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https://www.readbyqxmd.com/read/29106570/the-ucsc-genome-browser-database-2018-update
#1
Jonathan Casper, Ann S Zweig, Chris Villarreal, Cath Tyner, Matthew L Speir, Kate R Rosenbloom, Brian J Raney, Christopher M Lee, Brian T Lee, Donna Karolchik, Angie S Hinrichs, Maximilian Haeussler, Luvina Guruvadoo, Jairo Navarro Gonzalez, David Gibson, Ian T Fiddes, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Galt P Barber, Joel Armstrong, David Haussler, Robert M Kuhn, W James Kent
The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29084246/prevalence-risk-factors-and-virulence-genes-of-helicobacter-pylori-among-dyspeptic-patients-in-two-different-gastric-cancer-risk-regions-of-thailand
#2
Phawinee Subsomwong, Muhammad Miftahussurur, Tomohisa Uchida, Ratha-Korn Vilaichone, Thawee Ratanachu-Ek, Varocha Mahachai, Yoshio Yamaoka
Gastric cancer risk is varied among different regions of Thailand. We examined the characteristics of Helicobacter pylori infection in two regions of Thailand. The H. pylori status of 273 dyspeptic patients (136 from the South and 137 from the North; a low and high incidence of gastric cancer region, respectively) was evaluated, and virulence genotypes (cagA, vacA, hrgA and jhp0562-positive/β-(1,3)galT) were determined. The overall H. pylori infection rate was 34.1% (93/273). The prevalence was higher in the North than in the South (50...
2017: PloS One
https://www.readbyqxmd.com/read/29072057/nepalese-helicobacter-pylori-genotypes-reflects-a-geographical-diversity-than-a-true-virulence-factor
#3
Rabi Prakash Sharma, Muhammad Miftahussurur, Pradeep Krishna Shrestha, Phawinee Subsomwong, Tomohisa Uchida, Yoshio Yamaoka
Background: The data about the association between Helicobacter pylori putative virulence factors; iceA and jhp0562/β-(1,3)galT with clinical outcomes are still controversial. We identified and analyzed two putative H. pylori virulence factors in Nepalese strains. Methods: The iceA and jhp0562/β-(1,3)galT allelic types were determined by polymerase chain reaction amplification. Histological analysis were classified according to the updated Sydney system and the Operative Link on Gastritis Assessment (OLGA) system...
October 26, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29067747/effects-of-carbon-monoxide-on-early-dysfunction-and-microangiopathy-following-galt-ko-porcine-pulmonary-xenotransplantation-in-cynomolgus-monkeys
#4
Hisashi Sahara, Mitsuhiro Sekijima, Yuichi Ariyoshi, Akihiro Kawai, Kohei Miura, Shiori Waki, Louras Nathan, Yusuke Tomita, Takehiro Iwanaga, Kazuaki Nakano, Hitomi Matsunari, Hiroshi Date, Hiroshi Nagashima, Akira Shimizu, Kazuhiko Yamada
BACKGROUND: Despite progress in the current genetic manipulation of donor pigs, most non-human primates were lost within a day of receiving porcine lung transplants. We previously reported that carbon monoxide (CO) treatment improved pulmonary function in an allogeneic lung transplant (LTx) model using miniature swine. In this study, we evaluated whether the perioperative treatment with low-dose inhalation of CO has beneficial effects on porcine lung xenografts in cynomolgus monkeys (cynos)...
October 25, 2017: Xenotransplantation
https://www.readbyqxmd.com/read/29053834/effect-of-feed-supplementation-with-zinc-glycine-chelate-and-zinc-sulfate-on-cytokine-and-immunoglobulin-gene-expression-profiles-in-chicken-intestinal-tissue
#5
L Jarosz, A Marek, Z Gradzki, M Kwiecien, B Zylinska, B Kaczmarek
The aim of the study was to evaluate the effect of inorganic and organic forms of Zn on the expression of cytokines (IL-2, TNF-α, IFN-γ, IL-12, IL-17, IL-4, IL-10, and TGF-β) and immunoglobulins (IgA and IgG) in the tissues of the small intestine (jejunum and ileum) of broiler chickens. In the experiment, 90 broiler chickens were divided into 4 experimental groups and a control group, with 18 birds each. The birds received Zn supplements in inorganic form with and without phytase (ZnSO4 and ZnSO4 + F), and in organic form with glycine, with and without phytase (Zn-Gly and Zn-Gly + F)...
