Complete mitochondrial genome suggests diapsid affinities of turtles

Despite more than a century of debate, the evolutionary position of turtles (Testudines) relative to other amniotes (reptiles, birds, and mammals) remains uncertain. One of the major impediments to resolving this important evolutionary problem is the highly distinctive and enigmatic morphology of turtles that led to their traditional placement apart from diapsid reptiles as sole descendants of presumably primitive anapsid reptiles. To address this question, the complete (16,787-bp) mitochondrial genome sequence of the African side-necked turtle (Pelomedusa subrufa) was determined. This molecule contains several unusual features: a (TA)n microsatellite in the control region, the absence of an origin of replication for the light strand in the WANCY region of five tRNA genes, an unusually long noncoding region separating the ND5 and ND6 genes, an overlap between ATPase 6 and COIII genes, and the existence of extra nucleotides in ND3 and ND4L putative ORFs. Phylogenetic analyses of the complete mitochondrial genome sequences supported the placement of turtles as the sister group of an alligator and chicken (Archosauria) clade. This result clearly rejects the Haematothermia hypothesis (a sister-group relationship between mammals and birds), as well as rejecting the placement of turtles as the most basal living amniotes. Moreover, evidence from both complete mitochondrial rRNA genes supports a sister-group relationship of turtles to Archosauria to the exclusion of Lepidosauria (tuatara, snakes, and lizards). These results challenge the classic view of turtles as the only survivors of primary anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.

Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa

Fanconi anemia (FA) is a rare, genetically heterogeneous autosomal recessive disorder associated with progressive aplastic anemia, congenital abnormalities, and cancer. FA has a very high incidence in the Afrikaner population of South Africa, possibly due to a founder effect. Previously we observed allelic association between polymorphic markers flanking the FA group A gene (FANCA) and disease chromosomes in Afrikaners. We genotyped 26 FA families with microsatellite and single nucleotide polymorphic markers and detected five FANCA haplotypes. Mutation scanning of the FANCA gene revealed association of these haplotypes with four different mutations. The most common was an intragenic deletion of exons 12–31, accounting for 60% of FA chromosomes in 46 unrelated Afrikaner FA patients, while two other mutations accounted for an additional 20%. Screening for these mutations in the European populations ancestral to the Afrikaners detected one patient from the Western Ruhr region of Germany who was heterozygous for the major deletion. The mutation was associated with the same unique FANCA haplotype as in Afrikaner patients. Genealogical investigation of 12 Afrikaner families with FA revealed that all were descended from a French Huguenot couple who arrived at the Cape on June 5, 1688, whereas mutation analysis showed that the carriers of the major mutation were descendants of this same couple. The molecular and genealogical evidence is consistent with transmission of the major mutation to Western Germany and the Cape near the end of the 17th century, confirming the existence of a founder effect for FA in South Africa.

Rolling-circle transposons in eukaryotes

All eukaryotic DNA transposons reported so far belong to a single category of elements transposed by the so-called “cut-and-paste” mechanism. Here, we report a previously unknown category of eukaryotic DNA transposons, Helitron, which transpose by rolling-circle replication. Autonomous Helitrons encode a 5′-to-3′ DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. Helitron-like transposons have conservative 5′-TC and CTRR-3′ termini and do not have terminal inverted repeats. They contain 16- to 20-bp hairpins separated by 10–12 nucleotides from the 3′-end and transpose precisely between the 5′-A and T-3′, with no modifications of the AT target sites. Together with their multiple diverged nonautonomous descendants, Helitrons constitute ≈2% of both the Arabidopsis thaliana and Caenorhabditis elegans genomes and also colonize the Oriza sativa genome. Sequence conservation suggests that Helitrons continue to be transposed.

Postembryonic segregation of the germ line in sea urchins in relation to indirect development.

The four small micromeres of the sea urchin embryo contribute only to the coelomic sacs, which produce major components of the adult body plan during postembryonic development. To test the proposition that the small micromeres are the definitive primordial germ cell lineage of the sea urchin, we deleted their 4th cleavage parents, and raised the deleted embryos through larval life and metamorphosis to sexual maturity. Almost all of the experimental animals produced functional gametes, excluding the possibility that the germ cell lineage arises exclusively and obligatorily from descendants of the small micromeres; rather, the germ cell lineage arises during the postembryonic development of the rudiment. A survey of the literature indicates that there is no known case of an embryonic primordial germ cell lineage in a bilaterian species that displays maximal indirect development.

