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https://www.readbyqxmd.com/read/28632895/genome-mining-reveals-high-incidence-of-putative-lipopeptide-biosynthesis-nrps-pks-clusters-containing-fatty-acyl-amp-ligase-genes-in-biofilm-forming-cyanobacteria
#1
Tomáš Galica, Pavel Hrouzek, Jan Mareš
Cyanobacterial lipopeptides exhibit antimicrobial and antifungal bioactivities with potential for use in pharmaceutical research. However, due to their haemolytic activity and cytotoxic effects against human cells, they may pose a health issue if produced in substantial amounts in the environment. In bacteria, lipopeptides can be synthesized via several well-evidenced mechanisms. In one of them, fatty acyl-AMP ligase (FAAL) initiates the biosynthesis by activation of a fatty acyl residue. We have performed a bioinformatic survey of the cyanobacterial genomic information available in the public databases for the presence of FAAL-containing non-ribosomal peptide synthetase/polyketide synthetase (NRPS/PKS) biosynthetic clusters, as a genetic basis for lipopeptide biosynthesis...
June 20, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28626005/the-auxin-biosynthetic-tryptophan-aminotransferase-related-tatar2-1-3a-increases-wheat-grain-yield
#2
An Shao, Wenying Ma, Xueqiang Zhao, Mengyun Hu, Xue He, Wan Teng, Hui Li, Yiping Tong
Controlling the major auxin biosynthetic pathway to manipulate the auxin content could be a target for genetic engineering of crops with desired traits, but little progress had been made because low or high auxin contents often cause developmental inhibition. Here, we performed a genome-wide analysis of bread wheat (Triticum aestivum) to identify the tryptophan aminotransferase of Arabidopsis1/tryptophan aminotransferase-related (TAA1/TAR) genes that function in the tryptophan-dependent pathway of auxin biosynthesis...
June 16, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28625679/phenotype-databases-for-genetic-screens-in-human-cells
#3
Benedikt Rauscher, Erica Valentini, Ulrike Hardeland, Michael Boutros
Genetic screens are powerful tools to identify components that make up biological systems. Perturbations introduced by methods such as RNA interference (RNAi) or CRISPR/Cas9-mediated genome editing lead to biological phenotypes that can be examined to understand the molecular function of genes in the cell. Over the years, many of such experiments have been conducted providing a wealth of knowledge about genotype-to-phenotype relationships. These data are a rich source of information and it is in a common interest to make them available in a simplified and integrated format...
June 15, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28623888/ub-isap-a-streamlined-unix-pipeline-for-mining-unique-viral-vector-integration-sites-from-next-generation-sequencing-data
#4
Atul Kamboj, Claus V Hallwirth, Ian E Alexander, Geoffrey B McCowage, Belinda Kramer
BACKGROUND: The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. RESULTS: We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28619070/genome-and-transcriptome-sequence-of-finger-millet-eleusine-coracana-l-gaertn-provides-insights-into-drought-tolerance-and-nutraceutical-properties
#5
Shailaja Hittalmani, H B Mahesh, Meghana Deepak Shirke, Hanamareddy Biradar, Govindareddy Uday, Y R Aruna, H C Lohithaswa, A Mohanrao
BACKGROUND: Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful...
June 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28617548/bioinformatic-analysis-of-prognostic-value-of-arap3-in-breast-cancer-and-the-associated-signaling-pathways
#6
J-J Han, B-R Du, C-H Zhang
OBJECTIVE: In this study, we tried to pool previous annotated genomic data to assess the association between ARAP3 expression and metastatic relapse (MR) risk in patients with breast cancer. Moreover, we also investigated the signaling pathways in which ARAP3 might be involved in breast cancer. MATERIALS AND METHODS: The raw microarray data (GDS5666) that compared gene transcriptional profiles of 4T1 derived lung-aggressive explant and primary tumor explant were reanalyzed to identify the dysregulated genes...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28616744/demonstration-that-a-klebsiella-pneumoniae-subsp-pneumoniae-isolated-from-an-insect-nezara-viridula-harbors-a-plasmid-borne-type-iv-secretion-system
#7
Enrique Gino Medrano, Alois A Bell
Previously, we reported the isolation of Klebsiella pneumoniae subspecies pneumoniae strain Kp 5-1 from a southern green stink bug (Nezara viridula) that is a significant pest of numerous economically important crops. We subsequently sequenced the strains whole genome. Here, we report the presence of a functional plasmid-borne type IV secretion (TFSS) system that was identified using genomic mining of the annotated genome. Comparison of the Kp 5-1 resident 186 kb plasmid (pKp 5-1) with nine other Klebsiella with plasmids of comparable size from clinical and environmental strains revealed putative TFSS with identities ranging from 70 to 99%...
