Silvia C Galvan | Universidad Nacional Autónoma de México (original) (raw)
Papers by Silvia C Galvan
Bioinformatics and Biology Insights, 2017
BACkgRouND: Because the graphical presentation and analysis of motif distribution can provide ins... more BACkgRouND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. ReSulTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion.
Nucleic Acids Research, 1991
Rev. invest. clín, 2002
Base de dados : LILACS. Pesquisa : 332939 [Identificador único]. Referências encontradas : 1 [ref... more Base de dados : LILACS. Pesquisa : 332939 [Identificador único]. Referências encontradas : 1 [refinar]. Mostrando: 1 .. 1 no formato [Detalhado]. página 1 de 1, 1 / 1, LILACS, seleciona. para imprimir. Fotocópia. Texto completo SciELO México. experimental, Documentos relacionados ...
(HPV16) has a number of variants, each with a different geographic distri-bution and some that ar... more (HPV16) has a number of variants, each with a different geographic distri-bution and some that are associated more often with invasive neoplasias. We investigated whether the high inci-dence of cervical cancer in Mexico (50 cases per 100 000 women) may be asso-ciated with a high prevalence of onco-genic HPV16 variants. Methods: Cervi-cal samples were collected from 181 case patients with cervical cancer and from 181 age-matched control subjects, all from Mexico City. HPV16 was de-tected with an E6/E7 gene-specific polymerase chain reaction, and variant
Epigenetics, modifications of the genome, heritable during cell division, that do not involve cha... more Epigenetics, modifications of the genome, heritable during cell division, that do not involve changes in DNA sequences include several mechanisms mainly: histone modifications, DNA methy-lation and related modifications, non-coding RNAs (ncRNAs) and others that regulate gene expression. The past two decades has seen an explosion of interest for revealing mechanisms that control epigenetic modifications, mainly based on the influence they have on chromatin struc-ture and their impact in biological processes such as programmed DNA rearrangements, imprinting, germ line silencing, devel-opmentally cued stem cell division, and overall chromosomal stability and identity. It has also become obvious that epigenet-ics changes are fundamental in the interplay between viruses and their host cells. Generally speaking, when retroviruses and DNA viruses integrate their genomes into the host genome, they can
Expert Opinion on Environmental Biology, 2017
Exploring the Role of a Soil Microbial Consortium on the Biodegradation and Physical Alteration o... more Exploring the Role of a Soil Microbial Consortium on the Biodegradation and Physical Alteration of Low Density Polyethylene Background: Our study is a contribution to the searching for microorganisms capable of degrading low density polyethylene. A microbial consortium was detected on low density polyethylene wastes buried under soil in a composting area of a Mexico City landfill known as “Bordo Poniente”. Methods: Photomicrographs of the microbial consortium by optical microscopy and scanning electron microscope (SEM) were taken at different times during the microbial film development in low density polyethylene; specific culture media, with polyethylene as the only carbon source, were used for strain isolation of bacteria, yeast and filamentous fungi; polyethylene degradation was evaluated by observing the physical alteration of this material in the SEM and by quantifying its weight loss when the polyethylene was used as a carbon source and incubated at different temperatures under shaking conditions at different pH. Results and conclusions: Photomicrographs of the microbial consortium by SEM, show a wide variety of species. It was possible to observe not only the shape of the microbial colonies but also the progressive development of a biofilm. The higher microbial degradation activity (18% in 60 days) was attained when cultures were incubated at 24°C under shaking conditions at pH 5.0. This is one of the more efficient degradations reported up to date. In addition, paper and wood degrading activity by the same consortium was estimated.
