keyword
MENU ▼
Read by QxMD icon Read
search

Genome mining

keyword
https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#1
Bin Bai, Le Wang, Ying Jun Zhang, May Lee, Rahmadsyah Rahmadsyah, Yuzer Alfiko, Bao Qing Ye, Sigit Purwantomo, Antonius Suwanto, Nam-Hai Chua, Gen Hua Yue
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29324691/physiological-and-comparative-genomic-analysis-of-arthrobacter-sp-srs-w-1-2016-provides-insights-on-niche-adaptation-for-survival-in-uraniferous-soils
#2
Ashvini Chauhan, Ashish Pathak, Rajneesh Jaswal, Bobby Edwards Iii, Demario Chappell, Christopher Ball, Reyna Garcia-Sillas, Paul Stothard, John Seaman
Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29321918/reproductive-management-in-dairy-cows-the-future
#3
REVIEW
Mark A Crowe, Miel Hostens, Geert Opsomer
Background: Drivers of change in dairy herd health management include the significant increase in herd/farm size, quota removal (within Europe) and the increase in technologies to aid in dairy cow reproductive management. Main body: There are a number of key areas for improving fertility management these include: i) handling of substantial volumes of data, ii) genetic selection (including improved phenotypes for use in breeding programmes), iii) nutritional management (including transition cow management), iv) control of infectious disease, v) reproductive management (and automated systems to improve reproductive management), vi) ovulation / oestrous synchronisation, vii) rapid diagnostics of reproductive status, and viii) management of male fertility...
2018: Irish Veterinary Journal
https://www.readbyqxmd.com/read/29321052/asgdb-a-specialised-genomic-resource-for-interpreting-anopheles-sinensis-insecticide%C3%A2-resistance
#4
Dan Zhou, Yang Xu, Cheng Zhang, Meng-Xue Hu, Yun Huang, Yan Sun, Lei Ma, Bo Shen, Chang-Liang Zhu
BACKGROUND: Anopheles sinensis is an important malaria vector in Southeast Asia. The widespread emergence of insecticide resistance in this mosquito species poses a serious threat to the efficacy of malaria control measures, particularly in China. Recently, the whole-genome sequencing and de novo assembly of An. sinensis (China strain) has been finished. A series of insecticide-resistant studies in An. sinensis have also been reported. There is a growing need to integrate these valuable data to provide a comprehensive database for further studies on insecticide-resistant management of An...
January 10, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29320403/bacillibactin-and-bacillomycin-analogues-with-cytotoxicities-against-human-cancer-cell-lines-from-marine-bacillus-sp-pku-ma00093-and-pku-ma00092
#5
Mengjie Zhou, Fawang Liu, Xiaoyan Yang, Jing Jin, Xin Dong, Ke-Wu Zeng, Dong Liu, Yingtao Zhang, Ming Ma, Donghui Yang
Nonribosomal peptides from marine Bacillus strains have received considerable attention for their complex structures and potent bioactivities. In this study, we carried out PCR-based genome mining for potential nonribosomal peptides producers from our marine bacterial library. Twenty-one "positive" strains were screened out from 180 marine bacterial strains, and subsequent small-scale fermentation, HPLC and phylogenetic analysis afforded Bacillus sp. PKU-MA00092 and PKU-MA00093 as two candidates for large-scale fermentation and isolation...
January 10, 2018: Marine Drugs
https://www.readbyqxmd.com/read/29317492/a-protein-interaction-network-centered-on-leucine-rich-repeats-and-immunoglobulin-like-domains-1-lrig1-regulates-growth-factor-receptors
#6
Mahmood Faraz, Carl Herdenberg, Camilla Holmlund, Roger Henriksson, Håkan Hedman
Leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) is a tumor suppressor and a negative regulator of several receptor tyrosine kinases (RTKs). The molecular mechanisms by which LRIG1 mediates its tumor suppressor effects and regulates RTKs remain incompletely understood. Here, we performed a yeast two-hybrid screen to identify novel LRIG1-interacting proteins and mined data from the BioPlex (biophysical interactions of ORFeome-based complexes) protein interaction data repository. The putative LRIG1 interactors identified in the screen were functionally evaluated using a triple co-transfection system in which HEK293 cells were co-transfected with platelet-derived growth factor receptor alpha (PDGFRA), LRIG1, and shRNAs against the identified LRIG1 interactors...
