Despite the lack of robust empirical evidence, a growing number of media reports attempt to link climate change to the ongoing violent conflicts in Syria and other parts of the world, as well as to the migration crisis in Europe. Exploiting bilateral data on asylum seeking applications for 157 countries over the period 2006-2015, we assess the determinants of refugee flows using a gravity model which accounts for endogenous selection in order to examine the causal link between climate, conflict and forced migration. Our results indicate that climatic conditions, by affecting drought severity and the likelihood of armed conflict, played a significant role as an explanatory factor for asylum seeking in the period 2011-2015. The effect of climate on conflict occurrence is particularly relevant for countries in Western Asia in the period 2010-2012 during when many countries were undergoing political transformation. This finding suggests that the impact of climate on conflict and asylum seeking flows is limited to specific time period and contexts.

Retrovírus endógenos (ERVs) são vírus altamente difundidos no genoma de vertebrados. ERVs surgem quando retrovírus exógenos infectam células germinativas e se disseminam no genoma de seus hospedeiros, transmitindo seu material genético através das gerações por meio de herança mendeliana. ERVs são fundamentais na evolução dos genomas, sendo eles responsáveis por uma parte da diversidade genética de seus hospedeiros. O conhecimento sobre ERVs na família Felidae (Mammalia, Carnivora) estava praticamente restrito ao gato doméstico, e não se conhecia diversidade e padrões de evolução desses retroelementos em outras espécies. Este estudo teve como objetivo investigar diversidade, distribuição e padrões evolutivos de ERVs em espécies de gatos silvestres. Utilizando ferramentas de biologia molecular e bioinformática, foram identificadas e caracterizadas 85 sequências similares a retrovírus endógenos nos representantes das oito espécies brasileiras: Leopardus pardalis, L. wiedii, L. colocolo, L. geoffroyi, L. tigrinus, Puma concolor, P. yagouaroundi e Panthera onca. Encontrou-se uma predominância de ERVs similares a Gammaretrovirus, um padrão característico em muitas espécies de mamíferos. As análises filogenéticas evidenciaram três grupos principais de Gammaretrovirus, cada um evoluindo de maneira peculiar. Em uma visão geral, os ERVs provenientes de diferentes hospedeiros apresentaram-se distribuídos de forma heterogênea nas filogenias, dificultando a constatação de um padrão coevolutivo. No entanto, análises mais detalhadas de algumas sequências demonstraram peculiaridades, como no caso de um grupo de sequências similares a de um ERV oriundo do morcego Myotis lucifugus. Através de análises filogenéticas em comparação com dados obtidos na literatura, sugere-se que a infecção desse retrovírus ocorreu em uma espécie ancestral de felídeo, na segunda metade do Mioceno. Os resultados obtidos permitiram demonstrar que os felídeos neotropicais apresentam ERVs que seguem padrões semelhantes aos descritos a respeito de outros mamíferos, sugerindo também alguns casos de infecções de retrovírus muito similares entre diferentes ordens de mamíferos. / Endogenous retroviruses (ERVs) are widespread viruses in vertebrate genome. ERVs arise when exogenous retrovirus infects germinal cells and spread in the genome of their hosts, transmitting its genetic material throughout the generations by means of Mendelian inheritance. ERVs are fundamental for the evolution of genomes, being responsible for some part of the genetic diversity of their hosts. The knowledge on ERVs in felids (Mammalia, Carnivora, Felidae) was basically restricted to domestic cats, and the diversity and patterns of evolution of these retroviral elements in other species were not known. This study aimed to investigate diversity, distribution and evolutionary patterns of ERVs in wildcat species. Hence, by utilizing molecular biology and bioinformatics tools, 85 endogenous retrovirus-like sequences were identified and characterized in eight representative Brazilian species: Leopardus pardalis, L. wiedii, L. colocolo, L. geoffroyi, L. tigrinus, Puma concolor, P. yagouaroundi and Panthera onca. The analyses of these novel felid ERVs showed the predominance of Gammaretroviruslike sequences, which is a characteristic pattern present in many mammal species. Phylogenetic analyses have evidenced three major groups of Gammaretrovirus, each one evolving in a peculiar manner. ERVs from different hosts were distributed in a mixed way in the phylogenies, differently of a coevolutionary pattern. However, more detailed analyses of some sequences demonstrated peculiarities, as in the case of a group of sequences similar to an ERV from the bat Myotis lucifugus. Notably, through phylogenetic analyses, and in comparison to data obtained in the literature, it may be suggested that some infection by a retrovirus occurred in a felid ancestral species in the second half of the Miocene. Therefore, the results obtained demonstrate that ERVs from Neotropical felids follow patterns which are very similar to the ones described for other mammals, also suggesting some cases of similar retrovirus lineage infecting different mammal orders.

