The Mesoamerican Corpus of Formative Period Art and Writing

This project explores the origins and development of the first writing in the New World by constructing a comprehensive database of Formative period, 1500-400 BCE, iconography and a suite of database-driven digital tools. In collaboration with two of the largest repositories of Formative period Mesoamerican art in Mexico, the project integrates the work of archaeologists, art historians, and scientific computing specialists to plan and begin the production of a database, digital assets, and visual search software that permit the visualization of spatial, chronological, and contextual relationships among iconographic and archaeological datasets. These resources will eventually support mobile and web based applications that allow for the search, comparison, and analysis of a corpus of material currently only partially documented. The start-up phase will generate a functional prototype database, project website, wireframe user interfaces, and a report summarizing project development

Conservation genomics: speciation of the Neotropical damselfly species Megaloprepus caerulatus – as a model for insect speciation in tropical rainforests

The work presented in this thesis is located at the interface between ecology, evolution and developmental biology. It addresses theories and questions in population biology, phylogeography and speciation as well as methodological approaches for applying Next Generation Sequencing (NGS) data. In the center of this thesis stands the world’s largest extant damselfly, Megaloprepus caerulatus, as a model system for primary rainforests

História evolutiva das árvores de cuia (Crescentia cujete): uma integração entre genótipo, ambiente e cultura

Amazonia is a center of plant domestication, where high linguistic diversity, different artistic styles and subsistence strategies also developed. The role of humans in the geographical distribution of Amazonian biodiversity, and the different pressures they exerted in the life history of organisms are debated. The historical analyses of the use of a plant across its geographical distribution contributes to this debate, since it aims to identify the morphological and genetic modifications promoted by human activity, identify areas of biological and cultural diversity, as well as understand the factors that influence the dynamics of the use and management of plant varieties. In this context, the general objective of this thesis was to contribute to the reconstruction of the domestication history, dispersal and diversification of treegourds (Crescentia cujete, Bignoniaceae) in Brazilian Amazonia. The fruits (cuia) have symbolic and technological values for different native peoples across the Neotropics, and therefore, are good examples for the integration of the social and cultural aspects of the biology of domestication. From a genomic library of C. cujete, molecular markers were developed, which were the basis to analyze the genetic relationship between C. cujete and C. amazonica in the Amazon Basin and test Gentry’s (1980) and Ducke’s (1946) hypotheses about the origin of domestication and morphological diversification of treegourd fruits. The evaluation of how people perceive, use and propagate fruits of both species integrated with genetic, morphological and ethnobotanical analyses between Amazonia and Mesoamerica allowed discussion of alternative hypothesis of the origin of domestication, infer routes of the plant dispersal, and identify cultural and ecological factors of selection and diversification. The results showed that hybridization is important for the phenotypic diversity of the fruit. Local varieties (maracá, cuiupi, paranã) are intimately associated with gene flow between homegardens and flooded forests, and their specific uses suggest that management of hybridization is an ancient practice in Amazonia. It was demonstrated that domesticated C. cujete was introduced into the Amazon Basin and into Mexico, but its geographical origin of domestication remains unknown. The pattern of genetic diversification between Western and Eastern Amazonia allowed inferences of two routes of introduction. These agree with routes previously proposed for human groups and their plants. Mesoamerica and Amazonia have contrasting fruit morphological diversity, which suggests different cultural preferences along treegourd’s dispersal routes. Even after the demographic collapse of human populations and their plants caused by European conquest, fruit shapes and fruit sizes manipulated by modern Native Amazonians and riverine families are legacies of the pre-Columbian occupation in Amazonia.Amazônia é um centro de domesticação de plantas, onde também se desenvolveu alta diversidade linguística, diferentes estilos artísticos e estratégias de subsistência. O papel dos humanos na distribuição geográfica da biodiversidade amazônica e as diferentes pressões que exercem na história de vida dos organismos tem sido amplamente debatido. A análise histórica do uso de uma planta ao longo de sua distribuição geográfica contribui com este debate, uma vez que busca identificar as modificações morfológicas e genéticas promovidas pelas atividades humanas, identificar áreas de diversidade biológica e cultural, bem como entender os fatores que influenciam o dinamismo no uso e manejo de suas variedades. Nesta perspectiva, o objetivo geral da presente tese foi contribuir com a reconstrução da história de domesticação, dispersão e diversificação das cuieiras (Crescentia cujete, Bignoniaceae) na Amazônia brasileira. Os frutos (cuias) possuem valores simbólicos e tecnológicos entre diferentes povos nativos da região Neotropical e, portanto, podem ser bons exemplos para integrar aspectos sociais e culturais à biologia da domesticação. A partir do desenvolvimento de uma biblioteca genômica de C. cujete, foram desenvolvidos marcadores moleculares, os quais serviram de base para avaliar a relação genética entre C. cujete e C. amazonica na Bacia Amazônica e testar as hipóteses de Gentry (1980) e Ducke (1946) sobre a origem da domesticação e diversificação morfológica dos frutos. A avaliação de como as pessoas percebem, usam e propagam os frutos de ambas as espécies na Amazônia e a integração de análises genéticas, morfológicas e etnobotânicas entre Amazônia e Mesoamérica possibilitou discutir hipóteses alternativas de origem da domesticação, inferir rotas de dispersão da planta e identificar fatores culturais e ecológicos de seleção e diversificação. Os resultados mostraram que hibridização é importante na diversificação fenotípica da planta. Variedades locais (maracá, cuiupi, paranã) estão intimamente associadas ao fluxo gênico entre quintais e florestas alagáveis, e seus usos específicos sugerem que o manejo da hibridização é uma prática antiga na Amazônia. Foi demonstrado que C. cujete foi introduzida na Bacia Amazônica e no México, mas sua origem geográfica permanece desconhecida. O padrão de diversificação genética entre Leste e Oeste na Bacia Amazônica permitiu inferir duas rotas de introdução na Amazônia. A dispersão concorda com rotas anteriormente propostas para grupos humanos e suas plantas. Mesoamérica e Amazônia são contrastantes em termos da diversidade morfológica de frutos cultivados de C. cujete. A diversidade e distribuição do formato dos frutos revelam que, apesar do amplo uso utilitário dos frutos, existiram diferentes preferências culturais ao longo da distribuição da planta. Mesmo após o colapso demográfico de populações humanas e suas plantas causado pela conquista europeia, os formatos e tamanhos de frutos manipulados atualmente pelos povos indígenas e famílias ribeirinhas são legados da ocupação pré-colombiana na Amazônia

