Emerging pathways in colorectal-cancer development

The past decade has seen the emergence of new pathways in the development of colorectal cancer. There is now clear evidence that subsets of these tumours do not show chromosomal instability and do not follow the suppressor pathway. Instead, about 15% of colorectal cancers are characterised by microsatellite instability (MSI). This feature arises through defective DNA mismatch repair, which is related either to a germline mutation (as in hereditary non-polyposis colorectal carcinoma) or to failure to express a mismatch-repair gene. CpG-island methylation has been linked to sporadic cancers with a high frequency of MSI. This type of methylation leads to loss of gene expression when it occurs in the promoter region of a gene. Tumours may have high or low type C (cancer-related) CpG-island methylation. When methylation affects hMLH1 (mismatch repair gene), the resultant cancer has high MSI.

Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) revelas a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an intersubspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

Expression of a truncated Brca1 protein delays lactational mammary development in transgenic mice

To address the hypothesis that certain disease-associated mutants of the breast-ovarian cancer susceptibility gene BRCA1 have biological activity in vivo, we have expressed a truncated Brca1 protein (trBrca1) in cell-lines and in the mammary gland of transgenic mice. Immunofluorescent analysis of transfected cell-lines indicates that trBRCA1 is a stable protein and that it is localized in the cell cytoplasm. Functional analysis of these cell-lines indicates that expression of trBRCA1 confers an increased radiosensitivity phenotype on mammary epithelial cells, consistent with abrogation of the BRCA1 pathway. MMTV-trBrca1 transgenic mice from two independent lines displayed a delay in lactational mammary gland development, as demonstrated by altered histological profiles of lobuloalveolar structures. Cellular and molecular analyses indicate that this phenotype results from a defect in differentiation, rather than altered rates of proliferation or apoptosis. The results presented in this paper are consistent with trBrca1 possessing dominant-negative activity and playing an important role in regulating normal mammary development. They may also have implications for germline carriers of BRCA1 mutations.

Combining the analyses of introgressive hybridisation and linkage mapping to investigate the genetic architecture of population divergence in the lake whitefish (Coregonus clupeaformis, Mitchill)

Adaptation and reproductive isolation, the engines of biological diversity, are still elusive when discussing the genetic bases of speciation. Namely, the number of genes and magnitude of selection acting positively or negatively on genomic traits implicated in speciation is contentious. Here, we describe the first steps of an ongoing research program aimed at understanding the genetic bases of population divergence and reproductive isolation in the lake whitefish (Coregonus clupeaformis). A preliminary linkage map originating from a hybrid cross between dwarf and normal ecotypes is presented, whereby some of the segregating AFLP markers were found to be conserved among natural populations. Maximum-likelihood was used to estimate hybrid indices from non-diagnostic markers at 998 AFLP loci. This allowed identification of the most likely candidate loci that have been under the influence of selection during the natural hybridisation of whitefish originating from different glacial races. As some of these loci could be identified on the linkage map, the possibility that selection of traits in natural populations may eventually be correlated to specific chromosomal regions was demonstrated. The future prospects and potential of these approaches to elucidate the genetic bases of adaptation and reproductive isolation among sympatric ecotypes of lake whitefish is discussed.

Fast neutron mutagenesis of soybean (Glycine soja L.) produces a supernodulating mutant containing a large deletion in linkage group H

We describe for the first time the application of fast neutron mutagenesis to the genetic dissection of root nodulation in legumes. We demonstrate the utility of chromosomal deletion mutations through production of a soybean supernodulation mutant FN37 that lacks the internal autoregulation of nodulation mechanism. After inoculation with microsymbiont Bradyrhizobium japonicum, FN37 forms at least 10 times more nodules than the wild type G. soja parent and has a phenotype identical to that of chemically induced allelic mutants nts382 and nts1007 (NTS-1 locus). Reciprocal grafting of shoots and roots confirmed systemic shoot control of the FN37 nodulation phenotype. RFLP/PCR marker pUTG132a and AFLP marker UQC-IS1 which are tightly linked to NTS-1 allowed the isolation of BAC contigs delineating both ends of the deletion. The genetic/physical distance ratio in the NTS-1 region is 279 kb/cM. The deletion is estimated to be about 460 kb based on the absence of markers and bacterial artificial chromosomes (BAC) ends as well as genetic and physical mapping. Deletion break points were determined physically and placed within flanking BAC contigs.