As gorduras são componentes importantes em dietas para carnívoros, porém o aproveitamento pelos animais sofre influência de fatores inerentes à composição das dietas, principalmente fibras e minerais, que precisam ser melhor estudados. Os trabalhos que avaliam as perdas endógenas de gordura nas fezes (PEGF) e os efeitos na digestibilidade aparente da gordura são escassos e divergentes. Desta forma, os objetivos destes estudos foram: determinar as PEGF em cães e mink; utilizar as PEGF para obtenção dos valores de digestibilidade verdadeira da gordura; além de avaliar os efeitos da composição de fibras dietéticas e a inclusão de emulsificantes no aproveitamento da gordura por cães. No primeiro estudo, as PEGF foram mensuradas em cães adultos. Dietas com níveis crescentes de gordura de frango foram utilizadas e as PEGF dos cães foram determinadas a partir de análises de regressão. As PEGF foram expressas em relação ao peso corporal (PC) dos animais, 155 mg/kg PV/dia, ou em relação ao consumo de gordura na matéria seca (MS), 7,9 g/kg MS consumida. A digestibilidade aparente total da gordura apresentou aumento conforme o consumo. A digestibilidade verdadeira total da gordura, corrigida para PEGF, não variou mediante o consumo de gordura. A relação entre PEGF e consumo de gordura foi maior em dietas com baixa gordura e explica o aumento na digestibilidade aparente da gordura quando concentrações maiores são consumidas. No segundo estudo, as PEGF foram determinadas em mink. Dietas com níveis crescente de óleo de soja foram formuladas e as PEGF avaliadas por regressão. Foi obtido o valor de 0,5 g/100g MS consumida, próximo ao relatado em cães. No terceiro estudo foi avaliada a influência das fibras dietéticas e da lecitina de soja na digestibilidade aparente da gordura em dietas para cães adultos. Foram avaliadas três fontes de carboidratos, amido de milho, celulose e polpa de beterraba, combinadas ou não à lecitina de soja. A polpa de beterraba reduziu a digestibilidade aparente e verdadeira da gordura em cães, aumentou o teor de umidade e elevou o escore fecal, porém ainda dentro da faixa considerada ideal. A lecitina de soja não apresentou efeito de melhora na digestibilidade dos macronutrientes e da energia das dietas. / Fats are important components of carnivores diets, however inherent factors of diets composition, mainly fibers and minerals, may affect its use by the animals, requiring further studies. Studies evaluating endogenous fat loss (EFL) and the effects on apparent total tract digestibility of fat are limited and divergent. The objectives of these studies were: to determine the EFL in dogs and mink; apply the EFL to calculated the true total tract digestibility of fats; and to evaluate the effects of dietary fiber composition and an emulsifying agent on fats digestibility in dogs. On the first study, the EFL was evaluated in adult dogs. Diets with increasing levels of poultry fat were used and the EFL was determined by regression analysis. The EFL was obtained according to the dogs’ body weight (BW) as 155 mg/kg BW/day, or according to dry matter (DM) fat intake, as 7.9 g/kg DM intake. The apparent total tract digestibility of fat increases according to the intake level. However, the true total tract digestibility of fat, EFL corrected, remained unaffected by fat intake. The relation between EFL and fat intake is higher for low fat diets and explains why the apparent digestibility increases according to intake. On the second study, the EFL was measured in mink. Diets with graded levels of soybean oil were offered and the EFL evaluated by regression. The value of 0.5 g/100 g DM intake was obtained, close to the reported with dogs. The third study assessed the influences of dietary fibers and soy lecithin on apparent total tract digestibility of fat in adult dog diets. Were evaluated three carbohydrate sources; corn starch, cellulose and beet pulp; combined or not with soy lecithin. The beet pulp decreased apparent and true total tract digestibility of fat in dogs, increased the moisture level of faeces and the faecal score, yet the faeces still had good quality. The soy lecithin did not improve digestibility of macronutrients and energy of diets.