Frontiers Research Topics, 2015
Revista De Investigacion Clinica Organo Del Hospital De Enfermedades De La Nutricion, 2002
The purpose of the present investigation, was to analyze the sequences of 16S ribosomal genes par... more The purpose of the present investigation, was to analyze the sequences of 16S ribosomal genes partially amplified from 17 isolated Giardia intestinalis obtained from faces of 13 children with intestinal pathology and four symptoms-free children with intestinal pathology. Analysis was made also with Giardia Portland-I and four Giardias isolated from dogs. Children ages in both groups ranged from six to twelve years. Genomic DNA was isolated using the phenol-chloroform-isoamyl alcohol technique, and partial amplification of 16S rRNA ribosomal gene was carried out by the Polymerase Chain Reaction. Sequences of rDNA were compared with Portland-I by using CLUSTAL-W (1.81) and PHYLIP (3.6) software in order to determine phylogenic associations. Our results showed that only one isolate from symptoms-free children and three from the symptomatic children were associated with Portland I. The other isolated Giardias were associated between them and with two samples obtained from dogs that are phylogenetically distant from Portland-I. Two isolates from dog constituted a different group. These results suggest a zoonotic infection and presence of symptoms in children from the present investigation; probably it was associated with host or special characteristics of Giardia strains. The last two situations have a special epidemiological and public health interest.
Salud pública de México
This study evaluates, after a 10-year period, the attitudes of medical students towards research ... more This study evaluates, after a 10-year period, the attitudes of medical students towards research and learning at the National University of Mexico (UNAM), and tries to determine the role that experiences obtained during academic years could play in orienting these attitudes. Results indicate that all four groups of participant students,--1st and 4th-5th grades, in 1984 and in 1994--show slightly positive attitudes towards research and learning. No significant attitude changes were observed after the 10-year period in students who enter medical school nor in those who begin clinical practice. Besides, it was found a significant correlation between these two attitudinal factors. Some possible explanations for these results are discussed, as well as some steps that could help to promote positive attitudes towards research and learning.
Frontiers in Genetics, 2015
Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, 1983
1. Thirteen isoenzyme loci were analyzed electrophoretically for each of 13 isolates obtained fro... more 1. Thirteen isoenzyme loci were analyzed electrophoretically for each of 13 isolates obtained from Argentina. Costa Rica, Mexico and Venezuela to determine both genetic distance and time of evolutionary divergence between these populations.
BMC Infectious Diseases, 2014
Background: Anal cancer has become one of the most common non-AIDS-defined tumors among Human Imm... more Background: Anal cancer has become one of the most common non-AIDS-defined tumors among Human Immunodeficiency Virus-positive (HIV+) individuals, and a rise in its incidence among HIV+ Men who have Sex with Men (MSM) has been shown, despite the introduction of Highly Active Anti-Retroviral Therapy (HAART). Human Papillomavirus (HPV) infections are highly prevalent among HIV+ MSM and recent studies have shown high rates of HPV-associated anal intraepithelial neoplasia (AIN) and anal cancer among this population.
School Science and Mathematics, 1982
Mechanisms of Ageing and Development, 1986
The activities of brain initiation factor 2 and brain elongation factor 1, which function as rate... more The activities of brain initiation factor 2 and brain elongation factor 1, which function as rate-limiting in total protein synthesis, and estimations of brain weight were followed during postnatal life in the rat and the mouse. Both activities decreased in parallel while cumulative brain weight increased. Three exponential components were required for the mathematical expression of each of the three processes in semilogarithmic plots against time. The acceleration curves for the activities and tissue weight demonstrated a mirror image symmetry. Within the general pattern of diminution with age, the negative acceleration of the activities and the positive acceleration of the brain weight displayed repeated bursts. The activities of both factors could also be arranged into several regression lines in log/log plots against time. Significantly, in these plots, the regression line calculated for the whole set of data for each factor activity showed that the value of the ratio of the slopes (mouse to rat) was inversely related to the square root of the ratio of species longevity and was in agreement with the power law relating life spans of cells to species longevity (Röhme, Proc. Natl. Acad. Sci. U.S.A., 78 (1981) 5009).
