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Genome mining

Jyothi Padiadpu, Priyanka Baloni, Kushi Anand, MohamedHusen Munshi, Chandrani Thakur, Abhilash Mohan, Amit Singh, Nagasuma Chandra
The global mechanisms and associated molecular alterations that occur in drug-resistant mycobacteria are poorly understood. To address this, we obtain genomics data and then construct a genome-scale response network in isoniazid-resistant Mycobacterium smegmatis and apply a network-mining algorithm. Through this, we decipher global alterations in an unbiased manner and identify emergent vulnerabilities in resistant bacilli, of which redox response was prominent. Using phenotypic profiling, we find that resistant bacilli exhibit collateral sensitivity to several compounds that block antioxidant responses...
September 9, 2016: ACS Infectious Diseases
Bo Gao, Wang Sun, Xianzhi Meng, Dongbo Xue, Weihui Zhang
Hematological abnormalities are frequently observed in patients with liver cirrhosis (LC). A previous study demonstrated that the apoptosis and damage of endothelial cells could cause the hematological abnormalities in LC. Protein kinases are one of the most important factors that regulate cell behavior, and are potential therapeutic targets for the treatment of a number of diseases. In a previous study, whole genome profiling was used to identify differentially expressed genes in human bone marrow endothelial cells treated with serum from 26 patients with LC...
October 12, 2016: Molecular Medicine Reports
Xiaohui Yao, Jingwen Yan, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Mark Inlow, Jason H Moore, Andrew J Saykin, Li Shen
Enrichment analysis has been widely applied in the genome-wide association studies, where gene sets corresponding to biological pathways are examined for significant associations with a phenotype to help increase statistical power and improve biological interpretation. In this work, we expand the scope of enrichment analysis into brain imaging genetics, an emerging field that studies how genetic variation influences brain structure and function measured by neuroimaging quantitative traits (QT). Given the high dimensionality of both imaging and genetic data, we propose to study Imaging Genetic Enrichment Analysis (IGEA), a new enrichment analysis paradigm that jointly considers meaningful gene sets (GS) and brain circuits (BC) and examines whether any given GS-BC pair is enriched in a list of gene-QT findings...
May 13, 2016: Brain Informatics
Ji-Long Liu, Miao Zhao
Endometriosis affects 5-10% of women in reproductive age, leading to dysmenorrhea, pelvic pain and infertility; however, our understanding on the pathogenesis of this disease remains incomplete. In the present study, we performed a systematic analysis of endometriosis-related genes using text mining. Taking text mining results as input, we subsequently generated a filtered gene set by computing the likelihood of finding more than expected occurrences for every gene across the disease-centered subset of the PubMed database...
October 13, 2016: Genomics
Jin-Bo Han, Guo-Qing Li, Pin-Jun Wan, Tao-Tao Zhu, Qing-Wei Meng
Glutathione S-transferases (GSTs) is a family of multifunctional enzymes that are involved in detoxification of poisonous compounds. In the present paper, the Leptinotarsa decemlineata genome and transcriptome dataset were mined and 30 GST genes were identified. These GSTs belonged to cytosolic (29 genes) and microsomal (1 gene) classes. Among them 3 GSTs (LdGSTe2, LdGSTs4, and LdGSTo3) possessed splice variants. Of the 29 cytosolic LdGSTs, 3, 10, 5, 4, 4, and 1 members were classified as delta, epsilon, omega, sigma, theta, and zeta subclasses respectively, along with 2 unclassified genes...
October 2016: Pesticide Biochemistry and Physiology
Sietske Grijseels, Jens Christian Nielsen, Milica Randelovic, Jens Nielsen, Kristian Fog Nielsen, Mhairi Workman, Jens Christian Frisvad
A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311(T) = IBT 12289(T)). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases...
October 14, 2016: Scientific Reports
Ni Ai, Haoyang Cai, Caius Solovan, Michael Baudis
BACKGROUND: DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing methods. Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA quality is sometimes observed in genome screening experiments and may lead to unreliable copy number profiles. Depending on the extent of these artefacts and the resulting misidentification of copy number alterations/variations (CNA/CNV), it may be desirable to exclude such samples from analyses or to adapt the downstream data analysis strategy accordingly...
