Oscheius tipulae as an example of eEF1A gene diversity in nematodes

We characterized four eEF1A genes in the alternative rhabditid nematode model organism Oscheius tipulae. This is twice the copy number of eEF1A genes in C. elegans, C. briggsae, and, probably, many other free-living and parasitic nematodes. The introns show features remarkably different from those of other metazoan eEF1A genes. Most of the introns in the eEF1A genes are specific to O. tipulae and are not shared with any of the other genes described in metazoans. Most of the introns are phase 0 (inserted between two codons), and few are inserted in protosplice sites (introns inserted between the nucleotide sequence A/CAG and G/A). Two of these phase 0 introns are conserved in sequence in two or more of the four eEF1A gene copies, and are inserted in the same position in the genes. Neither of these characteristics has been detected in any of the nematode eEF1A genes characterized to date. The coding sequences were also compared with other eEF1A cDNAs from 11 different nematodes to determine the variability of these genes within the phylum Nematoda. Parsimony and distance trees yielded similar topologies, which were similar to those created using other molecular markers. The presence of more than one copy of the eEF1A gene with nearly identical coding regions makes it difficult to define the orthologous cDNAs. As shown by our data on O. tipulae, careful and extensive examination of intron positions in the eEF1A gene across the phylum is necessary to define their potential for use as valid phylogenetic markers.

Structural stability and reversible unfolding of recombinant porcine S100A12

Porcine S100A12 is a member of the S100 proteins, family of small acidic calcium-binding proteins characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events such as the regulation of protein phosphorylation, enzymatic activity, protein-protein interaction, Ca(2+) homeostasis, inflammatory processes and intermediate filament polymerization. In addition, members of this family bind Zn(2+) or Ca(2+) with cooperative effect on binding. In this study, the gene sequence encoding porcine S100A12 was obtained by the synthetic gene approach using E. coli codon bias. Additionally, we report a thermodynamic study of the recombinant S100A12 using circular dichroism, fluorescence and isothermal titration calorimetry. The results of urea and temperature induced unfolding and refolding processes indicated a reversible two-state process. Also, the ANS fluorescence studies showed that in presence of divalent ions the protein exposes hydrophobic sites which could facilitate the interaction with other proteins and trigger the physiological responses. (c) 2008 Elsevier B.V. All rights reserved.

Symmetry breaking in the genetic code: Finite groups

We investigate the possibility of interpreting the degeneracy of the genetic code, i.e., the feature that different codons (base triplets) of DNA are transcribed into the same amino acid, as the result of a symmetry breaking process, in the context of finite groups. In the first part of this paper, we give the complete list of all codon representations (64-dimensional irreducible representations) of simple finite groups and their satellites (central extensions and extensions by outer automorphisms). In the second part, we analyze the branching rules for the codon representations found in the first part by computational methods, using a software package for computational group theory. The final result is a complete classification of the possible schemes, based on finite simple groups, that reproduce the multiplet structure of the genetic code. (C) 2010 Elsevier Ltd. All rights reserved.

The differential roles of D-Pax2 variants in regulating Drosophila eye and bristle development

The ability to appropriately interact with the environment is crucial to an organism’s survival. The establishment of functional sensory systems, such as the bristles and eyes in Drosophila, is a critical event during the development of the organism. The transcription factor D Pax2 is involved in the differentiation of the shaft and glial cells in the developing bristle (Kavaler et al., Dev, 126:2261-2272, 1999) and of the cone and primary pigment cells in the developing eye (Fu and Noll, Genes Dev, 11:389-405, 1997). How D-Pax2 contributes to distinct differentiative pathways in different cell types is not known. Recent work by Anna Czechowski and Katherine Harmon (personal communication) identified a mutation in the D-Pax2 gene that introduced a stop codon at the end of exon 9, effectively truncating the protein. This mutation affects bristle, but not eye, development. We thus suspected regions after exon 9 are required for D-Pax2 function only in the bristles and may also be associated with alternative splicing of the D Pax2 transcript. We plan to assess the role of the carboxy terminal region of the protein by establishing transgenic lines bearing rescue constructs of D-Pax2 with either the complete coding sequence or with deletions of specific exons. To date, we have generated the first rescue construct bearing the complete coding region of the gene driven by a 3 KB upstream regulatory region of D-Pax2 and are currently generating transgenic fly lines with this construct.

