journal
MENU ▼
Read by QxMD icon Read
search

Journal of Genomics

journal
https://www.readbyqxmd.com/read/28698739/complete-genome-sequence-of-actinomadura-parvosata-subsp-kistnae-a-rich-source-of-novel-natural-product-bio-chemistry
#1
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/28698738/complete-genome-sequence-and-comparative-genomics-of-a-streptococcus-pyogenes-emm3-strain-m3-b-isolated-from-a-japanese-patient-with-streptococcal-toxic-shock-syndrome
#2
Kohei Ogura, Shinya Watanabe, Teruo Kirikae, Tohru Miyoshi-Akiyama
Epidemiologic typing of Streptococcus pyogenes (GAS) is frequently based on the genotype of the emm gene, which encodes M/Emm protein. In this study, the complete genome sequence of GAS emm3 strain M3-b, isolated from a patient with streptococcal toxic shock syndrome (STSS), was determined. This strain exhibited 99% identity with other complete genome sequences of emm3 strains MGAS315, SSI-1, and STAB902. The complete genomes of five additional strains isolated from Japanese patients with and without STSS were also sequences...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698737/draft-genome-sequence-of-a-virulent-strain-of-pasteurella-multocida-isolated-from-alpaca
#3
Raquel Enma Hurtado, Flavia Aburjaile, Diego Mariano, Marcus Vinicius Canário, Leandro Benevides, Daniel Antonio Fernandez, Nataly Olivia Allasi, Rocio Rimac, Julio Eduardo Juscamayta, Jorge Enrique Maximiliano, Raul Hector Rosadio, Vasco Azevedo, Lenin Maturrano
Pasteurella multocida is one of the most frequently isolated bacteria in acute pneumonia cases, being responsible for high mortality rates in Peruvian young alpacas, with consequent social and economic costs. Here we report the genome sequence of P. multocida strain UNMSM, isolated from the lung of an alpaca diagnosed with pneumonia, in Peru. The genome consists of 2,439,814 base pairs assembled into 82 contigs and 2,252 protein encoding genes, revealing the presence of known virulence-associated genes (ompH, ompA, tonB, tbpA, nanA, nanB, nanH, sodA, sodC, plpB and toxA)...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28698736/draft-genome-sequence-of-the-symbiotic-frankia-sp-strain-kb5-isolated-from-root-nodules-of-casuarina-equisetifolia
#4
Céline Pesce, Erik Swanson, Stephen Simpson, Krystalynne Morris, W Kelley Thomas, Louis S Tisa, Anita Sellstedt
Frankia sp. strain KB5 was isolated from Casuarina equisetifolia and previous studies have shown both nitrogenase and uptake hydrogenase activities under free-living conditions. Here, we report 5.5-Mbp draft genome sequence with a G+C content of 70.03 %, 4,958 candidate protein-encoding genes, and 2 rRNA operons.
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28611852/cnv-analysis-of-host-responses-to-porcine-reproductive-and-respiratory-syndrome-virus-infection
#5
El Hamidi A Hay, Igseo Choi, Lingyang Xu, Yang Zhou, Robert R R Rowland, Joan K Lunney, George E Liu
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28529652/de-novo-assembly-of-the-liver-transcriptome-of-the-european-starling-sturnus-vulgaris
#6
Mark F Richardson, William B Sherwin, Lee A Rollins
The European starling, Sturnus vulgaris, is a prolific and worldwide invasive species that also has served as an important model for avian ecological and invasion research. Although the genome sequence recently has become available, no transcriptome data have been published for this species. Here, we have sequenced and assembled the S. vulgaris liver transcriptome, which will provide a foundational resource for further annotation and validation of the draft genome. Moreover, it will be important for ecological and evolutionary studies investigating the genetic factors underlying rapid evolution and invasion success in this global invader...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28529651/draft-genome-sequence-of-roseovarius-sp-a-2-an-iodide-oxidizing-bacterium-isolated-from-natural-gas-brine-water-chiba-japan
#7
Tri Yuliana, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki, Seigo Amachi
Roseovarius sp. A-2 is a heterotrophic iodide (I(-))-oxidizing bacterium isolated from iodide-rich natural gas brine water in Chiba, Japan. This strain oxidizes iodide to molecular iodine (I2) by means of an extracellular multicopper oxidase. Here we report the draft genome sequence of strain A-2. The draft genome contained 46 tRNA genes, 1 copy of a 16S-23S-5S rRNA operon, and 4,514 protein coding DNA sequences, of which 1,207 (27%) were hypothetical proteins. The genome contained a gene encoding IoxA, a multicopper oxidase previously found to catalyze the oxidation of iodide in Iodidimonas sp...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348643/whole-genome-sequencing-of-vibrio-sinaloensis-t47-a-tropical-marine-isolate-with-quorum-sensing-properties