October 12, 2016: BMC Genomics
Lisa Hui, Diana W Bianchi
Noninvasive prenatal DNA testing is the vanguard of genomic medicine. In only four years, this screening test has revolutionized prenatal care globally and opened up new prospects for personalized medicine for the fetus. There are widespread implications for increasing the scope of human genetic variation that can be detected before birth, and for discovering more about materno-fetal and placental biology. These include an urgent need to develop pretest education for all pregnant women and consistent posttest management recommendations for those with discordant test results...
October 10, 2016: Annual Review of Medicine
Sabine Gollner, Heiko Stuckas, Terue C Kihara, Stefan Laurent, Sahar Kodami, Pedro Martinez Arbizu
Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance...
2016: PloS One
Adeline Feri, Raphaël Loll-Krippleber, Pierre-Henri Commere, Corinne Maufrais, Natacha Sertour, Katja Schwartz, Gavin Sherlock, Marie-Elisabeth Bougnoux, Christophe d'Enfert, Mélanie Legrand
: The diploid genome of the yeast Candida albicans is highly plastic, exhibiting frequent loss-of-heterozygosity (LOH) events. To provide a deeper understanding of the mechanisms leading to LOH, we investigated the repair of a unique DNA double-strand break (DSB) in the laboratory C. albicans SC5314 strain using the I-SceI meganuclease. Upon I-SceI induction, we detected a strong increase in the frequency of LOH events at an I-SceI target locus positioned on chromosome 4 (Chr4), including events spreading from this locus to the proximal telomere...
October 11, 2016: MBio
Dorcus C Gemenet, Willmar L Leiser, Francesca Beggi, Ludger H Herrmann, Vincent Vadez, Henry F W Rattunde, Eva Weltzien, Charles T Hash, Andreas Buerkert, Bettina I G Haussmann
West Africa (WA) is among the most food insecure regions. Rapid human population growth and stagnating crop yields greatly contribute to this fact. Poor soil fertility, especially low plant available phosphorus (P) is constraining food production in the region. P-fertilizer use in WA is among the lowest in the world due to inaccessibility and high prices, often unaffordable to resource-poor subsistence farmers. This article provides an overview of soil P-deficiency in WA and opportunities to overcome it by exploiting sorghum and pearl millet genetic diversity...
2016: Frontiers in Plant Science
Vikas Belamkar, Andrew D Farmer, Nathan T Weeks, Scott R Kalberer, William J Blackmon, Steven B Cannon
For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection...
October 10, 2016: Scientific Reports
Yingjia Han, Gen Xu, Hewei Du, Jieyun Hu, Zhanji Liu, Hui Li, Jiansheng Li, Xiaohong Yang
We identified 11 SAD genes, and mined their natural variations associated with the conservation of stearic to oleic acid, especially ZmSAD1 supported by both the QTL and an expression QTL. Maize oil is generally regarded as a healthy vegetable oil owing to its low abundance of saturated fatty acids. Stearoyl-ACP desaturase (SAD) is a key rate-limiting enzyme for the conservation of stearic (C18:0) to oleic (C18:1) acid. Here, 11 maize SAD genes were identified to have more divergent functions than Arabidopsis SAD genes...
October 7, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Alagu Manickavelu, Reem Joukhadar, Abdulqader Jighly, Caixia Lan, Julio Huerta-Espino, Ahmad Shah Stanikzai, Andrzej Kilian, Ravi P Singh, Tomohiro Ban
Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R(2)≈0.16 at 0cM) due to germplasm peerless diversity...