International Journal of Cancer, 1999
Background: Human papillomavirus 16 (HPV16) has a number of variants, each with a different geogr... more Background: Human papillomavirus 16 (HPV16) has a number of variants, each with a different geographic distribution and some that are associated more often with invasive neoplasias. We investigated whether the high incidence of cervical cancer in Mexico (50 cases per 100 000 women) may be associated with a high prevalence of oncogenic HPV16 variants. Methods: Cervical samples were collected from 181 case patients with cervical cancer and from 181 age-matched control subjects, all from Mexico City. HPV16 was detected with an E6/E7 gene-specific polymerase chain reaction, and variant HPV classes and subclasses were identified by sequencing regions of the E6 and L1/MY genes. Clinical data and data on tumor characteristics were also collected. All statistical tests were twosided. Results: HPV16 was detected in cervical scrapes from 50.8% 92 of 181) of case patients and from 11% (20 of 181) of control subjects. All HPV16positive samples, except one, contained European (E) or Asian-American (AA) variants. AA and E variants were found statistically significantly more often in case patients (AA = 23.2% [42 of 181]; E = 27.1% [49 of 181]) than in control subjects (AA = 1.1% [two of 181]; E = 10% [18 of 181]) (P<.001 for case versus control subjects for either E or AA variants . However, the frequency of AA variants was 21 times higher in cancer patients than in control subjects, whereas that ratio for E variants was only 2.7 (P = .006, 2 test). The odds ratio (OR) for cervical cancer associated with AA variants (OR = 27.0; 95% confidence interval [CI] = 6.4 to 113.7) was higher than that asso-ciated with E variants (OR = 3.4; 95% CI = 1.9 to 6.0). AA-positive case patients (46.2 ± 12.5 years [mean ± standard deviation]) were 7.7 years younger than E-positive case patients (53.9 ± 12.2 years) (P = .004, Student's t test). AA variants were associated with squamous cell carcinomas and adenocarcinomas, but E variants were associated with only squamous cell carcinomas (P = .014, Fisher's exact test). Conclusions: The high frequency of HPV16 AA variants, which appear to be more oncogenic than E variants, might contribute to the high incidence of cervical cancer in
Expert Review of Vaccines, 2007
Prophylactic vaccines against human papillomavirus (HPV) are on the market and will certainly red... more Prophylactic vaccines against human papillomavirus (HPV) are on the market and will certainly reduce the incidence of genital warts and the risk of developing cervical cancer. In addition, they will contribute to reducing anal as well as head and neck cancers. However, effort should be made in the short term in order for these vaccines to have a real impact in the developing world, where almost 80% of cervical cancer cases occur. Since the available vaccines include only two of the HPV types found in cancers (approximately 70%), improvements in current mass screening programs -with the use of molecular techniques -must be made, particularly in developing countries. Therapeutic vaccines have been designed to control advanced lesions and residual illness and, although success has usually been obtained in animal models, clinical studies have not yet provided the anticipated results. Finally, the next generations of prophylactic HPV vaccines will probably include subunit vaccines, transgenic bacteria and plants, among others, and could represent useful and cheaper alternatives for reducing cervical cancer, particularly in the developing world.
BMC Genomics, 2011
Background: The Human Papillomavirus (HPV) genome is divided into early and late coding sequences... more Background: The Human Papillomavirus (HPV) genome is divided into early and late coding sequences, including 8 open reading frames (ORFs) and a regulatory region (LCR). Viral gene expression may be regulated through epigenetic mechanisms, including cytosine methylation at CpG dinucleotides. We have analyzed the distribution of CpG sites and CpG islands/clusters (CGI) among 92 different HPV genomes grouped in function of their preferential tropism: cutaneous or mucosal. We calculated the proportion of CpG sites (PCS) for each ORF and calculated the expected CpG values for each viral type. Results: CpGs are underrepresented in viral genomes. We found a positive correlation between CpG observed and expected values, with mucosal high-risk (HR) virus types showing the smallest O/E ratios. The ranges of the PCS were similar for most genomic regions except E4, where the majority of CpGs are found within islands/clusters. At least one CGI belongs to each E2/E4 region. We found positive correlations between PCS for each viral ORF when compared with the others, except for the LCR against four ORFs and E6 against three other ORFs. The distribution of CpG islands/clusters among HPV groups is heterogeneous and mucosal HR-HPV types exhibit both lower number and shorter island sizes compared to cutaneous and mucosal Low-risk (LR) HPVs (all of them significantly different).
