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Molecular genetics

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https://www.readbyqxmd.com/read/27936210/genetic-analysis-and-qtl-mapping-of-fruit-peduncle-length-in-cucumber-cucumis-sativus-l
#1
Zi-Chao Song, Han Miao, Song Zhang, Ye Wang, Sheng-Ping Zhang, Xing-Fang Gu
Mechanized harvesting of cucumbers offers significant advantages compared to manual labor as both shortages and costs of labor increase. However the efficient use of machines depends on breeding plants with longer peduncles, but the genetic and molecular basis of fruit peduncle development in cucumber is not well understood. In this study, F2 populations were developed from a cross between two inbred lines, 1101 with a long peduncle and 1694 with a short peduncle. These were grown at two field sites, Hainan, with a tropical marine climate, in December 2014, and Beijing, with a warm temperate climate, in May 2015...
2016: PloS One
https://www.readbyqxmd.com/read/27936208/developmental-stage-muscle-and-genetic-type-modify-muscle-transcriptome-in-pigs-effects-on-gene-expression-and-regulatory-factors-involved-in-growth-and-metabolism
#2
Miriam Ayuso, Almudena Fernández, Yolanda Núñez, Rita Benítez, Beatriz Isabel, Ana I Fernández, Ana I Rey, Antonio González-Bulnes, Juan F Medrano, Ángela Cánovas, Clemente J López-Bote, Cristina Óvilo
Iberian pig production includes purebred (IB) and Duroc-crossbred (IBxDU) pigs, which show important differences in growth, fattening and tissue composition. This experiment was conducted to investigate the effects of genetic type and muscle (Longissimus dorsi (LD) vs Biceps femoris (BF)) on gene expression and transcriptional regulation at two developmental stages. Nine IB and 10 IBxDU piglets were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period). Carcass traits and LD intramuscular fat (IMF) content were measured...
2016: PloS One
https://www.readbyqxmd.com/read/27936105/serogroup-and-clonal-characterization-of-czech-invasive-neisseria-meningitidis-strains-isolated-from-1971-to-2015
#3
Zuzana Jandova, Martin Musilek, Zuzana Vackova, Jana Kozakova, Pavla Krizova
BACKGROUND: This study presents antigenic and genetic characteristics of Neisseria meningitidis strains recovered from invasive meningococcal disease (IMD) in the Czech Republic in 1971-2015. MATERIAL AND METHODS: A total of 1970 isolates from IMD, referred to the National Reference Laboratory for Meningococcal Infections in 1971-2015, were studied. All isolates were identified and characterized by conventional biochemical and serological tests. Most isolates (82...
2016: PloS One
https://www.readbyqxmd.com/read/27936082/three-molecular-markers-show-no-evidence-of-population-genetic-structure-in-the-gouldian-finch-erythrura-gouldiae
#4
Peri E Bolton, Andrea J West, Adam P A Cardilini, Jennalee A Clark, Kimberley L Maute, Sarah Legge, James Brazill-Boast, Simon C Griffith, Lee A Rollins
Assessment of genetic diversity and connectivity between regions can inform conservation managers about risk of inbreeding, potential for adaptation and where population boundaries lie. The Gouldian finch (Erythrura gouldiae) is a threatened species in northern Australia, occupying the savannah woodlands of the biogeographically complex monsoon tropics. We present the most comprehensive population genetic analysis of diversity and structure the Gouldian finch using 16 microsatellite markers, mitochondrial control region and 3,389 SNPs from genotyping-by-sequencing...
2016: PloS One
https://www.readbyqxmd.com/read/27936067/deletion-at-the-gcnt2-locus-causes-autosomal-recessive-congenital-cataracts
#5
Bushra Irum, Shahid Y Khan, Muhammad Ali, Muhammad Daud, Firoz Kabir, Bushra Rauf, Fareeha Fatima, Hira Iqbal, Arif O Khan, Saif Al Obaisi, Muhammad Asif Naeem, Idrees A Nasir, Shaheen N Khan, Tayyab Husnain, Sheikh Riazuddin, Javed Akram, Allen O Eghrari, S Amer Riazuddin
PURPOSE: The aim of this study is to identify the molecular basis of autosomal recessive congenital cataracts (arCC) in a large consanguineous pedigree. METHODS: All participating individuals underwent a detailed ophthalmic examination. Each patient's medical history, particularly of cataracts and other ocular abnormalities, was compiled from available medical records and interviews with family elders. Blood samples were donated by all participating family members and used to extract genomic DNA...
