Alfonso Méndez Tenorio - Academia.edu (original) (raw)
Papers by Alfonso Méndez Tenorio
Frontiers in Cellular and Infection Microbiology, Feb 28, 2017
Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of... more Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.
Health, 2013
The aim of this study was to determinate the gene expression levels of angiotensinogen, angiotens... more The aim of this study was to determinate the gene expression levels of angiotensinogen, angiotensin converting enzyme, renin, (pro)renin receptor, and the final rennin-angiotensin system (RAS) products Angiotensin (Ang) II and Ang 1-7 in the remnant kidney of 5/6 nephrectomized rats and its response to RAS pharmacological blockade. Male Wistar rats were divided into five groups: sham operated (SO), 5/6 nephrectomized (NFX), NFX + captopril (50 mg/ kg/day), NFX + losartan (10 mg/kg/day), and NFX + aliskiren (10 mg/kg/day). Animals were followed up for 60 days and protein urine excretion was measured. Systolic blood pressure, renal tissue RAS mRNA expression levels, plasma Ang II, and plasma Ang 1-7 were evaluated at day 60 after nephrectomy. Blood pressure and urine protein were increased after 5/6 nephrectomy. Ang II levels were increased 9.4 fold, whereas Ang 1-7 decreased 72.9% in NFX animals compared with SO rats. 5/6 nephrectomy increased renal angiotensinogen and (pro)renin receptor mRNA expression but down-regulated renin mRNA expression. RAS blockade restored the systolic blood pressure to normal values and slowed down urinary protein excretion, and also prevented changes in Ang II and Ang 1-7. RAS blockade reduced (pro)renin receptor, ACE, and AGT mRNA expression in the remnant kidney. However, renin mRNA expression increased compared with NFX rats. In conclusion these results suggest that inhibition of Ang II synthesis by RAS blockade is associated with renal regulation of RAS mRNA expression and this may be through a mechanism related with the Ang II/Ang 1-7 balance.
Frontiers in Cellular and Infection Microbiology
Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associate... more Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associated with pediatric and traveler’s diarrhea. Even without diarrhea, EAEC infections in children also lead to increased gut inflammation and growth shortfalls. EAEC strain’s defining phenotype is the aggregative adherence pattern on epithelial cells attributable to the aggregative adherence fimbriae (AAF). EAEC only causes diarrhea in humans; therefore, not much is known of the exact intestinal region of infection and damage or its interactions with intestinal enterocytes in vivo and in situ. This study aimed to develop a new tEAEC mouse model of infection, characterize the microbiota of infected mice, and evaluate in situ the expression of host adherence and surface molecules triggering EAEC infection and the role of the EAEC AAF-II in adherence. Six-week-old C57BL/6 mice, without previous antibiotic treatment, were orally challenged with EAEC 042 strain or EAEC 042 AAF-II mutant (ΔAAF/II) ...
![Research paper thumbnail of Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans](https://attachments.academia-assets.com/118577970/thumbnails/1.jpg)
](Virology, 2008
Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly ... more Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly speciesspecific. Interspecies virus transmission is thought to be one of the important contributors involved in the evolution and diversity of rotaviruses in nature. Human rotavirus (HRV) G3P[3] strains Ro1845 and HCR3A have been reported to be closely related genetically to certain canine and feline rotaviruses (RVs). Whole genome sequence and phylogenetic analyses of each of these 2 HRVs as well as 3 canine RVs (CU-1, K9 and A79-10, each with G3P[3] specificity) and 2 feline RVs (Cat97 with G3P[3] specificity and Cat2 with G3P[9] specificity) revealed that (i) each of 11 genes of the Ro1845 and HCR3A was of canine/feline origin; (ii) canine and feline rotaviruses with G3P[3] specificity bore highly conserved species-specific genomes; and (iii) the Cat2 strain may have evolved via multiple reassortment events involving canine, feline, human and bovine rotaviruses. Published by Elsevier Inc.
