Integrated functional genomics for improved manufacture of recombinant enveloped virus

Dissertation presented to obtain the Ph.D degree in Engineering and Technology Sciences-Biotechnology

Longitudinal comparison between plasma and seminal HIV-1 viral loads during antiretroviral treatment

This study was designed to investigate the impact of anti-retroviral therapy on both plasma and seminal HIV-1 viral loads and the correlation between viral loads in these compartments after treatment. Viral load, CD4+ and CD8+ T-cell counts were evaluated in paired plasma and semen samples from 36 antiretroviral therapy-naïve patients at baseline and on days 45, 90, and 180 of treatment. Slopes for blood and seminal viral loads in all treated patients were similar (p = 0.21). Median HIV-1 RNA titers in plasma and semen at baseline were 4.95 log10 and 4.48 log10 copies/ml, respectively. After 180 days of therapy, the median viral load declined to 3.15 log10 copies/ml (plasma) and 3.2 log10 copies/ml (semen). At this timepoint 22 patients presented HIV-1 viral load below 400 copies/ml in either plasma or semen, but only 9 had viral loads below 400 copies/ml in both compartments.

Using epidemiological survey data to infer geographic distributions of leishmaniasis vector species

An important aspect of tropical medicine is analysis of geographic aspects of risk of disease transmission, which for lack of detailed public health data must often be reduced to an understanding of the distributions of critical species such as vectors and reservoirs. We examine the applicability of a new technique, ecological niche modeling, to the challenge of understanding distributions of such species based on municipalities in the state of São Paulo in which a group of 5 Lutzomyia sandfly species have been recorded. The technique, when tested based on independent occurrence data, yielded highly significant predictions of species' distributions; minimum sample sizes for effective predictions were around 40 municipalities.

Avanços no tratamento da hepatite pelo vírus B

Nos últimos anos, houve um grande progresso no tratamento da hepatite B crônica. Cinco drogas são hoje aprovadas para tratamento dessa virose: intérferon alfa, lamivudina, adefovir, entecavir e telbivudina. Os intérferons (convencionais ou peguilados) foram as primeiras drogas utilizadas no tratamento dessas infecções podendo levar a resposta sustentada (perda do DNA-VHB e do AgHbe) em até um terço dos casos tratados. Um grande número de análogos de nucleosídeos/nucleotídeos estão no momento, disponíveis para tratar a hepatite B; a eficácia da lamivudina, o primeiro análogo de nucleosídeo utilizado, é limitada pela elevada incidência de resistência. O adefovir tem eficácia comparável à lamivudina porém baixa freqüência de resistência. Entecavir e tenofovir também se mostram muito ativos em controlar a replicação do vírus da hepatite B, e estão associados com mínimo desenvolvimento de resistência, mesmo em tratamento prolongados. Outras drogas, tais como telbivudina, emtricitabina e clevudine, se tornarão em futuro próximo, novas armas no controle dessa virose. Co-infectados HIV/VHB representam um grupo de doentes de difícil manuseio e que hoje se beneficiam com combinações de drogas no esquema anti-retroviral potente que devem atuar em ambas as viroses. O desenvolvimento de antivirais mais potentes e novas associações de medicamentos, conjuntamente com a melhor compreensão dos mecanismos de resistência do vírus da hepatite B a terapia são importantes conquistas para melhorar a eficácia do tratamento e diminuir no futuro, a carga global de portadores do vírus da hepatite B.

Acute Chagas disease outbreak associated with oral transmission

Seven individuals living in a town in the Southwest of Bahia developed sudden signs of cardiac and systemic impairment, with lethality of 28.6%. Serological tests were positive at least in one test in the five patients examined. Forty percent of the Triatoma sordida mynphs found inside or around Trypanosoma cruzi were found by blood culturig in there out five cases the homes of these cases were positive for Trypanosoma cruzi. Transmission probably occurred through consumption of water contaminated with triatomine feces. These findings emphasize the necessity to evaluation the importance of vectors like Triatoma sordida in maintaining the endemicity of this disease.

