L. M. , Kalem Murat C. , Panepinto John C. 
Published: July 2022

ABSTRACTIn response to the host environment, Cryptococcus neoformans must rapidly reprogram its translatome from one which promotes growth to one which is responsive to host temperature and oxidative stress. This reprogramming is primarily driven through the Gcn2-mediated repression of translation initiation and Ccr4-mediated removal of abundant pro-growth mRNAs from the translating pool. Here we investigate the contributions of these two pathways to the translational response to stress, and show that the response to oxidative stress is primarily driven by Gcn2 whereas temperature and oxidative stress both require Ccr4. Temperature stress, but not oxidative stress, result in an increase in RNase I resistant disome. Further, eIF2α phosphorylation varies in response to the type and magnitude of stress, yet all tested conditions induce translation of integrated stress response (ISR) transcription factor Gcn4, but not necessarily the Gcn4-dependent transcription. Finally, we define the ISR regulon in response to oxidative stress in C. neoformans. Together this study identifies the differential response to host-relevant stressors in an environmental fungus which can adapt to the environment inside the human host.
CGAN-Cmap: protein contact map prediction using deep generative adversarial neural networks
Authors: Madani Mohammad , Behzadi Mohammad Mahdi , Song Dongjin , Ilies Horea , Tarakanova Anna 
Published: July 2022

AbstractProtein contact maps represent spatial pairwise inter-residue interactions, providing a protein’s translationally and rotationally invariant topological representation. Accurate contact map prediction has been a critical driving force for improving protein structure prediction, one of computational biology’s most challenging problems in the last half-century. While many computational tools have been developed to this end, most fail to predict accurate contact maps for proteins with insufficient homologous protein sequences, and exhibit low accuracy for long-range contacts. To address these limitations, we develop a novel hybrid model, CGAN-Cmap, that uses a generative adversarial neural network embedded with a series of modified squeeze and excitation residual networks. To exploit features of different dimensions, we build the generator of CGAN-Cmap via two parallel modules: sequential and pairwise modules to capture and interpret distance profiles from 1D sequential and 2D pairwise feature maps, respectively, and combine them during the training process to generate the contact map. This novel architecture helps to improve the contact map prediction by surpassing redundant features and encouraging more meaningful ones from 1D and 2D inputs simultaneously. We also introduce a new custom dynamic binary cross-entropy (BCE) as the loss function to extract essential details from feature maps, and thereby address the input imbalance problem for highly sparse long-range contacts in proteins with insufficient numbers of homologous sequences. We evaluate the performance of CGAN-Cmap on the 11th, 12th, 13th, and 14th Critical Assessment of protein Structure Prediction (CASP 11, 12, 13, and 14) and CAMEO test sets. CGAN-Cmap significantly outperforms state-of-the-art models, and in particular, it improves the precision of medium and long-range contact by at least 3.5%. Furthermore, our model has a low dependency on the number of homologous sequences obtained via multiple sequence alignment, suggesting that it can predict protein contact maps with good accuracy for those proteins that lack homologous templates. These results demonstrate an efficient approach for fast and highly accurate contact map prediction toward construction of protein 3D structure from protein sequence.Data availabilityAll datasets and source codes are provided in: https://github.com/mahan-fcb/CGAN-Cmap-A-protein-contact-map-predictor
Reorganization of bird communities along a rainforest elevation gradient during a strong El Niño event in Papua New Guinea
Authors: Sam Katerina , Jorge Leonardo Ré , Koane Bonny , Hazell Richard , Shearman Phil , Novotny Vojtech 
Published: July 2022

