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https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#1
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29236161/genetic-analysis-of-adults-heterozygous-for-alpl-mutations
#2
Agnès Taillandier, Christelle Domingues, Annika Dufour, Françoise Debiais, Pascal Guggenbuhl, Christian Roux, Catherine Cormier, Bernard Cortet, Valérie Porquet-Bordes, Fabienne Coury, David Geneviève, Jean Chiesa, Thierry Colin, Elaine Fletcher, Agnès Guichet, Rose-Marie Javier, Michel Laroche, Michael Laurent, Ekkehart Lausch, Bruno LeHeup, Cédric Lukas, Georg Schwabe, Ineke van der Burgt, Christine Muti, Brigitte Simon-Bouy, Etienne Mornet
Hypophosphatasia (HPP) is a rare inherited metabolic bone disease due to a deficiency of the tissue nonspecific alkaline phosphatase isoenzyme (TNSALP) encoded by the ALPL gene. Patients have consistently low serum alkaline phosphatase (AP), so that this parameter is a good hallmark of the disease. Adult HPP is heterogeneous, and some patients present only mild nonpathognomonic symptoms which are also common in the general population such as joint pain, osteomalacia and osteopenia, chondrocalcinosis, arthropathy and musculoskeletal pain...
December 13, 2017: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/29235987/gene-free-methodology-for-cell-fate-dynamics-during-development
#3
Francis Corson, Eric D Siggia
Models of cell function that assign a variable to each gene frequently lead to systems of equations with many parameters whose behavior is obscure. Geometric models reduce dynamics to intuitive pictorial elements that provide compact representations for sparse in-vivo data and transparent descriptions of developmental transitions. To illustrate, a geometric model fit to vulval development in C. elegans, implies a phase diagram where cell-fate choices are displayed in a plane defined by EGF and Notch signaling levels...
December 13, 2017: ELife
https://www.readbyqxmd.com/read/29235260/functional-polymorphisms-of-innate-immunity-receptors-are-not-risk-factors-for-the-non-sbp-type-bacterial-infections-in-cirrhosis
#4
Tamas Dinya, Tamas Tornai, Zsuzsanna Vitalis, Istvan Tornai, Boglárka Balogh, David Tornai, Peter Antal-Szalmas, Andrea Sumegi, Hajnalka Andrikovics, Andras Bors, Attila Tordai, Maria Papp
BACKGROUND&AIMS: Pattern recognition receptors (PRRs) have a key role in the innate host defense. Functional polymorphisms of various PRRs have been established to contribute to an increased susceptibility to spontaneous bacterial peritonitis (SBP). Their role in the development of cirrhosis-associated bacterial infections (BI), beyond SBP or progressive disease course related to pathological bacterial translocation (BT) remains unknown. METHODS: 349 patients with cirrhosis were genotyped for common NOD2 (R702W, G908R and L1007PfsinsC), TLR2 (-16934T>A), and TLR4 (D299G) variants...
December 13, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/29234865/electromechanical-heterogeneity-in-the-heart-a%C3%A2-key-to-long-qt-syndrome
#5
REVIEW
F F Dressler, J Brado, K E Odening
In the healthy heart, physiological heterogeneities in structure and in electrical and mechanical activity are crucial for normal, efficient excitation and pumping. Alterations of heterogeneity have been linked to arrhythmogenesis in various cardiac disorders such as long QT syndrome (LQTS). This inherited arrhythmia disorder is caused by mutations in different ion channel genes and is characterized by (heterogeneously) prolonged cardiac repolarization and increased risk for ventricular tachycardia, syncope and sudden cardiac death...
December 12, 2017: Herzschrittmachertherapie & Elektrophysiologie
https://www.readbyqxmd.com/read/29234695/an-improved-draft-of-the-pigeonpea-cajanus-cajan-l-millsp-genome
#6
Ajay Kumar Mahato, Ajay Kumar Sharma, Tilak Raj Sharma, Nagendra Kumar Singh
The first draft of the pigeonpea (Cajanus cajan (L.) Millsp. cv. Asha) genome with 511 Mbp of assembled sequence information has low genome coverage of about sixty percent. Here we present an improved version of this genome with 648.2 Mbp of assembled sequence of this popular pigeonpea variety, which is liked by the millers and has resistance to fusarium wilt and sterility mosaic diseases. With the addition of 137 Mb of assembled sequence information the present version has the highest available genome coverage of pigeonpea till date...
