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Genome assembly

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https://www.readbyqxmd.com/read/28222188/the-thermodynamics-of-pr55gag-rna-interaction-regulate-the-assembly-of-hiv
#1
Hanumant S Tanwar, Keith K Khoo, Megan Garvey, Lynne Waddington, Andrew Leis, Marcel Hijnen, Tony Velkov, Geoff J Dumsday, William J McKinstry, Johnson Mak
The interactions that occur during HIV Pr55Gag oligomerization and genomic RNA packaging are essential elements that facilitate HIV assembly. However, mechanistic details of these interactions are not clearly defined. Here, we overcome previous limitations in producing large quantities of full-length recombinant Pr55Gag that is required for isothermal titration calorimetry (ITC) studies, and we have revealed the thermodynamic properties of HIV assembly for the first time. Thermodynamic analysis showed that the binding between RNA and HIV Pr55Gag is an energetically favourable reaction (ΔG<0) that is further enhanced by the oligomerization of Pr55Gag...
February 21, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28221953/comparative-evaluation-of-genomic-and-laboratory-approaches-for-determination-of-shiga-toxin-subtypes-in-escherichia-coli
#2
Catherine D Carrillo, Adam G Koziol, Amit Mathews, Noriko Goji, Dominic Lambert, George Huszczynski, Martine Gauthier, Kingsley Amoako, Burton W Blais
The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole genome sequence analysis using algorithms that can be readily incorporated into bioinformatics analysis pipelines for characterization of isolates by their genetic composition...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221768/formation-of-nitrogenase-nifdk-tetramers-in-the-mitochondria-of-saccharomyces-cerevisiae
#3
Stefan Burén, Eric M Young, Elizabeth A Sweeny, Gema López-Torrejón, Marcel Veldhuizen, Christopher A Voigt, Luis M Rubio
Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle's high O2 consumption and the presence of bacterial-type iron-sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae where transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome...
February 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28220435/rapid-construction-of-multiplexed-crispr-cas9-systems-for-plant-genome-editing
#4
Levi Lowder, Aimee Malzahn, Yiping Qi
Multiplex CRISPR-Cas9 nuclease mediated genome editing is an efficient method for disrupting gene function in plants. Use of CRISPR-Cas9 has escalated rapidly in recent years and is expected to become routine practice in molecular biology and related fields of research. Due to the relatively novel and widespread adoption of this technology, first-time users may not have regular access to experienced guidance or technical support from peers or mentors. Here, we offer guidance and technical support in the form of a detailed and tested protocol for simultaneous targeting of three separate loci on the TRANSPARENT TESTA 4 (TT4) gene in Arabidopsis thaliana using multiplex CRISPR-Cas9...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28220135/differential-gene-expression-analysis-in-polygonum-minus-leaf-upon-24-h-of-methyl-jasmonate-elicitation
#5
Reyhaneh Rahnamaie-Tajadod, Kok-Keong Loke, Hoe-Han Goh, Normah M Noor
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28219831/expression-and-characterization-of-the-major-capsid-protein-derived-from-a-gii-6-norovirus-strain-isolated-in-china
#6
Yuqi Huo, Lijun Zheng, Xuhui Chen, Lili Ge, Yumei Wang
The objective of this study was to express and characterize the major capsid protein (VP1) of a GII.6 Norovirus (NoV)strain isolated in China. The newly identified GII.6 NoV strain was isolated from a five-year old boy presenting acute gastroenteritis. The genome of the GII.6 strain was 7550 nucleotides in length, excluding the poly-adenylation tail. Multiple sequence alignment and phylogenetic analysis based on deduced VP1 amino acid sequences from different genotypes indicated close relationship between GII...
February 17, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28219787/a-novel-archaeal-species-belonging-to-methanoculleus-genus-identified-via-de-novo-assembly-and-metagenomic-binning-process-in-biogas-reactors
#7
Panagiotis G Kougias, Stefano Campanaro, Laura Treu, Xinyu Zhu, Irini Angelidaki
Recently, a first comprehensive catalogue of microbial genomes populating biogas reactors treating manure and agro-industrial residues was determined by sequencing samples collected from 22 biogas reactors including laboratory and full scale. Among the archaeal community, one of the most abundant methanogens belongs to Methanoculleus genus and for this reason it was provisionally named Methanoculleus sp. DTU006. Its full length 16S rRNA sequence is 97% similar to Methanoculleus marisnigri JR1 and to Methanoculleus palmolei DSM 4273...