Endogenous viral elements, or viral genomic fossils, have proven extremely valuable in the study of the macroevolution of viruses, providing important, and otherwise unobtainable, insights into the ancient origin of viruses, and how their ancestors might have co-evolved with their hosts in the distant past. This type of investigation falls within the realm of paleovirology—the study of ancient viruses. Investigations of extant viruses and paleovirological analyses, however, often give conflicting results, especially those concerning viral evolutionary rates and timescales. Reconciling these two types of analyses is a necessary step towards a better understanding of the overall long-term evolutionary dynamics of viruses. The main study system of this thesis is foamy viruses (FVs). FVs are characterised by their stable co-speciation history with their hosts, allowing their evolutionary dynamics to be modelled and investigated over various timescales. This unique evolutionary feature makes FVs one of the best subjects for connecting recent and ancient viral evolution. The work here reports the discovery of several endogenous mammalian FVs, and examines how mammalian FVs co-evolve with their hosts. Analyses reveal a co-diversifying history of the two that could be dated back to the basal radiation of eutherians more than 100 million years ago. However, a small number of ancient FV cross-species transmissions could still be found, mostly involving New World monkey FVs. Based on this extended FV-mammal co-speciation pattern, this thesis investigates the long-term evolutionary rate dynamics of FVs, and shows that the rate estimates of FV evolution appear to decrease continuously as the rate measurement timescale increases, following a power-law decay function. The work presented here also shows that this so-called 'time-dependent rate phenomenon' is in fact a pervasive evolutionary feature of all viruses, and surprisingly, the rate estimates of evolution of all viruses seem to decay at the same speed, decreasing by approximately half for every 3-fold increase in the measurement timescale. Based on this power-law rate-decay pattern, we could infer evolutionary timescales of modern-day lentiviruses that are consistent with paleovirological analyses for the first time. Finally, this thesis reports the discovery of basal FV-like endogenous retroviruses (FLERVs) in amphibian and fish genomes. Phylogenetic analyses reveal that the progenitors of ray-finned fish FLERVs co-diversify broadly with their fish hosts, but also suggest that there might have been several ancient viral cross-class transmissions, involving lobe-finned fish, shark, and frog FLERVs. Again, by using the power-law rate-decay model, analyses in this thesis suggest that this major retroviral clade has an ancient Ordovician marine origin, originating together with their jawed vertebrate hosts more than 450 million years ago. This finding implies that the origin of retroviruses as a whole must be in the early Paleozoic Era, if not earlier. The results presented here bridge ancient and recent viral evolution.

No description available.

Using a three-essay approach, I focus on two issues related to the labor market: the effect of changes in regulatory costs on informal sector employment, and the role of endogeneity in the relationship between education and earnings. In the first essay, I analyze the implications of regulatory costs on skill-based wage differences and informal sector employment. I use a two sector matching model with exogenous skill types for workers where firms have sector-specific costs and workers have sector-specific bargaining power. In general, there are multiple equilibria possible for this model. I focus on the equilibrium that best resembles the situation in the developing countries of sub-Saharan Africa and southern Asia. My results show that government policies which reduce regulatory costs decrease unemployment, earnings inequality, and the fraction of skilled workers in the informal sector. The different types of regulatory costs affect the skill premium differently and non-monotonically. In the second essay, I test the hypothesis of linearity in returns to education in the Mincer regression with endogenous schooling and earnings. I estimate the marginal rate of return to education using a polynomial model and a semiparametric partial linear model based on the standard Mincer regression. To perform the analysis, I use a control function approach for IV estimation with spousal and parental education as instruments. Results suggest that estimates not accounting for endogeneity understate returns at the tails of the education spectrum and overstate returns for education levels between middle-school and college. In the third essay, I empirically test the claim of Mookherjee and Ray (2010), based on a theoretical model of skill complexity, that "the return to human capital is endogenously nonconcave." I estimate the functional form of returns to education for India using a semiparametric partial linear model based on the standard Mincer regression. Marginal returns are estimated to test the nonconcavity of the functional form under both exogenous and endogenous schooling assumptions. My results show that the marginal rate of return declines during primary education and increases until high school, followed by stable returns for college and higher studies. However, the test of robustness of the functional form based on uniform confidence bands fails to reject the presence of nonconcavity in returns to education for India. This lends support to the claim of Mookherjee and Ray (2010).

