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Naša raziskava sovpada s porastom zanimanja za »novo porajajočo se« bolezen virusa hepatitisa E (HEV) v svetu in prinaša nove izsledke o razširjenosti okužbe v slovenskih rejah prašičev. Ker gre za zoonozo, smo z raziskavo želeli ugotoviti, kakšno je stanje v slovenskih klavnicah in ali hepatitis E virus ogroža zdravje ljudi. Vzorčenje prašičev je potekalo v štirih klavnicah po Sloveniji med junijem in septembrom 2014. Vzorce blata, jeter in žolča smo odvzeli 811 klinično zdravim prašičem različnih starostnih kategorij. Ob vzorčenju v klavnici smo jemali tudi brise površin na klavni liniji, vzorčili mleto meso in pečenice. Z metodo RT-PCR v realnem času smo dokazovali prisotnost nukleinske kisline HEV v odvzetih vzorcih. Istim prašičem smo odvzeli tudi vzorec krvi in določali prisotnosti protiteles IgG proti HEV. Največ HEV pozitivnih živali smo ugotovili med 322 odojki, in sicer 17 %. Med 400 pitanci smo ugotovili en pozitiven vzorec jeter in en pozitiven vzorec žolča, kar je bistveno manj, kot smo pričakovali. Med 89 plemenskimi svinjami nismo ugotovili pozitivne živali. Med 63 brisi površin smo odkrili dva pozitivna vzorca. V vzorcih pečenic in mletega mesa prisotnosti HEV nismo ugotovili. Z genetsko tipizacijo 45 HEV pozitivnih vzorcev in filogenetsko primerjavo nukleotidnih zaporedij slovenskih sevov skupaj z zaporedji sevov HEV, ki so dostopni v podatkovni zbirki GenBank, smo ugotovili pojav velike genetske raznolikosti med vzorci ter prisotnost štirih različnih podtipov genotipa 3 (3a, 3b, 3e in 3f) HEV v Sloveniji. V izvedeni študiji genotipa 4 nismo ugotovili. V določanje nukleotidnega zaporedja smo vključili tudi pet humanih vzorcev, pozitivnih na prisotnost HEV. Zaradi premajhne količine virusne RNA v HEV pozitivnih humanih vzorcih nam pri nobenem ni uspelo določiti nukleotidnega zaporedja. Z dvema komercialnima encimskoimunskima testoma (ID Screen® Hepatitis E Indirect Multi-species proizvajalca IDvet in HEV-IgG ELISA porcine proizvajalca Axiom) smo pregledali vzorce krvi domačih prašičev na prisotnost protiteles IgG proti HEV. Pregledali smo 351 vzorcev, naključno izbranih iz vzorcev odvzetih na celotnem območju Slovenije v okviru rednega monitoringa kužnih bolezni pri prašičih v letih 2013 in 2014, ter 359 vzorcev, odvzetih v klavnici ob zakolu leta 2014. Primerjava rezultatov obeh testov je pokazala, da je encimskoimunski test proizvajalca Axiom ustreznejši za presejalna testiranja. Za razjasnitev 38 rezultatov, ki se pri vzorcih iz klavnice pri obeh encimskoimunskih testih niso ujemali, smo uporabili modificiran humani imunoblot test recomLine HEV IgG/IgM (Mikrogen diagnostik). Izvedena raziskava je prva tovrstna študija, ki dokazuje prisotnost HEV pri prašičih na klavni liniji v Sloveniji, prav tako je prva izvedena sistematična raziskava v tako širokem obsegu v Sloveniji. Rezultati raziskave prispevajo k boljšemu razumevanju stanja okužb prašičev s HEV ob vstopu na klavno linijo, in podajajo natančnejšo sliko o stanju prekuženosti prašičev v rejah. Glede na številčnost pregledanih vzorcev in razpršenost rej po državi, iz katerih so izhajali vzorčeni prašiči, lahko z gotovostjo trdimo, da rezultati podajajo natančen podatek o razširjenosti okužb s HEV med domačimi prašiči v Sloveniji. Our research coincides with increasing interest in the newly emerging zoonosis, the hepatitis E virus, and provides new information regarding infection distribution in Slovenian pig herds. Since HEV is a zoonosis, our goal was to investigate the existing condition in Slovenian slaughterhouses and to assess associated health risks posed to consumers and personnel. Sampling of pigs was conducted in four Slovenian slaughterhouses, between June and September 2014. Feces, liver and bile samples were collected from 811 healthy pigs (different age categories). At the time of slaughter, swab samples of different surfaces and samples of minced meat and sausages were also taken. All samples were analyzed with real time PCR (RT-PCR) for the presence of HEV. Blood samples taken from the same pigs were analyzed for the presence of IgG HEV antibodies. The highest number of HEV positive animals was found in the 3 month old age group of pigs (322 animals), where 17% of animals were HEV positive. In the age group of 6 month old pigs (400 animals), only one liver sample and one bile sample was positive, which was significantly less than we would have expected. Out of 89 pigs that were older than 1 year, none was HEV positive. Out of 63 surface swabs, two were positive for the presence of HEV. None of the minced meat and sausage samples was positive. A phylogenetic tree, generated combining sequences obtained from Slovenian strains (45 positive samples) and nucleotide sequences of HEV strains derived from GeneBank, revealed high genetic variability between samples, allowing classification of the identified Slovenian strains into four different subtypes of genotype 3 (3a, 3b, 3e and 3f). Genotype 4 was not found. Additionally, five HEV positive human samples were sequenced, although sequencing was unsuccessful due to an insufficient amount of viral RNA. With two commercial ELISA (ID Screen® Hepatitis E Indirect Multi-species (IDvet) and HEV-IgG ELISA porcine (Axiom)) we analyzed blood samples from domestic pigs for the presence of IgG HEV antibodies. We analyzed 351 randomly selected serum samples collected from pigs located in different parts of Slovenia (these samples were collected within the scope of annual monitoring of infectious diseases in 2013 and 2014) and 359 samples collected from pigs at slaughter in 2014. Comparison of results from both ELISA showed that Axiom ELISA is more suitable as a screening method. A human immunoblot test was optimized and standardized to test 38 serum samples that showed discrepancies in results obtained with Axion and IDvet ELISA kits. The work presented herein represents the first systematic, wide scope analysis on the presence of HEV in pigs at slaughter in Slovenia. Results of the research have contributed to a better understanding of pig HEV infection status at slaughter and have shown a more detailed picture of seroprevalence status in pig farming. Since our research included a great number of samples and dispersion of different farms around the country, we can safely say that the obtained results show accurate information about pig HEV infections in Slovenia.

Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at >= 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples. Funding Agencies|ALF funding Region Orebro County; Orebro County Council Research committee

Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. The novel associations nearly double the number of genome-wide hits reported for SSc thus far. We define 95% credible sets of less than 5 likely causal variants in 12 loci. Additionally, we identify specific SSc subtype-associated signals. Functional analysis of high-priority variants shows the potential function of SSc signals, with the identification of 43 robust target genes through HiChIP. Our results point towards molecular pathways potentially involved in vasculopathy and fibrosis, two main hallmarks in SSc, and highlight the spectrum of critical cell types for the disease. This work supports a better understanding of the genetic basis of SSc and provides directions for future functional experiments., We thank Sofia Vargas, Sonia García, and Gema Robledo for their excellent technical assistance and all the patients and control donors for their essential collaboration. We thank National DNA Bank Carlos III (University of Salamanca, Spain) that supplied part of the control DNA samples from Spain, WTCCC and EIRA Consortiums, and PopGen 2.0 network. This work was supported by Spanish Ministry of Economy and Competitiveness (grant ref. SAF2015-66761-P), Consejeria de Innovacion, Ciencia y Tecnologia, Junta de Andalucía (P12-BIO-1395), Ministerio de Educación, Cultura y Deporte through the program FPU, Juan de la Cierva fellowship (FJCI-2015-24028), Red de Investigación en Inflamación y Enfermadades Reumaticas (RIER) from Instituto de Salud Carlos III (RD16/0012/0013), and Scleroderma Research Foundation and NIH P50- HG007735 (to H.Y.C.). H.Y.C. is an Investigator of the Howard Hughes Medical Institute. PopGen 2.0 is supported by a grant from the German Ministry for Education and Research (01EY1103). M.D.M and S.A. are supported by grant DoD W81XWH-18-1- 0423 and DoD W81XWH-16-1-0296, respectively

