scholarly journals Comparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species

Pathogens ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 899 ◽  
Author(s):  
Martin Hölzer ◽  
Lisa-Marie Barf ◽  
Kevin Lamkiewicz ◽  
Fabien Vorimore ◽  
Marie Lataretu ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Chlamydia Psittaci ◽  
Analysis Tool ◽  
Closely Related Species ◽  
Functional Studies ◽  
Tryptophan Operon ◽  
The Common ◽  
Characteristic Features ◽  
G 14

To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.

Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)

2020 ◽  
Vol 9 (3) ◽  
pp. 160-170
Author(s):  
Thumadath P.A. Krishna ◽  
Maharajan Theivanayagam ◽  
Gurusunathan V. Roch ◽  
Veeramuthu Duraipandiyan ◽  
Savarimuthu Ignacimuthu
Keyword(s):  
Molecular Marker ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Related Species ◽  
Finger Millet ◽  
Crop Improvement ◽  
Human Beings ◽  
Closely Related Species ◽  
Genome Amplification

Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to finger millet. Cross-genome transferability is the easiest and cheapest method to develop SSR markers. Many comparative mapping studies using microsatellite markers clearly revealed the presence of synteny within the genomes of closely related species/ genus. Sufficient homology exists among several crop plant genomes in the sequences flanking the SSR loci. Thus, the SSR markers are beneficial to amplify the target regions in the finger millet genome. Many SSR markers were used for the analysis of cross-genome amplification in various plants such as Setaria italica, Pennisetum glaucum, Oryza sativa, Triticum aestivum, Zea mays and Hordeum vulgare. However, there is very little information available about cross-genome amplification of these markers in finger millet. The only limited report is available for the utilization of cross-genome amplified microsatellite markers in genetic analysis, gene mapping and other applications in finger millet. This review highlights the importance and implication of microsatellite markers such as genomic SSR (gSSR) and Expressed Sequence Tag (EST)-SSR in cross-genome analysis in finger millet. Nowadays, crop improvement has been one of the major priority areas of research in agriculture. The genome assisted breeding and genetic engineering plays a very crucial role in enhancing crop productivity. The rapid advance in molecular marker technology is helpful for crop improvement. Therefore, this review will be very helpful to the researchers for understanding the importance and implication of SSR markers in closely related species.

scholarly journals 3D Ore Characterization as a Paradigm Shift for Process Design and Simulation in Mineral Processing

2021 ◽  
Author(s):  
Pratama Istiadi Guntoro ◽  
Yousef Ghorbani ◽  
Jan Rosenkranz
Keyword(s):  
Process Design ◽  
Paradigm Shift ◽  
Mineral Processing ◽  
Analysis Tool ◽  
Micro Computed Tomography ◽  
X Ray ◽  
Automated Mineralogy ◽  
Process Mineralogy ◽  
The Common ◽  
Ore Characterization

AbstractCurrent advances and developments in automated mineralogy have made it a crucial key technology in the field of process mineralogy, allowing better understanding and connection between mineralogy and the beneficiation process. The latest developments in X‑ray micro-computed tomography (µCT) have shown a great potential to let it become the next-generation automated mineralogy technique. µCT’s main benefit lies in its capability to allow 3D monitoring of the internal structure of the ore sample at resolutions down to a few hundred nanometers, thus excluding the common stereological error in conventional 2D analysis. Driven by the technological and computational progress, µCT is constantly developing as an analysis tool and successively it will become an essential technique in the field of process mineralogy. This study aims to assess the potential application of µCT systems, for 3D ore characterization through relevant case studies. The opportunities and platforms that µCT 3D ore characterization provides for process design and simulation in mineral processing are presented.