Qualidade da água da lagoa Juara (Serra/ES) : avaliações físicas, químicas e respostas fisiológicas e citogenéticas em plantas

A gestão dos recursos hídricos necessita da integração entre os critérios físicos e químicos, e os aspectos bióticos, os quais possibilitam identificar os efeitos combinados de substâncias e avaliar suas influências. Os sistemas testes Allium cepa e Tradescantia pallida, são utilizados para o estudo da poluição aquática a partir de aspectos citogenéticos. Além destes biomarcadores, os teores de clorofila também são utilizados em estudos de estresse devido ao reflexo a múltiplos fatores. Assim, o objetivo deste trabalho foi avaliar a qualidade da água da lagoa Juara (Município de Serra/ES) pela análise integrada de aspectos físicos, químicos e ecotoxicológicos a partir de estudos citogenéticos em A. cepa e T. pallida, e fotossintéticos nesta última espécie. Foram definidas três estações amostrais ao longo da lagoa e a partir de amostras de água foram analisados parâmetros tais como condutividade, oxigênio dissolvido, concentração de nutrientes e metais. A determinação dos metais ocorreu por análises de espectrometria de massa. O teste do A. cepa foi realizado a partir sementes germinadas em amostras de água da lagoa. Com plantas de T. pallida, foi realizado o ensaio da mitose em ponta de raiz de T. pallida e dosado os teores de pigmentos cloroplastídicos em folhas totalmente expandidas. Para tanto, foi realizado ensaio utilizando-se a água da lagoa como solvente para solução de Hoagland onde estacas previamente enraizadas de T. pallida foram expostas durante 24 horas e 40 dias para as avaliações citogenéticas e fotossintéticas, respectivamente. Foi realizado novo teste do A. cepa nas águas da lagoa após os 40 dias de ensaio para aferir a manutenção das propriedades químicas das amostras. A avaliação citogenética nas duas espécies envolveu a análise dos índice mitótico (IM), índice de aberrações cromossômicas (AC) e frequência de micronúcleos (MN). Para a análise estatística foi utilizada a análise de variância seguida pelo teste de Tukey (p < 0.05) para a comparação dos tratamentos durante a mesma campanha, e teste de Bonferroni (p < 0,05) para a comparação entre as campanhas. Os resultados físicos e químicos mensurados demonstram que a lagoa Juara apresenta indícios de eutroficação artificial. Duas estações amostrais, em pelo menos uma campanha amostral, apresentaram potenciais citotóxico, genotóxico e mutagênico. Todavia, esses potenciais não demonstram relação com os teores de Fe e Mn quantificados, levando a crer que tais pontos apresentam outros potenciais poluentes. Os danos citogenéticos observados apresentaram efeitos maximizados durante a segunda campanha, demostrando o efeito do período de chuva na intensificação da poluição nesse ambiente. O estudo do metabolismo fotossintético em T. pallida, demonstrou os teores de pigmentos cloroplastídicos relacionados ao elevado aporte de nutrientes presentes nas estações J2 e J3. Sendo o excesso destes, o provável responsável pelo teor inferior de pigmentos em J3. Observa-se que os ensaios com A. cepa e T. pallida responderam de maneira fidedigna ao risco potencial do ambiente, complementando as análises físicas e químicas usualmente utilizadas na avaliação da qualidade da água de ambientes lacustres.

