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https://www.readbyqxmd.com/read/29150974/reciprocal-interactions-between-bile-acids-and-gut-microbiota-in-human-liver-diseases
#1
REVIEW
Tadashi Ikegami, Akira Honda
The gut microbiota (GM) play a central role in their hosts' metabolism of bile acids (BAs) by regulating deconjugation, dehydroxylation, dehydrogenation, and epimerization reactions to generate unconjugated free BAs and secondary BAs. These BAs generated by the GM are potent signaling molecules that interact with BA receptors, such as the farnesoid X receptor (FXR) and Takeda G-protein-coupled receptor 5 (TGR5). Each BA has a differential affinity to these receptors; therefore, alterations in BA composition by GM could modify the intensity of receptor signaling...
November 18, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/29150962/genotype-and-diet-affect-resistance-survival-and-fecundity-but-not-fecundity-tolerance
#2
Megan A M Kutzer, Joachim Kurtz, Sophie A O Armitage
Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilising resistance improve fitness by clearing or reducing pathogen loads and hosts utilising tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on resistance and tolerance we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors...
November 18, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29150959/nono-ubiquitination-is-mediated-by-fbw7-and-gsk3-%C3%AE-via-a-degron-lost-upon-chromosomal-rearrangement-in-cancer
#3
Luigi Alfano, Antonella Caporaso, Angela Altieri, Caterina Costa, Iris M Forte, Carmelina A Iannuzzi, Daniela Barone, Luca Esposito, Antonio Giordano, Francesca Pentimalli
NONO is an RNA-binding protein involved in transcription, mRNA splicing, DNA repair and checkpoint activation in response to UV radiation. NONO expression has been found altered in several tumour types, including prostate, colon, breast, melanoma and in papillary renal carcinoma, in which an X chromosome inversion generates a NONO-TFE3 fusion protein. Upon such rearrangement, NONO loses its C-terminal domain. Through bioinformatics analysis, we identified a putative degron motif, known to be recognized by the Skp1-Cul1-F-box-protein (SCF) complex...
November 18, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29150927/identification-of-proteins-drying-oils-waxes-and-resins-in-the-works-of-art-micro-samples-by-chromatographic-and-mass-spectrometric-techniques
#4
Bartłomiej Witkowski, Anna Duchnowicz, Monika Ganeczko, Agnieszka Laudy, Tomasz Gierczak, Magdalena Biesaga
Simplified method for simultaneous identification of proteins, drying oils, waxes and resins in the works-of-art samples was developed. Liquid chromatography with mass spectrometry and gas chromatography with mass spectrometry were used to identify natural materials most frequently encountered in historical paintings. Protein binders were extracted with ammonia and purified using miniaturized solid-phase microextraction (Omix tips) to efficiently suppress matrix interferences. Zwitterionic stationary phase was used for separation of sixteen underivatized amino acids analysis with hydrophilic interaction liquid chromatography that were subsequently quantified with liquid chromatography with mass spectrometry...
November 18, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/29150924/comprehensive-profiling-of-lysine-acetylome-in-baculovirus-infected-silkworm-bombyx-mori-cells
#5
Dongbing Hu, Shengjie Xue, Cui Zhao, Ming Wei, Huihui Yan, Yanping Quan, Wei Yu
Bombyx mori is one of the key lepidopteran model species, and is economically important for silk production and proteinaceous drug expression. Baculovirus and insect host are important natural biological models for studying host-pathogen interactions. The impact of Bombyx mori nucleopolyhedrovirus (BmNPV) infection on the proteome and acetylome of Bombyx mori ovarian (BmN) cells were explored to facilitate a better understanding of infection-driven interactions between BmNPV and host in vitro. The proteome and acetylome were profiled through 6-plex Tandem mass tag (TMT) labelling-based quantitative proteomics...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150920/two-elution-mechanisms-of-mep-chromatography
#6
Tsutomu Arakawa, Masao Tokunaga, Takuya Maruyama, Kentarou Shiraki
MEP (mercapto-ethyl-pyridine) HyperCel is one of the hydrophobic charge induction chromatography (HCIC) resins. Under normal operation, proteins are bound to the MEP resin at neutral pH, at which MEP is not charged, mostly via hydrophobic interaction. MEP has a pyridine group, whose pK is 4.8, and hence is positively charged at acidic pH range. Based on the binding mechanism (i.e., hydrophobic interaction) and the induced positive charge at acidic pH, there may be two ways to elute the bound proteins. One way is to bring the pH down to protonate both MEP resin and the bound protein, leading to charge repulsion and thereby elution...