2016: PloS One
https://www.readbyqxmd.com/read/27935966/the-transcription-factor-nfatc2-regulates-%C3%AE-cell-proliferation-and-genes-associated-with-type-2-diabetes-in-mouse-and-human-islets
#6
Mark P Keller, Pradyut K Paul, Mary E Rabaglia, Donnie S Stapleton, Kathryn L Schueler, Aimee Teo Broman, Shuyun Isabella Ye, Ning Leng, Christopher J Brandon, Elias Chaibub Neto, Christopher L Plaisier, Shane P Simonett, Melkam A Kebede, Gloria M Sheynkman, Mark A Klein, Nitin S Baliga, Lloyd M Smith, Karl W Broman, Brian S Yandell, Christina Kendziorski, Alan D Attie
Human genome-wide association studies (GWAS) have shown that genetic variation at >130 gene loci is associated with type 2 diabetes (T2D). We asked if the expression of the candidate T2D-associated genes within these loci is regulated by a common locus in pancreatic islets. Using an obese F2 mouse intercross segregating for T2D, we show that the expression of ~40% of the T2D-associated genes is linked to a broad region on mouse chromosome (Chr) 2. As all but 9 of these genes are not physically located on Chr 2, linkage to Chr 2 suggests a genomic factor(s) located on Chr 2 regulates their expression in trans...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27935940/molecular-characterization-of-resistance-to-soybean-rust-phakopsora-pachyrhizi-syd-syd-in-soybean-cultivar-dt-2000-pi-635999
#7
Tri D Vuong, David R Walker, Binh T Nguyen, Tuyet T Nguyen, Hoan X Dinh, David L Hyten, Perry B Cregan, David A Sleper, Jeong D Lee, James G Shannon, Henry T Nguyen
Resistance to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd. & Syd., has been identified in many soybean germplasm accessions and is conferred by either dominant or recessive genes that have been mapped to six independent loci (Rpp1 -Rpp6), but No U.S. cultivars are resistant to SBR. The cultivar DT 2000 (PI 635999) has resistance to P. pachyrhizi isolates and field populations from the United States as well as Vietnam. A F6:7 recombinant inbred line (RIL) population derived from Williams 82 × DT 2000 was used to identify genomic regions associated with resistance to SBR in the field in Ha Noi, Vietnam, and in Quincy, Florida, in 2008...
2016: PloS One
https://www.readbyqxmd.com/read/27935899/-algorithm-for-selection-of-individual-therapy-with-clopidogrel-in-vascular-surgical-practice
#8
A I Shevela, A A Slepukhina, E M Zelenskaya, T A Seredina, G I Lifshits
For treatment of patients with diseases of lower limb arteries and prevention of cardiovascular complications in high-risk patients (those with diabetes mellitus, arterial hypertension, dyslipidemia, obesity) permanent antiplatelet therapy is indicated. A problem is variable individual sensitivity to therapeutic agents. For antiplatelet therapy in patients with atherosclerosis of lower limb arteries there has been obtained an evidence-supported base concerning efficacy of long-term administration of clopidogrel preparations, unlike patients with acute coronary syndrome, for whom there has been accumulated an evidence-confirmed base of administering clopidogrel preparations, as well as ticagrelor and prasugrel in various clinical situations...
2016: Angiologii︠a︡ i Sosudistai︠a︡ Khirurgii︠a︡, Angiology and Vascular Surgery
https://www.readbyqxmd.com/read/27935851/an-analysis-of-the-sequence-of-the-bad-gene-among-patients-with-maturity-onset-diabetes-of-the-young-mody
#9
Karolina Antosik, Piotr Gnyś, Przemysława Jarosz-Chobot, Małgorzata Myśliwiec, Agnieszka Szadkowska, Maciej Małecki, Wojciech Młynarski, Maciej Borowiec
BACKGROUND: Monogenic diabetes is a rare disease caused by single gene mutations. Maturity onset diabetes of the young (MODY) is one of the major forms of monogenic diabetes recognised in the paediatric population. To date, 13 genes have been related to MODY development. The aim of the study was to analyse the sequence of the BCL2-associated agonist of cell death (BAD) gene in patients with clinical suspicion of GCK-MODY, but who were negative for glucokinase (GCK) gene mutations. METHODS: A group of 122 diabetic patients were recruited from the "Polish Registry for Paediatric and Adolescent Diabetes - nationwide genetic screening for monogenic diabetes" project...
