Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around similar to 23,000 to similar to 19,000 years ago. Toward the end of the LGM, a strong population expansion started similar to 18,000 and finished similar to 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

The progesterone receptor exon 4 Va1660Leu G/T polymorphism and risk of breast cancer in Australian women

An Alu insertion polymorphism of the progesterone receptor (PR) was reported recently to be associated with a reduced risk of breast cancer, with risks of 0.8- and 0.3-fold associated with the heterozygote and homozygote genotypes, respectively. This intronic variant is considered to be in linkage disequilibrium with an exon 4 hinge region G to T Val660Leu polymorphism. We investigated whether the exon 4 PR polymorphism was associated with breast cancer in Australian women, using a population-based study of 1452 cases and 793 controls, half of whom were

Tissue engineering for bone regeneration using differentiated alveolar bone cells in collagen scaffolds

Regeneration of osseous defects by a tissue-engineering approach provides a novel means of treatment utilizing cell biology, materials science, and molecular biology. In this study the concept of tissue engineering was tested with collagen type I matrices seeded with cells with osteogenic potential and implanted into sites where osseous damage had occurred. Explant cultures of cells from human alveolar bone and gingiva were established. When seeded into a three-dimensional type I collagen-based scaffold, the bone-derived cells maintained their osteoblastic phenotype as monitored by mRNA and protein levels of the bone-related proteins including bone sialoprotein, osteocalcin, osteopontin, bone morphogenetic proteins 2 and 4, and alkaline phosphatase. These in vitro-developed matrices were implanted into critical-size bone defects in skulls of immunodeficient (SCID) mice. Wound healing was monitored for up to 4 weeks. When measured by microdensitometry the bone density within defects filled with osteoblast-derived matrix was significantly higher compared with defects filled with either collagen scaffold alone or collagen scaffold impregnated with gingival fibroblasts. New bone formation was found at all the sites treated with the osteoblast-derived matrix at 28 days, whereas no obvious new bone formation was identified at the same time point in the control groups. In situ hybridization for the human-specific Alu gene sequence indicated that the newly formed bone tissue resulted from both transplanted human osteoblasts and endogenous mesenchymal stem cells. The results indicate that cells derived from human alveolar bone can be incorporated into bioengineered scaffolds and synthesize a matrix, which on implantation can induce new bone formation.

Aula inaugural do curso de forma????o da carreira de EPPGG

A aula inaugural da primeira turma do curso de forma????o de Especialista em Pol??ticas P??blicas e Gest??o Governamental - EPPGG e da Escola Nacional de Administra????o P??blica - ENAP, preparada pelo presidente Jos?? Sarney e proferida pelo ministro Alu??zio Alves, em 1988, ?? documento de fundamental import??ncia para a carreira, para a ENAP e para a profissionaliza????o da Administra????o P??blica. A presente publica????o re??ne de maneira in??dita tr??s discursos que s??o refer??ncia obrigat??ria para os gestores governamentais: al??m da aula do presidente Jos?? Sarney, os pronunciamentos do ministro Alu??zio Alves e do presidente da Funda????o Centro de forma????o do Servidor P??blico - FUNCEP, Paulo Catalano, proferidos na mesma ocasi??o. Os textos traduzem as expectativas e as diretrizes para a consolida????o da ENAP e da carreira de EPPGGs, ressaltando sua import??ncia par uma gest??o p??blica voltada aos interesses dos cidad??os. Resgat??-los colabora para refor??ar a mem??ria e a hist??ria dos gestores governamentais, valorizando sua trajet??ria e seus objetivos. Vinte e cinco anos ap??s a aula inaugural, os prop??sitos e os princ??pios que nortearam a cria????o da carreira e da ENAP permanecem os mesmos, como ressaltado no discurso presidencial: "todos os atos do governo, do mais solene ao mais rotineiro, devem ter sempre no horizonte, o fim ??ltimo e a raz??o essencial do Estado que ?? a promo????o do bem-estar, a garantia de igualdade de chances, do direito ?? paz, ?? liberdade e ?? busca individual de felicidade para todos.