November 2016: Plant Science: An International Journal of Experimental Plant Biology
Isabel E Olivera, Katrina C Fins, Sara A Rodriguez, Sumayyah K Abiff, Jaime L Tartar, Aurélien Tartar
BACKGROUND: Although interest in animal pathogenic oomycetes is increasing, the molecular basis mediating oomycete-animal relationships remains virtually unknown. Crinkler (CRN) genes, which have been traditionally associated with the cytotoxic activity displayed by plant pathogenic oomycetes, were recently detected in transcriptome sequences from the entomopathogenic oomycete Lagenidium giganteum, suggesting that these genes may represent virulence factors conserved in both animal and plant pathogenic oomycetes...
October 6, 2016: BMC Microbiology
Jinwoo Park, Benjamin Hur, Sungmin Rhee, Sangsoo Lim, Min-Su Kim, Kwangsoo Kim, Wonshik Han, Sun Kim
A breast cancer subtype classification scheme, PAM50, based on genetic information is widely accepted for clinical applications. On the other hands, experimental cancer biology studies have been successful in revealing the mechanisms of breast cancer and now the hallmarks of cancer have been determined to explain the core mechanisms of tumorigenesis. Thus, it is important to understand how the breast cancer subtypes are related to the cancer core mechanisms, but multiple studies are yet to address the hallmarks of breast cancer subtypes...
August 29, 2016: Journal of Bioinformatics and Computational Biology
SriGanesh Jammula, Diego Pasini
BACKGROUND: In epigenetic research, both the increasing ease of high-throughput sequencing and a greater interest in genome-wide studies have resulted in an exponential flooding of epigenetic-related data in public domain. This creates an opportunity for exploring data outside the limits of any specific query-centred study. Such data have to undergo standard primary analyses that are accessible with multiple well-stabilized programs. Further downstream analyses, such as genome-wide comparative, correlative and quantitative analyses, are critical in deciphering key biological features...
2016: Epigenetics & Chromatin
Marta Maciejewska, Delphine Adam, Loïc Martinet, Aymeric Naômé, Magdalena Całusińska, Philippe Delfosse, Monique Carnol, Hazel A Barton, Marie-Pierre Hayette, Nicolas Smargiasso, Edwin De Pauw, Marc Hanikenne, Denis Baurain, Sébastien Rigali
Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical properties, thereby suggesting that its filamentous endemic actinobacterial population might be a source of natural products useful in human treatment. In this work, a screening approach was undertaken in order to isolate cultivable Actinobacteria from moonmilk of the Grotte des Collemboles in Belgium, to evaluate their taxonomic profile, and to assess their potential in biosynthesis of antimicrobials...
2016: Frontiers in Microbiology
Danielle S Kelley, Christopher W Lennon, Marlene Belfort, Olga Novikova
: Inteins are self-splicing protein elements that are mobile at the DNA level and are sporadically distributed across microbial genomes. Inteins appear to be horizontally transferred, and it has been speculated that phages may play a role in intein distribution. Our attention turns to mycobacteriophages, which infect mycobacteria, where both phage and host harbor inteins. Using bioinformatics, mycobacteriophage genomes were mined for inteins. This study reveals that these mobile elements are present across multiple mycobacteriophage clusters and are pervasive in certain genes, like the large terminase subunit TerL and a RecB-like nuclease, with the majority of intein-containing genes being phage specific...
October 4, 2016: MBio
Cun-Duo Tang, Hong-Ling Shi, Qing-Hai Tang, Jun-Shi Zhou, Lun-Guang Yao, Zhu-Jin Jiao, Yun-Chao Kan
Two novel glycosyl hydrolase family 5 (GH5) β-mannanases (AoMan5A and AoMan5B) were identified from Aspergillus oryzae RIB40 by genome mining. The AoMan5A contains a predicted family 1 carbohydrate binding module (CBM-1), located at its N-terminal. The AoMan5A, AoMan5B and truncated mutant AoMan5AΔCL (truncating the N-terminal CBM and linker of AoMan5A) were expressed retaining the N-terminus of the native protein in Pichia pastoris GS115 by pPIC9K(M). The specific enzyme activity of the purified reAoMan5A, reAoMan5B and reAoMan5AΔCL towards locust bean gum at pH 3...
November 2016: Enzyme and Microbial Technology
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