Nucleic Acids Research, 1991
EMBL accession nos X54474-X54479 (incl.) Ribosomal RNA (rRNA) molecules are considered very good ... more EMBL accession nos X54474-X54479 (incl.) Ribosomal RNA (rRNA) molecules are considered very good phylogenetic markers because they are shared by all prokaryotic and eukaryotic cells, as a constitutive part of the very ancient protein synthesis machinery, the ribosomes. It seems their primary and secondary structure as well as the relative position of the genes or gene fragments (exons) within the ribosomal cistron, reflect the phylogenetic distances between living groups of organisms. There are some remarkable differences between trypanosomatid rRNA molecules and those of most eukaryotic organisms. First, trypanosomatids have four very small rRNAs in addition to the typical eukaryotic 5S and 5.8S-like species and all six mature molecules are associated with the 28S-like species of the large ribosomal subunit. Second, the genes for three of the extra rRNAs: M2, M4 and M6, are coded near the 3' end of the genes for the 28S-like species and the gene for Ml is located between the two exons for the constituents (alpha and beta) of the 28S-like molecule (1, 2). The remaining species, M3 and M5 are considered 5.8S and 5S-like, respectively. These small rRNA molecules were directly sequenced employing the method of Donis-Keller (3) using the enzymes TI, U2, Phy M and B. cereus. The length, in number of bases, the relative composition of purine and pyrimidine bases, and the accession numbers in EMBL are presented in . The percent homology with the corresponding molecules of Crithidia fasciculata (4) and Trypanosoma brucei (5, 6) calculated with CLUSTAL package , shows the very close relationship between these molecules, but that M6 is relatively more variable .
Bioinformatics and Biology Insights, 2017
BACkgRouND: Because the graphical presentation and analysis of motif distribution can provide ins... more BACkgRouND: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. ReSulTS: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion.
Nucleic Acids Research, 1991
Rev. invest. clín, 2002
Base de dados : LILACS. Pesquisa : 332939 [Identificador único]. Referências encontradas : 1 [ref... more Base de dados : LILACS. Pesquisa : 332939 [Identificador único]. Referências encontradas : 1 [refinar]. Mostrando: 1 .. 1 no formato [Detalhado]. página 1 de 1, 1 / 1, LILACS, seleciona. para imprimir. Fotocópia. Texto completo SciELO México. experimental, Documentos relacionados ...
(HPV16) has a number of variants, each with a different geographic distri-bution and some that ar... more (HPV16) has a number of variants, each with a different geographic distri-bution and some that are associated more often with invasive neoplasias. We investigated whether the high inci-dence of cervical cancer in Mexico (50 cases per 100 000 women) may be asso-ciated with a high prevalence of onco-genic HPV16 variants. Methods: Cervi-cal samples were collected from 181 case patients with cervical cancer and from 181 age-matched control subjects, all from Mexico City. HPV16 was de-tected with an E6/E7 gene-specific polymerase chain reaction, and variant
Epigenetics, modifications of the genome, heritable during cell division, that do not involve cha... more Epigenetics, modifications of the genome, heritable during cell division, that do not involve changes in DNA sequences include several mechanisms mainly: histone modifications, DNA methy-lation and related modifications, non-coding RNAs (ncRNAs) and others that regulate gene expression. The past two decades has seen an explosion of interest for revealing mechanisms that control epigenetic modifications, mainly based on the influence they have on chromatin struc-ture and their impact in biological processes such as programmed DNA rearrangements, imprinting, germ line silencing, devel-opmentally cued stem cell division, and overall chromosomal stability and identity. It has also become obvious that epigenet-ics changes are fundamental in the interplay between viruses and their host cells. Generally speaking, when retroviruses and DNA viruses integrate their genomes into the host genome, they can
Expert Opinion on Environmental Biology, 2017