XRCC3241 Polymorphism influence on genotoxicity biomarkers frequency in workers occupationaly exposed to formaldehyde

Formaldehyde (FA) is ubiquitous in the environment and is a chemical agent that possesses high reactivity. Occupational exposure to FA has been shown to induce nasopharyngeal cancer and has been classified as carcinogenic to humans (group 1) on the basis of sufficient evidence in humans and sufficient evidence in experimental animals. The exposure to this substance is epidemiologically linked to cancer and nuclear changes detected by the cytokinesis-block micronucleus test (CBMN). This method is extensively used in molecular epidemiology, since it determines several biomarkers of genotoxicity, such as micronucleus (biomarkers of chromosomes breakage or loss), nucleoplasmic bridges (biomarker of chromosome rearrangement, poor repair and / or telomeres fusion) and nuclear buds (biomarker of elimination of amplified DNA). The gene X-ray repair cross-complementing group 3 (XRCC3) is involved in homologous recombination repair of cross-links and chromosomal double-strand breaks and at least one polymorphism has been reported in codon 241, a substitution of a methionine for a threonine.

Formaldehyde's genotoxicity effects in pathology anatomy technologists and medical pathologists

Formaldehyde (FA) had been considered to be carcinogenic by the International Agency for Research on Cancer (group1), on the basis of sufficient evidence both in humans and in experimental animals, making it a subject of major environmental concern, especially in the occupational context. Manifold in vitro studies clearly indicated that FA is genotoxic, inducing various genotoxic effects in proliferating cultured mammalian cells. Cytokinesis-blocked micronucleus (CBMN) assay is used extensively in molecular epidemiology, and the chromosomal alterations most reported and studied by the CBMN are: micronucleus (MN), nucleoplasmic bridges (NPB) and nuclear buds (NBUDs). The pathology anatomy laboratories are work places that manipulate routinely FA and pathology anatomy technologists and pathologists contact daily with this chemical compound particularly in the macroscopic exam and grossing procedures. The aim of this study was to identify genotoxicity biomarkers in the set workers groups, such as micronucleus (MN), nucleoplasmic bridges (NPB) and nuclear buds (NBUD) in peripheral blood lymphocytes.

Interaction of formaldehyde and tobacco smoking in the frequency of micronucleus and the XRCC3 Thr241Met polymorphism

Formaldehyde is classified by IARC as carcinogenic to humans (nasopharyngeal cancer). Tobacco smoke has been epidemiologically associated to a higher risk of development of cancer, especially in the oral cavity, larynx and lungs, as these are places of direct contact with many carcinogenic tobacco’s compounds. XRCC3 is involved in homologous recombination repair of cross-links and chromosomal double-strand breaks (Thr241Met polymorphism). The aim of the study is to determine whether there is an in vivo association between genetic polymorphism of the gene XRCC3 and the frequency of genotoxicity biomarkers in subjects exposed or not to formaldehyde and with or without tobacco consumption.

Genotoxicity biomarkers micronucleus, nucleoplasmic bridges and nuclear buds

The increase of mortality from cancer brought urgency in identification and validation of predictive markers of risk and therefore early diagnosis. There is evidence that cytogenetic biomarkers are positively correlated with risk of cancer, and this is validated by studies of cohort and case-control. Cytokinesis-blocked micronucleus (CBMN) assay is used extensively in molecular epidemiology, and can be considered as a “cytome” assay covering cell proliferation, apoptosis, necrosis and chromosomal changes. The chromosomal alterations most reported and studied by the CBMN are: micronucleus (MN), nucleoplasmic bridges (NPB) and nuclear buds (NBUDS). The use of the MN assay in biomonitoring studies had a large increase in the last 15 years and international projects such as the HUMN have helped to increase the applicability and reliability of these tests.

