Were bowerbirds part of the New Zealand fauna?

Bowerbirds (Ptilonorhynchidae) have previously been considered to be confined to the Australo-Papuan continental plate. We provide molecular evidence that the extinct New Zealand Piopio Turnagra capensis is, in fact, a bowerbird. Such a finding is surprising on biogeographical grounds. However, recent molecular evidence on the relationships of the New Zealand moas and kiwis with the Australo-Papuan flightless birds suggests the need for a reassessment of current views on the origins of New Zealand's fauna.

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

Variabilidade populacional em manguezais: análises moleculares e morfológicas em caranguejos Brachyura (Crustacea: Decapoda)

A análise da estruturação populacional de espécies codistribuídas permite a comparação de padrões de estruturação, fornecendo informações acerca dos fatores que influenciam a diferenciação em espécies pertencentes ao mesmo ecossistema. Este projeto teve como objetivo principal analisar a variabilidade intraespecífica em caranguejos habitantes de manguezais, codistribuídos ao longo do Oceano Atlântico Ocidental, por meio de ferramentas moleculares e morfológicas, visando testar a hipótese de elevada estruturação populacional em manguezais. Para este fim, cinco espécies foram utilizadas como modelo (Aratus pisonii, Goniopsis cruentata, Sesarma rectum, Uca thayeri e Ucides cordatus) e avaliadas por meio de marcadores mitocondriais COI e 16S e nuclear H3 e análises morfológicas comparativas e de morfometria. Os dados moleculares revelaram dois padrões, indicando elevada estruturação populacional para as espécies A. pisonii e U. thayeri e ausência de estruturação para G. cruentata, S. rectum e U. cordatus. Os dados morfológicos, no entanto, não acompanham esses padrões, já que não foram encontradas diferenças morfológicas ou morfométricas associadas aos grupos evidenciados pelas análises moleculares. A ausência de fluxo gênico entre regiões para algumas espécies deve-se, muito provavelmente, à existência de fatores que não se limitam ao isolamento por distância, mas também devido a diferenças na duração do estágio larval e a diferenças bruscas em alguns fatores abióticos, como a salinidade, por exemplo, que, associados às diferentes características do desenvolvimento larval de cada espécie, culminam na existência de estruturas populacionais diferentes. Além disso, os padrões de diferenciação genética observados concordam com os cenários biogeográficos propostos para o Atlântico Ocidental, no qual mudanças e flutuações geológicas, climáticas e oceanográficas, resultantes do fechamento do Istmo do Panamá e de ciclos glaciais na América do Norte, promoveram divergência genética.

Obesidade e genes candidatos: estudo de associação em populações quilombolas do Vale do Ribeira-SP

