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https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#1
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635424/genome-wide-linkage-and-haplotype-sharing-analysis-implicates-the-mcdr3-locus-as-a-candidate-region-for-a-developmental-macular-disorder-in-association-with-digit-abnormalities
#2
Valentina Cipriani, Ambreen Kalhoro, Gavin Arno, Raquel S Silva, Nikolas Pontikos, Virginie Puech, Michelle E McClements, David M Hunt, Veronica van Heyningen, Michel Michaelides, Andrew R Webster, Anthony T Moore, Bernard Puech
BACKGROUND: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second locus on 5p15-5p13 (MCDR3) has been implicated in a similar phenotype, but the disease-causing mechanism still remains unknown. METHODS: Two families affected by a dominant developmental macular disorder that closely resembles NCMD in association with digit abnormalities were included in the study...
March 2, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28634423/tumor-ras-gene-expression-levels-are-influenced-by-the-mutational-status-of-ras-genes-and-both-upstream-and-downstream-ras-pathway-genes
#3
Robert M Stephens, Ming Yi, Bailey Kessing, Dwight V Nissley, Frank McCormick
The 3 human RAS genes play pivotal roles regulating proliferation, differentiation, and survival in normal cells and become mutated in 15% to 20% of all human tumors and amplified in many others. In this report, we examined data from The Cancer Genome Atlas to investigate the relationship between RAS gene mutational status and messenger RNA expression. We show that all 3 RAS genes exhibit increased expression when they are mutated in a context-dependent manner. In the case of KRAS, this increase is manifested by a larger proportional increase in KRAS4A than KRAS4B, although both increase significantly...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28634337/evolutionary-and-network-analysis-of-virus-sequences-from-infants-infected-with-an-australian-recombinant-strain-of-human-parechovirus-type-3
#4
Soren Alexandersen, Tiffanie M Nelson, Jason Hodge, Julian Druce
We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012-2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28634269/human-development-heredity-and-evolution
#5
REVIEW
Ryuichi Nishinakamura, Minoru Takasato
From March 27-29 2017, the RIKEN Center for Developmental Biology held a symposium entitled 'Towards Understanding Human Development, Heredity, and Evolution' in Kobe, Japan. Recent advances in technologies including stem cell culture, live imaging, single-cell approaches, next-generation sequencing and genome editing have led to an expansion in our knowledge of human development. Organized by Yoshiya Kawaguchi, Mitinori Saitou, Mototsugu Eiraku, Tomoya Kitajima, Fumio Matsuzaki, Takashi Tsuji and Edith Heard, the symposium covered a broad range of topics including human germline development, epigenetics, organogenesis and evolution...
June 15, 2017: Development
https://www.readbyqxmd.com/read/28634246/assisted-reproductive-techniques-and-risk-of-beckwith-wiedemann-syndrome
#6
Alessandro Mussa, Cristina Molinatto, Flavia Cerrato, Orazio Palumbo, Massimo Carella, Giuseppina Baldassarre, Diana Carli, Clementina Peris, Andrea Riccio, Giovanni Battista Ferrero
BACKGROUND AND OBJECTIVES: The emerging association of assisted reproductive techniques (ART) with imprinting disorders represents a major issue in the scientific debate on infertility treatment and human procreation. We studied the prevalence of Beckwith-Wiedemann syndrome (BWS) in children conceived through ART to define the specific associated relative risk. METHODS: Patients with BWS born in Piemonte, Italy, were identified and matched with the general demographic data and corresponding regional ART registry...
June 20, 2017: Pediatrics
https://www.readbyqxmd.com/read/28634180/a-mutyh-germline-mutation-is-associated-with-small-intestinal-neuroendocrine-tumors
#7
Jan P Dumanski, Chiara Rasi, Peyman Björklund, Hanna Davies, Abir Salwa Ali, Malin Grönberg, Staffan Welin, Halfdan Sorbye, Henning Grønbæk, Janet Cunningham, Lars A Forsberg, Lars Lind, Erik Ingelsson, Peter Stalberg, Per Hellman, Eva Tiensuu Janson
The genetics behind predisposition to small intestinal neuroendocrine tumors (SI-NETs) is largely unknown, but there is growing awareness of a familial form of the disease. We aimed to identify germline mutations involved in the carcinogenesis of SI-NETs. The strategy included next-generation sequencing of exome- and/or whole-genome of blood DNA, and in selected cases tumor DNA, from 24 patients from 15 families with the history of SI-NETs. We identified seven candidate mutations in six genes that were further studied using 215 sporadic SI-NET patients...
