Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors

Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation-deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression

Robust Person Tracking Algorithm Based on Convolutional Neural Network for Indoor Video Surveillance Systems

In this paper, we present an algorithm for multi person tracking in indoor surveillance systems based on tracking-by-detection approach. Convolutional Neural Networks (CNNs) for detection and tracking both are used. CNN Yolov3 has been utilized as detector. Person features extraction is performed based on modified CNN ResNet. Proposed architecture includes 29 convolutional and one fully connected layer. Hungarian algorithm is applied for objects association. After that object visibility in the frame is determined based on CNN and color features. For algorithm evaluation prepared videos that was labeled and tested using MOT evaluation metric. The proposed algorithm efficiency is illustrated and confirmed by our experimental results

Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics.

Protective humoral memory forms in secondary lymphoid organs where B cells undergo affinity maturation and differentiation into memory or plasma cells. Here, we provide a comprehensive roadmap of human B cell maturation with single-cell transcriptomics matched with bulk and single-cell antibody repertoires to define gene expression, antibody repertoires, and clonal sharing of B cell states at single-cell resolution, including memory B cell heterogeneity that reflects diverse functional and signaling states. We reconstruct gene expression dynamics during B cell activation to reveal a pre-germinal center state primed to undergo class switch recombination and dissect how antibody class-dependent gene expression in germinal center and memory B cells is linked with a distinct transcriptional wiring with potential to influence their fate and function. Our analyses reveal the dynamic cellular states that shape human B cell-mediated immunity and highlight how antibody isotype may play a role during their antibody-based selection. This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution. The definitive version was published in Science Immunology on Science Immunology Vol. 6, Feb 2021, DOI: 10.1126/sciimmunol.abe6291

KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity

Wellcome Trust [102349/Z/13/Z to A.H.T., 099677/Z/12/Z to H.W.K., 098024/Z/11/Z, 209400/Z/17/Z to R.J.K.]; Lister Institute of Preventive Medicine; European Research Council [681440]; Japan Agency for Medical Research and Development, AMEDCREST Programme. Funding for open access charge: Wellcome Trus

Exosomes and the kidney: Blaming the messenger

Exosomes are membrane-bound vesicles of endosomal origin, present in awide range of biological fluids, including blood and urine. They rangebetween 30 and 100 nm in diameter, and consist of a limiting lipid bilayer,transmembrane proteins and a hydrophilic core containing proteins,mRNAs and microRNAs (miRNA). Exosomes can act as extracellular vehi-cles by which cells communicate, through the delivery of their functionalcargo to recipient cells, with many important biological, physiologicaland pathological implications. The exosome release pathway contributestowards protein secretion, antigen presentation, pathogen transfer andcancer progression. Exosomes and exosome-mediated signalling have beenimplicated in disease processes such as atherosclerosis, calcification andkidney diseases. Circulating levels of exosomes and extracellular vesicles canbe influenced by the progression of renal disease. Advances in methods forpurification and analysis of exosomes are leading to potential diagnostic andtherapeutic avenues for kidney diseases. This review will focus on biophysi-cal properties and biogenesis of exosomes, their pathophysiological rolesand their potential as biomarkers and therapeutics in kidney diseases

An Investigation into the Oil Transport and Starvation of Piston-Ring Pack

In order to accurately predict the lubricant film thickness and generated friction in any tribological contact, it is important to determine appropriate boundary conditions, taking into account the oil availability and extent of starvation. This paper presents a two-dimensional hydrodynamic model of a piston ring pack for prediction of lubricant film thickness, friction and total power loss. The model takes into account starvation caused by reverse flow at the conjunctional inlet wedge, and applied to a ring pack, comprising a compression and scraper ring. Inlet boundaries are calculated for an engine cycle of a four-cylinder, four-stroke gasoline engine operating at 1500 r/min with conditions pertaining to the New European Drive Cycle. The analysis shows the two main sources of starvation: first, due to a physical lack of inlet meniscus and second, due to reverse flow at the inlet wedge significantly affecting the prevailing conditions from the generally assumed idealised boundary conditions. Such an approach has not hitherto been reported in literature