January 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29305694/pervasiveness-of-uvc254-resistant-geobacillus-strains-in-extreme-environments
#7
Courtney Carlson, Nitin K Singh, Mohit Bibra, Rajesh K Sani, Kasthuri Venkateswaran
We have characterized a broad collection of extremophilic bacterial isolates from a deep subsurface mine, compost dumping sites, and several hot spring ecosystems. Spore-forming strains isolated from these environments comprised both obligate thermophiles/thermotolerant species (growing at > 55 °C; 240 strains) and mesophiles (growing at 15 to 40 °C; 12 strains). An overwhelming abundance of Geobacillus (81.3%) and Bacillus (18.3%) species was observed among the tested isolates. 16S rRNA sequence analysis documented the presence of 24 species among these isolates, but the 16S rRNA gene was shown to possess insufficient resolution to reliably discern Geobacillus phylogeny...
January 5, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29304277/photosynthetic-production-of-sunscreen-shinorine-using-an-engineered-cyanobacterium
#8
Guang Yang, Monica A Cozad, Destin A Holland, Yi Zhang, Hendrik Luesch, Yousong Ding
Mycosporine-like amino acids (MAAs) are secondary metabolites of a variety of marine organisms including cyanobacteria and macroalgae. These compounds have strong ultraviolet (UV) absorption maxima between 310 and 362 nm and are biological sunscreens for counteracting the damaging effects of UV radiation in nature. The common MAA shinorine has been used as one key active ingredient of environmentally friendly sunscreen creams. Commercially used shinorine is isolated from one red algae that is generally harvested from the wild...
January 5, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29301494/inducement-and-identification-of-chromosome-introgression-and-translocation-of-gossypium-australe-on-gossypium-hirsutum
#9
Yingying Wang, Shouli Feng, Sai Li, Dong Tang, Yu Chen, Yu Chen, Baoliang Zhou
BACKGROUND: We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G2G2 genome) into the most cultivated cotton, G. hirsutum (AADD). RESULTS: In the present report, the pollen from a pentaploid (2n = AADDG2) of G. hirsutum-G. australe was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of G...
January 4, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29301019/mining-of-the-uncharacterized-cytochrome-p450-genes-involved-in-alkaloid-biosynthesis-in-california-poppy-using-a-draft-genome-sequence
#10
Kentaro Hori, Yasuyuki Yamada, Purwanto Ratmoyo, Yohei Minakuchi, Atsushi Toyoda, Hideki Hirakawa, Fumihiko Sato
Land plants produce specialized low-molecular-weight metabolites to adapt to various environmental stressors, such as ultraviolet radiation, pathogen infection, wounding, and animal feeding damage. Due to the large variety of stresses, plants produce various chemicals, particularly plant species-specific alkaloids, through specialized biosynthetic pathways. In this study, using a draft genome sequence and querying known biosynthetic cytochrome P450 (P450) enzyme-encoding genes, we characterized the P450 genes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in California poppy (Eschscholzia californica), as P450s are key enzymes involved in the diversification of specialized metabolism...
December 29, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29297358/stable-solution-to-l-2-1-based-robust-inductive-matrix-completion-and-its-application-in-linking-long-noncoding-rnas-to-human-diseases
#11
Ashis Kumer Biswas, Dongchul Kim, Mingon Kang, Chris Ding, Jean X Gao
BACKGROUNDS: A large number of long intergenic non-coding RNAs (lincRNAs) are linked to a broad spectrum of human diseases. The disease association with many other lincRNAs still remain as puzzle. Validation of such links between the two entities through biological experiments are expensive. However, a plethora lincRNA-data are available now, thanks to the High Throughput Sequencing (HTS) platforms, Genome Wide Association Studies (GWAS), etc, which opens the opportunity for cutting-edge machine learning and data mining approaches to extract meaningful relationships among lincRNAs and diseases...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29295711/physical-mapping-and-candidate-gene-prediction-of-fertility-restorer-gene-of-cytoplasmic-male-sterility-in-cotton
#12
Cunpeng Zhao, Guiyuan Zhao, Zhao Geng, Zhaoxiao Wang, Kaihui Wang, Suen Liu, Hanshuang Zhang, Baosheng Guo, Junyi Geng
BACKGROUND: Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton...