Microorganisms, Aug 22, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cancers, May 7, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cancers, 2021
We previously reported that triple-negative breast cancer (BRCA) cells overexpress the cytokines ... more We previously reported that triple-negative breast cancer (BRCA) cells overexpress the cytokines GM-CSF, G-CSF, MCP-1, and RANTES, and when monocytes were 3-D co-cultured with them, M1-like macrophages were generated with the ability to induce aggressive features in luminal BRCA cell lines. These include upregulation of mesenchymal and stemness markers and invasion. In this study, we stimulated peripheral blood monocytes with the four cytokines and confirmed their capacity to generate protumoral M1-like macrophages. Using the METABRIC BRCA database, we observed that GM-CSF, MCP-1, and RANTES are associated with triple-negative BRCA and reduced overall survival, particularly in patients under 55 years of age. We propose an extended M1-like macrophage proinflammatory signature connected with these three cytokines. We found that the extended M1-like macrophage signature coexists with monocyte/macrophage, Th1 immune response, and immunosuppressive signatures, and all are enriched in cla...
Non-Coding RNA, Sep 26, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Journal of Molecular Evolution, 2022
Diverse studies have shown that the content of genes present in sequenced genomes does not seem t... more Diverse studies have shown that the content of genes present in sequenced genomes does not seem to correlate with the complexity of the organisms. However, various studies have shown that organism complexity and the size of the proteome has, indeed, a significant correlation. This characteristic allows us to postulate that some molecular mechanisms have permitted a greater functional diversity to some proteins to increase their participation in developing organisms with higher complexity. Among those mechanisms, the domain promiscuity, defined as the ability of the domains to organize in combination with other distinct domains, is of great importance for the evolution of organisms. Previous works have analyzed the degree of domain promiscuity of the proteomes showing how it seems to have paralleled the evolution of eukaryotic organisms. The latter has motivated the present study, where we analyzed the domain promiscuity in a collection of 84 eukaryotic proteomes representative of all the taxonomy groups of the tree of life. Using a grammar definition approach, we determined the architecture of 1,223,227 proteins, conformed by 2,296,371 domains, which established 839,184 bigram types. The phylogenetic reconstructions based on differences in the content of information from measures of proteome promiscuity confirm that the evolution of the promiscuity of domains in eukaryotic organisms resembles the evolutionary history of the species. However, a close analysis of the PHD and RING domains, the most promiscuous domains found in fungi and functional components of chromatin remodeling enzymes and important expression regulators, suggests an evolution according to their function.
European Journal of Cancer Prevention
Photodiagnosis and Photodynamic Therapy
Frontiers in Microbiology, 2021
Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks caus... more Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the is...
International Journal of Cancer, 2020
Novelty and Impact Statement: This study is the first to examine the associations of Helicobacter... more Novelty and Impact Statement: This study is the first to examine the associations of Helicobacter pylori (Hp) cag pathogenicity island sequence variants with gastric pathology in unselected gastric biopsy specimens, inclusive of un-culturable strains. Cumulative scores based on individual Hp polymorphisms associated with advanced gastric pre-malignant lesions or gastric cancer showed highly significant associations with these outcomes. These markers can potentially be used for risk stratification in the population, in view of targeting Hp eradication to high risk groups.
Scientific Reports, 2020
Helicobacter pylori (HP) colonizes the human stomach and induces acute gastritis, peptic ulcer di... more Helicobacter pylori (HP) colonizes the human stomach and induces acute gastritis, peptic ulcer disease, atrophic gastritis, and gastric adenocarcinoma. Increased virulence in HP isolates derives from harboring the cag (cytotoxin-associated genes) pathogenicity island (cagPAI). We analyzed the microvariants in cagPAI genes with the hypothesis that they may play an important role in determining HP virulence. We tested DNAs from cagA positive patients HP isolates; a total of 74 patients with chronic gastritis (CG, N = 37), intestinal metaplasia (IM, N = 21) or gastric cancer (GC, N = 16) from Mexico and Colombia. We selected 520 non-synonymous variants with at least 7.5% frequency in the original sequence outputs or with a minimum of 5 isolates with minor allele. After adjustment for multiple comparisons, no variants were statistically significantly associated with IM or GC. However, 19 non-synonymous showed conventional P-values < 0.05 comparing the frequency of the alleles between...