Submitted by Danilo Giorgi Abranches de Andrade null (dgaandrade@fmvz.unesp.br) on 2017-02-23T14:17:39Z No. of bitstreams: 1 dissertacao_danilo_g_a_andrade.pdf: 2560202 bytes, checksum: d847a79e450a463626e2d953a46fcc54 (MD5) Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-03-02T14:45:46Z (GMT) No. of bitstreams: 1 andrade_dga_me_bot.pdf: 2560202 bytes, checksum: d847a79e450a463626e2d953a46fcc54 (MD5) Made available in DSpace on 2017-03-02T14:45:46Z (GMT). No. of bitstreams: 1 andrade_dga_me_bot.pdf: 2560202 bytes, checksum: d847a79e450a463626e2d953a46fcc54 (MD5) Previous issue date: 2017-02-09 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Dermatosparaxia é uma enfermidade autossômica recessiva do tecido conjuntivo caracterizada clinicamente por fragilidade e hiperextensibilidade cutâneas. Estas características impedem que o animal seja mantido no sistema de criação, sendo descartado na maioria dos casos. Descrita em diversas espécies, a dermatosparaxia foi relatada também em algumas raças de ovinos. O polimorfismo de nucleotídeo único (SNP) c.421G>T no gene ADAMTS2 (a disintegrin and metalloproteinase with thrombospondin type I motif, 2), em homozigose, é responsável pela enfermidade em ovinos da raça White Dorper. Recentemente a doença foi descrita no Brasil, contudo acredita-se que possa ter sido subdiagnosticada, uma vez que a enfermidade já foi descrita em diversos países. O objetivo desta pesquisa foi estimar a frequência alélica do SNP c.421G>T no gene ADAMTS2 em ovinos da raça White Dorper do estado de São Paulo a partir de uma metodologia diagnóstica que utilizasse a reação em cadeia da polimerase (PCR) seguida do sequenciamento direto da região desse SNP. Neste estudo, foram coletadas amostras de sangue para extração do DNA de 303 ovinos da raça White Dorper. Após a extração do DNA, realizou-se PCR para amplificar a região do SNP e, então, o sequenciamento genético para determinar sua presença no gene ADAMTS2. A frequência alélica do SNP na população estudada foi de 7,8%. Este resultado indica que as medidas de controle devem ser adotadas para prevenir a propagação do SNP c.421G>T no gene ADAMTS2 nos rebanhos de ovinos White Dorper brasileiros. Dermatosparaxis is an autosomal recessive disorder of the connective tissue; the disorder is clinically characterized by skin fragility and hyperextensibility. These skin defects prevent affected animals from entering the breeding system because they are either discarded or removed from their usual activities. Described in several species, dermatosparaxis has also been reported in some sheep breeds. The single nucleotide polymorphism (SNP) c.421G>T in the ADAMTS2 (a disintegrin and metalloproteinase with thrombospondin type I motif, 2) gene, in homozygosity, is responsible for the disease in White Dorper sheep. Recently the disorder was described in Brazil, however, it might have been underdiagnosed since the disease has already been described in many countries. The aim of this study was to estimate the allelic frequency of SNP c.421G>T in the ADAMTS2 gene in the White Dorper herd of Sao Paulo state, Brazil using a diagnostic methodology with polymerase chain reaction (PCR) and then direct sequencing of the SNP region. In this study, we collected blood DNA samples from 303 White Dorper sheep and performed PCR to amplify the SNP region. The samples were sequenced to determine the presence of the SNP in the ADAMTS2 gene. The allelic frequency of the SNP in the studied population was 7.8%; this finding indicates that control measures should be adopted to prevent the inheritance of SNP c.421G>T in the ADAMTS2 gene in Brazilian White Dorper herds.

Summary Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l-1 of [U-13C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain. © 2008 The Authors. Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd.

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes., IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism’s biology.

Vascular wilts caused by Verticillium spp. are destructive plant diseases affecting hundreds of hosts. Only a few Verticillium spp. are causal agents of vascular wilt diseases, of which V. dahliae is the most notorious pathogen, and several V. dahliae genomes are available. In contrast, V. tricorpus is mainly known as a saprophyte and causal agent of opportunistic infections. Based on a hybrid approach that combines second and third generation sequencing, a near-gapless V. tricorpus genome assembly was obtained. With comparative genomics, we sought to identify genomic features in V. dahliae that confer the ability to cause vascular wilt disease. Unexpectedly, both species encode similar effector repertoires and share a genomic structure with genes encoding secreted proteins clustered in genomic islands. Intriguingly, V. tricorpus contains significantly fewer repetitive elements and an extended spectrum of secreted carbohydrate- active enzymes when compared with V. dahliae. In conclusion, we highlight the technical advances of a hybrid sequencing and assembly approach and show that the saprophyte V. tricorpus shares many hallmark features with the pathogen V. dahliae.

