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https://www.readbyqxmd.com/read/28715148/lineage-specific-epitope-profiles-for-hpai-h5-pre-pandemic-vaccine-selection-and-evaluation
#1
Xueting Qiu, Venkata R Duvvuri, Jonathan B Gubbay, Richard Webby, Ghazi Kayali, Justin Bahl
BACKGROUND: Multiple highly pathogenic avian influenza (HPAI) H5 viruses continue to co-circulate. This has complicated pandemic preparedness and confounded effective vaccine candidate selection and evaluation. OBJECTIVES: In this study we aim to predict and map the diversity of CD8+ T-cell epitopes among H5 Hemagglutinin (HA) gene lineages to estimate CD8+ T-cell immunity in humans induced by vaccine candidates. METHODS: A dataset consisting of 1125 H5 HA sequences collected between 1996 and 2017 from avian and humans was assembled for phylogenetic and lineage-specific epitope analyses...
July 17, 2017: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/28693426/evolution-gene-expression-profiling-and-3d-modeling-of-csld-proteins-in-cotton
#2
Yanpeng Li, Tiegang Yang, Dandan Dai, Ying Hu, Xiaoyang Guo, Hongxia Guo
BACKGROUND: Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. RESULTS: A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28691666/hymenobacter-tenuis-sp-nov-isolated-from-wastewater-of-an-acidic-water-neutralization-facility
#3
Joo Won Kang, Ji Hee Lee, Han Na Choe, Chi Nam Seong
A non-motile, red-pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine...
July 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28690608/phylogenetic-tracings-of-proteome-size-support-the-gradual-accretion-of-protein-structural-domains-and-the-early-origin-of-viruses-from-primordial-cells
#4
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28688656/notch-signaling-promotes-ductular-reactions-in-biliary-atresia
#5
Jessica A Zagory, William Dietz, Alex Park, Michael Fenlon, Jiabo Xu, Sarah Utley, Nirmala Mavila, Kasper S Wang
BACKGROUND: Biliary atresia (BA) is a congenital, progressive, fibro-obliterative disease of the extrahepatic biliary tree and the most common cause of end-stage liver disease in children. BA is characterized by extensive intrahepatic proliferating ductular reactions that may contribute to biliary fibrosis. Lineage tracing during experimental cholestasis indicates that cells within ductular reactions derive from PROM1-expressing hepatic progenitor cells. Given the role of Notch signaling in normal biliary development, we hypothesize that activated Notch signaling promotes the formation of ductular reactions in BA...
July 2017: Journal of Surgical Research
https://www.readbyqxmd.com/read/28687978/two-new-leptographium-spp-reveal-an-emerging-complex-of-hardwood-infecting-species-in-the-ophiostomatales
#6
Robert Jankowiak, Beata Strzałka, Piotr Bilański, Riikka Linnakoski, Truls Aas, Halvor Solheim, Małgorzata Groszek, Z Wilhelm de Beer
Species of Leptographium are generally characterized by mononematous conidiophores and are commonly associated with bark beetles and weevils. These species are responsible for sapstain and in some cases serious diseases on a range of primarily coniferous trees. In comparison with coniferous trees, the occurrence of Leptographium species on hardwood trees has been poorly studied in Europe. During a survey of ophiostomatoid fungi on various tree species in Norway and Poland, three unusual species, which fit the broader morphological description of Leptographium spp...
July 7, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28684519/origins-of-lymphatic-and-distant-metastases-in-human-colorectal-cancer
#7
Kamila Naxerova, Johannes G Reiter, Elena Brachtel, Jochen K Lennerz, Marc van de Wetering, Andrew Rowan, Tianxi Cai, Hans Clevers, Charles Swanton, Martin A Nowak, Stephen J Elledge, Rakesh K Jain
The spread of cancer cells from primary tumors to regional lymph nodes is often associated with reduced survival. One prevailing model to explain this association posits that fatal, distant metastases are seeded by lymph node metastases. This view provides a mechanistic basis for the TNM staging system and is the rationale for surgical resection of tumor-draining lymph nodes. Here we examine the evolutionary relationship between primary tumor, lymph node, and distant metastases in human colorectal cancer. Studying 213 archival biopsy samples from 17 patients, we used somatic variants in hypermutable DNA regions to reconstruct high-confidence phylogenetic trees...
