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https://www.readbyqxmd.com/read/28914754/investigation-of-antimicrobial-peptide-genes-associated-with-fungus-and-insect-resistance-in-maize
#1
Joseph Noonan, William Paul Williams, Xueyan Shan
Antimicrobial peptides (AMPs) are small defense proteins present in various organisms. Major groups of AMPs include beta-barrelin, hevein, knottin, lipid transfer protein (LTP), thionin, defensin, snakin, and cyclotide. Most plant AMPs involve host plant resistance to pathogens such as fungi, viruses, and bacteria, whereas a few plant AMPs from the cyclotide family carry insecticidal functions. In this research, a genome-wide investigation on antimicrobial peptide genes in maize genome was conducted. AMPs previously identified from various plant species were used as query sequences for maize genome data mining...
September 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28905086/identification-and-characterization-of-a-novel-vibo-quercitol-1-dehydrogenase-from-burkholderia-terrae-suitable-for-production-of-vibo-quercitol-from-2-deoxy-scyllo-inosose
#2
Nobuya Itoh, Junji Kurokawa, Hiroshi Toda, Kazunobu Konishi
(-)-vibo-Quercitol is a deoxyinositol (1L-1,2,4/3,5-cyclohexanepentol) that naturally occurs in oak species, honeydew honey, wines aged in oak barrels, and Gymnema sylvestre and is a potential intermediate for pharmaceuticals. We found that (-)-vibo-quercitol is stereoselectively synthesized from 2-deoxy-scyllo-inosose by the reductive reaction of a novel (-)-vibo-quercitol 1-dehydrogenase found in the proteomes of Burkholderia, Pseudomonas, and Arthrobacter. Among them, Burkholderia terrae sp. AKC-020 (40-1) produced a (-)-vibo-quercitol 1-dehydrogenase appropriate for synthesizing (-)-vibo-quercitol with a high diastereomeric excess...
September 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28902217/a-bifunctional-old-yellow-enzyme-from-penicillium-roqueforti-is-involved-in-ergot-alkaloid-biosynthesis
#3
Nina Gerhards, Shu-Ming Li
The blue cheese-making fungus Penicillium roqueforti produces isofumigaclavine A as the main ergot alkaloid. Recently, genome mining revealed the presence of two DNA loci bearing the genetic potential for its biosynthesis. In this study, a short-chain dehydrogenase/reductase (SDR) from one of the loci was proved to be responsible for the conversion of chanoclavine-I to its aldehyde. Furthermore, a putative gene coding for an enzyme with high homology to Old Yellow Enzymes (OYEs) involved in the ergot alkaloid biosynthesis was found outside the two clusters...
September 13, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28899484/rational-design-of-kluyveromyces-marxianus-zjb14056-aldo-keto-reductase-kmakr-to-enhance-diastereoselectivity-and-activity
#4
Ya-Jun Wang, Bin-Bin Ying, Wei Shen, Ren-Chao Zheng, Yu-Guo Zheng
t-Butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-1b) is a valuable chiral synthon of atorvastatin calcium. A novel NADPH-specific aldo-keto reductase (AKR) was identified from a thermotolerant yeast Kluyveromyces marxianus ZJB14056 by genome database mining, displaying t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1a) reducing activity and moderate diastereoselectivity (dep∼80.5%). Molecular homology modeling and docking studies demonstrated that the side chain of Trp297 blocks binding of (5R)-1a to KmAKR...
December 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28894971/identification-of-genes-associated-with-primary-open-angle-glaucoma-by-bioinformatics-approach
#5
Haiyan Qiu, Benhu Zhu, Shengrong Ni
PURPOSE: This study aimed to identify associated genes with primary open-angle glaucoma (POAG) and explore the potentially modular mechanism underlying POAG. METHODS: We downloaded gene expression profiles data GSE27276 from gene expression omnibus and identified differentially expressed genes between POAG patients and normal controls. Then, gene ontology analysis and kyoto encyclopedia of genes and genomes pathway enrichment were performed to predict the DEGs functions, followed with the construction, centrality analysis, and module mining of protein-protein interaction network...
