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https://www.readbyqxmd.com/read/27922118/mining-visualizing-and-comparing-multidimensional-biomolecular-data-using-the-genomics-data-miner-gmine-web-server
#1
Carla Proietti, Martha Zakrzewski, Thomas S Watkins, Bernard Berger, Shihab Hasan, Champa N Ratnatunga, Marie-Jo Brion, Peter D Crompton, John J Miles, Denise L Doolan, Lutz Krause
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921425/-oxldl-%C3%AE-2-glycoprotein-i-complex-as-a-pro-atherogenic-autoantigen-is-atherosclerosis-an-autoimmune-disease
#2
Pavel Kraml
Oxidation of atherogenic low-density lipoproteins (LDL) plays a key role in the pathogenesis of atherosclerosis. Oxidation stress and inflammation are closely interrelated and they can potentiate one another. In the subendothelial space of the arterial intima, monocytes/macrophages become activated and phagocyte oxidized LDL (oxLDL) via scavenger receptors. It has been demonstrated that oxLDL forms complex with plasma β2-glycoprotein I (β2GPI) and becomes autoantigenic triggering synthesis of specific antiphosholipid antibodies...
2016: Vnitr̆ní Lékar̆ství
https://www.readbyqxmd.com/read/27921293/coloniality-and-migration-are-related-to-selection-on-mhc-genes-in-birds
#3
Piotr Minias, Linda A Whittingham, Peter O Dunn
The Major Histocompatibility Complex (MHC) plays a key role in pathogen recognition as a part of vertebrate adaptive immune system. The great diversity of MHC genes in natural populations is maintained by different forms of balancing selection and its strength should correlate with the diversity of pathogens to which a population is exposed and the rate of exposure. Despite this prediction, little is known about how the life-history characteristics affect selection at the MHC. Here, we examined whether the strength of balancing selection on MHC class II genes in birds (as measured with nonsynonymous nucleotide substitutions, dN) was related to their social or migratory behaviour, two life-history characteristics correlated with pathogen exposure...
December 6, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27920779/functional-versatility-of-agy-serine-codons-in-immunoglobulin-variable-region-genes
#4
Thiago Detanico, Matthew Phillips, Lawrence J Wysocki
In systemic autoimmunity, autoantibodies directed against nuclear antigens (Ags) often arise by somatic hypermutation (SHM) that converts AGT and AGC (AGY) Ser codons into Arg codons. This can occur by three different single-base changes. Curiously, AGY Ser codons are far more abundant in complementarity-determining regions (CDRs) of IgV-region genes than expected for random codon use or from species-specific codon frequency data. CDR AGY codons are also more abundant than TCN Ser codons. We show that these trends hold even in cartilaginous fishes...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27920759/immune-responses-to-influenza-virus-and-its-correlation-to-age-and-inherited-factors
#5
REVIEW
Azadeh Bahadoran, Sau H Lee, Seok M Wang, Rishya Manikam, Jayakumar Rajarajeswaran, Chandramathi S Raju, Shamala D Sekaran
Influenza viruses belong to the family Orthomyxoviridae of enveloped viruses and are an important cause of respiratory infections worldwide. The influenza virus is able to infect a wide variety species as diverse as poultry, marine, pigs, horses, and humans. Upon infection with influenza virus the innate immunity plays a critical role in efficient and rapid control of viral infections as well as in adaptive immunity initiation. The humoral immune system produces antibodies against different influenza antigens, of which the HA-specific antibody is the most important for neutralization of the virus and thus prevention of illness...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920651/use-of-direct-acting-antivirals-for-the-treatment-of-hepatitis-c-virus-associated-oral-lichen-planus-a-case-report
#6
Kenji Misaka, Takashi Kishimoto, Yuji Kawahigashi, Michio Sata, Yumiko Nagao
Hepatitis C virus (HCV) is frequently associated with various extrahepatic manifestations such as autoimmune features and immune complex deposit diseases. Oral lichen planus (OLP) is one of the representative extrahepatic manifestations of HCV infection. Direct-acting antivirals (DAA) are highly effective and safe for the eradication of HCV. However, there is a lack of information regarding the association between HCV-associated OLP and interferon (IFN)-free DAA therapy. Herein, we present the case of a 60-year-old female who was diagnosed with OLP during routine periodontal treatment by a dentist...
