scholarly journals Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

2018 ◽  
Vol 37 (9) ◽  
pp. 2322-2338 ◽  
Author(s):  
V.R. Chechetkin ◽  
V.V. Lobzin
Keyword(s):  
Large Scale ◽  
Genomic Sequences ◽  
Genome Packaging

Rice Functional Genomics by Transposon Mutagenesis

2002 ◽  
Vol 06 (24) ◽  
pp. 930-935 ◽  
Author(s):  
Chang-deok Han
Keyword(s):  
Tissue Culture ◽  
Transposable Elements ◽  
Functional Genomics ◽  
Large Scale ◽  
Expression Patterns ◽  
Transposon Mutagenesis ◽  
Transposon Tagging ◽  
Genomic Sequences ◽  
Knock Out ◽  
Genetic Cross

Transposable elements are powerful mutagens. Along with genomic sequences, knock-out phenotypes and expression patterns are important information to elucidate the function of genes. In this review, I propose a strategy to develop tranposant lines on a large scale by combining genetic cross and tissue culture of Ac and Ds lines. Based on the facts that Ds tends to be inactive in F2 or later generation and Ds becomes reactivated via tissue culture, a large scale of transposants can be produced by tissue culture of seeds carrying Ac and inactive Ds. In this review, I describe limitations and considerations in operating transposon tagging systems in rice. Also, I discuss the efficiency of our gene trap system and technical procedures to clone Ds flanking DNA.

scholarly journals Local Evolutionary Patterns of Human Respiratory Syncytial Virus Derived from Whole-Genome Sequencing

2015 ◽  
Vol 89 (7) ◽  
pp. 3444-3454 ◽  
Author(s):  
Charles N. Agoti ◽  
James R. Otieno ◽  
Patrick K. Munywoki ◽  
Alexander G. Mwihuri ◽  
Patricia A. Cane ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Large Scale ◽  
Vaccine Development ◽  
Human Respiratory Syncytial Virus ◽  
Genomic Variation ◽  
Genomic Sequences ◽  
The Novel ◽  
Sequencing Method ◽  
The World ◽  
Syncytial Virus

ABSTRACTHuman respiratory syncytial virus (RSV) is associated with severe childhood respiratory infections. A clear description of local RSV molecular epidemiology, evolution, and transmission requires detailed sequence data and can inform new strategies for virus control and vaccine development. We have generated 27 complete or nearly complete genomes of RSV from hospitalized children attending a rural coastal district hospital in Kilifi, Kenya, over a 10-year period using a novel full-genome deep-sequencing process. Phylogenetic analysis of the new genomes demonstrated the existence and cocirculation of multiple genotypes in both RSV A and B groups in Kilifi. Comparison of local versus global strains demonstrated that most RSV A variants observed locally in Kilifi were also seen in other parts of the world, while the Kilifi RSV B genomes encoded a high degree of variation that was not observed in other parts of the world. The nucleotide substitution rates for the individual open reading frames (ORFs) were highest in the regions encoding the attachment (G) glycoprotein and the NS2 protein. The analysis of RSV full genomes, compared to subgenomic regions, provided more precise estimates of the RSV sequence changes and revealed important patterns of RSV genomic variation and global movement. The novel sequencing method and the new RSV genomic sequences reported here expand our knowledge base for large-scale RSV epidemiological and transmission studies.IMPORTANCEThe new RSV genomic sequences and the novel sequencing method reported here provide important data for understanding RSV transmission and vaccine development. Given the complex interplay between RSV A and RSV B infections, the existence of local RSV B evolution is an important factor in vaccine deployment.

scholarly journals Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

2001 ◽  
Vol 11 (5) ◽  
pp. 677-684
Author(s):  
Yutaka Suzuki ◽  
Tatsuhiko Tsunoda ◽  
Jun Sese ◽  
Hirotoshi Taira ◽  
Junko Mizushima-Sugano ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Genomic Sequences ◽  
Cdna Libraries ◽  
Promoter Regions ◽  
Specific Expression ◽  
Link Type ◽  
Potential Promoter ◽  
E Boxes