Polimorfismo I/D do gene da enzima conversora da angiotensina

Em Portugal, no ano de 2009, existiam 983 mil indivíduos com Diabetes mellitus (DM), dos quais 90% DM tipo 2 (DM2). Um dos principais factores de risco para o desenvolvimento da DM2 é a obesidade. A DM2 está, desta forma, associada a um estilo de vida sedentário, quer pela diminuição do metabolismo da glicose, quer pela sua associação à obesidade devido ao aumento dos níveis de glicose como consequência da sobrealimentação. Outros factores como a lipotoxicidade e o stress oxidativo também têm sido considerados como responsáveis pela disfunção das células-beta pancreáticas. O gene da enzima conversora da angiotensina (ECA) é altamente polimórfico, sendo associado como factor predisponente para diferentes patologias como a DM. O polimorfismo melhor descrito até à actualidade é o de Inserção/Delecção (I/D), consistindo na inserção de um fragmento Alu de 287bp no intrão 16 do gene DCP1. A actividade pró-inflamatória e pró-oxidativa desta enzima sobre o pâncreas, bem como a sua actuação nos processos de fibrose, podem em parte auxiliar na compreensão do processo que origina esta patologia. O polimorfismo I/D torna-se assim um óptimo candidato para a detecção de indivíduos susceptíveis.Este estudo tem como objectivo analisar a distribuição do polimorfismo I/D, bem como a sua possível relação com a incidência de DM e com os níveis de glicose.

Análise combinada de fatores genéticos e ambientais na hipertensão essencial em um município da região Amazônica

OBJETIVO: Este estudo avaliou a contribuição de seis polimorfismos genéticos presentes em genes do sistema renina-angiotensina-aldosterona (SRAA) e fatores de risco clínicos para o desenvolvimento da hipertensão arterial essencial em um município da região Amazônica. MÉTODOS: Oitenta e dois indivíduos hipertensos e setenta e oito indivíduos normotensos foram genotipados quanto à presença de polimorfismos REN-G1051A (renina), AGT-M235T (angiotensinogênio), ECA-Alu I/D (enzima conversora de angiotensina I), AGTR1-A1166C (receptor tipo 1 da angiotensina II) e CYP11B2-C344T (aldosterona sintetase) pela técnica de reação em cadeia da polimerase (PCR), com análise de restrição quando necessário. A influência de polimorfismos genéticos e fatores de risco clínicos na variação da pressão arterial foi avaliada por meio de regressão linear stepwise. RESULTADOS: Relatamos a co-ocorrência de fatores de risco clínicos e polimorfismo do gene da enzima conversora de angiotensina (ECA) na população de um município da região amazônica. Nossos resultados mostram que a elevação da pressão arterial sistólica é favorecida pelo alelo D do polimorfismo de inserção/deleção do gene da ECA e pelo aumento da idade, enquanto consumo de bebida alcoólica e envelhecimento estão associados ao aumento da pressão arterial diastólica (PAD). CONCLUSÃO: Esses achados indicam que os moradores de Santa Isabel do Rio Negro que possuem o alelo D da ECA ou têm o hábito de beber apresentam valores mais elevados de PAS e PAD, respectivamente, com o passar dos anos.

Molecular identification of similar species of the genus Biomphalaria (Mollusca: Planorbidae) determined by a polymerase chain reaction-restriction fragment length polymorphism

The freshwater snails Biomphalaria straminea, B. intermedia, B. kuhniana and B. peregrina, are morphologically similar; based on this similarity the first three species were therefore grouped in the complex B. straminea. The morphological identification of these species is based on characters such as vaginal wrinkling, relation between prepuce: penial sheath:deferens vas and number of muscle layers in the penis wall. In this study the polymerase chain reaction restriction fragment length polymorphism technique was used for molecular identification of these molluscs. This technique is based on the amplification of the internal transcribed spacer regions ITS1 e ITS2 of the ribosomal RNA gene and subsequent digestion of these fragments by restriction enzymes. Six enzymes were tested: Dde I, Mnl I, Hae III, Rsa I, Hpa II e Alu I. The restriction patterns obtained with DdeI presented the best profile for separation of the four species of Biomphalaria. The profiles obtained with all the enzymes were used to estimate the genetic distances among the species through analysis of common banding patterns.