Journal of proteomics, Jan 23, 2018
Gastric cancer is one of the most aggressive malignancies affecting humankind. With almost a mill... more Gastric cancer is one of the most aggressive malignancies affecting humankind. With almost a million cases globally, it sits in fifth position in terms of incidence, and third in terms of mortality. The progression of this disease is slow, with prolonged and sequential precancerous stages including chronic gastritis, intestinal metaplasia, dysplasia, and finally gastric cancer. Here we used the iTRAQ approach combined with high-resolution mass spectrometry analysis to describe the spectrum of the gastric cancer cascade. Biopsies from three stages: chronic gastritis, intestinal metaplasia, and gastric adenocarcinoma, were selected for analysis by quantitative proteomics. We identified and reported quantitative data for 3914 different proteins quantified with high confidence, uncovering pathways and processes dysregulated between the different stages. Intestinal metaplasia is characterized by the down-regulation of ribosomal proteins, with overexpression of cell survival proteins such...
Con el desarrollo del presente estudio se pretendio implementar estrategias que permitan evaluar ... more Con el desarrollo del presente estudio se pretendio implementar estrategias que permitan evaluar el proteoma embrionario permitiendo asi elevar las tasas de exito de los tratamientos de reproduccion asistida. El encontrar criterios eficaces y facilmente aplicables basados en la examinacion para la seleccion embrionaria es una finalidad en la biologia reproductiva ya que permite obtener buenos resultados con menos cantidad de ovocitos fecundados y por lo tanto menos embriones analizados, reduciendo el uso de material biologico y reduciendo los costos de proceso lo que beneficia a las parejas que deseen tener descendencia mediante este tipo de procedimientos. La manera como abordamos este problema fue realizando una busqueda mediante cromatografia liquida de alta eficacia en fase reversa (RP-HPLC) que es una poderosa herramienta que posee una gran sensibilidad, resolucion, utiliza muy poca muestra y es automatizable permitiendo analizar proteinas que pueden usarse como blancos para el diagnostico preimplantacional. Se extrajeron proteinas de muestras de zigotos, embriones y blastocistos, en el analisis de los cromatogramas se observaron las cumbres con los tiempos de retencion para los peptidos a una longitud de onda de 220nm. Estos peptidos fueron analizados por espectrometria de masas.
Archives of Microbiology, 2015
The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bact... more The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bacteria considered rare opportunistic pathogens in humans. Metagenomics was performed on the cerebrospinal fluid (CSF) of a pediatric patient with meningitis. Nucleic acids were extracted, randomly amplified, and sequenced with the 454 GS FLX Titanium next-generation sequencing (NGS) system. Sequencing reads were assembled, and potential virulence genes were predicted. Phylogenomic and phylogenetic studies were performed. Psychrobacter sp. 310 was identified, and several virulence genes characteristic of pathogenic bacteria were found. The phylogenomic study and 16S rRNA gene phylogenetic analysis showed that the closest relative of Psychrobacter sp. 310 was Psychrobacter sanguinis. To our knowledge, this is the first report of a meningitis case associated with Psychrobacter sp. identified by NGS metagenomics in CSF from a pediatric patient. The metagenomic strategy based on NGS was a powerful tool to identify a rare unknown pathogen in a clinical case. Communicated by Jorge Membrillo-Hernández.
