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Genome assembly

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https://www.readbyqxmd.com/read/28806750/characterization-of-novel-bangle-lectin-from-photorhabdus-asymbiotica-with-dual-sugar-binding-specificity-and-its-effect-on-host-immunity
#1
Gita Jančaříková, Josef Houser, Pavel Dobeš, Gabriel Demo, Pavel Hyršl, Michaela Wimmerová
Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P...
August 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28802692/de-novo-transcriptome-assembly-and-rna-seq-expression-analysis-in-blood-from-beluga-whales-of-bristol-bay-ak
#2
Jeanine S Morey, Kathy A Burek Huntington, Michelle Campbell, Tonya M Clauss, Caroline E Goertz, Roderick C Hobbs, Denise Lunardi, Amanda J Moors, Marion G Neely, Lori H Schwacke, Frances M Van Dolah
Assessing the health of marine mammal sentinel species is crucial to understanding the impacts of environmental perturbations on marine ecosystems and human health. In Arctic regions, beluga whales, Delphinapterus leucas, are upper level predators that may serve as a sentinel species, potentially forecasting impacts on human health. While gene expression profiling from blood transcriptomes has widely been used to assess health status and environmental exposures in human and veterinary medicine, its use in wildlife has been limited due to the lack of available genomes and baseline data...
August 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28802076/single-cell-sequencing-unveils-the-lifestyle-and-crispr-based-population-history-of-hydrotalea-sp-in-acid-mine-drainage
#3
J D Medeiros, L R Leite, V S Pylro, F S Oliveira, V M Almeida, G R Fernandes, A C M Salim, F M G Araújo, A C Volpini, G Oliveira, S Cuadros-Orellana
Acid mine drainage (AMD) is characterized by an acid and metal-rich runoff that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea, and is closely related to H. flava. The phylogeny and average nucleotide identity analysis suggest that all single-amplified genomes (SAGs) form two clades that may represent different strains...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28802047/dual-ifgmosaic-a-versatile-method-for-multispectral-and-combinatorial-mosaic-gene-function-analysis
#4
Samuel Pontes-Quero, Luis Heredia, Verónica Casquero-García, Macarena Fernández-Chacón, Wen Luo, Ana Hermoso, Mayank Bansal, Irene Garcia-Gonzalez, Maria S Sanchez-Muñoz, Juan R Perea, Adrian Galiana-Simal, Iker Rodriguez-Arabaolaza, Sergio Del Olmo-Cabrera, Susana F Rocha, Luis M Criado-Rodriguez, Giovanna Giovinazzo, Rui Benedito
Improved methods for manipulating and analyzing gene function have provided a better understanding of how genes work during organ development and disease. Inducible functional genetic mosaics can be extraordinarily useful in the study of biological systems; however, this experimental approach is still rarely used in vertebrates. This is mainly due to technical difficulties in the assembly of large DNA constructs carrying multiple genes and regulatory elements and their targeting to the genome. In addition, mosaic phenotypic analysis, unlike classical single gene-function analysis, requires clear labeling and detection of multiple cell clones in the same tissue...
August 10, 2017: Cell
https://www.readbyqxmd.com/read/28801606/linkage-mapping-aided-by-de-novo-genome-and-transcriptome-assembly-in-portunus-trituberculatus-applications-in-growth-related-qtl-and-gene-identification
#5
Jianjian Lv, Baoquan Gao, Ping Liu, Jian Li, Xianliang Meng
A high-resolution genetic linkage map is an essential tool for decoding genetics and genomics in non-model organisms. In this study, a linkage map was constructed for the swimming crab (Portunus trituberculatus) with 10,963 markers; as far as we know, this number of markers has never been achieved in any other crustacean. The linkage map covered 98.85% of the whole genome with a mean marker interval of 0.51 cM. The de novo assembly based on genome and transcriptome sequencing data enabled 2,378 explicit annotated markers to be anchored to the map...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800965/the-crispr-cas9-facilitated-multiplex-pathway-optimization-cfpo-technique-and-its-application-to-improve-the-escherichia-coli-xylose-utilization-pathway
#6
Xinna Zhu, Dongdong Zhao, Huanna Qiu, Feiyu Fan, Shuli Man, Changhao Bi, Xueli Zhang
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome...