Polymorphism in the Plasmodium vivax msp 3: gene in field samples from Tierralta, Colombia

We evaluated the Plasmodium vivax polymorphism by studying the Pvmsp-3 gene's polymorphic region by PCR-RFLP in 55 samples from patients living in Tierralta, Colombia. Three different sizes of the Pvmsp-3 gene were found, type A (1,900 bp), type B (1,500 bp) and type C (1,100 bp); most of the samples were type A (96.4 %). The Pvmsp-3 gene exhibited high polymorphism. Seven restriction patterns were found when using Alu I, and nine were found with Hha I; 12 different alleles were obtained when these patterns were combined. The findings suggest that this gene could be used in Colombia as a molecular epidemiologic marker for genotyping P. vivax.

Identification of blood meal sources of Lutzomyia longipalpis using polymerase chain reaction-restriction fragment length polymorphism analysis of the cytochrome B gene

An analysis of the dietary content of haematophagous insects can provide important information about the transmission networks of certain zoonoses. The present study evaluated the potential of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome B (cytb) gene to differentiate between vertebrate species that were identified as possible sources of sandfly meals. The complete cytb gene sequences of 11 vertebrate species available in the National Center for Biotechnology Information database were digested with Aci I, Alu I, Hae III and Rsa I restriction enzymes in silico using Restriction Mapper software. The cytb gene fragment (358 bp) was amplified from tissue samples of vertebrate species and the dietary contents of sandflies and digested with restriction enzymes. Vertebrate species presented a restriction fragment profile that differed from that of other species, with the exception of Canis familiaris and Cerdocyon thous. The 358 bp fragment was identified in 76 sandflies. Of these, 10 were evaluated using the restriction enzymes and the food sources were predicted for four: Homo sapiens (1), Bos taurus (1) and Equus caballus (2). Thus, the PCR-RFLP technique could be a potential method for identifying the food sources of arthropods. However, some points must be clarified regarding the applicability of the method, such as the extent of DNA degradation through intestinal digestion, the potential for multiple sources of blood meals and the need for greater knowledge regarding intraspecific variations in mtDNA.

The gene for the ligand binding chain of the human interferon gamma receptor.

In order to characterize the gene encoding the ligand binding (1(st); alpha) chain of the human IFN-gamma receptor, two overlapping cosmid clones were analyzed. The gene spans over 25 kilobases (kb) of the genomic DNA and has seven exons. The extracellular domain is encoded by exons 1 to 5 and by part of exon 6. The transmembrane region is also encoded by exon 6. Exon 7 encodes the intracellular domain and the 3' untranslated portion. The gene was located on chromosome 6q23.1, as determined by in situ hybridization. The 4 kb region upstream (5') of the gene was sequenced and analyzed for promoter activity. No consensus-matching TATA or CAAT boxes in the 5' region were found. Potential binding sites for Sp1, AP-1, AP-2, and CREB nuclear factors were identified. Compatible with the presence of the Sp1/AP-2 sites and the lack of TATA box, S1-nuclease mapping experiments showed multiple transcription initiation sites. Promoter activity of the 5' flanking region was analyzed with two different reporter genes: the Escherichia coli chloramphenicol acetyltransferase and human growth hormone. The smallest 5' region of the gene that still had full promoter activity was 692 base pairs in length. In addition, we found sequences belonging to the oldest family of Alu repeats, 2 - 3 kb upstream of the gene, which could be useful for genetic studies.

A large deletion in the adRP gene PRPF31: evidence that haploinsufficiency is the cause of disease.

PURPOSE: To report a large deletion that encompasses more than 90% of PRPF31 gene and two other neighboring genes in their entirety in an adRP pedigree that appears to show only the typical clinical features of retinitis pigmentosa. METHODS: To identify PRPF31 mutation in a dominant RP family (ADRP2) previously linked to the RP11 locus, the 14 exons of PRPF31 were screened for mutations by direct sequencing. To investigate the possibility of a large deletion, microsatellite markers near PRPF31 gene were analyzed by non-denaturing PAGE. RESULTS: Initial screening of PRPF31 gene in the ADRP2 family did not reveal an obvious mutation. A large deletion was however suspected due to lack of heterozygosity for nearly all PRPF31 intragenic single nucleotide polymorphysm (SNPs). In order to estimate the size of the deletion, SNPs and microsatellite markers spanning and flanking PRPF31 were analyzed in the entire ADRP2 family. Haplotype analysis with the above markers suggested a deletion of approximately 30 kb that included the putative promoter region of a novel gene OSCAR, the entire genomic content of genes NDUFA3, TFPT and more than 90% of PRPF31 gene. Sequence analysis of the region flanking the potential deletion showed a high presence of Alu elements implicating Alu mediated recombination as the mechanism responsible for this event. CONCLUSIONS: This mutation provides evidence that haploinsufficiency rather than aberrant function of mutated proteins is the cause of disease in these adRP patients with mutations in PRPF31 gene.