Moniliophthora perniciosa genome: assembly and annotation of mitochondrion and development of a semi-automatic system of genes annotation

Orientador: Gonçalo Amarante Guimarães PereiraTese (doutorado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: O genoma mitocondrial (mtDNA) do fungo Moniliophthora perniciosa foi completamente seqüenciado e contém 109103 pb, com 31% de bases GC, porcentagem menor que a encontrada nas seqüências do genoma nuclear (47%). É o maior genoma mitocondrial de fungos descrito até o momento, e seu tamanho é conseqüência de grande espaço intergênico, que contém diversas ORFs com possibilidade de serem confirmadas como novos genes. Análises computacionais indicam a presença de variação no número de mtDNAs/célula nas diferentes bibliotecas, com tendência significativa de menor número de mtDNAs/célula no grupo de bibliotecas proveniente de culturas submetidas a repetidas repicagens. A maioria dos genes típicos (atp6, atp9, nad1-6, nad4L, cox1-3, cob, sendo a exceção o atp8), todos os rRNAS, tRNAS (foi encontrado pelo menos um para cada aminoácido) e genes das ORFs intrônicas estão orientados no sentido horário. Foram identificados também um gene rps3 e um grupo de ORFs com características semelhantes às dos genes típicos. Surpreendentemente o mtDNA apresenta uma região ocupada por uma estrutura de invertron característica de plasmídeos kalilo-like, integrado de maneira estável ao genoma em todas as variedades do biótipo C, e presente nos demais biótipos testados. Esta seqüência está disponível no GenBank através do número de acesso: AY376688. A outra linha de trabalho foi desenvolvida juntamente com outros bioinformatas do Laboratório de Genômica e Expressão. Foram desenvolvidas ferramentas de mineração e anotação de genes para projetos genoma, sendo os maiores destaques o Gene Projects, que permite mineração e anotação de genes durante o processo de seqüenciamento, e a nova interface de anotação, desenvolvida para otimizar a qualidade e a eficiência da anotação de genesAbstract: The mitochondrial genome (mtDNA) of the fungus Moniliophthora perniciosa was completely sequenced and it contains 109103 bases pair, with 31% of bases GC, smaller percentage than found in the sequences of the nuclear genome (47%). It is the largest mitochondrial genome of fungus described to the moment, and its size is consequence of great intergenic space, with several ORFs who can be confirmed as new genes. Computational analyses show the presence of variation in the number of mtDNAs / cell in different libraries, with significant tendency of smaller mtDNAs / cell number in group of libraries originating from cultures undergoes to repeatedly reply. Most of the typical genes (atp6, atp9, nad1-6, nad4L, cox1-3, cob, being the exception the atp8), all of the rRNAS, tRNAS (it was found at least one for each amino acid) and genes of the intronic ORFs are guided in the hourly sense. Surprisingly the mtDNA presents one region occupied for a structure of invertron, characteristic of plasmids kalilo-like, integrated in stable way to the genome in all of the varieties of the biotype C, and present in other tested biotypes. This sequence is available in the GenBank through the accession number: AY376688. The other work line was developed together with other bioinformatics of the Genomic and Expression Laboratory. Data mining and annotation of genes tools were developed for projects genome, being the largest prominences the Gene Projects, that allows mining and annotation of genes during the sequencing process, and the new annotation interface, developed to optimize the quality and the efficiency of the annotation of genesDoutoradoBioquimicaDoutor em Biologia Funcional e Molecula

Before Kukulkán