October 5, 2017: Poultry Science
https://www.readbyqxmd.com/read/28990060/microrna-expression-profiling-of-intestinal-mucosa-tissue-predicts-multiple-crucial-regulatory-molecules-and-signaling-pathways-for-gut-barrier-dysfunction-of-aids-patients
#6
Yu Xu, Hua-Wei Wang, Hua-You Luo, Ruo Shu, Jia Liu, Liang Sun, Xue-Fei Han, Na Lin, Ting-Hua Wang, Yu-Jian Zeng, Kun-Hua Wang
Human immunodeficiency virus‑1 (HIV‑1) infection severely damages the gut‑associated lymphoid tissue (GALT), the immune system and the gut barrier, which leads to accelerating the disease progression for patients with acquired immune deficiency syndrome (AIDS). Dysregulation of microRNAs (miRNAs) may contribute to this process. However, few studies have investigated the importance of miRNAs in AIDS pathogenesis and progression. The whole miRNA profile of patients with HIV infection from southwest P.R...
December 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28971364/genetic-testing-in-pediatric-ophthalmology
#7
REVIEW
Ishwar Chander Verma, Preeti Paliwal, Kanika Singh
The authors review the utility of genetic testing in ophthalmic disorders - precise diagnosis, accurate prognosis, genetic counseling, prenatal diagnosis, and entry into gene-specific therapeutic trials. The prerequisites for a successful outcome of a genetic test are an accurate clinical diagnosis, a careful family history that guides which genes to study, and genetic counseling (both pre-test and post-test). The common eye disorders for which genetic testing is commonly requested are briefly discussed - anophthalmia, microphthalmia, coloboma, anterior segment dysgenesis, corneal dystrophies, cataracts, optic atrophy, congenital glaucoma, congenital amaurosis, retinitis pigmentosa, color blindness, juvenile retinoshisis, retinoblastoma etc...
October 2, 2017: Indian Journal of Pediatrics
https://www.readbyqxmd.com/read/28968888/tissue-pharmacologic-and-virologic-determinants-of-duodenal-and-rectal-gastrointestinal-associated-lymphoid-tissue-immune-reconstitution-in-hiv-infected-patients-initiating-antiretroviral-therapy
#8
David M Asmuth, Corbin G Thompson, Tae-Wook Chun, Zhong-Min Ma, Surinder Mann, Talia Sainz, Sergio Serrano-Villar, Netanya S Utay, Juan Carlos Garcia, Paolo Troia-Cancio, Richard B Pollard, Christopher J Miller, Alan Landay, Angela D Kashuba
Plasma, duodenal, and rectal tissue antiretroviral therapy (ART) drug concentrations, human immunodeficiency virus (HIV) RNA and HIV DNA copy numbers, and recovery of mucosal immunity were measured before and 9 months after initiation of 3 different ART regimens in 26 subjects. Plasma and tissue HIV RNA correlated at baseline and when 9-month declines were compared, suggesting that these compartments are tightly associated. Antiretroviral tissue:blood penetration ratios were above the 50% inhibitory concentration values in almost 100% of cases...
October 17, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28961353/the-evolution-of-a-web-resource-the-galactosemia-proteins-database-2-0
#9
Antonio d'Acierno, Bernardina Scafuri, Angelo Facchiano, Anna Marabotti
Galactosemia Proteins Database 2.0 is a Web-accessible resource collecting information about the structural and functional effects of the known variations associated to the three different enzymes of the Leloir pathway encoded by the genes GALT, GALE, and GALK1 and involved in the different forms of the genetic disease globally called "galactosemia." It represents an evolution of two available online resources we previously developed, with new data deriving from new structures, new analysis tools, and new interfaces and filters in order to improve the quality and quantity of information available for different categories of users...
September 29, 2017: Human Mutation
https://www.readbyqxmd.com/read/28949001/forearm-pronation-efficiency-in-a-l-288-1-australopithecus-afarensis-and-mh2-australopithecus-sediba-insights-into-their-locomotor-and-manipulative-habits
#10
Pere Ibáñez-Gimeno, Joan Manyosa, Ignasi Galtés, Xavier Jordana, Salvador Moyà-Solà, Assumpció Malgosa
OBJECTIVES: The locomotor and manipulative abilities of australopithecines are highly debated in the paleoanthropological context. Australopithecus afarensis and Australopithecus sediba likely engaged in arboreal locomotion and, especially the latter, in certain activities implying manipulation. Nevertheless, their degree of arboreality and the relevance of their manipulative skills remain unclear. Here we calculate the pronation efficiency of the forearm (Erot ) in these taxa to explore their arboreal and manipulative capabilities using a biomechanical approach...