Cancer Research, 2013
Non-Hodgkin Lymphoma (NHL) is a group of different kinds of cancer rising on the basis of monoclo... more Non-Hodgkin Lymphoma (NHL) is a group of different kinds of cancer rising on the basis of monoclonal expansion of B and T Lymphocytes. Over 90% of NHL has its origin in B lymphocytes. The causes of NHL are poorly understood. Diffuse large B-cell lymphoma (DLBCL), the most common lymphoma in adults, and Burkitt s lymphoma are highly aggressive forms of NHL. It is of interest to characterize diverse transcription factors that are involved in the development of lymphoid progenitors because of their potential therapeutic applications. Krüppel-like factor 4 (KLF4) is a member of the KLF zinc-finger-containing transcription factor family. Evidence has established KLF4 as an oncogene or a tumor suppressor. Recent studies indicated the involvement of KLF4 in the regulation of apoptosis, proliferation, and differentiation of B cells and B-cell malignancies. By using a Tissue Micro Array (TMA), we have recently shown that NHLs have high expression of KLF4. The underlying mechanisms of the re...
Bioinformation, 2012
There are very few antiviral drugs available to fight viral infections and the appearance of vira... more There are very few antiviral drugs available to fight viral infections and the appearance of viral strains resistant to these antivirals is not a rare event. Hence, the design of new antiviral drugs is important. We describe the prediction of peptides with antiviral activity (AVP) derived from the viral glycoproteins involved in the entrance of herpes simplex (HSV) and influenza A viruses into their host cells. It is known, that during this event viral glycoproteins suffer several conformational changes due to protein-protein interactions, which lead to membrane fusion between the viral envelope and the cellular membrane. Our hypothesis is that AVPs can be derived from these viral glycoproteins, specifically from regions highly conserved in amino acid sequences, which at the same time have the physicochemical properties of being highly exposed (antigenic), hydrophilic, flexible, and charged, since these properties are important for protein-protein interactions. For that, we separately analyzed the HSV glycoprotein H and B, and influenza A viruses hemagglutinin (HA), using several bioinformatics tools. A set of multiple alignments was carried out, to find the most conserved regions in the amino acid sequences. Then, the physicochemical properties indicated above were analyzed. We predicted several peptides 12-20 amino acid length which by docking analysis were able to interact with the fusion viral glycoproteins and thus may prevent conformational changes in them, blocking the viral infection. Our strategy to design AVPs seems to be very promising since the peptides were synthetized and their antiviral activities have produced very encouraging results.
Frontiers in Cellular and Infection Microbiology, Feb 28, 2017
Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of... more Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.
Health, 2013
The aim of this study was to determinate the gene expression levels of angiotensinogen, angiotens... more The aim of this study was to determinate the gene expression levels of angiotensinogen, angiotensin converting enzyme, renin, (pro)renin receptor, and the final rennin-angiotensin system (RAS) products Angiotensin (Ang) II and Ang 1-7 in the remnant kidney of 5/6 nephrectomized rats and its response to RAS pharmacological blockade. Male Wistar rats were divided into five groups: sham operated (SO), 5/6 nephrectomized (NFX), NFX + captopril (50 mg/ kg/day), NFX + losartan (10 mg/kg/day), and NFX + aliskiren (10 mg/kg/day). Animals were followed up for 60 days and protein urine excretion was measured. Systolic blood pressure, renal tissue RAS mRNA expression levels, plasma Ang II, and plasma Ang 1-7 were evaluated at day 60 after nephrectomy. Blood pressure and urine protein were increased after 5/6 nephrectomy. Ang II levels were increased 9.4 fold, whereas Ang 1-7 decreased 72.9% in NFX animals compared with SO rats. 5/6 nephrectomy increased renal angiotensinogen and (pro)renin receptor mRNA expression but down-regulated renin mRNA expression. RAS blockade restored the systolic blood pressure to normal values and slowed down urinary protein excretion, and also prevented changes in Ang II and Ang 1-7. RAS blockade reduced (pro)renin receptor, ACE, and AGT mRNA expression in the remnant kidney. However, renin mRNA expression increased compared with NFX rats. In conclusion these results suggest that inhibition of Ang II synthesis by RAS blockade is associated with renal regulation of RAS mRNA expression and this may be through a mechanism related with the Ang II/Ang 1-7 balance.
