keyword
MENU ▼
Read by QxMD icon Read
search

Translational genomics

keyword
https://www.readbyqxmd.com/read/29779130/the-present-and-the-future-of-genetic-testing-in-familial-hypercholesterolemia-opportunities-and-caveats
#1
REVIEW
Amanda J Hooper, John R Burnett, Damon A Bell, Gerald F Watts
PURPOSE OF REVIEW: We summarize recent advances in the understanding of genetic testing in familial hypercholesterolemia (FH), the use of expanded FH next-generation sequencing panels, and directions for future research. RECENT FINDINGS: The uptake of massively parallel sequencing in research and diagnostic laboratories has enabled expanded testing for FH and its phenocopies, with the added advantage that copy number variants can be detected. However, increasing the number of genes tested increases the number of variants detected, which may or may not be pathogenic...
May 19, 2018: Current Atherosclerosis Reports
https://www.readbyqxmd.com/read/29779058/genetics-of-resistant-hypertension-the-missing-heritability-and-opportunities
#2
REVIEW
Samantha K Teixeira, Alexandre C Pereira, Jose E Krieger
PURPOSE OF THE REVIEW: Blood pressure regulation in humans has long been known to be a genetically determined trait. The identification of causal genetic modulators for this trait has been unfulfilling at the least. Despite the recent advances of genome-wide genetic studies, loci associated with hypertension or blood pressure still explain a very low percentage of the overall variation of blood pressure in the general population. This has precluded the translation of discoveries in the genetics of human hypertension to clinical use...
May 19, 2018: Current Hypertension Reports
https://www.readbyqxmd.com/read/29778840/identification-of-a-novel-promoter-from-banana-aquaporin-family-gene-matip1-2-which-responses-to-drought-and-salt-stress-in-transgenic-arabidopsis-thaliana
#3
Shun Song, Yi Xu, Dongmei Huang, Hongxia Miao, Juhua Liu, Caihong Jia, Wei Hu, Ana Valeria Valarezo, Biyu Xu, Zhiqiang Jin
Drought and salt stresses often affect plant growth and crop yields. Identification of promoters involved in drought and salt stress responses is of great significance for genetic improvement of crop resistance. Our previous studies showed that aquaporin can respond to drought and salt stresses, but its promoter has not yet been reported in plants. In the present study, cis-acting elements of MaAQP family member promoters were systematically analyzed in banana. Expression of MaTIP1; 2 was induced by drought and salt stresses but not sensitive to cold stress, waterlogging stress, or mechanical damage, and its promoter contained five stress-related cis-acting elements...
May 17, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29778623/hypothesis-driven-versus-hypothesis-free-approaches-to-the-identification-of-genes-for-cleft-lip-and-palate
#4
Alexandre R Vieira
Much progress has been made in understanding the genetic contributions to isolated forms of cleft lip and palate, however this effort is yet to be translated to enhanced genetic counseling or prevention strategies. Interest in the topic was renewed with the ability to perform genome-wide genotyping and after a few of those relatively larger scale studies, many are considering more targeted efforts and to focus on specific genes and/or loci. Here we discuss this crossroad and suggest targeted approaches and rethought clinical descriptions are a better way to move the field forward...
May 16, 2018: Archives of Oral Biology
https://www.readbyqxmd.com/read/29777445/a-reverse-genetics-system-for-enterovirus-d68-using-human-rna-polymerase-i
#5
Minglei Pan, Shuai Gao, Zhenwei Zhou, Keke Zhang, Sihua Liu, Zhiyun Wang, Tao Wang
Human enterovirus D68 (EV-D68) is a highly contagious virus, which causes respiratory tract infections. However, no effective vaccines are currently available for controlling EV-D68 infection. Here, we developed a reverse genetics system to recover EV-D68 minireplicons and infectious EV-D68 from transfected plasmids using the RNA polymerase I (Pol I) promoter. The EV-D68 minireplicons contained the luciferase reporter gene, which flanked by the non-coding regions of the EV-D68 RNA. The luciferase signals could be detected in cells after transfection and Pol I promoter-mediated luciferase signal was significantly stronger than that mediated by the T7 promoter...