Comparison of feeding and defecation patterns between fifth-instar nymphs of Triatoma patagonica (Del Ponte, 1929) and Triatoma infestans (Klug, 1934) under laboratory conditions

Among the vectors of Chagas disease, Triatoma patagonica is a species in the process of adaptation to the human environment. However, its vector competence is not well known. This study had the aim of evaluating and comparing feeding and defecation patterns among fifth-instar nymphs of Triatoma patagonica and Triatoma infestans that were fed ad libitum. The results showed that nymphs of Triatoma patagonica had a feeding pattern similar to that of Triatoma infestans. Sixty nine percent and 58% of nymphs of Triatoma patagonica and Triatoma infestans, respectively, produced their first defecation within five minutes after being fed. Triatoma patagonica defecated during feeding, with an average time until first defecation that was shorter than that of Triatoma infestans (3.4 and 6.2 min, respectively). The nymphs of Triatoma patagonica were capable of defecating during or immediately after feeding.

Gold nanoparticles for plasmid delivery

Gene therapy presents an ideal strategy for the treatment of genetic as well as acquired diseases, such as cancer and typically involves the insertion of a functioning gene into cells to correct a cellular dysfunction or to provide a new cellular function. Gene delivery vectors are based in two models: viral and non-viral. Viral vectors have high transfection efficiency but their major barrier is immunogenicity. Since the non-viral vectors have no immunogenicity, these have been widely studied. Gold nanoparticles have been proposed as optimal delivery systems of genetic material, due their small size, high surface-to-volume ratio and the ability to be functionalized with multiple molecules. In the present work, an AuNP-based formulation was developed to deliver a plasmid in a colorectal cancer cell line, containing as reporter gene the gene encoding to EGFP. The delivery system resulted from the functionalization of 14 nm AuNP with a PEG layer (4300114 PEG chains/AuNP), which increases stability and biocompatibility of AuNPs; quaternary ammonium groups which provide positive charges that allow electrostatic binding of plasmid, which is considered the therapeutic agent to be transported into cells. The system developed was characterized by UV-vis spectroscopy, DLS, TEM and by electrophoretic mobility, yielding a formulation with 113.5 nm.Transfection efficiency of the formulation developed was evaluated through PCR and through EGFP expression by fluorescence microscopy and fluorescence spectroscopy. The internalization was observed 3h post transfection; however a low level of EGFP expression was achieved. After 24h of incubation, EGFP expression increases just 3 times compared to non-transfected cells. The commercial system (Lipofectamine) expressed EGFP 5 times more than the system developed AuNP@PEG@R4N+@pEGFP. This difference could be related to lower translocation to the nucleus.

Estudo das características epidemiológicas e clínicas de pacientes portadores do vírus da imunodeficiência humana em Pronto Atendimento do Hospital das Clínicas da Universidade Federal de Minas Gerais

Este trabalho objetiva a análise prospectiva das características clínicas e epidemiológicas que levam os pacientes adultos com HIV/AIDS a procurarem atendimento clínico de urgência em Pronto Atendimento do Hospital das Clínicas da Universidade Federal de Minas Gerais. Noventa e nove pacientes perfizeram 118 internações. A idade foi em média 39,4 anos. A relação homem e mulher foi de 1,35:1. O tempo desde o diagnóstico até a admissão situou-se de forma mais freqüente entre 0-5 anos em 40,4% dos casos. A terapêutica anti-retroviral era usada regularmente em 56,8% das admissões. A contagem de linfócitos T CD4+ foi inferior a 200 células/mm³ em 45,7% dos pacientes. As queixas mais freqüentes foram aumento da temperatura corpórea, diarréia, tosse e dispnéia. O aparelho respiratório foi o mais acometido. As doenças oportunistas mais freqüentes foram pneumocistose, pneumonia comunitária, síndrome diarréica, e candidiase oral. A demanda de internações de pacientes com HIV representou 2,8% das admissões, com tempo médio de permanência hospitalar de 4,6 dias. Os pacientes possuíam, em sua maioria, contagem de linfócitos TCD4+ baixa, quase metade não usava a terapia anti-retroviral altamente eficaz. Houve tendência à feminização. As doenças relacionadas à AIDS continuam sendo as mais freqüentes no nosso meio.