A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.

Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.

Death and resurrection of the human IRGM gene

Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for Crohn's disease. We analyzed the detailed structure of this gene family among primates and showed that most of the IRG gene cluster was deleted early in primate evolution, after the divergence of the anthropoids from prosimians ( about 50 million years ago). Comparative sequence analysis of New World and Old World monkey species shows that the single-copy IRGM gene became pseudogenized as a result of an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF). We find that the ORF was reestablished as a part of a polymorphic stop codon in the common ancestor of humans and great apes. Expression analysis suggests that this change occurred in conjunction with the insertion of an endogenous retrovirus, which altered the transcription initiation, splicing, and expression profile of IRGM. These data argue that the gene became pseudogenized and was then resurrected through a series of complex structural events and suggest remarkable functional plasticity where alleles experience diverse evolutionary pressures over time. Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites.

Ontología de ALUS

En este trabajo se describe una base de conocimiento de las ALU humanas. La ontología incorpora términos SO y GO y está orientada a describir el contexto genómico del conjunto de ALU. Para cada elemento ALU se almacenan el gen y transcrito más cercanos, así como su anotación funcional de acuerdo a GO, el estado de la cromatina circundante y los factores de transcripción presentes en la ALU. Se han incorporado reglas semánticas para facilitar el almacenamiento, consulta e integración de la información. La ontología de ALU es plenamente analizable mediante razonadores como Pellet y está parcialmente transferida a una wiki semántica.