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and theTM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos.AU098358–AU100608.]

scholarly journals Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

BMC Genomics ◽  
2006 ◽  
Vol 7 (1) ◽  
Author(s):  
George E Liu ◽  
Lakshmi K Matukumalli ◽  
Tad S Sonstegard ◽  
Larry L Shade ◽  
Curtis P Van Tassell
Keyword(s):  
Large Scale ◽  
Genomic Sequences

Visualizing large-scale genomic sequences

2001 ◽  
Vol 20 (4) ◽  
pp. 49-54 ◽  
Author(s):  
G. Glusman ◽  
D. Lancet
Keyword(s):  
Large Scale ◽  
Genomic Sequences

Efficient and Robust Analysis of Large Phylogenetic Datasets

2011 ◽  
pp. 104-117 ◽  
Author(s):  
Sven Rahmann ◽  
Tobias Muller ◽  
Thomas Dandekar ◽  
Matthias Wolf
Keyword(s):  
Phylogenetic Tree ◽  
Efficient Method ◽  
Software Package ◽  
Large Scale ◽  
Morphological Characteristics ◽  
Tree Topology ◽  
Genomic Sequences ◽  
Neighbor Joining ◽  
Phylogenetic Information ◽  
Robust Analysis

The goal of phylogenetics is to reconstruct ancestral relationships between different taxa, e.g., different species in the tree of life, by means of certain characters, such as genomic sequences. We consider the prominent problem of reconstructing the basal phylogenetic tree topology when several subclades have already been identified or are well known by other means, such as morphological characteristics. Whereas most available tools attempt to estimate a fully resolved tree from scratch, the profile neighbor-joining (PNJ) method focuses directly on the mentioned problem and has proven a robust and efficient method for large-scale datasets, especially when used in an iterative way. We describe an implementation of this idea, the ProfDist software package, which is freely available, and apply the method to estimate the phylogeny of the eukaryotes. Overall, the PNJ approach provides a novel effective way to mine large sequence datasets for relevant phylogenetic information.

scholarly journals Genomic Divergence Between Human and Chimpanzee Estimated from Large-Scale Alignments of Genomic Sequences

2001 ◽  
Vol 92 (6) ◽  
pp. 481-489 ◽  
Author(s):  
F.-C. Chen ◽  
E. J. Vallender ◽  
H. Wang ◽  
C.-S. Tzeng ◽  
W.-H. Li
Keyword(s):  
Large Scale ◽  
Genomic Sequences ◽  
Genomic Divergence

scholarly journals High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Julian R. Garneau ◽  
Véronique Legrand ◽  
Martial Marbouty ◽  
Maximilian O. Press ◽  
Dean R. Vik ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Computing Time ◽  
Rapid Identification ◽  
Viral Metagenomics ◽  
Genome Packaging ◽  
Viral Origin ◽  
Virus Identification ◽  
Viral Particles

AbstractViruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv.

Some comments about observations and image processing of comet 29P/Schwassmann-Wachmann 1

1999 ◽  
Vol 173 ◽  
pp. 243-248
Author(s):  
D. Kubáček ◽  
A. Galád ◽  
A. Pravda
Keyword(s):  
Image Processing ◽  
Large Scale ◽  
Harvard College ◽  
Oak Ridge ◽  
Large Scale Structures ◽  
Short Period Comet ◽  
Short Period ◽  
Scale Structures ◽  
Harvard College Observatory ◽  
Period Comet

AbstractUnusual short-period comet 29P/Schwassmann-Wachmann 1 inspired many observers to explain its unpredictable outbursts. In this paper large scale structures and features from the inner part of the coma in time periods around outbursts are studied. CCD images were taken at Whipple Observatory, Mt. Hopkins, in 1989 and at Astronomical Observatory, Modra, from 1995 to 1998. Photographic plates of the comet were taken at Harvard College Observatory, Oak Ridge, from 1974 to 1982. The latter were digitized at first to apply the same techniques of image processing for optimizing the visibility of features in the coma during outbursts. Outbursts and coma structures show various shapes.

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