Avaliação da adesão aos anti-retrovirais em um município no Sul do Brasil

O objetivo desta pesquisa foi avaliar os fatores preditores e o grau de adesão aos anti-retrovirais por meio de auto-relato e data de retirada da medicação. Trata-se de um estudo transversal em que foram entrevistados 67 pacientes. Foram considerados aderentes aqueles pacientes que utilizaram mais de 90% das doses. Os resultados de adesão foram: referida (72,7%); calculada por dose esquecida no último dia (70%); por três dias (76,1%); por sete dias (80,5%); e por quinze dias (80,5%); calculada pela data de retirada da medicação no período de três meses (53,7%); e em seis meses (47,8%). As variáveis associadas significativamente com a adesão foram: escolaridade, fato de viver com a família, referir boa adesão, avaliação positiva da terapia anti-retroviral, diagnóstico por doença oportunista, menor contagem de linfócitos CD4 maior que 200 células/mm³ e o fato de estar no primeiro tratamento. A partir da identificação dos fatores que comprometem a adesão, devem ser elaboradas estratégias individuais e coletivas para a promoção da adesão.

Semantic enrichment of knowledge sources supported by domain ontologies

This thesis introduces a novel conceptual framework to support the creation of knowledge representations based on enriched Semantic Vectors, using the classical vector space model approach extended with ontological support. One of the primary research challenges addressed here relates to the process of formalization and representation of document contents, where most existing approaches are limited and only take into account the explicit, word-based information in the document. This research explores how traditional knowledge representations can be enriched through incorporation of implicit information derived from the complex relationships (semantic associations) modelled by domain ontologies with the addition of information presented in documents. The relevant achievements pursued by this thesis are the following: (i) conceptualization of a model that enables the semantic enrichment of knowledge sources supported by domain experts; (ii) development of a method for extending the traditional vector space, using domain ontologies; (iii) development of a method to support ontology learning, based on the discovery of new ontological relations expressed in non-structured information sources; (iv) development of a process to evaluate the semantic enrichment; (v) implementation of a proof-of-concept, named SENSE (Semantic Enrichment kNowledge SourcEs), which enables to validate the ideas established under the scope of this thesis; (vi) publication of several scientific articles and the support to 4 master dissertations carried out by the department of Electrical and Computer Engineering from FCT/UNL. It is worth mentioning that the work developed under the semantic referential covered by this thesis has reused relevant achievements within the scope of research European projects, in order to address approaches which are considered scientifically sound and coherent and avoid “reinventing the wheel”.

Comparative biology of the two sister species of Triatominae (Hemiptera: Reduviidae)

INTRODUCTION: Triatoma pseudomaculata and T. wygodzinskyi (Hemiptera: Reduviidae: Triatominae) are two Brazilian vectors of Chagas disease. The first is an arboricolous species in sylvatic environment and considered a vector of T. cruzi in peridomestic structures; the second, a rupicolous species in the wild environment of no epidemiological importance. In order to test the assumption that sister species share biological traits, comparative studies of their development cycle and blood ingestion were conducted. METHODS: Eggs laid by five field females of each species were randomly selected. The nymphs were observed daily and fed on mice weekly. The time required to pass through the different stages to adulthood was recorded in days. The triatomines were weighed individually before and after feeding. The mortality rate according to each nymphal stage was calculated. RESULTS AND CONCLUSIONS: Analysis of the results shows that they display only minor biological differences even though they exhibit a distinct ecology. This suggests that the biological traits are important criteria to determine the relationship between species.

Effects of flooding of the River Paraná on the temporal activity of Anopheles (Nyssorhynchus) darlingi Root (Diptera: Culicidae), at the border state of Mato Grosso do Sul and São Paulo, Brazil

INTRODUCTION: Study of the temporal activity of malaria vectors during the implantation of a hydroelectric power station on the River Paraná, intended to generate electrical energy. The river separates the States of São Paulo and Mato Grosso do Sul, in Brazil. The objective was to verify whether alterations occurred in the wealth and diversity indices of Anopheles, following two successive floods, extended to the temporal activity and nycthemeral rhythm followed over a five year period. METHODS: Mosquito capture was performed monthly using the Human Attraction Technique and Shannon Traps. The first, executed for 24h, provided the nycthemeral rhythm and the second, lasting 15h, permitted the tracking of Anopheles during the two floods. RESULTS: The bimodal pattern of Anopheles darlingi defined before these floods was modified throughout the environment interventions. The same effect had repercussions on the populations of An albitarsis s.l., An triannulatus and An galvaoi. Activity prior to twilight was less affected by the environment alterations. CONCLUSIONS: The dam construction provoked changes in Anopheles temporal activity patterns, permitting classification of the area as an ecologically steady and unstable situation. Differences observed in Anopheles behavior due to the capture methods revealed the influence of solo and multiple attractiveness inside the populations studied.