AbstractThe El Niño 2015 event, most extreme since 1997, led to severe droughts in tropical wet Papua New Guinea (PNG), reducing May to October dry season rainfall by - 75% in the lowlands and 25% in the highlands. Such droughts are likely to have significant effects on terrestrial ecosystems, but they have been poorly explored in Papua New Guinea. Here we report changes in bird community composition prior, during and after 2015 El Niño event along the elevational gradient ranging from 200 m to 2,700 m a.s.l. at the Mt. Wilhelm rainforest in PNG. The abundance of birds in lowlands dropped by 60% but increased by 40% at elevations above 1700m during El Niño year. In the following year, the individual bird species reached mean population sizes similar to pre-El Niño years but did not fully recover. Species richness roughly followed the pattern of observed abundance and quickly and fully re-established after the event to the pre-El Niño values. Thus, at least some terrestrial birds seem to react quickly to the extreme droughts in lowlands and shifted to less affected mountain habitats. We recorded upper elevational range limits to shifts by more than 500m asl in 22 bird species (out of 237 recorded in total) during El Niño year, in contrast to their typical ranges. Our study suggests that a strong El Niño event can have strong but reversible effects on bird communities as long as they have an opportunity to move to more favourable sites through undisturbed habitats.
Hypoxia potentiates the inflammatory fibroblast phenotype promoted by pancreatic cancer cell-derived cytokines
Authors: Schwörer Simon , Ros Manon , Tsanov Kaloyan M. , Cimino Francesco V. , Lowe Scott W. , Carmona-Fontaine Carlos , Thompson Craig B. 
Published: July 2022

AbstractCancer-associated fibroblasts (CAFs) are a major cell type in the stroma of solid tumors and can exert both tumor-promoting and tumor-restraining functions. This functional heterogeneity is correlated with the existence of transcriptionally distinct subpopulations of CAFs. CAF heterogeneity is observed in pancreatic ductal adenocarcinoma (PDAC), a tumor characterized by a remarkably dense and hypoxic stroma that features tumor-restraining myofibroblastic CAFs (myCAFs) and tumor-supporting inflammatory CAFs (iCAFs). While CAF heterogeneity can be driven in part by tumor cell-produced cytokines, other determinants shaping CAF identity and function are largely unknown.In vivo, we found that iCAFs display a hypoxic gene expression and biochemical profile and are enriched in hypoxic regions of PDAC tumors. Hypoxia leads fibroblasts to acquire an inflammatory gene expression signature and synergizes with cancer cell-derived cytokines to promote an iCAF phenotype in a HIF-1α dependent fashion. Furthermore, we show that HIF-1α stabilization is sufficient to induce an iCAF phenotype in stromal cells introduced into PDAC organoid co-cultures and to promote PDAC tumor growth. These findings indicate hypoxia-induced HIF-1α as a regulator of CAF heterogeneity and promoter of tumor progression in PDAC.
Spatial structure formation by RsmE-regulated extracellular secretions in Pseudomonas fluorescens Pf0-1
Authors: Evans Anton , Wells Meghan , Denk Jordan , Mazza William , Santos Raziel , Delprince Amber , Kim Wook 
Published: July 2022

ABSTRACTCells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures manifest through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene are repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE’s primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identify the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses show that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community.IMPORTANCEIn densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces, however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE’s paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.
High Frequencies of Phenotypically and Functionally Senescent and Exhausted CD56+CD57+PD-1+ Natural Killer Cells, SARS-CoV-2-Specific Memory CD4+ and CD8+ T cells Associated with Severe Disease in Unvaccinated COVID-19 Patients
Authors: Srivastava Ruchi , Dhanushkodi Nisha , Prakash Swayam , Coulon Pierre Gregoire , Vahed Hawa , Zayou Latifa , Quadiri Afshana , BenMohamed Lbachir 
Published: July 2022

