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https://www.readbyqxmd.com/read/27899642/the-ucsc-genome-browser-database-2017-update
#1
Cath Tyner, Galt P Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steve Heitner, Angie S Hinrichs, Donna Karolchik, Brian T Lee, Christopher M Lee, Parisa Nejad, Brian J Raney, Kate R Rosenbloom, Matthew L Speir, Chris Villarreal, John Vivian, Ann S Zweig, David Haussler, Robert M Kuhn, W James Kent
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898686/gut-homing-cd4-and-cd8-t-cell-frequencies-in-hiv-infected-individuals-on-antiretroviral-treatment
#2
Olivia Briceño, Sandra Pinto-Cardoso, Nataly Rodríguez-Bernabe, Akio Murakami-Ogasawara, Gustavo Reyes-Terán
The depletion of mucosal CD4+ T-cells occurs early in HIV infection and despite years on antiretroviral treatment (ART), this population never reconstitutes to pre-HIV infection levels. In an effort to understand the effect of ART initiation and different ART regimens on the reconstitution of mucosal T cells within the gut associated lymphoid tissue (GALT), we quantified the frequency of CD4+ and CD8+ T cells expressing the gut homing receptors CCR9 and β7 in peripheral blood (PB) of HIV infected individuals naive to ART and treated individuals on both short-term (less than a year) and long-term ART (more than 2 years)...
2016: PloS One
https://www.readbyqxmd.com/read/27888523/the-cotton-%C3%AE-galactosyltransferase-1-galt1-that-galactosylates-arabinogalactan-proteins-participates-in-controlling-fiber-development
#3
Li-Xia Qin, Yun Chen, Wei Zeng, Yang Li, Lu Gao, Deng-Di Li, Antony Bacic, Wen-Liang Xu, Xue-Bao Li
Arabinogalactan-proteins (AGPs) are highly glycosylated proteins which play pivotal roles in diverse developmental processes in plants. Type II AG glycans, mostly O-linked to the hydroxyproline residues of the protein backbone, account for up to 95% w/w of the AGP, but their functions are still largely unclear. Cotton fibers are extremely elongated single-cell trichomes on the seed epidermis. However, little is known of the molecular basis governing the regulation of fiber cell development. Here, we characterized the role of a CAZy glycosyltransferase (GT) family 31 member GhGalT1 in cotton fiber development...
November 26, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27869292/model-based-investigation-of-intracellular-processes-determining-antibody-fc-glycosylation-under-mild-hypothermia
#4
Si Nga Sou, Philip M Jedrzejewski, Ken Lee, Christopher Sellick, Karen M Polizzi, Cleo Kontoravdi
Despite the positive effects of mild hypothermic conditions on monoclonal antibody (mAb) productivity (qmAb ) during mammalian cell culture, the impact of reduced culture temperature on mAb Fc-glycosylation and the mechanism behind changes in the glycan composition is not fully established. The lack of knowledge about the regulation of dynamic intracellular processes under mild hypothermia restricts bioprocess optimisation. To address this issue, a mathematical model that quantitatively describes CHO cell behaviour and metabolism, mAb synthesis and its N-linked glycosylation profiles before and after the induction of mild hypothermia is constructed using two sets of parameters...
November 21, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27863570/radionuclide-therapies-in-molecular-imaging-and-precision-medicine
#5
REVIEW
A Tuba Kendi, Valeria M Moncayo, Jonathon A Nye, James R Galt, Raghuveer Halkar, David M Schuster
This article reviews recent advances and applications of radionuclide therapy. Individualized precision medicine, new treatments, and the evolving role of radionuclide therapy are discussed.
January 2017: PET Clinics
https://www.readbyqxmd.com/read/27837085/kns4-upex1-a-type-ii-arabinogalactan-%C3%AE-1-3-galactosyltransferase-required-for-pollen-exine-development
#6
Toshiya Suzuki, Joan Oñate Narciso, Wei Zeng, Allison van de Meene, Masayuki Yasutomi, Shunsuke Takemura, Edwin R Lampugnani, Monika Susanne Doblin, Antony Bacic, Sumie Ishiguro
Pollen exine is essential for protection from the environment of the male gametes of seed-producing plants, but its assembly and composition remain poorly understood. We previously characterized Arabidopsis mutants with abnormal pollen exine structure and morphology which we named kaonashi (kns). Here we describe the identification of the causal gene of kns4 which was found to be a member of the CAZy glycosyltransferase (GT) 31 gene family, identical to UNEVEN PATTERN OF EXINE1 (UPEX1), and the biochemical characterization of the encoded protein...
