keyword
MENU ▼
Read by QxMD icon Read
search

Genome mining

keyword
https://www.readbyqxmd.com/read/28729898/draft-genome-sequences-of-strains-salinicola-socius-smb35-t-salinicola-sp-mh3r3-1-and-chromohalobacter-sp-smb17-from-the-verkhnekamsk-potash-mining-region-of-russia
#1
Björn E Olsson, Ekaterina S Korsakova, Lyudmila N Anan'ina, Anna A Pyankova, Olga V Mavrodi, Elena G Plotnikova, Dmitri V Mavrodi
Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35(T), Salinicola sp. MH3R3-1 and Chromohalobacter sp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28728936/cell-free-pipeline-for-discovery-of-thermotolerant-xylanases-and-endo-1-4-%C3%AE-glucanases
#2
Dejan Gagoski, Zhenyu Shi, Lars Keld Nielsen, Claudia E Vickers, Stephen Mahler, Robert Speight, Wayne A Johnston, Kirill Alexandrov
The rapid expansion in the number of sequenced genomes and metagenomes provides an exceptional resource for mining of the enzymes with biotechnologically relevant properties. However, the majority of protein production and analysis methods are not sufficiently cost-efficient and scalable to experimentally verify the results of computational genomic mining. Here, we present a pipeline based on Leishmania tarentolae cell-free system that was used to characterise 30 putative thermostable endo-1,4-β-glucanases and xylanases identified in public genomic databases...
July 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28724888/crosscheck-an-open-source-web-tool-for-high-throughput-screen-data-analysis
#3
Jamil Najafov, Ayaz Najafov
Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724061/multi-locus-mixed-model-analysis-of-stem-rust-resistance-in-winter-wheat
#4
Paul D Mihalyov, Virginia A Nichols, Peter Bulli, Matthew N Rouse, Michael O Pumphrey
Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f. sp. is a devastating disease that threatens wheat ( L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1411 hexaploid winter wheat accessions genotyped with 5390 single nucleotide polymorphism markers...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723273/the-repair-project-examining-the-biological-impacts-of-sub-background-radiation-exposure-within-snolab-a-deep-underground-laboratory
#5
Christopher Thome, Sujeenthar Tharmalingam, Jake Pirkkanen, Andrew Zarnke, Taylor Laframboise, Douglas R Boreham
Considerable attention has been given to understanding the biological effects of low-dose ionizing radiation exposure at levels slightly above background. However, relatively few studies have been performed to examine the inverse, where natural background radiation is removed. The limited available data suggest that organisms exposed to sub-background radiation environments undergo reduced growth and an impaired capacity to repair genetic damage. Shielding from background radiation is inherently difficult due to high-energy cosmic radiation...
July 19, 2017: Radiation Research
https://www.readbyqxmd.com/read/28720060/ppfia1-is-upregulated-in-liver-metastasis-of-breast-cancer-and-is-a-potential-poor-prognostic-indicator-of-metastatic-relapse
#6
Jing Yang, Ning-Ni Wu, De-Jia Huang, Yao-Chang Luo, Jun-Zhen Huang, Hai-Yuan He, Hai-Lin Lu, Wen-Ling Song
Although the oncogenic role of PPFIA1 (liprin-α1) in breast cancer has been reported, whether its dysregulation is associated with metastasis risk or survival outcomes in breast cancer patients is not clear. Our primary data showed that PPFIA1 expression was significantly higher in liver metastatic breast tumors than in the primary tumors. Then, we tried to pool previous annotated genomic data to assess the prognostic value of PPFIA1 in distant metastasis-free survival, the risk of metastatic relapse, and metastatic relapse-free survival in breast cancer patients by data mining in two large databases, Kaplan-Meier plotter and bc-GenExMiner 4...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28718375/emp3-is-induced-by-twist1-2-and-regulates-epithelial-to-mesenchymal-transition-of-gastric-cancer-cells
#7
Ming Han, Wanpeng Xu
In this study, we aimed to explore new downstream effectors of TWIST1/2 in inducing epithelial-to-mesenchymal transition in gastric cancer. Bioinformatic data mining was performed using data in The Cancer Genome Atlas Stomach Adenocarcinoma. Survival curves were generated using Kaplan-Meier plotter. Gastric cancer cell lines (AGS and SGC-7901) were used as in vitro cell model to investigate the regulative effect of TWIST1/2 on epithelial membrane protein 3 expression and the progression of epithelial-to-mesenchymal transition...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28716113/whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#8
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized...