A obesidade comum é atualmente um dos problemas de saúde pública mais importante no mundo, frequentemente associada a outros distúrbios tais como hipertensão, diabetes, doenças cardiovasculares e câncer. Apesar da alta prevalência de obesidade em diversas populações, muitos dos estudos relacionados aos seus fatores de risco genéticos foram realizados com indivíduos de ascendência europeia ou asiática, mas foram poucos os realizados com populações de origem africana ou nativas americanas. Nosso trabalho tem por objetivo geral investigar potenciais fatores de risco genéticos associados ao sobrepeso e à obesidade em populações afrodescendentes remanescentes de quilombos do Vale do Ribeira - SP, comunidades rurais semi-isoladas, previamente bem caracterizadas do ponto de vista clínico, genealógico e genético-populacional. Nossa amostra constituiu-se de 759 indivíduos, pertencentes a doze populações de remanescentes de quilombos (Abobral, São Pedro, Galvão, Ivaporunduva, Pedro Cubas, André Lopes, Nhunguara, Sapatu, Pilões, Maria Rosa, Poça e Reginaldo), dos quais foram obtidos amostras de DNA, dados clínicos, informações genealógicas e medidas antropométricas. A investigação dos fatores de risco genéticos associados ao sobrepeso/obesidade foi realizada por duas abordagens: (1) estudo de associação baseado em famílias (N = 584, 59 famílias) e (2) estudo de associação populacional com indivíduos não aparentados (N=305). Foram selecionados para estudo nove polimorfismos em oito genes candidatos: LEP rs2167270, LEPR rs1137101, ADRB2 rs1042713, PPARG rs1801282, PLIN1 rs2289487, RETN rs1862513, INSIG2 rs7566605, FTO rs1121980 e FTO rs1421085. As análises de associação baseadas em família indicaram que, nessas populações, apenas o polimorfismo PLIN1 rs2289487 está associado significativamente com o grupo de risco em relação à razão cintura-quadril (RCQ >=0,85 para mulheres e >=0,90 para homens; P=0,013). Aparentemente não existem trabalhos anteriores que verificaram a associação deste polimorfismo com a obesidade por essa metodologia. As análises do estudo populacional com indivíduos não aparentados mostraram associação significativa entre: (i) o alelo G no polimorfismo LEPR rs1137101 e a variação do índice de massa corporal (IMC; P=0,027); (ii) o alelo G do polimorfismo LEPR rs1137101 e o fenótipo de sobrepeso/obesidade (IMC>=25 Kg/m²; P=0,027); (iii) o alelo G no polimorfismo ADRB2 rs1042713 e o fenótipo de risco (IMC>=25 Kg/m²; P=0,029); (iv) o polimorfismo PLIN1 rs2289487 (genótipo GG) e os menores valores do IMC (P=0,025); (v) o polimorfismo FTO rs1121980 (alelo G) e o fenótipo de risco (IMC>=25 Kg/m²), assim como a variação do IMC (P=0,037 e P=0,022 respectivamente); e (vi) o alelo A no polimorfismo FTO rs1421085 e maiores valores da circunferência da cintura (Cc; P=0,016) e da razão cintura-quadril (RCQ; P=0,030). Tomados em conjunto, nossos resultados sugerem a participação dos genes LEP, LEPR, ADRB2, PLIN1 e FTO no aumento da predisposição ao sobrepeso e à obesidade nas populações remanescentes de quilombos. Por fim, as elevadas estimativas de herdabilidade dos três fenótipos investigados (IMC=33%, Cc=33% e RCQ=70%) reforçam a relevância do papel dos fatores genéticos no acúmulo de gordura corporal. O trabalho apresentado é resultado de uma investigação cuidadosa sobre os componentes genéticos associados à regulação do peso corporal em uma população brasileira afrodescendente (com características históricas, ambientais e genéticas peculiares), corroborando a hipótese de que a obesidade comum nas populações quilombolas do Vale do Ribeira é condicionada por um mecanismo poligênico modulado por fatores ambientais importantes como o sedentarismo e a transição nutricional

Maragogipinho - as vozes do barro: práxis educativa em culturas populares

Este trabalho apresenta uma observação acurada do universo da cerâmica no povoado de Maragogipinho, Bahia. A pesquisa revela quem são os mestres e mestras do barro, dá a conhecer o seu processo criativo e educativo. Esses homens e mulheres são protagonistas do patrimônio cultural imaterial brasileiro, eles detêm e socializam conhecimentos que perpassam gerações, saberes tecidos em práticas de ensino não sistematizadas e nem legitimadas pelas culturas hegemônicas. A educação artesanal está fundada na ancestralidade, na repetição e na invenção, no constante diálogo entre a tradição e a emergência da modernidade: novas formas de criação e antigos segredos de ofício se misturam, numa tensão permanente entre transformação e conservação. O artesão e a artesã vivem o seu legado cultural e o mantêm vivo, reinventando-o e atualizando-o eternamente. Essa herança conserva a conexão com o passado, mas se reveste de novos símbolos e significados no presente para fortalecer a identidade dos autores e de suas comunidades, e para dar sentido ao futuro.

Brewing Behind Barbed Wire: An Archaeology of Saké at Amache

After the Japanese attack at Pearl Harbor on December 7, 1941, approximately 120,000 people of Japanese ancestry living on the west coast of the United States were forcibly removed from their home communities. These people were designated as "evacuees" by the U.S. Government and were incarcerated within a network of federal government facilities the largest of which were internment centers operated by the War Relocation Authority that held mostly U.S. citizens. The Granada Relocation Center (Amache) was the smallest of these internment centers. The presence of saké at Amache indicates that Japanese Americans continued important practices of daily life despite restrictions under confinement. This thesis investigates the practices of saké production and consumption at Amache and examines the importance of these practices in Japanese American daily life. In order to understand these practices, this research draws on multiple lines of evidence. This includes investigations of an assemblage of the material culture associated with saké, research into the history and methods of production and consumption, collection of oral histories, review of archival data, and the application of practice theory. These data provide insight into practices that are not well understood by researchers of Japanese American internment due to their illicit nature. This research endeavors to characterize how saké was produced and used at Amache and provides a way to understand how cultural practices maintain aspects of everyday life in ways that may have little to do with intentional resistance.

