Characterization of the hypothetical proteins of Human Papillomavirus DNA consensus sequence

The diagnosis of HPV infection is generally carried out using immunological and molecular techniques based on high risk to probable high-risk HPV strains. The aim of this work is to generate a global representation of HPV strains for diagnosis and drug development. In this work, all the complete genomic DNA sequences of registered Human Papillomavirus (HPV) strains available in NCBI GenBank were used to obtain a consensus sequence of HPV using the Genetic Algorithm. The consensus DNA sequence was translated using the ExPASy software tool. In all, six longest amino acids frames were selected from the six translated frames. The amino acid sequence identity was carried out using the BLAST tool. The six amino acid sequences were identified as E1, E2, E6, E7, L1 and L2. The homology modeling method (Modeller Software Tool) was used to determine the secondary structure of these six identified primary amino acid sequence. The percentage of similarity ranged from 24% in L2 to 100% in E7 and L1. The functions of these structural domains were also determined from PDB databank, InterProScan and CATH. Hence the consensus sequence built using a genetic algorithm is representative of the HPV genome which can be used for diagnostics and drug development purposes.

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Insertion and excision of Caenorhabditis elegans transposable element Tc1

Molecular and Cellular Biology ◽

10.1128/mcb.8.2.737-746.1988 ◽

1988 ◽

Vol 8 (2) ◽

pp. 737-746

Author(s):

D Eide ◽

P Anderson

Keyword(s):

Amino Acid ◽

Caenorhabditis Elegans ◽

Transposable Element ◽

Dna Sequences ◽

Germ Line ◽

Consensus Sequence ◽

Somatic Cells ◽

Chain Gene ◽

Imprecise Excision ◽

Insertion Sites

The transposable element Tc1 is responsible for most spontaneous mutations that occur in Caenorhabditis elegans variety Bergerac. We investigated the genetic and molecular properties of Tc1 transposition and excision. We show that Tc1 insertion into the unc-54 myosin heavy-chain gene was strongly site specific. The DNA sequences of independent Tc1 insertion sites were similar to each other, and we present a consensus sequence for Tc1 insertion that describes these similarities. We show that Tc1 excision was usually imprecise. Tc1 excision was imprecise in both germ line and somatic cells. Imprecise excision generated novel unc-54 alleles that had amino acid substitutions, amino acid insertions, and, in certain cases, probably altered mRNA splicing. The DNA sequences remaining after Tc1 somatic excision were the same as those remaining after germ line excision, but the frequency of somatic excision was at least 1,000-fold higher than that of germ line excision. The genetic properties of Tc1 excision, combined with the DNA sequences of the resulting unc-54 alleles, demonstrated that excision was dependent on Tc1 transposition functions in both germ line and somatic cells. Somatic excision was not regulated in the same strain-specific manner as germ-line excision was. In a genetic background where Tc1 transposition and excision in the germ line was not detectable, Tc1 excision in the soma still occurred at high frequency.

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Rapid purification and characterization of human platelet glycoprotein V: the amino acid sequence contains leucine-rich repetitive modules as in glycoprotein Ib

Blood ◽

10.1182/blood.v75.12.2349.bloodjournal75122349 ◽

1990 ◽

Vol 75 (12) ◽

pp. 2349-2356 ◽

Cited By ~ 1

Author(s):

T Shimomura ◽

K Fujimura ◽

S Maehama ◽

M Takemoto ◽

K Oda ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Structural Model ◽

Consensus Sequence ◽

Reversed Phase ◽

Platelet Glycoprotein ◽

Lectin Affinity Chromatography ◽

Glycoprotein Ib ◽

Simple Method ◽

Carbohydrate Chains

Glycoprotein V (GPV) is a membrane-associated, 82 Kd platelet glycoprotein that is hydrolyzed during thrombin activation to yield 69 Kd fragment. We have developed a rapid and simple method for isolation of the protein from platelet extracts using a combination of gel permeation, anion-exchange, and lectin affinity chromatography. The partial amino acid sequence was determined by analysis of peptides generated by digestion of the S-carboxyamido-methylated protein with Achromobacter protease I or cyanogen bromide. The sequence shows a remarkable periodicity of leucine residues, which is homologous to the consensus sequence of a highly diversified protein super-family with a common repetitive module. Thrombin cleavage site was determined to be located at the C-terminal region of GPV by analysis of the products separated by sizing and reversed-phase high performance liquid chromatography. By lectin blot analysis, the existence of mucin-type carbohydrate chains was indicated, as well as the existence of asparagine-linked carbohydrate chains shown by the amino acid sequence analysis. From these data, we report a structural model of GPV that is analogous to glycoprotein Ib.