July 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28715095/a-self-sacrificing-n-methyltransferase-is-the-precursor-of-the-fungal-natural-product-omphalotin
#9
Sascha Ramm, Bartlomiej Krawczyk, Agnes Mühlenweg, Annette Poch, Eva Mösker, Roderich D Süssmuth
Research on ribosomally synthesized and posttranslationally modified peptides (RiPPs) has led to an increasing understanding of biosynthetic mechanisms, mostly drawn from bacterial examples. In contrast, reports on RiPPs from fungal producers, apart from the amanitins and phalloidins, are still scarce. The fungal cyclopeptide omphalotin A carries multiple N-methylations on the peptide backbone, a modification previously known only from nonribosomal peptides. Mining the genome of the omphalotin-producing fungus for a precursor peptide led to the identification of two biosynthesis genes, one encoding a methyltransferase OphMA that catalyzes the automethylation of its C-terminus, which is then released and cyclized by the protease OphP...
July 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28707409/chilling-responsive-demeter-like-dna-demethylase-mediates-in-poplar-bud-break
#10
Daniel Conde, Anne-Laure Le Gac, Mariano Perales, Christopher Dervinis, Matias Kirst, Stéphane Maury, Pablo González-Melendi, Isabel Allona
Annual dormancy-growth cycle is a developmental and physiological process essential for the survival of deciduous trees in temperate and boreal forests. Seasonal control of shoot growth in woody perennials requires specific genetic programs responding to environmental signals. The environmental-controlled mechanisms that regulate the shift between winter dormancy and the growth promoting genetic programs are still unknown. Here, we show that dynamics in genomic DNA (gDNA) methylation levels are involved in the regulation of dormancy-growth cycle in poplar...
July 13, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28706523/identification-of-optimal-reference-genes-for-normalization-of-qpcr-analysis-during-pepper-fruit-development
#11
Yuan Cheng, Xin Pang, Hongjian Wan, Golam J Ahammed, Jiahong Yu, Zhuping Yao, Meiying Ruan, Qingjing Ye, Zhimiao Li, Rongqing Wang, Yuejian Yang, Guozhi Zhou
Due to its high sensitivity and reproducibility, quantitative real-time PCR (qPCR) is practiced as a useful research tool for targeted gene expression analysis. For qPCR operations, the normalization with suitable reference genes (RGs) is a crucial step that eventually determines the reliability of the obtained results. Although pepper is considered an ideal model plant for the study of non-climacteric fruit development, at present no specific RG have been developed or validated for the qPCR analyses of pepper fruit...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28705974/draft-genome-sequence-of-klebsiella-michiganensis-3t412c-harboring-an-arsenic-resistance-genomic-island-isolated-from-mine-tailings-in-peru
#12
Robert Ccorahua-Santo, Miguel Cervantes, Yerson Duran, Mac Aguirre, Claudia Marin, Pablo Ramírez
An arsenic resistance genomic island in the bacterium Klebsiella michiganensis 3T412C was isolated from mine tailings from Peru. This genomic island confers adaptation to extreme environments with high concentrations of arsenic. Isolate 3T412C contained a complete set of genes involved in resistance to arsenic. This operon is surrounded by putative genes for resistance to other heavy metals.
July 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28705677/hyicin-4244-the-first-sactibiotic-described-in-staphylococci-exhibits-an-anti-staphylococcal-biofilm-activity
#13
Andreza Freitas de Souza Duarte, Hilana Ceotto-Vigoder, Emile Santos Barrias, Thaïs Cristina Baeta Soares Souto-Padrón, Ingolf Figved Nes, Maria do Carmo de Freire Bastos
Hyicin 4244 is a small antimicrobial peptide with a broad-spectrum of activity found in the culture supernatant of Staphylococcus hyicus 4244, whose genome was then sequenced. The bacteriocin gene cluster (hyiSABCDEFG) was mined from its single chromosome and exhibited a genetic organization similar to that of subtilosin A. All genes involved in hyicin 4244 biosynthesis proved to be transcribed and encode proteins that share at least 42 % similarity to proteins encoded by the subtilosin A gene cluster. Due to its resemblance to subtilosin A and the presence of three thioether bonds in its structure, hyicin 4244 is assumed to be a 35 amino acid circular sactibiotic, the first to be described in staphylococci...
July 10, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28702355/whole-genome-sequencing-and-annotation-of-halophilic-salinicoccus-sp-bab-3246-isolated-from-the-coastal-region-of-gujarat
#14
Vishal Mevada, Shradhdha Patel, Jignesh Pandya, Himani Joshi, Rajesh Patel
Salinicoccus sp. BAB 3246 is a halophilic bacterium isolated from a marine water sample collected from the coastal region of Gujarat, India, from a surface water stream. Based on 16sRNA sequencing, the organism was identified as Salinicoccus sp. BAB 3246 (Genebank ID: KF889285). The present work was performed to determine the whole genome sequence of the organism using Ion Torrent PGM platform followed by assembly using the CLC genomics workbench and genome annotation using RAST, BASys and MaGe. The complete genome sequence was 713,204 bp identified by with second largest size for Salinicoccus sp...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28700235/quantitative-crassphage-pcr-assays-for-human-fecal-pollution-measurement
#15
Elyse Stachler, Catherine Kelty, Mano Sivaganesan, Xiang Li, Kyle Bibby, Orin C Shanks
Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal indicator bacteria are used; however, they cannot distinguish human fecal waste from other animal pollution sources. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome...
