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Gene Mapping

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https://www.readbyqxmd.com/read/28938400/il-1%C3%AE-inhibits-connexin-43-and-disrupts-decidualization-of-human-endometrial-stromal-cells-through-erk1-2-and-p38-map-kinase
#1
Jie Yu, Sarah L Berga, Wei Zou, D Grace Yook, Joshua C Pan, Aurora Arroyo Andrade, Lijuan Zhao, Neil Sidell, Indrani C Bagchi, Milan K Bagchi, Robert N Taylor
Inflammation can interfere with endometrial receptivity. We examined how IL-1β affects expression of the uterine gap junction protein, Cx43, which is known to be critical for embryonic implantation. We used an in vitro model of human endometrial stromal cells (ESC), Western blotting and a combination of validated, selective kinase inhibitors to evaluate five canonical IL-1β signaling pathways. Cx43 and two other markers of ESC differentiation (prolactin and VEGF) were inhibited predominantly via IL-1β-activated ERK1/2 and p38 MAP kinase cascades...
September 11, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938018/genome-wide-identification-of-bacterial-plant-colonization-genes
#2
Benjamin J Cole, Meghan E Feltcher, Robert J Waters, Kelly M Wetmore, Tatiana S Mucyn, Elizabeth M Ryan, Gaoyan Wang, Sabah Ul-Hasan, Meredith McDonald, Yasuo Yoshikuni, Rex R Malmstrom, Adam M Deutschbauer, Jeffery L Dangl, Axel Visel
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28938012/f-map-a-bayesian-approach-to-infer-the-gene-regulatory-network-using-external-hints
#3
Maryam Shahdoust, Hamid Pezeshk, Hossein Mahjub, Mehdi Sadeghi
The Common topological features of related species gene regulatory networks suggest reconstruction of the network of one species by using the further information from gene expressions profile of related species. We present an algorithm to reconstruct the gene regulatory network named; F-MAP, which applies the knowledge about gene interactions from related species. Our algorithm sets a Bayesian framework to estimate the precision matrix of one species microarray gene expressions dataset to infer the Gaussian Graphical model of the network...
2017: PloS One
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#4
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
September 22, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28936945/sources-of-fungal-genetic-variation-and-associating-it-with-phenotypic-diversity
#5
John W Taylor, Sara Branco, Cheng Gao, Chris Hann-Soden, Liliam Montoya, Iman Sylvain, Pierre Gladieux
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability...
September 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28936718/identification-of-candidate-genes-for-generalized-tonic-clonic-seizures-in-noda-epileptic-rat
#6
Takashi Kuramoto, Birger Voigt, Satoshi Nakanishi, Kazuhiro Kitada, Tadashi Nakamura, Kaori Wakamatsu, Minako Yoshihara, Mikita Suyama, Risa Uemura, Miyuu Tanaka, Mitsuru Kuwamura, Saki Shimizu, Yukihiro Ohno, Masashi Sasa, Tadao Serikawa
The Noda epileptic rat (NER) exhibits generalized tonic-clonic seizures (GTCS). A genetic linkage analysis identified two GTCS-associated loci, Ner1 on Chr 1 and Ner3 on Chr 5. The wild-type Ner1 and Ner3 alleles suppressed GTCS when combined in double-locus congenic lines, but not when present in single-locus congenic lines. Global expression analysis revealed that cholecystokinin B receptor (Cckbr) and suppressor of tumorigenicity 5 (St5), which map within Ner1, and PHD finger protein 24 (Phf24), which maps within Ner3, were significantly downregulated in NER...