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Characterization of two newly isolated Staphylococcus aureus bacteriophages from Japan belonging to the genus Silviavirus

Archives of Virology ◽

10.1007/s00705-020-04749-6 ◽

2020 ◽

Vol 165 (10) ◽

pp. 2355-2359

Author(s):

Naoya Kitamura ◽

Eri Sasabe ◽

Shigenobu Matsuzaki ◽

Masanori Daibata ◽

Tetsuya Yamamoto

Keyword(s):

Staphylococcus Aureus ◽

Amino Acid ◽

Amino Acid Sequence ◽

Dna Sequences ◽

Related Gene ◽

Bacteriophage Therapy ◽

Dna Rearrangements ◽

Site Specific

Abstract Two Staphylococcus aureus bacteriophages, KSAP7 and KSAP11, were isolated from sewage and characterized. Based on morphology and DNA sequences, they were assigned to the genus Silviavirus, subfamily Twortvirinae, family Herelleviridae, whose members are hypothesized to be suitable for bacteriophage therapy. The KSAP7 and KSAP11 genomes were 137,950 and 138,307 bp in size, respectively. Although their DNA sequences were almost identical, evidence of site-specific DNA rearrangements was found in two regions. Changes in the number of PIEPEK amino acid sequence repeats encoded by orf10 and the insertion/deletion of a 541-bp sequence that includes a possible tail-related gene were identified.

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Prevalence and Distribution of High-Risk Human Papillomavirus Genotypes in Invasive Carcinoma of the Uterine Cervix in Uruguay

International Journal of Gynecological Cancer ◽

10.1097/igc.0b013e318285e753 ◽

2013 ◽

Vol 23 (3) ◽

pp. 527-532 ◽

Cited By ~ 9

Author(s):

Nora Berois ◽

Patricia De Cremoux ◽

Daniel Mazal ◽

Adela Sica ◽

Mabel Cedeira ◽

...

Keyword(s):

Human Papillomavirus ◽

High Risk ◽

Dna Sequences ◽

Invasive Cervical Cancer ◽

Human Papillomaviruses ◽

Geographical Differences ◽

Hpv Dna ◽

High Prevalence ◽

Hpv Types ◽

High Risk Hpv

ObjectivesPersistent infection with specific genotypes of human papillomaviruses (HPVs) is the main cause of invasive cervical cancer (ICC). Only a few of the various HPV types account for most of the cases worldwide, and geographical differences in their distribution are evident. Data from locally prevalent genotypes are essential in view of introduction of HPV type-specific prophylactic vaccines.MethodsIn this work, we have investigated HPV type distribution in samples of ICC cases that occurred in Uruguayan women. DNA extracted from ICC treated in Centro Hospitalario Pereira Rossell of Montevideo between 1999 and 2007 were analyzed. Search and typing were performed by polymerase chain reaction using generic GP5+/GP6+ primers and specific primers for HPV types 16, 18, 33, and 45. Positive GP5+/GP6+ samples, which were negative for all 4 high-risk HPV-specific types screened were further analyzed by sequencing.ResultsHuman papillomavirus DNA sequences were found in 163 (92.6%) of 176 cases. The most prevalent genotypes were HPV16 (67.6%) and HPV18 (8.5%) followed by HPV45 (6.8%) and HPV33 (3.4%), as single or mixed infection. Other less frequent genotypes were HPV31, HPV35, HPV39, HPV51, HPV52, HPV58, HPV66, and HPV73. The viral type could not be determined (HPV X) in 1 case (0.6%) of the HPV DNA–positive cervical cancers and double infections were found in 1.7% of the cases. The higher percentage of most aggressive HPV (16/18/45) genotypes was detected in cases diagnosed at younger than 60 years old, whereas these genotypes were less frequent in older patients.ConclusionWe conclude that HPV types 16, 18, and 45 have a very high prevalence in ICC of Uruguayan women. Results provide evidence that 16 of 18 infections are more aggressive, but most cancers could be vaccine preventable.