This volume illuminates human lifeways in the northern Maya lowlands prior to the rise of Chichén Itzá. This period and area have been poorly understood on their own terms, obscured by scholarly focus on the central lowland Maya kingdoms. "Before Kukulkán" is anchored in three decades of interdisciplinary research at the Classic Maya capital of Yaxuná, located at a contentious crossroads of the northern Maya lowlands. Using bioarchaeology, mortuary archaeology, and culturally sensitive mainstream archaeology, the authors create an in-depth regional understanding while also laying out broader ways of learning about the Maya past. Part 1 examines ancient lifeways among the Maya at Yaxuná, while part 2 explores different meanings of dying and cycling at the settlement and beyond: ancestral practices, royal entombment and desecration, and human sacrifice. The authors close with a discussion of the last years of occupation at Yaxuná and the role of Chichén Itzá in the abandonment of this urban center. "Before Kukulkán" provides a cohesive synthesis of the evolving roles and collective identities of locals and foreigners at the settlement and their involvement in the region’s trajectory. Theoretically informed and contextualized discussions offer unique glimpses of everyday life and death in the socially fluid Maya city. These findings, in conjunction with other documented series of skeletal remains from this region, provide a nuanced picture of the social and biocultural dynamics that operated successfully for centuries before the arrival of the Itzá

Investigating the potential causes of Mesoamerican Nephropathy (MeN)

Mesoamerican Nephropathy (MeN) has emerged as a major public health concern in Central America. MeN is not associated with traditional chronic kidney disease (CKD) risk factors, and the cause remains unknown. Our aim was to bring together evidence for and against potential causes of MeN. We used biosamples collected from 350 initially apparently healthy men and women aged 18-30 years from a population at risk of MeN to: (i) explore potential early biomarkers of kidney dysfunction, and (ii) quantify associations between possible nephrotoxins and change in renal function over a 2-year follow-up period. We quantified a range of serum and urinary markers of renal injury. Twelve metals and metalloids were analysed by inductively-coupled plasma-mass spectrometry. Twelve pesticides, their metabolites and two mycotoxins were analysed by liquid chromatography coupled to mass spectrometry. Differences in the creatinine-corrected urinary and serum concentrations of the measured exposures were examined between participants in different kidney function decline groups. Furthermore, the effect of heat and elevated fructose individually and in combination was assessed in vitro. The levels of urinary RBP, NGAL and serum UA were significantly elevated in the established kidney dysfunction group but did not help identify those with a normal baseline but declining function. Elevated levels of aluminium and total arsenic were observed across the population but no differences were identified between the different groups. Finally, in vitro experiments showed that heat stress suppressed the mRNA expression of MCP-1 but caused an early increase in expression of fibrogenic genes. Elevated fructose led to early mRNA increase in MCP-1, KIM-1, TGF-β, COLA1 and KIM-1 secretion. However, a number of these molecules were suppressed after longer term exposure. These findings provide evidence against the xenobiotic hypothesis investigated in this thesis as the primary cause(s) of MeN in Nicaragua. Future research priorities include examining alternative toxins not included in the present study and identification of more accurate biomarkers for the early detection of MeN