November 16, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/29150788/ck4-ck6-cyclin-d1-p16-ink4a-and-egfr-expression-in-glioblastoma-with-a-primitive-neuronal-component
#7
Guiyan Xu, Jian Yi Li
Glioblastoma with primitive neuroectodermal tumor-like component (GBM-PNET) is a rare variant of glioblastoma, which was renamed as glioblastoma with a primitive neuronal component (GBM-PN) in new WHO classification of tumours of the central nervous system in 2016. There are few publications on the investigation of GBM-PN. In this study, PCR mRNA arrays on 6 cases of conventional GBM and 10 cases of GBM-PN showed high mRNA level of CDK4 in GBM-PN and low mRNA level of EGFR in GBM-PN. Immunohistochemical stains on tissue microarrays with 28 cases of conventional GBM and 13 cases of GBM-PN demonstrated that CDK4 was selectively expressed in the primitive neuronal component of all GBM-PN cases while EGFR was positive in conventional GBM and glial component of GBM-PN, but was negative in the primitive neuronal component of all GBM-PN cases...
November 17, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29150669/genome-wide-survey-indicates-diverse-physiological-roles-of-the-turnip-brassica-rapa-var-rapa-calcium-dependent-protein-kinase-genes
#8
Qiuli Wang, Xin Yin, Qian Chen, Nan Xiang, Xudong Sun, Yunqiang Yang, Yongping Yang
Calcium-dependent protein kinases (CDPKs) as crucial sensors of calcium concentration changes play important roles in responding to abiotic and biotic stresses. In this study, 55 BrrCDPK genes, which were phylogenetically clustered into four subfamilies, were identified. Chromosome locations indicated that the CDPK family in turnip expanded by segmental duplication and genome rearrangement. Moreover, gene expression profiles showed that different BrrCDPKs were expressed in specific tissues or stages. Transcript levels of BrrCDPKs indicated that they were involved in abiotic and biotic stresses and that paralogs exhibited functional divergence...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150636/a-genetic-system-for-targeted-mutations-to-disrupt-and-restore-genes-in-the-obligate-bacterium-ehrlichia-chaffeensis
#9
Ying Wang, Lanjing Wei, Huitao Liu, Chuanmin Cheng, Roman R Ganta
Obligate intracellular bacteria (obligates) belonging to Rickettsiales and Chlamydiales cause diseases in hundreds of millions of people worldwide and in many animal species. Lack of an efficient system for targeted mutagenesis in obligates remains a major impediment in understanding microbial pathogenesis. Challenges in creating targeted mutations may be attributed to essential nature of majority of the genes and intracellular replication dependence. Despite success in generating random mutations, a method that works well in creating mutations in specific genes of interest followed by complementation remains problematic for obligates and is a highly sought-after goal...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#10
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150605/global-role-of-the-bacterial-post-transcriptional-regulator-csra-revealed-by-integrated-transcriptomics
#11
Anastasia H Potts, Christopher A Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo
CsrA is a post-transcriptional regulatory protein that is widely distributed among bacteria. This protein influences bacterial lifestyle decisions by binding to the 5' untranslated and/or early coding regions of mRNA targets, causing changes in translation initiation, RNA stability, and/or transcription elongation. Here, we assess the contribution of CsrA to gene expression in Escherichia coli on a global scale. UV crosslinking immunoprecipitation and sequencing (CLIP-seq) identify RNAs that interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA abundance, and RNA stability...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150600/mapping-tenascin-c-interaction-with-toll-like-receptor-4-reveals-a-new-subset-of-endogenous-inflammatory-triggers
#12
Lorena Zuliani-Alvarez, Anna M Marzeda, Claire Deligne, Anja Schwenzer, Fiona E McCann, Brian D Marsden, Anna M Piccinini, Kim S Midwood
Pattern recognition underpins innate immunity; the accurate identification of danger, including infection, injury, or tumor, is key to an appropriately targeted immune response. Pathogen detection is increasingly well defined mechanistically, but the discrimination of endogenous inflammatory triggers remains unclear. Tenascin-C, a matrix protein induced upon tissue damage and expressed by tumors, activates toll-like receptor 4 (TLR4)-mediated sterile inflammation. Here we map three sites within tenascin-C that directly and cooperatively interact with TLR4...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29150526/the-devil-is-in-the-domain-understanding-protein-recognition-of-multiple-rna-targets
#13
REVIEW
Glen R Gronland, Andres Ramos
RNA regulation provides a finely tuned and highly co-ordinated control of gene expression. Regulation is mediated by hundreds to thousands of multi-functional RNA-binding proteins which often interact with large sets of RNAs. In this brief review, we focus on a recent work that highlights how the proteins use multiple RNA-binding domains to interact selectively with the different RNA targets. Deconvoluting the molecular complexity of the RNA regulatory network is essential to understanding cell differentiation and function, and requires accurate models for protein-RNA recognition and protein target selectivity...
