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https://www.readbyqxmd.com/read/28088540/multiplexed-site-specific-genome-engineering-for-overproducing-bioactive-secondary-metabolites-in-actinomycetes
#1
Lei Li, Guosong Zheng, Jun Chen, Mei Ge, Weihong Jiang, Yinhua Lu
Actinomycetes produce a large variety of pharmaceutically active compounds, yet production titers often require to be improved for discovery, development and large-scale manufacturing. Here, we describe a new technique, multiplexed site-specific genome engineering (MSGE) via the 'one integrase-multiple attB sites' concept, for the stable integration of secondary metabolite biosynthetic gene clusters (BGCs). Using MSGE, we achieved five-copy chromosomal integration of the pristinamycin II (PII) BGC in Streptomyces pristinaespiralis, resulting in the highest reported PII titers in flask and batch fermentations (2...
January 11, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#2
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#3
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077090/gbs-based-single-dosage-markers-for-linkage-and-qtl-mapping-allow-gene-mining-for-yield-related-traits-in-sugarcane
#4
Thiago Willian Almeida Balsalobre, Guilherme da Silva Pereira, Gabriel Rodrigues Alves Margarido, Rodrigo Gazaffi, Fernanda Zatti Barreto, Carina Oliveira Anoni, Cláudio Benício Cardoso-Silva, Estela Araújo Costa, Melina Cristina Mancini, Hermann Paulo Hoffmann, Anete Pereira de Souza, Antonio Augusto Franco Garcia, Monalisa Sampaio Carneiro
BACKGROUND: Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28074120/complete-genome-sequence-of-the-heavy-metal-resistant-bacterium-agromyces-aureus-ar33-t-and-comparison-with-related-actinobacteria
#5
Erika Corretto, Livio Antonielli, Angela Sessitsch, Stéphane Compant, Christoph Höfer, Markus Puschenreiter, Günter Brader
Agromyces aureus AR33(T) is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#6
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28065665/unbiased-identification-of-blood-based-biomarkers-for-pulmonary-tuberculosis-by-modeling-and-mining-molecular-interaction-networks
#7
Awanti Sambarey, Abhinandan Devaprasad, Abhilash Mohan, Asma Ahmed, Soumya Nayak, Soumya Swaminathan, George D'Souza, Anto Jesuraj, Chirag Dhar, Subash Babu, Annapurna Vyakarnam, Nagasuma Chandra
Efficient diagnosis of tuberculosis (TB) is met with multiple challenges, calling for a shift of focus from pathogen-centric diagnostics towards identification of host-based multi-marker signatures. Transcriptomics offer a list of differentially expressed genes, but cannot by itself identify the most influential contributors to the disease phenotype. Here, we describe a computational pipeline that adopts an unbiased approach to identify a biomarker signature. Data from RNA sequencing from whole blood samples of TB patients were integrated with a curated genome-wide molecular interaction network, from which we obtain a comprehensive perspective of variations that occur in the host due to TB...
February 2017: EBioMedicine
https://www.readbyqxmd.com/read/28061369/employing-image-processing-techniques-for-cancer-detection-using-microarray-images
#8
Nastaran Dehghan Khalilabad, Hamid Hassanpour
Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes...
December 21, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28060710/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#9
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28053166/world-data-centre-for-microorganisms-an-information-infrastructure-to-explore-and-utilize-preserved-microbial-strains-worldwide
#10
Linhuan Wu, Qinglan Sun, Philippe Desmeth, Hideaki Sugawara, Zhenghong Xu, Kevin McCluskey, David Smith, Vasilenko Alexander, Nelson Lima, Moriya Ohkuma, Vincent Robert, Yuguang Zhou, Jianhui Li, Guomei Fan, Supawadee Ingsriswang, Svetlana Ozerskaya, Juncai Ma
The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC)-Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28043922/reconstruction-of-a-genome-scale-metabolic-model-and-in-silico-analysis-of-the-polymalic-acid-producer-aureobasidium-pullulans-cctcc-m2012223
#11
Jun Feng, Jing Yang, Xiaorong Li, Meijin Guo, Bochu Wang, Shang-Tian Yang, Xiang Zou
Aureobasidium pullulans is a yeast-like fungus used for producing biopolymers e.g. polymalic acid (PMA) and pullulan. A high PMA producing strain, A. pullulans CCTCC M2012223, was isolated and sequenced in our previous study. To understand its metabolic performance, a genome-scale metabolic model, iZX637, consisting of 637 genes, 1347 reactions and 1133 metabolites, was reconstructed based on genome annotation and literature mining studies. The iZX637 model was validated by simulating cell growth, utilization of carbon and nitrogen sources, and gene essentiality analysis in A...