The aim of this study was to determine the frequency and allele associations of locus of enterocyte effacement encoded esp and tir genes among 181 enteropathogenic Escherichia coli (EPEC) strains (90 diarrhoea-associated and 91 controls) isolated from Peruvian children under 18 months of age. We analysed espA, espB, espD and tir alleles by PCR-RFLP. EPEC strains were isolated with higher frequency from healthy controls (91/424, 21.7 %) than from diarrhoeal samples (90/936, 9.6 %) (P

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19-12 thousand years (ka) ago. M.P. was supported by Marie Curie Early Stage Training “Advanced Genetic Analysis in the Postgenomic Era” (European Union MEST-CT-2004-504318) and by a Newton International Fellowship. This research was also supported by the Italian Ministry of Education, University, and Research: Progetti FIRB-Futuro in Ricerca 2008 (to A.A. and A.O.), and Progetti Ricerca Interesse Nazionale 2009 (to A.A., O.S. and A.T.); Fondazione Alma Mater Ticinensis (to A.T. and O.S.); the European Commission, Directorate-General for Research (FP7 Ecogene grant number 205419, to R.V.); the European Union Regional Development Fund (through the Centre of Excellence in Genomics, to R.V.); the Estonian Ministry of Education and Research (Basic Research grant numbers SF 0270177As08, to R.V., and SF 0270177Bs08, to E.M.); the Estonian Science Foundation (grant number 7858, to E.M.); and the FCT (Portuguese Foundation for Science and Technology), through research project PTDC/CS-ANT/113832/2009 and personal grants to J.B.P. (SFRH/BD/45657/2008) and P.S. (SFRH/BPD/64233/2009). P.S. also received support from the DeLaszlo Foundation. N.A.-Z. was supported by the Institute of International Education fellowship. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology, and Higher Education (FCT) and is partially supported by FCT.

Orientador: Reginaldo Palazzo Júnior Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação Resumo: Um dos grandes desafios da comunidade científica em teorias da informação genética, comunicação genética e codificação genética é verificar a existência de uma estrutura matemática relacionada com a estrutura do DNA. Este trabalho propõe modelos para o sistema de comunicação de informação genética e genômica análogos ao modelo de um sistema de comunicação digital. Ambos os modelos são capazes de identificar, reproduzir e classificar matematicamente diferentes sequências de DNA. O primeiro identifica e reproduz a sequência de nucleotídeos de uma fita simples do DNA através da codificação genética e, o segundo identifica e reproduz a sequência das bases complementares da fita dupla do DNA através da codificação genômica. Os objetivos principais do presente trabalho são: a) caracterização matemática dos modelos de codificação genética e codificação genômica, b) proposta de um algoritmo para identificação de sequências de DNA; c) mostrar que sequências de DNA com características biológicas distintas, incluindo proteínas, gene e genoma em termos das fitas simples do DNA e da dupla hélice do DNA são identificadas como palavras-código dos códigos G-linearidade (BCH sobre corpos e BCH sobre anéis), reproduzidas e classificadas matematicamente, d) representação algébrica via polinômios primitivos/geradores e seus polinômios recíprocos das fitas simples do DNA (fita codante e fita não codante) e da dupla hélice do DNA, e) mostrar a existência de códigos concatenados (nested codes) entre algumas sequências de direcionamento e suas respectivas proteínas organelares, f) mostrar a arquitetura biológica (Biological frame) do genoma do plasmídeo Lactococcus lactis. Os resultados apresentados neste trabalho contribuem para o desenvolvimento de uma metodologia que poderá ser aplicada em análises mutacionais e de polimorfismos, produção de novos fármacos, melhoramento genético, entre outros, reduzindo tempo e custos laboratoriais Abstract: One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to the structure of DNA. This thesis proposes a model of a communication system for genetic and genomic information similar to the model of a digital communication system. Both models are able to identify, reproduce and classify mathematically different sequences of DNA. The first model identifies and reproduces the nucleotide sequence of a single DNA strand via the genetic encoding. The latter identifies and reproduces the sequence of the complementary bases of the double DNA strand through genomic encoding. The aims of this work are: a) a mathematical characterization of the models of genetic coding and genomic coding, b) the proposal of an algorithm for the identification of DNA sequences, c) to show that DNA sequences with distinct biological characteristics, including protein, gene and genome in terms of the single strands of DNA and of the double helix of DNA are identified as codewords of the G-linearity codes (BCH codes over fields and BCH codes over rings), mathematically reproduced and classified, d) algebraic representation via primitive/generator polynomials and their reciprocal polynomials of single DNA strands (coding strand and non-coding strand) and the double DNA strand, e) to show the existence of concatenated codes (nested codes) between some targeting sequences and their corresponding organelles proteins, f) to show the biological architecture (Biological frame) of the plasmid Lactococcus lactis genome. The results presented in this work contribute to the development of a methodology that can be applied to mutational analysis and polymorphisms, production of new drugs, genetic improvement, among others, reducing time and laboratory costs Doutorado Telecomunicações e Telemática Doutor em Engenharia Elétrica

