scholarly journals Characterization of a new genotype of Betapapillomavirus HPV 17 through L1, E7, E7 and LCR sequences

2018 ◽  
Author(s):  
Ledy H Oliveira ◽  
Larissa Silva Santos ◽  
Felipe P G Neves
Keyword(s):  
Amino Acid ◽  
Evolutionary Process ◽  
Long Control Region ◽  
Nucleotide Substitutions ◽  
Specific Primers ◽  
E6 Oncoprotein ◽  
Potential Binding ◽  
New Genotype ◽  
Zinc Binding Domain

Background. Human papillomavirus (HPV) exhibits epithelial and mucosal tropism. HPV type 17 belongs to the Betapapillomavirus genus and molecular cloning experiments have identified two subtypes (17a and 17b) isolated from epidermodysplasia verruciformis (EV). HPV subtypes are characterized by dissimilarities from 2 to 10% at the nucleotide level from their referenced HPV. The aim of this study was to characterize the L1, E6, E7 and LCR sequences from an isolate from the oral mucosa of an asymptomatic woman. Methods. The whole late gene 1 (L1) was amplified using several sets of primers. The complete early genes 6 and 7 (E6, E7) and the long control region (LCR) were amplified using specific primers. Potential binding sites for transcriptional factors within the LCR were also investigated. Results. Within these sets, the DNA sequence was altered at 91 positions (68 in L1, 13 in E6, 8 in E7, and 2 in LCR sequences). L1 analysis showed high dissimilarity compared with the HPV 17 prototype, reaching 4% of nucleotide substitutions and leading to a probability third 17 subtype. The E6 oncoprotein presented the highest modification among the sequences !2 studied, with four amino acid changes in comparison with the prototype isolate. The amino acid was modified at a position 62 (S-T), a zinc-binding domain (CxxC(C)29 CxxC). Discussion. Our findings provide data on genetic variations seen in this genotype, reaching to dichotomic branching and pointing to an evolutionary process. The oral cavity has a large HPV spectrum and may be implicated in the evolution of this virus, allowing it to adapt to sites other than its original niche, may drive to produce adaptive variants of this genotype

scholarly journals Characterization of a new genotype of Betapapillomavirus HPV 17 through L1, E7, E7 and LCR sequences

2018 ◽  
Author(s):  
Ledy H Oliveira ◽  
Larissa Silva Santos ◽  
Felipe P G Neves
Keyword(s):  
Amino Acid ◽  
Evolutionary Process ◽  
Long Control Region ◽  
Nucleotide Substitutions ◽  
Specific Primers ◽  
E6 Oncoprotein ◽  
Potential Binding ◽  
New Genotype ◽  
Zinc Binding Domain

Background. Human papillomavirus (HPV) exhibits epithelial and mucosal tropism. HPV type 17 belongs to the Betapapillomavirus genus and molecular cloning experiments have identified two subtypes (17a and 17b) isolated from epidermodysplasia verruciformis (EV). HPV subtypes are characterized by dissimilarities from 2 to 10% at the nucleotide level from their referenced HPV. The aim of this study was to characterize the L1, E6, E7 and LCR sequences from an isolate from the oral mucosa of an asymptomatic woman. Methods. The whole late gene 1 (L1) was amplified using several sets of primers. The complete early genes 6 and 7 (E6, E7) and the long control region (LCR) were amplified using specific primers. Potential binding sites for transcriptional factors within the LCR were also investigated. Results. Within these sets, the DNA sequence was altered at 91 positions (68 in L1, 13 in E6, 8 in E7, and 2 in LCR sequences). L1 analysis showed high dissimilarity compared with the HPV 17 prototype, reaching 4% of nucleotide substitutions and leading to a probability third 17 subtype. The E6 oncoprotein presented the highest modification among the sequences !2 studied, with four amino acid changes in comparison with the prototype isolate. The amino acid was modified at a position 62 (S-T), a zinc-binding domain (CxxC(C)29 CxxC). Discussion. Our findings provide data on genetic variations seen in this genotype, reaching to dichotomic branching and pointing to an evolutionary process. The oral cavity has a large HPV spectrum and may be implicated in the evolution of this virus, allowing it to adapt to sites other than its original niche, may drive to produce adaptive variants of this genotype

scholarly journals Nucleotide Sequence and Characterization of a Novel Cefotaxime-Hydrolyzing β-Lactamase (CTX-M-10) Isolated in Spain