December 30, 2016: Gene
https://www.readbyqxmd.com/read/28036252/pseudaminobacter-manganicus-sp-nov-isolated-from-sludge-of-a-manganese-mine
#12
Jiahong Li, Jing Huang, Shuijiao Liao, Gejiao Wang
A Gram-staining-negative, aerobic, non-motile, capsule-forming and rod-shaped bacterium, designated JH-7T, was isolated from sludge of a manganese mine. The 16S rRNA gene sequence of strain JH-7T showed highest similarities to Pseudaminobacter salicylatoxidans BN12T (97.4 %), Mesorhizobium thiogangeticum SJTT (97.0 %) and Pseudaminobacter defluvii THI 051T (96.5 %). Phylogenetic trees clustered strain JH-7T together with P. salicylatoxidans BN12T and P. defluvii THI 051T. The DNA-DNA hybridization values between strain JH-7T and P...
December 30, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28029655/identifying-prognostic-biomarkers-based-on-aberrant-dna-methylation-in-kidney-renal-clear-cell-carcinoma
#13
Guang Chen, Yihan Wang, Lu Wang, Wanhai Xu
The outcome of kidney renal clear cell carcinoma (KIRC) differs even among individuals with similar clinical characteristics. DNA methylation is regarded as a regulator of gene expression in cancers, which may be a molecular marker of prognosis. In this study, we aimed to mine novel methylation markers of the prognosis of KIRC. We revealed a total of 2793 genes differentially methylated in their promoter regions (DMGs) and 2979 differentially expressed genes (DEGs) in KIRC tissues compared with normal tissues using The Cancer Genome Atlas datasets...
December 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/28029220/exome-sequencing-provides-additional-evidence-for-the-involvement-of-arhgap29-in-mendelian-orofacial-clefting-and-extends-the-phenotypic-spectrum-to-isolated-cleft-palate
#14
Huan Liu, Tamara Busch, Steven Eliason, Deepti Anand, Steven Bullard, Lord J J Gowans, Nichole Nidey, Aline Petrin, Eno-Abasi Augustine-Akpan, Irfan Saadi, Martine Dunnwald, Salil A Lachke, Ying Zhu, Adebowale Adeyemo, Brad Amendt, Tony Roscioli, Robert Cornell, Jeffrey Murray, Azeez Butali
BACKGROUND: Recent advances in genomics methodologies, in particular the availability of next-generation sequencing approaches have made it possible to identify risk loci throughout the genome, in particular the exome. In the current study, we present findings from an exome study conducted in five affected individuals of a multiplex family with cleft palate only. METHODS: The GEnome MINIng (GEMINI) pipeline was used to functionally annotate the single nucleotide polymorphisms, insertions and deletions...
December 28, 2016: Birth Defects Research. Part A, Clinical and Molecular Teratology
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#15
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28025338/tbro-visualization-and-management-of-de-novo-transcriptomes
#16
Markus J Ankenbrand, Lorenz Weber, Dirk Becker, Frank Förster, Felix Bemm
RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28018846/developing-integrated-crop-knowledge-networks-to-advance-candidate-gene-discovery
#17
Keywan Hassani-Pak, Martin Castellote, Maria Esch, Matthew Hindle, Artem Lysenko, Jan Taubert, Christopher Rawlings
The chances of raising crop productivity to enhance global food security would be greatly improved if we had a complete understanding of all the biological mechanisms that underpinned traits such as crop yield, disease resistance or nutrient and water use efficiency. With more crop genomes emerging all the time, we are nearer having the basic information, at the gene-level, to begin assembling crop gene catalogues and using data from other plant species to understand how the genes function and how their interactions govern crop development and physiology...
December 2016: Applied & Translational Genomics
https://www.readbyqxmd.com/read/28018385/chloroplast-genome-sequence-of-pigeonpea-cajanus-cajan-l-millspaugh-and-cajanus-scarabaeoides-l-thouars-genome-organization-and-comparison-with-other-legumes
#18
Tanvi Kaila, Pavan K Chaduvla, Swati Saxena, Kaushlendra Bahadur, Santosh J Gahukar, Ashok Chaudhury, T R Sharma, N K Singh, Kishor Gaikwad
Pigeonpea (Cajanus cajan (L.) Millspaugh), a diploid (2n = 22) legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides (L.) Thouars were generated. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harboring the C...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28013273/catchup-a-web-database-for-spatiotemporally-regulated-genes
#19
Yukino Nakamura, Toru Kudo, Shin Terashima, Misa Saito, Eiji Nambara, Kentaro Yano
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of genome-scale functional gene networks. However, comprehensive information on spatiotemporally expressed genes is lacking in plants. To collect such information, we devised a new index, δdmax, which is the maximum difference in relative gene expression levels between sample runs which are neighboring when sorted by the levels...
December 23, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28013086/rational-synthetic-pathway-refactoring-of-natural-products-biosynthesis-in-actinobacteria
#20
REVIEW
Gao-Yi Tan, Tiangang Liu
Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency...
January 2017: Metabolic Engineering
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