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.

An ethnopharmacological and historical analysis of “Dictamnus”, a European traditional herbal medicine

Ethnopharmacological relevance and background: “Dictamnus” was a popular name for a group of medicinal herbaceous plant species of the Rutaceae and Lamiaceae, which since the 4th century have been used for gynaecological problems and other illnesses BCE and still appear in numerous ethnobotanical records. Aims: This research has as four overarching aims: Determining the historical evolution of medical preparations labelled “Dictamnus” and the different factors affecting this long-standing herbal tradition. Deciphering and differentiating those medicinal uses of “Dictamnus” which strictly correspond to Dictamnus (Rutaceae), from those of Origanum dictamnus and other Lamiaceae species. Quantitatively assessing the dependence from herbal books, and pharmaceutical tradition, of modern Dictamnus ethnobotanical records. Determining whether differences between Western and Eastern Europe exist with regards to the Dictamnus albus uses in ethnopharmacology and ethnomedicine. Methods: An exhaustive review of herbals, classical pharmacopoeias, ethnobotanical and ethnopharmacological literature was conducted. Systematic analysis of uses reported which were standardized according to International Classification of Diseases – 10 and multivariate analysis using factorial, hierarchical and neighbour joining methods was undertaken. Results and discussion: The popular concept “Dictamnus” includes Origanum dictamnus L., Ballota pseudodictamnus (L.) Benth. and B. acetabulosa (L.) Benth. (Lamiaceae), as well as Dictamnus albus L. and D. hispanicus Webb ex Willk. (Rutaceae), with 86 different types of uses. Between 1000 and 1700 CE numerous complex preparations with “Dictamnus” were used in the treatment of 35 different pathologies. On biogeographical grounds the widespread D. albus is a far more likely prototypical “Dictamnus” than the Cretan endemic Origanum dictamnus. However both form integral parts of the “Dictamnus” complex. Evidence exists for a sufficiently long and coherent tradition for D. albus and D. hispanicus, use to treat 47 different categories of diseases. Conclusions: This approach is a model for understanding the cultural history of plants and their role as resources for health care. “Dictamnus” shows how transmission of traditional knowledge about materia medica, over 26 centuries, represents remarkable levels of development and innovation. All this lead us to call attention to D. albus and D. hispanicus which are highly promising as potential herbal drug leads. The next steps of research should be to systematically analyse phytochemical, pharmacological and clinical evidence and to develop safety, pharmacology and toxicology profiles of the traditional preparations.

Ethnogenesis and Craniofacial Change in Japan from the Perspective of Nonmetric Traits

To examine population affinities in light of the ‘dual structure model’, frequencies of 21 nonmetric cranial traits were analyzed in 17 prehistoric to recent samples from Japan and five from continental northeast Asia. Eight bivariate plots, each representing a different bone or region of the skull, as well as cluster analysis of 21-trait mean measures of divergence using multidimensional scaling and additive tree techniques, revealed good discrimination between the Jomon-Ainu indigenous lineage and that of the immigrants who arrived from continental Asia after 300 BC. In Hokkaido, in agreement with historical records, Ainu villages of Hidaka province were least, and those close to the Japan Sea coast were most, hybridized with Wajin. In the central islands, clines were identified among Wajin skeletal samples whereby those from Kyushu most resembled continental northeast Asians, while those from the northernmost prefectures of Tohoku apparently retained the strongest indigenous heritage. In the more southerly prefectures of Tohoku, stronger traces of Jomon ancestry prevailed in the cohort born during the latest Edo period than in the one born after 1870. Thus, it seems that increased inter-regional mobility and gene flow following the Meiji Restoration initiated the most recent episode in the long process of demic diffusion that has helped to shape craniofacial change in Japan.