June 20, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28634106/biology-evolution-and-medical-importance-of-polyomaviruses-an-update
#8
REVIEW
Ugo Moens, Andi Krumbholz, Bernhard Ehlers, Roland Zell, Reimar Johne, Sébastien Calvignac-Spencer, Chris Lauber
The family Polyomaviridae encompasses non-enveloped viruses with a circular dsDNA genome that is typically approximately 5000bp in length. Originally isolated from mammals, polyomavirus sequences have now been detected in invertebrates, fish, amphibians, reptiles and birds, although it remains to be determined whether all these animals are genuine hosts. The genomes of all polyomaviruses encode at least two regulatory proteins (large and small tumour antigen) and two structural proteins (capsid proteins VP1 and VP2) whose functions have been defined...
June 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28633944/gene-expression-analysis-identify-a-metabolic-and-cell-function-alterations-as-a-hallmark-of-obesity-without-metabolic-syndrome-in-peripheral-blood-a-pilot-study
#9
Daniel Antonio de Luis, Raquel Almansa, Rocío Aller, Olatz Izaola, E Romero
BACKGROUND: Understanding molecular basis involved in overweight is an important first step in developing therapeutic pathways against excess in body weight gain. OBJECTIVE: The purpose of our pilot study was to evaluate the gene expression profiles in the peripheral blood of obese patients without other metabolic complications. DESIGN: A sample of 17 obese patients without metabolic syndrome and 15 non obese control subjects was evaluated in a prospective way...
June 10, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28633664/a-review-of-sarcoptes-scabiei-past-present-and-future
#10
REVIEW
Larry G Arlian, Marjorie S Morgan
The disease scabies is one of the earliest diseases of humans for which the cause was known. It is caused by the mite, Sarcoptes scabiei, that burrows in the epidermis of the skin of humans and many other mammals. This mite was previously known as Acarus scabiei DeGeer, 1778 before the genus Sarcoptes was established (Latreille 1802) and it became S. scabiei. Research during the last 40 years has tremendously increased insight into the mite's biology, parasite-host interactions, and the mechanisms it uses to evade the host's defenses...
June 20, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-non-coding-sequences-on-embryonic-brain-development
#11
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633450/comparative-genomics-of-all-three-campylobacter-sputorum-biovars-and-a-novel-cattle-associated-c-sputorum-clade
#12
William G Miller, Emma Yee, Mary H Chapman, James L Bono
Campylobacter sputorum is a non-thermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase negative, urease negative), bv. fecalis (catalase positive, urease negative), and bv. paraureolyticus (catalase negative, urease positive). A multi-locus sequence typing (MLST) method was recently constructed for C...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633445/bpp-a-sequence-based-algorithm-for-branch-point-prediction
#13
Qing Zhang, Xiaodan Fan, Yejun Wang, Mingan Sun, Jianlin Shao, Dianjing Guo
Motivation: Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results: We here propose a novel branch point prediction algorithm that utilises information on the branch point sequence and the polypyrimidine tract...
June 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633280/motifhyades-expectation-maximization-for-de-novo-dna-motif-pair-discovery-on-paired-sequences
#14
Ka-Chun Wong
Motivation: In higher eukaryotes, protein-DNA binding interactions are the central activities in gene regulation. In particular, DNA motifs such as transcription factor binding sites are the key components in gene transcription. Harnessing the recently available chromatin interaction data, computational methods are desired for identifying the coupling DNA motif pairs enriched on long-range chromatin-interacting sequence pairs (e.g. promoter-enhancer pairs) systematically. Results: To fill the void, a novel probabilistic model (namely, MotifHyades) is proposed and developed for de novo DNA motif pair discovery on paired sequences...
June 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633085/biotechnological-production-of-recombinant-tissue-plasminogen-activator-protein-reteplase-from-transplastomic-tobacco-cell-cultures
#15
Diego Hidalgo, Maryam Abdoli-Nasab, Mokhtar Jalali-Javaran, Roque Bru-Martínez, Rosa M Cusidó, Purificación Corchete, Javier Palazon
Transplastomic plants are a system of choice for the mass production of biopharmaceuticals due to the polyploidy of the plastid genome and the low risk of pollen-mediated outcrossing because of maternal inheritance. However, as field-grown plants, they can suffer contamination by agrochemicals and fertilizers, as well as fluctuations in yield due to climatic changes and infections. Tissue-type plasminogen activator (tPA), a protein used to treat heart attacks, converts plasminogen into plasmine, which digests fibrin and induces the dissolution of fibrin clots...