Desenvolvimento de um sistema de expressão em Metarhizium anisopliae baseado no promotor homólogo do gene tef-1 α

Vetores de expressão são ferramentas moleculares úteis para investigar a função de genes tanto em sistemas procarióticos quanto eucarióticos. O fungo Metarhizium anisopliae, utilizado no controle biológico de artrópodes, é bem caracterizado em nível molecular. Genes candidatos a participar do processo de infecção de hospedeiros tem sido isolados utilizando estratégias em que o gene candidato é predefinido (enzimas hidrolíticas, por exemplo) ou estratégias mais globais como projetos de ESTs e a análise de bibliotecas de subtração. A superexpressão tem sido o método adotado para verificar a participação de genes isolados no processo de infecção. Esta estratégia tem sido baseada no promoter heterólogo PgpdA de Aspergillus nidulans. Neste trabalho, o gene que codifica o fator de alongamento de tradução tef-1 α de Metarhizium anisopliae foi clonado e a sua região promotora foi localizada e utilizada na construção de um vetor de expressão. Somente uma cópia do gene tef-1α está presente no genoma de M. anisopliae e o seu perfil de expressão foi analisado. Uma árvore filogenética foi construída baseada nos ortógos de tef-1 α e mostrou uma alta correlação com o fungo Cordyceps taii. A região de 639 pb à montante do codon de iniciação (ATG) foi utilizada com sucesso para a expressão do gene repórter sGFP e do gene bar, que confere resistência ao glifosinato de amônio, em M. anisopliae. Os transformantes construídos não apresentaram alteração na sua virulência em bioensaios com carrapatos, em relação a linhagem receptora. Além disso, demonstramos que o nível de expressão permite a detecção óptica da fluorescência de sGFP durante a infecção dos carrapatos. Desta forma, o vetor desenvolvido será uma ferramenta útil para a superexpressão em Metarhizium.

Caracterização molecular e laboratorial da talassemia beta e da interação hemoglobina s/talassemia beta

Beta thalassemia arises as a consequence of the reduction (β+, β++, βsilent) or absence (β0) of beta globin chain synthesis and results from a number of mechanisms that lead to genetic defects. The inheritance of beta thalassemia is characterized by the existence of heterozygous individuals, compound heterozygotes, homozygotes and those with coinheritance of beta thalassemia allele and other thalassemias and/or hemoglobin variants. The aim of this study was to perform molecular and laboratory characterization of beta thalassemia in heterozygous and homozygous individuals and in those with coinheritance of S beta thalassemia. A total of 48 individuals were included (35 heterozygotes, 4 homozygotes and 9 S beta thalessemia carriers) referred to the Integrated Laboratory of Clinical Analyses of the Federal University of Rio Grande do Norte (UFRN) and the Hematology Ambulatory Facility of the Dalton Barbosa Cunha Hemocenter (Hemonorte Natal, Brazil). Peripheral blood samples form each patient underwent the following laboratory examinations: erythrogram, hemoglobin electrophoresis at alkaline pH, measurements of Hb A2, Fetal Hb and serum ferritin. DNA was extracted using the illustra blood genomicPrep Mini Spin Kit and molecular characterization was performed by the PCR/RFLP technique, which involves digestion with specific restriction enzymes for IVS-1 nt 1 (G®A), IVS-1 nt 6 (T®C) and codon 39 (CAG®TAG) mutations. Of the 35 heterozygotes, 37.1% showed IVS-1 nt 6 mutation, 42.9% IVS-1 nt 1 and 20% were carriers of other mutations not identified by the technique used. The four homozygous patients presented with the IVS-1 nt 6 mutation, while 66.7% of the individuals with S beta thalassemia had the IVS-1 nt 1 mutation. Codon 39 was not detected in any of the patients investigated. Of the thallasemic alleles found, 40.4% were IVS- 1 nt 1, 40.4% IVS-1 nt 6 and 19.2% were not identified. Laboratory data showed that the heterozygotes exhibited microcytosis and hypochromia, evidenced by MCV ranging from 57 to 75fL and MCH from 15.9 to 23.6 pg. Hemoglobin A2 varied between 3.7 and 7.2%. The homogygotes also showed reduced MCV and MCH and elevated HbA2.. Comparison of laboratory data between heterozygous individuals with IVS-1 nt 1 and IVS-1 nt 6 mutations showed that heterozygotes for the IVS1-1 mutation had significantly lower mean MCV and MCH (p = 0.023 and 0.007, respectively) and significantly higher hemoglobin A2 (p < 0.001) when compared to heterozygotes for the IVS-1 nt 6 mutation. PCR/RFLP was useful in identifying the presence or absence of IVS-1 nt 6, IVS-1 nt 1 and codon 39 mutations in most of the patients investigated here. This is the first study conducted in the state of Rio Grande do Norte, Brazil aimed at identifying beta thalassemia mutations and represents an important contribution to the knowledge regarding the molecular profile of beta thalassemia in our country