Heart failure in an elderly population

2001 ◽  
Vol 11 (4) ◽  
pp. 311-321
Author(s):  
DN Carmichael ◽  
Michael Lye
Keyword(s):  
Heart Failure ◽  
Treatment Options ◽  
Clinical Syndrome ◽  
Point Of View ◽  
Diagnostic Challenge ◽  
The Common ◽  
Characteristic Features ◽  
The Many ◽  
Neuroendocrine Activation ◽  
Symptoms And Signs

Heart failure has been defined in many ways and definitions change over time. The multiplicity of definitions reflect the paucity of our understanding of the primary underlying physiology of heart failure and the many diseases for which heart failure is the common end-point. Fundamentally, heart failure represents a failure of the heart to meet the body’s requirement for blood supply for whatever reason. It is thus a clinical syndrome with characteristic features – not a single disease in its own right. The syndrome includes symptoms and signs of organ underperfusion, fluid retention and neuroendocrine activation. The syndrome arises from a range of possible causes of which ischaemic heart disease is the commonest. From the point of view of a clinician, the underlying pathology will determine treatment options and prognosis. The extensive range of possible aetiologies present a diagnostic challenge both to correctly identify the syndrome amongst all other causes of dyspnoea and to identify the aetiology, allowing optimization of treatment.

scholarly journals Evolutionary Spread and Recombination of Porcine Endogenous Retroviruses in the Suiformes

2005 ◽  
Vol 79 (1) ◽  
pp. 649-654 ◽  
Author(s):  
Marcus Niebert ◽  
Ralf R. Tönjes
Keyword(s):  
Long Terminal Repeat ◽  
Related Species ◽  
Sus Scrofa ◽  
Endogenous Retroviruses ◽  
Phylogenetic Distance ◽  
African Origin ◽  
Closely Related Species ◽  
Separate Event ◽  
Porcine Endogenous Retroviruses ◽  
The Common

ABSTRACT Different Suiformes with increasing phylogenetic distance to the common pig (Sus scrofa) were assayed for the presence of porcine endogenous retroviruses (PERV) in general (pol gene), while the distribution of long terminal repeat (LTR) types (with or without repeats in U3) and env genes (classes A, B, and C) were determined in detail. PERV was not detectable in the most distantly related species, while classes PERV-A and PERV-B are present in Suiformes originating in the Pliocene epoch, and class PERV-C was detectable only in S. scrofa and in closely related species originating in the Holocene epoch. This distribution pattern of PERV classes is in line with our previous study on the age of PERV (45) and suggests an African origin of about 7.5 million years ago (MYA) and a gradual spread of PERV through the Suiformes. It seems likely that PERV-C originated more recently (1.5 to 3.5 MYA) by recombination with a homologue of unknown descent, while the origin of the repeatless LTR was a separate event approximately 3.5 MYA.

scholarly journals QUEER CRITICISM AS A POST-MODERNIST APPROACH

2015 ◽  
Vol 1 (1) ◽  
pp. 132
Author(s):  
Hamdi Hameed Yousif
Keyword(s):  
Literary Criticism ◽  
Literary Work ◽  
First Century ◽  
Critical Approach ◽  
The Social ◽  
Late Twentieth ◽  
The Common ◽  
Characteristic Features ◽  
The One ◽  
Late Twentieth Century

One of the post-modernist approaches to literary criticism is the queer criticism which has not been evaluated properly. Queer criticism can refer to any piece of literary criticism that interprets a text from a non-straight perspective. Therefore, it includes both lesbian and gay criticism. The aim of this paper, therefore, is to trace the social and political reasons behind the emergence of Queer criticism in the late twentieth century till it acquired momentum in the twenty-first century. After trying to define the terms related to the Queer criticism, the paper tries to examine the poetics of queer (gay and lesbian) literary works and to point out the main characteristic features of this critical approach by identifying the criteria and the textual evidence by which a literary work is labeled queer. It, also tries to shed light on the common features between queer criticism and feminism, on the one hand, and queer criticism and the deconstructuralist approach on the other hand. The final section of the study is a critique which points out the negative aspects of this approach.

scholarly journals Whole genome analysis of the common pathogens associated with microbial keratitis

