Orientador: João Aristeu da Rosa / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-08T20:03:24Z (GMT). No. of bitstreams: 1 Mendonca_VagnerJose_M.pdf: 9704244 bytes, checksum: c343d08640ae10d944866e45beb0b3ae (MD5) Previous issue date: 2007 / Resumo: Triatomíneos silvestres coletados por Cerqueira em 1975 em Santo Inácio/BA foram estudados por Papa et al. (2002) que concluíram tratar-se de uma nova espécie, denominada T. sherlocki ao compará-la com outros Triatominae. No intuito de ampliar o conhecimento dessa nova espécie e inferir relação filogenética para as espécies da subfamília Triatominae foram seqüenciados genes nucleares, ITS-2 e 28S, e mitocondriais, citocromo b e 16S, de T. sherlocki e T. brasiliensis. As seqüências foram alinhadas no programa Clustal W do BioEdit e as relações filogenéticas construídas utilizando metodologias de distâncias com os parâmetros p-distance e Kimura-2 do algoritimo Neighbor-Joining, do programa MEGA 3.1, e Máxima Parsimônia, do programa PAUP 4.1. A filogenia baseada nos dois genes mitocondriais revelou que a espécie T. sherlocki é estritamente relacionada com a espécie T. melanica, e que T. brasiliensis aparece como espécieirmã dessas duas, exceção para a análise de Parcimônia do gene 16S que apresenta T. melanica como espécie-irmã da relação mais estreita entre T. sherlocki e T. brasiliensis. P. megistus e T. infestans aparecem relacionadas com espécies norte-americanas nas filogenias inferidas do gene 16S e das seqüências dos aminoácido do citocromo b, respectivamente. A filogenia baseada no gene nuclear 28S revelou uma politomia envolvendo as espécies T. sherlocki, T. brasiliensis e T. melanica. Essa filogenia foi subestimada pelo baixo número de espécies presentes na árvore. Essa mesma relação ocorreu na filogenia do gene do ITS-2 na análise baseada em Parcimônia. A análise de distância desse gene revelou a proximidade entre T. sherlocki e T. brasiliensis, com T. melanica como espécie-irmã. Essa filogenia apresentou as espécies T. maculata, T. brasiliensis e T. infestans estritamente relacionadas com espécies de triatomíneos norte-americanas. Algumas espécies como T. infestans e P. megistus apresentaram mais de uma topologia dependendo do gene analisado, sendo necessários mais estudos para definir uma posição filogenética dessas espécies. A proximidade de T. sherlocki com os haplótipos de T. brasiliensis, principalmente com a espécie T. melanica, pode inferir uma possível filogeografia a partir de ancestrais de T. brasiliensis, tratando-se portanto de espécies derivadas / Abstract: Wild triatomines collected by Cerqueira in 1975 in Santo Inácio,BA, Brazil were studied by Papa et al. (2002), who observed morphological differences from other species of the Triatominae, concluding that they represented a new species, named Triatoma sherlocki. Mitochondrial (cytocrome b and 16S) and nuclear (ITS-2 and 28S) gene sequencing of T. sherlocki and T. brasiliensis was carried out with the aim of learning more about the new species and its phylogenetic relationship to the species of the Triatominae subfamily. The sequences ware aligned with the Clustal W application of the BioEdit freeware program and the phylogenetic relationship inferred by estimating distances with the Kimura 2-parameter and p-distance methods of the Neighbor-Joining algorithm in the MEGA 3.1 program and Maximum Parsimony (MP) method of the PAUP 4.1 program. The phylogeny based on the two mitochondrial genes disclosed that T. sherlocki and T. melanica were closely related and that T. brasiliensis was a sister species of the two, with the exception that in for the Parsimony analysis of the 16S gene, T. melanica appeared as a sister species of the clade formed by T. sherlocki and T. brasiliensis. The species Panstrongylus megistus and T. infestans are related to North American species in phylogenetic analyses of the large subunit ribosomal RNA mitochondrial gene (16S) and the amino acid sequences of cytocrome b, respectively. The phylogeny based on the large subunit ribosomal D2 (28S) nuclear gene revealed to a polytomy involving T. sherlocki, T. brasiliensis and T. melanica. This phylogeny was underestimated due to the small number of species present in the tree. This same relationship occurred in the phylogeny of internally transcribed spacer 2 (ITS-2) nuclear gene, in analysis based on Maximum Parsimony. The analysis of distance in this gene revealed proximity between T. sherlocki and T. brasiliensis, with T. melanica as sister species. This phylogeny showed T. maculata, T. brasiliensis and T. infestans to be closely related to North American triatomines. Certain species, such as T. infestans and P. megistus, exhibited more than one topology with different genes, and fusther study is needed to define the phylogenetic positions of these species. The proximity of T. sherlocki to the T. brasiliensis haplotypes, especially with the species T. melanica, may reveal a possible phylogeography originaling from T. brasiliensis ancestors, thus implying derived species / Mestrado / Mestre em Parasitologia

Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Thesis advisor: Marc-Jan Gubbels / Thesis advisor: Sarah McMenamin / Toxoplasma gondii, an obligate intracellular parasite, infects nearly one-third of the global population, causing the disease toxoplasmosis. Despite its significant health impact, the molecular mechanisms governing its lytic cycle and stress-induced adaptation remain incompletely understood. The unique asexual cell division mechanism, endodyogeny, used by T. gondii to expand its parasitic biomass in intermediate hosts, including humans, leads to severe pathological consequences through repeated rounds of the lytic cycle, resulting in acute toxoplasmosis. The parasite’s cell cycle is characterized by a prolonged G1 phase, with centrosome duplication marking the onset of the S phase, followed by a transient G2 phase and a near-simultaneous onset of mitosis and cytokinesis. These overlapping division processes, coupled with the challenges of synchronizing T. gondii, obscure the precise molecular mechanisms of its transcriptional programs. To address these challenges, we employed single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq), combined with advanced machine learning tools, to reveal ‘transition points’ in gene expression and chromatin accessibility that correspond to shifts in biological activity during the lytic cycle. RNA velocity and time-course clustering analyses uncovered a significant G1a transcriptional burst and identified specific AP2 family transcription factors (TFs) that peak during the C-to-G1a transition, likely driving this burst to regulate G1 progression. Further, we conducted an in-depth functional characterization of G1-specific TFs, focusing on AP2XII-8, which plays a critical role in activating a ribosome regulon to promote G1 progression. The study identified combinatorial binding motifs and suggested the existence of a large AP2XII-8 protein complex, involving other TFs and epigenetic factors, that reuglates the intricate processes of T. gondii cell cycle replication. Additionally, we examined stress-responsive AP2 TFs associated with enhanced virulence during in vitro evolution, providing insights into adaptive mechanisms that enable T. gondii to thrive under extracellular stress conditions. Collectively, these findings enhance our understanding of T. gondii’s complex regulatory networks, offering potential targets for therapeutic intervention against acute toxoplasmosis. This dissertation provides the time-resolved transcriptional and chromatin accessibility landscapes of T. gondii’s lytic cycle, resolves transcriptional programs to DNA motifs, and identifies key regulatory elements involved in its cell cycle progression and stress response. / Thesis (PhD) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

This project represents the first comprehensive study applying molecular and genetic methods to study historical contexts such as migration and trade based on human parasites. Using specially developed techniques, the study focused on parasites with minor symptoms which allowed the infected person to go about their daily business. The combination of state of the art techniques in archaeology, molecular methods and phylogenetic analysis enabled us to develop a novel powerful tool to study historic events. Diseases have a considerable impact on societies. Various publications indicate that human intestinal parasites are commonly found in a variety of archaeological contexts, including latrines, graves and mummies. These parasites can be detected by microscopy which focuses the work on samples which do close association to humans; widespread prevalence and the possibility for reliable microscopic diagnostics suggest that these parasites are an attractive study system for human activities. Infectious diseases have a much short generation time which offers greater opportunity to track historical events at higher resolution. Looking at a range of human parasites, their different life-cycles allowed insight into various aspects of human culture, comparing different origins of the samples allows an estimation of the epidemiological burden of ancient populations. Application of a parallel sequencing approach (MiSeq) enabled building a comprehensive database of sequences from various archaeological sites dating as far back as 3630 BCE. Indepth phylogenetic analysis reveals patterns in the genetic signatures of both coding and non-coding genetic regions, taking various levels of selective pressure into account. This project has produced the oldest pathogen sequence and the most comprehensive database of ancient pathogen sequences.