Exploring the Role of a Soil Microbial Consortium on the Biodegradation and Physical Alteration o... more Exploring the Role of a Soil Microbial Consortium on the Biodegradation and Physical Alteration of Low Density Polyethylene Background: Our study is a contribution to the searching for microorganisms capable of degrading low density polyethylene. A microbial consortium was detected on low density polyethylene wastes buried under soil in a composting area of a Mexico City landfill known as “Bordo Poniente”. Methods: Photomicrographs of the microbial consortium by optical microscopy and scanning electron microscope (SEM) were taken at different times during the microbial film development in low density polyethylene; specific culture media, with polyethylene as the only carbon source, were used for strain isolation of bacteria, yeast and filamentous fungi; polyethylene degradation was evaluated by observing the physical alteration of this material in the SEM and by quantifying its weight loss when the polyethylene was used as a carbon source and incubated at different temperatures under shaking conditions at different pH. Results and conclusions: Photomicrographs of the microbial consortium by SEM, show a wide variety of species. It was possible to observe not only the shape of the microbial colonies but also the progressive development of a biofilm. The higher microbial degradation activity (18% in 60 days) was attained when cultures were incubated at 24°C under shaking conditions at pH 5.0. This is one of the more efficient degradations reported up to date. In addition, paper and wood degrading activity by the same consortium was estimated.
Frontiers Research Topics, 2015
Revista De Investigacion Clinica Organo Del Hospital De Enfermedades De La Nutricion, 2002
The purpose of the present investigation, was to analyze the sequences of 16S ribosomal genes par... more The purpose of the present investigation, was to analyze the sequences of 16S ribosomal genes partially amplified from 17 isolated Giardia intestinalis obtained from faces of 13 children with intestinal pathology and four symptoms-free children with intestinal pathology. Analysis was made also with Giardia Portland-I and four Giardias isolated from dogs. Children ages in both groups ranged from six to twelve years. Genomic DNA was isolated using the phenol-chloroform-isoamyl alcohol technique, and partial amplification of 16S rRNA ribosomal gene was carried out by the Polymerase Chain Reaction. Sequences of rDNA were compared with Portland-I by using CLUSTAL-W (1.81) and PHYLIP (3.6) software in order to determine phylogenic associations. Our results showed that only one isolate from symptoms-free children and three from the symptomatic children were associated with Portland I. The other isolated Giardias were associated between them and with two samples obtained from dogs that are phylogenetically distant from Portland-I. Two isolates from dog constituted a different group. These results suggest a zoonotic infection and presence of symptoms in children from the present investigation; probably it was associated with host or special characteristics of Giardia strains. The last two situations have a special epidemiological and public health interest.
Salud pública de México
This study evaluates, after a 10-year period, the attitudes of medical students towards research ... more This study evaluates, after a 10-year period, the attitudes of medical students towards research and learning at the National University of Mexico (UNAM), and tries to determine the role that experiences obtained during academic years could play in orienting these attitudes. Results indicate that all four groups of participant students,--1st and 4th-5th grades, in 1984 and in 1994--show slightly positive attitudes towards research and learning. No significant attitude changes were observed after the 10-year period in students who enter medical school nor in those who begin clinical practice. Besides, it was found a significant correlation between these two attitudinal factors. Some possible explanations for these results are discussed, as well as some steps that could help to promote positive attitudes towards research and learning.
Frontiers in Genetics, 2015
Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, 1983
1. Thirteen isoenzyme loci were analyzed electrophoretically for each of 13 isolates obtained fro... more 1. Thirteen isoenzyme loci were analyzed electrophoretically for each of 13 isolates obtained from Argentina. Costa Rica, Mexico and Venezuela to determine both genetic distance and time of evolutionary divergence between these populations.
