Whole sequencing of the mitochondrial genome of breast cancer tissue in Mexican-mestizo postmenopausal women with different body mass index

Abstract Background Mitochondrial and oxidative stress has been related to obesity and breast cancer being this cancer more frequent and more aggressive in postmenopausal women with obesity. Objective The objective of this study was to investigate whether Mexican-Mestizo postmenopausal women with breast cancer and obesity present different somatic mutations in the mitochondrial DNA (mtDNA) when compared to women with normal body mass index (BMI). Subjects and Methods We included six Mexican-Mestizo postmenopausal women bearing breast cancer and who underwent mastectomy or breast-conserving surgery. BMI was determined in each case. Patients’ genomic DNA was isolated from blood leukocytes and tumor tissue samples. Whole mtDNA sequence was determined by MitoChip v2.0 mitochondrial resequencing array, and data were analyzed using the GeneChip Sequence Analysis Software. Tumor mtDNA sequence was compared with matched leukocyte mtDNA sequence. Results Three women had a normal BMI and three presented obesity. Overall, we found 64 genetic variants: 53.1% were somatic mutations and 46.9% were polymorphisms; 44.1% were in the non-coding region and 55.9% were in genes that encode for mitochondrial proteins. Among the somatic mutations, 67.7% were in patients with normal BMI and 32.3% in patients with obesity. Conclusions We did not find a higher frequency of mitochondrial somatic mutations in postmenopausal women with breast cancer and obesity compared to those with normal BMI. However, results could be due to the small number of women studied.

Genoma mitocondrial de Simulium spp. e Onchocerca volvulus na Amazônia brasileira / Mitochondrial genome of Simulium spp. and Onchocerca volvulus in the Brazilian Amazon

As espécies de simulídeos são vetores de filárias, como as do gênero Onchocerca e Mansonella, que são os agentes etiológicos da oncocercose e mansonellose, respectivamente. Essas duas filárias ocorrem na região Amazônica brasileira e são transmitidas pelas seguintes espécies de vetores: Simulium incrustatum, S. limbatum, S. oyapockense, S. exiguum, S. guianense, e S. roraimense. As espécies de Simulium tem sido designada com base em caracteres morfológicos, os quais, em alguns casos, não são bem discriminativos. Recentemente, o gene mitocondrial Citocromo c-oxidase 1 (CO1) e a região nuclear Internal Transcribed Spacer (ITS) tem sido utilizados para descriminar espécies e definir populações dentro deste gênero. Entretanto, existe um grande gap acerca da informação genética de Simulium, o qual é considerado a linha de base para estudos ecológicos e populacionais. Considerando este cenário, nosso objetivo foi aplicar a metagenômica para recuperar genomas mitocondriais de amostras brasileiras S. incrustatum e S. oyapockense do foco de oncocercose e também a informação genética a respeito de seus microbiomas. O DNA total de dez simulídeos, morfologicamente identificados como S. incrustatum (3) e S. oyapockense (7) foram sequenciados randomicamente na plataforma Illumina HiSeq 2500. Nós recuperamos dez genomas mitocondriais com cobertura média de 15,591 bp e conteúdo médio de GC de 22,94 %, apresentando o mesmo conteúdo gênico e em sintenia. Baseado nestes mitogenomas, no gene mitocondrial CO1, e também na região nuclear (ITS), realizamos análises filogenéticas que mostraram a presença de três espécies conhecidas dentre as amostras: S. incrustatum, S. oyapockense e S. guianense, e também um grupo de amostras pertencentes à Simulium spp. Nós também recuperamos um genoma mitocondrial de Onchocerca volvulus da amostra aqui identificada como S. guianense.