Frontiers in Cellular and Infection Microbiology
Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associate... more Typical enteroaggregative Escherichia coli (tEAEC) is a diarrheagenic E. coli pathotype associated with pediatric and traveler’s diarrhea. Even without diarrhea, EAEC infections in children also lead to increased gut inflammation and growth shortfalls. EAEC strain’s defining phenotype is the aggregative adherence pattern on epithelial cells attributable to the aggregative adherence fimbriae (AAF). EAEC only causes diarrhea in humans; therefore, not much is known of the exact intestinal region of infection and damage or its interactions with intestinal enterocytes in vivo and in situ. This study aimed to develop a new tEAEC mouse model of infection, characterize the microbiota of infected mice, and evaluate in situ the expression of host adherence and surface molecules triggering EAEC infection and the role of the EAEC AAF-II in adherence. Six-week-old C57BL/6 mice, without previous antibiotic treatment, were orally challenged with EAEC 042 strain or EAEC 042 AAF-II mutant (ΔAAF/II) ...
Virology, 2008
Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly ... more Rotaviruses, the major causative agents of infantile diarrhea worldwide, are, in general, highly speciesspecific. Interspecies virus transmission is thought to be one of the important contributors involved in the evolution and diversity of rotaviruses in nature. Human rotavirus (HRV) G3P[3] strains Ro1845 and HCR3A have been reported to be closely related genetically to certain canine and feline rotaviruses (RVs). Whole genome sequence and phylogenetic analyses of each of these 2 HRVs as well as 3 canine RVs (CU-1, K9 and A79-10, each with G3P[3] specificity) and 2 feline RVs (Cat97 with G3P[3] specificity and Cat2 with G3P[9] specificity) revealed that (i) each of 11 genes of the Ro1845 and HCR3A was of canine/feline origin; (ii) canine and feline rotaviruses with G3P[3] specificity bore highly conserved species-specific genomes; and (iii) the Cat2 strain may have evolved via multiple reassortment events involving canine, feline, human and bovine rotaviruses. Published by Elsevier Inc.
Microorganisms, Aug 22, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cancers, May 7, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Cancers, 2021
We previously reported that triple-negative breast cancer (BRCA) cells overexpress the cytokines ... more We previously reported that triple-negative breast cancer (BRCA) cells overexpress the cytokines GM-CSF, G-CSF, MCP-1, and RANTES, and when monocytes were 3-D co-cultured with them, M1-like macrophages were generated with the ability to induce aggressive features in luminal BRCA cell lines. These include upregulation of mesenchymal and stemness markers and invasion. In this study, we stimulated peripheral blood monocytes with the four cytokines and confirmed their capacity to generate protumoral M1-like macrophages. Using the METABRIC BRCA database, we observed that GM-CSF, MCP-1, and RANTES are associated with triple-negative BRCA and reduced overall survival, particularly in patients under 55 years of age. We propose an extended M1-like macrophage proinflammatory signature connected with these three cytokines. We found that the extended M1-like macrophage signature coexists with monocyte/macrophage, Th1 immune response, and immunosuppressive signatures, and all are enriched in cla...
Non-Coding RNA, Sep 26, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Journal of Molecular Evolution, 2022
Diverse studies have shown that the content of genes present in sequenced genomes does not seem t... more Diverse studies have shown that the content of genes present in sequenced genomes does not seem to correlate with the complexity of the organisms. However, various studies have shown that organism complexity and the size of the proteome has, indeed, a significant correlation. This characteristic allows us to postulate that some molecular mechanisms have permitted a greater functional diversity to some proteins to increase their participation in developing organisms with higher complexity. Among those mechanisms, the domain promiscuity, defined as the ability of the domains to organize in combination with other distinct domains, is of great importance for the evolution of organisms. Previous works have analyzed the degree of domain promiscuity of the proteomes showing how it seems to have paralleled the evolution of eukaryotic organisms. The latter has motivated the present study, where we analyzed the domain promiscuity in a collection of 84 eukaryotic proteomes representative of all the taxonomy groups of the tree of life. Using a grammar definition approach, we determined the architecture of 1,223,227 proteins, conformed by 2,296,371 domains, which established 839,184 bigram types. The phylogenetic reconstructions based on differences in the content of information from measures of proteome promiscuity confirm that the evolution of the promiscuity of domains in eukaryotic organisms resembles the evolutionary history of the species. However, a close analysis of the PHD and RING domains, the most promiscuous domains found in fungi and functional components of chromatin remodeling enzymes and important expression regulators, suggests an evolution according to their function.