November 9, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27822211/cd4-t-follicular-helper-and-iga-b-cell-numbers-in-gut-biopsies-from-hiv-infected-subjects-on-antiretroviral-therapy-are-similar-to-hiv-uninfected-individuals
#7
John Zaunders, Mark Danta, Michelle Bailey, Gerald Mak, Katherine Marks, Nabila Seddiki, Yin Xu, David J Templeton, David A Cooper, Mark A Boyd, Anthony D Kelleher, Kersten K Koelsch
BACKGROUND: Disruption of gastrointestinal tract epithelial and immune barriers contribute to microbial translocation, systemic inflammation, and progression of HIV-1 infection. Antiretroviral therapy (ART) may lead to reconstitution of CD4(+) T cells in gut-associated lymphoid tissue (GALT), but its impact on humoral immunity within GALT is unclear. Therefore, we studied CD4(+) subsets, including T follicular helper cells (Tfh), as well as resident B cells that have switched to IgA production, in gut biopsies, from HIV(+) subjects on suppressive ART compared to HIV-negative controls (HNC)...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27818646/immunoprotective-efficacy-of-six-in-vivo-induced-antigens-against-actinobacillus-pleuropneumoniae-as-potential-vaccine-candidates-in-murine-model
#8
Fei Zhang, Sanjie Cao, Zhuang Zhu, Yusheng Yang, Xintian Wen, Yung-Fu Chang, Xiaobo Huang, Rui Wu, Yiping Wen, Qigui Yan, Yong Huang, Xiaoping Ma, Qin Zhao
Six in vivo-induced (IVI) antigens-RnhB, GalU, GalT, Apl_1061, Apl_1166, and HflX were selected for a vaccine trial in a mouse model. The results showed that the IgG levels in each immune group was significantly higher than that of the negative control (P < 0.001). Except rRnhB group, proliferation of splenocytes was observed in all immunized groups and a relatively higher proliferation activity was observed in rGalU and rGalT groups (P < 0.05). In the rGalT vaccinated group, the proportion of CD4+ T cells in spleen was significant higher than that of negative control (P < 0...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27810921/gut-dysbiosis-impairs-recovery-after-spinal-cord-injury
#9
Kristina A Kigerl, Jodie C E Hall, Lingling Wang, Xiaokui Mo, Zhongtang Yu, Phillip G Popovich
The trillions of microbes that exist in the gastrointestinal tract have emerged as pivotal regulators of mammalian development and physiology. Disruption of this gut microbiome, a process known as dysbiosis, causes or exacerbates various diseases, but whether gut dysbiosis affects recovery of neurological function or lesion pathology after traumatic spinal cord injury (SCI) is unknown. Data in this study show that SCI increases intestinal permeability and bacterial translocation from the gut. These changes are associated with immune cell activation in gut-associated lymphoid tissues (GALTs) and significant changes in the composition of both major and minor gut bacterial taxa...
November 14, 2016: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/27798903/gut-associated-lymphoid-tissue-galt-carcinoma-or-dome-carcinoma
#10
Carlos A Rubio, Peter T Schmidt
BACKGROUND/AIM: The vast majority of colorectal carcinomas (CRCs) evolve from mucosa not associated to lymphoid tissues aggregates via the adenoma-carcinoma sequence or via the serrated pathway. Rarely CRCs evolve from gut mucosa associated to lymphoid tissue (GALT). MATERIALS AND METHODS: Based on the presence of a circumscribed elevation in the colorectal mucosa, GALT carcinomas are also referred to as dome carcinomas (DC). Descriptions of the surface mucosa covering 21 GALT-CRCs appearing in pathological reports were reviewed...