September 11, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28894827/the-genetic-landscape-of-programmed-death-ligand-1-pd-l1-alterations-in-head-and-neck-cancer
#6
Thomas E Heineman, Adam Widman, Edward C Kuan, Maie St John
OBJECTIVES: Nivolumab has recently been shown in the phase III clinical trial CheckMate-141 to have superior survival rates compared to the current standard of care chemotherapy for recurrent or metastatic platinum-resistant head and neck squamous cell carcinoma (HNSCC). Nivolumab targets the immune inhibitory receptor programmed cell death 1 (PD-1). Programmed cell death ligand 1 (PD-L1) genomics have been poorly characterized in the context of HNSCC, including expression levels of PD-L1 in individual tumors as well as related up or down-regulated genes that might function as co-targets...
June 2017: Laryngoscope Investigative Otolaryngology
https://www.readbyqxmd.com/read/28893840/the-monoplastidic-bottleneck-in-algae-and-plant-evolution
#7
REVIEW
Jan de Vries, Sven B Gould
Plastids in plants and algae evolved from the endosymbiotic integration of a cyanobacterium by a heterotrophic eukaryote. New plastids can only emerge through fission; thus, the synchronization of bacterial division with the cell cycle of the eukaryotic host was vital to the origin of phototrophic eukaryotes. Most of the sampled algae house a single plastid per cell and basal-branching relatives of polyplastidic lineages are all monoplastidic, as are some non-vascular plants during certain stages of their life cycle...
September 11, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28892736/five-distinct-reassortants-of-h5n6-highly-pathogenic-avian-influenza-a-viruses-affected-japan-during-the-winter-of-2016-2017
#8
Nobuhiro Takemae, Ryota Tsunekuni, Kirill Sharshov, Taichiro Tanikawa, Yuko Uchida, Hiroshi Ito, Kosuke Soda, Tatsufumi Usui, Ivan Sobolev, Alexander Shestopalov, Tsuyoshi Yamaguchi, Junki Mine, Toshihiro Ito, Takehiko Saito
To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016-2017 and 117 AIV/HPAIVs isolated in Japan and Russia. Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that period. Japanese H5N6 isolates shared a common genetic ancestor in 6 of 8 genomic segments, and the PA and NS genes demonstrated 4 and 2 genetic origins, respectively...
September 8, 2017: Virology
https://www.readbyqxmd.com/read/28887351/using-predictive-analytics-and-big-data-to-optimize-pharmaceutical-outcomes
#9
Inmaculada Hernandez, Yuting Zhang
PURPOSE: The steps involved, the resources needed, and the challenges associated with applying predictive analytics in healthcare are described, with a review of successful applications of predictive analytics in implementing population health management interventions that target medication-related patient outcomes. SUMMARY: In healthcare, the term big data typically refers to large quantities of electronic health record, administrative claims, and clinical trial data as well as data collected from smartphone applications, wearable devices, social media, and personal genomics services; predictive analytics refers to innovative methods of analysis developed to overcome challenges associated with big data, including a variety of statistical techniques ranging from predictive modeling to machine learning to data mining...
