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Protein function prediction

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https://www.readbyqxmd.com/read/29149660/a-systems-level-approach-for-investigating-organophosphorus-pesticide-toxicity
#1
Jingbo Zhu, Jing Wang, Yan Ding, Baoyue Liu, Wei Xiao
The full understanding of the single and joint toxicity of a variety of organophosphorus (OP) pesticides is still unavailable, because of the extreme complex mechanism of action. This study established a systems-level approach based on systems toxicology to investigate OP pesticide toxicity by incorporating ADME/T properties, protein prediction, and network and pathway analysis. The results showed that most OP pesticides are highly toxic according to the ADME/T parameters, and can interact with significant receptor proteins to cooperatively lead to various diseases by the established OP pesticide -protein and protein-disease networks...
November 14, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29149510/transferrin-as-a-predictor-of-survival-in-cirrhosis
#2
André Viveiros, Armin Finkenstedt, Benedikt Schaefer, Mattias Mandorfer, Bernhard Scheiner, Konrad Lehner, Moritz Tobiasch, Thomas Reiberger, Herbert Tilg, Michael Edlinger, Heinz Zoller
BACKGROUND AND AIMS: Patients with cirrhosis frequently present with high serum ferritin and low transferrin concentrations, reflecting impaired liver function and inflammation. Recent studies have shown that transferrin and its saturation with iron are MELD-independent predictors of mortality in patients with acute on chronic liver failure or decompensated cirrhosis. The aim of this study was to evaluate the prognostic utility of serum iron parameters in relation to markers of liver function and immune activation...
November 17, 2017: Liver Transplantation
https://www.readbyqxmd.com/read/29149426/relationship-between-lat1-expression-and-resistance-to-chemotherapy-in-pancreatic-ductal-adenocarcinoma
#3
Bolag Altan, Kyoichi Kaira, Akira Watanabe, Norio Kubo, Pinjie Bao, Gantumur Dolgormaa, Erkhem-Ochir Bilguun, Kenichiro Araki, Yoshikatsu Kanai, Takehiko Yokobori, Tetsunari Oyama, Masahiko Nishiyama, Hiroyuki Kuwano, Ken Shirabe
PURPOSE: L-type amino acid transporter 1 (LAT1) is linked to tumor cell proliferation, angiogenesis, and survival in various human cancers. Although the expression of LAT1 was identified as a significant prognostic predictor after surgery in patients with pancreatic ductal adenocarcinoma (PDAC), little is known about the clinical significance of LAT1 as a chemotherapeutic resistance factor in PDAC. METHODS: A total of 110 patients with surgically resected PDAC were retrospectively reviewed as the training set...
November 17, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/29149403/structure-function-relationship-of-tctp
#4
Beatriz Xoconostle-Cázares, Roberto Ruiz-Medrano
The translationally controlled tumor protein (TCTP) is a small, multifunctional protein found in most, if not all, eukaryotic lineages, involved in a myriad of key regulatory processes. Among these, the control of proliferation and inhibition of cell death, as well as differentiation, are the most important, and it is probable that other responses are derived from the ability of TCTP to influence them in both unicellular and multicellular organisms. In the latter, an additional function for TCTP stems from its capacity to be secreted via a nonclassical pathway and function in a non-cell autonomous (paracrine) manner, thus affecting the responses of neighboring or distant cells to developmental or environmental stimuli (as in the case of serum TCTP/histamine-releasing factor in mammals and phloem TCTP in Arabidopsis)...
2017: Results and Problems in Cell Differentiation
https://www.readbyqxmd.com/read/29148771/an-qm-mm-study-of-the-reaction-catalyzed-by-alkyladenine-dna-glycosylase-examination-of-the-substrate-specificity-of-a-dna-repair-enzyme
#5
Stefan A P Lenz, Stacey D Wetmore
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a non-specific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a non-substrate (G), or a cationic substrate (7-methylguanine (7MeG)), and probe changes in the reaction pathway that occur when AAG targets different nucleotides...
