scholarly journals Utility of phylogenetic studies in the identification ofLeptospirastrains

2007 ◽  
Vol 135 (8) ◽  
pp. 1266-1273 ◽  
Author(s):  
G. RESCH ◽  
M. AWAD-MASALMEH ◽  
P. BAKOSS ◽  
J. JAREKOVÁ
Keyword(s):  
Phylogenetic Tree ◽  
Central Europe ◽  
Computer Software ◽  
Digital Reading ◽  
Phylogenetic Studies ◽  
Wild Strains ◽  
Software Programs ◽  
Reference Strains

SUMMARYA phylogenetic tree, which distinguishes between the serovars and serogroups of leptospires common in Central Europe was constructed using an established RAPD procedure together with digital reading and evaluation (using different computer software programs) of the generated amplified DNA patterns. The application of this procedure has revealed a consistent correspondence between serogroup and genotype (position in constructed tree) in 69 cases, and serovar and genotype in 72 cases, of wild strains of leptospires. There was an agreement between serovar and genotype in cases of strains of Grippotyphosa, Pomona, Mozdok, Arborea and Sorexjalna as well as between serogroup and genotype in cases of Australis, Bataviae and Sejroe. With the procedure used in this study, it was not possible to distinguish between reference strains of serovars Jalna, Bratislava and Lora (all serogroup Australis) as well as between serovars Icterohaemorrhagiae and Copenhageni (both of serogroup Icterohaemorrhagiae). In contrast to this, wild strains belonging to serogroup Sejroe were distributed between Polonica, Istrica, Saxkoebing and Sejroe serovars. Endemic strains of leptospires tested, were also distinguishable.

Contemporary media forum: Books, videos, and computer software programs

1996 ◽  
Vol 26 (3) ◽  
pp. 307-318
Author(s):  
Erwin Randolph Parson ◽  
Robert S. Pepper ◽  
Francine Schwartz
Keyword(s):  
Computer Software ◽  
Contemporary Media ◽  
Software Programs ◽  
Media Forum

scholarly journals The Diverse Applications of Tree Set Visualization and Exploration

2020 ◽  
Author(s):  
Jeremy M. Brown ◽  
Genevieve G. Mount ◽  
Kyle A. Gallivan ◽  
James Wilgenbusch
Keyword(s):  
Phylogenetic Tree ◽  
Software Package ◽  
Species Tree ◽  
Model Based ◽  
Phylogenetic Studies ◽  
Tree Inference ◽  
Visualization Techniques ◽  
Species Tree Inference

All phylogenetic studies are built around sets of trees. Tree sets carry different kinds of information depending on the data and approaches used to generate them, but ultimately the variation they contain and their structure is what drives new phylogenetic insights. In order to better understand the variation in and structure of phylogenetic tree sets, we need tools that are generic, flexible, and exploratory. These tools can serve as natural complements to more formal, statistical investigations and allow us to flag surprising or unexpected observations, better understand the results of model-based studies, as well as build intuition. Here, we describe such a set of tools and provide examples of how they can be applied to relevant questions in phylogenetics, phylogenomics, and species-tree inference. These tools include both visualization techniques and quantitative summaries and are currently implemented in the TreeScaper software package (Huang et al. 2016).

scholarly journals So Dark the Con(tu) of Man: The Quest for a Software Derivative Work Right in Section 117

2008 ◽  
Vol 70 (1) ◽  
Author(s):  
Lateef Mtima
Keyword(s):  
Computer Software ◽  
Copyright Law ◽  
Copyright Holder ◽  
User Adaptation ◽  
New Public ◽  
Derivative Work ◽  
Software Programs ◽  
Exclusive Right ◽  
The Impact ◽  
Judicial Recognition

Computer software programs have various unique characteristics as copyrightable works. Among other things, unlike traditional copyrightable works, it is necessary to copy and often to modify software programs in order to use them. In addition, as functional works, the development of additional programs, an overarching goal of copyright protection, often requires the “efficient reuse” of protected elements of preexisting programs. The copyright law currently provides an ambiguous and contradictory response to these issues. While section 117 of the Copyright Act provides program users with the privilege to prepare “adaptations” of copyrighted programs, section 106 reserves to copyright holders the exclusive right to prepare derivative versions of their programs. This article proposes that user adaptation privileges can be distinguished from, and reconciled with, copyright holder derivative work exclusive rights by virtue of the impact that a user-prepared adaptation will have upon the market for the original copyrighted program: “market benign” adaptations should be treated as privileged adaptations, while “market pernicious” adaptations should be treated as derivative works and therefore, subject to the rights of the copyright holder in the original program. In addition, the “practical-use versus market-impact” balancing rationale used to draw the foregoing distinction can also be used to reconstruct the traditional derivative work right into a narrower “software derivative work right.” This software derivative work right would limit the copyright holder’s exclusive right to that of creating derivative programs that are likely to compete with, or otherwise have an undue impact on the market for, the original copyrighted software program. This would enable judicial recognition of a new “public derivative work privilege” to create non-competitive derivative software programs from preexisting works.