December 9, 2016: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/27935838/the-paralogous-histone-deacetylases-rpd3-and-rpd31-play-opposing-roles-in-regulating-the-white-opaque-switch-in-the-fungal-pathogen-candida-albicans
#10
Jing Xie, Sabrina Jenull, Michael Tscherner, Karl Kuchler
: Chromatin modifications affect gene regulation in response to environmental stimuli in numerous biological processes. For example, N-acetyl-glucosamine and CO2 induce a morphogenetic conversion between white (W) and opaque (O) cells in MTL (mating-type locus) homozygous and heterozygous ( A: /α) strains of the human fungal pathogen Candida albicans Here, we identify 8 histone-modifying enzymes playing distinct roles in the regulation of W/O switching in MTL homozygous and heterozygous strains...
November 15, 2016: MBio
https://www.readbyqxmd.com/read/27935690/an-international-inter-laboratory-digital-pcr-study-demonstrates-high-reproducibility-for-the-measurement-of-a-rare-sequence-variant
#11
Alexandra S Whale, Alison S Devonshire, George A Karlin-Neumann, Jack Regan, Leanne Javier, Simon Cowen, Ana Fernandez-Gonzalez, Gerwyn M Jones, Nicholas Redshaw, Julia Beck, Andreas W Berger, Valerie Combaret, Nina Dahl Kjersgaard, Lisa Davis, Frederic Fina, Tim Forshew, Rikke Fredslund Andersen, Silvia Galbiati, Álvaro González Hernández, Charles A Haynes, Filip Janku, Roger Lacave, Justin Lee, Vilas Mistry, Alexandra Pender, Anne Pradines, Charlotte Proudhon, Lao H Saal, Elliot Stieglitz, Bryan Ulrich, Carole A Foy, Helen Parkes, Svilen Tzonev, Jim Francis Huggett
This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate labs. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using qPCR or NGS due to the presence of competing wild type sequences and the need for calibration. Using dPCR, eighteen laboratories were able to quantify the G12D marker within 12% of each other in all samples...
December 9, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27935588/single-cell-mass-spectrometry-reveals-the-importance-of-genetic-diversity-and-plasticity-for-phenotypic-variation-in-nitrogen-limited-chlamydomonas
#12
Jasmin Krismer, Manu Tamminen, Simone Fontana, Renato Zenobi, Anita Narwani
Phenotypic variation is vital for microbial populations to survive environmental perturbations. Both genetic and non-genetic factors contribute to an organism's phenotypic variation and therefore its fitness. To investigate the correlation between genetic diversity and phenotypic variation, we applied our recently developed mass spectrometry method that allows for the simultaneous measurement of more than 25 different lipids and pigments with high throughput in the unicellular microalga Chlamydomonas reinhardtii...
December 9, 2016: ISME Journal
https://www.readbyqxmd.com/read/27935054/damaging-effects-of-ultraviolet-radiation-on-the-cornea
#13
Naomi C Delic, J Guy Lyons, Nick Di Girolamo, Gary M Halliday
The cornea sits at the anterior aspect of the eye and additionally to the skin, is highly exposed to ultraviolet radiation (UVR). The cornea blocks a significant proportion of UVB from reaching the posterior structures of the eye. However, UVA can penetrate the full thickness of the cornea, even reaching the anterior portion of the lens. Epidemiological data indicate that UVR is a contributing factor for a multitude of corneal diseases of the cornea including pterygium, photokeratitis, climatic droplet keratopathy, (CDK) and ocular surface squamous neoplasia (OSSN), although the pathogenic mechanisms of each require further elucidation...
December 9, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27935041/avrpm2-encodes-an-rnase-like-avirulence-effector-which-is-conserved-in-the-two-different-specialized-forms-of-wheat-and-rye-powdery-mildew-fungus
#14
Coraline R Praz, Salim Bourras, Fansong Zeng, Javier Sánchez-Martín, Fabrizio Menardo, Minfeng Xue, Lijun Yang, Stefan Roffler, Rainer Böni, Gerard Herren, Kaitlin E McNally, Roi Ben-David, Francis Parlange, Simone Oberhaensli, Simon Flückiger, Luisa K Schäfer, Thomas Wicker, Dazhao Yu, Beat Keller
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3(a2/f2) that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2...