February 2018: Data in Brief
https://www.readbyqxmd.com/read/29234311/the-slzrt1-gene-encodes-a-plasma-membrane-located-zip-zrt-irt-like-protein-transporter-in-the-ectomycorrhizal-fungus-suillus-luteus
#7
Laura Coninx, Anneleen Thoonen, Eli Slenders, Emmanuelle Morin, Natascha Arnauts, Michiel Op De Beeck, Annegret Kohler, Joske Ruytinx, Jan V Colpaert
Zinc (Zn) is an essential micronutrient but may become toxic when present in excess. In Zn-contaminated environments, trees can be protected from Zn toxicity by their root-associated micro-organisms, in particular ectomycorrhizal fungi. The mechanisms of cellular Zn homeostasis in ectomycorrhizal fungi and their contribution to the host tree's Zn status are however not yet fully understood. The aim of this study was to identify and characterize transporters involved in Zn uptake in the ectomycorrhizal fungus Suillus luteus, a cosmopolitan pine mycobiont...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29234056/identification-and-characterization-of-two-functional-variants-in-the-human-longevity-gene-foxo3
#8
Friederike Flachsbart, Janina Dose, Liljana Gentschew, Claudia Geismann, Amke Caliebe, Carolin Knecht, Marianne Nygaard, Nandini Badarinarayan, Abdou ElSharawy, Sandra May, Anne Luzius, Guillermo G Torres, Marlene Jentzsch, Michael Forster, Robert Häesler, Kathrin Pallauf, Wolfgang Lieb, Céline Derbois, Pilar Galan, Dmitriy Drichel, Alexander Arlt, Andreas Till, Ben Krause-Kyora, Gerald Rimbach, Hélène Blanché, Jean-François Deleuze, Lene Christiansen, Kaare Christensen, Michael Nothnagel, Philip Rosenstiel, Stefan Schreiber, Andre Franke, Susanne Sebens, Almut Nebel
FOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown. Here, we perform resequencing of the FOXO3 locus and single-nucleotide variant (SNV) genotyping in three European populations. We find two FOXO3 SNVs, rs12206094 and rs4946935, to be most significantly associated with longevity and further characterize them functionally. We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233840/microbiome-in-pten-hamartoma-tumor-syndrome
#9
Victoria Byrd, Ted M Getz, Roshan Padmanabhan, Hans Arora, Charis Eng
Germline PTEN mutations defining PTEN hamartoma tumor syndrome [PHTS] confer heritable predisposition to breast, endometrial, thyroid, and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA-gene sequencing...
December 12, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29233721/antitumor-mir-150-5p-and-mir-150-3p-inhibit-cancer-cell-aggressiveness-by-targeting-spock1-in-head-and-neck-squamous-cell-carcinoma
#10
Keiichi Koshizuka, Toyoyuki Hanazawa, Naoko Kikkawa, Koji Katada, Atsushi Okato, Takayuki Arai, Tetsuya Idichi, Yusaku Osako, Yoshitaka Okamoto, Naohiko Seki
OBJECTIVE: Our recent studies have revealed that both strands of pre-miRNAs, the guide strand and the passenger strand, are involved in cancer pathogenesis. Analyses of miRNA expression signatures by RNA sequencing in head and neck squamous cell carcinoma (HNSCC) showed that both of the strands of pre-miR-150 (miR-150-5p and miR-150-3p) were significantly downregulated, and that these miRNAs acted as antitumor miRNAs in HNSCC cells. The aim of this study was to identify oncogenic genes in HNSCC cells that were regulated by miR-150-5p and miR-150-3p...