November 17, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29150508/community-composition-and-ultrastructure-of-a-nitrate-dependent-anaerobic-methane-oxidizing-enrichment-culture
#14
Lavinia Gambelli, Simon Guerrero-Cruz, Rob J Mesman, Geert Cremers, Mike S M Jetten, Huub J M Op den Camp, Boran Kartal, Claudia Lueke, Laura van Niftrik
Methane is a very potent greenhouse gas and can be oxidized aerobically or anaerobically through microbial-mediated processes, thus decreasing methane emissions to the atmosphere. Using a complementary array of methods including phylogenetic analysis, physiological experiments, and light and electron microscopy techniques (including electron tomography), we investigated the community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150497/low-molecular-weight-thiols-and-thioredoxins-are-important-players-in-hg-ii-resistance-in-thermus-thermophilus-hb27
#15
J Norambuena, Y Wang, T Hanson, J M Boyd, T Barkay
Mercury (Hg), one of the most toxic and widely distributed heavy metals, has a high affinity for thiol groups. Thiol groups reduce and sequester Hg. Therefore, low molecular weight and protein thiols may be important cell components used in Hg resistance. To date, the role of low molecular weight thiols in Hg-detoxification remains understudied. The mercury resistance (mer) operon of Thermus thermophilus suggests an evolutionary link between Hg(II) resistance and low molecular weight thiol metabolism. This mer operon encodes for an enzyme involved in methionine biosynthesis, Oah...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150495/small-dense-high-density-lipoproteins-display-potent-vasorelaxing-activity-reflecting-their-elevated-content-of-sphingosine-1-phosphate
#16
Laurence Persegol, Maryam Darabi, Carolane Dauteuille, Marie Lhomme, Sandrine Chantepie, Kerry-Anne Rye, Patrice Therond, M John Chapman, Robert Salvayre, Anne Negre-Salvayre, Philippe Lesnik, Serge Monier, Anatol Kontush
AIMS: Functional heterogeneity of HDL is attributed to its diverse bioactive components. We evaluated whether vasodilatory effects of HDL differed across HDL subpopulations, reflecting their distinct molecular composition. METHODS: Capacity of five major HDL subfractions to counteract inhibitory effects of oxidized low-density lipoprotein on acetylcholine-induced vasodilation was tested in a rabbit aortic rings model. Nitric oxide (NO) production, an essential pathway in endothelium-dependent vasorelaxation, was studied in SV40-transformed murine endothelial cells (SVEC)...
November 17, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/29150461/gabaa-receptor-activation-in-the-allosteric-coagonist-model-framework-relationship-between-ec50-and-basal-activity
#17
Gustav Akk, Daniel J Shin, Allison L Germann, Joseph H Steinbach
The concerted transition model for multimeric proteins is a simple formulation for analyzing the behavior of transmitter-gated ion channels. Here, we use the model to examine the relationship between the EC50 for activation of the GABAA receptor by the transmitter GABA and basal activity employing concatemeric ternary GABAA receptors expressed in Xenopus oocytes. The basal activity reflects receptor function in the absence of transmitter, and can be changed either by mutation to increase constitutive activity, or by addition of a second agonist (acting at a different site) to increase background activity...
November 17, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/29150446/biogenesis-of-the-bacterial-cbb3-cytochrome-c-oxidase-active-subcomplexes-support-a-sequential-assembly-model
#18
Anne Durand, Marie-Line Bourbon, Anne-Soisig Steunou, Bahia Khalfaoui-Hassani, Camille Legrand, Audrey Guitton, Chantal Astier, Soufian Ouchane
The cbb3 oxidase has a high affinity for oxygen and is required for growth of bacteria, including pathogens, in oxygen-limited environments. However, the assembly of this oxidase is poorly understood. Most cbb3 are composed of four subunits: the catalytic CcoN subunit, the two cytochromes c subunits (CcoO and CcoP) involved in electron transfer and the small CcoQ subunit with an unclear function. Here, we address the role of these four subunits in cbb3 biogenesis in the purple bacterium Rubrivivax gelatinosus Analyses of membrane proteins from different mutants revealed the presence of active CcoNQO and CcoNO subcomplexes and also showed that the CcoP subunit is not essential for their assembly...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29150445/the-antiapoptotic-protein-hax-1-mediates-half-of-phospholamban-s-inhibitory-activity-on-calcium-cycling-and-contractility-in-the-heart
#19
Philip A Bidwell, Kobra Haghighi, Evangelia G Kranias
The antiapoptotic protein HS-associated protein X-1 (HAX-1) localizes to sarcoplasmic reticulum (SR) in the heart and interacts with the small membrane protein phospholamban (PLN), inhibiting the cardiac sarco/endoplasmic reticulum calcium ATPase (SERCA2a) in the regulation of overall calcium handling and heart muscle contractility. However, because global HAX-1 deletion causes early lethality, how much endogenous HAX-1 contributes to PLN's inhibitory activity on calcium cycling is unknown. We therefore generated a cardiac-specific and inducible knockout mouse model...
November 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29150441/co-ii-and-ni-ii-binding-of-the-escherichia-coli-transcriptional-repressor-rcnr-orders-its-n-terminus-alters-helix-dynamics-and-reduces-dna-affinity
#20
Hsin-Ting Huang, Cedric E Bobst, Jeffrey S Iwig, Peter T Chivers, Igor A Kaltashov, Michael J Maroney
RcnR, a transcriptional regulator in Escherichia coli, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered the flexibility from the N-terminus through helix 1 and modulated the RcnR-DNA interaction...
November 17, 2017: Journal of Biological Chemistry
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