In the development of noninvasive optical biopsy, normal tissues can be statistically differentiated from precancerous and cancerous tissues by analyzing their autofluorescence spectra. The observed cancer hallmarks in the spectra are manifestations of biochemical and morphological changes in tissue during cancerous transformation. For detection of colorectal cancers, it has been hypothesized that the major contributors to tissue fluorescence are three endogenous fluorophores – reduced nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD) and collagen. Separating and identifying endogenous fluorophores in cells/tissues using capillary electrophoresis (CE) with laser–induced fluorescence (LIF) detection holds promise as a simple and fast method to analyze fluorophore compositions in tissues during the cancerous transformation. To this end, we have established the extraction and separation protocols for quantifying endogenous fluorophores in Chinese Hamster Ovary (CHO) cells, human colorectal adenocarcinoma cells (HT–29) and human normal colon cells (FHC). Flavin mononucleotide (FMN), FAD, NADH and nicotinamide adenine dinucleotide phosphate (NADPH) have been identified in the cell extracts by spiking them with standards and quantified by standard addition methods. The influence of cell densities and cell growth stages on fluorophore composition has been closely examined. Two–dimensional (2D) correlation coefficient mapping of electropherograms of HT–29 and FHC cell extracts reveals that the HT–29 cell extracts with higher cell density can be differentiated from FHC and HT–29 cell extracts with lower cell density, which is also demonstrated by the comparison of peak area ratios of NADH and NADPH. The electropherograms for 2D correlation analysis are pretreated by aligning their prominent peaks to account for peak shifting. A challenge in biological spectroscopy of cells and tissue is the identification of endogenous components that contribute to the overall complex spectra and the diagnostic signature. We propose 2D generalized correlation of CE–LIF electropherograms and fluorescence spectra in order to resolve the overlapped fluorescence spectra into their individual components. Separation of the endogenous fluorophores in normal and cancer cells by CE–LIF has provided us insight into fluorophore compositions and tools for classifications of cells. It has also prepared us for extraction and separation of tissues under different physiological conditions to assist cancer diagnosis.

Placebo treatments are inert but are known to alleviate symptoms across numerous clinical conditions. One of the most studied placebo effects is placebo analgesia, which is a placebo effect limited to pain relief. This thesis aims to introduce the current state of research regarding the neuroscience of placebo analgesia and specifically to present research findings regarding the neurotransmission. Studies have demonstrated that placebo analgesia can be elicited through two separate processes interacting with each other; manipulation of expectations and through conditioning. These processes seem to affect neurotransmission in different ways. Many brain areas have been found to be correlated to placebo analgesia. Besides the pain-processing brain areas, studies point to that the prefrontal cortex can have a vital role in the placebo analgesic effect. Known neurotransmitters that have shown to be involved in placebo analgesia are endogenous opioids, cholecystokinin (CCK), and endocannabinoids. Studies point to that endogenous opioids are involved in the placebo analgesic effect when elicited by expectation or conditioned by an opioid drug. CCK act on placebo analgesia by affecting the release of endogenous opioids and endocannabinoids seem to be involved in placebo analgesia while it occurs due to conditioning with non-opioid drugs. Getting a better understanding of placebo analgesia and find ways to apply this knowledge in the clinical context could powerfully develop the whole medical society.