February 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28219018/selective-incorporation-of-vrnp-into-influenza-a-virions-determined-by-its-specific-interaction-with-m1-protein
#8
Chutikarn Chaimayo, Tsuyoshi Hayashi, Andrew Underwood, Erin Hodges, Toru Takimoto
Influenza A viruses contain eight single-stranded, negative-sense RNA segments as viral genomes in the form of viral ribonucleoproteins (vRNPs). During genome replication in the nucleus, positive-sense complementary RNPs (cRNPs) are produced as replicative intermediates, which are not incorporated into progeny virions. To analyze the mechanism of selective vRNP incorporation into progeny virions, we quantified vRNPs and cRNPs in the nuclear and cytosolic fractions of infected cells, using a strand-specific qRT-PCR...
February 17, 2017: Virology
https://www.readbyqxmd.com/read/28218837/rapid-and-efficient-genome-editing-in-staphylococcus-aureus-by-using-an-engineered-crispr-cas9-system
#9
Weizhong Chen, Yifei Zhang, Won-Sik Yeo, Taeok Bae, Quanjiang Ji
Staphylococcus aureus, a major human pathogen, has been the cause of serious infectious diseases with a high mortality rate. Although genetics is a key means to study S. aureus physiology, such as drug resistance and pathogenesis, genetic manipulation in S. aureus is always time consuming and labor intensive. Here, we report a CRISPR/Cas9 system (pCasSA) for rapid and efficient genome editing, including gene deletion, insertion and single-base substitution mutation in S. aureus. The designed pCasSA system is amenable to assembly of spacers and repair arms by Golden Gate assembly and Gibson assembly, respectively, enabling rapid construction of the plasmids for editing...
February 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28218240/scaffolding-and-completing-genome-assemblies-in-real-time-with-nanopore-sequencing
#10
Minh Duc Cao, Son Hoang Nguyen, Devika Ganesamoorthy, Alysha G Elliott, Matthew A Cooper, Lachlan J M Coin
Third generation sequencing technologies provide the opportunity to improve genome assemblies by generating long reads spanning most repeat sequences. However, current analysis methods require substantial amounts of sequence data and computational resources to overcome the high error rates. Furthermore, they can only perform analysis after sequencing has completed, resulting in either over-sequencing, or in a low quality assembly due to under-sequencing. Here we present npScarf, which can scaffold and complete short read assemblies while the long read sequencing run is in progress...
February 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28217858/golden-gate-assembly-system-dedicated-to-complex-pathway-manipulation-in-yarrowia-lipolytica
#11
Ewelina Celińska, Rodrigo Ledesma-Amaro, Macarena Larroude, Tristan Rossignol, Cyrille Pauthenier, Jean-Marc Nicaud
In this study, we have adopted Golden Gate modular cloning strategy to develop a robust and versatile DNA assembly platform for the nonconventional yeast Yarrowia lipolytica. To this end, a broad set of destination vectors and interchangeable building blocks have been constructed. The DNA modules were assembled on a scaffold of predesigned 4 nt overhangs covering three transcription units (each bearing promoter, gene and terminator), selection marker gene and genomic integration targeting sequences, constituting altogether thirteen elements...
February 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28217442/whole-genome-sequencing-and-analysis-of-campylobacter-coli-yh502-from-retail-chicken-reveals-a-plasmid-borne-type-vi-secretion-system
#12
Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin
Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28217138/using-population-and-comparative-genomics-to-understand-the-genetic-basis-of-effector-driven-fungal-pathogen-evolution
#13
REVIEW
Clémence Plissonneau, Juliana Benevenuto, Norfarhan Mohd-Assaad, Simone Fouché, Fanny E Hartmann, Daniel Croll
Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28217111/integration-of-metagenomic-and-stable-carbon-isotope-evidence-reveals-the-extent-and-mechanisms-of-carbon-dioxide-fixation-in-high-temperature-microbial-communities
#14
Ryan de Montmollin Jennings, James J Moran, Zackary J Jay, Jacob P Beam, Laura M Whitmore, Mark A Kozubal, Helen W Kreuzer, William P Inskeep
Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable (13)C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous "streamer" communities) were investigated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28216647/an-adaptive-decorrelation-method-removes-illumina-dna-base-calling-errors-caused-by-crosstalk-between-adjacent-clusters
#15
Bo Wang, Lin Wan, Anqi Wang, Lei M Li
Base-calling accuracy is crucial for high-throughput DNA sequencing and downstream analysis such as read mapping and genome assembly. Accordingly, we made an endeavor to reduce DNA sequencing errors of Illumina systems by correcting three kinds of crosstalk in the cluster intensity data. We discovered that signal crosstalk between adjacent clusters accounts for a large portion of sequencing errors in Illumina systems, even after correcting color crosstalk caused by the overlap of dye emission spectra and phasing/pre-phasing caused by out-of-step nucleotide synthesis...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216230/activation-of-a-cryptic-splice-site-in-the-mitochondrial-elongation-factor-gfm1-causes-combined-oxphos-deficiency
#16
Mariella T Simon, Bobby G Ng, Marisa W Friederich, Raymond Y Wang, Monica Boyer, Martin Kircher, Renata Collard, Kati J Buckingham, Richard Chang, Jay Shendure, Deborah A Nickerson, Michael J Bamshad, Johan L K Van Hove, Hudson H Freeze, Jose E Abdenur
We report the clinical, biochemical, and molecular findings in two brothers with encephalopathy and multi-systemic disease. Abnormal transferrin glycoforms were suggestive of a type I congenital disorder of glycosylation (CDG). While exome sequencing was negative for CDG related candidate genes, the testing revealed compound heterozygous mutations in the mitochondrial elongation factor G gene (GFM1). One of the mutations had been reported previously while the second, novel variant was found deep in intron 6, activating a cryptic splice site...