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Thrombophilic dysfibrinogen Tokyo V with the amino acid substitution of γ Ala327Thr: formation of fragile but fibrinolysis-resistant fibrin clots and its relevance to arterial thromboembolism

Blood ◽

10.1182/blood-2003-07-2569 ◽

2004 ◽

Vol 103 (8) ◽

pp. 3045-3050 ◽

Cited By ~ 20

Author(s):

Akiei Hamano ◽

Jun Mimuro ◽

Motonori Aoshima ◽

Takeyoshi Itoh ◽

Noboru Kitamura ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Amino Acid Substitution ◽

Factor Xiii ◽

Consensus Sequence ◽

Fibrin Networks ◽

Tissue Plasminogen ◽

Fibrin Monomers ◽

Partial Correction ◽

Fibrin Clots

Abstract Thrombophilic dysfibrinogen Tokyo V was identified in a 43-year-old man with recurrent thromboembolism. Based on analyses of the patient fibrinogen genes, the amino acid sequence of the aberrant fibrinogen peptide, and deglycosylation experiments, fibrinogen Tokyo V was shown to have an amino acid substitution of γ Ala327Thr and possibly extra glycosylation at γ Asn325 because the mutation confers the N-linked glycosylation consensus sequence Asn-X-Thr. The mutation resulted in impaired function and hypofibrinogenemia (hypodysfibrinogen). Polymerization of fibrin monomers derived from patient fibrinogen was severely impaired with a partial correction in the presence of calcium, resulting in very low clottability. Additionally, a large amount of soluble cross-linked fibrin was formed upon thrombin treatment in the presence of factor XIII and calcium. However, Tokyo V–derived fibrin was resistant to degradation by tissue plasminogen activator (tPA)–catalyzed plasmin digestion. The structure of Tokyo V fibrin appeared severely perturbed, since there are large pores inside the tangled fibrin networks and fiber ends at the boundaries. Taken together, these data suggest that Tokyo V fibrin clots are fragile, so that fibrinolysis-resistant insoluble fibrin and soluble fibrin polymers may be released to the circulation, partly accounting for the recurrent embolic episodes in the patient. (Blood. 2004;103:3045-3050)

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Detection of high-risk human papillomavirus by two molecular techniques: Hybrid capture and linear array

Journal of Virological Methods ◽

10.1016/j.jviromet.2008.01.021 ◽

2008 ◽

Vol 149 (1) ◽

pp. 163-166 ◽

Cited By ~ 8

Author(s):

Jesús Chacón de Antonio ◽

Ana Fernández-Olmos ◽

María Mercadillo ◽

María Luisa Mateos Lindemann ◽

Fernando Baquero Mochales

Keyword(s):

Human Papillomavirus ◽

High Risk ◽

Linear Array ◽

Molecular Techniques ◽

Hybrid Capture

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Putative amino acid sequence of HLA-DRB chain contributing to rheumatoid arthritis susceptibility.

Journal of Experimental Medicine ◽

10.1084/jem.169.6.2263 ◽

1989 ◽

Vol 169 (6) ◽

pp. 2263-2268 ◽

Cited By ~ 70

Author(s):

Y Watanabe ◽

K Tokunaga ◽

K Matsuki ◽

F Takeuchi ◽

K Matsuta ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Amino Acid ◽

Amino Acid Sequence ◽

Dna Sequences ◽

Strong Association ◽

Amino Acid Residues ◽

Net Charge ◽

Drb Gene ◽

Polymerase Chain

The association between HLA-DR4 and rheumatoid arthritis (RA) has been established in many ethnic groups. To clarify the determinant of susceptibility to RA, a polymorphic segment of the HLA-DRB gene was amplified in vitro by polymerase chain reaction and analyzed with oligonucleotide probes specific for the HLA-DR4 DNA sequences. A particular sequence encoding amino acids Gln70-Arg71-Arg72-Ala73-Ala74 showed a strong association with RA (p less than 0.005, relative risk 6.0). This amino acid sequence occurs in the DRB molecules with three RA-associated specificities, DR4/Dw14, DR4/Dw15, and DR1. DR4/Dw4, which is common in Caucasian RA patients, has a strikingly similar amino acid sequence Gln70-Lys71-Arg72-Ala73-Ala74 in terms of polarity and charge profiles. Other RA nonassociated sequences differ from this sequence by at least one amino acid substitution that causes the change of the net charge. The composition of amino acid residues at the positions 70-74 may play a crucial role in the pathogenesis of RA.

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