ABSTRACTUnvaccinated COVID-19 patients display a large spectrum of symptoms, ranging from asymptomatic to severe symptoms, the latter even causing death. Distinct Natural killer (NK) and CD4+ and CD8+ T cells immune responses are generated in COVID-19 patients. However, the phenotype and functional characteristics of NK cells and T-cells associated with COVID-19 pathogenesis versus protection remain to be elucidated. In this study, we compared the phenotype and function of NK cells SARS-CoV-2-specific CD4+ and CD8+ T cells in unvaccinated symptomatic (SYMP) and unvaccinated asymptomatic (ASYMP) COVID-19 patients. The expression of senescent CD57 marker, CD45RA/CCR7differentiation status, exhaustion PD-1 marker, activation of HLA-DR, and CD38 markers were assessed on NK and T cells from SARS-CoV-2 positive SYMP patients, ASYMP patients, and Healthy Donors (HD) using multicolor flow cytometry. We detected significant increases in the expression levels of both exhaustion and senescence markers on NK and T cells from SYMP patients compared to ASYMP patients and HD controls. In SYMP COVID-19 patients, the T cell compartment displays several alterations involving naive, central memory, effector memory, and terminally differentiated T cells. The senescence CD57 marker was highly expressed on CD8+ TEM cells and CD8+ TEMRA cells. Moreover, we detected significant increases in the levels of proinflammatory TNF-α, IFN-γ, IL-6, IL-8, and IL-17 cytokines from SYMP COVID-19 patients, compared to ASYMP COVID-19 patients and HD controls. The findings suggest exhaustion and senescence in both NK and T cell compartment is associated with severe disease in critically ill COVID-19 patients.IMPORTANCEUnvaccinated COVID-19 patients display a large spectrum of symptoms, ranging from asymptomatic to severe symptoms, the latter even causing death. Distinct Natural killer (NK) and CD4+ and CD8+ T cells immune responses are generated in COVID-19 patients. In this study, we detected significant increases in the expression levels of both exhaustion and senescence markers on NK and T cells from unvaccinated symptomatic (SYMP) compared to unvaccinated asymptomatic (ASYMP) COVID-19 patients. Moreover, we detected significant increases in the levels of proinflammatory TNF-α, IFN-γ, IL-6, IL-8, and IL-17 cytokines from SYMP COVID-19 patients, compared to ASYMP COVID-19 patients. The findings suggest exhaustion and senescence in both NK and T cell compartment is associated with severe disease in critically ill COVID-19 patients.TWEETSignificant exhaustion and senescence in both NK and T cells were detected in unvaccinated symptomatic COVID-19 patients, suggesting a weakness in both innate and adaptive immune systems leads to severe disease in critically ill COVID-19 patients.
Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction
Authors: Kusch Stefan , Singh Mansi , Thieron Hannah , Spanu Pietro D. , Panstruga Ralph 
Published: July 2022

AbstractThe establishment of host-microbe interactions requires molecular communication between both partners, which involves the mutual transfer of noncoding small RNAs. Previous evidence suggests that this is also true for the barley powdery mildew disease, which is caused by the fungal pathogen Blumeria hordei. However, previous studies lacked spatial resolution regarding the accumulation of small RNAs upon host infection by B. hordei. Here, we analysed site-specific small RNA repertoires in the context of the barley-B. hordei interaction. To this end, we dissected infected leaves into separate fractions representing different sites that are key to the pathogenic process: epiphytic fungal mycelium, infected plant epidermis, isolated haustoria, a vesicle-enriched fraction from infected epidermis, and extracellular vesicles. Unexpectedly, we discovered enrichment of specific 31- to 33-base long 5’-terminal fragments of barley 5.8S ribosomal RNA (rRNA) in extracellular vesicles and infected epidermis, as well as particular B. hordei tRNA fragments in haustoria. We describe canonical small RNAs from both the plant host and the fungal pathogen that may confer cross-kingdom RNA interference activity. Interestingly, we found first evidence of phased small RNAs (phasiRNAs) in B. hordei, a feature usually attributed to plants, which may be associated with the post-transcriptional control of fungal coding genes, pseudogenes, and transposable elements. Our data suggests a key and possibly site-specific role for cross-kingdom RNA interference and noncoding RNA fragments in the host-pathogen communication between B. hordei and its host barley.
Aptamer Proteomics for Biomarker Discovery in Heart Failure with Reduced Ejection Fraction
Authors: Zhang Luqing , Cunningham Jonathan W. , Claggett Brian L. , Jacob Jaison , Mendelson Mike , Serrano-Fernandez Pablo , Kaiser Sergio , Yates Denise , Healey Margaret , Chen Chien-Wei , Turner Gordon , Patel-Murray Natasha , Zhao Faye , Beste Michael T. , Laramie Jason M. , Abraham William T. , Jhund Pardeep S. , Kober Lars , Packer Milton , Rouleau Jean , Zile Michael R. , Prescott Margaret F. , Lefkowitz Martin , McMurray John J.V. , Solomon Scott D. , Chutkow William 
Published: July 2022

