keyword
MENU ▼
Read by QxMD icon Read
search

Reference gene

keyword
https://www.readbyqxmd.com/read/28724077/physical-map-of-the-short-arm-of-bread-wheat-chromosome-3d
#1
Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723903/automatic-analysis-and-3d-modelling-of-hi-c-data-using-tadbit-reveals-structural-features-of-the-fly-chromatin-colors
#2
François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume Filion, Marc A Marti-Renom
The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions...
July 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28723513/the-natural-history-and-outcome-predictors-of-metastatic-castration-resistant-prostate-cancer
#3
REVIEW
Robert J van Soest, Jason A Efstathiou, Cora N Sternberg, Bertand Tombal
CONTEXT: Biomarkers for the treatment of metastatic castration-resistant prostate cancer (mCRPC) are urgently needed by clinicians to facilitate treatment decisions. OBJECTIVE: To review current prognostic and predictive biomarkers in mCRPC. EVIDENCE ACQUISITION: We performed a nonsystematic review of the literature from 2004 to August 2016 by searching in Medline. Cross-matching references were used to search for additional articles. We reviewed clinical research and review articles written in the English language...
December 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723080/an-orthogonal-multi-input-integration-system-to-control-gene-expression-in-escherichia-coli
#4
Fabio Annunziata, Antoni Matyjaszkiewicz, Gianfranco Fiore, Claire Grierson, Lucia Marucci, Mario di Bernardo, Nigel Savery
In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behaviour. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their relative abundance. The computation is performed via molecular titration between an orthogonal σ factor and its cognate anti-σ factor. We use mathematical modelling and experiments to show that the computation system is predictable and able to adapt GFP expression dynamically to a wide range of combinations of the two signals, and our model qualitatively captures most of these behaviours...
July 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28721981/detection-of-clostridium-difficile-antigen-and-toxin-in-stool-specimens-comparison-of-the-c-difficile-quik-chek-complete-enzyme-immunoassay-and-genexpert-c-difficile-polymerase-chain-reaction-assay
#5
Abiola C Senok, Kamel M Aldosari, Rayan A Alowaisheq, Othman A Abid, Khalid A Alsuhaibani, Mohammad A Khan, Ali M Somily
BACKGROUND/AIMS: Accurate and rapid laboratory diagnosis of Clostridium difficile infections (CDI) remains a significant challenge. A two-step algorithm for detection of toxigenic C. difficile in stool based on initial screening for glutamate dehydrogenase assay followed by confirmation by toxin A+B detection using an enzyme immunoassay (EIA) or molecular assay has been proposed. We aimed to evaluate the C. difficile Quik Chek Complete® (QCC-EIA) versus the GeneXpert® C. difficile polymerase chain reaction (PCR) assay in this two-step algorithm...
July 2017: Saudi Journal of Gastroenterology: Official Journal of the Saudi Gastroenterology Association
https://www.readbyqxmd.com/read/28721848/evaluation-of-biofilm-specific-antimicrobial-resistance-genes-in-pseudomonas-aeruginosa-isolates-in-farabi-hospital
#6
Mahmood Saffari, Shabnam Karami, Farzaneh Firoozeh, Mojtaba Sehat
BACKGROUND: Biofilm produced from Pseudomonas aeruginosa is the cause of infection induced by contact lenses, trauma and post-surgery infection. The aim of this study was to evaluate biofilm formation and the presence of the genes ndvB and tssC1 in ocular infection isolates of P. aeruginosa. METHODS: A total of 92 P. aeruginosa strains were collected from patients with ocular infection referred to Farabi Hospital between March 2014 and July 2015. Antibiotic susceptibility patterns were evaluated by the agar disc-diffusion method according to CLSI guidelines...
July 18, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28721485/non-additive-and-epistatic-effects-of-hla-polymorphisms-contributing-to-risk-of-adult-glioma
#7
Chenan Zhang, Adam J de Smith, Ivan V Smirnov, John K Wiencke, Joseph L Wiemels, John S Witte, Kyle M Walsh
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described...
July 18, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28721157/micrornas-and-metabolic-disorders-where-are-we-heading
#8
Agnieszka Sliwinska, Marta A Kasinska, Jozef Drzewoski
MicroRNAs (miRNAs, miRs) are short, non-coding molecules engaged in normal functioning of eukaryotic cells, as negative regulators of gene expression. Since the first discovery of miRNA in the early 1990s, hundreds of different miRNAs and their targets have been identified. A growing number of studies have aimed to search for microRNAs which have a key role in the regulation of insulin signaling and metabolic homeostasis. Recent evidence indicates that dysregulation of miRNA expression is involved in the development of various diseases, including type 2 diabetes mellitus (T2DM), obesity and cardiovascular diseases...
June 2017: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/28720979/first-report-of-phyllosticta-citricarpa-and-description-of-two-new-species-p-%C3%A2-paracapitalensis-and-p-%C3%A2-paracitricarpa-from-citrus-in-europe
#9
V Guarnaccia, J Z Groenewald, H Li, C Glienke, E Carstens, V Hattingh, P H Fourie, P W Crous
The genus Phyllosticta occurs worldwide, and contains numerous plant pathogenic, endophytic and saprobic species. Phyllosticta citricarpa is the causal agent of Citrus Black Spot disease (CBS), affecting fruits and leaves of several citrus hosts (Rutaceae), and can also be isolated from asymptomatic citrus tissues. Citrus Black Spot occurs in citrus-growing regions with warm summer rainfall climates, but is absent in countries of the European Union (EU). Phyllosticta capitalensis is morphologically similar to P...
