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https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#1
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29028986/a-new-haplotype-block-detection-method-for-dense-genome-sequencing-data-based-on-interval-graph-modeling-of-clusters-of-highly-correlated-snps
#2
Sun Ah Kim, Chang-Sung Cho, Suh-Ryung Kim, Shelley B Bull, Yun Joo Yoo
Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation...
September 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028613/divergent-biology-of-facultative-heavy-metal-plants
#3
REVIEW
Hermann Bothe, Aneta Słomka
Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred...
September 7, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29027357/studies-on-the-aerobic-utilization-of-synthesis-gas-syngas-by-wild-type-and-recombinant-strains-of-ralstonia-eutropha-h16
#4
Daniel Heinrich, Matthias Raberg, Alexander Steinbüchel
The biotechnical platform strain Ralstonia eutropha H16 was genetically engineered to express a cox subcluster of the carboxydotrophic Oligotropha carboxidovoransOM5, including (i) the structural genes coxM, -S and -L, coding for an aerobic carbon monoxide dehydrogenase (CODH) and (ii) the genes coxD, -E, -F and -G, essential for the maturation of CODH. The coxOc genes expressed under control of the CO2 -inducible promoter PL enabled R. eutropha to oxidize CO to CO2 for the use as carbon source, as demonstrated by (13) CO experiments, but the recombinant strains remained dependent on H2 as external energy supply...
October 13, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29027297/factors-associated-with-ambulatory-care-sensitive-emergency-department-visits-for-south-carolina-medicaid-members-with-intellectual-disability
#5
S McDermott, J Royer, J R Mann, B S Armour
INTRODUCTION: Ambulatory care sensitive conditions (ACSCs) can be seen as failure of access or management in primary care settings. Identifying factors associated with ACSCs for individuals with an Intellectual Disability (ID) provide insight into potential interventions. METHOD: To assess the association between emergency department (ED) ACSC visits and a number of demographic and health characteristics of South Carolina Medicaid members with ID. A retrospective cohort of adults with ID was followed from 2001 to 2011...
October 13, 2017: Journal of Intellectual Disability Research: JIDR
https://www.readbyqxmd.com/read/29026447/epigenome-alterations-in-aortic-valve-stenosis-and-its-related-left-ventricular-hypertrophy
#6
REVIEW
Igor Gošev, Martina Zeljko, Željko Đurić, Ivana Nikolić, Milorad Gošev, Sanja Ivčević, Dino Bešić, Zoran Legčević, Frane Paić
Aortic valve stenosis is the most common cardiac valve disease, and with current trends in the population demographics, its prevalence is likely to rise, thus posing a major health and economic burden facing the worldwide societies. Over the past decade, it has become more than clear that our traditional genetic views do not sufficiently explain the well-known link between AS, proatherogenic risk factors, flow-induced mechanical forces, and disease-prone environmental influences. Recent breakthroughs in the field of epigenetics offer us a new perspective on gene regulation, which has broadened our perspective on etiology of aortic stenosis and other aortic valve diseases...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29026162/improving-membrane-protein-expression-and-function-using-genomic-edits
#7
Heather M Jensen, Thomas Eng, Victor Chubukov, Robin A Herbert, Aindrila Mukhopadhyay
Expression of membrane proteins often leads to growth inhibition and perturbs central metabolism and this burden varies with the protein being overexpressed. There are also known strain backgrounds that allow greater expression of membrane proteins but that differ in efficacy across proteins. We hypothesized that for any membrane protein, it may be possible to identify a modified strain background where its expression can be accommodated with less burden. To directly test this hypothesis, we used a bar-coded transposon insertion library in tandem with cell sorting to assess genome-wide impact of gene deletions on membrane protein expression...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025584/regulatory-mechanisms-of-long-noncoding-rnas-on-gene-expression-in-cancers
#8
REVIEW
Weiliang Sun, Yunben Yang, Chunjing Xu, Junming Guo
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. HOTAIR and ANRIL function in chromatin remodeling...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#9
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29024003/molecular-characterization-of-the-llama-fgf5-gene-and-identification-of-putative-loss-of-function-mutations
#10
M S Daverio, L Vidal-Rioja, E N Frank, F Di Rocco
Llama, the most numerous domestic camelid in Argentina, has good fiber-production ability. Although a few genes related to other productive traits have been characterized, the molecular genetic basis of fiber growth control in camelids is still poorly understood. Fibroblast growth factor 5 (FGF5) is a secreted signaling protein that controls hair growth in humans and other mammals. Mutations in the FGF5 gene have been associated with long-hair phenotypes in several species. Here, we sequenced the llama FGF5 gene, which consists of three exons encoding 813 bp...
October 11, 2017: Animal Genetics
https://www.readbyqxmd.com/read/29023628/ethnic-derivation-of-the-ainu-inferred-from-ancient-mitochondrial-dna-data
#11
Noboru Adachi, Tsuneo Kakuda, Ryohei Takahashi, Hideaki Kanzawa-Kiriyama, Ken-Ichi Shinoda
OBJECTIVES: The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined...