2019 ◽  
Vol 1 (1A) ◽  
Author(s):  
Michael Glenn ◽  
Stephen Kaye ◽  
Timothy Neal ◽  
Paul Roberts ◽  
Craig Winstanley ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Microbial Keratitis ◽  
Whole Genome Analysis ◽  
The Common

scholarly journals Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

GigaScience ◽  
2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Harry A Thorpe ◽  
Sion C Bayliss ◽  
Samuel K Sheppard ◽  
Edward J Feil
Keyword(s):  
Genome Analysis ◽  
Large Scale ◽  
Analysis Tool ◽  
Pan Genome ◽  
Intergenic Regions

scholarly journals Isostatic postglacial rebound over Fennoscandia with a self-gravitating spherical visco-elastic Earth model

1996 ◽  
Vol 23 ◽  
pp. 318-327 ◽  
Author(s):  
E. Le Meur
Keyword(s):  
Present Model ◽  
Short Review ◽  
Earth Model ◽  
Postglacial Rebound ◽  
Mantle Viscosity ◽  
Surface Displacements ◽  
Grounding Line ◽  
The Common ◽  
Characteristic Features ◽  
Sensitive Issues

Accounting for isostasy in glaciological models has always been a necessity but these models mostly use very simple parameterizations (Le Meur and Huybrechts, 1996). The need for more realistic isostatic parameterizations rapidly became apparent, especially in the treatment of bedrock-sensitive issues such as the grounding-line migration (Huybrechts, 1990a, b). To this end, a rather sophisticated Earth model, avoiding most of the common assumptions, has been developed and is presented here. The two key groups of parameters, to which the model is most sensitive, are the Earth properties and the rheological law used for the mantle. The aim of this paper is first to justify the use of Maxwell rheology for the mantle and then to tune the most sensitive Earth parameter, namely the mantle viscosity, in order to match the numerous present-day uplift data over Fennoscandia. So, in the first instance, a short review of the different available rheologies is presented and discussed. The visco-elastic theory, as well as the mathematical background used in the present model, is also briefly sketched. Secondly, a glacial scenario over Fennoscandia served as an input for the model in a calibration test on the mantle-viscosity values. The degree of agreement of the model outputs with the present-day measurements gives a reference set of Green functions, to which one can reasonably refer when modelling the isostatic response over areas where such a control is not possible (Le Meur and Huybrechts, 1996). Finally, a closer look to the time-dependent surface displacements will confirm the ability for the model to reproduce correctly the main postglacial rebound characteristic features.

scholarly journals Comparative transcriptomics of the venoms of continental and insular radiations of West African cones

2020 ◽  
Vol 287 (1929) ◽  
pp. 20200794
Author(s):  
Samuel Abalde ◽  
Manuel J. Tenorio ◽  
Carlos M. L. Afonso ◽  
Rafael Zardoya
Keyword(s):  
Related Species ◽  
Common Ancestor ◽  
West African ◽  
Generic Level ◽  
Closely Related Species ◽  
Functional Convergence ◽  
Venom Glands ◽  
Phylogenetic Framework ◽  
The Common ◽  
Secreted Peptides

The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera Africonus and Varioconus were sequenced and venom repertoires compared within a phylogenetic framework using one Kalloconus species as outgroup. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one-fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species, and the phylogenetical signal was totally eroded at the inter-generic level (no sequence was identified as shared derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2 and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum-likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of Varioconus . Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.

scholarly journals Transposable Elements and the Evolution of Insects

2021 ◽  
Vol 66 (1) ◽  
pp. 355-372
Author(s):  
Clément Gilbert ◽  
Jean Peccoud ◽  
Richard Cordaux
Keyword(s):  
Transposable Elements ◽  
Related Species ◽  
Horizontal Transfer ◽  
Population Genomics ◽  
Antiviral Immunity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Functional Studies ◽  
Insect Symbionts

Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.

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