January 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29295704/acyl-coa-binding-protein-family-members-in-laticifers-are-possibly-involved-in-lipid-and-latex-metabolism-of-hevea-brasiliensis-the-para-rubber-tree
#13
Zhiyi Nie, Yihang Wang, Chuntai Wu, Yu Li, Guijuan Kang, Huaide Qin, Rizhong Zeng
BACKGROUND: Acyl-CoA-binding proteins (ACBPs) are mainly involved in acyl-CoA ester binding and trafficking in eukaryotic cells, and their various functions have been characterized in model plants, such as Arabidopsis thaliana (A. thaliana), Oryza sativa (rice), and other plant species. In the present study, genome-wide mining and expression analysis of ACBP genes was performed on Hevea brasiliensis (the para rubber tree), the most important latex-producing crop in the world. RESULTS: Six members of the H...
January 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29288438/synthetic-biology-genome-mining-and-combinatorial-biosynthesis-of-nrps-derived-antibiotics-a-perspective
#14
Richard H Baltz
Combinatorial biosynthesis of novel secondary metabolites derived from nonribosomal peptide synthetases (NRPSs) has been in slow development for about a quarter of a century. Progress has been hampered by the complexity of the giant multimodular multienzymes. More recently, advances have been made on understanding the chemical and structural biology of these complex megaenzymes, and on learning the design rules for engineering functional hybrid enzymes. In this perspective, I address what has been learned about successful engineering of complex lipopeptides related to daptomycin, and discuss how synthetic biology and microbial genome mining can converge to broaden the scope and enhance the speed and robustness of combinatorial biosynthesis of NRPS-derived natural products for drug discovery...
December 29, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29288427/comparative-wgbs-identifies-genes-that-influence-non-ripe-phenotype-in-tomato-epimutant-colourless-non-ripening
#15
Weiwei Chen, Zhiming Yu, Junhua Kong, Hui Wang, Yichen Li, Mei Zhao, Xiaohong Wang, Qianqian Zheng, Nongnong Shi, Pengcheng Zhang, Silin Zhong, Paul Hunter, Mahmut Tör, Yiguo Hong
Whole-genome bisulfite sequencing (WGBS) allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals. This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation. However, naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define. In tomato, fruit development and ripening are a complex process that involves epigenetic control...
December 27, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29288361/genome-sequence-and-comparative-analysis-of-jiangella-alba-yim-61503t-isolated-from-a-medicinal-plant-maytenus-austroyunnanensis
#16
Jian-Yu Jiao, Nimaichand Salam, Lan Liu, Manik Prabhu Narsing Rao, Xiao-Tong Zhang, Bao-Zhu Fang, Ming-Xian Han, Zi-Tong Zhang, Jing Chen, Jiao Zhao, Yu Zhou, Dalal Hussien M Alkhalifah, Qing Liu, Min Xiao, Hans-Peter Klenk, Wen-Jun Li
A draft genome sequence of Jiangella alba YIM 61503T revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503T with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503T and J. muralis DSM 45357T, while indicating a high divergence between J. gansuensis YIM 002T and other Jiangella species...
December 29, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29286517/distribution-of-rs2124594-genotypes-in-chronic-lymphocytic-leukemia-patients-depending-on-radiation-anamnesis
#17
N I Bilous, I V Abramenko, A A Chumak, I S Diagil, Z V Martina
OBJECTIVE: to test the method of polymerase chain reaction with following fragments' length restriction to deter mine the rs2124594 polymorphism and to study its contribution in the development of chronic lymphocytic leukemia (CLL) in the post Chornobyl period. METHODS: Genotypes of rs2124594 were determined in 109 patients with CLL of B cell origin including 53 patients irradiated due to the Chornobyl NPP accident. Genotypes distribution among CLL patients was compared with healthy persons of European origin (the 1000 Genomes Project data set was used as a reference)...
December 2017: Problemy Radiat︠s︡iĭnoï Medyt︠s︡yny Ta Radiobiolohiï
https://www.readbyqxmd.com/read/29283433/congems-condensed-gene-co-expression-module-discovery-through-rule-based-clustering-and-its-application-to-carcinogenesis
#18
Saurav Mallik, Zhongming Zhao
For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores...
December 28, 2017: Genes
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#19
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29273003/an-integrated-and-comparative-approach-towards-identification-characterization-and-functional-annotation-of-candidate-genes-for-drought-tolerance-in-sorghum-sorghum-bicolor-l-moench
#20
Adugna Abdi Woldesemayat, Peter Van Heusden, Bongani K Ndimba, Alan Christoffels
BACKGROUND: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait...
December 22, 2017: BMC Genetics
keyword
keyword
78757
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"