Cytogenetic Mapping of 5S and 18S rRNAs and H3 Histone Genes in 4 Ancient Proscopiidae Grasshopper Species: Contribution to Understanding the Evolutionary Dynamics of Multigene Families

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Leishmanial antigens in the diagnosis of active lesions and ancient scars of American tegumentary leishmaniasis patients

Cutaneous biopsies (n = 94) obtained from 88 patients with American tegumentary leishmaniasis were studied by conventional and immunohistochemical techniques. Specimens were distributed as active lesions of cutaneous leishmaniasis (n = 53) (Group I), cicatricial lesions of cutaneous leishmaniasis (n = 35) (Group II) and suggestive scars of healed mucosal leishmaniasis patients (n = 6) (Group III). In addition, active cutaneous lesions of other etiology (n = 24) (Group C1) and cutaneous scars not related to leishmaniasis (n = 10) (Group C2) were also included in the protocol. Amastigotes in Group I biopsies were detected by routine histopathological exam (30.2%), imprint (28.2%), culture (43.4%), immunofluorescence (41.4%) and immunoperoxidase (58.5%) techniques; and by the five methods together (79.3%). In Group II, 5.7% of cultures were positive. Leishmanial antigen was also seen in the cytoplasm of macrophages and giant cells (cellular pattern), vessel walls (vascular pattern) and dermal nerves (neural pattern). Positive reaction was detected in 49 (92.5%), 20 (57%) and 4 (67%) biopsies of Groups I, II and III, respectively. Antigen persistency in cicatricial tissue may be related to immunoprotection or, on the contrary, to the development of late lesions. We suggest that the cellular, vascular and neural patterns could be applied in the immunodiagnosis of active and cicatricial lesions in which leishmaniasis is suspected.

Myths and facts in the chronicles of the conquest of Ancient Peru

The chronicles of historical sources are difficult because they are a mix of myths and facts experienced by their authors. Starting from this premise, this study analyzes some of the Spanish and indigenous sources on the conquest of the Inca people and the description of this world and people who were so different. Among the chroniclers chosen, the article highlights the reports by Jose de Acosta on the Mundus Novus and by Cieza de Leon and Garcilaso de la Vega on the myths of the first Inca chief; finally, Francisco de Xerez, Juan de Betanzos, among others, on the event of the imprisonment and murder of Atahualpa, which resulted in the conquest of the "Tahuantinsuyu" by the Spanish.

The discovery of Foxl2 paralogs in chondrichthyan, coelacanth and tetrapod genomes reveals an ancient duplication in vertebrates

The Foxl2 (forkhead box L2) gene is an important member of the forkhead domain family, primarily responsible for the development of ovaries during female sex differentiation. The evolutionary studies conducted previously considered the presence of paralog Foxl2 copies only in teleosts. However, to search for possible paralog copies in other groups of vertebrates and ensure that all predicted copies were homolog to the Foxl2 gene, a broad evolutionary analysis was performed, based on the forkhead domain family. A total of 2464 sequences for the forkhead domain were recovered, and subsequently, 64 representative sequences for Foxl2 were used in the evolutionary analysis of this gene. The most important contribution of this study was the discovery of a new subgroup of Foxl2 copies (ortholog to Foxl2B) present in the chondrichthyan Callorhinchus milii, in the coelacanth Latimeria chalumnae, in the avian Taeniopygia guttata and in the marsupial Monodelphis domestica. This new scenario indicates a gene duplication event in an ancestor of gnathostomes. Furthermore, based on the analysis of the syntenic regions of both Foxl2 copies, the duplication event was not exclusive to Foxl2. Moreover, the duplicated copy distribution was shown to be complex across vertebrates, especially in tetrapods, and the results strongly support a loss of this copy in eutherian species. Finally, the scenario observed in this study suggests an update for Foxl2 gene nomenclature, extending the actual suggested teleost naming of Foxl2A and Foxl2B to all vertebrate sequences and contributing to the establishment of a new evolutionary context for the Foxl2 gene. © 2013 Macmillan Publishers Limited All rights reserved.