#8
Nur Izzati Mohamad, Kah Yan How, Wai-Fong Yin, Kok-Gan Chan
A large number of Vibrio sp. thrive in the marine environment and they are notable to cause food borne infection associated with undercooked seafood. In this study, we report the whole genome sequence of Vibrio sinaloensis T47 which was isolated from coastal marine water in Morib Beach, Hulu Selangor. The genome is made up of approximately 4.59 Mbp with 80 contigs and 46% G+C content. From the annotated genome, genes associated with quorum sensing (QS) were identified. This research provides a genetic basis for better understanding of QS pathway which contributes to the physiological traits of strain T47 to thrive in the marine environment...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348642/metagenomic-analysis-of-a-complex-community-present-in-pond-sediment
#9
Vivek Negi, Rup Lal
The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348641/complete-genome-sequence-and-functional-study-of-the-fibrinolytic-enzyme-producing-bacterium-leuconostoc-holzapfelii-5h4-a-silage-probiotic
#10
Hye Sun Kim, Ouk Kyu Han, Youn-Sig Kwak
To process silage, rye is usually removed before the heading stage but the rye biomass increased up to 30% after the heading stage. However, after the heading stage, lignification rapidly accelerated and it resulted in a poor NDF digestibility problem. This has led to a demand for a strong fibrinolytic enzyme-producing probiotic for rye silage. The Gram-positive Leuconostoc holzapfelii 5H4 was selected as a fibrinolytic enzyme-producing probiotic to overcome lignification of rye silage. The L. holzapfelii 5H4 has a relatively small circular chromosome (1,885,398 bp), but the strain has one cellulase, two xylanase, and five esterase in its genome sequence...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28348640/exploration-of-small-rna-seq-data-for-small-non-coding-rnas-in-human-colorectal-cancer
#11
Srinivas V Koduru, Amit K Tiwari, Sprague W Hazard, Milind Mahajan, Dino J Ravnic
Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28138345/genomic-characterization-of-eight-ensifer-strains-isolated-from-pristine-caves-and-a-whole-genome-phylogeny-of-ensifer-sinorhizobium
#12
Heerman Kumar Sandra Kumar, Han Ming Gan, Mun Hua Tan, Wilhelm Wei Han Eng, Hazel A Barton, André O Hudson, Michael A Savka
A total of eight Ensifer sp. strains were isolated from two pristine cave environments. One strain was isolated from a cave water pool located in the Wind Cave National Park, South Dakota, USA and the remaining seven strains were isolated from Lechuguilla Cave of Carlsbad Caverns National Park, New Mexico, USA. Whole genome sequencing and comparative genomic analyses of the eight isolates compared to various type strains from the genera Ensifer and Sinorhizobium demonstrates that although members in these genera can be phylogenetically separated into two distinct clades, the percentage of conserved proteins (POCP) between various type strains from Ensifer and Sinorhizobium are consistently higher than 50%, providing strong genomic evidence to support the classification of the genera Ensifer and Sinorhizobium into a single genus...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28138344/detection-of-intestinal-pathogens-in-river-shore-and-drinking-water-in-lima-peru
#13
David C Grothen, Sydney J Zach, Paul H Davis
Water quality management is an ongoing struggle for many locations worldwide. Current testing of water supplies can be time-consuming, expensive, and lack sensitivity. This study describes an alternative, easy-to-use, and inexpensive method to water sampling and testing at remote locations. This method was employed to detect a number of intestinal pathogens in various locations of Lima, Peru. A total of 34 PCR primer pairs were tested for specificity and high-yield amplification for 12 different pathogens using known DNA templates...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28138343/first-draft-genome-sequence-of-the-dourine-causative-agent-trypanosoma-equiperdum-strain-ovi
#14
Laurent Hébert, Bouziane Moumen, Anthony Madeline, Sascha Steinbiss, Latifa Lakhdar, Nick Van Reet, Philippe Büscher, Claire Laugier, Julien Cauchard, Sandrine Petry
