mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences

The mitochondrial genome, contained in the subcellular mitochondrial network, encodes a small number of peptides pivotal for cellular energy production. Mitochondrial genes are highly polymorphic and cataloguing existing variation is of interest for medical scientists involved in the identification of mutations causing mitochondrial dysfunction, as well as for population genetics studies. Human Mitochondrial Genome Database (mtDB) (http://www.genpat.uu.se/mtDB) has provided a comprehensive database of complete human mitochondrial genomes since early 2000. At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. As of August 2005 this database contains 2104 sequences (1544 complete genome and 560 coding region) available to download or search for specific polymorphisms. Of special interest to medical researchers and population geneticists evaluating specific positions is a complete list of (currently 3311) mitochondrial polymorphisms among these sequences. Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variant

mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences

The mitochondrial genome, contained in the subcellular mitochondrial network, encodes a small number of peptides pivotal for cellular energy production. Mitochondrial genes are highly polymorphic and cataloguing existing variation is of interest for medical scientists involved in the identification of mutations causing mitochondrial dysfunction, as well as for population genetics studies. Human Mitochondrial Genome Database (mtDB) () has provided a comprehensive database of complete human mitochondrial genomes since early 2000. At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. As of August 2005 this database contains 2104 sequences (1544 complete genome and 560 coding region) available to download or search for specific polymorphisms. Of special interest to medical researchers and population geneticists evaluating specific positions is a complete list of (currently 3311) mitochondrial polymorphisms among these sequences. Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variants

Global and unbiased detection of splice junctions from RNA-seq data

SplitSeek can be used to detect novel splicing events in SOLiD RNA-seq data without the need for a pre-defined library

Genome-wide analysis of chimpanzee genes with premature termination codons

<p>Abstract</p> <p>Background</p> <p>Premature termination codons (PTCs) cause mRNA degradation or a truncated protein and thereby contribute to the transcriptome and proteome divergence between species. Here we present the first genome-wide study of PTCs in the chimpanzee. By comparing the human and chimpanzee genome sequences we identify and characterize genes with PTCs, in order to understand the contribution of these mutations to the transcriptome diversity between the species.</p> <p>Results</p> <p>We have studied a total of 13,487 human-chimpanzee gene pairs and found that ~8% were affected by PTCs in the chimpanzee. A majority (764/1,109) of PTCs were caused by insertions or deletions and the remaining part was caused by substitutions. The distribution of PTC genes varied between chromosomes, with Y having the highest proportion. Furthermore, the density of PTC genes varied on a megabasepair scale within chromosomes and we found the density to be correlated both with indel divergence and proximity to the telomere. Within genes, PTCs were more common close to the 5' and 3' ends of the amino acid sequence. Gene Ontology classification revealed that olfactory receptor genes were over represented among the PTC genes.</p> <p>Conclusion</p> <p>Our results showed that the density of PTC genes fluctuated across the genome depending on the local genomic context. PTCs were preferentially located in the terminal parts of the transcript, which generally have a lower frequency of functional domains, indicating that selection was operating against PTCs at sites central to protein function. The enrichment of GO terms associated with olfaction suggests that PTCs may have influenced the difference in the repertoire of olfactory genes between humans and chimpanzees. In summary, 8% of the chimpanzee genes were affected by PTCs and this type of variation is likely to have an important effect on the transcript and proteomic divergence between humans and chimpanzees.</p

Lifestyle, Genetics, and Disease in Sami

Aim: To present a summary of the lifestyle, genetic origin, diet, and disease in the population of Sami, indigenous people of northern Fennoscandia. Method: A survey of the available scientific literature and preliminary results from our own study of the Swedish Sami population. Results: The Sami probably have a heterogeneous genetic origin, with a major contribution of continental or Eastern European tribes and a smaller contribution from Asia. The traditional Sami diet, high in animal products, persists in Sami groups still involved with reindeer herding, but others have adopted a diet typical of Western cultures. Early reports indicated a lower prevalence of heart disease and most cancers, except stomach cancer. Recent studies have not found a lower risk of heart disease, but have consistently shown an overall reduced cancer risk. Sami have been reported to share some specific health-related genetic polymorphisms with other European populations, but none that would explain the observed differences in disease risk. Conclusion: The genetic structure of the Sami population makes it suitable for studies of the genetic and environmental factors influencing the development of common diseases. The difference in incidence of heart disease between studies may reflect the ongoing transition from a traditional to a more Westernized lifestyle. The ability to compare population segments with different lifestyles, combined with the genetic structure of the population, creates unusual possibilities for studies of the genetic and environmental factors involved in the development of common disease