Pea formaldehyde-active class III alcohol dehydrogenase: common derivation of the plant and animal forms but not of the corresponding ethanol-active forms (classes I and P).

A plant class III alcohol dehydrogenase (or glutathione-dependent formaldehyde dehydrogenase) has been characterized. The enzyme is a typical class III member with enzymatic parameters and substrate specificity closely related to those of already established animal forms. Km values with the pea enzyme are 6.5 microM for NAD+, 2 microM for S-hydroxymethylglutathione, and 840 microM for octanol versus 9, 4, and 1200 microM, respectively, with the human enzyme. Structurally, the pea/human class III enzymes are closely related, exhibiting a residue identity of 69% and with only 3 of 23 residues differing among those often considered in substrate and coenzyme binding. In contrast, the corresponding ethanol-active enzymes, the long-known human liver and pea alcohol dehydrogenases, differ more (47% residue identities) and are also in functionally important active site segments, with 12 of the 23 positions exchanged, including no less than 7 at the usually much conserved coenzyme-binding segment. These differences affect functionally important residues that are often class-distinguishing, such as those at positions 48, 51, and 115, where the plant ethanol-active forms resemble class III (Thr, Tyr, and Arg, respectively) rather than the animal ethanol-active class I forms (typically Ser, His, and Asp, respectively). Calculations of phylogenetic trees support the conclusions from functional residues in subgrouping plant ethanol-active dehydrogenases and the animal ethanol-active enzymes (class I) as separate descendants from the class III line. It appears that the classical plant alcohol dehydrogenases (now called class P) have a duplicatory origin separate from that of the animal class I enzymes and therefore a paralogous relationship with functional convergence of their alcohol substrate specificity. Combined, the results establish the conserved nature of class III also in plants, and contribute to the molecular and functional understanding of alcohol dehydrogenases by defining two branches of plant enzymes into the system.

DNA sequences of Alu elements indicate a recent replacement of the human autosomal genetic complement.

DNA sequences of neutral nuclear autosomal loci, compared across diverse human populations, provide a previously untapped perspective into the mode and tempo of the emergence of modern humans and a critical comparison with published clonally inherited mitochondrial DNA and Y chromosome measurements of human diversity. We obtained over 55 kilobases of sequence from three autosomal loci encompassing Alu repeats for representatives of diverse human populations as well as orthologous sequences for other hominoid species at one of these loci. Nucleotide diversity was exceedingly low. Most individuals and populations were identical. Only a single nucleotide difference distinguished presumed ancestral alleles from descendants. These results differ from those expected if alleles from divergent archaic populations were maintained through multiregional continuity. The observed virtual lack of sequence polymorphism is the signature of a recent single origin for modern humans, with general replacement of archaic populations.

Restriction-modification systems as genomic parasites in competition for specific sequences.

Restriction-modification (RM) systems are believed to have evolved to protect cells from foreign DNA. However, this hypothesis may not be sufficient to explain the diversity and specificity in sequence recognition, as well as other properties, of these systems. We report that the EcoRI restriction endonuclease-modification methylase (rm) gene pair stabilizes plasmids that carry it and that this stabilization is blocked by an RM of the same sequence specificity (EcoRI or its isoschizomer, Rsr I) but not by an RM of a different specificity (PaeR7I) on another plasmid. The PaeR7I rm likewise stabilizes plasmids, unless an rm gene pair with identical sequence specificity is present. Our analysis supports the following model for stabilization and incompatibility: the descendants of cells that have lost an rm gene pair expose the recognition sites in their chromosomes to lethal attack by any remaining restriction enzymes unless modification by another RM system of the same specificity protects these sites. Competition for specific sequences among these selfish genes may have generated the great diversity and specificity in sequence recognition among RM systems. Such altruistic suicide strategies, similar to those found in virus-infected cells, may have allowed selfish RM systems to spread by effectively competing with other selfish genes.