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of the tropical and subtropical climate zones where the species normally occurs. In every case, the causative agent belongs to a previously rare genotype of C. gattii called AFLP6/VGII, but the origin of the outbreak clades remains enigmatic. Here we used phylogenetic and recombination analyses, based on AFLP and multiple MLST datasets, and coalescence gene genealogy to demonstrate that these outbreaks have arisen from a highly-recombining C. gattii population in the native rainforest of Northern Brazil. Thus the modern virulent C. gattii AFLP6/VGII outbreak lineages derived from mating events in South America and then dispersed to temperate regions where they cause serious infections in humans and animals.

Transmissable Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage

Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.

Book Review of Stone by Stone: Exploring Ancient Sites on the Canadian Plains by Liz Bryan

Liz Bryan begins her book with a description of the Canadian Plains:" . .. a voluptuous landscape of hills and valleys and plains, of lakes and tiny twinkling potholes, of flower-filled coulees and vast sand dunes." Her emphasis throughout on the landscape of southern Saskatchewan and Alberta is necessary since the ancient monuments she describes only truly resonate within this setting. Indeed, almost every page of this attractive book is adorned with at least two color images-of scenery, stone features, artifacts, and aboriginal events. She then proceeds to an eclectic overview of the archaeological record of the Plains of Saskatchewan and Alberta, including the earliest human evidence, such as the Clovis points from the Wally's Beach site, Alberta, where the trackways of mammoths, camels, and muskoxen were miraculously and briefly exposed in the late 1990s. There is one perplexing error, however-the attribution of the extinction of the ice age bestiary, about 12,000 years ago, to the meteorite that felled the dinosaurs!

Hunting in Ancient and Modern Amazonia: Rethinking Sustainability

We use a recently developed computerized modeling technique to explore the long-term impacts of indigenous Amazonian hunting in the past, present, and future. The model redefines sustainability in spatial and temporal terms, a major advance over the static "sustainability indices" currently used to study hunting in tropical forests. We validate the model's projections against actual field data from two sites in contemporary Amazonia and use the model to assess various management scenarios for the future of Manu National Park in Peru. We then apply the model to two archaeological contexts, show how its results may resolve long-standing enigmas regarding native food taboos and primate biogeography, and reflect on the ancient history and future of indigenous people in the Amazon.

An ancient founder mutation in PROKR2 impairs human reproduction

Congenital gonadotropin-releasing hormone (GnRH) deficiency manifests as absent or incomplete sexual maturation and infertility. Although the disease exhibits marked locus and allelic heterogeneity, with the causal mutations being both rare and private, one causal mutation in the prokineticin receptor, PROKR2 L173R, appears unusually prevalent among GnRH-deficient patients of diverse geographic and ethnic origins. To track the genetic ancestry of PROKR2 L173R, haplotype mapping was performed in 22 unrelated patients with GnRH deficiency carrying L173R and their 30 first-degree relatives. The mutations age was estimated using a haplotype-decay model. Thirteen subjects were informative and in all of them the mutation was present on the same approximate to 123 kb haplotype whose population frequency is 10. Thus, PROKR2 L173R represents a founder mutation whose age is estimated at approximately 9000 years. Inheritance of PROKR2 L173R-associated GnRH deficiency was complex with highly variable penetrance among carriers, influenced by additional mutations in the other PROKR2 allele (recessive inheritance) or another gene (digenicity). The paradoxical identification of an ancient founder mutation that impairs reproduction has intriguing implications for the inheritance mechanisms of PROKR2 L173R-associated GnRH deficiency and for the relevant processes of evolutionary selection, including potential selective advantages of mutation carriers in genes affecting reproduction.

ANCIENT LAW – UM CLÁSSICO REVISITADO 150 ANOS DEPOIS

Este artigo pretende realçar a importância desempenhada pela obra de Henry James Sumner Maine na formação da antropologia jurídica e da sociologia do direito. Mediante a recuperação da tese central de sua obra Ancient Law, procura ressaltar o papel por ela desempenhado no delineamento de uma nova forma de abordagem da relação entre direito e sociedade. Para tanto, recupera traços gerais das análises de Norbert Rouland e de Niklas Luhmann acerca da importância das ideias do autor.