June 15, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28611742/analysis-of-the-genome-and-mobilome-of-a-dissimilatory-arsenate-reducing-aeromonas-sp-o23a-reveals-multiple-mechanisms-for-heavy-metal-resistance-and-metabolism
#8
Witold Uhrynowski, Przemyslaw Decewicz, Lukasz Dziewit, Monika Radlinska, Pawel S Krawczyk, Leszek Lipinski, Dorota Adamska, Lukasz Drewniak
Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28611492/genome-mining-and-predictive-functional-profiling-of-acidophilic-rhizobacterium-pseudomonas-fluorescens-pt14
#9
Pooja Rani, Nitish Kumar Mahato, Anukriti Sharma, Desiraju Lakshmi Narsimha Rao, Komal Kamra, Rup Lal
Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P...
June 2017: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/28608126/complete-genome-sequence-of-halomonas-ventosae-virulent-halovirus-qhhsv-1
#10
Chaoqun Fu, Qin Zhao, Zhiying Li, Yongxia Wang, Shiying Zhang, Yonghong Lai, Wei Xiao, Xiaolong Cui
A virulent halovirus QHHSV-1 which lyses Halomonas ventosae QH52-2 originating from the Qiaohou salt mine in Yunnan, Southwest China was characterized. The complete genome of QHHSV-1 is composed of a circular double-stranded DNA of 37,270 base pairs in length, with 66.8% G+C content and 69 putative open reading frames (ORFs), which were classified into five functional groups, including morphogenesis, replication/regulation, packaging, lysis and lysogeny. A putative Cro repressor gene and an integrase gene were found in the genome, showing that QHHSV-1 may utilize a lambda-like repression system under unfavorable conditions...
June 12, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28606152/heterologous-expression-of-cytotoxic-sesquiterpenoids-from-the-medicinal-mushroom-lignosus-rhinocerotis-in-yeast
#11
Hui-Yeng Yeannie Yap, Mariano Jordi Muria-Gonzalez, Boon-Hong Kong, Keith A Stubbs, Chon-Seng Tan, Szu-Ting Ng, Nget-Hong Tan, Peter S Solomon, Shin-Yee Fung, Yit-Heng Chooi
BACKGROUND: Genome mining facilitated by heterologous systems is an emerging approach to access the chemical diversity encoded in basidiomycete genomes. In this study, three sesquiterpene synthase genes, GME3634, GME3638, and GME9210, which were highly expressed in the sclerotium of the medicinal mushroom Lignosus rhinocerotis, were cloned and heterologously expressed in a yeast system. RESULTS: Metabolite profile analysis of the yeast culture extracts by GC-MS showed the production of several sesquiterpene alcohols (C15H26O), including cadinols and germacrene D-4-ol as major products...
June 12, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28603140/mining-the-genome-for-therapeutic-targets
#12
Jose C Florez
Current pharmacological options for type 2 diabetes do not cure the disease. Despite the availability of multiple drug classes that modulate glycemia effectively and minimize long-term complications, these agents do not reverse pathogenesis, and in practice they are not selected to correct the molecular profile specific to the patient. Pharmaceutical companies find drug development programs increasingly costly and burdensome, and many promising compounds fail before launch to market. Human genetics can help advance the therapeutic enterprise...