BMC Infectious Diseases, 2014
Background: Anal cancer has become one of the most common non-AIDS-defined tumors among Human Imm... more Background: Anal cancer has become one of the most common non-AIDS-defined tumors among Human Immunodeficiency Virus-positive (HIV+) individuals, and a rise in its incidence among HIV+ Men who have Sex with Men (MSM) has been shown, despite the introduction of Highly Active Anti-Retroviral Therapy (HAART). Human Papillomavirus (HPV) infections are highly prevalent among HIV+ MSM and recent studies have shown high rates of HPV-associated anal intraepithelial neoplasia (AIN) and anal cancer among this population.
School Science and Mathematics, 1982
Mechanisms of Ageing and Development, 1986
The activities of brain initiation factor 2 and brain elongation factor 1, which function as rate... more The activities of brain initiation factor 2 and brain elongation factor 1, which function as rate-limiting in total protein synthesis, and estimations of brain weight were followed during postnatal life in the rat and the mouse. Both activities decreased in parallel while cumulative brain weight increased. Three exponential components were required for the mathematical expression of each of the three processes in semilogarithmic plots against time. The acceleration curves for the activities and tissue weight demonstrated a mirror image symmetry. Within the general pattern of diminution with age, the negative acceleration of the activities and the positive acceleration of the brain weight displayed repeated bursts. The activities of both factors could also be arranged into several regression lines in log/log plots against time. Significantly, in these plots, the regression line calculated for the whole set of data for each factor activity showed that the value of the ratio of the slopes (mouse to rat) was inversely related to the square root of the ratio of species longevity and was in agreement with the power law relating life spans of cells to species longevity (Röhme, Proc. Natl. Acad. Sci. U.S.A., 78 (1981) 5009).
International Journal of Cancer, 1999
Background: Human papillomavirus 16 (HPV16) has a number of variants, each with a different geogr... more Background: Human papillomavirus 16 (HPV16) has a number of variants, each with a different geographic distribution and some that are associated more often with invasive neoplasias. We investigated whether the high incidence of cervical cancer in Mexico (50 cases per 100 000 women) may be associated with a high prevalence of oncogenic HPV16 variants. Methods: Cervical samples were collected from 181 case patients with cervical cancer and from 181 age-matched control subjects, all from Mexico City. HPV16 was detected with an E6/E7 gene-specific polymerase chain reaction, and variant HPV classes and subclasses were identified by sequencing regions of the E6 and L1/MY genes. Clinical data and data on tumor characteristics were also collected. All statistical tests were twosided. Results: HPV16 was detected in cervical scrapes from 50.8% 92 of 181) of case patients and from 11% (20 of 181) of control subjects. All HPV16positive samples, except one, contained European (E) or Asian-American (AA) variants. AA and E variants were found statistically significantly more often in case patients (AA = 23.2% [42 of 181]; E = 27.1% [49 of 181]) than in control subjects (AA = 1.1% [two of 181]; E = 10% [18 of 181]) (P<.001 for case versus control subjects for either E or AA variants . However, the frequency of AA variants was 21 times higher in cancer patients than in control subjects, whereas that ratio for E variants was only 2.7 (P = .006, 2 test). The odds ratio (OR) for cervical cancer associated with AA variants (OR = 27.0; 95% confidence interval [CI] = 6.4 to 113.7) was higher than that asso-ciated with E variants (OR = 3.4; 95% CI = 1.9 to 6.0). AA-positive case patients (46.2 ± 12.5 years [mean ± standard deviation]) were 7.7 years younger than E-positive case patients (53.9 ± 12.2 years) (P = .004, Student's t test). AA variants were associated with squamous cell carcinomas and adenocarcinomas, but E variants were associated with only squamous cell carcinomas (P = .014, Fisher's exact test). Conclusions: The high frequency of HPV16 AA variants, which appear to be more oncogenic than E variants, might contribute to the high incidence of cervical cancer in
Expert Review of Vaccines, 2007
Prophylactic vaccines against human papillomavirus (HPV) are on the market and will certainly red... more Prophylactic vaccines against human papillomavirus (HPV) are on the market and will certainly reduce the incidence of genital warts and the risk of developing cervical cancer. In addition, they will contribute to reducing anal as well as head and neck cancers. However, effort should be made in the short term in order for these vaccines to have a real impact in the developing world, where almost 80% of cervical cancer cases occur. Since the available vaccines include only two of the HPV types found in cancers (approximately 70%), improvements in current mass screening programs -with the use of molecular techniques -must be made, particularly in developing countries. Therapeutic vaccines have been designed to control advanced lesions and residual illness and, although success has usually been obtained in animal models, clinical studies have not yet provided the anticipated results. Finally, the next generations of prophylactic HPV vaccines will probably include subunit vaccines, transgenic bacteria and plants, among others, and could represent useful and cheaper alternatives for reducing cervical cancer, particularly in the developing world.
