PubMed Health⌕ Search

Biomedical subjects

S D Pena

Publications and source records attributed to S D Pena.

At least 19 recordsLinked to original sources
PubMed2006

Characterization of promoter regulatory elements involved in downexpression of the DNA polymerase kappa in colorectal cancer.

The low-fidelity DNA polymerases thought to be specialized in DNA damage processing are frequently misregulated in cancers. We show here that DNA polymerase kappa (polkappa), prone to replicate across oxidative and aromatic adducts and known to function in nucleotide excision repair (NER), is downregulated in colorectal tumour biopsies. Contrary to the replicative poldelta and polalpha, for which only activating domains were described, we identified an upstream 465-bp-long repressor region in the promoter of POLK. We also found an activating 237-bp region that includes stimulating protein-1 (SP1) and cyclic AMP-responsive element (CRE)-binding sites. Mutations at one CRE-binding site led to a dramatic 80% decrease in promoter activity. Alterations of the SP1-binding site also affected, to a lesser extent, the transcription. Gel shift assays confirmed the role played by CRE/SP1 recognition sequences. Moreover, ectopic expression of SP1 or CRE-binding protein (CREB) protein favoured polkappa transcription. Finally, we found that polkappa downexpression in colorectal biopsies correlated with a decreased level of CREB and SP1 transcripts. This work shows that the promoter of POLK is cis-controlled and suggests that silencing of CREB and SP1 proteins could contribute to downregulation of this repair polymerase in colorectal tumours.

Acetylation↗
PubMed2001

Molecular cloning and characterization of the DNA mismatch repair gene class 2 from the Trypanosoma cruzi.

Genes with homology to the bacterial mutS gene, which encodes a protein involved in post-replication DNA mismatch repair, are known in several organisms. Using a degenerate PCR strategy, we cloned a Trypanosoma cruzi genomic DNA fragment homologous to the mutS gene class two (MSH2). This fragment was used as a probe to select the corresponding cDNAs from a T. cruzi cDNA library. The complete sequence of the gene (3304 bp), denominated TcMSH2, was obtained. The sequence contained an open reading frame of 2889 bp coding for a putative protein of 962 amino acids. Computational analyses of the amino acid sequence showed 36% identity with MSH2 proteins from other eukaryotes and revealed the presence of all functional domains of MutS proteins. Hybridization analyses indicated that the TcMSH2 gene is present as a single copy gene that is expressed in all forms of the T. cruzi life cycle. The role of the product of the TcMSH2 gene in mismatch repair was investigated by negative dominance phenotype analyses in Escherichia coli. When eukaryotic muts genes are expressed in a prokaryotic system, they increase the bacterial mutation rate. The same phenomenon was observed with the TcMSH2 cDNA, indicating that T. cruzi MSH2 interferes with the bacterial mismatch system. Phylogenetic analyses showed that the T. cruzi gene grouped with the MSH2 clade confirming the nature of the gene isolated in this work.

Amino Acid Sequence↗
PubMed2001

Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome.

The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome-linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations-settled in the Amazonian region, the central Brazilian plateau, and the Chaco region-have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.

Cultural Diversity↗
PubMed2001

Microsatellite instability as a tool for the classification of gastric cancer.

Microsatellite instability (MSI) is a common feature of gastric cancers that reflects underlying mismatch-repair deficiency in the tumor, caused most frequently by methylation of the hMLH1 promoter. Tumors with MSI have been found to inactivate certain target genes by permitting an increased frequency of mutations in mononucleotide runs in their coding regions. Gastric tumors with MSI have a distinct clinicopathological profile with a relatively good prognosis. Using the simple and robust methodologies available, MSI detection in gastrointestinal tumors promises to be one of the first widely used molecular prognostic tests for human cancer. Here, we review the molecular context of this exciting prospect with respect to one of the world's most prevalent cancers, that of the stomach.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade.

The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (-3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (+/-14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.

Africa↗
PubMed2001

Usefulness of microsatellite typing in population genetic studies of Trypanosoma cruzi.