Summary Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l-1 of [U-13C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain. © 2008 The Authors. Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd.

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.

Inbred mouse strains have been maintained for more than 100 years, and they are thought to be a mixture of four different mouse subspecies. Although genealogies have been established, female inbred mouse phylogenies remain unexplored. By a phylogenetic analysis of newly generated complete mitochondrial DNA sequence data in 16 strains, we show here that all common inbred strains descend from the same Mus musculus domesticus female wild ancestor, and suggest that they present a different mitochondrial evolutionary process than their wild relatives with a faster accumulation of replacement substitutions. Our data complement forthcoming results on resequencing of a group of priority strains, and they follow recent efforts of the Mouse Phenome Project to collect and make publicly available information on various strains. This work was partially supported by Fundação para a Ciência e a Tecnologia through a research grant to A.G. (SFRH/BD/16518/2004) and by “Programa Operacional Ciência, e Inovação 2010” (POCI 2010), VI Programa-Quadro (2002–2006).

In order to study the matrilineal genetic composition in Cabo Verde (Republic of Cape Verde), an archipelago that used to serve as a Portuguese entrepôt of the Atlantic slave trade, we have analysed a total of 292 mtDNAs sampled from the seven inhabited islands for the hypervariable segment I (HVS-I) and some characteristic RFLPs of the coding regions. The different settlement history of the northwestern group of the islands is well reflected in the mtDNA pool. The total Cabo Verde sample clearly displays the characteristic mitochondrial features of the Atlantic fringe of western Africa and testifies to almost no mitochondrial input from the Portuguese colonizers. LP was supported by a Ph.D. grant from Fundacao para a Ciencia e a Tecnologia (PRAXIS XXI/BD/13632/97).

Background Land plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown to participate in post-transcriptional events involved in organellar gene expression, and this type of function is now thought to be their main biological role. Among PPR genes, restorers of fertility (Rf) of cytoplasmic male sterility systems constitute a peculiar subgroup that is thought to evolve in response to the presence of mitochondrial sterility-inducing genes. Rf genes encoding PPR proteins are associated with very close relatives on complex loci. Results We sequenced a non-restoring allele (L7rfo) of the Rfo radish locus whose restoring allele (D81Rfo) was previously described, and compared the two alleles and their PPR genes. We identified a ca 13 kb long fragment, likely originating from another part of the radish genome, inserted into the L7rfo sequence. The L7rfo allele carries two genes (PPR-1 and PPR-2) closely related to the three previously described PPR genes of the restorer D81Rfo allele (PPR-A, PPR-B, and PPR-C). Our results indicate that alleles of the Rfo locus have experienced complex evolutionary events, including recombination and insertion of extra-locus sequences, since they diverged. Our analyses strongly suggest that present coding sequences of Rfo PPR genes result from intragenic recombination. We found that the 10 C-terminal PPR repeats in Rfo PPR gene encoded proteins result from the tandem duplication of a 5 PPR repeat block. Conclusions The Rfo locus appears to experience more complex evolution than its flanking sequences. The Rfo locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination. It is therefore not possible to determine which genes on the two alleles are direct orthologs. Our observations recall some previously reported data on pathogen resistance complex loci.