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https://www.readbyqxmd.com/read/28227172/path-based-connectivity-for-clustering-genome-sequences
#1
Oznur Sengel, Olcay Kursun, Oznur Sengel, Olcay Kursun, Olcay Kursun, Oznur Sengel
Clustering is an unsupervised data mining tool and in bioinformatics, clustering genome sequences is used to group related biological sequences when there is no additional supervision. Sequence clusters are often related with gene/protein families, which can shed some light onto determining tertiary structures. To extract such hidden and valuable structures in a data set of genome sequences can benefit from better clustering methods such as the recently popular Spectral Clustering. In this study, we apply spectral clustering and its improved variations to sequence clustering task in our efforts to develop a novel approach for improving it...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28222763/the-discovery-of-novel-lpmo-families-with-a-new-hidden-markov-model
#2
Gerben P Voshol, Erik Vijgenboom, Peter J Punt
BACKGROUND: Renewable biopolymers, such as cellulose, starch and chitin are highly resistance to enzymatic degradation. Therefore, there is a need to upgrade current degradation processes by including novel enzymes. Lytic polysaccharide mono-oxygenases (LPMOs) can disrupt recalcitrant biopolymers, thereby enhancing hydrolysis by conventional enzymes. However, novel LPMO families are difficult to identify using existing methods. Therefore, we developed a novel profile Hidden Markov model (HMM) and used it to mine genomes of ascomycetous fungi for novel LPMOs...
February 21, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28222662/foxf2-promoter-methylation-is-associated-with-prognosis-in-esophageal-squamous-cell-carcinoma
#3
Xiaoying Chen, Haochang Hu, Jing Liu, Yong Yang, Guili Liu, Xiuru Ying, Yingmin Chen, Bin Li, Cong Ye, Dongping Wu, Shiwei Duan
Esophageal squamous cell carcinoma is a commonly malignant tumor of digestive tract with poor prognosis. Previous studies suggested that forkhead box F2 ( FOXF2) could be a candidate gene for assessing and predicting the prognosis of human cancers. However, the relationship between FOXF2 promoter methylation and the prognosis of esophageal squamous cell carcinoma remained unclear. Formalin-fixed, paraffin-embedded esophageal squamous cell carcinoma tissues of 135 esophageal squamous cell carcinoma patients were detected for FOXF2 promoter methylation status by methylation-specific polymerase chain reaction approach...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#4
Michael Knowles, Sara Stinson, Dominic Lambert, Catherine Carrillo, Adam Koziol, Martine Gauthier, Burton Blais
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221784/development-of-a-biosensor-concept-to-detect-the-production-of-cluster-specific-secondary-metabolites
#5
Yi-Qian Sun, Tobias Busche, Christian Rückert, Constanze Paulus, Yuriy Rebets, Renata Novakova, Joern Kalinowski, Andriy Luzhetskyy, Jan Kormanec, Olga N Sekurova, Sergey B Zotchev
Genome mining of actinomycete bacteria aims at the discovery of novel bioactive secondary metabolites that can be developed into drugs. A new repressor-based biosensor to detect activated secondary metabolite biosynthesis gene clusters in Streptomyces was developed. Biosynthetic gene clusters for undecylprodigiosin and coelimycin in the genome of Streptomyces lividans TK24, which encoded TetR-like repressors and appeared to be almost "silent" based on the RNA-seq data were chosen for the proof-of-principle studies...
February 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28217441/genome-sequence-of-the-acid-tolerant-desulfovibrio-sp-dv-isolated-from-the-sediments-of-a-pb-zn-mine-tailings-dam-in-the-chita-region-russia
#6
Anastasiia Kovaliova, Vitaly V Kadnikov, Dmitrii V Antsiferov, Alexey V Beletsky, Ehrzena V Danilova, Marat R Avakyan, Andrey V Mardanov, Olga V Karnachuk
Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K(+)-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28216008/computational-tools-for-exploring-sequence-databases-as-a-resource-for-antimicrobial-peptides
#7
REVIEW
W F Porto, A S Pires, O L Franco
Data mining has been recognized by many researchers as a hot topic in different areas. In the post-genomic era, the growing number of sequences deposited in databases has been the reason why these databases have become a resource for novel biological information. In recent years, the identification of antimicrobial peptides (AMPs) in databases has gained attention. The identification of unannotated AMPs has shed some light on the distribution and evolution of AMPs and, in some cases, indicated suitable candidates for developing novel antimicrobial agents...