Indiana University-Purdue University Indianapolis (IUPUI) / Histone acetylation has been linked to developmental changes in gene expression and is a validated drug target of apicomplexan parasites, but little is known about the roles of individual histone modifying enzymes and how they are recruited to target genes. The protozoan parasite Toxoplasma gondii (phylum Apicomplexa) is unusual among invertebrates in possessing two GCN5-family lysine acetyltransferases (KATs). While GCN5a is required for gene expression in response to alkaline stress, this KAT is dispensable for parasite proliferation in normal culture conditions. In contrast, GCN5b cannot be disrupted, suggesting it is essential for Toxoplasma viability. To further explore the function of GCN5b, we generated clonal parasites expressing an inducible HA-tagged form of GCN5b containing a point mutation that ablates enzymatic activity (E703G). Stabilization of this dominant-negative form of GCN5b was mediated through ligand-binding to a destabilization domain (dd) fused to the protein. Induced accumulation of the ddHAGCN5b(E703G) protein led to a rapid arrest in parasite replication. Growth arrest was accompanied by a decrease in histone H3 acetylation at specific lysine residues as well as reduced expression of GCN5b target genes in GCN5b(E703G) parasites, which were identified using chromatin immunoprecipitation coupled with microarray hybridization (ChIP-chip). We also demonstrate that GCN5b interacts with AP2-domain proteins, which are plant-like transcription factors in Apicomplexa. The interactions between GCN5b, AP2IX-7, and AP2X-8 were confirmed by reciprocal co-immunoprecipitation and revealed a “core complex” that includes the co-activator ADA2-A, TFIID subunits, LEO1 polymerase-associated factor (Paf1) subunit, and RRM proteins. The dominant-negative phenotype of ddHAGCN5b(E703G) parasites, considered with the proteomics and ChIP-chip data, indicate that GCN5b plays a central role in transcriptional and chromatin remodeling complexes. We conclude that GCN5b has a non-redundant and indispensable role in regulating gene expression required during the Toxoplasma lytic cycle.

Comparer les structures génétiques des populations d’un couple hôte-parasite permet d’évaluer les facteurs qui façonnent la dispersion ainsi que la potentialité d’adaptation locale de ces espèces. Le modèle étudié est le crabe ectoparasite Dissodactylus primitivus et son oursin-hôte Meoma ventricosa, endémiques des Caraïbes et des côtes américaines voisines. <p>En étudiant des populations le long de l’arc antillais et de la côte panaméenne, ce travail a mis en évidence que la structure génétique des populations du parasite D. primitivus diffère fortement de celle de son hôte M. ventricosa (microsatellites et cytochrome oxydase I). En effet, alors que les populations du parasite présentent une différenciation au sein de cette région, celles de l’hôte sont génétiquement homogènes. Ce contraste peut être expliqué par des caractères biologiques et écologiques (fécondité, habilité à la nage, disponibilité de l’habitat) et suggère des potentialités d’adaptation locale distinctes. La distance géographique semble être importante dans la structuration des populations du crabe mais la courantologie ou encore des évènements passés (glaciations) jouent également un rôle. A l’échelle d’une même île, les crabes ne présentent pas de différenciation entre des sites distincts. En outre, nous avons pu montrer que des crabes issus d’hôtes d’espèces différentes ne sont pas différenciés génétiquement ce qui pourrait être liée à la mobilité des crabes adultes. Par des analyses de paternité, nous avons souligné cette mobilité, démontrant que le mode de reproduction du crabe est de la polygamie mais aussi que des accouplements pouvaient avoir lieu entre crabes d’espèces hôtes distinctes.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished