Hirschmackinnon1244

By contrast, TNFα treatment of HOB cells (but not in MG63) leads to the upregulation of several key enzymes involved in the biosynthesis of sex steroids, which is proposed to lead to higher levels of estrogen production. These data also suggest that at least with respect to the topic of this study the cell line MG63 is not a good representative for osteoblasts and that it is preferential to use primary osteoblasts instead. This article is protected by copyright. learn more All rights reserved.Serial blockface scanning electron microscopy (SBSEM) is used to describe the sensory peripheral nervous system (PNS) in the tail of a cephalochordate, Asymmetron lucayanum. The reconstructed region extends from the tail tip to the origin of the most posterior peripheral nerves from the dorsal nerve cord. As peripheral nerves ramify within the dermis, all the nuclei along their course belong to glial cells. Invaginations in the glial cell cytoplasm house the neurites, an association reminiscent of the non-myelinated Schwann cells of vertebrates. Peripheral nerves pass from the dermis to the epidermis via small fenestrae in the sub-epidermal collagen fibril layer; most nerves exit abruptly, but a few run obliquely within the collagen fibril layer for many micrometers before exiting. Within the epidermis, each nerve begins ramifying repeatedly, but the branches are too small to be followed to their tips with SBSEM at low magnification (previous studies on other cephalochordates indicate that the branches end freely or in association with epidermal sensory cells). In Asymmetron, two morphological kinds of sensory cells are scattered in the epidermis, usually singly, but sometimes in pairs, evidently the recent progeny of a single precursor cell. The discussion considers the evolution of the sensory PNS in the phylum Chordata. In cephalochordates, Retzius bipolar neurons with intramedullary perikarya likely correspond to the Rohon-Beard cells of vertebrates. However, extramedullary neurons originating from ventral epidermis in cephalochordates (and presumably in ancestral chordates) contrast with vertebrate sensory neurons, which arise from placodes and neural crest. This article is protected by copyright. All rights reserved. © 2020 Wiley Periodicals, Inc.Maintenance of homeostasis at body barriers that are constantly challenged by microbes, toxins and potentially bioactive (macro)molecules requires complex, highly-orchestrated mechanisms of protection. Recent discoveries in respiratory research have shed light on the unprecedented role of airway epithelial cells (AEC), which, besides immune cells homing to the lung, also significantly contribute to host defense by expressing membrane-bound and soluble pattern recognition receptors (sPRR). Recent evidence suggests that distinct, evolutionary ancient, sPRR secreted by AEC might become activated by usually innocuous proteins, commonly referred to as allergens. We here provide a systematic overview on sPRR detectable in the mucus lining of AEC. Some of them become actively produced and secreted by AECs (like the pentraxins C-reactive protein and pentraxin 3; the collectins mannose binding protein and surfactant proteins A and D; H-ficolin; serum amyloid A; and the complement components C3 and C5). Others are elaborated by innate and adaptive immune cells such as monocytes/macrophages and T cells (like the pentraxins C-reactive protein and pentraxin 3; L-ficolin; serum amyloid A; and the complement components C3 and C5). Herein we discuss how sPRRs may contribute to homeostasis but sometimes also to overt disease (e.g., airway hyperreactivity and asthma) at the alveolar-air interface. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.MOTIVATION Identifying the genes regulated by a given transcription factor (its "target genes") is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method (CisMapper) for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TF's binding site and the expression of the gene across a set of tissues or cell lines. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene. RESULTS We present the T-Gene algorithm, which overcomes these limitations. It can be used to predict which genes are most likely to be regulated by a TF, and which of the TF's binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a gene's promoter, achieving median precision above 60%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median precision above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions. AVAILABILITY The T-Gene web server, source code, histone/expression data and genome annotation files are provided at http//meme-suite.org. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. For Permissions, please email journals.permissions@oup.com.MOTIVATION Programmed DNA elimination plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific to the detection of DNA splicing events is scarce. In this paper, we describe ADFinder, an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software will facilitate research of programmed DNA eliminations and all down-stream analyses. RESULTS By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila we prove that ADFinder is effective in predicting large scale programmed DNA eliminations. AVAILABILITY The source codes and manual of ADFinder are available in our GitHub website https//github.