BMC Genomics, 2011
Background: The Human Papillomavirus (HPV) genome is divided into early and late coding sequences... more Background: The Human Papillomavirus (HPV) genome is divided into early and late coding sequences, including 8 open reading frames (ORFs) and a regulatory region (LCR). Viral gene expression may be regulated through epigenetic mechanisms, including cytosine methylation at CpG dinucleotides. We have analyzed the distribution of CpG sites and CpG islands/clusters (CGI) among 92 different HPV genomes grouped in function of their preferential tropism: cutaneous or mucosal. We calculated the proportion of CpG sites (PCS) for each ORF and calculated the expected CpG values for each viral type. Results: CpGs are underrepresented in viral genomes. We found a positive correlation between CpG observed and expected values, with mucosal high-risk (HR) virus types showing the smallest O/E ratios. The ranges of the PCS were similar for most genomic regions except E4, where the majority of CpGs are found within islands/clusters. At least one CGI belongs to each E2/E4 region. We found positive correlations between PCS for each viral ORF when compared with the others, except for the LCR against four ORFs and E6 against three other ORFs. The distribution of CpG islands/clusters among HPV groups is heterogeneous and mucosal HR-HPV types exhibit both lower number and shorter island sizes compared to cutaneous and mucosal Low-risk (LR) HPVs (all of them significantly different).
Nucleic Acids Research, 1991
EMBL accession nos X54474-X54479 (incl.) Ribosomal RNA (rRNA) molecules are considered very good ... more EMBL accession nos X54474-X54479 (incl.) Ribosomal RNA (rRNA) molecules are considered very good phylogenetic markers because they are shared by all prokaryotic and eukaryotic cells, as a constitutive part of the very ancient protein synthesis machinery, the ribosomes. It seems their primary and secondary structure as well as the relative position of the genes or gene fragments (exons) within the ribosomal cistron, reflect the phylogenetic distances between living groups of organisms. There are some remarkable differences between trypanosomatid rRNA molecules and those of most eukaryotic organisms. First, trypanosomatids have four very small rRNAs in addition to the typical eukaryotic 5S and 5.8S-like species and all six mature molecules are associated with the 28S-like species of the large ribosomal subunit. Second, the genes for three of the extra rRNAs: M2, M4 and M6, are coded near the 3' end of the genes for the 28S-like species and the gene for Ml is located between the two exons for the constituents (alpha and beta) of the 28S-like molecule (1, 2). The remaining species, M3 and M5 are considered 5.8S and 5S-like, respectively. These small rRNA molecules were directly sequenced employing the method of Donis-Keller (3) using the enzymes TI, U2, Phy M and B. cereus. The length, in number of bases, the relative composition of purine and pyrimidine bases, and the accession numbers in EMBL are presented in . The percent homology with the corresponding molecules of Crithidia fasciculata (4) and Trypanosoma brucei (5, 6) calculated with CLUSTAL package , shows the very close relationship between these molecules, but that M6 is relatively more variable .