Análises taxonômicas do microbioma dos simulídeos revelaram Proteobacteria e Ascomycota como os filos mais abundantes. A análise funcional revelou que a família de enzimas das Transcriptases Reversas são as mais abundantes. Portanto, nós contribuímos com informação genética original preenchendo parte do viés a respeito das espécies de Simulium associadas ao foco brasileiro de oncocercose. (AU)

The comparative mitogenomics and phylogenetics of the two grouse-grasshoppers (Insecta, Orthoptera, Tetrigoidea)

OBJECTIVE: This study aimed to reveal the mitochondrial genomes (mtgenomes) of Tetrix japonica and Alulatettix yunnanensis, and the phylogenetics of Orthoptera species. METHODS: The mtgenomes of A. yunnanensis and T. japonica were firstly sequenced and assembled through partial sequences amplification, and then the genome organization and gene arrangement were analyzed. Based on nucleotide/amino acid sequences of 13 protein-coding genes and whole mtgenomes, phylogenetic trees were established on 37 Orthoptera species and 5 outgroups, respectively. RESULTS: Except for a regulation region (A+T rich region), a total of 37 genes were found in mtgenomes of T. japonicaand A. yunnanensis, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Orthoptera species. Phylogenetic tree based on 13 concatenated protein-coding nucleotide sequences were considered to be more suitable for phylogenetic reconstruction of Orthoptera species than amino acid sequences and mtgenomes. The phylogenetic relationships of Caelifera species were Acridoidea and Pamphagoidea > Pyrgomorphoidea > Pneumoroidea > Eumastacoidea > Tetrigoidea > Tridactyloidea. Besides, a sister-group relationship between Tettigonioidea and Rhaphidophoroidea was revealed in Ensifera. CONCLUSION: Concatenated protein-coding nucleotide sequences of 13 genes were suitable for reconstruction of phylogenetic relationship in orthopteroid species. Tridactyloidea was a sister group of Tetrigoidea in Caelifera, and Rhaphidophoroidea was a sister group of Tettigonioidea in Ensifera.

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

O mitogenoma completo de Corydoras nattereri , uma espécie de bagres encouraçados do sudeste do Brasil, foi reconstruído através de técnicas de sequencimento de DNA de próxima geração. O mitogenoma foi produzido a partir de produtos de transcrição mitocondrial dos transcriptomas hepáticos de três indivíduos, resultando numa sequência de DNA circular de 16.557 nucleotídeos abrangendo 22 genes de tRNA, dois genes de rRNA, 13 genes codificadores de proteínas e duas regiões de controle não codificadoras (D-loop, OrigL). A análise filogenética de sequências proximamente relacionadas da subunidade I do gene Citocrome Oxidase C (COI) demonstrou a existência de elevada diversidade entre populações morfologicamente similares de C. nattereri . Corydoras nattereri está inserida num complexo de populações atualmente identificadas como C. paleatus e C. ehrhardti . A análise da estrutura do mitogenoma demonstra que a inserção de uma sequência de 21 nucleotídeos entre os genes da subunidade 6 da ATPase e do COIII representa um caráter filogeneticamente informativo associado à evolução de Corydoradinae.

Repetitive element palindromic PCR (rep-PCR) as a genetic tool to study interspecific diversity in Euphorbiaceae family

Background The classification of diversity in germplasm collections is important for plant breeding. The repetitive element palindromic-polymerase chain reaction (rep-PCR) technique was used to investigate inter-specific diversity within 17 species from the Euphorbiaceae family using REP and BOX primers. Results The agglomerative cluster analysis was used to evaluate the scoring data. BOX and REP gave amplification with polymorphism of 98.84% and 100% respectively. REP marker demarcated between the subgenus peltatae. Both markers confirmed Jatropha tanjorensis as a natural hybrid between Jatropha gossypifolia and Jatropha curcas. Five random sequences from the rep-PCR gels were chosen, cloned and sequenced. The blast results demonstrated that the amplified products were from the mitochondrial genomes. Conclusion The rep-PCR molecular tool can be used to characterize diversity in plants as they are suitable for distinguishing eukaryotic genomes effectively.