June 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28720171/pacbio-assembly-of-a-plasmodium-knowlesi-genome-sequence-with-hi-c-correction-and-manual-annotation-of-the-sicavar-gene-family
#10
S A Lapp, J A Geraldo, J-T Chien, F Ay, S B Pakala, G Batugedara, J Humphrey, J D DeBARRY, K G Le Roch, M R Galinski, J C Kissinger
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features...
July 19, 2017: Parasitology
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#11
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28718045/full-length-genome-sequence-analysis-of-four-subgroup-j-avian-leukosis-virus-strains-isolated-from-chickens-with-clinical-hemangioma
#12
Lulu Lin, Peikun Wang, Yongli Yang, Haijuan Li, Teng Huang, Ping Wei
Since 2014, cases of hemangioma associated with avian leukosis virus subgroup J (ALV-J) have been emerging in commercial chickens in Guangxi. In this study, four strains of the subgroup J avian leukosis virus (ALV-J), named GX14HG01, GX14HG04, GX14LT07, and GX14ZS14, were isolated from chickens with clinical hemangioma in 2014 by DF-1 cell culture and then identified with ELISA detection of ALV group specific antigen p27, the detection of subtype specific PCR and indirect immunofluorescence assay (IFA) with ALV-J specific monoclonal antibody...
July 17, 2017: Virus Genes
https://www.readbyqxmd.com/read/28717847/exploring-the-genomic-diversity-and-cariogenic-differences-of-streptococcus-mutans-strains-through-pan-genome-and-comparative-genome-analysis
#13
Peiqi Meng, Chang Lu, Qian Zhang, Jiuxiang Lin, Feng Chen
Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35...
July 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28717674/exactly-zero-or-once-a-clinically-helpful-guide-to-assessing-genetic-variants-in-mild-epilepsies
#14
Caitlin A Bennett, Slavé Petrovski, Karen L Oliver, Samuel F Berkovic
OBJECTIVE: To assist the interpretation of genomic data for common epilepsies, we asked whether variants implicated in mild epilepsies in autosomal dominant families are present in the general population. METHODS: We studied 12 genes for the milder epilepsies and identified published variants with strong segregation support (de novo germline mutation or ≥4 affected family members). These variants were checked in the Exome Aggregation Consortium (ExAC), a database of genetic variation in over 60,000 individuals...
August 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28717592/epas1-variants-in-high-altitude-tibetan-wolves-were-selectively-introgressed-into-highland-dogs
#15
Bridgett vonHoldt, Zhenxin Fan, Diego Ortega-Del Vecchyo, Robert K Wayne
BACKGROUND: Admixture can facilitate adaptation. For example, black wolves have obtained the variant causing black coat color through past hybridization with domestic dogs and have higher fitness than gray colored wolves. Another recent example of the transfer of adaptive variation between the two species has been suggested by the similarity between high altitude Tibetan mastiffs and wolves at the EPAS1 gene, a transcription factor induced in low oxygen environments. METHODS: Here, we investigate the directionality of admixture in EPAS1 between 28 reference highland gray wolves, 15 reference domestic dogs, and 21 putatively admixed highland wolves...
2017: PeerJ
https://www.readbyqxmd.com/read/28717051/detection-of-markers-predictive-of-macrolide-and-fluoroquinolone-resistance-in-mycoplasma-genitalium-from-patients-attending-sexual-health-services-in-england
#16
Rachel Pitt, Helen Fifer, Neil Woodford, Sarah Alexander
OBJECTIVES: Resistance to both macrolides and fluoroquinolones has been reported in Mycoplasma genitalium; however, due to limited diagnostics, studies are often small and confined to specific geographical areas. This study sought to determine the rate of predicted resistance in M. genitalium-positive specimens referred for diagnostic testing. METHODS: Seventy-four M. genitalium-positive specimens, referred to the national reference laboratory (2010-2013) from 19 centres across England, were blinded and anonymised...
July 17, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/28717002/human-ribonuclease-h1-resolves-r-loops-and-thereby-enables-progression-of-the-dna-replication-fork
#17
Shankar Parajuli, Daniel C Tealsey, Bhavna Murali, Jessica Jackson, Alessandro Vindigni, Sheila A Stewart
Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA:DNA hybrids, commonly referred to as R-loops. While R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression...
July 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28716134/detecting-protein-variants-by-mass-spectrometry-a-comprehensive-study-in-cancer-cell-lines
#18
Javier A Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C Boutros, Thomas Kislinger
BACKGROUND: Onco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database. METHODS: We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28716078/cognate-comparative-gene-annotation-characterizer
#19
Jeanne Wilbrandt, Bernhard Misof, Oliver Niehuis
BACKGROUND: The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28715930/transcription-analysis-of-cochlear-development-in-minipigs
#20
Qinghua Wang, Yan Zhang, Weiwei Guo, Yu Liu, Hong Wei, Shiming Yang
CONCLUSIONS: The critical stage for cochlear gene regulation in the embryo is E49-E56. These data provide a valuable resource to help elucidate gene regulation in cochlear development and will benefit ear-related studies, especially those that focus on gene and stem cell therapies in hearing loss. OBJECTIVES: To investigate gene regulation in cochlear development and provide reference information for ear-related research. METHODS: Total RNA extraction from the Bama miniature pig cochlea was performed at five time points that covered most of the cochlea development process (E42, E49, E56, E91, P13)...
July 18, 2017: Acta Oto-laryngologica
keyword
keyword
109419
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"