September 15, 2017: American Journal of Health-system Pharmacy: AJHP
https://www.readbyqxmd.com/read/28881617/germline-whole-exome-sequencing-and-large-scale-replication-identifies-fancm-as-a-likely-high-grade-serous-ovarian-cancer-susceptibility-gene
#10
Ed Dicks, Honglin Song, Susan J Ramus, Elke Van Oudenhove, Jonathan P Tyrer, Maria P Intermaggio, Siddhartha Kar, Patricia Harrington, David D Bowtell, Aocs Study Group, Mine S Cicek, Julie M Cunningham, Brooke L Fridley, Jennifer Alsop, Mercedes Jimenez-Linan, Anna Piskorz, Teodora Goranova, Emma Kent, Nadeem Siddiqui, James Paul, Robin Crawford, Samantha Poblete, Shashi Lele, Lara Sucheston-Campbell, Kirsten B Moysich, Weiva Sieh, Valerie McGuire, Jenny Lester, Kunle Odunsi, Alice S Whittemore, Natalia Bogdanova, Matthias Dürst, Peter Hillemanns, Beth Y Karlan, Aleksandra Gentry-Maharaj, Usha Menon, Marc Tischkowitz, Douglas Levine, James D Brenton, Thilo Dörk, Ellen L Goode, Simon A Gayther, D P Paul Pharoah
We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one HGSOC case. Gene-set enrichment analysis showed enrichment for genes involved in DNA repair (p = 1.8×10(-3)). Twelve DNA repair genes - APEX1, APLF, ATX, EME1, FANCL, FANCM, MAD2L2, PARP2, PARP3, POLN, RAD54L and SMUG1 - were prioritized for targeted sequencing in up to 3,107 HGSOC cases, 1,491 cases of other epithelial ovarian cancer (EOC) subtypes and 3,368 unaffected controls of European origin...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28881274/novel-bacterial-selenite-reductase-csrf-responsible-for-se-iv-and-cr-vi-reduction-that-produces-nanoparticles-in-alishewanella-sp-wh16-1
#11
Xian Xia, Shijuan Wu, Nuohan Li, Dan Wang, Shixue Zheng, Gejiao Wang
Alishewanella sp. WH16-1 is a facultative anaerobic bacterium isolated from mining soil. Under aerobic conditions, this bacterium efficiently reduces selenite and chromate. A flavoprotein showing 37% amino acid identity to E. coli chromate reductase ChrR was identified from the genome (named CsrF). Gene mutation and complementation along with heterologous expression revealed the ability of CsrF to reduce selenite and chromate in vivo. The purified CsrF was yellow and showed an absorption spectra similar to that of FMN...
August 24, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28875065/biofueldb-a-database-and-prediction-server-of-enzymes-involved-in-biofuels-production
#12
Nikhil Chaudhary, Ankit Gupta, Sudheer Gupta, Vineet K Sharma
BACKGROUND: In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes...
2017: PeerJ
https://www.readbyqxmd.com/read/28874672/unravelling-a-stearidonic-acid-rich-triacylglycerol-biosynthetic-pathway-in-the-developing-seeds-of-buglossoides-arvensis-a-transcriptomic-landscape
#13
R V Sreedhar, P Prasad, L Prasanna Anjaneya Reddy, Ram Rajasekharan, Malathi Srinivasan
Buglossoides arvensis is an emerging oilseed crop that is rich in stearidonic acid (SDA) and has several potential applications in human health and nutrition. The molecular basis of SDA biosynthesis in this plant remains unknown due to lack of genomic information. To unravel key genes involved in SDA-rich triacylglycerol (TAG) biosynthesis, we performed transcriptome sequencing of pooled mRNA from five different developmental stages of B. arvensis seeds using Illumina NextSeq platform. De novo transcriptome assembly generated 102,888 clustered transcripts from 39...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28873253/tomexpress-a-unified-tomato-rna-seq-platform-for-visualization-of-expression-data-clustering-and-correlation-networks
#14
Mohamed Zouine, Elie Maza, Anis Djari, Mattieu Lauvernier, Pierre Frasse, Abdelaziz Smouni, Julien Pirrello, Mondher Bouzayen
The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA-Seq data visualization and data mining. To avoid major biases that can result from the use of different mapping and statistical processing methods, RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence and post-processed using the same pipeline with accurate parameters. Following the calculation of the number of counts per gene in each RNA-Seq sample, a communal global normalization method was applied to all expression values...
September 5, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28871139/a-strategy-for-the-identification-of-patterns-in-the-biosynthesis-of-nonribosomal-peptides-by-betaproteobacteria-species
#15
João Luiz Baldim, Bruna Lidiane da Silva, Daniela Aparecida Chagas-Paula, João Henrique G Lago, Marisi G Soares
Nonribosomal peptides have an important pharmacological role due to their extensive biological properties. The singularities in the biosynthesis of these natural products allowed the development of genome-mining strategies which associate them to their original biosynthetic gene clusters. Generally, these compounds present complex architectures that make their identification difficult. Based on these evidences, genomes from species of the class Betaproteobacteria were studied with the purpose of finding biosynthetic similarities among them...