September 21, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28936424/acid-stress-response-mechanisms-of-group-b-streptococci
#7
REVIEW
Sarah Shabayek, Barbara Spellerberg
Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple different host niches. The pathophysiology of this bacterium reveals an outstanding ability to withstand varying pH fluctuations of the surrounding environments inside the human host. GBS host pathogen interations include colonization of the acidic vaginal mucosa, invasion of the neutral human blood or amniotic fluid, breaching of the blood brain barrier as well as survival within the acidic phagolysosomal compartment of macrophages...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28936222/the-soybean-rfg1-gene-restricts-nodulation-by-sinorhizobium-fredii-usda193
#8
Yinglun Fan, Jinge Liu, Shanhua Lyu, Qi Wang, Shengming Yang, Hongyan Zhu
Sinorhizobium fredii is a fast-growing rhizobial species that can establish a nitrogen-fixing symbiosis with a wide range of legume species including soybeans (Glycine max). In soybeans, this interaction shows a high level of specificity such that particular S. fredii strains nodulate only a limited set of plant genotypes. Here we report the identification of a dominant gene in soybeans that restricts nodulation with S. fredii USDA193. Genetic mapping in an F2 population revealed co-segregation of the underlying locus with the previously cloned Rfg1 gene...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28936219/a-high-density-genetic-map-derived-from-rad-sequencing-and-its-application-in-qtl-analysis-of-yield-related-traits-in-vigna-unguiculata
#9
Lei Pan, Nian Wang, Zhihua Wu, Rui Guo, Xiaolu Yu, Yu Zheng, Qiuju Xia, Songtao Gui, Chanyou Chen
Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28935754/pervasive-genome-wide-transcription-in-the-organelle-genomes-of-diverse-plastid-bearing-protists
#10
Matheus Sanitá Lima, David Roy Smith
Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing (NGS) technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in non-model species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts...
September 21, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28935715/identification-of-the-centromeres-of-leishmania-major-revealing-the-hidden-pieces
#11
Maria-Rosa Garcia-Silva, Lauriane Sollelis, Cameron Ross MacPherson, Slavica Stanojcic, Nada Kuk, Lucien Crobu, Frédéric Bringaud, Patrick Bastien, Michel Pagès, Artur Scherf, Yvon Sterkers
Leishmania affects millions of people worldwide. Its genome undergoes constitutive mosaic aneuploidy, a type of genomic plasticity that may serve as an adaptive strategy to survive distinct host environments. We previously found high rates of asymmetric chromosome allotments during mitosis that lead to the generation of such ploidy. However, the underlying molecular events remain elusive. Centromeres and kinetochores most likely play a key role in this process, yet their identification has failed using classical methods...
September 21, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#12
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28934385/hearing-loss-without-overt-metabolic-acidosis-in-atp6v1b1-deficient-mrl-mice-a-new-genetic-model-for-non-syndromic-deafness-with-enlarged-vestibular-aqueducts
#13
Cong Tian, Leona H Gagnon, Chantal Longo-Guess, Ron Korstanje, Susan M Sheehan, Kevin K Ohlemiller, Angela D Schrader, Jaclynn M Lett, Kenneth R Johnson
Mutations of the human ATP6V1B1 gene cause distal renal tubular acidosis (dRTA; OMIM #267300) often associated with sensorineural hearing impairment; however, mice with a knockout mutation of Atp6v1b1 were reported to exhibit a compensated acidosis and normal hearing. We discovered a new spontaneous mutation (vortex, symbol vtx) of Atp6v1b1 in an MRL/MpJ (MRL) colony of mice. In contrast to the reported phenotype of the knockout mouse, which was developed on a primarily C57BL/6 (B6) strain background, MRL-Atp6v1b1vtx/vtx mutant mice exhibit profound hearing impairment, which is associated with enlarged endolymphatic compartments of the inner ear...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#14
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28933027/learning-directed-acyclic-graphs-from-large-scale-genomics-data
#15
Fabio Nikolay, Marius Pesavento, George Kritikos, Nassos Typas
In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactions-Detector (GENIE) to identify the complex biological dependencies among genes and to compute the DAG topology that matches the DK measurements best...