European Journal of Cancer Prevention
Photodiagnosis and Photodynamic Therapy
Frontiers in Microbiology, 2021
Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks caus... more Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the is...
International Journal of Cancer, 2020
Novelty and Impact Statement: This study is the first to examine the associations of Helicobacter... more Novelty and Impact Statement: This study is the first to examine the associations of Helicobacter pylori (Hp) cag pathogenicity island sequence variants with gastric pathology in unselected gastric biopsy specimens, inclusive of un-culturable strains. Cumulative scores based on individual Hp polymorphisms associated with advanced gastric pre-malignant lesions or gastric cancer showed highly significant associations with these outcomes. These markers can potentially be used for risk stratification in the population, in view of targeting Hp eradication to high risk groups.
Scientific Reports, 2020
Helicobacter pylori (HP) colonizes the human stomach and induces acute gastritis, peptic ulcer di... more Helicobacter pylori (HP) colonizes the human stomach and induces acute gastritis, peptic ulcer disease, atrophic gastritis, and gastric adenocarcinoma. Increased virulence in HP isolates derives from harboring the cag (cytotoxin-associated genes) pathogenicity island (cagPAI). We analyzed the microvariants in cagPAI genes with the hypothesis that they may play an important role in determining HP virulence. We tested DNAs from cagA positive patients HP isolates; a total of 74 patients with chronic gastritis (CG, N = 37), intestinal metaplasia (IM, N = 21) or gastric cancer (GC, N = 16) from Mexico and Colombia. We selected 520 non-synonymous variants with at least 7.5% frequency in the original sequence outputs or with a minimum of 5 isolates with minor allele. After adjustment for multiple comparisons, no variants were statistically significantly associated with IM or GC. However, 19 non-synonymous showed conventional P-values < 0.05 comparing the frequency of the alleles between...
Journal of proteomics, Jan 23, 2018
Gastric cancer is one of the most aggressive malignancies affecting humankind. With almost a mill... more Gastric cancer is one of the most aggressive malignancies affecting humankind. With almost a million cases globally, it sits in fifth position in terms of incidence, and third in terms of mortality. The progression of this disease is slow, with prolonged and sequential precancerous stages including chronic gastritis, intestinal metaplasia, dysplasia, and finally gastric cancer. Here we used the iTRAQ approach combined with high-resolution mass spectrometry analysis to describe the spectrum of the gastric cancer cascade. Biopsies from three stages: chronic gastritis, intestinal metaplasia, and gastric adenocarcinoma, were selected for analysis by quantitative proteomics. We identified and reported quantitative data for 3914 different proteins quantified with high confidence, uncovering pathways and processes dysregulated between the different stages. Intestinal metaplasia is characterized by the down-regulation of ribosomal proteins, with overexpression of cell survival proteins such...
Con el desarrollo del presente estudio se pretendio implementar estrategias que permitan evaluar ... more Con el desarrollo del presente estudio se pretendio implementar estrategias que permitan evaluar el proteoma embrionario permitiendo asi elevar las tasas de exito de los tratamientos de reproduccion asistida. El encontrar criterios eficaces y facilmente aplicables basados en la examinacion para la seleccion embrionaria es una finalidad en la biologia reproductiva ya que permite obtener buenos resultados con menos cantidad de ovocitos fecundados y por lo tanto menos embriones analizados, reduciendo el uso de material biologico y reduciendo los costos de proceso lo que beneficia a las parejas que deseen tener descendencia mediante este tipo de procedimientos. La manera como abordamos este problema fue realizando una busqueda mediante cromatografia liquida de alta eficacia en fase reversa (RP-HPLC) que es una poderosa herramienta que posee una gran sensibilidad, resolucion, utiliza muy poca muestra y es automatizable permitiendo analizar proteinas que pueden usarse como blancos para el diagnostico preimplantacional. Se extrajeron proteinas de muestras de zigotos, embriones y blastocistos, en el analisis de los cromatogramas se observaron las cumbres con los tiempos de retencion para los peptidos a una longitud de onda de 220nm. Estos peptidos fueron analizados por espectrometria de masas.