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing

Background: We profile the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver, aiming to quantify expression of known genes and to identify novel transcribed regions. Results: Using stringent criteria for transcription, we identify 12,843 expressed genes, with a majority being found in both tissues. We further identify 9,826 novel transcribed regions that are not overlapping with annotated exons, mRNAs or ESTs. Over 80 % of the novel transcribed regions map within or in the vicinity of known genes, and by combining sequencing data with de novo splice predictions we predict several of the novel transcribed regions to be new exons or 3 &apos; UTRs. For approximately 350 novel transcribed regions, the corresponding DNA sequence is absent in the human reference genome. The presence of novel transcribed regions in five genes and in one intergenic region is further validated with RT-PCR. Finally, we describe and experimentally validate a putative novel multi-exon gene that belongs to the ATP-cassette transporter gene family. This gene does not appear to be functional in human since one exon is absent from the human genome. In addition to novel exons and UTRs, novel transcribed regions may also stem from different types of noncoding transcripts. We note that expressed repeats and introns from unspliced mRNAs are especially common in our data. Conclusions: Our results extend the chimpanzee gene catalogue with a large number of novel exons and 3 &apos; UTRs an

Lifestyle, Genetics, and Disease in Sami

Aim: To present a summary of the lifestyle, genetic origin, diet, and disease in the population of Sami, indigenous people of northern Fennoscandia. Method: A survey of the available scientific literature and preliminary results from our own study of the Swedish Sami population. Results: The Sami probably have a heterogeneous genetic origin, with a major contribution of continental or Eastern European tribes and a smaller contribution from Asia. The traditional Sami diet, high in animal products, persists in Sami groups still involved with reindeer herding, but others have adopted a diet typical of Western cultures. Early reports indicated a lower prevalence of heart disease and most cancers, except stomach cancer. Recent studies have not found a lower risk of heart disease, but have consistently shown an overall reduced cancer risk. Sami have been reported to share some specific health-related genetic polymorphisms with other European populations, but none that would explain the observed differences in disease risk. Conclusion: The genetic structure of the Sami population makes it suitable for studies of the genetic and environmental factors influencing the development of common diseases. The difference in incidence of heart disease between studies may reflect the ongoing transition from a traditional to a more Westernized lifestyle. The ability to compare population segments with different lifestyles, combined with the genetic structure of the population, creates unusual possibilities for studies of the genetic and environmental factors involved in the development of common disease

Fas and FasL gene polymorphisms are not associated with cervical cancer but differ among Black and Mixed-ancestry South Africans

© 2009 Williamson et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Petrolio e politica nella decolonizzazione Algerina: verso un network energetico Europeo?

Le relazioni tra Francia e Italia nella guerra d’Algeria sono state oggetto di diverse analisi storiche; questo lavoro si concentra sul ruolo dell’industria petrolifera nelle relazioni tra i due paesi nel periodo specifico. Le riserve d’idrocarburi algerine furono scoperte nel 1956, due anni dopo l’inizio della guerra. I ritrovamenti ebbero una notevole eco in Francia, e la possibilità di diventare un paese produttore di petrolio rese più urgente il dibattito sull’amministrazione del Sahara e sull’opportunità di aprire le porte alle compagnie straniere. Questa ricerca ha come obiettivo l’esame delle azioni intraprese dalla Francia per la messa a punto di un’industria petrolifera nel Sahara, e le parallele strategie dell’industria petrolifera internazionale per la penetrazione in un nuovo territorio e in un’area contestata. In particolare, l’analisi si concentra sulla strategia dell’Eni, la compagnia di Stato Italiana, che rifiutò apertamente di collaborare con il governo francese per mantenere un atteggiamento pro-arabo. L’articolo punta a ricostruire il dibattito sulle risorse del sottosuolo sahariano, il problema del controllo del territorio e le frizioni tra l’industria petrolifera di Stato europea e le grandi multinazionali americane, nel contesto più ampio della decolonizzazione, dei negoziati per la costruzione dell’Unione Europea e della ricerca di una maggiore indipendenza dagli Stati Uniti. Italian-French relations during the Algerian war have been the subject of thorough historical investigations; this paper concentrates on the hydrocarbon industry and its role in the Algerian decolonization process and in the Italian-French relations. Algerian hydrocarbon reserves were found in 1956, two years after the outbreak of the war. The discovery had a considerable impact in France, where the possibility of becoming an oil exporting country reinvigorated the debate over the management of the Saharan area and on whether (and to which degree) to allow the presence of foreign oil companies in its exploitation. The research aims to investigate the actions taken by the French government for the set-up of an oil industry in the Sahara and the parallel strategies of the international oil industry for the penetration of a new territory in a contented area. In particular, the paper focuses on the Italian State company ENI, which openly refused to collaborate with the French government in order to maintain a pro-Arab approach. This paper aims to reconstruct the debate over the Saharan oil resources, the control over the territory and the frictions between European SOEs and the American oil giants, in the broader contest of decolonization, the negotiations for the construction of the European Union and the research for more independence from the United States

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

<p>Abstract</p> <p>Background</p> <p>Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.</p> <p>Results</p> <p>Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures.</p> <p>Conclusions</p> <p>Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health.</p