September 20, 2017: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28932231/addition-of-aegilops-u-and-m-chromosomes-affects-protein-and-dietary-fiber-content-of-wholemeal-wheat-flour
#16
Marianna Rakszegi, István Molnár, Alison Lovegrove, Éva Darkó, András Farkas, László Láng, Zoltán Bedő, Jaroslav Doležel, Márta Molnár-Láng, Peter Shewry
Cereal grain fiber is an important health-promoting component in the human diet. One option to improve dietary fiber content and composition in wheat is to introduce genes from its wild relatives Aegilops biuncialis and Aegilops geniculata. This study showed that the addition of chromosomes 2U(g), 4U(g), 5U(g), 7U(g), 2M(g), 5M(g), and 7M(g) of Ae. geniculata and 3U(b), 2M(b), 3M(b), and 7M(b) of Ae. biuncialis into bread wheat increased the seed protein content. Chromosomes 1U(g) and 1M(g) increased the proportion of polymeric glutenin proteins, while the addition of chromosomes 1U(b) and 6U(b) led to its decrease...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28932230/high-density-linkage-map-construction-and-qtl-detection-for-three-silique-related-traits-in-orychophragmus-violaceus-derived-brassica-napus-population
#17
Yi Yang, Yusen Shen, Shunda Li, Xianhong Ge, Zaiyun Li
Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28931804/cross-ethnic-meta-analysis-identifies-association-of-the-gpx3-tnip1-locus-with-amyotrophic-lateral-sclerosis
#18
Beben Benyamin, Ji He, Qiongyi Zhao, Jacob Gratten, Fleur Garton, Paul J Leo, Zhijun Liu, Marie Mangelsdorf, Ammar Al-Chalabi, Lisa Anderson, Timothy J Butler, Lu Chen, Xiang-Ding Chen, Katie Cremin, Hong-Weng Deng, Matthew Devine, Janette Edson, Jennifer A Fifita, Sarah Furlong, Ying-Ying Han, Jessica Harris, Anjali K Henders, Rosalind L Jeffree, Zi-Bing Jin, Zhongshan Li, Ting Li, Mengmeng Li, Yong Lin, Xiaolu Liu, Mhairi Marshall, Emily P McCann, Bryan J Mowry, Shyuan T Ngo, Roger Pamphlett, Shu Ran, David C Reutens, Dominic B Rowe, Perminder Sachdev, Sonia Shah, Sharon Song, Li-Jun Tan, Lu Tang, Leonard H van den Berg, Wouter van Rheenen, Jan H Veldink, Robyn H Wallace, Lawrie Wheeler, Kelly L Williams, Jinyu Wu, Xin Wu, Jian Yang, Weihua Yue, Zong-Hong Zhang, Dai Zhang, Peter G Noakes, Ian P Blair, Robert D Henderson, Pamela A McCombe, Peter M Visscher, Huji Xu, Perry F Bartlett, Matthew A Brown, Naomi R Wray, Dongsheng Fan
Cross-ethnic genetic studies can leverage power from differences in disease epidemiology and population-specific genetic architecture. In particular, the differences in linkage disequilibrium and allele frequency patterns across ethnic groups may increase gene-mapping resolution. Here we use cross-ethnic genetic data in sporadic amyotrophic lateral sclerosis (ALS), an adult-onset, rapidly progressing neurodegenerative disease. We report analyses of novel genome-wide association study data of 1,234 ALS cases and 2,850 controls...
September 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28931651/region-specific-rna-m-6-a-methylation-represents-a-new-layer-of-control-in-the-gene-regulatory-network-in-the-mouse-brain
#19
Mengqi Chang, Hongyi Lv, Weilong Zhang, Chunhui Ma, Xue He, Shunli Zhao, Zhi-Wei Zhang, Yi-Xin Zeng, Shuhui Song, Yamei Niu, Wei-Min Tong
N(6)-methyladenosine (m(6)A) is the most abundant epitranscriptomic mark found on mRNA and has important roles in various physiological processes. Despite the relatively high m(6)A levels in the brain, its potential functions in the brain remain largely unexplored. We performed a transcriptome-wide methylation analysis using the mouse brain to depict its region-specific methylation profile. RNA methylation levels in mouse cerebellum are generally higher than those in the cerebral cortex. Heterogeneity of RNA methylation exists across different brain regions and different types of neural cells including the mRNAs to be methylated, their methylation levels and methylation site selection...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28931644/ufm1-founder-mutation-in-the-roma-population-causes-recessive-variant-of-h-abc
#20
Eline M C Hamilton, Enrico Bertini, Luba Kalaydjieva, Bharti Morar, Dana Dojčáková, Judy Liu, Adeline Vanderver, Julian Curiel, Claudia M Persoon, Daria Diodato, Lorenzo Pinelli, Nathalie L van der Meij, Barbara Plecko, Susan Blaser, Nicole I Wolf, Quinten Waisfisz, Truus E M Abbink, Marjo S van der Knaap
OBJECTIVE: To identify the gene defect in patients with hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC) who are negative for TUBB4A mutations. METHODS: We performed homozygosity mapping and whole exome sequencing (WES) to detect the disease-causing variant. We used a Taqman assay for population screening. We developed a luciferase reporter construct to investigate the effect of the promoter mutation on expression. RESULTS: Sixteen patients from 14 families from different countries fulfilling the MRI criteria for H-ABC exhibited a similar, severe clinical phenotype, including lack of development and a severe epileptic encephalopathy...
September 20, 2017: Neurology
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