September 26, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28921534/exploring-cellular-behaviour-under-transient-gene-expression-and-its-impact-on-mab-productivity-and-fc-glycosylation
#11
Si Nga Sou, Ken Lee, Kalpana Nayyar, Karen M Polizzi, Christopher Sellick, Cleo Kontoravdi
Transient gene expression (TGE) is a methodology employed in bioprocessing for the fast provision of recombinant protein material. Mild hypothermia is often introduced to overcome the low yield typically achieved with TGE and improve specific protein productivity. It is therefore of interest to examine the impact of mild hypothermic temperatures on both the yield and quality of transiently-expressed proteins and the relationship to changes in cellular processes and metabolism. In this study, we focus on the ability of a Chinese hamster ovary cell line to galactosylate a recombinant monoclonal antibody (mAb) product...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28913702/impaired-fertility-and-motor-function-in-a-zebrafish-model-for-classic-galactosemia
#12
Jo M Vanoevelen, M Estela Rubio-Gozalbo, Britt van Erven, Jörgen Bierau, Xiaoping Huang, Gerard T Berry, Rein Vos, Ana I Coelho
Classic galactosemia is a genetic disorder of galactose metabolism, caused by severe deficiency of galactose-1-phosphate uridylyltransferase (GALT) enzyme activity due to mutations of the GALT gene. Its pathogenesis is still not fully elucidated, and a therapy that prevents chronic impairments is lacking. In order to move research forward, there is a high need for a novel animal model, which allows organ studies throughout development and high-throughput screening of pharmacologic compounds. Here, we describe the generation of a galt knockout zebrafish model and present its phenotypical characterization...
September 14, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28910600/an-acceptor-analogue-of-%C3%AE-1-4-galactosyltransferase-substrate-inhibitor-or-both
#13
Jingqian Jiang, Gerd K Wagner
Many glycosyltransferase inhibitors in the literature are structurally derived from the donor or acceptor substrate of the respective enzyme. A representative example is 2-naphthyl β-d-GlcNAc, a synthetic GlcNAc glycoside that has been reported as a galactosyltransferase inhibitor. This GlcNAc derivative is attractive as a chemical tool compound for biological and biochemical studies because of its reported potency as an inhibitor, and its short and straightforward synthesis from readily available starting materials...
October 10, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28882590/targeted-deletion-of-rankl-in-m-cell-inducer-cells-by-the-col6a1-cre-driver
#14
Kazuki Nagashima, Shinichiro Sawa, Takeshi Nitta, Alejandro Prados, Vasiliki Koliaraki, George Kollias, Tomoki Nakashima, Hiroshi Takayanagi
The gut-associated lymphoid tissues (GALTs), including Peyer's patches (PPs), cryptopatches (CPs) and isolated lymphoid follicles (ILFs), establish a host-microbe symbiosis by the promotion of immune reactions against gut microbes. Microfold cell inducer (MCi) cells in GALTs are the recently identified mesenchymal cells that express the cytokine RANKL and initiate bacteria-specific immunoglobulin A (IgA) production via induction of microfold (M) cell differentiation. In the previous study, the Twist2-Cre driver was utilized for gene deletion in mesenchymal cells including MCi cells...
November 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28859865/ischemic-stroke-damages-the-intestinal-mucosa-and-induces-alteration-of-the-intestinal-lymphocytes-and-ccl19-mrna-in-rats
#15
Yaning Liu, Shijian Luo, Li Kou, Chaogang Tang, Ruxun Huang, Zhong Pei, Zhendong Li
The immunoreaction has a pivotal effect on ischemic stroke. It has been demonstrated that intestinal lymphocytes infiltrate into the brain and aggravate tissue injury after stroke. However, less attention has been paid to the influence on the intestinal immunology as well as morphology. Here, we utilized a rat permanent middle cerebral artery occlusion (MCAO) model to investigate the influences on intestinal mucosa, lymphocytes of the gut-associated lymphoid tissue (GALT), and the intestinal expression of CCL25 mRNA and CCL19 mRNA of stroke...