September 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28862994/fc1000-normalized-gene-expression-changes-of-systematically-perturbed-human-cells
#16
Ingrid M Lönnstedt, Sven Nelander
The systematic study of transcriptional responses to genetic and chemical perturbations in human cells is still in its early stages. The largest available dataset to date is the newly released L1000 compendium. With its 1.3 million gene expression profiles of treated human cells it offers many opportunities for biomedical data mining, but also data normalization challenges of new dimensions. We developed a novel and practical approach to obtain accurate estimates of fold change response profiles from L1000, based on the RUV (Remove Unwanted Variation) statistical framework...
September 26, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28861098/development-of-an-efficient-protein-extraction-method-compatible-with-lc-ms-ms-for-proteome-mapping-in-two-australian-seagrasses-zostera-muelleri-and-posidonia-australis
#17
Zhijian Jiang, Manoj Kumar, Matthew P Padula, Mathieu Pernice, Tim Kahlke, Mikael Kim, Peter J Ralph
The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28860565/interleukin-6-dependent-growth-in-a-newly-established-plasmablastic-lymphoma-cell-line-and-its-therapeutic-targets
#18
Sohtaro Mine, Tsunekazu Hishima, Akihiko Suganuma, Hitomi Fukumoto, Yuko Sato, Michiyo Kataoka, Tsuyoshi Sekizuka, Makoto Kuroda, Tadaki Suzuki, Hideki Hasegawa, Masashi Fukayama, Harutaka Katano
Plasmablastic lymphoma (PBL) is a rare, highly aggressive subtype of non-Hodgkin lymphoma with plasma-cell differentiation occurring typically in immune-suppressed patients such as those with AIDS. This study reports the establishment and characterization of a new cell line, PBL-1, derived from a patient with AIDS-associated PBL. Morphological assessment of PBL-1 indicated plasma-cell differentiation with a CD20(-) CD38(+) CD138(+) immunophenotype and IgH/c-myc translocation. The cell line harbours Epstein-Barr virus, but a 52...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28859688/a-13-gene-expression-based-radioresistance-score-highlights-the-heterogeneity-in-the-response-to-radiation-therapy-across-hpv-negative-hnscc-molecular-subtypes
#19
Jean-Philippe Foy, Louis Bazire, Sandra Ortiz-Cuaran, Sophie Deneuve, Janice Kielbassa, Emilie Thomas, Alain Viari, Alain Puisieux, Patrick Goudot, Chloé Bertolus, Nicolas Foray, Youlia Kirova, Pierre Verrelle, Pierre Saintigny
BACKGROUND: Radiotherapy for head and neck squamous cell carcinomas (HNSCC) is associated with a substantial morbidity and inconsistent efficacy. Human papillomavirus (HPV)-positive status is recognized as a marker of increased radiosensitivity. Our goal was to identify molecular markers associated with benefit to radiotherapy in patients with HPV-negative disease. METHODS: Gene expression profiles from public repositories were downloaded for data mining. Training sets included 421 HPV-negative HNSCC tumors from The Cancer Genome Atlas (TCGA) and 32 HNSCC cell lines with available radiosensitivity data (GSE79368)...
September 1, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28855510/mining-novel-starch-converting-glycoside-hydrolase-70-enzymes-from-the-nestl%C3%A3-culture-collection-genome-database-the-lactobacillus-reuteri-ncc-2613-gtfb
#20
Joana Gangoiti, Sander S van Leeuwen, Xiangfeng Meng, Stéphane Duboux, Christina Vafiadi, Tjaard Pijning, Lubbert Dijkhuizen
The Glycoside hydrolase (GH) family 70 originally was established for glucansucrases of lactic acid bacteria (LAB) converting sucrose into α-glucan polymers. In recent years we have identified 3 subfamilies of GH70 enzymes (designated GtfB, GtfC and GtfD) as 4,6-α-glucanotransferases, cleaving (α1 → 4)-linkages in maltodextrins/starch and synthesizing new (α1 → 6)-linkages. In this work, 106 putative GtfBs were identified in the Nestlé Culture Collection genome database with ~2700 genomes, and the L...
August 30, 2017: Scientific Reports
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