August 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28800596/fungal-genome-and-mating-system-transitions-facilitated-by-chromosomal-translocations-involving-intercentromeric-recombination
#7
Sheng Sun, Vikas Yadav, R Blake Billmyre, Christina A Cuomo, Minou Nowrousian, Liuyang Wang, Jean-Luc Souciet, Teun Boekhout, Betina Porcel, Patrick Wincker, Joshua A Granek, Kaustuv Sanyal, Joseph Heitman
Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million infections globally annually. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes...
August 11, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28800158/using-kbase-to-assemble-and-annotate-prokaryotic-genomes
#8
Benjamin Allen, Meghan Drake, Nomi Harris, Tarah Sullivan
The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) is an open-access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next-Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes...
August 11, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28799737/method-to-assemble-genomic-dna-fragments-or-genes-on-human-artificial-chromosome-with-regulated-kinetochore-using-a-multi-integrase-system
#9
Nicholas C O Lee, Jung-Hyun Kim, Nikolai Petrov, Hee-Sheung Lee, Hiroshi Masumoto, William C Earnshaw, Vladimir Larionov, Natalay Kouprina
The production of cells capable of carrying multiple transgenes to Mb-size genomic loci has multiple applications in biomedicine and biotechnology. In order to achieve this goal, three key steps are required: i) Cloning of large genomic segments; ii) Insertion of multiple DNA blocks at a precise location and iii) The capability to eliminate the assembled region from cells. In this study, we designed the Iterative Integration System (IIS) that utilizes recombinases Cre, ΦC31 and ΦBT1, and combined it with Human Artificial Chromosome (HAC) possessing a regulated kinetochore (alphoid(tetO)-HAC)...
August 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28798728/draft-genome-sequence-of-the-nitrogen-fixing-rhizobium-sullae-type-strain-is123-t-focusing-on-the-key-genes-for-symbiosis-with-its-host-hedysarum-coronarium-l
#10
Gaurav Sablok, Riccardo Rosselli, Torsten Seeman, Robin van Velzen, Elisa Polone, Alessio Giacomini, Nicola La Porta, Rene Geurts, Rosella Muresu, Andrea Squartini
The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123(T) nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798311/genomic-regions-and-genes-related-to-inter-population-differences-in-body-size-in-the-ground-beetle-carabus-japonicus
#11
Ryohei Komurai, Tomochika Fujisawa, Yutaka Okuzaki, Teiji Sota
Body size is a key trait in diversification among animal species, and revealing the gene regions responsible for body size diversification among populations or related species is important in evolutionary biology. We explored the genomic regions associated with body size differences in Carabus japonicus ground beetle populations by quantitative trait locus (QTL) mapping of F2 hybrids from differently sized parents from two populations using restriction site-associated DNA sequencing and de novo assembly of the beetle whole genome...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798190/draft-genome-sequence-of-thiohalobacter-thiocyanaticus-strain-fokn1-a-neutrophilic-halophile-capable-of-thiocyanate-degradation
#12
Mamoru Oshiki, Toshikazu Fukushima, Shuichi Kawano, Junichi Nakagawa
A draft genome sequence of a neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter thiocyanaticus FOKN1, was determined using a PacBio RSII sequencer. A 3.23-Mb circular genome sequence was assembled, in which 3,026 gene-coding sequences, 45 tRNAs, and 1 rrn operon were annotated.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798184/complete-genome-sequence-and-annotation-of-the-staphylococcus-aureus-strain-hg001
#13
Isabelle Caldelari, Béatrice Chane-Woon-Ming, Céline Noirot, Karen Moreau, Pascale Romby, Christine Gaspin, Stefano Marzi
Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a positive activator of SigB).