July 7, 2017: Science
https://www.readbyqxmd.com/read/28659877/dynamic-acquisition-and-loss-of-dual-obligate-symbionts-in-the-plant-sap-feeding-adelgidae-hemiptera-sternorrhyncha-aphidoidea
#8
Carol D von Dohlen, Usha Spaulding, Kistie B Patch, Kathryn M Weglarz, Robert G Foottit, Nathan P Havill, Gaelen R Burke
Sap-sucking insects typically engage in obligate relationships with symbiotic bacteria that play nutritional roles in synthesizing nutrients unavailable or in scarce supply from the plant-sap diets of their hosts. Adelgids are sap-sucking insects with complex life cycles that involve alternation between conifer tree species. While all adelgid species feed on spruce during the sexual phase of their life cycle, each adelgid species belongs to a major lineage that feeds on a distinct genus of conifers as their alternate host...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28651571/expression-and-phylogenetic-analyses-reveal-paralogous-lineages-of-putatively-classical-and-non-classical-mhc-i-genes-in-three-sparrow-species-passer
#9
Anna Drews, Maria Strandh, Lars Råberg, Helena Westerdahl
BACKGROUND: The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells...
June 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28584083/gene-regulatory-networks-and-cell-lineages-that-underlie-the-formation-of-skeletal-muscle
#10
Margaret Buckingham
Skeletal muscle in vertebrates is formed by two major routes, as illustrated by the mouse embryo. Somites give rise to myogenic progenitors that form all of the muscles of the trunk and limbs. The behavior of these cells and their entry into the myogenic program is controlled by gene regulatory networks, where paired box gene 3 (Pax3) plays a predominant role. Head and some neck muscles do not derive from somites, but mainly form from mesoderm in the pharyngeal region. Entry into the myogenic program also depends on the myogenic determination factor (MyoD) family of genes, but Pax3 is not expressed in these myogenic progenitors, where different gene regulatory networks function, with T-box factor 1 (Tbx1) and paired-like homeodomain factor 2 (Pitx2) as key upstream genes...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28582478/model-based-branching-point-detection-in-single-cell-data-by-k-branches-clustering
#11
Nikolaos K Chlis, F Alexander Wolf, Fabian J Theis
Motivation: The identification of heterogeneities in cell populations by utilizing single-cell technologies such as single-cell RNA-Seq, enables inference of cellular development and lineage trees. Several methods have been proposed for such inference from high-dimensional single-cell data. They typically assign each cell to a branch in a differentiation trajectory. However, they commonly assume specific geometries such as tree-like developmental hierarchies and lack statistically sound methods to decide on the number of branching events...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28564607/specification-and-diversification-of-pericytes-and-smooth-muscle-cells-from-mesenchymoangioblasts
#12
Akhilesh Kumar, Saritha Sandra D'Souza, Oleg V Moskvin, Huishi Toh, Bowen Wang, Jue Zhang, Scott Swanson, Lian-Wang Guo, James A Thomson, Igor I Slukvin
Elucidating the pathways that lead to vasculogenic cells, and being able to identify their progenitors and lineage-restricted cells, is critical to the establishment of human pluripotent stem cell (hPSC) models for vascular diseases and development of vascular therapies. Here, we find that mesoderm-derived pericytes (PCs) and smooth muscle cells (SMCs) originate from a clonal mesenchymal progenitor mesenchymoangioblast (MB). In clonogenic cultures, MBs differentiate into primitive PDGFRβ(+)CD271(+)CD73(-) mesenchymal progenitors, which give rise to proliferative PCs, SMCs, and mesenchymal stem/stromal cells...
