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https://www.readbyqxmd.com/read/28822173/-breakthrough-in-key-science-and-technologies-in-dendrobium-catenatum-industry
#1
Ji-Ping Si, Qi Wang, Zhong-Jian Liu, Jing-Jing Liu, Yi-Bo Luo
In view of the significant difficulties of propagation, planting and simple product in Dendrobium catenatum(D. officinale)industry development, a series of research were carried out. Genome study showed that D. catenatum is a specie of diploid with 38 chromosomes and 28 910 protein-coding genes. It was identified that specific genes accumulated in different organs at the transcriptome level. We got an insight into the gene regulation mechanism of the loss of the endospermous seed, the wide ecological adaptability and the synthesis of polysaccharides, which provided a theoretical basis for genetic engineering breeding and development and utilization of active pharmaceutical ingredients...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#2
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820180/osteogenesis-imperfecta
#3
REVIEW
Joan C Marini, Antonella Forlino, Hans Peter Bächinger, Nick J Bishop, Peter H Byers, Anne De Paepe, Francois Fassier, Nadja Fratzl-Zelman, Kenneth M Kozloff, Deborah Krakow, Kathleen Montpetit, Oliver Semler
Skeletal deformity and bone fragility are the hallmarks of the brittle bone dysplasia osteogenesis imperfecta. The diagnosis of osteogenesis imperfecta usually depends on family history and clinical presentation characterized by a fracture (or fractures) during the prenatal period, at birth or in early childhood; genetic tests can confirm diagnosis. Osteogenesis imperfecta is caused by dominant autosomal mutations in the type I collagen coding genes (COL1A1 and COL1A2) in about 85% of individuals, affecting collagen quantity or structure...
August 18, 2017: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/28819569/a-study-on-il8rb-gene-polymorphism-as-a-potential-immuno-compromised-adherent-in-exaggeration-of-parenteral-and-mammo-crine-oxidative-stress-during-mastitis-in-buffalo
#4
S M El Nahas, A H El Kasas, A A Abou Mossallem, M I Abdelhamid, Mohamad Warda
The genetic markers in inflammatory responses during mastitis afford a reasonable way for improving milk production in the Egyptian buffalo breed. Among them is the interleukin 8 Receptor Gene (IL8RB) (CXCR2); a chemokine receptor gene augments the neutrophil migration during infection. To understand its role better during mastitis in Egyptian buffalos, twenty-five dairy animals representing the normal, sub-clinically, clinically and chronically affected buffalos were randomly selected from different districts...
November 2017: Journal of Advanced Research
https://www.readbyqxmd.com/read/28815929/aggregation-of-population-based-genetic-variation-over-protein-domain-homologues-and-its-potential-use-in-genetic-diagnostics
#5
Laurens Wiel, Hanka Venselaar, Joris A Veltman, Gerrit Vriend, Christian Gilissen
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains"...
August 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28815618/effect-on-gene-expression-of-three-allelic-variants-in-gata-motifs-of-abo-rhd-and-rhce-regulatory-elements
#6
Katie Fennell, Roser Hoffman, Ken Yoshida, Sadahiko Iwamoto, Lavendri Govender, Kuben Vather, Ashika Sookraj, Ute Jentsch, Chantale Pambrun, Catherine McAuley, Margaret A Keller, Gorka Ochoa-Garay
BACKGROUND: Only a few genetic variants have been reported in regulatory elements of blood group genes. Most of them affect GATA motifs, binding sites for the GATA-1 transcription factor. STUDY DESIGN AND METHODS: Samples from two patients and one donor with unusual or discrepant serology for ABO, RhD, and RhCE antigens were analyzed by DNA sequencing. Analyzed regions included the coding sequence and portions of regulatory elements. The effect of some variants on gene expression was evaluated in reporter gene assays...
August 16, 2017: Transfusion
https://www.readbyqxmd.com/read/28815538/long-noncoding-rnas-in-the-yeast-s-%C3%A2-cerevisiae
#7
Rachel O Niederer, Evan P Hass, David C Zappulla
Long noncoding RNAs have recently been discovered to comprise a sizeable fraction of the RNA World. The scope of their functions, physical organization, and disease relevance remain in the early stages of characterization. Although many thousands of lncRNA transcripts recently have been found to emanate from the expansive DNA between protein-coding genes in animals, there are also hundreds that have been found in simple eukaryotes. Furthermore, lncRNAs have been found in the bacterial and archaeal branches of the tree of life, suggesting they are ubiquitous...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#8
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814280/assisted-clustering-of-gene-expression-data-using-ancut
#9
Sebastian J Teran Hidalgo, Mengyun Wu, Shuangge Ma
BACKGROUND: In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can reveal the (previously unknown) interconnections among genes. With the high dimensionality of gene expression data, many of the existing clustering methods and results are not as satisfactory...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28812986/epigenome-aberrations-emerging-driving-factors-of-the-clear-cell-renal-cell-carcinoma
#10
REVIEW
Ali Mehdi, Yasser Riazalhosseini
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#11
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812463/novel-col1a1-mutation-c-3290g-t-associated-with-severe-form-of-osteogenesis-imperfecta-in-a-fetus
#12
Laura Tanner, Paula Vainio, Minna Sandell, Jukka Laine
Osteogenesis imperfecta is a genetically and clinically heterogenous group of skeletal dysplasias characterized by bone fragility. Its severity ranges from nearly asymptomatic individuals to perinatal lethality. The majority of cases are caused by mutations in either the COL1A1 or the COL1A2 gene coding for alpha 1 and alpha 2 chains of collagen type 1, respectively, and a large number of pathogenic variants of these genes has been identified. We describe a novel COL1A1 mutation associated with prenatally diagnosed severe form of osteogenesis imperfecta...