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798176/draft-genome-sequence-of-magnetospirillum-sp-strain-15-1-a-denitrifying-toluene-degrader-isolated-from-a-planted-fixed-bed-reactor
#14
Ingrid Meyer-Cifuentes, Stefan Fiedler, Jochen A Müller, Uwe Kappelmeyer, Ines Mäusezahl, Hermann J Heipieper
Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was isolated from a planted fixed-bed reactor based on its ability to degrade toluene under anaerobic conditions. The genome assembly consists of 5.4 Mb in 28 contigs and 5,095 coding sequences containing the genes involved in anaerobic toluene degradation.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798170/whole-genome-sequence-of-the-soil-bacterium-micrococcus-sp-kbs0714
#15
V Kuo, W R Shoemaker, M E Muscarella, J T Lennon
We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from agricultural soil. The genome provides insight into the strategies that Micrococcus spp. use to contend with environmental stressors such as desiccation and starvation in environmental and host-associated ecosystems.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798164/draft-nuclear-genome-complete-chloroplast-genome-and-complete-mitochondrial-genome-for-the-biofuel-bioproduct-feedstock-species-scenedesmus-obliquus-strain-doe0152z
#16
S R Starkenburg, J E W Polle, B Hovde, H E Daligault, K W Davenport, A Huang, P Neofotis, Z McKie-Krisberg
The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28797211/disulfide-bonds-a-key-modification-in-bacterial-extracytoplasmic-proteins
#17
S F Lee, L Davey
Disulfide bonds are a common posttranslational modification that contributes to the folding and stability of extracytoplasmic proteins. Almost all organisms, from eukaryotes to prokaryotes, have evolved enzymes to make and break these bonds. Accurate and efficient disulfide bond formation can be vital for protein function; therefore, the enzymes that catalyze disulfide bond formation are involved in multiple biological processes. Recent advances clearly show that oral bacteria also have the ability to from disulfide bonds, and this ability has an effect on a range of dental plaque-related phenotypes...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28795188/filovirus-structural-biology-the-molecules-in-the-machine
#18
Robert N Kirchdoerfer, Hal Wasserman, Gaya K Amarasinghe, Erica Ollmann Saphire
In this chapter, we describe what is known thus far about the structures and functions of the handful of proteins encoded by filovirus genomes. Amongst the fascinating findings of the last decade is the plurality of functions and structures that these polypeptides can adopt. Many of the encoded proteins can play multiple, distinct roles in the virus life cycle, although the mechanisms by which these functions are determined and controlled remain mostly veiled. Further, some filovirus proteins are multistructural: adopting different oligomeric assemblies and sometimes, different tertiary structures to achieve their separate, and equally essential functions...
August 10, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28794988/whole-genome-sequencing-of-microbacterium-sp-aiso3-from-polluted-san-jacinto-river-sediment-reveals-high-bacterial-mobility-metabolic-versatility-and-heavy-metal-resistance
#19
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794924/expression-of-tomato-yellow-leaf-curl-virus-coat-protein-using-baculovirus-expression-system-and-evaluation-of-its-utility-as-a-viral-antigen
#20
Lamiaa Elgaied, Reda Salem, Wael Elmenofy
DNA encoding the coat protein (CP) of an Egyptian isolate of tomato yellow leaf curl virus (TYLCV) was inserted into the genome of Autographa californica nucleopolyhedrovirus (AcNPV) under the control of polyhedrin promoter. The generated recombinant baculovirus construct harboring the coat protein gene was characterized using PCR analysis. The recombinant coat protein expressed in infected insect cells was used as a coating antigen in an indirect Enzyme-linked immunosorbent assay (ELISA) and dot blot to test its utility for the detection of antibody generated against TYLCV virus particles...
August 2017: 3 Biotech
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