Archives of Microbiology, 2015
The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bact... more The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bacteria considered rare opportunistic pathogens in humans. Metagenomics was performed on the cerebrospinal fluid (CSF) of a pediatric patient with meningitis. Nucleic acids were extracted, randomly amplified, and sequenced with the 454 GS FLX Titanium next-generation sequencing (NGS) system. Sequencing reads were assembled, and potential virulence genes were predicted. Phylogenomic and phylogenetic studies were performed. Psychrobacter sp. 310 was identified, and several virulence genes characteristic of pathogenic bacteria were found. The phylogenomic study and 16S rRNA gene phylogenetic analysis showed that the closest relative of Psychrobacter sp. 310 was Psychrobacter sanguinis. To our knowledge, this is the first report of a meningitis case associated with Psychrobacter sp. identified by NGS metagenomics in CSF from a pediatric patient. The metagenomic strategy based on NGS was a powerful tool to identify a rare unknown pathogen in a clinical case. Communicated by Jorge Membrillo-Hernández.
Cancer Research, 2013
Non-Hodgkin Lymphoma (NHL) is a group of different kinds of cancer rising on the basis of monoclo... more Non-Hodgkin Lymphoma (NHL) is a group of different kinds of cancer rising on the basis of monoclonal expansion of B and T Lymphocytes. Over 90% of NHL has its origin in B lymphocytes. The causes of NHL are poorly understood. Diffuse large B-cell lymphoma (DLBCL), the most common lymphoma in adults, and Burkitt s lymphoma are highly aggressive forms of NHL. It is of interest to characterize diverse transcription factors that are involved in the development of lymphoid progenitors because of their potential therapeutic applications. Krüppel-like factor 4 (KLF4) is a member of the KLF zinc-finger-containing transcription factor family. Evidence has established KLF4 as an oncogene or a tumor suppressor. Recent studies indicated the involvement of KLF4 in the regulation of apoptosis, proliferation, and differentiation of B cells and B-cell malignancies. By using a Tissue Micro Array (TMA), we have recently shown that NHLs have high expression of KLF4. The underlying mechanisms of the re...
Bioinformation, 2012
There are very few antiviral drugs available to fight viral infections and the appearance of vira... more There are very few antiviral drugs available to fight viral infections and the appearance of viral strains resistant to these antivirals is not a rare event. Hence, the design of new antiviral drugs is important. We describe the prediction of peptides with antiviral activity (AVP) derived from the viral glycoproteins involved in the entrance of herpes simplex (HSV) and influenza A viruses into their host cells. It is known, that during this event viral glycoproteins suffer several conformational changes due to protein-protein interactions, which lead to membrane fusion between the viral envelope and the cellular membrane. Our hypothesis is that AVPs can be derived from these viral glycoproteins, specifically from regions highly conserved in amino acid sequences, which at the same time have the physicochemical properties of being highly exposed (antigenic), hydrophilic, flexible, and charged, since these properties are important for protein-protein interactions. For that, we separately analyzed the HSV glycoprotein H and B, and influenza A viruses hemagglutinin (HA), using several bioinformatics tools. A set of multiple alignments was carried out, to find the most conserved regions in the amino acid sequences. Then, the physicochemical properties indicated above were analyzed. We predicted several peptides 12-20 amino acid length which by docking analysis were able to interact with the fusion viral glycoproteins and thus may prevent conformational changes in them, blocking the viral infection. Our strategy to design AVPs seems to be very promising since the peptides were synthetized and their antiviral activities have produced very encouraging results.