A imunidade inata na interface materno-fetal é um dos mecanismos de proteção essenciais na resposta antiviral, sobretudo, na infecção por HIV-1. Neste trabalho, avaliamos a influência da infecção materna por HIV-1 na expressão de fatores antivirais, nas moléculas do complexo inflamassoma e de retrovírus endógenos (HERV), em células mononucleares (CMN) maternas, células do cordão umbilical (recém-natos, RN), colostro e no tecido placentário. Os resultados mostraram que no vilo das placentas de mães infectadas há um aumento na expressão de mRNA dos fatores antivirais, como IFN tipo I e III, DAMPs damage-associated molecular patterns e HERVs. Entretanto, na análise proteica, essas diferenças não se confirmam, indicando que o sistema imune inato é capaz de reconhecer o vírus, ou ainda, o dano causado pela infecção, mas controla a produção exacerbada da proteína. Sob estímulo de agonista de TLRs Toll-like receptor, em CMNs a expressão de HERVs não se altera entre RNs. Além disto, avaliando os níveis de &#223-quimiocinas, CCL5 e CCL3, e de IFN-&#967 nos sobrenadantes das culturas de CMNs, a ativação por LPS foi capaz de diminuir a produção de CCL3 e CCL5 nas CMNs de mães infectadas por HIV em relação às mães controles, contudo o CL097 promoveu níveis similares às mães do grupo controle. Nos RNs, enquanto os níveis de CCL5 são inferiores aos de adultos, os níveis de CCL3 são semelhantes. Já o ligante TLR7/8 foi capaz de restaurar a secreção de IFN-&#945 no grupo infectado por HIV-1. Além disso, no vilo das placentas das mães infectadas por HIV, há intensa modificação na expressão de mRNA dos fatores analisados, sejam antivirais, como IFN tipo I (IFN-&#945), tipo III (IFN-&#955), fatores relacionados ao dano celular (DAMPs e seus receptores). Entre os DAMPs, um aumento da expressão de S100A9 e HMGB1 e seus receptores RAGE, TLR4 e TLR9 foi observado nos vilos de placentas de mães infectadas por HIV-1, contudo, os níveis séricos de HMGB1 estão diminuídos em mães infectadas e RN expostos. Quanto aos níveis séricos de citocinas, foram observados níveis reduzidos de HMGB1, IL-6 e IL-1&#223 nos RNs expostos, o que evidencia um controle do estado inflamatório na exposição ao HIV-1. Também observamos presença de níveis séricos de HERV-W, livre ou em exossomas, em ambos os grupos analisados. Já no colostro, não encontramos diferenças nas análises de fatores inflamatórios e HERVs indicando que, nesse compartimento, a infecção não altera os padrões de expressão desses alvos. A vigência do estado antiviral e a supressão do ambiente inflamatório podem equilibrar a resposta imune placentária, promovendo a homeostase para o desenvolvimento do feto e de proteção à infecção por HIV-1 nos neonatos. / Innate immunity at the maternal-fetal interface is one of the main protection mechanisms in the antiviral response, especially in HIV-1 infection. In this work, we present the influence of maternal HIV-1 infection on the expression of antiviral factors, inflammasome molecular complex and human endogenous retroviruses (HERV), in maternal mononuclear cells (MNCs), umbilical cord cells (newborns, NB), colostrum and placental tissue. The results show that in infected mothers cells has an increase in mRNA expression of antiviral factors, such as IFN type I and III, DAMPs (damage-associated molecular patterns) and HERVs. However, in protein analysis, these differences are not confirmed, indicating that the immune system is able to detect the virus, or even the damage caused by the infection, but controls the exacerbated protein production. Under stimulation of the TLR (Toll-like receptor) agonist, CMNs do not change among the RNs. In addition, by evaluating the levels of &#223-chemokines, CCL5 and CCL3, and of IFN-&#945 in the supernatants of CMNs cultures, LPS activation was able to decrease the production of CCL3 and CCL5 in CMNs of HIV-infected mothers compared to control mothers, nevertheless CL097 promoted similar levels between HIV-infected mothers and control group. In RNs, while CCL5 levels are lower than in adults, CCL3 levels are similar. TLR7/8 agonist was able to restore IFN- secretion in the HIV-infected group. In contrast, the TLR7/8 agonist was able to restore IFN- secretion in HIV-infected group. In addition, in placental villi, there is intense modification in the mRNA expression of the analyzed factors, whether they are antiviral, such as IFN type I (IFN-&#945), type III (IFN-&#955), related to cell damage (DAMPs and their receptors). Among DAMPs, increased expression of S100A9 and HMGB1 and their receptors RAGE, TLR4 and TLR9 was observed in placental villi of HIV-infected mothers, however, serum HMGB1 levels are decreased in infected-mothers and exposed-newborns. About the cytokines serum levels, reduced levels of HMGB1, IL-6 and IL-1&#223 were observed in the exposed-NBs, which evidences an inflammatory status control in HIV-1 exposure. We also observed the presence of free HERV-W or exosomes levels in serum in both groups analyzed. In colostrum, we did not find differences in inflammatory factors and HERVs analysis indicating that, in this compartment, the infection does not alter the expression patterns of these targets. The effectiveness of antiviral status and suppression of the inflammatory environment can balance the placental immune response, promoting homeostasis for fetal development and protection of HIV-1 infection in neonates.