September 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#13
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810830/annotating-long-intergenic-non-coding-rnas-under-artificial-selection-during-chicken-domestication
#14
Yun-Mei Wang, Hai-Bo Xu, Ming-Shan Wang, Newton Otieno Otecko, Ling-Qun Ye, Dong-Dong Wu, Ya-Ping Zhang
BACKGROUND: Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. RESULTS: We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome...
August 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28809007/method-to-identify-silent-codon-mutations-that-may-alter-peptide-elongation-kinetics-and-co-translational-protein-folding
#15
Ronald Worthington, Elijah Ball, Brentsen Wolf, Gregory Takacs
Due to the redundancy of the protein genetic code, mutational changes in the second or third nucleotide of an existing codon may not change the amino acid specification of the resulting modified codon. When peptide primary sequence is unchanged by mutation, that mutation is assumed to have no functional consequences. However, for one key gene involved in drug transport, MDR-1, several silent, synonymous mutations have been shown to alter protein structure and substrate affinity (Kimchi-Sarfaty et al., Science 315:525-528, 2007)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808380/identification-and-analysis-of-jasmonate-pathway-genes-in-coffea-canephora-robusta-coffee-by-in-silico-approach
#16
Kosaraju Bharathi, H L Sreenath
BACKGROUND: Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica. Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808237/coding-and-small-non-coding-transcriptional-landscape-of-tuberous-sclerosis-complex-cortical-tubers-implications-for-pathophysiology-and-treatment
#17
James D Mills, Anand M Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J Anink, Bart Janssen, Till S Zimmer, Wim G Spliet, Peter C van Rijen, Floor E Jansen, Martha Feucht, Johannes A Hainfellner, Pavel Krsek, Josef Zamecnik, Katarzyna Kotulska, Sergiusz Jozwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J Kwiatkowski, R Jeroen Pasterkamp, Ketharini Senthilkumar, Lars von Oerthel, Marco F Hoekman, Jan A Gorter, Peter B Crino, Angelika Mühlebner, Brendon P Scicluna, Eleonora Aronica
Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28805541/lack-of-foxe3-coding-mutation-in-a-case-of-congenital-aphakia
#18
Yusuke Sano, Yusuke Matsukane, Akihisa Watanabe, Ko-Hei Sonoda, Hiroyuki Kondo
PURPOSE: To report the findings in a patient with congenital primary aphakia, a rare disease known to be caused by mutations in the FOXE3 gene. METHODS: The clinical appearances and visual functions of the patient were determined from the medical records. Genetic analyses were performed to search for mutations in the FOXE3 gene by Sanger sequencing and whole exome sequencing. RESULTS: The 2-month-old male patient first presented with bilateral congenital aphakia associated with microphthalmia, corneal opacity, and dysplasia of the anterior segment...
August 14, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28805485/transcriptional-activity-of-transposable-elements-may-contribute-to-gene-expression-changes-in-the-syncytium-formed-by-cyst-nematode-in-arabidopsis-roots
#19
Sarbottam Piya, Morgan Bennett, Aditi Rambani, Tarek Hewezi
Transposable elements (TEs) are mobile genetic materials that constitute a large fraction of plant genomes. Recent experimental evidences indicate that TEs can play key regulatory roles in controlling the expression of adjacent genes during plant development and stress responses. Nevertheless, information about the transcriptional activity of TEs and their impact on proximal genes during plant-nematode interaction remains largely unknown. Here, we identify of differentially expressed TEs and report their possible influence on the expression of nearby genes during the susceptible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis thaliana...
August 14, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28805191/presenting-a-new-kinetic-model-for-methanol-to-light-olefins-reactions-over-a-hierarchical-sapo-34-catalyst-using-the-langmuir-hinshelwood-hougen-watson-mechanism
#20
Mohammad Javad Azarhoosh, Rouein Halladj, Sima Askari
In this study, a new kinetic model for methanol to light olefins (MTO) reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson mechanism was presented and the kinetic parameters was obtained using genetic algorithm (GA) and genetic programming (GP). Several kinetic models for the MTO reactions, have been presented. However, due to the complexity of the reactions, most reactions are considered lumped and elementary, which cannot be deemed a completely accurate kinetic model of the process...
August 14, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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