Anemia de Fanconi em Portugal: estudo retrospetivo de 34 anos de investigação no INSA (1980-2014)

A Anemia de Fanconi (AF) é uma doença recessiva rara, com uma frequência estimada de 4 a 7 por 1 000 000 de nascimentos. Caraterizase por malformações congénitas, falência medular e hipersensibilidade a agentes clastogénicos de DNA. Devido à grande complexidade desta patologia a primeira abordagem de diagnóstico, consiste na análise da instabilidade cromossómica, após cultura celular com estimulação com agentes clastogénicos diepoxibutano (DEB) ou mitomicina C (MMC). Realizou- se um estudo retrospetivo de 34 anos (1980-2014) em 243 amostras com suspeita de AF e de 25 amostras de familiares de doentes de AF, num total de 268 amostras. Nas 243 amostras suspeitas de Anemia de Fanconi, foram identificadas 37 com AF. A idade média ao diagnóstico foi de 7 anos, existindo um ligeiro predomínio da incidência no sexo feminino (59%). Uma amostra foi classificada como AF(-/+). Nos familiares de doentes com AF foram identificados 2 casos positivos, o que perfaz 39 amostras de AF positivas. Em quatro das amostras AF negativas, observaram-se cariotipos anormais. Estes resultados não permitem estimar uma frequência de doentes de AF em Portugal, uma vez que não englobam indivíduos de todas as regiões portuguesas, mas permitem uma estimativa da frequência espectável.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Multi-dimensional scaling applied to histogram-based DNA analysis

This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method’s artifacts.

Mutation accumulation in Tetrahymena

Background - The rate and fitness effects of mutations are key in understanding the evolution of every species. Traditionally, these parameters are estimated in mutation accumulation experiments where replicate lines are propagated in conditions that allow mutations to randomly accumulate without the purging effect of natural selection. These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists. Results - We performed a mutation accumulation (MA) experiment in Tetrahymena thermophila, a species that can reproduce sexually and asexually in nature, and measured both the mean decline and variance increase in fitness of 20 lines. The results obtained with T. thermophila were compared with T. pyriformis that is an obligate asexual species. We show that MA lines of T. thermophila go to extinction at a rate of 1.25 clonal extinctions per bottleneck. In contrast, populations of T. pyriformis show a much higher resistance to extinction. Variation in gene copy number is likely to be a key factor in explaining these results, and indeed we show that T. pyriformis has a higher mean copy number per cell than T. thermophila. From fitness measurements during the MA experiment, we infer a rate of mutation to copy number variation of 0.0333 per haploid MAC genome of T. thermophila and a mean effect against copy number variation of 0.16. A strong effect of population size in the rate of fitness decline was also found, consistent with the increased power of natural selection. Conclusions - The rate of clonal extinction measured for T. thermophila is characteristic of a mutational degradation and suggests that this species must undergo sexual reproduction to avoid the deleterious effects detected in the laboratory experiments. We also suggest that an increase in chromosomal copy number associated with the phenotypic assortment of amitotic divisions can provide an alternative mechanism to escape the deleterious effect of random chromosomal copy number variation in species like T. pyriformis that lack the resetting mechanism of sexual reproduction. Our results are relevant to the understanding of cell line longevity and senescence in ciliates.

Identification of a 0.4 Kb deletion region in 10q26 associated with endometrial carcinoma

We have identified an allelic deletion common region in the q26 region of chromosome 10 in endometrial carcinomas, which has been reported previously as a potential target of genetic alterations related to this neoplasia. An allelotyping analysis of 19 pairs of tumoral and non-tumoral samples was accomplished using seven microsatellite polymorphic markers mapping in the 10q26 chromosomal region. Loss of heterozygosity for one or more loci was detected in 29% of the endometrial carcinoma samples. The observed pattern of loss enabled the identification of a 3.5 Mb common deleted region located between the D10S587 and D10S186 markers. An additional result from an endometrial sample with evidence of a RER phenotype may suggest a more centromeric region of loss within the above-mentioned interval. This 401.84 Kb interval flanked by the D10S587 and D10S216 markers may be a plausible location for a putative suppressor gene involved in early stage endometrial carcinogenesis.