September 2016: Case Reports in Gastroenterology
https://www.readbyqxmd.com/read/27920254/casein-kinase-2-is-linked-to-stress-granule-dynamics-through-phosphorylation-of-the-stress-granule-nucleating-protein-g3bp1
#7
Lucas C Reineke, Wei-Chih Tsai, Antrix Jain, Jason T Kaelber, Sung Yun Jung, Richard E Lloyd
Stress granules are large macromolecular aggregates that contain translation initiation complexes and mRNAs. Stress granule formation coincides with translational repression, and stress granules actively signal to mediate cell fate decisions by a) signaling to the translation apparatus to maintain translational repression, b) mount various transcriptional responses including innate immunity, and c) to repress apoptosis. Previous work showed G3BP1 is phosphorylated at serine 149, which regulates G3BP1 oligomerization, stress granule assembly, and RNase activity intrinsic to G3BP1...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920204/studies-on-the-detection-expression-glycosylation-dimerization-and-ligand-binding-properties-of-mouse-siglec-e
#8
Shoib Siddiqui, Flavio Schwarz, Stevan Springer, Zahra Khedri, Hai Yu, Lingquan Deng, Andrea Verhagen, Yuko Naito-Matsui, Weiping Jiang, Daniel Kim, Jie Zhou, Beibei Ding, Xi Chen, Nissi Varki, Ajit Varki
CD33-related Siglecs are a family of proteins widely expressed on innate immune cells. Binding of sialylated glycans or other ligands triggers signals that inhibit or activate inflammation. Immunomodulation by Siglecs has been extensively studied, but relationships between structure and functions are poorly explored. Here we present new data relating the structure and function of Siglec-E, the major CD33-related Siglec expressed on mouse neutrophils, monocytes, macrophages, and dendritic cells. We generated nine new rat monoclonal antibodies specific to mouse Siglec-E, with no cross-reactivity to Siglec-F...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27920181/chikungunya-virus-vaccines-viral-vector-based-approaches
#9
Katrin Ramsauer, Frédéric Tangy
In 2013, a major chikungunya virus (CHIKV) epidemic reached the Americas. In the past 2 years, >1.7 million people have been infected. In light of the current epidemic, with millions of people in North and South America at risk, efforts to rapidly develop effective vaccines have increased. Here, we focus on CHIKV vaccines that use viral-vector technologies. This group of vaccine candidates shares an ability to potently induce humoral and cellular immune responses by use of highly attenuated and safe vaccine backbones...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27919524/demystifying-the-cytokine-network-mathematical-models-point-the-way
#10
REVIEW
Penelope A Morel, Robin E C Lee, James R Faeder
Cytokines provide the means by which immune cells communicate with each other and with parenchymal cells. There are over one hundred cytokines and many exist in families that share receptor components and signal transduction pathways, creating complex networks. Reductionist approaches to understanding the role of specific cytokines, through the use of gene-targeted mice, have revealed further complexity in the form of redundancy and pleiotropy in cytokine function. Creating an understanding of the complex interactions between cytokines and their target cells is challenging experimentally...
December 2, 2016: Cytokine
https://www.readbyqxmd.com/read/27919440/partnered-sexual-activity-moderates-menstrual-cycle-related-changes-in-inflammation-markers-in-healthy-women-an-exploratory-observational-study
#11
Tierney K Lorenz, Gregory E Demas, Julia R Heiman
OBJECTIVE: To examine differences in inflammation markers in sexually active versus abstinent women and observe changes in inflammation markers across the menstrual cycle. Cycle-related immune fluctuations may have evolved to reduce interference with conception. If so, reproductively active (i.e., sexually active) women should show the most variability in cytokine expression. DESIGN: Participants provided serum samples at menses and ovulation (from which cytokines were assayed) and saliva samples at menses and during follicular, ovulation, and luteal phases (from which C-reactive protein [CRP] was assayed)...
December 2, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27919436/complement-in-basic-processes-of-the-cell
#12
Anaïs Jiménez-Reinoso, Ana V Marin, José R Regueiro
The complement system is reemerging in the last few years not only as key element of innate immunity against pathogens, but also as a main regulator of local adaptive responses, affecting dendritic cells as well as T and B lymphocytes. We review data showing that leucocytes are capable of significant autocrine synthesis of complement proteins, and express a large range of complement receptors, which in turn regulate their differentiation and effector functions while cross talking with other innate receptors such as Toll-like receptors...
December 2, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27918526/mycobacterium-tuberculosis-esxh-inhibits-escrt-dependent-cd4-t-cell-activation
#13
Cynthia Portal-Celhay, JoAnn M Tufariello, Smita Srivastava, Aleena Zahra, Thais Klevorn, Patricia S Grace, Alka Mehra, Heidi S Park, Joel D Ernst, William R Jacobs, Jennifer A Philips
Mycobacterium tuberculosis (Mtb) establishes a persistent infection, despite inducing antigen-specific T-cell responses. Although T cells arrive at the site of infection, they do not provide sterilizing immunity. The molecular basis of how Mtb impairs T-cell function is not clear. Mtb has been reported to block major histocompatibility complex class II (MHC-II) antigen presentation; however, no bacterial effector or host-cell target mediating this effect has been identified. We recently found that Mtb EsxH, which is secreted by the Esx-3 type VII secretion system, directly inhibits the endosomal sorting complex required for transport (ESCRT) machinery...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27918208/investigational-hemagglutinin-targeted-influenza-virus-inhibitors
#14
Li-Yan Zeng, Jie Yang, Shuwen Liu
Seasonal influenza and pandemic outbreaks typically result in high mortality and morbidity associated with severe economic burdens. Vaccines and anti-influenza drugs have made great contributions to control the infection. However, antigenic drifts and shifts allow influenza viruses to easily escape immune neutralization and antiviral drug activity. Hemagglutinin (HA)is an important envelope protein for the entry of influenza viruses into host cells, thus, HA-targeted agents may be potential anti-influenza drugs...