2001 ◽  
Vol 45 (2) ◽  
pp. 616-620 ◽  
Author(s):  
Antonio Oliver ◽  
José Claudio Pérez-Dı́az ◽  
Teresa M. Coque ◽  
Fernando Baquero ◽  
Rafael Cantón
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence Identity ◽  
Penicillin G ◽  
Nucleotide Substitutions ◽  
Sequence Identity ◽  
M 10 ◽  
Hydrolysis Rates ◽  
Kluyvera Ascorbata

ABSTRACT A cefotaxime-resistant, ceftazidime-susceptible Escherichia coli isolate was obtained from a patient with sepsis in 1997, from which a β-lactamase with a pI of 8.1 was cloned. Cephaloridine and cefotaxime relative hydrolysis rates were 167 and 81, respectively (penicillin G rate = 100), whereas ceftazidime hydrolysis was not detected. The nucleotide sequence revealed a bla gene related to that coding for CTX-M-3. Despite 21 nucleotide substitutions, only 2 determined amino acid changes (Ala27Val and Arg38Gln). The amino acid sequence identity between this enzyme, designated CTX-M-10, and the chromosomal β-lactamase ofKluyvera ascorbata was 81%.

Phylogeny and Polymorphism in the Long Control Region, E6, and L1 of Human Papillomavirus Types 53, 56, and 66 in Central Brazil

2011 ◽  
Vol 21 (2) ◽  
pp. 222-229 ◽  
Author(s):  
Patrícia Soares Wyant ◽  
Daniela Marreco Cerqueira ◽  
Daniella Sousa Moraes ◽  
José Paulo Gagliardi Leite ◽  
Cláudia Renata Fernandes Martins ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Variability ◽  
Binding Sites ◽  
Long Control Region ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Central Brazil ◽  
Hpv Types ◽  
Genomic Regions

Introduction:Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates.Methods:The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases.Results:Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants.Conclusions:The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

scholarly journals Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD)

2002 ◽  
Vol 184 (4) ◽  
pp. 1019-1027 ◽  
Author(s):  
Vladimir L. Motin ◽  
Anca M. Georgescu ◽  
Jeffrey M. Elliott ◽  
Ping Hu ◽  
Patricia L. Worsham ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Evolutionary Process ◽  
Nucleotide Substitutions ◽  
Neighboring Gene ◽  
Specific Primers ◽  
Gene Encoding ◽  
Close Relationship ◽  
Genes Encoding ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Negative Phenotype

ABSTRACT A PCR-based genotyping system that detects divergence of IS100 locations within the Yersinia pestis genome was used to characterize a large collection of isolates of different biovars and geographical origins. Using sequences derived from the glycerol-negative biovar orientalis strain CO92, a set of 27 locus-specific primers was designed to amplify fragments between the end of IS100 and its neighboring gene. Geographically diverse members of the orientalis biovar formed a homogeneous group with identical genotype with the exception of strains isolated in Indochina. In contrast, strains belonging to the glycerol-positive biovar antiqua showed a variety of fingerprinting profiles. Moreover, strains of the biovar medievalis (also glycerol positive) clustered together with the antiqua isolates originated from Southeast Asia, suggesting their close phylogenetic relationships. Interestingly, a Manchurian biovar antiqua strain Nicholisk 51 displayed a genotyping pattern typical of biovar orientalis isolates. Analysis of the glycerol pathway in Y. pestis suggested that a 93-bp deletion within the glpD gene encoding aerobic glycerol-3-phosphate dehydrogenase might account for the glycerol-negative phenotype of the orientalis biovar. The glpD gene of strain Nicholisk 51 did not possess this deletion, although it contained two nucleotide substitutions characteristic of the glpD version found exclusively in biovar orientalis strains. To account for this close relationship between biovar orientalis strains and the antiqua Nicholisk 51 isolate, we postulate that the latter represents a variant of this biovar with restored ability to ferment glycerol. The fact that such a genetic lesion might be repaired as part of the natural evolutionary process suggests the existence of genetic exchange between different Yersinia strains in nature. The relevance of this observation on the emergence of epidemic Y. pestis strains is discussed.

scholarly journals Molecular characterization of pncA gene mutations in Mycobacterium tuberculosis clinical isolates from China