Trypanosoma equiperdum is the causative agent of dourine, a sexually-transmitted infection of horses. This parasite belongs to the subgenus Trypanozoon that also includes the agent of sleeping sickness (Trypanosoma brucei) and surra (Trypanosoma evansi). We herein report the genome sequence of a T. equiperdum strain OVI, isolated from a horse in South-Africa in 1976. This is the first genome sequence of the T. equiperdum species, and its availability will provide important insights for future studies on genetic classification of the subgenus Trypanozoon...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/27672405/whole-genome-sequence-analysis-of-an-alachlor-and-endosulfan-degrading-micrococcus-sp-strain-2385-isolated-from-ochlockonee-river-florida
#15
Ashish Pathak, Ashvini Chauhan, Ayman Y I Ewida, Paul Stothard
We recently isolated Micrococcus sp. strain 2385 from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides- alachlor [(2-chloro-2`,6`-diethylphenyl-N (methoxymethyl)acetanilide)] and endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. To further identify the repertoire of metabolic functions possessed by strain 2385, a draft genome sequence was obtained, assembled, annotated and analyzed...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27672404/de-novo-assembly-and-analysis-of-the-chilean-pencil-catfish-trichomycterus-areolatus-transcriptome
#16
Thomas T Schulze, Jonathan M Ali, Maggie L Bartlett, Madalyn M McFarland, Emalie J Clement, Harim I Won, Austin G Sanford, Elyssa B Monzingo, Matthew C Martens, Ryan M Hemsley, Sidharta Kumar, Nicolas Gouin, Alan S Kolok, Paul H Davis
Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512520/pseudomonas-lini-strain-zbg1-revealed-carboxylic-acid-utilization-and-copper-resistance-features-required-for-adaptation-to-vineyard-soil-environment-a-draft-genome-analysis
#17
Kok-Gan Chan, Teik-Min Chong, Tan-Guan-Sheng Adrian, Heng Leong Kher, Catherine Grandclément, Denis Faure, Wai-Fong Yin, Yves Dessaux, Kar-Wai Hong
Pseudomonas lini strain ZBG1 was isolated from the soil of vineyard in Zellenberg, France and the draft genome was reported in this study. Bioinformatics analyses of the genome revealed presence of genes encoding tartaric and malic acid utilization as well as copper resistance that correspond to the adaptation this strain in vineyard soil environment.
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512519/draft-genome-sequence-of-carotenoid-producing-yellow-pigmented-planococcus-maritimus-mku009
#18
Ashok Ganapathy, Sridhar Jayavel, Sivakumar Natesan
Planococcus maritimus MKU009 is a Gram positive cocci and a moderate halophilic bacterium isolated from marine water of Pichavaram, South East Coast of India. Here we report the draft genome of Planococcus maritimus MKU009 with a total size of 3,251,644 bp with N50 value of 1681571 bp. The overall G+C content of the genome was 47.27%. The carotenoid producing crtN, crtB, crtP and crtI genes were located within the first contig of the genome assembly. This genome source will provide insights into functional genomics of carotenoid production and metabolic engineering...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27512518/external-rna-controls-consortium-beta-version-update
#19
Hangnoh Lee, P Scott Pine, Jennifer McDaniel, Marc Salit, Brian Oliver
Spike-in RNAs are valuable controls for a variety of gene expression measurements. The External RNA Controls Consortium developed test sets that were used in a number of published reports. Here we provide an authoritative table that summarizes, updates, and corrects errors in the test version that ultimately resulted in the certified Standard Reference Material 2374. We have noted existence of anti-sense RNA controls in the material, corrected sub-pool memberships, and commented on control RNAs that displayed inconsistent behavior...
2016: Journal of Genomics
https://www.readbyqxmd.com/read/27326264/draft-genome-sequence-of-kocuria-rhizophila-strain-tpw45-an-actinobacterium-isolated-from-freshwater
#20
Tan-Guan-Sheng Adrian, Pui-Wan Tan, Jian-Woon Chen, Wai-Fong Yin, Kok-Gan Chan
Kocuria rhizophila is a ubiquitous bacterium which is well known for its industrial value. Here, we present the draft genome of Kocuria rhizophila strain TPW45 which was isolated from Sungai Gabai, Selangor, Malaysia. The assembled genome comprised of 46 contigs and the estimated genome size is 2.7 Mb. Based on the RAST annotation, a gene cluster responsible for aromatic compound degradation was identified in this strain.
2016: Journal of Genomics
journal
journal
48757
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"