Genoma de Moniliophthora perniciosa: montagem e anotação da mitocôndria e desenvolvimento de sistema de anotação semi-automática de genes.

Tese (Doutorado) - Universidade Estadual de Campinas, Instituto de Biologia, Campinas, SP

Étude phylogéographique pancanadienne du sapin baumier (Abies balsamea [L.] Mill.) et de ses relations avec le sapin subalpin (Abies lasiocarpa [Hook] Nutt.) dans l’ouest du Canada

La structure phylogéographique et l’histoire postglaciaire du sapin baumier (Abies balsamea), ont été étudiées en utilisant l’ADN mitochondrial (ADNmt) et l’ADN chloroplastique (ADNcp). La différenciation génétique entre populations est ainsi apparue importante pour l’ADNmt (dispersé par les graines) et pour l’ADNcp (dispersé par le pollen puis par les graines), impliquant donc un flux de gènes par le pollen plus restreint chez le sapin baumier que celui habituellement observé chez d’autres conifères boréaux. Cette faible dispersion du pollen est supposée due aux propriétés structurales et la faible production de pollen, mais aussi à la récurrence des épidémies de tordeuse du bourgeon de l’épinette limitant les efforts reproductifs du sapin baumier. Par ailleurs, les polymorphismes de l’ADNmt et de l’ADNcp sont apparus géographiquement structurés, mettant en évidence une concordance incomplète d’au moins cinq lignées chloroplastiques et cinq lignées mitochondriales, résultante des flux de gènes chloroplastiques en place depuis l’Holocène. Enfin, de nouvelles combinaisons de génomes cytoplasmiques ont été observées permettant la détection de plusieurs cas de capture de génome cytoplasmique. L’étude de l’étendue et de la direction de l’introgression cytoplasmique est utile pour comprendre la dynamique des zones hybrides entre espèces interfécondes. L’introgression cytoplasmique entre Abies lasiocarpa x Abies balsamea a été caractérisée en utilisant des marqueurs de l’ADNmt et de l’ADNcp. L’utilisation des données génétiques et paléobotaniques a permis de définir la dynamique de la zone hybride en évaluant la concordance entre les localisations actuelle et historique de la zone hybride. Les flux de gènes de l’ADNcp sont apparus plus importants que ceux de l’ADNmt et la distribution géographique des mitotypes était plus concordante avec la répartition des espèces. Ces évidences génétiques, en accord avec un modèle de zone hybride stable, ont été confirmées par la chronologie de colonisation postglaciaire dérivée de données fossiles publiées, contrastant avec les attendus d’un scénario de zone hybride mobile et les observations habituellement faites chez les conifères. Enfin, bien que les flux de gènes interspécifiques de l’ADNcp semblent principalement conditionnés par les vents d’ouest dominants, des facteurs non-neutres pourraient aussi jouer un rôle dans le maintien de cette zone hybride stable

Investigación de la distribución de los alelos HLA en poblaciones sanas y enfermas mediante la aplicación de nuevas metodologías de secuenciación