June 11, 2017: Diabetes
https://www.readbyqxmd.com/read/28596936/new-bioengineering-breakthroughs-and-enabling-tools-in-regenerative-medicine
#13
REVIEW
Alvaro Mata, Helena S Azevedo, Lorenzo Botto, Nuria Gavara, Lei Su
PURPOSE OF REVIEW: In this review, we provide a general overview of recent bioengineering breakthroughs and enabling tools that are transforming the field of regenerative medicine (RM). We focus on five key areas that are evolving and increasingly interacting including mechanobiology, biomaterials and scaffolds, intracellular delivery strategies, imaging techniques, and computational and mathematical modeling. RECENT FINDINGS: Mechanobiology plays an increasingly important role in tissue regeneration and design of therapies...
2017: Current Stem Cell Reports
https://www.readbyqxmd.com/read/28595570/plant-pectin-acetylesterase-structure-and-function-new-insights-from-bioinformatic-analysis
#14
Florian Philippe, Jérôme Pelloux, Catherine Rayon
BACKGROUND: Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. RESULTS: In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases...
June 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28591748/clinical-roles-of-the-aberrantly-expressed-lncrnas-in-lung-squamous-cell-carcinoma-a-study-based-on-rna-sequencing-and-microarray-data-mining
#15
Wen-Jie Chen, Rui-Xue Tang, Rong-Quan He, Dong-Yao Li, Liang Liang, Jiang-Hui Zeng, Xiao-Hua Hu, Jie Ma, Shi-Kang Li, Gang Chen
Lung squamous cell carcinoma (LUSC) accounts for a significant proportion of lung cancer and there have been few therapeutic alternatives for recurrent LUSC due to the lack of specific driver molecules. To investigate the prospective role of lncRNAs in the tumorigenesis and progression of LUSC, the aberrantly expressed lncRNAs were calculated based on The Cancer Genome Atlas RNA-seq data. Of 7589 lncRNAs with 504 LUSC cases, 884 lncRNAs were identified as being aberrantly expressed (|log2 fold change| >2 and adjusted P<0...
May 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28588587/a-dynamic-tandem-repeat-in-monocotyledons-inferred-from-a-comparative-analysis-of-chloroplast-genomes-in-melanthiaceae
#16
Hoang Dang Khoa Do, Joo-Hwan Kim
Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28587624/genome-analysis-of-the-thermoacidophilic-archaeon-acidianus-copahuensis-focusing-on-the-metabolisms-associated-to-biomining-activities
#17
María Sofía Urbieta, Nicolás Rascovan, Martín P Vázquez, Edgardo Donati
BACKGROUND: Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potential and metabolic pathways involved in the biomining activity of this group, we sequenced the genome of Acidianus copahuensis ALE1 strain, a novel thermoacidophilic crenarchaeon (optimum growth: 75 °C, pH 3) isolated from the volcanic geothermal area of Copahue at Neuquén province in Argentina...
June 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28587290/interpreting-microbial-biosynthesis-in-the-genomic-age-biological-and-practical-considerations
#18
REVIEW
Ian J Miller, Marc G Chevrette, Jason C Kwan
Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction...
June 6, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28587273/proteases-of-dermatophagoides-pteronyssinus
#19
Thomas A Randall, Robert E London, Michael C Fitzgerald, Geoffrey A Mueller
Since the discovery that Der p 1 is a cysteine protease, the role of proteolytic activity in allergic sensitization has been explored. There are many allergens with proteolytic activity; however, exposure from dust mites is not limited to allergens. In this paper, genomic, transcriptomic and proteomic data on Dermatophagoides pteronyssinus (DP) was mined for information regarding the complete degradome of this house dust mite. D. pteronyssinus has more proteases than the closely related Acari, Dermatophagoides farinae (DF) and Sarcoptes scabiei (SS)...
June 6, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28586416/bridging-the-gap-between-reproducibility-and-translation-data-resources-and-approaches
#20
Caroline J Zeiss, Linda K Johnson
Animal research has constituted a fundamental means to achieve groundbreaking therapies for human disease. However, for complex diseases, promising preclinical results have failed to translate to the clinic. Reasons for this disparity are multifactorial. These include the challenges inherent in modeling complex disease in animals, as well issues of study design, reproducibility and operational norms within the biomedical research enterprise. In this issue, we explore the range of information resources available for the comparative study of disease, as well as challenges to the ultimate translation of preclinical findings...
June 6, 2017: ILAR Journal
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