scholarly journals Integrative Conjugative Elements and Related Elements Are Major Contributors to the Genome Diversity of Streptococcus agalactiae

2008 ◽  
Vol 190 (20) ◽  
pp. 6913-6917 ◽  
Author(s):  
Mathieu Brochet ◽  
Elisabeth Couvé ◽  
Philippe Glaser ◽  
Gérard Guédon ◽  
Sophie Payot
Keyword(s):  
Streptococcus Agalactiae ◽  
Wide Distribution ◽  
High Plasticity ◽  
Genome Diversity ◽  
Site Specific ◽  
Five Elements ◽  
Macroarray Analysis ◽  
Integrative Conjugative Elements

ABSTRACT Thirty-five putative integrative conjugative elements and related elements were identified at 15 locations in the eight sequenced genomes of Streptococcus agalactiae. Twelve are composite, likely resulting from site-specific accretions. Circular forms were detected for five elements. Macroarray analysis confirmed their high plasticity and wide distribution in S. agalactiae.

scholarly journals Malarial parasites as geographical markers in migratory birds?

2006 ◽  
Vol 2 (2) ◽  
pp. 213-216 ◽  
Author(s):  
Sylvia M Fallon ◽  
Robert C Fleischer ◽  
Gary R Graves
Keyword(s):  
North America ◽  
Migratory Birds ◽  
Wide Distribution ◽  
Specific Information ◽  
Population Movements ◽  
Site Specific ◽  
Dendroica Caerulescens ◽  
Bird Populations ◽  
Breeding Populations ◽  
Wintering Range

We tested the hypothesis that malarial parasites ( Plasmodium and Haemoproteus ) of black-throated blue warblers ( Dendroica caerulescens ) provide sufficient geographical signal to track population movements between the warbler's breeding and wintering habitats in North America. Our results from 1083 warblers sampled across the species' breeding range indicate that parasite lineages are geographically widespread and do not provide site-specific information. The wide distribution of malarial parasites probably reflects postnatal dispersal of their hosts as well as mixing of breeding populations on the wintering range. When compared to geographically structured parasites of sedentary Caribbean songbirds, patterns of malarial infections in black-throated blue warblers suggest that host–malaria dynamics of migratory and sedentary bird populations may be subject to contrasting selection pressures.

scholarly journals Conjugative Transfer of the Integrative Conjugative Elements ICESt1 and ICESt3 from Streptococcus thermophilus

2009 ◽  
Vol 191 (8) ◽  
pp. 2764-2775 ◽  
Author(s):  
Xavier Bellanger ◽  
Adam P. Roberts ◽  
Catherine Morel ◽  
Frédéric Choulet ◽  
Guillaume Pavlovic ◽  
...  
Keyword(s):  
Streptococcus Thermophilus ◽  
Genomic Islands ◽  
Conjugative Transfer ◽  
Integrase Gene ◽  
Site Specific ◽  
Integrative And Conjugative Elements ◽  
Conjugative Transposons ◽  
Site Specific Integration ◽  
The One ◽  
Integrative Conjugative Elements

ABSTRACT Integrative and conjugative elements (ICEs), also called conjugative transposons, are genomic islands that excise, self-transfer by conjugation, and integrate in the genome of the recipient bacterium. The current investigation shows the intraspecies conjugative transfer of the first described ICEs in Streptococcus thermophilus, ICESt1 and ICESt3. Mitomycin C, a DNA-damaging agent, derepresses ICESt3 conjugative transfer almost 25-fold. The ICESt3 host range was determined using various members of the Firmicutes as recipients. Whereas numerous ICESt3 transconjugants of Streptococcus pyogenes and Enterococcus faecalis were recovered, only one transconjugant of Lactococcus lactis was obtained. The newly incoming ICEs, except the one from L. lactis, are site-specifically integrated into the 3′ end of the fda gene and are still able to excise in these transconjugants. Furthermore, ICESt3 was retransferred from E. faecalis to S. thermophilus. Recombinant plasmids carrying different parts of the ICESt1 recombination module were used to show that the integrase gene is required for the site-specific integration and excision of the ICEs, whereas the excisionase gene is required for the site-specific excision only.

scholarly journals Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256451
Author(s):  
Najia Karim Ghanchi ◽  
Asghar Nasir ◽  
Kiran Iqbal Masood ◽  
Syed Hani Abidi ◽  
Syed Faisal Mahmood ◽  
...  
Keyword(s):  
Mutation Rates ◽  
Entropy Analysis ◽  
Genome Diversity ◽  
Genome Sequences ◽  
Rna Dependent Rna Polymerase ◽  
Site Specific ◽  
Specific Entropy ◽  
Before And After ◽  
Frequent Mutations ◽  
Selection Of

Background We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. Materials and methods We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. Results In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10−4. The most frequent mutations were 5’ UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. Conclusions The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.

Immune Electron Microscopy (IEM) of a Canine Adeno-Associated Virus

1974 ◽  
Vol 32 ◽  
pp. 256-257
Author(s):  
Gunter F. Thomas ◽  
M. David Hoggan
Keyword(s):  
Electron Microscopy ◽  
Cell Cultures ◽  
Complement Fixation ◽  
Hepatitis Virus ◽  
Wide Distribution ◽  
Immune Electron Microscopy ◽  
Adeno Associated Virus ◽  
Virus Like Particle ◽  
Dog Kidney ◽  
Green Monkeys

In 1968, Sugimura and Yanagawa described a small 25 nm virus like particle in association with the Matsuda strain of infectious canine hepatitis virus (ICHV). Domoto and Yanagawa showed that this particle was dependent on ICHV for its replication in primary dog kidney cell cultures (PDK) and was resistant to heating at 70°C for 10 min, and concluded that it was a canine adeno-associated virus (CAAV). Later studies by Onuma and Yanagawa compared CAAV with the known human serotypes (AAV 1, 2, 3) and AAV-4, known to be associated with African Green Monkeys. Using the complement fixation (CF) test, they found that CAAV was serologically related to AAV-3 and had wide distribution in the dog population of Japan.

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

MEMORY EFFECTS IN THE FRAGMENTATION OF MOLECULES FOLLOWING SITE-SPECIFIC CORE EXCITATION

1987 ◽  
Vol 48 (C9) ◽  
pp. C9-741-C9-744 ◽  
Author(s):  
W. HABENICHT ◽  
L. A. CHEWTER ◽  
M. SANDER ◽  
K. MÜLLER-DETHLEFS ◽  
E. W. SCHLAG
Keyword(s):  
Memory Effects ◽  
Core Excitation ◽  
Site Specific
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