Community dynamics of stabilized dune xerophytic shrubs

Tese de doutoramento, Biologia (Ecologia), Universidade de Lisboa, Faculdade de Ciências, 2016

Análise genética com Y-SNPs de subgrupos populacionais residentes no Sul de Portugal

Tese de mestrado, Medicina Legal e Ciências Forenses, Universidade de Lisboa, Faculdade de Medicina, 2016

Genetic association of CD247 (CD3ζ) with SLE in a large-scale multiethnic study

A classic T-cell phenotype in systemic lupus erythematosus (SLE) is the downregulation and replacement of the CD3ζ chain that alters T-cell receptor signaling. However, genetic associations with SLE in the human CD247 locus that encodes CD3ζ are not well established and require replication in independent cohorts. Our aim was therefore to examine, localize and validate CD247-SLE association in a large multiethnic population. We typed 44 contiguous CD247 single-nucleotide polymorphisms (SNPs) in 8922 SLE patients and 8077 controls from four ethnically distinct populations. The strongest associations were found in the Asian population (11 SNPs in intron 1, 4.99 × 10(-4) < P < 4.15 × 10(-2)), where we further identified a five-marker haplotype (rs12141731-rs2949655-rs16859085-rs12144621-rs858554; G-G-A-G-A; P(hap) = 2.12 × 10(-5)) that exceeded the most associated single SNP rs858554 (minor allele frequency in controls = 13%; P = 4.99 × 10(-4), odds ratio = 1.32) in significance. Imputation and subsequent association analysis showed evidence of association (P < 0.05) at 27 additional SNPs within intron 1. Cross-ethnic meta-analysis, assuming an additive genetic model adjusted for population proportions, showed five SNPs with significant P-values (1.40 × 10(-3) < P< 3.97 × 10(-2)), with one (rs704848) remaining significant after Bonferroni correction (P(meta) = 2.66 × 10(-2)). Our study independently confirms and extends the association of SLE with CD247, which is shared by various autoimmune disorders and supports a common T-cell-mediated mechanism.

Drivers of multi-scale plant community structure in agricultural field margins of South Korea

This data set describes the distribution of a total of 90 plant species growing on field margins of an agricultural landscape in the Haean-myun catchment in South Korea. We conducted our survey between July and August 2011 in 100 sampling plots, covering the whole catchment. In each plot we measured three environmental variables: slope, width of the field margin, and management type (i.e. "managed" for field margins that had signs of management activities from the ongoing season such as cutting or spraying herbicides and "unmanaged" for field margins that had been left untouched in the season). For the botanical survey each plot was sampled using three subplots of one square meter per subplot; subplots were 4 m apart from each other. In each subplot, we estimated three different vegetation characteristics: vegetation cover (i.e. the percentage of ground covered by vegetation), species richness (i.e. the number of observed species) and species abundance (i.e. the number of observed individuals / species). We calculated the percentage of the non-farmed habitats by creating buffer zones of 100, 200, 300, 400 and 500 m radii around each plot using data provided by (Seo et al. 2014). Non-farmed habitats included field margins, fallows, forest, riparian areas, pasture and grassland.

Alkenones and SST of surface sediments (Appendix)

We have analysed alkenones in 149 surface sediments from the eastern South Atlantic in order to establish a sediment-based calibration of the U37K' paleotemperature index. Our study covers the major tropical to subpolar production systems and sea-surface temperatures (SST's) between 0° and 27°C. In order to define the most suitable calibration for this region, the U37K' values were correlated to seasonal, annual, and production-weighted annual mean atlas temperatures and compared to previously published culture and core-top calibrations. The best linear correlation between U37K' and SST was obtained using annual mean SST from 0 to 10 m water depth (U37K' = 0.033 T + 0.069, r**2 = 0.981). Data scattering increased significantly using temperatures of waters deeper than 20 m, suggesting that U37K' reflects mixed-layer SST and that alkenone production at thermocline depths was not high enough to significantly bias the mixed-layer signal. Regressions based on both production-weighted and on actual annual mean atlas SST were virtually identical, indicating that regional variations in the seasonality of primary production have no discernible effect on the U37K' vs. SST relationship. Comparison with published core-top calibrations from other oceanic regions revealed a high degree of accordance. We, therefore, established a global core-top calibration using U37K' data from 370 sites between 60°S and 60°N in the Atlantic, Indian, and Pacific Oceans and annual mean atlas SST (0-29°C) from 0 m water depth. The resulting relationship (U37K' = 0.033 T + 0.044, r**2 = 958) is identical within error limits to the widely used E. huxleyi calibrations of and attesting their general applicability. The observation that core-top calibrations extending over various biogeographical coccolithophorid zones are strongly linear and in better accordance than culture calibrations suggests that U37K' is less species-dependent than is indicated by culture experiments. The results also suggest that variations in growth rate of algae and nutrient availability do not significantly affect the sedimentary record of U37K' in open ocean environments.