December 9, 2017: Auris, Nasus, Larynx
https://www.readbyqxmd.com/read/29233120/prediction-of-5-year-overall-survival-in-cervical-cancer-patients-treated-with-radical-hysterectomy-using-computational-intelligence-methods
#11
Bogdan Obrzut, Maciej Kusy, Andrzej Semczuk, Marzanna Obrzut, Jacek Kluska
BACKGROUND: Computational intelligence methods, including non-linear classification algorithms, can be used in medical research and practice as a decision making tool. This study aimed to evaluate the usefulness of artificial intelligence models for 5-year overall survival prediction in patients with cervical cancer treated by radical hysterectomy. METHODS: The data set was collected from 102 patients with cervical cancer FIGO stage IA2-IIB, that underwent primary surgical treatment...
December 12, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29232918/population-specific-associations-of-deleterious-rare-variants-in-coding-region-of-p2ry1-p2ry12-purinergic-receptor-genes-in-large-vessel-ischemic-stroke-patients
#12
Piotr K Janicki, Ceren Eyileten, Victor Ruiz-Velasco, Khaled Anwar Sedeek, Justyna Pordzik, Anna Czlonkowska, Iwona Kurkowska-Jastrzebska, Shigekazu Sugino, Yuka Imamura-Kawasawa, Dagmara Mirowska-Guzel, Marek Postula
The contribution of low-frequency and damaging genetic variants associated with platelet function to ischemic stroke (IS) susceptibility remains unknown. We employed a deep re-sequencing approach in Polish patients in order to investigate the contribution of rare variants (minor allele frequency, MAF < 1%) to the IS genetic susceptibility in this population. The genes selected for re-sequencing consisted of 26 genes coding for proteins associated with the surface membrane of platelets. Targeted pooled re-sequencing (Illumina HiSeq 2500) was performed on genomic DNA of 500 cases (patients with history of clinically proven diagnosis of large-vessel IS) and 500 controls...
December 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29232857/mir-34a-regulates-sperm-motility-in-zebrafish
#13
Wenjie Guo, Binyue Xie, Shuting Xiong, Xufang Liang, Jian-Fang Gui, Jie Mei
Increasing attention has been focused on the role of microRNAs in post-transcription regulation during spermatogenesis. Recently, the miR-34 family has been shown to be involved in the spermatogenesis, but the clear function of the miR-34 family in spermatogenesis is still obscure. Here we analyzed the function of miR-34a, a member of the miR-34 family, during spermatogenesis using miR-34a knockout zebrafish generated by the clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system...
December 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29232848/a-metagenomic-and-in-silico-functional-prediction-of-gut-microbiota-profiles-may-concur-in-discovering-new-cystic-fibrosis-patient-targeted-probiotics
#14
Pamela Vernocchi, Federica Del Chierico, Andrea Quagliariello, Danilo Ercolini, Vincenzina Lucidi, Lorenza Putignani
Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction...
December 9, 2017: Nutrients
https://www.readbyqxmd.com/read/29232328/novel-cyp2a6-diplotypes-identified-through-next-generation-sequencing-are-associated-with-in-vitro-and-in-vivo-nicotine-metabolism
#15
Julie-Anne Tanner, Andy Z Zhu, Katrina G Claw, Bhagwat Prasad, Viktoriya Korchina, Jianhong Hu, HarshaVardhan Doddapaneni, Donna M Muzny, Erin G Schuetz, Caryn Lerman, Kenneth E Thummel, Steven E Scherer, Rachel F Tyndale
OBJECTIVES: Smoking patterns and cessation rates vary widely across smokers and can be influenced by variation in rates of nicotine metabolism [i.e. cytochrome P450 2A6 (CYP2A6), enzyme activity]. There is high heritability of CYP2A6-mediated nicotine metabolism (60-80%) owing to known and unidentified genetic variation in the CYP2A6 gene. We aimed to identify and characterize additional genetic variants at the CYP2A6 gene locus. METHODS: A new CYP2A6-specific sequencing method was used to investigate genetic variation in CYP2A6...