O português de herança em território fronteiriço: a LH em Olivença como arma para preservação de um grupo minoritário

Esta pesquisa tem como objetivo investigar a língua portuguesa nativa e de herança sobreviventes em território fronteiriço de língua oficial espanhola. Como locus de pesquisa selecionamos Olivença, uma cidade da Espanha em que a língua portuguesa se faz em situações específicas de uso. A relevância desta pesquisa traduz-se no fato de que espaços fronteiriços mantêm sobrepostas em espaços geográficos contíguos algumas realidades que se sobrepõem: a realidade da oficialidade linguística e a realidade do sentimento de pertença sociolinguística. Nesta tese, partimos da identificação, em trabalho de campo, da presença da língua portuguesa no território atualmente espanhol (mas historicamente português) e na constatação de que há uma flutuação de identificação-identidade linguística. No espaço geográfico em que fizemos incursão científica, duas cidades sobrepõem-se historicamente e duas geografias políticas, por outro lado, avizinham-se e roçam-se continuamente. Ao tomar contato com essa cidade, hipotetizamos que o sentimento de pertença linguística estaria presente entre os falantes mais velhos, que manteriam a herança de traços lusitanos em sua comunicação, mesmo ao falar o espanhol. A justificativa é que, logo de chegada, já avistáramos recintos comerciais com nomes portugueses e, contrariamente, não ouvíamos o som lusitano nas ruas. Sabemos que o domínio espanhol numa cidade outrora portuguesa tenderia a apagar vestígios portugueses. No entanto, em grupos íntimos pressupúnhamos o português como língua corrente. Durante o trabalho de campo, identificamos fortes valores culturais sendo empunhados como armas de resistência entre descendentes de portugueses, fazendo correr numa velocidade acentuada a reorganização dos valores lusitanos em redutos da cidade espanhola. Essa força e essa velocidade pareciam ser as molas propulsoras de uma mudança linguística muito sorrateira, que impactava o sentimento de unidade de um segmento social da comunidade sociolinguística. Isso nos inspirou a dar um passo investigativo seguinte em direção aos mais jovens, que tinham o espanhol como língua materna, mas tinham o português como língua de herança. À pergunta central sobre a força do português como língua de herança buscamos respostas por meio de duas outras questões mais indiretas feitas aos sujeitos entrevistados: será que os mais jovens percebiam-se como portugueses? será que os elementos culturais lusitanos presentes nas ruas eram reconhecidos como vinculados à língua de herança? Foi assim que passamos a recolher pistas sobre os traços de resiliência do português como língua incrustada na região espanhola de Olivença.

Geologia econômica da região de Currais Novos - RN

O presente trabalho descreve a geologia econômica da região de Currais Novos, no Rio Grande do Norte, onde estão as principais jazidas de scheelita e de molibdenita do Brasil: jazidas Brejuí e Barra Verde. As rochas metamórficas da área pertencem à Série Ceará e são constituídas por gnaisses, calcários e tactitos. O autor evidenciou a existência de duas fases metamórficas no desenvolvimento dessas rochas. A primeira, datada de 750 \'+ OU -\' 50 M.A. possibilitou o desenvolvimento das texturas e dos minerais essenciais dos gnaisses e calcários e a formação dos tactitos compostos essencialmente de epidoto, diopsídio, granada, quartzo, calcita e vesuvianita. Ainda nessa fase ocorreu o empurrão das rochas da área oeste sôbre o gnaisse da Formação Seridó, ocasionando inversões de camadas nas áreas de Brejuí, Barra Verde, Quixabeiral, etc. Na segunda fase, com 550 \'+ OU -\' M.A. de idade, ocorreu microclinização dos gnaisses biotíticos das formações Parelhas e Quixaba e a mineralização dos tactitos, devido ao aporte de tungstênio, molibdênio, flúor, cobre, etc., provenientes do granito de Acari. Na etapa final dessa fase houve a intrusão do granodiorito Acauã. As rochas \"magmáticas da região estão representadas por: a) um grande batólito granítico heterogêneo - o maciço Acari -, constituído por quatro fácies petrográficas: um granodiorito pórfiro, um granito monzonítico, um diorito e pequenos corpos granodioriticos. b) um pequeno stock granodiorítico homogêneo e intrusivo - o. granodiorito Acauã. c) Diques de basaltos, aplitos e pegmatites. O minério da região é o tácito, que apresenta nítidos contrôles estratigráficos e estruturais, os quais servem de guias para a prospecção. Têm as jazidas Brejuí e Barra Verde um teor médio da ordem de 0,6% em \'W IND. O 3\' e 0,2% em Mo e uma espessura média de 2m. Nas outras ocorrências sua possança média é inferior a 1 m e o teor médio inferior a 0,5% em \'W IND. O 3\'. Sendo mantida a atual produção da região, cerca de 650 t métricas/ano de concentrados com 75% de \'W IND. O 3\', só as reservas conhecidas nas jazidas Brejuí e Barra Verde serão suficientes para abastecer o mercado por mais 20 anos