Study of materials and technology of ancient floor mosaics' substrate

Ancient pavements are composed of a variety of preparatory or foundation layers constituting the substrate, and of a layer of tesserae, pebbles or marble slabs forming the surface of the floor. In other cases, the surface consists of a mortar layer beaten and polished. The term mosaic is associated with the presence of tesserae or pebbles, while the more general term pavement is used in all the cases. As past and modern excavations of ancient pavements demonstrated, all pavements do not necessarily display the stratigraphy of the substrate described in the ancient literary sources. In fact, the number and thickness of the preparatory layers, as well as the nature and the properties of their constituent materials, are often varying in pavements which are placed either in different sites or in different buildings within a same site or even in a same building. For such a reason, an investigation that takes account of the whole structure of the pavement is important when studying the archaeological context of the site where it is placed, when designing materials to be used for its maintenance and restoration, when documenting it and when presenting it to public. Five case studies represented by archaeological sites containing floor mosaics and other kind of pavements, dated to the Hellenistic and the Roman period, have been investigated by means of in situ and laboratory analyses. The results indicated that the characteristics of the studied pavements, namely the number and the thickness of the preparatory layers, and the properties of the mortars constituting them, vary according to the ancient use of the room where the pavements are placed and to the type of surface upon which they were built. The study contributed to the understanding of the function and the technology of the pavements’ substrate and to the characterization of its constituent materials. Furthermore, the research underlined the importance of the investigation of the whole structure of the pavement, included the foundation surface, in the interpretation of the archaeological context where it is located. A series of practical applications of the results of the research, in the designing of repair mortars for pavements, in the documentation of ancient pavements in the conservation practice, and in the presentation to public in situ and in museums of ancient pavements, have been suggested.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Genetic characterisation and global comparison of ancient Mediterranean Great White Sharks population (Carcharodon carcharias, L.1758)

This study poses as its objective the genetic characterization of the ancient population of the Great White shark, Carcharodon carcharias, L.1758, present in the Mediterranean Sea. Using historical evidence, for the most part buccal arches but also whole, stuffed examples from various national museums, research institutes and private collections, a dataset of 18 examples coming from the Mediterranean Sea has been created, in order to increase the informations regarding this species in the Mediterranean. The importance of the Mediterranean provenance derives from the fact that a genetic characterization of this species' population does not exist, and this creates gaps in the knowledge of this species in the Mediterranean. The genetic characterization of the individuals will initially take place by the extraction of the ancient DNA and the analysis of the variations in the sequence markers of the mitochondrial DNA. This approach has allowed the genetic comparison between ancient populations of the Mediterranean and contemporary populations of the same geographical area. In addition, the genetic characterization of the population of white sharks of the Mediterranean, has allowed a genetic comparison with populations from global "hot spots", using published sequences in online databases (NCBI, GenBank). Analyzing the variability of the dataset, both in terms space and time, I assessed the evolutionary relationships of the Mediterranean population of Great Whites with the global populations (Australia/New Zealand, South Africa, Pacific USA, West Atlantic), and the temporal trend of the Mediterranean population variability. This method based on the sequencing of two portions of mitochondrial DNA genes, markers showed us how the population of Great White Sharks in the Mediterranean, is genetically more similar to the populations of the Australia Pacific ocean, American Pacific Ocean, rather than the population of South Africa, and showing also how the population of South Africa is abnormally distant from all other clusters. Interestingly, these results are inconsistent with the results from tagging of this species. In addition, there is evidence of differences between the ancient population of the Mediterranean with the modern one. This differentiation between the ancient and modern population of white shark can be the result of events impacting on this species occurred over the last two centuries.

Seismic vulnerability of the ancient albergotti's manor in Arezzo, Italy

The thesis moves from the need of understanding how a historical building would behave in case of earthquake and this purpose is strongly linked to the fact that the majority of Italian structures are old ones placed in seismic sites. Primarily an architectural and chronological research is provided in order to figure out how the building has developed in time; then, after the reconstruction of the skeleton of the analyzed element (“Villa i Bossi” in Gragnone, AR), a virtual model is created such that the main walls and sections are tested according to the magnitude of expected seismic events within the reference area. This approach is basically aimed at verifying the structure’s reliability as composed by single units; the latter are treated individually in order to find out all the main critical points where rehabilitation might be needed. Finally the most harmful sections are studied in detail and proper strengthening is advised according to the current know-how.