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https://www.readbyqxmd.com/read/28728360/isolation-and-characterization-of-a-novel-gossypol-degrading-bacteria-bacillus-subtilis-strain-rbs
#1
Yunhua Zhang, Lijuan Chen, Zhengyou Zhang, Li Dai, Ying Liu, Maoji Cheng
Objective: An experiment was conducted to isolate gossypol-degrading bacteria and assessed its potential for gossypol degradation. Methods: Rumen liquid was collected from the rumen of cows through fistula from the experimental pasture. Approximately 1 ml of the rumen liquid was spread onto basal medium plates containing 2 g/l gossypol as the only source of carbon and was then cultured at 39°C to isolate gossypol-degrading bacteria. The isolated colonies were cultured for 6 h and then observed their size and shape by the microscope and scanning electron microscope...
June 27, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28725556/de-novo-transcriptome-assembly-for-the-lung-of-the-ornamented-pygmy-frog-microhyla-fissipes
#2
Lusha Liu, Shouhong Wang, Lanying Zhao, Jianping Jiang
Microhyla fissipes, belonging to Neobatrachia, is a new model organism to study developmental biology, adaptive mechanisms from aquatic to terrestrial life, environmental toxicology, and human disease. M. fissipes use of lungs soon after hatching makes it extremely valuable for the study of lung function and development mechanisms. However, our knowledge of genes and pathways associated with lung development in M. fissipes is very limited. In this study, we conducted de novo transcriptome assembly for the lung of M...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28725438/nickel-resistant-bacteria-isolated-in-human-microbiome
#3
E A Lusi, T Patrissi, P Guarascio
Nickel-resistant bacteria have been isolated so far only in contaminated soils and wastewaters polluted with different industrial sources. The aim of our study was to determine if nickel-resistant bacteria could also be isolated from human samples. In this brief communication, we describe how we were able to isolate human bacterial strains that grew without oxygen and in the presence of high concentrations of nickel. The identification was made by phenotypic and genetic techniques. The bacterial sequences have been deposited in the NCBI database repository...
September 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28724769/stlv-1-infection-of-papio-anubis-tax-sequence-heterogeneity-and-t-cell-recognition
#4
James M Termini, Diogo M Magnani, Helen S Maxwell, William Lauer, Iris Castro, Jerilyn Pecotte, Glen N Barber, David I Watkins, Ronald C Desrosiers
Natural infection of baboons with simian T lymphotropic virus (STLV) is a potentially useful model system for study of vaccination against the human virus HTLV. Here we expand the number of available full-length STLV-1 baboon sequences from one to three and relate T cell responses that recognize the immunodominant Tax protein to the tax sequences present in two individual baboons. Continuously growing T cell lines were established from two baboons, 12141 and 12752. Next-generation sequencing (NGS) of complete STLV genome sequences from these lines revealed them to be closely related but distinct from each other and from the STLV-1 baboon sequence in the NCBI sequence database...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28721853/us10-a-novel-npro-interacting-protein-inhibits-classical-swine-fever-virus-replication
#5
Huifang Lv, Wang Dong, Gui Qian, Jie Wang, Xiaomeng Li, Zhi Cao, Qizhuang Lv, Chengbao Wang, Kangkang Guo, Yanming Zhang
Classical swine fever (CSF) is a severe, febrile and highly contagious disease caused by classical swine fever virus (CSFV) that has resulted in huge economic losses in the pig industry worldwide. CSFV Npro has been actively studied but remains incompletely understood. Few studies have investigated the cellular proteins that interact with Npro and their participation in viral replication. Here, the yeast two-hybrid (Y2H) system was employed to screen Npro-interacting proteins from a porcine alveolar macrophage (PAM) cDNA library, and a blast search of the NCBI database revealed that 15 cellular proteins interact with Npro...
July 18, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28721204/initial-genome-sequencing-of-the-sugarcane-cp-96-1252-complex-hybrid
#6
Jason R Miller, Kari A Dilley, Derek M Harkins, Manolito G Torralba, Kelvin J Moncera, Karen Beeri, Karrie Goglin, Timothy B Stockwell, Granger G Sutton, Reed S Shabman
The CP 96-1252 cultivar of sugarcane is a complex hybrid of commercial importance. DNA was extracted from lab-grown leaf tissue and sequenced. The raw Illumina DNA sequencing results provide 101 Gbp of genome sequence reads. The dataset is available from https://www.ncbi.nlm.nih.gov/bioproject/PRJNA345486/.