Caught in the act: gas and stellar velocity dispersions in a fast Quenching compact star-forming galaxy at z ~ 1.7

We present Keck I MOSFIRE spectroscopy in the Y and H bands of GDN-8231, a massive, compact, star-forming galaxy at a redshift of z ~ 1.7. Its spectrum reveals both Hα and [Nii] emission lines and strong Balmer absorption lines. The Hα and Spitzer MIPS 24 μm fluxes are both weak, thus indicating a low star-formation rate of SFR≲5-10 M_⨀ yr−1. This, added to a relatively young age of ~700 Myr measured from the absorption lines, provides the first direct evidence for a distant galaxy being caught in the act of rapidly shutting down its star formation. Such quenching allows GDN-8231 to become a compact, quiescent galaxy, similar to three other galaxies in our sample, by z ~ 1.5. Moreover, the color profile of GDN-8231 shows a bluer center, consistent with the predictions of recent simulations for an early phase of inside-out quenching. Its line-of-sight velocity dispersion for the gas, σ_LOG^gas = 127 ± 32 km s^−1, is nearly 40% smaller than that of its stars, σ_LOG^* = 215 ± 35 km s^−1. High-resolution hydro-simulations of galaxies explain such apparently colder gas kinematics of up to a factor of ~1.5 with rotating disks being viewed at different inclinations and/or centrally concentrated star-forming regions. A clear prediction is that their compact, quiescent descendants preserve some remnant rotation from their star-forming progenitors.

Da luta pela terra à territorialização quilombola: o caso da comunidade Porto Velho, Iporanga/SP

As mudanças nas formas de apropriação do espaço na região do Vale do Ribeira têm proporcionado metamorfoses da territorialidade de populações camponesas. É nessa conjuntura que a luta pela terra de trabalho ganha nova expressão: resistência e permanência no território ancestral por meio da construção da identidade quilombola. Portanto, a territorialização da comunidade remanescente de quilombo Porto Velho é analisada frente aos desafios e estratégias de resistência para permanecer no território ancestral. O histórico de origem deste bairro rural identifica estes sujeitos sociais como descendentes dos escravos que habitavam estas terras desde 1860. Todavia, entre as décadas de 1950 e 1980, houve um período importante de submissão e relações de trabalho precárias a fazendeiros e terceiros. No final dos anos 1980, os camponeses enfrentaram ameaças que culminaram em expropriações e expulsões de boa parte dos quilombolas do território. No contexto marcado pela emergência do conflito, o grupo negro se organiza e inicia a luta pela terra com apoio da Pastoral da Terra, MOAB e EAACONE. A pesquisa sobre a população remanescente de quilombo Porto Velho, situada no município de Iporanga (SP), refletiu a perspectiva geográfica de como estes sujeitos sociais constroem suas relações no território quilombola, sua organização comunitária e sociabilidade, e as transformações no âmbito material e imaterial. Trata-se de um estudo cuja metodologia é constituída por trabalhos de campo, entrevistas, pesquisa bibliográfica e documental. O estudo realizado identificou a complexidade do processo de transformação deste território quilombola na busca por autonomia e liberdade. Os impactos de novas demandas, justapostas sobre o território e sobre a vida destes sujeitos sociais, trouxeram a necessidade de criar e recriar estratégias para a conservação de costumes e de luta pela terra e permanência no território que habitam há gerações. Entende-se que neste processo de conflitos por terra, a lógica imposta pelo capital não só provocou forte transformação no território ancestral, como ofereceu situação de risco social e cultural à própria sobrevivência da comunidade quilombola.

Looking Back: A Granddaughter's Quest for Redemption and Understanding

On December 7th, 1941 Japan attacked Pearl Harbor in Hawaii. This event signaled the beginning of America's involvement in World War II. It also signaled the beginning of a change of life for the Japanese living in the United States. Following the attack, 120,000 persons of Japanese ancestry were placed in ten internment camps across the United States. Two-thirds of those interned were American citizens, including my grandmother. The fact that these American citizens were treated as prisoners in their own country had a devastating effect on the relationships of those interned and the generations of Japanese Americans that followed. This essay recounts my grandma's experience and explores how her internment changed her life and the lives of her descendants.