Examining the Relationships among the Coaching Climate, Life Skills Development and Well-Being in Sport

Using Benson and Saito's framework for positive youth development, we investigated the relationships between the coaching climate, young people's perceived life skills development within sport, and their psychological well-being. British youth sport participants (N=326, Mage=13.81, range=11–18 years) completed a survey assessing the coaching climate, participants' perceived life skills development (teamwork, goal setting, time management, emotional skills, interpersonal communication, social skills, leadership, and problem solving and decision making) and psychological well-being (self-esteem, positive affect, and satisfaction with life). In all analyses, the coaching climate was positively related to young peoples' perceived development of life skills within sport and their psychological well-being. Total life skills development (a summative score of all eight life skills scores) was positively related to all three psychological well-being indicators – providing support for the "pile-up" effect – and partially mediated the relationships between the coaching climate and participants' psychological well-being. Interpretation of the results indicated that coaches should foster the development of multiple life skills in youth sport participants, as they are associated with participants' psychological well-being. One way this can be achieved is through autonomy-supportive coaching behaviours

Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming

Epiblast cells in the early post-implantation stage mammalian embryo undergo a transition described as lineage priming before cell fate allocation, but signaling pathways acting upstream remain ill defined. Genetic studies demonstrate that Smad2/3 double-mutant mouse embryos die shortly after implantation. To learn more about the molecular disturbances underlying this abrupt failure, here we characterized Smad2/3-deficient embryonic stem cells (ESCs). We found that Smad2/3 double-knockout ESCs induced to form epiblast-like cells (EpiLCs) display changes in naive and primed pluripotency marker gene expression, associated with the disruption of Oct4-bound distal regulatory elements. In the absence of Smad2/3, we observed enhanced Bmp target gene expression and de-repression of extra-embryonic gene expression. Cell fate allocation into all three embryonic germ layers is disrupted. Collectively, these experiments demonstrate that combinatorial Smad2/3 functional activities are required to maintain distinct embryonic and/or extra-embryonic cell identity during lineage priming in the epiblast before gastrulation. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved

Protein interactions in Xenopus germ plasm RNP particles

Hermes is an RNA-binding protein that we have previously reported to be found in the ribonucleoprotein (RNP) particles of Xenopus germ plasm, where it is associated with various RNAs, including that encoding the germ line determinant Nanos1. To further define the composition of these RNPs, we performed a screen for Hermes-binding partners using the yeast two-hybrid system. We have identified and validated four proteins that interact with Hermes in germ plasm: two isoforms of Xvelo1 (a homologue of zebrafish Bucky ball) and Rbm24b and Rbm42b, both RNA-binding proteins containing the RRM motif. GFP-Xvelo fusion proteins and their endogenous counterparts, identified with antisera, were found to localize with Hermes in the germ plasm particles of large oocytes and eggs. Only the larger Xvelo isoform was naturally found in the Balbiani body of previtellogenic oocytes. Bimolecular fluorescence complementation (BiFC) experiments confirmed that Hermes and the Xvelo variants interact in germ plasm, as do Rbm24b and 42b. Depletion of the shorter Xvelo variant with antisense oligonucleotides caused a decrease in the size of germ plasm aggregates and loosening of associated mitochondria from these structures. This suggests that the short Xvelo variant, or less likely its RNA, has a role in organizing and maintaining the integrity of germ plasm in Xenopus oocytes. While GFP fusion proteins for Rbm24b and 42b did not localize into germ plasm as specifically as Hermes or Xvelo, BiFC analysis indicated that both interact with Hermes in germ plasm RNPs. They are very stable in the face of RNA depletion, but additive effects of combinations of antisense oligos suggest they may have a role in germ plasm structure and may influence the ability of Hermes protein to effectively enter RNP particles