2017: F1000Research
https://www.readbyqxmd.com/read/28713815/bioinformatic-prediction-of-possible-targets-and-mechanisms-of-action-of-the-green-tea-compound-epigallocatechin-3-gallate-against-breast-cancer
#7
Xinqiang Song, Mu Zhang, Lei Chen, Qingsong Lin
Epigallocatechin-3-gallate (EGCG), a bioactive compound in green tea, is the most abundant and biologically active catechin, and it exerts multiple effects in humans through mechanisms that remain to be clarified. The present study used bioinformatics to identify possible mechanisms by which EGCG reduces risk of breast cancer. Possible human protein targets of EGCG were identified in the PubChem database, possible human gene targets were identified in the NCBI database, and then both sets of targets were analyzed using Ingenuity Pathway Analysis to predict molecular networks affected by EGCG in breast cancer...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28713559/draft-genome-sequencing-of-the-sugarcane-hybrid-sp80-3280
#8
Diego Mauricio Riaño-Pachón, Lucia Mattiello
Sugarcane commercial cultivar SP80-3280 has been used as a model for genomic analyses in Brazil. Here we present a draft genome sequence employing Illumina TruSeq Synthetic Long reads. The dataset is available from NCBI BioProject with accession PRJNA272769.
2017: F1000Research
https://www.readbyqxmd.com/read/28713404/genome-wide-identification-and-analysis-of-genes-conserved-between-japonica-and-indica-rice-cultivars-that-respond-to-low-temperature-stress-at-the-vegetative-growth-stage
#9
Manu Kumar, Yun-Shil Gho, Ki-Hong Jung, Seong-Ryong Kim
Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711973/piwi-interacting-rnas-as-novel-regulators-of-pancreatic-beta-cell-function
#10
Imène Sarah Henaoui, Cécile Jacovetti, Inês Guerra Mollet, Claudiane Guay, Jonathan Sobel, Lena Eliasson, Romano Regazzi
AIMS/HYPOTHESIS: P-element induced Wimpy testis (PIWI)-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and guide them to silence transposable elements. They are abundantly expressed in germline cells and play key roles in spermatogenesis. There is mounting evidence that piRNAs are also present in somatic cells, where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta cell activities...
July 16, 2017: Diabetologia
https://www.readbyqxmd.com/read/28710456/genomic-insights-into-the-virulence-and-salt-tolerance-of-staphylococcus-equorum
#11
Do-Won Jeong, Sojeong Heo, Sangryeol Ryu, Jochen Blom, Jong-Hoon Lee
To shed light on the genetic background behind the virulence and salt tolerance of Staphylococcus equorum, we performed comparative genome analysis of six S. equorum strains. Data on four previously published genome sequences were obtained from the NCBI database, while those on strain KM1031 displaying resistance to multiple antibiotics and strain C2014 causing haemolysis were determined in this study. Examination of the pan-genome of five of the six S. equorum strains showed that the conserved core genome retained the genes for general physiological processes and survival of the species...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28709399/draft-sequencing-and-assembly-of-the-genome-of-the-world-s-largest-fish-the-whale-shark-rhincodon-typus-smith-1828
#12
Timothy D Read, Robert A Petit, Sandeep J Joseph, Md Tauqeer Alam, M Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S Vuong, Chad P Haase, D Harry Webb, Milton Tan, Alistair D M Dove
BACKGROUND: The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem...
July 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28708831/biochem4j-integrated-and-extensible-biochemical-knowledge-through-graph-databases
#13
Neil Swainston, Riza Batista-Navarro, Pablo Carbonell, Paul D Dobson, Mark Dunstan, Adrian J Jervis, Maria Vinaixa, Alan R Williams, Sophia Ananiadou, Jean-Loup Faulon, Pedro Mendes, Douglas B Kell, Nigel S Scrutton, Rainer Breitling
Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes...