February 12, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28216101/genome-sequence-of-methanobacterium-congolense-strain-buetzberg-a-hydrogenotrophic-methanogenic-archaeon-isolated-from-a-mesophilic-industrial-scale-biogas-plant-utilizing-bio-waste
#17
Gonzalo Torres Tejerizo, Yong Sung Kim, Irena Maus, Daniel Wibberg, Anika Winkler, Sandra Off, Alfred Pühler, Paul Scherer, Andreas Schlüter
Methanogenic Archaea are of importance at the end of the anaerobic digestion (AD) chain for biomass conversion. They finally produce methane, the end-product of AD. Among this group of microorganisms, members of the genus Methanobacterium are ubiquitously present in anaerobic habitats, such as bioreactors. The genome of a novel methanogenic archaeon, namely Methanobacterium congolense Buetzberg, originally isolated from a mesophilic biogas plant, was completely sequenced to analyze putative adaptive genome features conferring competitiveness of this isolate within the biogas reactor environment...
February 16, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28216038/de-novo-transcriptome-of-the-muga-silkworm-antheraea-assamensis-helfer
#18
Hasnahana Chetia, Debajyoti Kabiraj, Deepika Singh, Ponnala Vimal Mosahari, Suradip Das, Pragya Sharma, Kartik Neog, Swagata Sharma, P Jayaprakash, Utpal Bora
Antheraea assamensis (Lepidoptera: Saturniidae), is a semi-domesticated silkworm known to be endemic to Assam and the adjoining hilly areas of Northeast India. It is the only producer of a unique, commercially important variety of golden silk called "muga silk". Herein, we report the de novo transcriptome of A. assamensis reared on Machilus bombycina leaves for the first time. Short reads generated by high throughput sequencing of cDNA libraries from multiple tissues, viz. alimentary canal, silk gland and residual body were assembled into transcripts via a de novo assembly pipeline followed by functional annotation and classification...
February 16, 2017: Gene
https://www.readbyqxmd.com/read/28215351/a-genomic-comparison-of-putative-pathogenicity-related-gene-families-in-five-members-of-the-ophiostomatales-with-different-lifestyles
#19
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/28213905/a-ten-gene-containing-genomic-island-determines-flagellin-glycosylation-implication-for-its-regulatory-role-in-motility-and-virulence-of-xanthomonas-oryzae-pv-oryzae
#20
Chao Yu, Huamin Chen, Fang Tian, Fenghuan Yang, Xiaochen Yuan, Ching-Hong Yang, Chenyang He
Flagellin glycosylation plays crucial roles in flagellar assembly, motility and virulence in several pathogenic bacteria. However, little is known about the genetic determinants and biological functions of flagellin glycosylation in Xanthomonas oryzae pv. oryzae (Xoo), the causal pathogen of bacterial blight of rice. Here, the structure, regulation and functions of a ten-gene cluster gigX (glycosylation island genes of Xoo), which was embedded in a flagellar regulon were characterized. gigX1 through gigX10, encoded putative enzymes or proteins involved in glycan biosynthesis and transfer, including a nucleotide sugar transaminase, an acyl-carrier protein (ACP), a 3-oxoacyl-ACP synthase, a 3-oxoacyl-ACP reductase, a dehydrogenase, an acetyltransferase, a ring hydroxylating dioxygenase, a hypothetical protein, a methyltransferanse, and a glycosyltransferase, respectively...
February 18, 2017: Molecular Plant Pathology
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