February 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28215351/a-genomic-comparison-of-putative-pathogenicity-related-gene-families-in-five-members-of-the-ophiostomatales-with-different-lifestyles
#8
Ljerka Lah, Ulrike Löber, Tom Hsiang, Stefanie Hartmann
Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera)...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28215046/genome-resolved-metagenomics-of-a-bioremediation-system-for-degradation-of-thiocyanate-in-mine-water-containing-suspended-solid-tailings
#9
Sumayah F Rahman, Rose S Kantor, Robert Huddy, Brian C Thomas, Andries W van Zyl, Susan T L Harrison, Jillian F Banfield
Thiocyanate (SCN(-) ) is a toxic compound that forms when cyanide (CN(-) ), used to recover gold, reacts with sulfur species. SCN(-) -degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory-based reactors operated without suspended solids...
February 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28212290/defining-clinical-response-criteria-and-early-response-criteria-for-precision-oncology-current-state-of-the-art-and-future-perspectives
#10
Vivek Subbiah, Hubert H Chuang, Dhiraj Gambhire, Kalevi Kairemo
In this era of precision oncology, there has been an exponential growth in the armamentarium of genomically targeted therapies and immunotherapies. Evaluating early responses to precision therapy is essential for "go" versus "no go" decisions for these molecularly targeted drugs and agents that arm the immune system. Many different response assessment criteria exist for use in solid tumors and lymphomas. We reviewed the literature using the Medline/PubMed database for keywords "response assessment" and various known response assessment criteria published up to 2016...
February 15, 2017: Diagnostics
https://www.readbyqxmd.com/read/28210247/genome-insight-and-comparative-pathogenomic-analysis-of-nesterenkonia-jeotgali-strain-cd08_7-isolated-from-duodenal-mucosa-of-celiac-disease-patient
#11
Atul M Chander, Ramesan G Nair, Gurwinder Kaur, Rakesh Kochhar, Devinder K Dhawan, Sanjay K Bhadada, Shanmugam Mayilraj
Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1(T), Nesterenkonia sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28210246/prospects-of-in-vivo-incorporation-of-non-canonical-amino-acids-for-the-chemical-diversification-of-antimicrobial-peptides
#12
Tobias Baumann, Jessica H Nickling, Maike Bartholomae, Andrius Buivydas, Oscar P Kuipers, Nediljko Budisa
The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28204976/variation-in-whole-dna-methylation-in-red-maple-acer-rubrum-populations-from-a-mining-region-association-with-metal-contamination-and-cation-exchange-capacity-cec-in-podzolic-soils
#13
K N Kalubi, M Mehes-Smith, G Spiers, A Omri
Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications...
February 15, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28204975/surface-and-exoproteomes-of-gram-positive-pathogens-for-vaccine-discovery
#14
Massimiliano Biagini, Fabio Bagnoli, Nathalie Norais
Reverse vaccinology has been very successful in the discovery of vaccine candidates against many pathogenic bacteria by integrating genome and proteome mining. This great achievement was facilitated by the complementarity of the in silico prediction of antigens and the empirical data on protein localization, expression, and immunogenicity obtained through different techniques based on electrophoresis, immunoblotting and mass spectrometry. An iterative process between information provided by DNA sequence analysis and proteomic data has been established leading to precise antigen identification...
February 16, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28195566/rgs2-expression-predicts-amyloid-%C3%AE-sensitivity-mci-and-alzheimer-s-disease-genome-wide-transcriptomic-profiling-and-bioinformatics-data-mining
#15
A Hadar, E Milanesi, A Squassina, P Niola, C Chillotti, M Pasmanik-Chor, O Yaron, P Martásek, M Rehavi, D Weissglas-Volkov, N Shomron, I Gozes, D Gurwitz
No abstract text is available yet for this article.