The initial focus of this PhD project was on comparative gene mapping. Comparative gene mapping is facilitated by consensus PCR primers which amplify homologous gene fragments in many species. As a part of an international co-ordinated programme of comparative mapping in pigs, 47 CATS (Comparative Anchor Tagged Sequence) consensus primer pairs for loci located on human chromosomes 9, 10, 20, and 22, were used for amplifying homologous loci in pigs. After optimization of PCR conditions, 23 CATS products have confirmed by comparison with homologous sequences in GenBank. A French somatic cell hybrid panel was used to physically map the 6 porcine CATS products distinguishable from rodent background product, namely ADRA1A, ADRA2A, ARSA, GNAS1, OXT and TOP1. Of these, the map location of ADRA1A and OXT showed inconsistency with the previously recognised conserved relationship between human and pig. The other four loci mapped to positions consistent with known syntenic relationships. Despite low levels of polymorphism, frequently indistinguishable rodent and porcine products in somatic hybrids and some confusion of identity of gene family members, these CATS primers have made a useful contribution to the porcine-human comparative map. The focus of the project then changed to genetic and molecular characterisation of endogenous retroviruses in pigs and their relatives. Pigs are regarded as a potentially good source of organs and tissues for transplantation into humans. However, porcine endogenous retroviruses have emerged as a possible problem as they can infect cultured human cells. Two main types of pig retrovirus, determined by envelope protein, PERV-A and PERV-B, are widely distributed in different pig breeds and a third less common type, PERV-C, has also been recognised. Endogenous retroviruses were analyzed from the Westran (Westmead transplantation) inbred line of pig, specially bred for biomedical research. Thirty-one 1.8 kb env PCR product clones were sequenced after preliminary screening with the restriction enzymes KpnI and MboI. Five recombinant clones between A and B were identified. 55% of clones (17/31) sequenced had stop codons within the envelope protein-encoding region, which would prevent the retrovirus from making full-length envelope protein recognizable by cell-surface receptors of the virus. The endogenous viruses were physically mapped in Westran pigs by FISH (Fluorescence In Situ Hybridisation) using PERV-A and PERV-B envelope clones as probes. Preliminary FISH data suggest that there are at least 22 PERVs (13 PERV-A and 9 PERV-B) and the chromosomal locations of these in the Westran strain are quite different from European Large White pigs. The sequences and mapping results of inbred Westran pig suggest that there are relatively few PERV integration sites compared with commercial pigs and further that a large proportion of clones are defective due to premature stop codons in the envelope gene. To investigate the relationship of endogenous retroviruses in peccaries and pigs, a set of degenerate primers was used to amplify peccary retroviral sequences. The sequences of two putative retroviral clones showed close homology, albeit with a 534 bp deletion, to mouse and pig retroviral sequences. Also, four non-target sequences were amplified from peccary with the degenerate retroviral primers. They are a part of the peccary cofilin gene, a SINE, and a sequence containing a microsatellite. The peccary endogenous retroviral sequences are significant in that they are the first such sequences reported in peccary species and repudiate old claims in the literature that peccaries do not have C-type retroviral sequences.