scholarly journals A review of vision screening methods for children

2018 ◽  
Vol 77 (1) ◽  
Author(s):  
Ingrid T. Metsing ◽  
Wanda Jacobs ◽  
Rekha Hansraj
Keyword(s):  
Screening Method ◽  
Computer Software ◽  
Cost Effective ◽  
Screening Tests ◽  
Screening Methods ◽  
Vision Screening ◽  
Inclusion Criteria ◽  
Manual Search ◽  
Screening Protocol ◽  
Software Programs

Background: What constitutes an appropriate vision screening protocol is controversial, because the tests or methods are expected to be cost-effective, expedient and easy but efficient in detecting visual anomalies among children.Aim: This review intends to compare the different vision screening tests for children and methods in the interest of identifying the most effective screening method from the standpoint of validity, public acceptance, expediency and cost.Method: The literature search was performed for this review using the Medline, Science Direct and EBSCOhost databases. The search terms used were vision screening methods or tests, children’s vision screenings, computer software programs and vision screening instruments. The inclusion criteria for the articles reviewed were all types of articles related to vision screening methods. The exclusion criteria were all articles for which full text was not available and those not available in English. Eighty articles were analysed, of which 33 were found to have complied with the inclusion criteria and were selected. From the first round of articles retrieved, additional references were identified by a manual search among the cited references.Results: Evidence from the literature reviewed demonstrated that the conventional vision screening method (isolated and combination tests) is the method commonly used to detect a range of relevant visual anomalies among the schoolgoing age group (≥ 6 years) and drew attention to the need for training of vision screening personnel. However, in addition to the conventional method, other vision screening methods include instruments as an adjunct for screening preschoolers and those difficult to screen (≤ 6 years).Conclusion: Inconsistencies in what constitutes an appropriate vision screening method still exist, especially with the booming market of using computer software programs, which still needs to be validated.

scholarly journals Empirical Analysis of Phylogenetic Quasi-Terraces

2019 ◽  
Author(s):  
Paula Breitling ◽  
Alexandros Stamatakis ◽  
Olga Chernomor ◽  
Ben Bettisworth ◽  
Lukasz Reszczynski
Keyword(s):  
Phylogenetic Tree ◽  
Search Algorithms ◽  
Data Sets ◽  
Tree Search ◽  
Significance Tests ◽  
Analogous Structure ◽  
Phylogenetic Studies ◽  
Log Likelihood ◽  
Tree Space ◽  
Nearest Neighborhood

AbstractTerraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.

scholarly journals Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

2019 ◽  
Vol 48 (4) ◽  
pp. 1099-1106
Author(s):  
Emre Sevindik ◽  
Zehra Tuğba Murathan ◽  
Sümeyye Filiz ◽  
Kübra Yalçin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nucleotide Composition ◽  
Neighbor Joining ◽  
Sequencing Data ◽  
F Region ◽  
Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

scholarly journals Sequence-Based Classification Scheme for the GenusLegionella Targeting the mip Gene

1998 ◽  
Vol 36 (6) ◽  
pp. 1560-1567 ◽  
Author(s):  
Rodney M. Ratcliff ◽  
Janice A. Lanser ◽  
Paul A. Manning ◽  
Michael W. Heuzenroeder
Keyword(s):  
Gene Amplification ◽  
Classification Scheme ◽  
Amplicon Sequencing ◽  
Cross Reactivity ◽  
Classification Techniques ◽  
Wild Strains ◽  
Reference Strains ◽  
Phenotypic Classification ◽  
Nucleotide Bases