October 2016: Anticancer Research
https://www.readbyqxmd.com/read/27783170/assessment-of-ataxia-phenotype-in-a-new-mouse-model-of-galactose-1-phosphate-uridylyltransferase-galt-deficiency
#11
Wyman Chen, Rose Caston, Bijina Balakrishnan, Anwer Siddiqi, Kamalpreet Parmar, Manshu Tang, Merry Feng, Kent Lai
Despite adequate dietary management, patients with classic galactosemia continue to have increased risks of cognitive deficits, speech dyspraxia, primary ovarian insufficiency, and abnormal motor development. A recent evaluation of a new galactose-1 phosphate uridylyltransferase (GALT)-deficient mouse model revealed reduced fertility and growth restriction. These phenotypes resemble those seen in human patients. In this study, we further assess the fidelity of this new mouse model by examining the animals for the manifestation of a common neurological sequela in human patients: cerebellar ataxia...
October 25, 2016: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/27766282/induction-of-gut-regulatory-cd39-t-cells-by-teriflunomide-protects-against-eae
#12
Javier Ochoa-Repáraz, Sara L Colpitts, Christopher Kircher, Eli J Kasper, Kiel M Telesford, Sakhina Begum-Haque, Anudeep Pant, Lloyd H Kasper
OBJECTIVE: To determine whether as an orally delivered treatment, teriflunomide, an inhibitor of the mitochondrial enzyme dihydroorotate dehydrogenase approved to treat relapsing forms of multiple sclerosis, could affect gut-associated lymphoid tissue (GALT) immune responses functionally. METHODS: C57BL/6 mice were treated orally with teriflunomide and flow cytometric analysis of immune GALT cells performed ex vivo, and adoptive transfer experiments were used to test the protective effects of GALT regulatory T (Treg) cells...
December 2016: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/27697560/genomic-structure-and-expression-pattern-of-mhc-ii%C3%AE-and-ii%C3%AE-genes-reveal-an-unusual-immune-trait-in-lined-seahorse-hippocampus-erectus
#13
Wei Luo, Xin Wang, Hongyue Qu, Geng Qin, Huixian Zhang, Qiang Lin
The major histocompatibility complex (MHC) genes are crucial in the adaptive immune system, and the gene duplication of MHC in animals can generally result in immune flexibility. In this study, we found that the lined seahorse (Hippocampus erectus) has only one gene copy number (GCN) of MHC IIα and IIβ, which is different from that in other teleosts. Together with the lack of spleen and gut-associated lymphatic tissue (GALT), the seahorse may be referred to as having a partial but natural "immunodeficiency"...
September 30, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27693367/the-immune-system-of-the-gut-and-potential-adverse-effects-of-oral-nanocarriers-on-its-function
#14
REVIEW
Erik Őrfi, János Szebeni
There is substantial effort in modern pharmacotherapy to use nanoparticle-based drug delivery systems (nDDS) for improving the oral absorption of drugs. An often neglected circumstance regarding this approach is that the gut is a major part of the immune system that may be vulnerable for immune-cell toxicity, or mediate humoral immune response against various components of nDDS, recognized as foreign. This review recapitulates the structure and function of gut-associated lymphoid tissue (GALT), i.e., the enteral section of mucosa-associated lymphoid tissue (MALT) and reminds how virus-like nDDS may potentially induce immunogenicity just as attenuated or killed viruses do in oral vaccines...
November 15, 2016: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/27689995/probiotics-differently-affect-gut-associated-lymphoid-tissue-indolamine-2-3-dioxygenase-mrna-and-cerebrospinal-fluid-neopterin-levels-in-antiretroviral-treated-hiv-1-infected-patients-a-pilot-study
#15
Carolina Scagnolari, Giuseppe Corano Scheri, Carla Selvaggi, Ivan Schietroma, Saeid Najafi Fard, Andrea Mastrangelo, Noemi Giustini, Sara Serafino, Claudia Pinacchio, Paolo Pavone, Gianfranco Fanello, Giancarlo Ceccarelli, Vincenzo Vullo, Gabriella d'Ettorre
Recently the tryptophan pathway has been considered an important determinant of HIV-1 infected patients' quality of life, due to the toxic effects of its metabolites on the central nervous system (CNS). Since the dysbiosis described in HIV-1 patients might be responsible for the microbial translocation, the chronic immune activation, and the altered utilization of tryptophan observed in these individuals, we speculated a correlation between high levels of immune activation markers in the cerebrospinal fluid (CSF) of HIV-1 infected patients and the over-expression of indolamine-2,3-dioxygenase (IDO) at the gut mucosal surface...