Through microsatellite analysis of 53 monoclonal populations of Trypanosoma cruzi, we found a remarkable degree of genetic polymorphism with no single multilocus genotype being observed more than once. The microsatellite profile proved to be stable during 70 generations of the CL Brener clone in culture. The microsatellite profiling presented also high diagnostic sensitivity since DNA amplifications could be achieved with less than 100 fg DNA, corresponding to half parasite total DNA content. Based on these technical attributes the microsatellite assay turns out to be an important tool for direct typing T. cruzi in biological samples. By using this approach we were able to type T. cruzi in feces of artificially infected bugs and in single cells sorted by FACS. The microsatellites have shown to be excellent markers for T. cruzi phylogenetic reconstruction. We used maximum parsimony based on the minimum number of mutational steps to build an unrooted Wagner network, which confirms previous conclusions based on the analysis of the D7 domain of the LSU rDNA gene that T. cruzi is composed by two major groups. We also obtained evidence that strains belonging to rRNA group 2 are subdivided into two genetically distant clusters, and that one of these clusters is more related to rRNA group (1/2). These results suggest different origins for these strains.

Animals↗
PubMed2001

Relationship between Trypanosoma cruzi and human chagasic megaesophagus: blood and tissue parasitism.

The persistence of Trypanosoma cruzi in tissue and blood of 52 patients in the digestive form of chronic Chagas disease was studied. These patients had chagasic megaesophagus and underwent corrective surgery. Parasitologic (xenodiagnosis, hemoculture, or both), histopathologic (hematoxylin and eosin, and peroxidase-anti-peroxidase staining), and molecular (polymerase chain reaction [PCR] followed by slot-blot hybridization) tests were used in the analysis. The presence of T. cruzi, its genomic fragments, or its antigens could be detected in 98% (51 of 52) of the patients. The parasite was randomly identified in 76.9% of esophageal tissues and in 90.4% by PCR and in 73.1% by parasitologic methods from the blood. Fifty percent (26 of 52) of tissue samples had inflammation, 80.8% of which was associated with the parasite. Trypanosoma cruzi was also identified unassociated with inflammatory alterations. Higher tissue parasitism and intense inflammatory processes were observed in esophageal tissue from patients with Grade IV megaesophagus. These data demonstrate that in the digestive form of Chagas' disease, particularly in cases of megaesophagus, T. cruzi is frequently found, both in blood and tissues and may contribute to the pathogenic mechanisms involved.

Adult↗
PubMed2000

The phylogeography of Brazilian Y-chromosome lineages.

We examined DNA polymorphisms in the nonrecombining portion of the Y-chromosome to investigate the contribution of distinct patrilineages to the present-day white Brazilian population. Twelve unique-event polymorphisms were typed in 200 unrelated males from four geographical regions of Brazil and in 93 Portuguese males. In our Brazilian sample, the vast majority of Y-chromosomes proved to be of European origin. Indeed, there were no significant differences when the haplogroup frequencies in Brazil and Portugal were compared by means of an exact test of population differentiation. Y-chromosome typing was quite sensitive in the detection of regional immigration events. Distinct footprints of Italian immigration to southern Brazil, migration of Moroccan Jews to the Amazon region, and possible relics of the 17th-century Dutch invasion of northeast Brazil could be seen in the data. In sharp contrast with our mtDNA data in white Brazilians, which showed that > or =60% of the matrilineages were Amerindian or African, only 2.5% of the Y-chromosome lineages were from sub-Saharan Africa, and none were Amerindian. Together, these results configure a picture of strong directional mating between European males and Amerindian and African females, which agrees with the known history of the peopling of Brazil since 1500.

Black People↗
PubMed2000

The ancestry of Brazilian mtDNA lineages.

We have analyzed 247 Brazilian mtDNAs for hypervariable segment (HVS)-I and selected restriction fragment-length-polymorphism sites, to assess their ancestry in different continents. The total sample showed nearly equal amounts of Native American, African, and European matrilineal genetic contribution but with regional differences within Brazil. The mtDNA pool of present-day Brazilians clearly reflects the imprints of the early Portuguese colonization process (involving directional mating), as well as the recent immigrant waves (from Europe) of the last century. The subset of 99 mtDNAs from the southeastern region encompasses nearly all mtDNA haplogroups observed in the total Brazilian sample; for this regional subset, HVS-II was analyzed, providing, in particular, some novel details of the African mtDNA phylogeny.

Africa↗
PubMed2000

Molecular characterization and population study of an X chromosome homolog of the Y-linked microsatellite DYS391.