Anemia falciforme: desafios e avanços na busca de novos fármacos

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

EBNA-1 gene sequences in Brazilian and American patients with Hodgkin's disease

We examined the types of Epstein-Barr virus-associated nuclear antigen-1 (EBNA-1) gene carboxy (C)-terminal mutations occurring in Hodgkin's disease (HD) and reactive tissues from two different geographic regions. Previously reported EBNA-1 C-terminal region amino acid sequence variants, based on the amino acid at codon 487, include Prototype (P)-ala, which is found in the B95.8-derived prototype virus, P-thr, Variant (V)-leu, V-val, and V-pro. Using polymerase chain reaction (PCR) to amplify portions of the EBNA-1 gene, followed by DNA sequencing, we found a single EBNA-1 gene sequence variant in each tissue, whether reactive or neoplastic and whether from Brazil or the United States. Variant EBNA-1 gene sequences were more common in both neoplastic and non-neoplastic tissues from different geographic areas than the so-called prototype sequence. In the 17 Brazilian HD cases, 4 cases had P-thr variants and 13 had V-leu variants. In the six reactive tissues from Brazil, one had a P-ala variant, two had P-thr variants, and three had V-leu variants. In the 12 American HD cases, 2 had P-ala variants, 6 had P-thr variants, and 4 had V-leu variants. The 11 American reactive tissues included 2 P ala variants, 5 P-thr variants, and 4 V-leu variants. In both countries, there were similar variant EBNA-1 sequences present in normal tissues and HD cases. Compared with the P ala and P-thr cases, the V-leu cases were more likely to have the 30-bp latent membrane protein 1 (LMP1) gene deletion (P = 0.0075). In addition, cases of HD with the V-leu were statistically associated with a substitution of asparagine for glutamine at codon 322 of the C-terminal portion of the LMP1 gene. Our results suggest that any variation in EBNA-1 gene sequence is caused by a polymorphism present in pre-existing viral strains in the underlying population, and not a mutation occurring during oncogenesis. (C) 1999 by the American Society of Hematology.

A nonsense mutation in the tyrosinase gene causes albinism in water buffalo

Background: Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to determine the clinical presentation and genetic basis of albinism in this species.Results: Clinical examinations and pedigree analysis were performed in an affected herd, and wild-type and OCA tyrosinase mRNA sequences were obtained. The main clinical findings were photophobia and a lack of pigmentation of the hair, skin, horns, hooves, mucosa, and iris. The results of segregation analysis suggest that this disease is acquired through recessive inheritance. In the OCA buffalo, a single-base substitution was detected at nucleotide 1,431 (G to A), which leads to the conversion of tryptophan into a stop codon at residue 477.Conclusion: This premature stop codon produces an inactive protein, which is responsible for the OCA buffalo phenotype. These findings will be useful for future studies of albinism in buffalo and as a possible model to study diseases caused by a premature stop codon.

Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the Lmbr1 gene

Acheiropodia is an autosomal recessive developmental disorder presenting with bilateral congenital amputations of the upper and lower extremities and aplasia of the hands and feet. This severely handicapping condition appears to affect only the extremities, with no other systemic manifestations reported. Recently, a locus for acheiropodia was mapped on chromosome 7q36. Herein we report the narrowing of the critical region for the acheiropodia gene and the subsequent identification of a common mutation in C7orf2-the human orthologue of the mouse Lmbr1 gene-that is responsible for the disease. Analysis of five families with acheiropodia, by means of 15 polymorphic markers, narrowed the critical region to 1.3 cM, on the basis of identity by descent, and to <0.5 Mb, on the basis of physical mapping. Analysis of C7orf2, the human orthologue of the mouse Lmbr1 gene, identified a deletion in all five families, thus identifying a common acheiropodia mutation. The deletion was identified at both the genomic-DNA and mRNA level. It leads to the production of a C7orf2 transcript lacking exon 4 and introduces a premature stop codon downstream of exon 3. Given the nature of the acheiropodia phenotype, it appears likely that the Lmbr1 gene plays an important role in limb development.

Cyclin D1 gene polymorphism as a risk factor for squamous cell carcinoma of the upper aerodigestive system in non-alcoholics

Squamous cell carcinoma of the upper aerodigestive tract (UADT) is associated with environmental factors, especially tobacco and alcohol consumption. Genetic factors, including cyclin D1 (CCND1) polymorphism have been suggested to play an important rote in tumorigenesis and progression of UADT cancer. To investigate the relationship between CCND1 polymorphism on susceptibility for UADT cancers, 147 cancer and 135 non-cancer subjects were included in this study. CCND1 genotype at codon 242(G870A) in exon 4 was undertaken using denaturing high performance liquid chromatography (DHPLC) and DNA sequencing. Significant odds ratio (OR) of the AA + GA genotypes [OR = 7.5 (95% Cl: 1.4-39.7)] was observed in non-drinkers but for non-smokers a non-significant [OR = 5.4 (95% Cl: 0.9-31.4)] was found in the adjusted model. These results suggest that allele A may be a risk factor for UADT cancer, especially in non-alcoholics. However, further epidemiological studies are needed to establish the exact role of CCND1 polymorphism and the development of UADT cancers. (C) 2004 Elsevier Ltd. All rights reserved.

A single nucleotide deletion at the C1 inhibitor gene as the cause of hereditary angioedema: insights from a Brazilian family

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Avaliação eletroforética, cromatográfica e molecular da Hb D Los Angeles no Brasil

A variante de hemoglobina (Hb) D mais comum, Hb D Los Angeles ou D Punjab, é originada de uma transversão GAA->CAA no códon 121 da globina beta; essa mutação resulta na substituição do ácido glutâmico por glutamina na proteína. É a terceira variante de hemoglobina mais freqüente da população brasileira. Como as hemoglobinas D apresentam migração similar à hemoglobina S em pH alcalino, e com a hemoglobina A em pH ácido, são necessários vários testes para o correto diagnóstico. No presente estudo objetivou-se relacionar os diferentes procedimentos laboratoriais de rotina diagnóstica, além da análise molecular, para estabelecer o perfil de Hb D Los Angeles no Brasil. Foram analisados 47 indivíduos da população brasileira com provável Hb D Los Angeles, por vários procedimentos eletroforéticos em diferentes condições de pH, além da cromatografia líquida de alta pressão, e testes moleculares para confirmação da mutação. Foram encontrados quatro tipos de combinações de hemoglobinas: 42 indivíduos portadores de hemoglobina AD Los Angeles, dois indivíduos com doença de Hb S/D Los Angeles, dois indivíduos com Hb D Los Angeles e talassemia beta e um indivíduo com Hb D Los Angeles e Hb Lepore. Os indivíduos heterozigotos para D Los Angeles são assintomáticos, entretanto, em associação com outras variantes e talassemias podem apresentar graus variáveis de manifestações clínicas. Os resultados apresentados enfatizaram a necessidade da associação de várias metodologias para a identificação da Hb D Los Angeles, além de auxiliar na elucidação de combinações raras.

Gene Mutations in Esophageal Mucosa of Chagas Disease Patients

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gene Mutations and Polymorphisms of TP53 and FHIT in Chronic Esophagitis and Esophageal Carcinoma

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)