September 29, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28851631/strain-specific-helper-t-cell-profile-in-the-gut-associated-lymphoid-tissue
#16
Suzana Stanisavljević, Neda Đedović, Milica Vujičić, Tamara Saksida, Bojan Jevtić, Boško Milovanović, Miljana Momčilović, Đorđe Miljković, Ivana Stojanović
C57BL/6, BALB/c and NOD mice are among the most frequently used strains in autoimmunity research. NOD mice spontaneously develop type 1 diabetes (T1D) and they are prone to induction of experimental autoimmune encephalomyelitis (EAE). Both diseases can be routinely induced in C57BL/6 mice, but not in BALB/c mice. Also, C57BL/6 mice are generally considered T helper (Th)1-biased and BALB/c Th2-biased mice. Having in mind increasingly appreciated role of gut associated lymphoid tissue (GALT) cells in autoimmunity, especially in relation to gut Th17 and regulatory T (Treg) cells, our aim was to determine if there are differences in proportion of CD4(+) T cell populations in mesenteric lymph nodes and Peyer's patches of these mouse strains...
August 26, 2017: Immunology Letters
https://www.readbyqxmd.com/read/28844959/reversal-of-aberrant-pi3k-akt-signaling-by-salubrinal-in-a-galt-deficient-mouse-model
#17
B Balakrishnan, C Nicholas, A Siddiqi, W Chen, E Bales, M Feng, J Johnson, K Lai
Classic Galactosemia is an autosomal recessive disorder caused by deleterious mutations in the GALT gene, which encodes galactose-1 phosphate uridylyltransferase enzyme (GALT: EC 2.7.7.12). Recent studies of primary skin fibroblasts isolated from the GalT-deficient mice demonstrated a slower growth rate, a higher level of endoplasmic reticulum (ER) stress, and down-regulation of the Phosphoinositide 3 kinase/Protein kinase B (PI3K/Akt) signaling pathway. In this study, we compared the expression levels of the PI3K/Akt signaling pathway in normal and GalT-deficient mouse tissues...
August 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28832609/distinct-aging-profiles-of-cd8-t-cells-in-blood-versus-gastrointestinal-mucosal-compartments
#18
Jeffrey Dock, Christina M Ramirez, Lance Hultin, Mary Ann Hausner, Patricia Hultin, Julie Elliott, Otto O Yang, Peter A Anton, Beth D Jamieson, Rita B Effros
A hallmark of human immunosenescence is the accumulation of late-differentiated memory CD8+ T cells with features of replicative senescence, such as inability to proliferate, absence of CD28 expression, shortened telomeres, loss of telomerase activity, enhanced activation, and increased secretion of inflammatory cytokines. Importantly, oligoclonal expansions of these cells are associated with increased morbidity and mortality risk in elderly humans. Currently, most information on the adaptive immune system is derived from studies using peripheral blood, which contains approximately only 2% of total body lymphocytes...
2017: PloS One
https://www.readbyqxmd.com/read/28816213/association-of-presenile-cataract-with-galactose-1-phosphate-uridyl-transferase-gene-mutations
#19
Nitin Nema, Ravindra Kumar, Abha Verma, Sonam Verma, Kiran Chaturvedi
BACKGROUND: Presenile cataract is commonly idiopathic in origin. However, patients with presenile cataract could have an underlying genetic abnormality of galactose metabolism. We studied the association, if any, between idiopathic presenile cataract and galactose-1 -phosphate uridyl transferase (GALT) gene mutation. METHODS: We selected 50 patients with idiopathic presenile cataract, <45 years of age, and 50 age- and sex-matched controls for the study. Mutations in the GALT gene were determined by polymerase chain reaction restriction fragment length polymorphism...
March 2017: National Medical Journal of India
https://www.readbyqxmd.com/read/28782046/circulating-loxl2-levels-reflect-severity-of-intestinal-fibrosis-and-galt-cd4-t-lymphocyte-depletion-in-treated-hiv-infection
#20
Sophie Seang, Anoma Somasunderam, Maitreyee Nigalye, Ma Somsouk, Timoty W Schacker, Joyce L Sanchez, Peter W Hunt, Netanya S Utay, Jordan E Lake
BACKGROUND: Incomplete immune reconstitution may occur despite successful antiretroviral therapy (ART). Gut-associated lymphoid tissue (GALT) fibrosis may contribute via local CD4(+) T lymphocyte depletion, intestinal barrier disruption, microbial translocation, and immune activation. METHODS: In a cross-sectional analysis, we measured circulating fibrosis biomarker levels on cryopreserved plasma from adult HIV-infected (HIV+) SCOPE study participants on suppressive ART who also had fibrosis quantification on recto-sigmoid biopsies...
2017: Pathogens & Immunity
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