July 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28698739/complete-genome-sequence-of-actinomadura-parvosata-subsp-kistnae-a-rich-source-of-novel-natural-product-bio-chemistry
#16
Kalina Kusserow, Tobias A M Gulder
The soil dwelling actinomycete strain Actinomadura parvosata subsp. kistnae is the producer of the antiviral antibiotics kistamicin A and B. Genome sequencing and bioinformatic analysis revealed the presence of the kistamycin biosynthetic gene cluster responsible for the formation of these non-ribosomal peptides as well as an impressive number of yet uncharacterized biosynthetic pathways. This includes polyketide, ribosomal and non-ribosomal peptide and a large number of terpenoid biosynthetic loci encoding yet unknown natural products...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28696895/urinary-bladder-cancer-risk-factors-in-an-area-of-former-coal-iron-and-steel-industries-in-germany
#17
Eugen Krech, Silvia Selinski, Meinolf Blaszkewicz, Hannah Bürger, Thura Kadhum, Jan G Hengstler, Michael C Truß, Klaus Golka
This study was performed to investigate the frequency of bladder cancer in patients with an occupational history such as underground hard coal mining and/or painting after the structural change in the local industry. A total of 206 patients with bladder cancer and 207 controls were enlisted regarding occupational and nonoccupational bladder cancer risk factors by questionnaire. The phase II enzymes N-acetyltransferase 2 (NAT2), glutathione S-transferases M1 (GSTM1), and T1 (GSTT1) and the single nucleotide polymorphism (SNP) rs11892031[A/C] reported to be associated with bladder cancer in genome-wide association studies were genotyped...
July 11, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28696412/whole-genome-dna-methylation-status-associated-with-clinical-ptsd-measures-of-oif-oef-veterans
#18
R Hammamieh, N Chakraborty, A Gautam, S Muhie, R Yang, D Donohue, R Kumar, B J Daigle, Y Zhang, D A Amara, S-A Miller, S Srinivasan, J Flory, R Yehuda, L Petzold, O M Wolkowitz, S H Mellon, L Hood, F J Doyle, C Marmar, M Jett
Emerging knowledge suggests that post-traumatic stress disorder (PTSD) pathophysiology is linked to the patients' epigenetic changes, but comprehensive studies examining genome-wide methylation have not been performed. In this study, we examined genome-wide DNA methylation in peripheral whole blood in combat veterans with and without PTSD to ascertain differentially methylated probes. Discovery was initially made in a training sample comprising 48 male Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) veterans with PTSD and 51 age/ethnicity/gender-matched combat-exposed PTSD-negative controls...
July 11, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28694302/up-regulation-of-ankdr49-a-poor-prognostic-factor-regulates-cell-proliferation-of-gliomas
#19
Chunyan Hao, Hubin Duan, Hao Li, Mingyang Pei, Yueting Liu, Yimin Fan, Ce Zhang
The Ankyrin repeat domain 49 (ANKRD49) is an evolutionarily conserved protein, which is related to mediate protein-protein interaction. However, the function of ANKRD49 in human glioma remains elusive. Through mining The Cancer Genome Atlas (TCGA) database, we found that the expression of ANKRD49 was increased in glioma tissues and that high expression of ANKRD49 was strongly associated with high disease grade and poor overall survival. To investigate the role of ANKRD49 in malignant glioma, lentivirus expressing shRNA targeting ANKRD49 was constructed in U251 and U87 malignant glioma cells...
July 10, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28692290/top-down-atmospheric-ionization-mass-spectrometry-microscopy-combined-with-proteogenomics
#20
Cheng-Chih Hsu, Michael W Baker, Terry Gaasterland, Michael J Meehan, Eduardo R Macagno, Pieter C Dorrestein
Mass spectrometry-based protein analysis has become an important methodology for proteogenomic mapping by providing evidence for the existence of proteins predicted at the genomic level. However, screening and identification of proteins directly on tissue samples, where histological information is preserved, remain challenging. Here we demonstrate that the ambient ionization source, nanospray desorption electrospray ionization (nanoDESI), interfaced with light microscopy allows for protein profiling directly on animal tissues at the microscopic scale...
July 10, 2017: Analytical Chemistry
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"