A novel microsatellite homologous to DYS391, a (GATA)(n) short tandem repeat on the human Y chromosome, was identified and characterized in the present work. Employing somatic cell hybrid and deletion panels in a PCR-based approach, we found out that the new microsatellite is located in Xp21.2-22.3, while its Y counterpart mapped to Yq11.21. This X-linked locus (provisionally called DXYS391) and its Y homolog constitute one more example of similarity outside the pseudoautosomal regions between the two human sex chromosomes. Sequencing data showed high levels of homology in the flanking regions of DXYS391 and DYS391 that differ primarily by the presence of a (GACA)(3) motif in the Y locus. Both loci were detected in chimpanzee DNA, suggesting that a putative transposition from the X to the Y occurred before the human/chimpanzee split. The allele frequencies of DYS391 and DXYS391 were investigated, respectively, in 271 Y and 337 X chromosomes from distinct human populations worldwide. DYS391 consistently displayed greater among-population component of the variance of the allele frequencies than DXYS391, as expected due to the three-times lower effective population size of Y chromosomes relative to the X. The intra-population diversity of DYS391, measured by Nei's locus diversity as well as by allele size variance, was lowest in Amerindians, while very low diversity of DXYS391 was seen in Africans. Since our African data are based on a small sample, further studies will be necessary to evaluate better this observation.

Alleles↗
PubMed2000

Microsatellite instability in tumors as a model to study the process of microsatellite mutations.

We screened 42 sporadic gastric tumors and found that seven of them had significant microsatellite instability. These were then studied at 26 microsatellite loci, comprising di-, tri- and tetranucleotide repeats. The instability level of individual microsatellites in the tumors was found to be positively correlated with the population average heterozygosity and variance of repeat number of the microsatellite loci, as predicted by the stepwise mutation model. Moreover, as is known to occur in human populations, instability was strongly correlated with the number of repeats at each microsatellite locus and with the perfection of the reiterated sequence. These results demonstrate that microsatellite mutations in unstable tumors show similarities to germline mutations and suggest that their study may be useful in understanding the mechanisms that generate microsatellite variability in human populations. We used this model to test the claims that the microsatellite mutation process is biased towards increased size and heterozygosity with wide differences in allele sizes. These assertions were not confirmed.

Adenocarcinoma↗
PubMed2000

Genetic characterization of Trypanosoma cruzi directly from tissues of patients with chronic Chagas disease: differential distribution of genetic types into diverse organs.

We have previously shown that a low-stringency single-specific primer-polymerase chain reaction (LSSP- PCR) is a highly sensitive and reproducible technique for the genetic profiling of Trypanosoma cruzi parasites directly in tissues from infected animals and humans. By applying LSSP-PCR to the study of the variable region of kinetoplast minicircle from T. cruzi, the intraspecific polymorphism of the kinetoplast-deoxyribonucleic acid (kDNA) sequence can be translated into individual kDNA signatures. In the present article, we report on our success using the LSSP-PCR technique in profiling the T. cruzi parasites present in the hearts of 13 patients with chagasic cardiopathy and in the esophagi of four patients (three of them with chagasic megaesophagus). In two patients, one with the cardiodigestive clinical form of Chagas disease and the other with cardiopathy and an esophageal inflammatory process, we could study both heart and esophagus and we detected distinct kDNA signatures in the two organs. This provides evidence of a differential tissue distribution of genetically diverse T. cruzi populations in chronic Chagas disease, suggesting that the genetic variability of the parasite is one of the determining factors of the clinical form of the disease.

Adult↗
PubMed1999

Analysis of the gene expression profile of Schistosoma mansoni cercariae using the expressed sequence tag approach.

ESTs constitute rapid and informative tools with which to study gene-expression profiles of the diverse stages of the schistosome life cycle. Following a comprehensive EST study of adult worms, analysis has now targeted the cercaria, the parasite larval form responsible for infection of the vertebrate host. Two Schistosoma mansoni cercarial cDNA libraries were examined and partial sequence obtained from 957 randomly selected clones. On the basis of database searches, 551 (57.6%) ESTs generated had no homologs in the public databases whilst 308 (32.2%) were putatively identified, totaling 859 informative ESTs. The remaining 98 (10.2%) were uninformative ESTs (ribosomal RNA and non-coding mitochondrial sequences). By clustering analysis we have identified 453 different genes. The most common sequences in both libraries represented Sm8 calcium binding protein (8% of ESTs), fructose-1,6-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase, cytochrome oxidase subunit 1, ATP guanidine kinase and triose phosphate isomerase. One hundred and nineteen identified genes were sorted into 11 functional categories, with genes associated with energy metabolism being the most abundant (13%) and diverse. The diversity and abundance of genes associated with the transcription/translation machinery and with regulatory/signaling functions were also marked. A paramyosin transcript was identified, indicating that this gene is not exclusively expressed in adult worms and sporocysts (as had been suggested previously). The possible physiological relevance to cercariae of the presence of transcripts with homology to calcium binding proteins of the EF-hand superfamily, Gq-coupled rhodopsin photoreceptor, rod phosphodiesterase 8 subunit and peripheral-type benzodiazepine receptor is discussed.