Suomen kaupan ja teollisuuden rakenne kuljetusten näkökulmasta

Tässä selvityksessä on tarkasteltu Suomen kaupan ja teollisuuden rakennetta tarkoituk-sena löytää SPC Finlandin tärkeimmät kohderyhmät tuojien ja viejien joukosta. Samalla tavoitteena on ollut muodostaa kokonaiskuva kaupan ja teollisuuden toiminnasta ulko-maan kuljetusten näkökulmasta. Selvitys jakaantuu nimensä mukaisesti erikseen kauppaan ja teollisuuteen. Teollisuuden tarkastelussa keskitytään merikuljetusten kannalta tärkeimpiin toimialoihin metsäteolli-suuteen, teknologiateollisuuteen kuuluvaan metalliteollisuuteen ja kemianteollisuuteen. Ulkomaankauppaan liittyvien kotimaassa tapahtuvien kuljetusten kannalta oleellista on ollut toimialojen maantieteellisen sijainnin ja alueittaisen viennin jakautumisen kartoit-taminen. Suomen vienti on toimijoittain tarkasteltuna hyvin keskittynyttä. Puolet Suomen viennin arvosta muodostuu 21 suurimman vientiyrityksen viennistä. Toisaalta yli miljoonan euron vuosittaiseen vientiin yltäviä yrityksiä on lähes 2 000. Keskittyneisyys vaihtelee teollisuudessa toimialoittain. Vienti on keskittyneintä paperiteollisuudessa ja perusme-tallien valmistuksessa, jotka ovat myös merikuljetusten tärkeimpiä rahdinantajia. Vienti painottuu rannikolle ja muutamaan sisämaan voimakkaasti teollistuneeseen alu-eeseen. Tuotantolaitosten maantieteellisessä sijoittautumisessa on toimialakohtaisia ero-ja. Kemiallisen metsäteollisuuden sisämaan keskukset tarjoavat mahdollisuuden kehit-tää intermodaalisia kuljetusvirtoja, jos kontitusta siirtyy tehtaille. Intermodaalikuljetuk-sissa käytetään kahta tai useampaa kuljetusmuotoa ja runkokuljetus tapahtuu rautateitse tai vesitse. Kuljetusyksikkö, esimerkiksi kontti, ei yleensä vaihdu kuljetuksen aikana. Teknologiateollisuus jakaantuu moneen alatoimialaan. Suomen teollisuuden kasvu on ollut nopeaa erityisesti elektroniikka- ja sähköteknisessä teollisuudessa, joka ei kuiten-kaan kuulu suuriin merikuljettajiin. Kone- ja metallituoteteollisuudessa useat tuotteet soveltuvat suuryksiköitäviksi. Kemianteollisuus on jakautunut hyvin erilaisiin alatoimialoihin. Peruskemikaaleissa merkittävä tuoteryhmä on muun muassa metsäteollisuuden kemikaalit. Rannikolla on merkittäviä kemianalan keskittymiä, joista suurin on Porvoon Kilpilahdessa. Sinne saa-puu öljyä kemian teollisuuden raaka-aineeksi. Muovi- ja kumiteollisuus käyttävät tuote-kuljetuksissa erityisesti maantiekuljetuksia. Vientimäärät ovat melko vähäisiä. Muovi- ja kumiteollisuuden raaka-aineet ovat tuontitavaraa. Kaupan kehitys riippuu suuresti demografisista tekijöistä ja ostovoiman alueellisesta jakautumisesta. Ostovoima keskittyy Suomessa väestöltään suurimpiin seutukuntiin, joista kahdessa, Helsingissä ja Turussa, sijaitsee kaupan tuonnin tärkeimmät satamat. Kaupan tuonti keskittyy yhä voimakkaammin näihin kahteen seutukuntaan, vaikka myös Pohjois-Pohjanmaalla on potentiaalia kaupan tuontiin. Toimijoittain tukkukaupan tuonti on vielä melko vähän keskittynyttä. Alalla on paljon maahantuontiyrityksiä. Kes-kittyminen kuitenkin jatkuu ja suuret ketjut ohittavat suoralla tuonnilla pienet maahan-tuojat. Erikoistavarakaupassa Suomeen etabloituu lisää ulkomaisia ketjuja. Ketjuohjauksella tehdään päätökset hankinnoista ja logistiikasta. Kaupan valikoimissa ulkomais-ten tuotteiden määrä kasvaa. Intermodaalisuus lisääntyy, vaikka perusteollisuuden tuotannon kasvu hidastuisi tai kääntyisi laskuun. Jalostusasteen noston seurauksena suuryksiköidyt ja intermodaaliset kuljetukset lisääntyvät. Aiemmin suuryksiköimättömänä kuljetettua lastia, kuten irtota-varaa, siirtyy kuljetettavaksi konteissa. Sisäiset Suomen ja muun Euroopan väliset kont-tikuljetukset ovat vielä vähäisiä. Logistiikkaketjujen tehostaminen johtaa komodaali-suuden lisääntymiseen niin, että eri liikennemuotojen yhteiskäyttö tehostuu myös bulk-kuljetuksissa. Suomen teollisuuden ja kaupan alueellinen rakenne ei tue intermodaalisuuden kehittä-mistä kotimaan kuljetusosuuksilla kovinkaan voimakkaasti. Intermodaalikuljetusten osuuden nostamiseksi tarvitaan uusia innovaatioita ja palveluita, joita myös SPC Fin-land voi olla mukana tuottamassa. Suomen viennin voimakkaan toimijakohtaisen keskittymisen takia SPC Finlandin on helppo saavuttaa viejät, jotka vastaavat suurimmasta osasta Suomen viennistä. Pk-yritykset käyttävät viennissään todennäköisesti hyvin laajasti huolintaliikkeiden palve-luita. Tuonnin kenttä on hajanaisempi, vaikka tuonnissakin keskittyminen lisääntyy. Toisaalta yhä useammat yritykset ovat potentiaalisia SPC Finlandin palveluiden tarvitsi-joita, koska pienenkin yrityksen on helppo tuoda tavaraa EU:n alueelta. Selvityksen perusteella voidaan päätellä, että teollisuuden jalostusasteen nousu ja sen seurauksena tapahtuva intermodaalikuljetusten määrän kasvu näyttäisivät lisäävän tar-vetta SPC Finlandin palveluihin teollisuuden kokonaiskuljetusmäärien kehityksestä riippumatta. Kaupan kansainvälistyminen ja ulkomaisten tuotteiden määrän lisääntymi-nen vaikuttavat samaan suuntaan. Kun vielä otetaan huomioon, että viennin osuus brut-tokansantuotteesta todennäköisesti nousee lähemmäksi muiden pienten eurooppalaisten maiden tasoa, näyttäisi siltä, että SPC Finlandin palveluille lähimerenkulkusidonnaisten intermodaalikuljetusten edistämisessä on olemassa tarvetta myös tulevaisuudessa.