December 9, 2016: New Phytologist
https://www.readbyqxmd.com/read/27935012/mutational-analysis-of-agxt-in-tunisian-population-with-primary-hyperoxaluria-type-1
#15
Saoussen M'dimegh, Asma Omezzine, Ibtihel M'barek, Amira Moussa, Sameh Mabrouk, Hayet Kaarout, Geneviéve Souche, Jalel Chemli, Sabra Aloui, Cécile Aquaviva-Bourdain, Abdellatif Achour, Saoussen Abroug, Ali Bouslama
BACKGROUND: Primary hyperoxaluria type 1 (PH1) is an autosomal recessive metabolic disorder caused by inherited mutations in the AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT). PH1 is a clinically and genetically heterogeneous disorder. The aim of our study was to analyze and characterize the mutational spectrum of PH1 in Tunisian patients. MATERIALS AND METHODS: Molecular studies of 146 Tunisian patients suspected with PH were performed by PCR/Restriction fragment length polymorphism (RFLP) to detect seven mutations described as the most common...
December 9, 2016: Annals of Human Genetics
https://www.readbyqxmd.com/read/27934695/overview-of-crispr-cas9-biology
#16
Hannah K Ratner, Timothy R Sampson, David S Weiss
Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress...
December 1, 2016: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/27934583/bacillus-cereus-induced-food-borne-outbreaks-in-france-2007-to-2014-epidemiology-and-genetic-characterisation
#17
Benjamin Glasset, Sabine Herbin, Laurent Guillier, Sabrina Cadel-Six, Marie-Léone Vignaud, Joel Grout, Sylvie Pairaud, Valérie Michel, Jacques-Antoine Hennekinne, Nalini Ramarao, Anne Brisabois
The aim of this study was to identify and characterise Bacillus cereus from a unique national collection of 564 strains associated with 140 strong-evidence food-borne outbreaks (FBOs) occurring in France during 2007 to 2014. Starchy food and vegetables were the most frequent food vehicles identified; 747 of 911 human cases occurred in institutional catering contexts. Incubation period was significantly shorter for emetic strains compared with diarrhoeal strains A sub-panel of 149 strains strictly associated to 74 FBOs and selected on Coliphage M13-PCR pattern, was studied for detection of the genes encoding cereulide, diarrhoeic toxins (Nhe, Hbl, CytK1 and CytK2) and haemolysin (HlyII), as well as panC phylogenetic classification...
December 1, 2016: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/27933932/mechanism-of-the-pseudoirreversible-binding-of-amantadine-to-the-m2-proton-channel
#18
Salomé Llabrés, Jordi Juárez-Jiménez, Matteo Masetti, Rosana Leiva, Santiago Vázquez, Sabrina Gazzarrini, Anna Moroni, Andrea Cavalli, F Javier Luque
The M2 proton channel of influenza A virus is an integral membrane protein involved in the acidification of the viral interior, a step necessary for the release of the viral genetic material and replication of new virions. The aim of this study is to explore the mechanism of drug (un)binding to the M2 channel in order to gain insight into the structural and energetic features relevant for the development of novel inhibitors. To this end, we have investigated the binding of amantadine (Amt) to the wild type (wt) M2 channel and its V27A variant using multiple independent molecular dynamics simulations, exploratory conventional metadynamics, and multiple-walkers well-tempered metadynamics calculations...
November 30, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27933721/shared-molecular-networks-in-orofacial-and-neural-tube-development
#19
Youssef A Kousa, Tamer A Mansour, Haitham Seada, Samaneh Matoo, Brian C Schutte
BACKGROUND: Single genetic variants can affect multiple tissues during development. Thus it is possible that disruption of shared gene regulatory networks might underlie syndromic presentations. In this study, we explore this idea through examination of two critical developmental programs that control orofacial and neural tube development and identify shared regulatory factors and networks. Identification of these networks has the potential to yield additional candidate genes for poorly understood developmental disorders and assist in modeling and perhaps managing risk factors to prevent morbidly and mortality...
December 9, 2016: Birth Defects Research. Part A, Clinical and Molecular Teratology
https://www.readbyqxmd.com/read/27933683/genetics-and-the-conservation-of-natural-populations-allozymes-to-genomes
#20
Fred W Allendorf
I consider how the study of genetic variation has influenced efforts to conserve natural populations over the last 50 years. Studies with allozymes in the 1970s provided the first estimates of the amount of genetic variation within and between natural populations at multiple loci. These early studies played an important role in developing plans to conserve species. The description of genetic variation in mitochondrial DNA in the early 1980s laid the foundation for the field of phylogeography, which provided a deeper look in time of the relationships and connectivity among populations...
December 9, 2016: Molecular Ecology
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