May 17, 2018: Virus Genes
https://www.readbyqxmd.com/read/29777131/activity-of-acetyltransferase-toxins-involved-in-salmonella-persister-formation-during-macrophage-infection
#6
Julian A Rycroft, Bridget Gollan, Grzegorz J Grabe, Alexander Hall, Angela M Cheverton, Gerald Larrouy-Maumus, Stephen A Hare, Sophie Helaine
Non-typhoidal Salmonella strains are responsible for invasive infections associated with high mortality and recurrence in sub-Saharan Africa, and there is strong evidence for clonal relapse following antibiotic treatment. Persisters are non-growing bacteria that are thought to be responsible for the recalcitrance of many infections to antibiotics. Toxin-antitoxin systems are stress-responsive elements that are important for Salmonella persister formation, specifically during infection. Here, we report the analysis of persister formation of clinical invasive strains of Salmonella Typhimurium and Enteritidis in human primary macrophages...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#7
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29771278/a-pelota-like-gene-regulates-root-development-and-defence-responses-in-rice
#8
Wona Ding, Jing Wu, Jin Ye, Wenjuan Zheng, Shanshan Wang, Xinni Zhu, Jiaqin Zhou, Zhichong Pan, Botao Zhang, Shihua Zhu
Background and Aims: Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). Methods: A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed...
May 16, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29771001/total-chemical-synthesis-of-sumo-and-sumo-abps-to-profile-activity-of-sumo-specific-proteases
#9
Monique Priscilla Catharina Mulder, Remco Merkx, Katharina Witting, Dharjath Hameed, Dris El Atmioui, Lindsey Lelieveld, Frauke Liebelt, Jacques Neefjes, Ilana Berlin, Alfred Vertegaal, Huib Ovaa
SUMO, a post-translational modifier critical for cell cycle progression and genome stability, plays a role in tumorigenesis rendering SUMO-specific enzymes as potential pharmacological targets. However, systematic generation of tools for activity profiling of SUMO-specific enzymes has proven challenging, leading us to develop a diversifiable synthetic platform for a SUMO toolbox using a direct linear synthesis protocol, permitting N- and C-terminal labeling strategies to incorporate dyes and reactive warheads, respectively...
May 17, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29770522/conclusive-evidence-for-oct4-transcription-in-human-cancer-cell-lines-possible-role-of-a-small-oct4-positive-cancer-cell-population
#10
Tomoyuki Miyamoto, Nobuhiko Mizuno, Mitsuko Kosaka, Yoko Fujitani, Eiji Ohno, Aiji Ohtsuka
The role of octamer-binding transcription factor 4 (OCT4) in human cancer is still debated. Although many studies have been published on human OCT4, determining which of the findings are accurate or which are false-positives is currently challenging. We thus developed the most reliable method to date for highly specific and comprehensive detection of genuine OCT4-transcript variants without false-positive results. Our results provided clear evidence that the transcripts of OCT4A, OCT4B, OCT4B1 and other novel splicing variants are indeed present in many cancer cell lines, but are rarely detected in normal tissue-derived differentiated cells...
May 17, 2018: Stem Cells
https://www.readbyqxmd.com/read/29769529/methionine-metabolism-influences-genomic-architecture-and-gene-expression-through-h3k4me3-peak-width
#11
Ziwei Dai, Samantha J Mentch, Xia Gao, Sailendra N Nichenametla, Jason W Locasale
Nutrition and metabolism are known to influence chromatin biology and epigenetics through post-translational modifications, yet how this interaction influences genomic architecture and connects to gene expression is unknown. Here we consider, as a model, the metabolically-driven dynamics of H3K4me3, a histone methylation mark that is known to encode information about active transcription, cell identity, and tumor suppression. We analyze the genome-wide changes in H3K4me3 and gene expression in response to alterations in methionine availability in both normal mouse physiology and human cancer cells...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29769341/mutational-analysis-of-the-bovine-hepacivirus-internal-ribosome-entry-site
#12
A L Baron, A Schoeniger, P Becher, C Baechlein
In recent years, hepatitis C virus (HCV)-related viruses were identified in several species including dogs, horses, bats and rodents. Additionally, a novel virus of the genus Hepacivirus has been discovered in bovine samples and was termed bovine hepacivirus (BovHepV). Prediction of the BovHepV IRES (internal ribosome entry site) structure revealed strong similarities to the HCV IRES structure comprising domains II, IIIabcde, pseudoknot IIIf and domain IV with the initiation codon AUG. Unlike HCV, only one microRNA-122 (miR-122) binding site could be identified in the BovHepV 5' NTR...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769273/genome-wide-posttranscriptional-dysregulation-by-micrornas-in-human-asthma-as-revealed-by-frac-seq
#13
Rocio T Martinez-Nunez, Hitasha Rupani, Manuela Platé, Mahesan Niranjan, Rachel C Chambers, Peter H Howarth, Tilman Sanchez-Elsner
MicroRNAs are small noncoding RNAs that inhibit gene expression posttranscriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing subcellular fractionation and RNA sequencing (Frac-seq) in human primary bronchoepithelium from healthy controls and severe asthmatics...
May 16, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29768440/transcriptome-analysis-reveals-a-stress-response-of-shewanella-oneidensis-deprived-of-background-levels-of-ionizing-radiation
#14
Hugo Castillo, Xiaoping Li, Faye Schilkey, Geoffrey B Smith
Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72...