May 30, 2017: Cell Reports
https://www.readbyqxmd.com/read/28533395/integrative-modeling-of-gene-and-genome-evolution-roots-the-archaeal-tree-of-life
#13
Tom A Williams, Gergely J Szöllősi, Anja Spang, Peter G Foster, Sarah E Heaps, Bastien Boussau, Thijs J G Ettema, T Martin Embley
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28533331/chronic-stimulation-of-renin-cells-leads-to-vascular-pathology
#14
Masafumi Oka, Silvia Medrano, Maria Luisa S Sequeira-Lόpez, R Ariel Gómez
Experimental or spontaneous genomic mutations of the renin-angiotensin system or its pharmacological inhibition in early life leads to renal abnormalities, including poorly developed renal medulla, papillary atrophy, hydronephrosis, inability to concentrate the urine, polyuria, polydipsia, renal failure, and anemia. At the core of such complex phenotype is the presence of unique vascular abnormalities: the renal arterioles do not branch or elongate properly and they have disorganized, concentric hypertrophy...
July 2017: Hypertension
https://www.readbyqxmd.com/read/28528574/esc-track-a-computer-workflow-for-4-d-segmentation-tracking-lineage-tracing-and-dynamic-context-analysis-of-escs
#15
Laura Fernández-de-Manúel, Covadonga Díaz-Díaz, Daniel Jiménez-Carretero, Miguel Torres, María C Montoya
Embryonic stem cells (ESCs) can be established as permanent cell lines, and their potential to differentiate into adult tissues has led to widespread use for studying the mechanisms and dynamics of stem cell differentiation and exploring strategies for tissue repair. Imaging live ESCs during development is now feasible due to advances in optical imaging and engineering of genetically encoded fluorescent reporters; however, a major limitation is the low spatio-temporal resolution of long-term 3-D imaging required for generational and neighboring reconstructions...
May 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28508298/stability-of-control-networks-in-autonomous-homeostatic-regulation-of-stem-cell-lineages
#16
Natalia L Komarova, P van den Driessche
Design principles of biological networks have been studied extensively in the context of protein-protein interaction networks, metabolic networks, and regulatory (transcriptional) networks. Here we consider regulation networks that occur on larger scales, namely the cell-to-cell signaling networks that connect groups of cells in multicellular organisms. These are the feedback loops that orchestrate the complex dynamics of cell fate decisions and are necessary for the maintenance of homeostasis in stem cell lineages...
May 15, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28446158/parameter-inference-for-stochastic-single-cell-dynamics-from-lineage-tree-data
#17
Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash
BACKGROUND: With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods suitable for parameter inference with this type of data. Most of currently available methods treat single-cell trajectories independently, ignoring the mother-daughter relationships and the information provided by the population structure. However, this information is essential if a process of interest happens at cell division, or if it evolves slowly compared to the duration of the cell cycle...
April 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28424352/chromatin-module-inference-on-cellular-trajectories-identifies-key-transition-points-and-poised-epigenetic-states-in-diverse-developmental-processes
#18
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we developed a method called Chromatin Module INference on Trees (CMINT), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
July 2017: Genome Research
https://www.readbyqxmd.com/read/28399402/hematopoiesis-lineage-tree-uprooted-every-cell-is-a-rainbow
#19
Karen K Hirschi, Stefania Nicoli, Kenneth Walsh
Differentiation of hematopoietic stem cells into distinct cell types was thought to occur through a series of discrete, stable progenitor states. Work from Velten et al. (2017) now shows that hematopoietic cells differentiate via a mechanism of continuous lineage priming and thus represent a CLOUD-HSPC.
April 10, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28376782/image-analysis-driven-single-cell-analytics-for-systems-microbiology
#20
Athanasios D Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P Tampakaki, Konstantinos P Koutsoumanis, Elias S Manolakos
BACKGROUND: Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. RESULTS: BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view...
April 4, 2017: BMC Systems Biology
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