bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxidative stress induced by tBHP in human normal colon cells by label free Raman spectroscopy and imaging. The protective role of natural antioxidants in the form of β-carotene
Authors: Brozek-Pluska B. , Beton K. 
Published: February 2021

AbstractThe present study aimed to investigate the protective effect of β-carotene on the oxidative stress injury of human normal colon cell line CCD-18Co triggered by tert-Butyl hydroperoxide (tBHP). XTT examination was used to determine cell viability after β-carotene supplementation and to determine the optimal concentration of antioxidant in spectroscopic studies. Cell biochemistry for CCD-18Co control group, after tBHP adding and for cells in β-carotene - tBHP model was studied by using label-free Raman microspectroscopy. Results for stress treated CCD-18Co human colon normal cells and human colon cancer cells Caco-2 based on vibration features were also compared. Pretreatment with β-carotene alleviated damages in CCD-18Co human normal colon cells induced by tBHP and showed the preventative effect on cells apoptosis. Treatment with β-carotene altered the level of ROS investigated based on intensities of Raman peaks typical for lipids, proteins and nucleic acids. Presented study confirmed the antioxidant, protective role of β-carotene against ROS by using spectroscopic label-free Raman techniques.
HLA binding of self-peptides is biased towards proteins with specific molecular functions
Authors: Karnaukhov Vadim , Paes Wayne , Woodhouse Isaac B. , Partridge Thomas , Nicastri Annalisa , Brackenridge Simon , Scherbinin Dmitrii , Chudakov Dmitry M. , Zvyagin Ivan V. , Ternette Nicola , Koohy Hashem , Borrow Persephone , Shugay Mikhail 
Published: February 2021

AbstractHuman leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.
Size matters: An analytical study on the role of tissue size in spatiotemporal distribution of morphogens unveils a transition between different Reaction-Diffusion regimes
Authors: Ceccarelli Alberto S. , Borges Augusto , Chara Osvaldo 
Published: February 2021

AbstractThe reaction-diffusion model constitutes one of the most influential mathematical models to study distribution of morphogens in tissues. Despite its widespread use, the effect of finite tissue size on model-predicted spatiotemporal morphogen distributions has not been completely elucidated. In this study, we analytically investigated the spatiotemporal distributions of morphogens predicted by a reaction-diffusion model in a finite 1D domain, as a proxy for a biological tissue, and compared it with the solution of the infinite-domain model. We explored the reduced parameter, the tissue length in units of a characteristic reaction-diffusion length, and identified two reaction-diffusion regimes separated by a crossover tissue size estimated in ∼3.3 characteristic reaction-diffusion lengths. While above this crossover the infinite-domain model constitutes a good approximation, it breaks below this crossover, whereas the finite-domain model faithfully describes the entire parameter space. We evaluated whether the infinite-domain model renders accurate estimations of diffusion coefficients when fitted to finite spatial profiles, a procedure typically followed in Fluorescence Recovery After Photobleaching (FRAP) experiments. We found that the infinite-domain model overestimates diffusion coefficients when the domain is smaller than the crossover tissue size. Thus, the crossover tissue size may be instrumental in selecting the suitable reaction-diffusion model to study tissue morphogenesis.
Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains
Authors: Peng Jie , Joshi Ishita , Alvino Gina , Kwan Elizabeth , Feng Wenyi 
Published: February 2021