2018: PloS One
https://www.readbyqxmd.com/read/29767398/bioinformatic-analysis-of-the-metal-response-element-and-zinc-dependent-gene-regulation-via-the-metal-response-element-binding-transcription-factor-1-in-caco-2-cells
#15
Michael Francis, Arthur Grider
The purpose of this study was to determine the correlation between the position or number of metal regulatory elements (MREs) near gene transcriptional or translational start sites, and the strength of metal response element-binding transcription factor 1 (MTF-1) regulation. A secondary analysis was performed in silico on published results measuring the effects of Zn and MTF-1 on transcriptional regulation of genes (n = 120) in the Caco-2 cell line. MRE sequence variations throughout the human genome were sorted using a position weight matrix...
May 16, 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29766023/adeno-associated-virus-genome-population-sequencing-achieves-full-vector-genome-resolution-and-reveals-human-vector-chimeras
#16
Phillip W L Tai, Jun Xie, Kaiyuen Fong, Matthew Seetin, Cheryl Heiner, Qin Su, Michael Weiand, Daniella Wilmot, Maria L Zapp, Guangping Gao
Recombinant adeno-associated virus (rAAV)-based gene therapy has entered a phase of clinical translation and commercialization. Despite this progress, vector integrity following production is often overlooked. Compromised vectors may negatively impact therapeutic efficacy and safety. Using single molecule, real-time (SMRT) sequencing, we can comprehensively profile packaged genomes as a single intact molecule and directly assess vector integrity without extensive preparation. We have exploited this methodology to profile all heterogeneic populations of self-complementary AAV genomes via bioinformatics pipelines and have coined this approach AAV-genome population sequencing (AAV-GPseq)...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/29765862/genomic-imprinting-and-the-regulation-of-postnatal-neurogenesis
#17
REVIEW
Anna Lozano-Ureña, Raquel Montalbán-Loro, Anne C Ferguson-Smith, Sacri R Ferrón
Most genes required for mammalian development are expressed from both maternally and paternally inherited chromosomal homologues. However, there are a small number of genes known as " imprinted genes " that only express a single allele from one parent, which is repressed on the gene from the other parent. Imprinted genes are dependent on epigenetic mechanisms such as DNA methylation and post-translational modifications of the DNA-associated histone proteins to establish and maintain their parental identity...
November 9, 2017: Brain Plasticity
https://www.readbyqxmd.com/read/29765372/is-iqg-607-a-potential-metallodrug-or-metallopro-drug-with-a-defined-molecular-target-in-mycobacterium-tuberculosis
#18
REVIEW
Bruno L Abbadi, Valnês da Silva Rodrigues-Junior, Adilio da Silva Dadda, Kenia Pissinate, Anne D Villela, Maria M Campos, Luiz G de França Lopes, Cristiano V Bizarro, Pablo Machado, Eduardo H S Sousa, Luiz A Basso
The emergence of strains of Mycobacterium tuberculosis resistant to isoniazid (INH) has underscored the need for the development of new anti-tuberculosis agents. INH is activated by the mycobacterial katG -encoded catalase-peroxidase, forming an acylpyridine fragment that is covalently attached to the C4 of NADH. This isonicotinyl-NAD adduct inhibits the activity of 2- trans -enoyl-ACP(CoA) reductase (InhA), which plays a role in mycolic acid biosynthesis. A metal-based INH analog, Na3 [FeII (CN)5 (INH)]·4H2 O, IQG-607, was designed to have an electronic redistribution on INH moiety that would lead to an intramolecular electron transfer to bypass KatG activation...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29762088/an-updated-taxonomy-and-a-graphical-summary-tool-for-optimal-classification-and-comprehension-of-omics-research
#19
Nina Pirih, Tanja Kunej
The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e...
May 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29761930/multiple-phosphorylation-sites-on-%C3%AE-tubulin-are-essential-and-contribute-to-the-biogenesis-of-basal-bodies-in-tetrahymena
#20
Ewa Joachimiak, Maria Jerka-Dziadosz, Łucja Krzemień-Ojak, Ewa Wacławek, Katarzyna Jedynak, Paulina Urbanska, Wojciech Brutkowski, Hanna Sas-Nowosielska, Hanna Fabczak, Jacek Gaertig, Dorota Wloga
The mechanisms that regulate γ-tubulin, including its post-translational modifications, are poorly understood. γ-Tubulin is important for the duplication of centrioles and structurally similar basal bodies (BBs), organelles which contain a ring of nine triplet microtubules. The ciliate Tetrahymena thermophila carries hundreds of cilia in a single cell and provides an excellent model to specifically address the role of γ-tubulin in the BBs assembly and maintenance. The genome of Tetrahymena contains a single γ-tubulin gene...
May 15, 2018: Journal of Cellular Physiology
keyword
keyword
29666
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"