Malaria in the State of Amazonas: a typical Brazilian tropical disease influenced by waves of economic development

In Brazil, more than 99% of malaria cases are reported in the Amazon, and the State of Amazonas accounts for 40% of this total. However, the accumulated experience and challenges in controlling malaria in this region in recent decades have not been reported. Throughout the first economic cycle during the rubber boom (1879 to 1912), malaria was recorded in the entire state, with the highest incidence in the villages near the Madeira River in the Southern part of the State of Amazonas. In the 1970s, during the second economic development cycle, the economy turned to the industrial sector and demanded a large labor force, resulting in a large migratory influx to the capital Manaus. Over time, a gradual increase in malaria transmission was observed in peri-urban areas. In the 1990s, the stimulation of agroforestry, particularly fish farming, led to the formation of permanent Anopheline breeding sites and increased malaria in settlements. The estimation of environmental impacts and the planning of measures to mitigate them, as seen in the construction of the Coari-Manaus gas pipeline, proved effective. Considering the changes occurred since the Amsterdam Conference in 1992, disease control has been based on early diagnosis and treatment, but the development of parasites that are resistant to major antimalarial drugs in Brazilian Amazon has posed a new challenge. Despite the decreased lethality and the gradual decrease in the number of malaria cases, disease elimination, which should be associated with government programs for economic development in the region, continues to be a challenge.

Genomic study of Anopheles (Nyssorhynchus) aquasalis, Curry 1932. A Neotropical human malaria vector

A malária humana é uma doença provocada por parasitas do gênero Plasmodium, os quais na natureza requerem de um mosquito anofelíno para completar o seu ciclo de vida e serem transmitidos a um hospedeiro humano. Nas Américas, o Brasil tem a maior incidência de malária, sendo responsável por 41% dos casos. Com o aparecimento do sequenciamento de nova geração e das ferramentas bioinformática relacionados, grandes avanços foram alcançados em relação à montagem de genomas e transcriptomas de anofelinos, assim como na exploração de estratégias de paratransgenesis para interromper a transmissão da malária. No entanto, os vetores neotropicais da malária encontram-se longe dos vetores da África e Ásia no que refere a estes conhecimentos. Este estudo é parte de um esforço contínuo para montar o genoma do Anopheles aquasalis, um vetor neotropical da malária humana, que atualmente posiciona-se como um excelente modelo de transmissão da malária no Brasil. Em paralelo ao sequenciamento do genoma, e para maximizar os dados gerados, optamos por focar em duas tarefas pontuais e viáveis: explorar a diversidade e composição do consórcio bacteriano associado ao anofelino; assim como montar e caracterizar o genoma mitocondrial desta espécie.

O sequenciamento metagenômico ̈shotgun ̈ e o programa MG-RAST foram utilizados para fazer um ̈screening ̈ das bactérias associadas à pupas de A .aquasalis criadas em laboratório. O consórcio bacteriano predito é composto por 74 gêneros contendo bactérias marinhas e bioluminescentes. No nível taxonômico de família bacteriana, identificamos 14 OTUs compartilhadas entre anofelinos americanos e africanos. Além disso, foram comparadas cinco comunidades bacterianas associadas a duas espécies de anofelinos: A. aquasalis e Anopheles gambiae. Foi identificada uma associação significativa (NPMANOVA p <0,05) entre a composição da comunidade bacteriana e o ambiente aquático (laboratório ou condições semi-naturais) nas quais cada hospedeiro anofelino foi criado. Atualmente, o entendimento da filogenia do gênero Anopheles é limitado e as informações sobre o tempo de divergência dentro da linhagem de mosquitos é escassa.

Apresentamos a sequencia de 15,393 pb correspondente ao genoma mitocondrial de A. aquasalis. Quando comparado com outros mitogenomas anofelinos relevantes, observou-se alta similaridade na composição dos genomas assim como características estruturais conservadas. Através de análises Bayesianas, reconstruímos as relações filogenéticas e estimamos a data de divergência entre 22 anofelinos e outras espécies de dípteros. Descobrimos que o mais recente ancestral entre as subfamílias Nyssorhynchus e Anopheles +Cellia existiu ~ 83 milhões anos atrás (MYA). Estimou-se que A. aquasalis divergiu do complexo do Anopheles albitarisis faz ~ 28 MYA, e faz ~ 38 MYA do Anopheles darlingi. A distribuição estreita e o peculiar nicho ecológico do A. aquasalis, além de considerar a sua adaptação a ambientes larvários com água salobra fizeram nos perguntar se a sua história evolutiva deixou uma marca na arquitetura do seu genoma, assim como sobre a estrutura da comunidade bacteriana associada a este anofelino.