AbstractWe performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two common laboratory strains ofSaccharomyces cerevisiaechallenged by hydroxyurea (HU), an inhibitor of the ribonucleotide reductase. By doing so we gained understanding of the impact on origin activation by three factors: replication checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit. Our analysis recapitulated the previous finding that the majority of origins are subject to checkpoint control by the Rad53 kinase when cells were treated with HU. In addition, origins either subject to Rad53 checkpoint control or impervious to it are largely concordant between the two strains. However, these two strains also produced different dynamics of origin activation. First, the W303-RAD53cells showed a significant reduction of fork progression than A364a-RAD53cells. This phenotype was accompanied by an elevated level of Rad53 phosphorylation in W303-RAD53cells. Second, W303-rad53K227Acheckpoint-deficient cells activated a greater number of origins accompanied by global reduction of ssDNA across all origins compared to A364a-rad53K227Acells; and this is correlated with lower expression level of the mutant protein in W303 than in A364a. We also show that sequence polymorphism in the consensus motifs of the replication origins plays a minor role in determining origin usage. Remarkably, eight strain-specific origins lack the canonical 11-bp consensus motif for autonomously replicating sequences in either strain background. Finally, we identified a new class of origins that are only active in checkpoint-proficient cells, which we named “Rad53-dependent origins”. The only discernible feature of these origins is that they tend to overlap with an open reading frame, suggesting previously unexplored connection between transcription and origin activation. Our study presents a comprehensive list of origin usage in two diverse yeast genetic backgrounds, fine-tunes the different categories of origins with respect to checkpoint control, and provokes further exploration of the interplay between origin activation and transcription.Author SummaryComparative analysis of origins of replication in two laboratory yeast strains reveals new insights into origin activation, regulation and dependency on the Rad53 checkpoint kinase.
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction
Authors: Yang Xiaodi , Yang Shiping , Lian Xianyi , Wuchty Stefan , Zhang Ziding 
Published: February 2021

AbstractTo predict interactions between human and viral proteins, we combine evolutionary sequence profile features with a Siamese convolutional neural network (CNN) architecture and a multi-layer perceptron (MLP). Our architecture outperforms various feature encodings-based machine learning and state-of-the-art prediction methods. As our main contribution, we introduce two types of transfer learning methods (i.e., ‘frozen’ type and ‘fine-tuning’ type) that reliably predict interactions in a target human-virus domain based on training in a source human-virus domain, by retraining CNN layers. Our transfer learning strategies can effectively apply prior knowledge transfer from large source dataset/task to small target dataset/task to improve prediction performance. Finally, we utilize the ‘frozen’ type of transfer learning to predict human-SARS-CoV-2 PPIs, indicating that our predictions are topologically and functionally similar to experimentally known interactions. Source code and datasets are available athttps://github.com/XiaodiYangCAU/TransPPI/.
Organic electron donors and terminal electron acceptors structure anaerobic microbial communities and interactions in a permanently stratified sulfidic lake
Authors: Rojas Connie A. , De Santiago Torio Ana , Park Serry , Bosak Tanja , Klepac-Ceraj Vanja 
Published: February 2021

AbstractThe extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (~52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin’s index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose much below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities by interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
Metabolic constraints on nitrogen fixation by rhizobia in legume nodules
Authors: Schulte Carolin C. M. , Borah Khushboo , Wheatley Rachel M. , Terpolilli Jason J. , Saalbach Gerhard , Crang Nick , de Groot Daan H. , Ratcliffe R. George , Kruger Nicholas J. , Papachristodoulou Antonis , Poole Philip S. 
Published: February 2021

AbstractRhizobia induce nodule formation on legume roots and differentiate into bacteroids, which use plant-derived dicarboxylates as energy and electron sources for reduction of atmospheric N2into ammonia for secretion to plants. Using heterogeneous genome-scale datasets, we reconstructed a model of bacteroid metabolism to investigate the effects of varying dicarboxylate and oxygen supply on carbon and nitrogen allocation. Modelling and13C metabolic flux analysis in bacteroids indicate that microaerobiosis restricts the decarboxylating arm of the TCA cycle and limits ammonia assimilation into glutamate. Catabolism of dicarboxylates induces a higher oxygen demand but also a higher NADH/NAD+ratio compared to sugars. Carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules with alanine secretion increasing as oxygen tension decreases. Our results provide a framework for understanding fundamental constraints on rhizobial metabolism during symbiotic nitrogen fixation.
THE COMPLEX HODOLOGICAL ARCHITECTURE OF THE MACAQUE DORSAL INTRAPARIETAL AREAS AS EMERGING FROM NEURAL TRACERS AND DW-MRI TRACTOGRAPHY
Authors: Caminiti Roberto , Girard Gabriel , Battaglia-Mayer Alexandra , Borra Elena , Schito Andrea , Innocenti Giorgio M. , Luppino Giuseppe 
Published: February 2021