January 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29231860/predicting-the-functional-impact-of-cdh1-missense-mutations-in-hereditary-diffuse-gastric-cancer
#16
REVIEW
Soraia Melo, Joana Figueiredo, Maria Sofia Fernandes, Margarida Gonçalves, Eurico Morais-de-Sá, João Miguel Sanches, Raquel Seruca
The role of E-cadherin in Hereditary Diffuse Gastric Cancer (HDGC) is unequivocal. Germline alterations in its encoding gene (CDH1) are causative of HDGC and occur in about 40% of patients. Importantly, while in most cases CDH1 alterations result in the complete loss of E-cadherin associated with a well-established clinical impact, in about 20% of cases the mutations are of the missense type. The latter are of particular concern in terms of genetic counselling and clinical management, as the effect of the sequence variants in E-cadherin function is not predictable...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231144/qsar-of-natural-sesquiterpene-lactones-as-inhibitors-of-myb-dependent-gene-expression
#17
Gloria Castellano, Lucia Redondo, Francisco Torrens
Protein c-Myb is a therapeutic target. Some sesquiterpene lactones suppress Myb-dependent gene expression, which results in a mechanism for their potential anti-cancer activity. Database ChEMBL is representative of lactones for physicochemical and physiochemical properties. Data presented for 31 natural lactones are discussed in terms of quantitative structure-activity relationships, which objective is to predict inhibitors of Myb-induced gene expression. Several constitutional descriptors are related to structure-activity...
December 11, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/29230893/microbial-communities-exhibit-host-species-distinguishability-and-phylosymbiosis-along-the-length-of-the-gastrointestinal-tract
#18
Kevin D Kohl, Denise M Dearing, Seth R Bordenstein
Host-associated microbial communities consist of stable and transient members that can assemble through purely stochastic processes associated with the environment or by interactions with the host. Phylosymbiosis predicts that if host-microbiota interactions impact assembly patterns, then one conceivable outcome is concordance between host evolutionary histories (phylogeny) and the ecological similarities in microbial community structures (microbiota dendrogram). This assembly pattern has been demonstrated in several clades of animal hosts in laboratory and natural populations, but in vertebrates it has only been investigated using samples from feces or the distal colon...
December 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29230620/long-non-coding-rnas-in-metastasis
#19
Qihong Huang, Jinchun Yan, Reuven Agami
Long non-coding RNA (lncRNA) genes have recently been discovered as key regulators of developmental, physiological, and pathological processes in humans. Recent studies indicate that lncRNAs regulate every step of gene expression, and their aberrant expression can be found in the majority of cancer types. Particularly, lncRNAs were found to function in tumor development and metastasis, which is the major cause of cancer-related death. Thus, exploring key roles of lncRNAs in metastasis is predicted to enhance our knowledge of metastasis, and uncover novel therapeutic targets and biomarkers of this process...
December 11, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/29230365/identification-and-characterization-of-a-novel-zebrafish-danio-rerio-pentraxin-carbonic-anhydrase
#20
Maarit S Patrikainen, Martti E E Tolvanen, Ashok Aspatwar, Harlan R Barker, Csaba Ortutay, Janne Jänis, Mikko Laitaoja, Vesa P Hytönen, Latifeh Azizi, Prajwol Manandhar, Edit Jáger, Daniela Vullo, Sampo Kukkurainen, Mika Hilvo, Claudiu T Supuran, Seppo Parkkila
Background: Carbonic anhydrases (CAs) are ubiquitous, essential enzymes which catalyze the conversion of carbon dioxide and water to bicarbonate and H+ ions. Vertebrate genomes generally contain gene loci for 15-21 different CA isoforms, three of which are enzymatically inactive. CA VI is the only secretory protein of the enzymatically active isoforms. We discovered that non-mammalian CA VI contains a C-terminal pentraxin (PTX) domain, a novel combination for both CAs and PTXs. Methods: We isolated and sequenced zebrafish (Danio rerio) CA VI cDNA, complete with the sequence coding for the PTX domain, and produced the recombinant CA VI-PTX protein...
2017: PeerJ
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