The identification and speciation of strains ofLegionella is often difficult, and even the more successful chromatographic classification techniques have struggled to discriminate newly described species. A sequence-based genotypic classification scheme is reported, targeting approximately 700 nucleotide bases of the mip gene and utilizing gene amplification and direct amplicon sequencing. With the exception ofLegionella geestiana, for which an amplicon was not produced, the scheme clearly and unambiguously discriminated among the remaining 39 Legionella species and correctly grouped 26 additional serogroup and reference strains within those species. Additionally, the genotypic classification of approximately 150 wild strains from several continents was consistent with their phenotypic classification, with the exception of a few strains where serological cross-reactivity was complex, potentially confusing the latter classification. Strains thought to represent currently uncharacterized species were also found to be genotypically unique. The scheme is technically simple for a laboratory with even basic molecular capabilities and equipment, if access to a sequencing laboratory is available.

scholarly journals A Comparison of Three Circular Mitochondrial Genomes of Fagus sylvatica from Germany and Poland Reveals Low Variation and Complete Identity of the Gene Space

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 571
Author(s):  
Bagdevi Mishra ◽  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Sebastian Ploch ◽  
Jaroslaw Burczyk ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Central Europe ◽  
Glacial Refugia ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Organelle Dna ◽  
Phylogenetic Studies ◽  
Low Degree ◽  
Multiple Copies ◽  
Mitochondrial Sequences

Similar to chloroplast loci, mitochondrial markers are frequently used for genotyping, phylogenetic studies, and population genetics, as they are easily amplified due to their multiple copies per cell. In a recent study, it was revealed that the chloroplast offers little variation for this purpose in central European populations of beech. Thus, it was the aim of this study to elucidate, if mitochondrial sequences might offer an alternative, or whether they are similarly conserved in central Europe. For this purpose, a circular mitochondrial genome sequence from the more than 300-year-old beech reference individual Bhaga from the German National Park Kellerwald-Edersee was assembled using long and short reads and compared to an individual from the Jamy Nature Reserve in Poland and a recently published mitochondrial genome from eastern Germany. The mitochondrial genome of Bhaga was 504,730 bp, while the mitochondrial genomes of the other two individuals were 15 bases shorter, due to seven indel locations, with four having more bases in Bhaga and three locations having one base less in Bhaga. In addition, 19 SNP locations were found, none of which were inside genes. In these SNP locations, 17 bases were different in Bhaga, as compared to the other two genomes, while 2 SNP locations had the same base in Bhaga and the Polish individual. While these figures are slightly higher than for the chloroplast genome, the comparison confirms the low degree of genetic divergence in organelle DNA of beech in central Europe, suggesting the colonisation from a common gene pool after the Weichsel Glaciation. The mitochondrial genome might have limited use for population studies in central Europe, but once mitochondrial genomes from glacial refugia become available, it might be suitable to pinpoint the origin of migration for the re-colonising beech population.

scholarly journals Escherichia coliH-Genotyping PCR: a Complete and Practical Platform for Molecular H Typing

2018 ◽  
Vol 56 (6) ◽  
Author(s):  
Masaya Banjo ◽  
Atsushi Iguchi ◽  
Kazuko Seto ◽  
Taisei Kikuchi ◽  
Tetsuya Harada ◽  
...  
Keyword(s):  
Low Cost ◽  
Epidemiological Studies ◽  
Pathogenic Potential ◽  
Content Type ◽  
E Coli ◽  
Outbreak Investigations ◽  
Pcr Products ◽  
Wild Strains ◽  
Encoding Genes ◽  
Reference Strains

ABSTRACTInEscherichia coli, more than 180 O groups and 53 H types have been recognized. The O:H serotyping ofE. colistrains is an effective method for identifying strains with pathogenic potential and classifying them into clonal groups. In particular, the serotyping of Shiga toxin-producingE. coli(STEC) strains provides valuable information to evaluate the routes, sources, and prevalence of agents in outbreak investigations and surveillance. Here, we present a complete and practical PCR-based H-typing system,E. coliH-genotyping PCR, consisting of 10 multiplex PCR kits with 51 single PCR primer pairs. Primers were designed based on a detailed comparative analysis of sequences from all H-antigen (flagellin)-encoding genes,fliCand its homologs. The specificity of this system was confirmed by using all H type reference strains. Additionally, 362 serotyped wild strains were also used to evaluate its practicality. All 277 H-type-identified isolates gave PCR products that corresponded to the results of serological H typing. Moreover, 76 nonmotile and nine untypeable strains could be successfully subtyped into any H type by the PCR system. TheE. coliH-genotyping PCR developed here allows broader, rapid, and low-cost subtyping of H types and will assist epidemiological studies as well as surveillance of pathogenicE. coli.

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