October 11, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29023486/the-sea-cucumber-genome-provides-insights-into-morphological-evolution-and-visceral-regeneration
#12
Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean-François Hamel, Chengzhang Liu, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Songjun Jin, Peng Xu, Kenneth B Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers...
October 2017: PLoS Biology
https://www.readbyqxmd.com/read/29023445/identifying-direct-contacts-between-protein-complex-subunits-from-their-conditional-dependence-in-proteomics-datasets
#13
Kevin Drew, Christian L Müller, Richard Bonneau, Edward M Marcotte
Determining the three dimensional arrangement of proteins in a complex is highly beneficial for uncovering mechanistic function and interpreting genetic variation in coding genes comprising protein complexes. There are several methods for determining co-complex interactions between proteins, among them co-fractionation / mass spectrometry (CF-MS), but it remains difficult to identify directly contacting subunits within a multi-protein complex. Correlation analysis of CF-MS profiles shows promise in detecting protein complexes as a whole but is limited in its ability to infer direct physical contacts among proteins in sub-complexes...
October 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29022581/the-impact-of-rare-variation-on-gene-expression-across-tissues
#14
Xin Li, Yungil Kim, Emily K Tsang, Joe R Davis, Farhan N Damani, Colby Chiang, Gaelen T Hess, Zachary Zappala, Benjamin J Strober, Alexandra J Scott, Amy Li, Andrea Ganna, Michael C Bassik, Jason D Merker, Ira M Hall, Alexis Battle, Stephen B Montgomery
Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022495/genetic-polymorphisms-of-hotair-gene-are-associated-with-the-risk-of-breast-cancer-in-a-sample-of-southeast-iranian-population
#15
Shekoufeh Hassanzarei, Mohammad Hashemi, Hedieh Sattarifard, Seyed Mehdi Hashemi, Gholamreza Bahari, Saeid Ghavami
There is an increasing body of evidence which highlights the critical functions of long non-coding RNAs in the carcinogenicity mechanism of a variety of cancers. It has been reported that HOX transcript antisense intergenic RNA, a member of long non-coding RNA family, increases breast cancer risk. To date, no data regarding the association between HOX transcript antisense intergenic RNA polymorphisms and the risk of breast cancer development has been reported in Iran. Here, we examine the possible association between HOX transcript antisense intergenic RNA gene polymorphisms and breast cancer in a sample of southeast Iranian female population...
October 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29020744/fastbma-scalable-network-inference-and-transitive-reduction
#16
Ling-Hong Hung, Kaiyuan Shi, Migao Wu, William Chad Young, Adrian E Raftery, Ka Yee Yeung
Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29020618/hotspots-of-de-novo-point-mutations-in-induced-pluripotent-stem-cells
#17
Masahito Yoshihara, Ryoko Araki, Yasuji Kasama, Misato Sunayama, Masumi Abe, Kohji Nishida, Hideya Kawaji, Yoshihide Hayashizaki, Yasuhiro Murakawa
Induced pluripotent stem cells (iPSCs) are generated by direct reprogramming of somatic cells and hold great promise for novel therapies. However, several studies have reported genetic variations in iPSC genomes. Here, we investigated point mutations identified by whole-genome sequencing in mouse and human iPSCs in the context of epigenetic status. In contrast to disease-causing single-nucleotide polymorphisms, de novo point mutations introduced during reprogramming were underrepresented in protein-coding genes and in open chromatin regions, including transcription factor binding sites...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/29019003/role-of-dynein-axonemal-heavy-chain-6-gene-expression-as-a-possible-biomarker-for-huntington-s-disease-a-translational-study
#18
Lorena B Areal, Lorraine P Pereira, Fabiola M Ribeiro, Isabella G Olmo, Marcelo R Muniz, Maria do Carmo Rodrigues, Patrik F Costa, Cristina Martins-Silva, Stephen S G Ferguson, Daniela A M Guimarães, Rita G W Pires
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder characterized by motor dysfunction, cognitive deficits, and psychiatric symptoms. The primary genetic cause is an expansion of cytosine adenine guanine (CAG) nucleotides of the huntingtin gene, which codes an important protein involved with neuronal signaling. The severity of HD correlates with the number of CAG repeats and individuals with longer expansions have an earlier onset and more severe symptoms. A microarray study conducted by our research group showed alteration in DNAH6 gene (encoding dynein axonemal heavy chain 6)...
October 10, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/29018616/integration-of-lncrna-mirna-mrna-reveals-novel-insights-into-oviposition-regulation-in-honey-bees
#19
Xiao Chen, Ce Ma, Chao Chen, Qian Lu, Wei Shi, Zhiguang Liu, Huihua Wang, Haikun Guo
BACKGROUND: The honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation and oviposition processes on a molecular level, a genome-wide analysis of lncRNAs, miRNAs and mRNA expression in the ovaries of the queens was performed to screen for differentially expressed coding and noncoding RNAs. Further analysis identified relevant candidate genes or RNAs...
2017: PeerJ
https://www.readbyqxmd.com/read/29018283/codon-optimality-bias-and-usage-in-translation-and-mrna-decay
#20
REVIEW
Gavin Hanson, Jeff Coller
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery...
October 11, 2017: Nature Reviews. Molecular Cell Biology
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