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Medicina, Departamento de Inmunología, Oftalmología y ORL, leída el 09/03/2021Increasing our knowledge of the HLA system, including both the complete sequence description and the assessment of its diversity at the worldwide human population-level, is of great importance for elucidating the molecular functional mechanisms of the immune system and its regulation in health and disease. Furthermore, assessment of HLA allelic and haplotypic diversity of each human population is essential in the clinical histocompatibility and transplantation setting as well as in the pharmacogenetics, immunotherapy and anthropology fields. Nevertheless, the inherent vast polymorphism and high complexity presented by the HLA system have been an important challenge for its unambiguous and in-depth (high-resolution) characterization by previously available legacy molecular HLA genotyping methods (e.g. SSP, SSO and even SBT). Recent application of novel next-generation sequencing (NGS) technology for high-resolution molecular HLA genotyping has enabled to obtain, at a high-throughput mode and larger scale, full-length and/or extended sequences and genotypes of all major HLA genes, thus overcoming most of these previous limitations. Objectives: I) Characterization of HLA allele and haplotype diversity of all major classical HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5) by application of NGS of a first representative cohort of the Spanish population that could also serve as a healthy control reference group. Respective statistical analyses were performed for this immunogenetic population data. II) Characterization of HLA allele and haplotype diversity of all major classical HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5) by application of NGS of a respective cohort of multiple sclerosis (MS) patients in the Spanish population (recruited at the Department of Neurology, Hospital Clínic, Barcelona, Catalonia, Spain). A first case-control study was carried out to examine HLA-disease associations with MS in these Spanish population cohorts as well as to attempt a fine-mapping of these allele and haplotype associations by full gene resolution level via NGS. In addition, a second analysis exercise (i.e. test case) of this case-control study was carried out using an alternative healthy control group dataset, exclusively from the Spanish northeastern region of Catalonia in this second case, to evaluate possible differences in the findings of HLA-disease association with MS due to plausible regional HLA genetic variation within mainland Spain (i.e. as a statistical way to try controlling for any possible existing population stratification)...El estudio del sistema HLA, incluyendo la descripción completa de su secuencia y de la diversidad de este complejo HLA a nivel poblacional, es de gran importancia de cara a poder entender los mecanismos moleculares y funciones del sistema inmune así como su regulación en individuos sanos y enfermos. Además, la caracterización exhaustiva de la diversidad de alelos y haplotipos HLA de cada población humana es esencial en el campo de la inmunología de trasplante e histocompatibilidad al igual que en las áreas de farmacogenética e inmunoterapia. El inmenso polimorfismo y gran complejidad que presenta el sistema HLA han sido hasta ahora importantes barreras de cara a poder caracterizarlo en gran detalle (por alta resolución) y sin ambigüedades mediante métodos de genotipaje HLA tradicionales disponibles (como son SSP, SSO o incluso SBT). La reciente aplicación de la novedosa tecnología de secuenciación masiva NGS para el genotipaje molecular HLA por alta resolución ha posibilitado obtener secuencias completas o mucho más extendidas para genotipos de los principales genes de HLA, superándose así estas previas limitaciones. Objetivos: I) Caracterización de la diversidad alélica y haplotípica de los principales genes HLA (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 y -DRB3/4/5) mediante la aplicación de NGS en una primera cohorte representativa de la población española que, igualmente, constituirá una población control de referencia para estudios de asociación de HLA y enfermedades. También, respectivos análisis estadísticos se realizaron para estos resultados de genotipaje HLA. II) Caracterización de la diversidad alélica y haplotípica de los principales genes HLA (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 y -DRB3/4/5) mediante la aplicación de NGS en una correspondiente cohorte de pacientes con esclerosis múltiple (EM) de la población española (reclutados y procedentes del Departamento de Neurología del Hospital Clínic (Barcelona, Cataluña)). Un primer estudio de asociación HLA tomando casos (pacientes EM) frente a controles sanos se llevó a cabo para examinar la asociación de genes HLA y la enfermedad de EM en estas cohortes de población española antes mencionadas. Así se buscaba realizar un mapeo fino de las respectivas asociaciones alélicas y haplotípicas de HLA mediante la gran resolución alélica proporcionada por esta metodología de secuenciación masiva. De modo adicional, y como un segundo ejercicio de análisis en este estudio de asociación HLA, se utilizó un grupo control sano alternativo al previo, que incluía individuos procedentes de la región de Cataluña (situada al noreste de España) exclusivamente en este caso, para evaluar así posibles diferencias dadas en la asociación de HLA con EM debido a la probable variación genética en HLA existente a nivel regional dentro del territorio de España...Fac. de MedicinaTRUEunpu