December 5, 2016: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/27917914/t-cells-mediate-autoantibody-induced-cutaneous-inflammation-and-blistering-in-epidermolysis-bullosa-acquisita
#15
Katja Bieber, Mareike Witte, Shijie Sun, Jennifer E Hundt, Kathrin Kalies, Sören Dräger, Anika Kasprick, Trix Twelkmeyer, Rudolf A Manz, Peter König, Jörg Köhl, Detlef Zillikens, Ralf J Ludwig
T cells are key players in autoimmune diseases by supporting the production of autoantibodies. However, their contribution to the effector phase of antibody-mediated autoimmune dermatoses, i.e., tissue injury and inflammation of the skin, has not been investigated. In this paper, we demonstrate that T cells amplify the development of autoantibody-induced tissue injury in a prototypical, organ-specific autoimmune disease, namely epidermolysis bullosa acquisita (EBA) - characterized and caused by autoantibodies targeting type VII collagen...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917879/colonic-luminal-microbiota-and-bacterial-metabolite-composition-in-pregnant-huanjiang-mini-pigs-effects-of-food-composition-at-different-times-of-pregnancy
#16
Xiang-Feng Kong, Yu-Jiao Ji, Hua-Wei Li, Qian Zhu, F Blachier, Mei-Mei Geng, Wen Chen, Yu-Long Yin
The gut harbours diverse and complex microbiota, which influence body health including nutrient metabolism, immune development, and protection from pathogens. Pregnancy is associated with immune and metabolic changes that might be related to microbiota compositional dynamics. We therefore investigated the colonic luminal bacteria community in Huanjiang mini-pigs fed diets with different nutrient levels from the first to third trimester of pregnancy. The concentrations of intestinal metabolites including short-chain fat acids, NH3-N, indole, skatole, and bioamines were also determined...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917878/spatiotemporal-control-of-interferon-induced-jak-stat-signalling-and-gene-transcription-by-the-retromer-complex
#17
Daniela Chmiest, Nanaocha Sharma, Natacha Zanin, Christine Viaris de Lesegno, Massiullah Shafaq-Zadah, Vonick Sibut, Florent Dingli, Philippe Hupé, Stephan Wilmes, Jacob Piehler, Damarys Loew, Ludger Johannes, Gideon Schreiber, Christophe Lamaze
Type-I interferons (IFNs) play a key role in the immune defences against viral and bacterial infections, and in cancer immunosurveillance. We have established that clathrin-dependent endocytosis of the type-I interferon (IFN-α/β) receptor (IFNAR) is required for JAK/STAT signalling. Here we show that the internalized IFNAR1 and IFNAR2 subunits of the IFNAR complex are differentially sorted by the retromer at the early endosome. Binding of the retromer VPS35 subunit to IFNAR2 results in IFNAR2 recycling to the plasma membrane, whereas IFNAR1 is sorted to the lysosome for degradation...
December 5, 2016: Nature Communications
https://www.readbyqxmd.com/read/27917442/polymorphisms-in-ten-candidate-genes-are-associated-with-conformational-and-locomotive-traits-in-spanish-purebred-horses
#18
Natalia Sevane, Susana Dunner, Ana Boado, Javier Cañon
The Spanish Purebred horses, also known as Andalusian horses, compete to the highest standards in international dressage events. Gait and conformation could be used as early selection criteria to detect young horses with promising dressage ability. Although the genetic background of equine size variation has been recently uncovered, the genetic basis of horse conformational and locomotive traits is not known, hampered by the complex genetic architecture underlying quantitative traits and the lack of phenotypic data...
December 5, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27917375/recombinant-lipoprotein-rv1016c-derived-from-mycobacterium-tuberculosis-is-a-tlr-2-ligand-that-induces-macrophages-apoptosis-and-inhibits-mhc-ii-antigen-processing
#19
Haibo Su, Shenglin Zhu, Lin Zhu, Wei Huang, Honghai Wang, Zhi Zhang, Ying Xu
TLR2-dependent cellular signaling in Mycobacterium tuberculosis-infected macrophages causes apoptosis and inhibits class II major histocompatibility complex (MHC-II) molecules antigen processing, leading to evasion of surveillance. Mycobacterium tuberculosis (MTB) lipoproteins are an important class of Toll-like receptor (TLR) ligand, and identified as specific components that mediate these effects. In this study, we identified and characterized MTB lipoprotein Rv1016c (lpqT) as a cell wall associated-protein that was exposed on the cell surface and enhanced the survival of recombinants M...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27917262/toll-like-receptors-in-pathophysiology-of-liver-diseases
#20
REVIEW
Safak Kiziltas
Toll-like receptors (TLRs) are pattern recognition receptors that participate in host defense by recognizing pathogen-associated molecular patterns alongside inflammatory processes by recognizing damage associated molecular patterns. Given constant exposure to pathogens from gut, strict control of TLR-associated signaling pathways is essential in the liver, which otherwise may lead to inappropriate production of pro-inflammatory cytokines and interferons and may generate a predisposition to several autoimmune and chronic inflammatory diseases...
November 18, 2016: World Journal of Hepatology
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