2000 ◽  
Vol 124 (2) ◽  
pp. 227-232 ◽  
Author(s):  
L. HOU ◽  
D. OSEI-HYIAMAN ◽  
Z. ZHANG ◽  
B. WANG ◽  
A. YANG ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Molecular Basis ◽  
Gene Mutations ◽  
Clinical Isolates ◽  
Start Codon ◽  
Nucleotide Position ◽  
Nucleotide Substitutions ◽  
Base Pair Deletion

A sample of 35 pyrazinamide (PZA)-resistant and 30 PZA-susceptible clinical isolates recovered from Beijing and Taiyuan City, China were characterized by SSCP and sequence analysis for mutations in the pncA gene that encodes the Mycobacterium tuberculosis PZase. The purpose of this study was to understand the molecular basis and the characteristics of pncA gene mutations and its relation to PZA resistance in M. tuberculosis strains from China. Several mutations with base changes leading to amino acid substitutions were found in the PZA-resistant isolates. No mutations were seen in the 243 PZA-susceptible isolates. Among the 35 PZA-resistant isolates, 32 isolates (91·4%) had nucleotide substitutions, insertions and deletions that resulted in amino-acid substitution; or frameshifts in some strains. Other previously uncharacterized mutations were found as follows: Asn118→Thr, CG insertion at position 501; CC insertion at nucleotide position 403; a 8 base-pair deletion at start codon; Pro54→Thr; AG insertion at 368; Tyr41→His, Ser88→stop, and A insertion at nucleotide position 301. IS6110 subtyping revealed that each strain was unique; indicative of the epidemiologic independence of the isolates.

PURIFICATION AND PARTIAL CHEMICAL CHARACTERIZATION OF SHEEP NEUROPHYSIN

1973 ◽  
Vol 74 (2) ◽  
pp. 226-236 ◽  
Author(s):  
Michel Chrétien ◽  
Claude Gilardeau
Keyword(s):  
Amino Acid ◽  
Polyacrylamide Gel Electrophoresis ◽  
Chemical Characterization ◽  
Terminal Amino Acid ◽  
Amino Acid Determination ◽  
Pituitary Glands ◽  
Terminal Amino ◽  
Partial Chemical ◽  
Acid Determination

ABSTRACT A protein isolated from ovine pituitary glands has been purified, and its homogeneity assessed by NH2- and COOH-terminal amino acid determination, ultracentrifugation studies, and polyacrylamide gel electrophoresis after carboxymethylation. Its chemical and immunochemical properties are closely similar to those of beef and pork neurophysins, less similar to those of human neurophysins. It contains no tryptophan (like other neurophysins) or histidine (like all except bovine neurophysin-I and human neurophysins). It has alanine at the NH2-terminus and valine at the COOH-terminus. Its amino acid composition is similar to, but not identical with those of porcine and bovine neurophysins.

Phylogeny Characterization of Seb Gene Encoding Enterotoxins in Staphylococcus aureus Isolated from Raw Milk and Cheese

2019 ◽  
Vol 9 (o3) ◽  
Author(s):  
Fatima N. Aziz ◽  
Laith Abdul Hassan Mohammed-Jawad
Keyword(s):  
Staphylococcus Aureus ◽  
Food Poisoning ◽  
Raw Milk ◽  
Staphylococcal Enterotoxin B ◽  
Human Pathogen ◽  
Conventional Pcr ◽  
Biochemical Tests ◽  
Specific Primers ◽  
Gene Encoding

Food poisoning due to the bacteria is a big global problem in economically and human's health. This problem refers to an illness which is due to infection or the toxin exists in nature and the food that use. Milk is considered a nutritious food because it contains proteins and vitamins. The aim of this study is to detect and phylogeny characterization of staphylococcal enterotoxin B gene (Seb). A total of 200 milk and cheese samples were screened. One hundred ten isolates of Staphylococcus aureus pre-confirmed using selective and differential media with biochemical tests. Genomic DNA was extracted from the isolates and the SEB gene detects using conventional PCR with specific primers. Three staphylococcus aureus isolates were found to be positive for Seb gene using PCR and confirmed by sequencing. Sequence homology showed variety range of identity starting from (100% to 38%). Phylogenetic tree analyses show that samples (6 and 5) are correlated with S. epidermidis. This study discovered that isolates (A6-RLQ and A5-RLQ) are significantly clustered in a group with non- human pathogen Staphylococcus agnetis.

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