Caraterização da tomada de decisão em organizações hospitalares : impacto do estatuto jurídico

RESUMO - O decisor hospitalar tem como função decidir os recursos de uma organização de saúde, sejam estes financeiros, materiais ou humanos, sendo decisivo o conhecimento e informação que o apoiem na aplicabilidade nas tomadas de decisão e na solução dos problemas. As tomadas de decisão suportam-se em modelos reproduzidos pelos decisores, em processos, modelos, e em princípios, que podem ou não assumir intuição, objetividade, racionalidade e ética, bem como de técnicas várias que podem ser limitativas ou condicionadas, por força de fatores vários, como: a falta de informação inerente de uma multidisciplinaridade do processo; de condicionalismos organizacionais, internos ou externos, associados à envolvente e cultura organizacional e influências políticas e macroeconómicas; ao fator tempo; a tecnologia; a estrutura e desenho organizacional; a autoridade/poder e a autonomia para decidir; a liderança, e do estatuto jurídico que o hospital possui. Este último ponto será esmiuçado, mais profundamente, neste estudo. Iremos, através do estudo, compreender se os elementos componentes das decisões tomadas nos hospitais, são ou não adaptadas em consonância com diferentes políticas de governação hospitalar, em contextos e dinâmicas organizacionais diferenciadas, por diferentes Estatutos Jurídicos Hospitalares - EPE, SPA, PPP e Privados. Foi realizado um estudo de caráter exploratório, descritivo-correlacional e transversal, baseou-se num questionário aplicado a decisores hospitalares, incidindo nos dois vetores centrais do estudo, na tomada de decisão e no estatuto jurídico hospitalar. A decisão é então, um valiosíssimo veículo na persecução das estratégias e planos formulados pelo hospital, esperando-se destes produzir consequentes resultados eficientes, eficazes e efetivos na sua aplicação.

Cocirculation of two dengue virus serotypes in individual and pooled samples of Aedes aegypti and Aedes albopictus larvae

INTRODUCTION: To detect dengue virus, eggs of Aedes sp were collected in the city of Belo Horizonte, Brazil, in 2007. METHODS: Egg samples were subsequently hatched and the larvae were tested for the presence of dengue virus RNA by RT-PCR. RESULTS: Among the Aedes aegypti larvae samples, 163 (37.4%) out of 435 were positive, including 32 (10.9%) of 293 individual larvae samples concomitantly positive for two serotypes. CONCLUSIONS: Virological surveillance detecting coinfected vectors in the field could represent an important strategy for understanding the numerous factors involved in the transmission and clinical presentation of dengue.

Rabies diagnosis and serology in bats from the State of São Paulo, Brazil

INTRODUCTION: Bats are one of the most important reservoirs and vectors of the rabies virus in the world. METHODS: From 1988 to 2003, the Zoonosis Control Center in São Paulo City performed rabies diagnosis on 5,670 bats by direct immunofluorescent test and mouse inoculation test. Blood samples were collected from 1,618 bats and the sera were analyzed using the rapid fluorescent focus inhibition test to confirm rabies antibodies. RESULTS: Forty-four (0.8%) bats were positive for rabies. The prevalence of rabies antibodies was 5.9% using 0.5IU/ml as a cutoff. Insectivorous bats (69.8%) and bats of the species Molossus molossus (51.8%) constituted the majority of the sample; however, the highest prevalence of antibodies were observed in Glossophaga soricina (14/133), Histiotus velatus (16/60), Desmodus rotundus (8/66), Artibeus lituratus (5/54), Nyctinomops macrotis (3/23), Tadarida brasiliensis (3/48), Carollia perspicillata (3/9), Eumops auripendulus (2/30), Nyctinomops laticaudatus (2/16), Sturnira lilium (2/17) and Eumops perotis (1/13). The prevalence of rabies antibodies was analyzed by species, food preference and sex. CONCLUSIONS: The expressive levels of antibodies associated with the low virus positivity verified in these bats indicate that rabies virus circulates actively among them.