ABSTRACTIn macaque monkeys, dorsal intraparietal areas are involved in several daily visuo-motor actions. However, their border and sources of cortical afferents remain loosely defined. Through a retrograde tracer and MRI diffusion-based tractography study here we show a complex organization of the dorsal bank of the IPS, which can be subdivided into a rostral area PEip, projecting to the spinal cord, and a caudal area MIP lacking such projections. Both areas include a rostral and a caudal sector, emerging from their ipsilateral, gradient-like connectivity profiles. As tractography estimations, we used the cross-sectional volume of the white matter bundles connecting each area with other parietal and frontal regions, after selecting ROIs corresponding to the injection sites of retrograde tracers. A quantitative analysis between the proportions of cells projecting to all sectors of PEip and MIP along the continuum of the dorsal bank of the IPS and tractography revealed a significant correlation between the two data sets for most connections. Moreover, tractography revealed “false positive” but plausible streamlines awaiting histological validation.
Col6a1+/CD201+mesenchymal cells regulate intestinal morphogenesis and homeostasis
Authors: Melissari Maria-Theodora , Henriques Ana , Tzaferis Christos , Prados Alejandro , Sarris Michalis E. , Chouvardas Panagiotis , Grammenoudi Sofia , Kollias George , Koliaraki Vasiliki 
Published: February 2021

AbstractIntestinal mesenchymal cells encompass multiple subsets, whose origins, functions, and pathophysiological importance are still not clear. Here, we used theCol6a1Cremouse, which targets telocytes and perivascular cells that can be further distinguished by the combination of the CD201, PDGFRα and αSMA markers. Developmental studies revealed that theCol6a1Cremouse also targets mesenchymal aggregates that are crucial for intestinal morphogenesis and patterning, suggesting an ontogenic relationship between them and homeostatic telocytes. Cell depletion experiments in adulthood showed that Col6a1+/CD201+mesenchymal cells regulate homeostatic enteroendocrine cell differentiation and epithelial proliferation. During acute colitis, they expressed an inflammatory and extracellular matrix remodeling gene signature, but they also retained their properties and topology. Notably, both in homeostasis and tissue regeneration, they were dispensable for normal organ architecture, while CD34+mesenchymal cells expanded, localised at the top of the crypts and showed increased expression of villous-associated morphogenetic factors, providing thus evidence for the plasticity potential of distinct mesenchymal populations in the intestine. Our results provide a comprehensive analysis of the identities, origin, and functional significance of distinct mesenchymal populations in the intestine.
Cardiac Specific Overexpression of Transcription Factor EB (TFEB) in Normal Hearts Induces Pathologic Cardiac Hypertrophy and Lethal Cardiomyopathy
Authors: Kenny Helena C. , Weatherford Eric T. , Collins Greg V. , Allamargot Chantal , Gesalla Taha , Zimmerman Kathy , Goel Harsh , McLendon Jared M. , Dai Dao-Fu , Romac Theo , Streeter Jennifer , Sharafuddin Jacob , Diwan Abhinav , Pereira Renata , Song Long-Sheng , Abel E. Dale 
Published: February 2021

AbstractTFEB promotes lysosomal biogenesis, autophagy, and lysosomal exocytosis. The present study characterized the consequence of inducible TFEB overexpression in cardiomyocytes in vivo. We generated cardiomyocyte-specific doxycycline inducible (Tet off) mice to achieve spatial and temporal control of TFEB overexpression, by crossing TFEB transgenic mice with mice harboring the tTA transgene (TFEB/tTA). Two weeks after doxycycline removal, an 8-fold increase in TFEB protein expression was observed in transgenic hearts. Heart weight normalized to tibia length was increased by 2.5-fold following TFEB overexpression (TFEB/tTA), characterized by induction of markers of pathological hypertrophy, such asNppa, NppbandActa1, progressive contractile dysfunction and cardiac dilatation. Overexpression of TFEB resulted in premature death, associated with high degree AV block. Reversal of TFEB overexpression normalized cardiac structure and function. Mitochondrial respiration and ATP levels were preserved after 2-weeks of TFEB induction, despite reduced mitochondrial (OXPHOS) protein expression, mtDNA content, and altered mitochondrial morphology. Signaling through mTOR was induced in TFEB/tTA mice, and when inhibited by rapamycin treatment for 4 weeks, partially offset left ventricular dysfunction. Transcriptome analysis revealed early suppression of mitochondrial metabolic pathways, induction of fibrosis and altered calcium signaling. MCOLN1, a lysosomal calcium release channel, the calcineurin target RCAN1.4, and the mitochondrial calcium uniporter (MCU) were strikingly induced in TFEB/tTA mice. In summary, persistent overexpression of TFEB at high levels (8-fold protein upregulation) in cardiomyocytes promotes pathologic cardiac hypertrophy via suppression of mitochondrial bioenergetic pathways and activation of pro-fibrotic and calcium regulatory pathways.
A unified genealogy of modern and ancient genomes
Authors: Wohns Anthony Wilder , Wong Yan , Jeffery Ben , Akbari Ali , Mallick Swapan , Pinhasi Ron , Patterson Nick , Reich David , Kelleher Jerome , McVean Gil 
Published: February 2021

AbstractThe sequencing of modern and ancient genomes from around the world has revolutionised our understanding of human history and evolution1,2. However, the general problem of how best to characterise the full complexity of ancestral relationships from the totality of human genomic variation remains unsolved. Patterns of variation in each data set are typically analysed independently, and often using parametric models or data reduction techniques that cannot capture the full complexity of human ancestry3,4. Moreover, variation in sequencing technology5,6, data quality7and in silico processing8,9, coupled with complexities of data scale10, limit the ability to integrate data sources. Here, we introduce a non-parametric approach to inferring human genealogical history that overcomes many of these challenges and enables us to build the largest genealogy of both modern and ancient humans yet constructed. The genealogy provides a lossless and compact representation of multiple datasets, addresses the challenges of missing and erroneous data, and benefits from using ancient samples to constrain and date relationships. Using simulations and empirical analyses, we demonstrate the power of the method to recover relationships between individuals and populations, as well as to identify descendants of ancient samples. Finally, we show how applying a simple non-parametric estimator of ancestor geographical location to the inferred genealogy recapitulates key events in human history. Our results demonstrate that whole-genome genealogies are a powerful means of synthesising genetic data and provide rich insights into human evolution.
Shared long-term and short-term memory representational formats in occipital and parietal cortex
Authors: Vo Vy A. , Sutterer David W. , Foster Joshua J. , Sprague Thomas C. , Awh Edward , Serences John T. 
Published: February 2021

AbstractCurrent theories propose that the short-term retention of information in working memory (WM) and the recall of information from long-term memory (LTM) are supported by overlapping neural mechanisms in occipital and parietal cortex. Both are thought to rely on reinstating patterns of sensory activity evoked by the perception of the remembered item. However, the extent of the shared representations between WM and LTM are unclear, and it is unknown how WM and LTM representations may differ across cortical regions. We designed a spatial memory task that allowed us to directly compare the representations of remembered spatial information in WM and LTM. Critically, we carefully matched the precision of behavioral responses in these tasks. We used fMRI and multivariate pattern analyses to examine representations in (1) retinotopic cortex and (2) lateral parietal cortex (LPC) regions previously implicated in LTM. We show that visual memories were represented in a sensory-like code in both tasks across retinotopic regions in occipital and parietal cortex. LPC regions also encoded remembered locations in both WM and LTM, but in a format that differed from the sensory-evoked activity. These results suggest a striking correspondence in the format of WM and LTM representations across occipital and parietal cortex. On the other hand, we show that activity patterns in nearly all parietal regions, but not occipital regions, contained information that could discriminate between WM trials and LTM trials. Our data provide new evidence for theories of memory systems and the representation of mnemonic content.