November 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29147019/identification-and-characterization-of-serine-protease-inhibitors-in-a-parasitic-wasp-pteromalus-puparum
#6
Lei Yang, Yaotian Mei, Qi Fang, Jiale Wang, Zhichao Yan, Qisheng Song, Zhe Lin, Gongyin Ye
Serine protease inhibitors (SPIs) regulate protease-mediated activities by inactivating their cognate proteinases, and are involved in multiple physiological processes. SPIs have been extensively studied in vertebrates and invertebrates; however, little SPI information is available in parasitoids. Herein, we identified 57 SPI genes in total through the genome of a parasitoid wasp, Pteromalus puparum. Gene structure analyses revealed that these SPIs contain 7 SPI domains. Depending on their mode of action, these SPIs can be categorized into serpins, canonical inhibitors and alpha-2-macroglobulins (A2Ms)...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146583/comparison-of-chip-seq-data-and-a-reference-motif-set-for-human-krab-c2h2-zinc-finger-proteins
#7
Marjan Barazandeh, Sam Lambert, Mihai Albu, Timothy R Hughes
KRAB C2H2 zinc finger proteins (KZNFs) are the largest and most diverse family of human transcription factors, likely due to diversifying selection driven by novel endogenous retroelements (EREs), but the vast majority lack binding motifs or functional data. Two recent studies analyzed a majority of the human KZNFs using either ChIP-seq (60 proteins) or ChIP-exo (221 proteins) in the same cell type (HEK293). The ChIP-exo paper did not describe binding motifs, however. Thirty-nine proteins are represented in both studies, enabling the systematic comparison of the data sets presented here...
November 16, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29146477/a-review-of-s100-protein-family-in-lung-cancer
#8
REVIEW
Ting Wang, Xiaoying Huo, Zhaoyang Chong, Hamadhaider Khan, Rui Liu, Ting Wang
S100 protein family, representing 25 relatively small calcium binding proteins, has been reported to be involved in multiple stages of tumorigenesis and progression. These proteins are considered having potential value to be adopted as novel biomarkers in the detection and accurate prediction of many kinds of tumors, including lung cancer. As the one having the highest morbidity and mortality among all cancers, lung carcinoma is still occult for detection, especially at early stage. S100 proteins take participation in the lung neoplasia through playing intracellular and/or extracellular functions, therefore getting involved in a variety of biological processes such as differentiation, proliferation, and migration...
November 13, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29145896/downregulation-of-mir-31-stimulates-expression-of-lats2-via-the-hippo-pathway-and-promotes-epithelial-mesenchymal-transition-in-esophageal-squamous-cell-carcinoma
#9
Yanping Gao, Jun Yi, Kai Zhang, Fan Bai, Bing Feng, Rui Wang, Xiaoyuan Chu, Longbang Chen, Haizhu Song
BACKGROUND: Dysregulation of miRNAs is associated with cancer development by coordinately suppressing abundant target genes. Emerging evidence indicates that miR-31 plays a dual role in tumorigenicity. However, whether miR-31 plays as an oncogene in esophageal squamous cell carcinoma (ESCC) and the potential target molecules are still unclear. MiR-31 role in ESCC was investigated and an association of the target molecules with EMT was identified in the progression of ESCC. METHODS: Western blot assays and qRT-PCR was performed to detect the protein and mRNA levels...
November 16, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29145829/effect-of-a-rare-genetic-variant-of-tm7sf4-gene-on-osteoclasts-of-patients-with-paget-s-disease-of-bone
#10
Emilie Laurier, Nathalie Amiable, Edith Gagnon, Jacques P Brown, Laëtitia Michou
BACKGROUND: Dendritic Cell-Specific Transmembrane Protein (DC-STAMP) is involved in osteoclastogenesis with a key role in mononucleated osteoclasts fusion. We reported in patients with Paget's disease of bone (PDB) a rare variant (rs62620995) in the TM7SF4 gene, encoding for DC-STAMP, which changes a highly conserved amino acid, possibly damaging according to in silico predictions. This study aimed at determining the functional effects of this variant on osteoclast phenotype in PDB. METHODS: Fifty ml of peripheral blood were collected in pagetic patients carrier of this variant (n = 4) or not (n = 4) and healthy controls (n = 4)...