June 13, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28632924/metabolomics-as-a-driver-in-advancing-precision-medicine-in-sepsis
#16
Michelle Eckerle, Lilliam Ambroggio, Michael Puskarich, Brent Winston, Alan E Jones, Theodore J Standiford, Kathleen A Stringer
OBJECTIVE: The objective of this review is to explain the science of metabolomics-a science of systems biology that measures and studies endogenous small molecules (metabolites) that are present in a single biological sample-and its application to the diagnosis and treatment of sepsis. In addition, we discuss how discovery through metabolomics can contribute to the development of precision medicine targets for this complex disease state and the potential avenues for those new discoveries to be applied in the clinical environment...
June 20, 2017: Pharmacotherapy
https://www.readbyqxmd.com/read/28632895/genome-mining-reveals-high-incidence-of-putative-lipopeptide-biosynthesis-nrps-pks-clusters-containing-fatty-acyl-amp-ligase-genes-in-biofilm-forming-cyanobacteria
#17
Tomáš Galica, Pavel Hrouzek, Jan Mareš
Cyanobacterial lipopeptides exhibit antimicrobial and antifungal bioactivities with potential for use in pharmaceutical research. However, due to their haemolytic activity and cytotoxic effects against human cells, they may pose a health issue if produced in substantial amounts in the environment. In bacteria, lipopeptides can be synthesized via several well-evidenced mechanisms. In one of them, fatty acyl-AMP ligase (FAAL) initiates the biosynthesis by activation of a fatty acyl residue. We have performed a bioinformatic survey of the cyanobacterial genomic information available in the public databases for the presence of FAAL-containing non-ribosomal peptide synthetase/polyketide synthetase (NRPS/PKS) biosynthetic clusters, as a genetic basis for lipopeptide biosynthesis...
June 20, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28632820/the-nexus-of-stem-cell-derived-beta-cells-and-genome-engineering
#18
Sara D Sackett, Aida Rodriguez, Jon S Odorico
Diabetes, type 1 and type 2 (T1D and T2D), are diseases of epidemic proportions, which are complicated and defined by genetics, epigenetics, environment, and lifestyle choices. Current therapies consist of whole pancreas or islet transplantation. However, these approaches require life-time immunosuppression, and are compounded by the paucity of available donors. Pluripotent stem cells have advanced research in the fields of stem cell biology, drug development, disease modeling, and regenerative medicine, and importantly allows for the interrogation of therapeutic interventions...
2017: Review of Diabetic Studies: RDS
https://www.readbyqxmd.com/read/28632398/the-mitochondrial-protein-atlas-a-database-of-experimentally-verified-information-on-the-human-mitochondrial-proteome
#19
Noa Godin, Jerry Eichler
Given its central role in various biological systems, as well as its involvement in numerous pathologies, the mitochondrion is one of the best-studied organelles. However, although the mitochondrial genome has been extensively investigated, protein-level information remains partial, and in many cases, hypothetical. The Mitochondrial Protein Atlas (MPA; URL: lifeserv.bgu.ac.il/wb/jeichler/MPA ) is a database that provides a complete, manually curated inventory of only experimentally validated human mitochondrial proteins...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28631672/-the-influence-of-interleukin-gene-polymorphism-on-the-serum-cytokine-level-in-the-patients-presenting-with-chonic-suppurative-otitis-media
#20
E V Baike, Yu A Vitkovsky, A A Dutova
The objective of the present work was to study the influence of allelic variant associations of 1-beta interleukin (C3953T, &511C, T31C), interleukin-6 (C174G), and tumour necrosis factor-alpha (G308A) gene polymorphisms on the serum cytokine level in the patients presenting with chronic suppurative otitis media. A total of 299 patients at the age varying from 16 to 55 years with this condition divided into three groups were examined. Group 1 was comprised of 146 patients suffering from the tubotympanic form of chronic suppurative otitis media (CSOM)...
2017: Vestnik Otorinolaringologii
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