Elucidation of rRNA Secondary Structure and Phylogenetic  Analysis of Salmonella enterica based on 16S RNA

The influence of a temperature default on ribosomal RNA (rRNA) secondary structure models was studied with the "Mfold" energy-optimization program. Folding models of the internal transcribed spacer (ITS) 1 rRNA for both Drosophila simulans (Insecta) and Isabellaria adriani (Gastropoda) were generated at two different temperatures. The folding models are compared with the models previously shown for the ITS-1 of D. melanogaster Oregon R strain and I. adriani. A search for phylogenetically informative ITS-1 folding motifs was conducted for D. simulans. In I. adriani, a new approach for ITS-1 secondary structure analyses is suggested. The paper also elucidates results inferred from three energy-optimizing programs (Mfold, GeneBee, and STAR). These three folding programs give different information on the structure and free energy of a ITS-1 rRNA molecule. Furthermore, secondary-structure models of the small subunit (ssu) rRNA of Daphnia pulex (Crustacea: Cladocera) were investigated. The ssu rRNA molecule is usually folded according to alignment information. Here, ssu folding patterns are computed with Mfold using two temperature conditions. The two Mfold models are compared with the alignment model previously suggested for D. pulex. Three cladoceran-specific motifs and a short stem motif within the ssu rRNA of eukaryotes are discussed with respect to structure and phylogenetic information.

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Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil: TABLE 1

Genome Announcements ◽

10.1128/genomea.00892-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 3

Author(s):

Fernanda Almeida ◽

Marta Inês Cazentini Medeiros ◽

Dália Prazeres Rodrigues ◽

Justin Payne ◽

Ruth E. Timme ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Health Problem ◽

Salmonella Enterica ◽

Salmonella Enterica Serovar Typhimurium ◽

Draft Genome ◽

Genome Sequences ◽

Serovar Typhimurium ◽

Important Health

Salmonellosis is an important health problem worldwide and Salmonella enterica serovar Typhimurium is one of the most common isolated serovars. Here, we reported the draft genomes of 40 S . Typhimurium strains isolated from humans and food in Brazil. These draft genomes will improve phylogenetic analysis and will help enhance our understanding of strains of this serovar isolated in Brazil.

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The 16S-like, 5.8S and 23S-like rRNAs of the two varieties ofCryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms

Medical Mycology ◽

10.1080/02681219480000231 ◽

1994 ◽

Vol 32 (3) ◽

pp. 163-180 ◽

Cited By ~ 23

Author(s):

M. Fan ◽

B.P. Currie ◽

R.R. Gutell ◽

M.A. Ragan ◽

A. Casadevall

Keyword(s):

Phylogenetic Analysis ◽

Secondary Structure ◽

Restriction Fragment

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Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

Journal of Clinical Microbiology ◽

10.1128/jcm.02200-15 ◽

2015 ◽

Vol 54 (2) ◽

pp. 289-295 ◽

Cited By ~ 54

Author(s):

S. Bekal ◽

C. Berry ◽

A. R. Reimer ◽

G. Van Domselaar ◽

G. Beaudry ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Salmonella Enterica ◽

Core Genome ◽

Phage Type ◽

Epidemiological Data ◽

Single Nucleotide Variant ◽

High Quality ◽

Typing Method ◽

Single Nucleotide ◽

Content Type

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

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Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)

Journal of Zoological Systematics & Evolutionary Research ◽

10.1111/j.1439-0469.2009.00553.x ◽

2009 ◽

pp. no-no ◽

Cited By ~ 6

Author(s):

Berit Ullrich ◽

Klaus Reinhold ◽

Oliver Niehuis ◽

Bernhard Misof

Keyword(s):

Phylogenetic Analysis ◽

Secondary Structure ◽

Internal Transcribed Spacers ◽

Bush Crickets

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Phylogenetic Analysis and Structural Predictions of Human Adenovirus Penton Proteins as a Basis for Tissue-Specific Adenovirus Vector Design

Journal of Virology ◽

10.1128/jvi.00048-07 ◽

2007 ◽

Vol 81 (15) ◽

pp. 8270-8281 ◽

Cited By ~ 31

Author(s):

Ijad Madisch ◽

Soeren Hofmayer ◽

Christian Moritz ◽

Alexander Grintzalis ◽

Jens Hainmueller ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Secondary Structure ◽

Rational Design ◽

Immune Escape ◽

Adenovirus Vector ◽

Human Adenovirus ◽

Site Directed Mutagenesis ◽

Penton Base ◽

Base Function ◽

Tissue Specific

ABSTRACT The penton base is a major capsid protein of human adenoviruses (HAdV) which forms the vertices of the capsid and interacts with hexon and fiber protein. Two hypervariable loops of the penton are exposed on the capsid surface. Sequences of these and 300 adjacent amino acid residues of all 51 HAdV and closely related simian adenoviruses were studied. Adjacent sequences and predicted overall secondary structure were conserved. Phylogenetic analysis revealed clustering corresponding to the HAdV species and recombination events in the origin of HAdV prototypes. All HAdV except serotypes 40 and 41 of species F exhibited an integrin binding RGD motif in the second loop. The lengths of the loops (HVR1 and RGD loops) varied significantly between HAdV species with the longest RGD loop observed in species C and the longest HVR1 in species B. Long loops may permit the insertion of motifs that modify tissue tropism. Genetic analysis of HAdV prime strain p17′H30, a neutralization variant of HAdV-D17, indicated the significance of nonhexon neutralization epitopes for HAdV immune escape. Fourteen highly conserved motifs of the penton base were analyzed by site-directed mutagenesis of HAdV-D8 and tested for sustained induction of early cytopathic effects. Thus, three new motifs essential for penton base function were identified additionally to the RGD site, which interacts with a secondary cellular receptor responsible for internalization. Therefore, our penton primary structure data and secondary structure modeling in combination with the recently published fiber knob sequences may permit the rational design of tissue-specific adenoviral vectors.

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