Mitochondrial genome sequence diversity of Indian Plasmodium falciparum isolates

We have analysed the whole mitochondrial (mt) genome sequences (each ~6 kilo nucleotide base pairs in length) of four field isolates of the malaria parasite Plasmodium falciparum collected from different locations in India. Comparative genomic analyses of mt genome sequences revealed three novel India-specific single nucleotide polymorphisms. In general, high mt genome diversity was found in Indian P. falciparum, at a level comparable to African isolates. A population phylogenetic tree placed the presently sequenced Indian P. falciparum with the global isolates, while a previously sequenced Indian isolate was an outlier. Although this preliminary study is limited to a few numbers of isolates, the data have provided fundamental evidence of the mt genome diversity and evolutionary relationships of Indian P. falciparum with that of global isolates.

Influencia del tipo de alimentación en el desarrollo de la alergia a la leche de vaca en niños pequeños factores involucrados en el proceso por el cual se adquiere la enfermedad / nfluence of the type of power supply in the development of cow's milk allergy in young children factors involved in the process by which it acquires the disease

Antecedentes: Los resultados de las investigaciones sobre la historia natural de la alergia a la leche de vaca (ALV) no han provisto aún, de un cuadro claro y consistente que ayude en la práctica al médico tratante. Objetivos: Identificar los factores involucrados en el desarrollo de la enfermedad en lactantes pequeños, con el fin de determinar perfiles específicos e índices predictivos. Estudiar la influencia de haplogrupos mitocondriales en un grupo de niños ALV, con el fin de arribar a un mejor conocimiento de la herencia biológica y genética en la etiología de la enfermedad. Lugar de realización: Río Cuarto, Córdoba, Argentina. Diseño:Análisis observacional y retrospectivo.Análisis de mutaciones o variantes de la región D-loop del ADN mitocondrial.Población: 91 niños con diagnóstico de ALV y 91 controles, de ambos sexos, menores de 6 años, mientras que 11 niños con diagnóstico de ALV y 30 controles, de ambos sexos, menores de 2 años, conformaron la población del estudio de haplogrupos mitocondriales.Método: Análisis de factores seleccionados de las historias clínicas, su relación individual con el diagnóstico (prueba X2, Odds Ratios, diferencias de medias) y su incidencia conjunta en la probabilidad de ser ALV para determinar perfiles (Análisis de Correspondencia Múltiple y Regresión Logística). Elaboración de 3 índices predictivos basados en: Odds Ratios individuales, los correspondientes a la Regresión Logística y la identificación de criterios mayores y menores, con su respectiva evaluación de efectividad diagnóstica (sensibilidad, especificidad, valores predictivos y curva ROC). Para el procesamiento de datos y obtención de los resultados empleados en el análisis de mutaciones o variantes de la región D-loop del genoma mitocondrial y en el estudio filogenético se utilizaron diferentes programas específicos (software) disponibles.

ABSTRACT: Background: The results of the research on the natural history of allergy to cow's milk allergy (CMA) still have not provided a clear picture and consistent that in practice helps the attending physician. Objectives: To identify the factors involved in the development of the disease in young infants, in order to determine specific profiles and predictive clinical indexes.Study the influence of haplogroup mitochondrial in a group of children ALV, in order to arrive at a better understanding of the biological and genetic heritage in the etiology of the disease. Setting: Río Cuarto, Córdoba, Argentina. Design: Observational and retrospective analysis. Analysis of mutations or variants of the mitochondrial DNA D-loop region.Population: 91 children with a diagnosis of CMA and 91 controls, of both sexes, under the age of 6 years, while 11 children with a diagnosis of CMA and 30 controls, of both sexes, under 2 years old, formed the population of the study of mitochondrial haplogroups. Methods:Analysis of selected factors of the clinical histories, their relationship with the individual diagnosis (test X2, Odds Ratios, differences in average) and their combined impact on the probability of being CMA to determine profiles (multiple correspondence analysis and logistic regression). Elaboration of 3 predictive indices based on: individual Odds Ratios, corresponding to the logistic regression and the identification of greater and smaller criteria, with its respective evaluation of effectiveness diagnoses (predictive sensitivity, specificity, values and ROC curve).For data processing and the results used for the analysis of mutations or variants of the D-loop of mitochondrial genome region and the phylogenetic study used different specific programmes (software) available.

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.