November 16, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/29145801/comparative-genomics-of-coniophora-olivacea-reveals-different-patterns-of-genome-expansion-in-boletales
#11
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt LaButti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V Grigoriev, Antonio G Pisabarro, Lucía Ramírez
BACKGROUND: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. RESULTS: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145755/defining-recognizing-and-reporting-malnutrition
#12
Marinos Elia
Although malnutrition is a common health and social care problem, there is no universal agreement about its definition, prevalence, or method of identification and report. Fifteen definitions of malnutrition were critically examined to assess their variability. They ranged from descriptions of undernutrition alone to under- and overnutrition, with intakes ranging from dietary protein and energy alone to dietary and nondietary sources of all nutrients and energy. Definitions also varied from non-outcome based to those based on functional, physiological, and/or clinical outcomes...
November 1, 2017: International Journal of Lower Extremity Wounds
https://www.readbyqxmd.com/read/29145147/up-regulation-of-mir-299-suppressed-the-invasion-and-migration-of-htr-8-svneo-trophoblast-cells-partly-via-targeting-hdac2-in-pre-eclampsia
#13
Yu Gao, Ruilian She, Qian Wang, Yan Li, Haiying Zhang
Pre-eclampsia (PE), a pregnancy-associated disorder, is a major contributor to maternal mortality and morbidity worldwide. Recently, microRNAs (miRNAs) were found to be associated with the pathogenesis of PE. The present study investigated the function of miR-299 in HTR-8/SVneo trophoblast cells and explored its underlying mechanism in the pathogenesis of PE. The miR-299 and histone deacetylase 2 (HDAC2) mRNA expression levels were determined by quantitative real-time PCR. Transwell invasion and wound healing assays were used to measure cell invasive and migratory ability...
November 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29145093/proteomic-profile-and-toxicity-pathway-analysis-in-zebrafish-embryos-exposed-to-bisphenol-a-and-di-n-butyl-phthalate-at-environmentally-relevant-levels
#14
Xing Dong, Xuchun Qiu, Shunlong Meng, Hai Xu, Xiangyang Wu, Ming Yang
Bisphenol A (BPA) and di-n-butyl phthalate (DBP) are well-known endocrine-disrupting chemicals (EDCs) that have human health risks. Chronic exposure to BPA and DBP increases the occurrence of human disease. Despite the potential for exposure in embryonic development, the mechanism of action of BPA and DBP on vertebrate development and disease still remains unclear. In the present study, we identified proteins and protein networks that are perturbed by BPA and DBP during zebrafish (Danio rerio) development. Zebrafish embryos were exposed to environmentally relevant levels of BPA (10 μg/L) and DBP (50 μg/L) for 96 h...
November 10, 2017: Chemosphere
https://www.readbyqxmd.com/read/29144802/lipid-accumulation-product-visceral-adiposity-index-and-chinese-visceral-adiposity-index-as-markers-of-cardiometabolic-risk-in-adult-growth-hormone-deficiency-patients-a-cross-sectional-study
#15
Xin Xie, Qing Li, Lingmin Zhang, Wei Ren
OBJECTIVE: Adult growth hormone deficiency (AGHD) is associated with cardiometabolic risk factors. Given that cardiovascular disease (CVD) is an important cause of morbidity and mortality in the AGHD population, there is a need for alternative, non-invasive methods of assessing cardiometabolic risk in this population. Chinese visceral adiposity index (CVAI) is a new marker of visceral fat dysfunction that is based on age, body mass index (BMI), waist circumference (WC) and metabolic parameters...