Proline and pyrrolidine derivatives: new drug cadidates for hepatitis C treatment

The more advantageous hepatitis C virus (HCV) inhibitors (most of them incorporating polysubstituted prolines or pyrrolidines) are detailed in this paper. The improvement of current treatments by combination of antiviral drugs is the driving force of this race to reduce the fast proliferation of this virus. The enhancement of efficiency in short periods of treatment is crucial in the economical point of view and for the hope of all infected people. New protease or polymerase inhibitors have been recently developed in order to substitute the traditional highly toxic PEG-interferon α-2b/ribavirin tandem. The contribution of our group in this field concerns the elaboration of the first and second generation GSK polymerase inhibitors through enantioselective processes based on silver(I)- and gold(I)-catalyzed 1,3-dipolar cycloadditions of azomethine ylides.

On the nature of the galactic early-B hypergiants

Aims. Despite their importance to a number of astrophysical fields, the lifecycles of very massive stars are still poorly defined. In order to address this shortcoming, we present a detailed quantitative study of the physical properties of four early-B hypergiants (BHGs) of spectral type B1-4 Ia+; Cyg OB2 #12, ζ1 Sco, HD 190603 and BP Cru. These are combined with an analysis of their long-term spectroscopic and photometric behaviour in order to determine their evolutionary status. Methods. Quantitative analysis of UV–radio photometric and spectroscopic datasets was undertaken with a non-LTE model atmosphere code in order to derive physical parameters for comparison with apparently closely related objects, such as B supergiants (BSGs) and luminous blue variables (LBVs), and theoretical evolutionary predictions. Results. The long-term photospheric and spectroscopic datasets compiled for the early-B HGs revealed that they are remarkably stable over long periods ( ≥ 40 yrs), with the possible exception of ζ1 Sco prior to the 20th century; in contrast to the typical excursions that characterise LBVs. Quantitative analysis of ζ1 Sco, HD 190603 and BP Cru yielded physical properties intermediate between BSGs and LBVs; we therefore suggest that BHGs are the immediate descendants and progenitors (respectively) of such stars, for initial masses in the range ~30−60 M⊙. Comparison of the properties of ζ1 Sco with the stellar population of its host cluster/association NGC 6231/Sco OB1 provides further support for such an evolutionary scenario. In contrast, while the wind properties of Cyg OB2 #12 are consistent with this hypothesis, the combination of extreme luminosity and spectroscopic mass (~110 M⊙) and comparatively low temperature means it cannot be accommodated in such a scheme. Likewise, despite its co-location with several LBVs above the Humphreys-Davidson (HD) limit, the lack of long term variability and its unevolved chemistry apparently excludes such an identification. Since such massive stars are not expected to evolve to such cool temperatures, instead traversing an O4-6Ia → O4-6Ia+ → WN7-9ha pathway, the properties of Cyg OB2 #12 are therefore difficult to understand under current evolutionary paradigms. Finally, we note that as with AG Car in its cool phase, despite exceeding the HD limit, the properties of Cyg OB2 #12 imply that it lies below the Eddington limit – thus we conclude that the HD limit does not define a region of the HR diagram inherently inimical to the presence of massive stars.

College Book 6, 1726-1790

College Book 6 is often referred to as the Hollis book, reflecting its contents. It was created following an April 4, 1726 Corporation vote that "Mr. Treasurer procure a Book, into which shall be transmitted, and a Register kept of, Mr Hollis's Rules, orders, Gifts & Bounties past & to come; together with ye Names & age, & Charecter of his Scholars, ye time of their Entry and Dismission; and also all ye Votes of ye Overseers & Corporation from time to time relating to ye said orders, Bounties & Scholars of the said Mr Hollis." Entries are primarily in Benjamin Wadsworth's hand and record donations from Thomas Hollis and his descendants, with transcriptions of related Corporation minutes. They also provide detailed information about the allocation of Hollis funds and scholarships, and the rules governing the Hollis Professorship of Divinity (established in 1721) and the Hollis Professorship of Mathematics and Natural Philosophy (established in 1727). The volume also contains inventories of books in the official library of the Hollis Professor of Divinity and two inventories – created in 1779 and in 1790 – of the mathematical and philosophical apparatus purchased with Hollis funds. Many entries related to the purchase of scientific instruments and supplies include the cost in sterling of each item. Also included are entries related to financial accounts and expenditures, as well as copies of letters from Nathaniel Hollis.