February 14, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28193326/properties-of-a-novel-thermostable-glucose-isomerase-mined-from-thermus-oshimai-and-its-application-to-preparation-of-high-fructose-corn-syrup
#16
Dong-Xu Jia, Lin Zhou, Yu-Guo Zheng
Glucose isomerase (GI) is used in vitro to convert d-glucose to d-fructose, which is capable of commercial producing high fructose corn syrup (HFCS). To manufacture HFCS at elevated temperature and reduce the cost of enriching syrups, novel refractory GIs from Thermoanaerobacterium xylanolyticum (TxGI), Thermus oshimai (ToGI), Geobacillus thermocatenulatus (GtGI) and Thermoanaerobacter siderophilus (TsGI) were screened via genome mining approach. The enzymatic characteristics research showed that ToGI had higher catalytic efficiency and superior thermostability toward d-glucose among the screened GIs...
April 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/28182651/a-comprehensive-software-suite-for-protein-family-construction-and-functional-site-prediction
#17
David Renfrew Haft, Daniel H Haft
In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling) is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins...
2017: PloS One
https://www.readbyqxmd.com/read/28181736/high-throughput-mining-of-e-genome-specific-snps-for-characterizing-thinopyrum-elongatum-introgressions-in-common-wheat
#18
Haijuan Lou, Lingli Dong, Kunpu Zhang, Da-Wei Wang, Maolin Zhao, Yiwen Li, Chaowu Rong, Huanju Qin, Aimin Zhang, Zhenying Dong, Daowen Wang
Diploid Thinopyrum elongatum (EE, 2n = 2x = 14) and related polyploid species constitute an important gene pool for improving Triticeae grain and forage crops. However, the genomic and molecular marker resources are generally poor for these species. To aid the genetic, molecular, breeding and ecological studies involving Thinopyrum species, we developed a strategy for mining and validating E-genome specific SNPs using Th. elongatum and common wheat (Triticum aestivum, AABBDD, 2n = 6x = 42) as experimental materials...
February 9, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28181423/next-generation-sequencing-of-mirnas-in-clinical-samples-of-epstein-barr-virus-associated-b-cell-lymphomas
#19
Kouta Sakamoto, Tsuyoshi Sekizuka, Taeko Uehara, Tsunekazu Hishima, Sohtaro Mine, Hitomi Fukumoto, Yuko Sato, Hideki Hasegawa, Makoto Kuroda, Harutaka Katano
Epstein-Barr virus (EBV) encodes 49 microRNAs (miRNAs) in the BART and BHRF1 regions of its genome. Although expression profiles of EBV-encoded miRNAs have been reported for EBV-positive cell lines and nasopharyngeal carcinoma, to date there is little information about total miRNA expression, including cellular and viral miRNAs, in the primary tumors of EBV-associated B-lymphoproliferative disorders. In this study, next-generation sequencing and quantitative real-time reverse transcription-PCR were used to determine the expression profiles of miRNAs in EBV-infected cell lines and EBV-associated B-cell lymphomas, including AIDS-related diffuse large B-cell lymphoma (DLBCL), pyothorax-associated lymphoma, methotrexate-associated lymphoproliferative disorder, EBV-positive DLBCL of the elderly, and Hodgkin lymphoma...
February 9, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28174677/macfp-maximal-approximate-consecutive-frequent-pattern-mining-under-edit-distance
#20
Jingbo Shang, Jian Peng, Jiawei Han
Consecutive pattern mining aiming at finding sequential patterns substrings, is a special case of frequent pattern mining and has been played a crucial role in many real world applications, especially in biological sequence analysis, time series analysis, and network log mining. Approximations, including insertions, deletions, and substitutions, between strings are widely used in biological sequence comparisons. However, most existing string pattern mining methods only consider hamming distance without insertions/deletions (indels)...
May 2016: Proceedings of the ... SIAM International Conference on Data Mining
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