2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27604178/collagenvi-cre-mice-a-new-tool-to-target-stromal-cells-in-secondary-lymphoid-organs
#16
Alejandro Prados, George Kollias, Vasiliki Koliaraki
Stromal cells in secondary lymphoid organs (SLOs) are non-hematopoietic cells involved in the regulation of adaptive immune responses. Three major stromal populations have been identified in adult SLOs: fibroblastic reticular cells (FRCs), follicular dendritic cells (FDCs) and marginal reticular cells (MRCs). The properties of these individual populations are not clearly defined, mainly due to the lack of appropriate genetic tools, especially for MRCs. Here, we analyzed stromal cell targeting in SLOs from a transgenic mouse strain that expresses Cre recombinase under the CollagenVI promoter, using lineage tracing approaches...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27603904/identification-of-multiple-gene-mutations-accounts-for-a-new-genetic-architecture-of-primary-ovarian-insufficiency
#17
Justine Bouilly, Isabelle Beau, Sara Barraud, Valérie Bernard, Kemal Azibi, Jérôme Fagart, Anne Fèvre, Anne Laure Todeschini, Reiner A Veitia, Chérif Beldjord, Brigitte Delemer, Catherine Dodé, Jacques Young, Nadine Binart
CONTEXT: Idiopathic primary ovarian insufficiency (POI) is a major cause of amenorrhea and infertility. POI affects 1% of women before age 40, and several genetic causes have been reported. To date, POI has been considered a monogenic disorder. OBJECTIVE: The aim of this study was to identify novel gene variations and to investigate if individuals with POI harbor mutation in multiple loci. PATIENTS AND METHODS: One hundred well-phenotyped POI patients were systematically screened for variants in 19 known POI loci (and potential candidate genes) using next-generation sequencing...
September 7, 2016: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/27578510/a-population-based-genomic-study-of-inherited-metabolic-diseases-detected-through-newborn-screening
#18
Kyoung Jin Park, Seungman Park, Eunhee Lee, Jong Ho Park, June Hee Park, Hyung Doo Park, Soo Youn Lee, Jong Won Kim
BACKGROUND: A newborn screening (NBS) program has been utilized to detect asymptomatic newborns with inherited metabolic diseases (IMDs). There have been some bottlenecks such as false-positives and imprecision in the current NBS tests. To overcome these issues, we developed a multigene panel for IMD testing and investigated the utility of our integrated screening model in a routine NBS environment. We also evaluated the genetic epidemiologic characteristics of IMDs in a Korean population...
November 2016: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/27570813/contribution-of-mesenteric-lymph-nodes-and-galt-to-the-intestinal-foxp3-regulatory-t-cell-compartment
#19
Duke Geem, Vu Ngo, Akihito Harusato, Benoit Chassaing, Andrew T Gewirtz, Rodney D Newberry, Timothy L Denning
: This study showed that the absence of CCR7 or mesenteric lymph nodes/gut-associated lymphoid tissue did not appreciably impact total intestinal Foxp3+ regulatory T cell representation in the steady-state. However, mesenteric lymph nodes/GALT are required for normal peripherally induced Foxp3+ regulatory T cell differentiation in the small intestine, but not in the large intestine. BACKGROUND & AIMS: Foxp3+ regulatory T cells (Tregs) in the intestine promote immune tolerance to enteric antigens...
May 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27562100/acute-and-long-term-outcomes-in-a-drosophila-melanogaster-model-of-classic-galactosemia-occur-independently-of-galactose-1-phosphate-accumulation
#20
Jennifer M I Daenzer, Patricia P Jumbo-Lucioni, Marquise L Hopson, Kerry R Garza, Emily L Ryan, Judith L Fridovich-Keil
Classic galactosemia (CG) is a potentially lethal inborn error of metabolism that results from the profound loss of galactose-1-phosphate uridylyltransferase (GALT), the second enzyme in the Leloir pathway of galactose metabolism. Neonatal detection and dietary restriction of galactose minimizes or resolves the acute sequelae of CG, but fails to prevent the long-term complications experienced by a majority of patients. One of the substrates of GALT, galactose-1-phosphate (Gal-1P), accumulates to high levels in affected infants, especially following milk exposure, and has been proposed as the key mediator of acute and long-term pathophysiology in CG...
November 1, 2016: Disease Models & Mechanisms
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