AbstractBackgroundSystematically characterizing associations between circulating proteins and risk for subsequent clinical events may improve clinical risk prediction and shed light on unrecognized biological pathways in heart failure (HF). Large-scale assays measuring thousands of proteins now enable broad proteomic investigation in clinical trials.MethodsSerum levels of 4076 proteins were measured at baseline in the ATMOSPHERE (n=1258, 487 events over 6 years) and PARADIGM-HF (n=1257, 287 events over 4 years) trials of chronic HF with reduced ejection fraction using a modified aptamer-based proteomics assay. Proteins associated with the primary endpoint of HF hospitalization or cardiovascular death were identified in the ATMOSPHERE discovery cohort by Cox regression adjusted for age, sex, treatment arm, and anticoagulant use (false discovery rate<0.05), and were replicated in PARADIGM-HF (Bonferroni-corrected p<0.05). A proteomic risk score was derived in ATMOSPHERE using Cox LASSO penalized regression and evaluated in PARADIGM-HF compared to the MAGGIC clinical risk score and N-terminal pro-B-type natriuretic peptide (NT-proBNP) immunoassay. For proteins that were associated with the primary endpoint, two-sample Mendelian randomization was performed using genetic and outcome data from both trials and protein quantitative trait loci from deCODE to infer causal associations.ResultsWe identified 377 serum proteins that were associated with the primary endpoint in ATMOSPHERE and replicated 167 in PARADIGM-HF. Prognostic proteins included known HF biomarkers such as Growth Differentiation Factor 15, NT-BNP, and Angiopoietin-2, and also a previously unrecognized HF biomarker: Sushi, Von Willebrand Factor Type A, EGF and Pentraxin Domain Containing 1 (SVEP1, HR 1.60 [95% CI 1.44-1.79] per standard deviation [SD], p=2×10−17). A 64-protein risk score derived in ATMOSPHERE predicted the primary endpoint in PARADIGM-HF with greater discrimination (C-statistic 0.70) than the MAGGIC clinical score (C-statistic 0.61), NT-proBNP (C-statistic 0.65), or both (C-statistic 0.66). Genetically controlled levels of BNP, WISP2, FSTL1, and CTSS were associated with the primary endpoint by Mendelian randomization.ConclusionsWe identified SVEP1, an extracellular matrix protein known to cause inflammation in vascular smooth muscle cells, as a new HF biomarker associated with risk of hospitalization or death. A 64-protein score improved risk discrimination compared with NT-proBNP and may assist in identifying high-risk patients.
Pioneer activity distinguishes activating from non-activating pluripotency transcription factor binding sites
Authors: Maresca Michela , van den Brand Teun , Li Hangpeng , Teunissen Hans , Davies James , de Wit Elzo 
Published: July 2022

AbstractGenome-wide transcriptional activity involves the binding of many transcription factors to thousands of sites in the genome. Determining which sites are directly driving transcription remains a challenge. Here we use acute protein depletion of the pioneer transcription factors OCT4 and SOX2 to establish their functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of pioneer factors. To understand the relationship with transcription we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to SOX2 binding sites that do not maintain accessibility. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted largely at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.
The hidden secrets of the dental calculus: Calibration of a mass spectrometry protocol for dental calculus protein analysis
Authors: Bender Omer , Tzabag Dana , Gavish Talia , Meyrom Noa , Zamir Neta , May Hila , Sarig Rachel , Bar Daniel Z. 
Published: July 2022

AbstractDental calculus is a solid deposit that forms and accumulates on the tooth surface, entrapping oral microorganisms, biomolecules, and other micro-debris found in the oral cavity. Mass spectrometry analysis of its protein content opens a vista into the subject’s diet, oral flora, and even some aspects of health, thus providing new insight and expanding our knowledge of archaic cultures. Multiple experimental protocols have been proposed for the optimal extraction of proteins from dental calculus. Herein, we compared various experimental conditions in order to calibrate and validate a protocol for protein extraction. Our results show that a high concentration of acetic acid followed by mechanical crushing and sonication provided the highest protein yield, while acetone precipitation enabled the identification of more distinct proteins. We validated this protocol using archeological samples, identifying human and microbial proteins in specimens from the 8th and 17th centuries (approximately 250–1300 years ago). These findings demonstrate that the developed protocol is useful for studying excavated archaeological samples and that it might be utilized to explore the biohistory, dietary habits, and microbiome of archaic populations.