scholarly journals A Solution for Universal Classification of Species Based on Genomic DNA

2007 ◽  
Vol 2007 ◽  
pp. 1-8 ◽  
Author(s):  
Mariko Kouduka ◽  
Daisuke Sato ◽  
Manabu Komori ◽  
Motohiro Kikuchi ◽  
Kiyoshi Miyamoto ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Genomic Dna ◽  
Phylogenetic Trees ◽  
Sequencing Technology ◽  
Vast Number ◽  
Number Of Species ◽  
Genome Profiling ◽  
Single Probe ◽  
The Cost

Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact.

Classification of the factors forming the cost of the web-site

2017 ◽  
Vol 31 (2) ◽  
pp. 82-89
Author(s):  
E. S. Epifanov
Keyword(s):  
Web Site ◽  
Internet Site ◽  
Advantages And Disadvantages ◽  
Major Factors ◽  
The Cost ◽  
The Web

This article presents a classification of major factors that shape the cost of Internet site. Also discusses the limitations in determining the objectives of the web site; advantages and disadvantages of different factors.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals Protected Areas in Forest Conservation: Challenges and Opportunities

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 488
Author(s):  
Panayiotis G. Dimitrakopoulos ◽  
Nikoleta Jones
Keyword(s):  
Protected Areas ◽  
Forest Conservation ◽  
Forest Ecosystems ◽  
Vast Number ◽  
Number Of Species ◽  
Challenges And Opportunities

Forest ecosystems are important habitats for a vast number of species worldwide[...]

scholarly journals Antibacterial Activity of Polymer Nanocomposites Incorporating Graphene and Its Derivatives: A State of Art

Polymers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 2105
Author(s):  
Ana M. Díez-Pascual ◽  
José A. Luceño-Sánchez
Keyword(s):  
Graphene Oxide ◽  
Polymeric Nanocomposites ◽  
Natural Polymers ◽  
Vast Number ◽  
Antimicrobial Materials ◽  
Reduced Graphene ◽  
Different Shapes ◽  
Different Characteristics ◽  
State Of Art

The incorporation of carbon-based nanostructures into polymer matrices is a relevant strategy for producing novel antimicrobial materials. By using nanofillers of different shapes and sizes, and polymers with different characteristics, novel antimicrobial nanocomposites with synergistic properties can be obtained. This article describes the state of art in the field of antimicrobial polymeric nanocomposites reinforced with graphene and its derivatives such as graphene oxide and reduced graphene oxide. Taking into account the vast number of articles published, only some representative examples are provided. A classification of the different nanocomposites is carried out, dividing them into acrylic and methacrylic matrices, biodegradable synthetic polymers and natural polymers. The mechanisms of antimicrobial activity of graphene and its derivatives are also reviewed. Finally, some applications of these antimicrobial nanocomposites are discussed. We aim to enhance understanding in the field and promote further work on the development of polymer-based antimicrobial nanocomposites incorporating graphene-based nanomaterials.

scholarly journals Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm

2020 ◽  
Vol 36 (12) ◽  
pp. 3669-3679 ◽  
Author(s):  
Can Firtina ◽  
Jeremie S Kim ◽  
Mohammed Alser ◽  
Damla Senol Cali ◽  
A Ercument Cicek ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Supplementary Information ◽  
Third Generation ◽  
Sequencing Technology ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Generation Sequencing ◽  
Large Genomes

Abstract Motivation Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively. Results We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward–Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts. Availability and implementation Source code is available at https://github.com/CMU-SAFARI/Apollo. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Classification of cesarean section through Robson criteria: an emerging concept to audit the increasing cesarean section rate

2018 ◽  
Vol 7 (11) ◽  
pp. 4674
Author(s):  
Anita Kant ◽  
Shweta Mendiratta
Keyword(s):  
Cesarean Section ◽  
Sedentary Lifestyle ◽  
Health Concern ◽  
Vaginal Birth After Cesarean ◽  
Public Health Concern ◽  
Cesarean Deliveries ◽  
Poor Tolerance ◽  
Group 5 ◽  
The Cost

Background: There has been an increase in rate of cesarean section over last five decades. This is a matter of international public health concern as it increases the cesarean section related maternal morbidity. The aim of the present study was to audit the increasing rate of caesarean section.Methods: In the present study, all cases delivered by cesarean section during the period of six months were recorded and classified according to Robson's 10 group classification system. This was an attempt to see which clinically relevant groups contributed most to the cesarean deliveries.Results: There was a trend of increased percentage of cesarean section in group 5 and 2 respectively in present study. Increasingly sedentary lifestyle and poor tolerance to pain are adding to cesarean delivery on maternal request.Conclusions: We should judiciously make use of vaginal birth after cesarean section but not at the cost of maternal or fetal health. Standardization of indication of cesarean deliveries, regular audits and definite protocols in                                                                                                                                                                                                                                                                                                                                 hospital will aid in curbing the rate of cesarean deliveries in hospitals.

scholarly journals Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Shu-Ting Cho ◽  
Hung-Jui Kung ◽  
Weijie Huang ◽  
Saskia A. Hogenhout ◽  
Chih-Horng Kuo
Keyword(s):  
Molecular Markers ◽  
Genome Analysis ◽  
Species Boundaries

OnAcanthogyrusn.g. from the Intestine of the Indian FishLabeo rohita, with a Note on the Classification of the Acanthocephala

1927 ◽  
Vol 5 (2) ◽  
pp. 109-120 ◽  
Author(s):  
Gobind Singh Thapar
Keyword(s):  
External Morphology ◽  
General Belief ◽  
Number Of Species ◽  
Single Genus

Of the various groups of Helminths, Acanthocephala has received the least attention from Helminthologists; so much so that even its classification is based on very arbitrary characters. This may partly be due to the general belief that infestation with these worms is very rare. The earlier accounts, such as that of Diesing (1851), which deals with a number of species from fishes, giving brief descriptions of their external morphology and a few generalised drawings, describe the various species under a single genus,Echinorhynchus.

scholarly journals Color Metallography

2005 ◽  
Vol 13 (6) ◽  
pp. 22-27 ◽  
Author(s):  
George F. Vander Voort
Keyword(s):  
Digital Imaging ◽  
Color Images ◽  
Vast Number ◽  
Human Eye ◽  
Black And White ◽  
Color Metallography ◽  
The Cost

Color has historically seen limited use in metallography, mainly due to the cost of film and prints and the difficulty and cost of reproducing images in publications. However, with the growth of digital imaging, capturing color images is much simpler and cheaper. Also, printing images in color is inexpensive for in-house reports, and can be distributed cheaply on CDs, although reproduction in journals is still expensive. Color does have many advantages over black and white. First, the human eye is sensitive to only about forty shades of gray from white to black, but is sensitive to a vast number of colors. Tint etchants reveal features in the microstructure that often cannot be revealed using standard black and white etchants.

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