Animals↗
PubMed1999

Fully mutated and gray-zone FRAXA alleles in Brazilian mentally retarded boys.

We used a non-isotopic polymerase chain reaction (PCR) technique for fragile X syndrome diagnosis to screen 256 mentally retarded boys who were selected randomly from special schools. Patients identified as pre- or full-mutation carriers were further investigated by Southern blot analysis with the StB12.3 probe. The PCR-based test identified five boys with the expanded allele and 17 other patients as carriers of either premutated or gray-zone alleles. The full mutation was confirmed in four cases after Southern blotting and a fifth patient carried a normal allele. Of the 17 patients identified with a premutation allele by PCR, one individual was diagnosed as mosaic by Southern blotting, 12 individuals displayed fragments of 2.90 kb or 2.85 kb, and the remaining four individuals showed apparently normal-sized fragments. However, sizing of these 16 alleles by further PCR analysis showed them to be in the gray-zone range (40-60 repeats). Therefore, the frequency of the full mutation in this cohort of mentally retarded boys was close to 2% (5/256). The prevalence of gray-zone alleles among those mentally impaired boys who did not carry the full mutation was 6.4% (16/251) and, although more than twice the prevalence of these alleles among a cohort of unaffected Brazilian males 2.8% (71251), the difference did not reach statistical significance.

Alleles↗
PubMed1999

Differential tissue distribution of diverse clones of Trypanosoma cruzi in infected mice.

Chagas disease, caused by the protozoan Trypanosoma cruzi, presents variable clinical course but the phenomena underlying this variability remain largely unknown. T. cruzi has a clonal population structure and infecting strains are often multiclonal. T. cruzi genetic variability could be a determinant of differential tissue tropism or distribution and consequently of the clinical forms of the disease. We tested this hypothesis by using low-stringency single specific primer polymerase chain reaction (LSSP-PCR) to type genetically the parasites in tissues of experimental infected mice. BALB/c mice were simultaneously inoculated with two different T. cruzi populations (JG strain and Coll.7G2 clone). Doubly infected animals showed clear differential tissue distribution for the two populations (chronic phase). Our results indicate a significant influence of the genetic polymorphism of infecting T. cruzi populations in the pathogenesis of chronic Chagas disease.

Acute Disease↗
PubMed1999

Divergent human Y-chromosome microsatellite evolution rates.

In this work, we analyze several characteristics influencing the low variability of the microsatellite DYS19 in the major founder Amerindian Y chromosome lineage containing the point mutation DYS199-T. Variation of DYS19 was compared with that of five other Y-linked tetranucleotide repeat loci (DYS389A, DYS389B, DYS390, DYS391, and DYS393) in the DYS199-T lineage. All the other microsatellites showed significantly higher levels of variability than DYS19 as measured by gene diversity and repeat number variance. Moreover, we had previously shown that DYS19 had high diversity in Brazilians and in several other populations worldwide. Thus, the slow DYS19 evolution in the DYS199-T lineage seems to be both locus and allele specific. To understand the slow DYS19 evolutionary rate, the microsatellite loci were compared according to their mapping on the Y chromosome and also on the basis of structural aspects such as the base composition of the repeat motif and flanking regions and the degree of perfection and size (repeat number) of the variable blocks. The only observed difference that might be related to the low DYS19 variability is its small average number of repeats, a value expected to be closer to the founder DYS19 allele in the DYS199-T lineage. These data were also compared to other derived Y lineages. The Tat-C lineage displayed a lower DYS19 variability correlated to a small average repeat number, while in the DYS234-G lineage, a high DYS19 variability was found associated to a larger average repeat number. This approach reveals that evolution of Y microsatellites in lineages defined by slowly evolving markers, such as point mutations, can be greatly influenced by the size (number of repeats of the variable block) of the founder allele in each microsatellite locus. Thus lineage-dating methods using microsatellite variation should be practiced with great care.

Base Sequence↗