November 16, 2017: Endocrine Practice
https://www.readbyqxmd.com/read/29144398/predict-the-relationship-between-gene-and-large-yellow-croaker-s-economic-traits
#16
Xiangxiang Zeng, Shuting Jin, Jin Jiang, Kunhuang Han, Xiaoping Min, Xiangrong Liu
The importance of a gene's impact on traits is well appreciated. Gene expression will affect the growth, immunity, reproduction and environmental resistance of some fish, and then affect the economic performance of fish-related business. Studying the connection between gene and character can help elucidate the growth of fishes. Thus far, a collected database containing large yellow croaker (Larimichthys crocea) genes does not exist. The gene having to do with the growth efficiency of fish will have a huge impact on research...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29144204/specific-hypersensitive-response-associated-recognition-of-new-apoplastic-effectors-from-cladosporium-fulvum-in-wild-tomato
#17
Carl H Mesarich, Bilal Ӧkmen, Hanna Rovenich, Scott A Griffiths, Changchun Wang, Mansoor Karimi Jashni, Aleksandar Mihajlovski, Jérôme Collemare, Lukas Hunziker, Cecilia H Deng, Ate van der Burgt, Henriek G Beenen, Matthew D Templeton, Rosie E Bradshaw, Pierre J G M de Wit
Tomato leaf mold disease is caused by the biotrophic fungus Cladosporium fulvum. During infection, C. fulvum produces extracellular small secreted protein (SSP) effectors that function to promote colonization of the leaf apoplast. Resistance to the disease is governed by Cf immune receptor genes that encode receptor-like proteins (RLPs). These RLPs recognize specific SSP effectors to initiate a hypersensitive response (HR) that renders the pathogen avirulent. C. fulvum strains capable of overcoming one or more of all cloned Cf genes have now emerged...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29144203/suppression-or-activation-of-immune-responses-by-predicted-secreted-proteins-of-the-soybean-rust-pathogen-phakopsora-pachyrhizi
#18
Mingsheng Qi, James P Grayczyk, Janina M Seitz, Youngsill Lee, Tobias I Link, Doil Choi, Kerry F Pedley, Ralf T Voegele, Thomas J Baum, Steven A Whitham
Rust fungi, such as the soybean rust pathogen Phakopsora pachyrhizi, are major threats to crop production. They form specialized haustoria that are hyphal structures intimately associated with host-plant cell membranes. These haustoria have roles in acquiring nutrients and secreting effector proteins that manipulate host immune systems. Functional characterization of effector proteins of rust fungi is important for understanding mechanisms that underlie their virulence and pathogenicity. Hundreds of candidate effector proteins have been predicted for rust pathogens, but it is not clear how to prioritize these effector candidates for further characterization...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29143455/understanding-the-functional-role-of-microrna-214-3p-in-atherosclerosis-for-the-identification-of-novel-targeted-therapies-to-prevent-or-reverse-endothelial-cell-dysfunction-and-stimulate-autophagy
#19
EDITORIAL
Adriana Georgescu
The original article by Jing Wang and collaborators, entitled "MicroRNA-214-3p: A Link between Autophagy and Endothelial Cell Dysfunction in Atherosclerosis", brings new data concerning molecular mechanisms linking decreased autophagy to endothelial dysfunction in atherosclerosis. In this issue of Acta Physiologica, the authors concluded that microRNA-214-3p (miR-214-3p) controls oxidized low-density lipoprotein (ox-LDL)-induced autophagy in human umbilical vein endothelial cells (HUVECs) by regulating intracellular levels of autophagy-related protein 5 (ATG5), and may have a relevant role in the pathogenesis of atherosclerosis...
November 16, 2017: Acta Physiologica
https://www.readbyqxmd.com/read/29143394/bactericera-cockerelli-vitellogenin-6-like-a-vitellogenin-without-a-direct-reproductive-function
#20
F Ibanez, X Tang, C Tamborindeguy
Vitellogenin-like proteins are members of the large lipid transfer proteins, a family of proteins involved in reproduction, lipid circulation and immune defences. In this study, we identified a new Bactericera cockerelli vitellogenin-like (Vg-like) transcript, and named it BcVg6-like based on its similarity to Acyrthosiphon pisum Vg6. In silico analyses predicted different conserved domains in BcVg6-like compared with the conventional Ba. cockerelli vitellogenin, BcVg1-like, previously described by our research group...
November 16, 2017: Insect Molecular Biology
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