scholarly journals Genomes of Wolbachia endosymbionts from the human filarial parasites Mansonella perstans and Mansonella ozzardi

2021 ◽  
Author(s):  
Amit Sinha ◽  
Zhiru Li ◽  
Catherine B Poole ◽  
Laurence Ettwiller ◽  
Nathália F Lima ◽  
...  
Keyword(s):  
Data Analysis ◽  
Metagenomic Data ◽  
Clinical Samples ◽  
Valuable Resource ◽  
Genome Sequences ◽  
High Quality ◽  
Metagenome Assembly ◽  
Mansonella Perstans ◽  
Symbiosis Evolution ◽  
Alpha Proteobacteria

Mansonella ozzardi and Mansonella perstans, filarial parasites infecting millions of people worldwide, harbor their unique obligate endosymbionts, the alpha-proteobacteria WolbachiawMoz and wMpe, respectively. Currently, little is known about these Wolbachia and no genome sequences are available. In the current study, high quality draft genomes of wMoz and wMpe were assembled from complex clinical samples using a metagenome assembly and binning approach. These represent the first genomes from supergroup F Wolbachia originating from human parasites and share features characteristic of filarial as well arthropod Wolbachia, consistent with their position in supergroup F. Metagenomic data analysis was also used to estimate Wolbachia titers, which revealed wide variation in levels across different clinical isolates, addressing the contradicting reports on presence or absence of Wolbachia in M. perstans. These findings may have implications for the use antibiotics to treat mansonellosis. The wMoz and wMpe genome sequences provide a valuable resource for further studies on symbiosis, evolution and drug discovery.

scholarly journals MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

2018 ◽  
Author(s):  
Gherman V Uritskiy ◽  
Jocelyne DiRuggiero ◽  
James Taylor
Keyword(s):  
Data Analysis ◽  
Shotgun Sequencing ◽  
Metagenomic Analysis ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
High Quality ◽  
Single Genome ◽  
Significant Burden ◽  
Versatile Tool ◽  
Genome Level

AbstractBackground:The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization.Results:To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP’s hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real datasets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization.Conclusions:MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP.

scholarly journals Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sten Ilmjärv ◽  
Fabien Abdul ◽  
Silvia Acosta-Gutiérrez ◽  
Carolina Estarellas ◽  
Ioannis Galdadas ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Spike Protein ◽  
Genome Sequences ◽  
Viral Polymerase ◽  
Rna Dependent Rna Polymerase ◽  
High Quality

AbstractThe D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.

scholarly journals High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

2018 ◽  
Vol 6 (19) ◽  
pp. e00383-18 ◽  
Author(s):  
David K. Ngugi ◽  
Ulrich Stingl
Keyword(s):  
Single Cell ◽  
Lake Sediments ◽  
Red Sea ◽  
Genome Sequence ◽  
Soda Lake ◽  
Genome Sequences ◽  
High Quality ◽  
Candidate Division ◽  
Cell Genome ◽  
Single Cell Genome

ABSTRACT Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

scholarly journals ANALISIS TINGKAT KEPUASAN PELANGGAN TERHADAP PELAYANAN PT PELNI (PERSERO)

2018 ◽  
Vol 1 (2) ◽  
Author(s):  
Arif Fatkur Rohman ◽  
Bambang Syairudin ◽  
Endah Angreni
Keyword(s):  
Data Analysis ◽  
Customer Satisfaction ◽  
Continuous Improvement ◽  
Shopping Centers ◽  
Analysis Method ◽  
Clean Room ◽  
High Quality ◽  
Repair Service ◽  
Research Results ◽  
Sample Data

Development and competition business of transporting had been restrictive. Each operators race competition do innovation, efficiency, and continuous improvement. The customers of PT Pelni from year to year continues to decrease. Although actually PT Pelni also improve themselves, repair service and innovation, but still be unable to improve the number of passengers. This study attempts to know the level customer satisfaction PT Pelni to make known well and innovation that has done is in line with hope customers. The measurement of the customer satisfaction PT Pelni done with the approach servqual method. Aspects which are under consideration includes 5 dimensions main namely tangibles, reliability, responsiveness, assurance, and empathy which divided in 29 indicators variable. This research using respondents as the sample. Data analysis used the analysis method servqual and cartesious diagrams. The research results show that there are inconquirity between hope customers by the fact experienced. The largest is in dimension tangible, with the gap an average of -1,3.While gap smallest there are in dimension responsiveness -0,42. Analysis by diagram cartecious show you some attribute in the main priority improvement: furnishings that high quality (2), facilities shopping centers on a vessel (4), the availability of a bed with the corresponding numbers of a ticket (6), size cabin large (7), and the condition a clean room (8). All those attributes including in dimension of tangible.

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

2021 ◽  
Author(s):  
Kevin S Kuchinski ◽  
Jason Nguyen ◽  
Tracy D Lee ◽  
Rebecca Hickman ◽  
Agatha N Jassem ◽  
...  
Keyword(s):  
British Columbia ◽  
Laboratory Data ◽  
Genomic Sequencing ◽  
Genome Sequences ◽  
High Quality ◽  
Laboratory Methods ◽  
Clinical Specimens ◽  
Recent Outbreak ◽  
High Quality Genome

Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance.

scholarly journals Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA

2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Robbie M. Martin ◽  
Michael Kausch ◽  
Kimarie Yap ◽  
John D. Wehr ◽  
Gregory L. Boyer ◽  
...  
Keyword(s):  
New York ◽  
Cyanobacterial Bloom ◽  
Genome Sequences ◽  
High Quality ◽  
Planktothrix Agardhii ◽  
Content Type ◽  
Fresh Waters

ABSTRACT Raphidiopsis raciborskii and Planktothrix agardhii are filamentous, potentially toxin-producing cyanobacteria that form nuisance blooms in fresh waters. Here, we report high-quality metagenome-assembled genome sequences of R. raciborskii and P. agardhii collected from a bloom in Kissena Lake, New York.

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