2017: PloS One
https://www.readbyqxmd.com/read/28708504/study-of-lysophosphatidic-acid-receptors-lpars-in-buffalo-uterus-demonstrated-upregulation-of-lpar1-and-lpar6-in-early-pregnancy
#14
Abdul Sadam, Subhashree Parida, Amol R Padol, Ankita D Verma, Naseer Ahmad Baba, Wanta M Khuman, Vivek Srivastava, Manjit Panigrahi, Thakur Uttam Singh, Souvendra Nath Sarkar
Lysophosphatidic acid (LPA) is an important factor involved in embryo implantation and pregnancy establishment in humans and domestic livestock. LPA exerts its action through six G-protein-coupled receptors (LPA1-LPA6). We investigated the types of LPA receptors expressed in buffalo uterus and also their differential expression in the nonpregnant, and early-pregnant endometrium. The nonpregnant, and early-pregnant (<42 days) uteri were collected from the local slaughterhouse. RT-PCR experiments detected mRNAs of all the six LPA receptors (LPAR1-LPAR6) in both nonpregnant, and early-pregnant endometrial tissues...
May 27, 2017: Theriogenology
https://www.readbyqxmd.com/read/28702355/whole-genome-sequencing-and-annotation-of-halophilic-salinicoccus-sp-bab-3246-isolated-from-the-coastal-region-of-gujarat
#15
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/28702047/transcriptome-analysis-of-al-induced-genes-in-buckwheat-fagopyrum-esculentum-moench-root-apex-new-insight-into-al-toxicity-and-resistance-mechanisms-in-an-al-accumulating-species
#16
Jia Meng Xu, Wei Fan, Jian Feng Jin, He Qiang Lou, Wei Wei Chen, Jian Li Yang, Shao Jian Zheng
Relying on Al-activated root oxalate secretion, and internal detoxification and accumulation of Al, buckwheat is highly Al resistant. However, the molecular mechanisms responsible for these processes are still poorly understood. It is well-known that root apex is the critical region of Al toxicity that rapidly impairs a series of events, thus, resulting in inhibition of root elongation. Here, we carried out transcriptome analysis of the buckwheat root apex (0-1 cm) with regards to early response (first 6 h) to Al stress (20 μM), which is crucial for identification of both genes and processes involved in Al toxicity and tolerance mechanisms...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28699823/the-gmz2-malaria-vaccine-from-concept-to-efficacy-in-humans
#17
Michael Theisen, Bright Adu, Benjamin Mordmüller, Subhash Singh
GMZ2 is a recombinant protein consisting of conserved domains of GLURP and MSP3, two asexual blood-stage antigens of Plasmodium falciparum, and is designed with the aim of mimicking naturally acquired anti-malarial immunity. The rationale for combining these two antigens is based on a series of immune epidemiological studies from geographically diverse malaria endemic regions; functional in vitro studies; and pre-clinical studies in rodents and New World monkeys. GMZ2 adjuvanted with alhydrogel® (alum) was well tolerated and immunogenic in three phase 1 studies...
July 12, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28698996/genome-sequencing-of-strain-cellulosimicrobium-sp-th-20-with-ginseng-biotransformation-ability
#18
REVIEW
Fei Zheng, Wei Zhang, Xiaodan Chu, Yulin Dai, Jing Li, Huanxi Zhao, Liankui Wen, Hao Yue, Shanshan Yu
Biotransformation for increasing the pharmaceutical effect of ginsenosides is getting more and more attractions. Strain Cellulosimicrobium sp. TH-20 isolated from ginseng soil samples was identified to produce enzymes contributing to its excellent biotransformation activity against ginsenosides, the main active components of ginseng. Based on phylogenetic tree and homology analysis, the strain can be designated as Cellulosimicrobium sp. Genome sequencing was performed using the Illumina Miseq to explore the functional genes involved in ginsenoside transformation...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#19
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28688945/purification-and-structural-characterization-of-a-novel-anti-tumor-protein-from-arca-inflata
#20
Jianhua Zhu, Jian Xu, Yanqing Wang, Chunlei Li, Zhiyan Chen, Liyan Song, Jingjing Gao, Rongmin Yu
A novel in vitro anti-tumor protein (J2-C2) with a molecular weight of 27,153.0Da was isolated from the edible portion of Arca inflata. Physical and structural properties of J2-C2 were characterized using physicochemical and instrumental analyses. Gel electrophoresis analysis showed that J2-C2 is a homogeneous, monomeric protein with an isoelectric point of 6.3. The purity of the isolated native J2-C2 was >99%, as determined by RP-HPLC. The carbohydrate content assay showed that J2-C2 was not a glycoprotein...
July 5, 2017: International Journal of Biological Macromolecules
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