Evolution of the Human Immunodeficiency Virus Type 2 Envelope in the First Years of Infection is Associated with the Dynamics of the Neutralizing Antibody Response

Background: Differently from HIV-1, HIV-2 disease progression usually takes decades without antiretroviral therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4+ T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected at birth. Results: CD4+ T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4+ T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Conclusion: Our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.

Chromosomal structure: a selectable trait for evolution

Dissertation presented to obtain the Ph.D degree in Evolutionary Biology

Intron evolution in primates

Dissertation presented to obtain a Ph.D degree in Evolutionary Biology

Intention recognition, commitment and their roles in the evolution of cooperation

Dissertação para obtenção do Grau de Doutor em Informática

Human mucocutaneous leishmaniasis in Três Braços, Bahia - Brazil: an area of Leishmania braziliensis braziliensis transmission. II. Cutaneous disease. Presentation and evolution

The clinical records of 182 patients with cutaneous leishmaniasis probably due to Leishmania braziliensis braziliensis are analysed. 68% had a single lesion which was usually an ulceron the lower anterior tibial third. Many had short histories of one to two months and all age groups were represented 13% had closed lesions of a verrucose or plaque like nature. Evolution of these skin lesions after treatment was related to the regularity of antimony therapy. Although healing usually occurred in three months, the time to scarring after commencing treatment was variable and related to the size ofthe lesion (p < 0.01). Usually if sufficient antimony treatment was given the lesion closed. Seven of the ten patients with initially negative leishmanin skin tests converted to positive after treatment. A significant decline of indirect fluorescent antibody titres occurred in patients followed, during and after therapy.

Evolution of sarcoma 180 (ascitic tumor) in mice infected with Schistosoma mansoni

Mice infected with 60 cercariae of Schistosoma mansoni were more resistant to the sarcoma 180 ascites tumor. Tumor inoculation was performed 50 days after schistosoma infection and the animals were observed and weighed at 48 hours intervals for development and progression of malignancy. In infected mice the weight gain (ascites formation) started later and was shorter than in uninfected Controls. Also, the number of tumor cells into the peritoneal cavity 72h after tumor implantation was shorter in infected group than incontrols. This in creased resistance against a transplantable tumor probably is related to the effect of endotoxin on tumoricidal activity of macrophages activated by the infection. The immunodepression induced by Schistosoma mansoni infection enhances the proliferation of endogenous bacteria increasing the amount of endotoxin absorbed from the gut.

Evolution in public procurement and the impact of e-procurement platforms: A case study

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

The Evolution of Population Distribution on the Iberian Peninsula: A Transnational Approach (1877–2001)

Surpassing the national perspective usually adopted, the authors confirmed the existence of a pattern of population distribution common to the whole Iberian Peninsula in the long run. This pattern is clearly associated with geographical factors. These variables seem to have more weight in explaining changes between 1877/78 and 1940 than in the period from 1940 to 2001. The observation of the cross-border region has shown that proximity to the frontier has not generated any distinct pattern of population density on either side of the boundary line. The spatial coherence of the observed phenomena throughout the Peninsula and of its evolution, independent of the border between states, reinforces the importance of geographic factors in their explanation. At the same time, this verification opens up new issues related to the effect of national political and economic policies.

The evolution of design with concerns on sustainability

This paper aims to analyse the birth and evolution of design with concerns over sustainability, in the context of social and civilizational changes experienced since the industrial revolution, with particular focus since the post-war period and in the context of sustainable development. It will examine several factors that influenced this design approach and that drove its evolution through different stages of maturity and complexity. It will analyse the various forms of design with environmental concerns, as well as the inclusion of other criteria in the context of sustainability, namely social ones. The aim is to settle knowledge that can allow us to draw some lessons to meet the challenges we face today.

Italian interlocking directorates: structure, evolution and cross-country comparisons

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Evolution of methodology for the study of adaptability and stability in cultivated species.

The GxE interaction only became widely discussed from evolutionary studies and evaluations of the causes of behavioral changes of species cultivated in environments. In the last 60 years, several methodologies for the study of adaptability and stability of genotypes in multiple environments trials were developed in order to assist the breeder's choice regarding which genotypes are more stable and which are the most suitable for the crops in the most diverse environments. The methods that use linear regression analysis were the first to be used in a general way by breeders, followed by multivariate analysis methods and mixed models. The need to identify the genetic and environmental causes that are behind the GxE interaction led to the development of new models that include the use of covariates and which can also include both multivariate methods and mixed modeling. However, further studies are needed to identify the causes of GxE interaction as well as for the more accurate measurement of its effects on phenotypic expression of varieties in competition trials carried out in genetic breeding programs.

The Evolution of Function in the Rab family of Small GTPases

Dissertation presented to obtain the PhD degree in Computational Biology.

Clinical and laboratory findings related to a favorable evolution of hantavirus pulmonary syndrome

The medical records of 27 patients with hantavirus pulmonary syndrome were analyzed according to the need for invasive mechanical ventilation in relation to the following data up on hospital admission: age, gender, fever, cough, dyspnea, systolic arterial blood pressure, heart rate, levels of hemoglobin, hematocrit, leukocytes, lymphocytes, platelets, creatinine and arterial blood gases. The volume infused during the first 24 hours after admission, the use of inotropic agents, the use of corticosteroids and the patient outcomes were also evaluated. A favorable outcome was related to systolic blood pressure³ 100mmHg, heart rate lower than 100 beats per minute, creatinine below 1.6mg/dl, arterial blood pH³ 7.35, bicarbonate higher than 15mEq/dl, oxygen saturation higher than 84.1%, lower rehydration volume in the first 24 hours of hospitalization and no use of inotropic agents. Absence of clinical and laboratory signs of circulatory shock up on admission was associated with a favorable outcome of the patients.

Evolution of Diplodocid Sauropod dinosaurs with emphasis on specimens from Howe Ranch, Wyoming (USA)

Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, as well as possibly Spain, England, and Asia. To date, the clade includes about 12 to 15 different species, some of them with questionable taxonomic status (e.g. ‘Diplodocus’ hayi or Dyslocosaurus polyonychius). However, intrageneric relationships of the multi-species, iconic genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which was done for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. New material from different localities and stratigraphic levels on the Howe Ranch (Shell,Wyoming, USA) sheds additional light on the evolution of Diplodocidae. Three new specimens are described herein, considerably increasing our knowledge of the anatomy of the group. The new specimens (SMA 0004, SMA 0011, and SMA 0087) represent two, to possibly three new diplodocid species. They preserve material from all parts of the skeleton, including two nearly complete skulls, as well as fairly complete manus and pedes, material which is generally rare in diplodocids. Thereby, they considerably increase anatomical overlap between the sometimes fragmentary holotype specimens of the earlier described diplodocid species, allowing for significant results in a specimenbased phylogenetic analysis. Furthermore, clavicles and interclavicles are identified, the latter for the first time in dinosaurs. Their presence seems restricted to early sauropods, flagellicaudatans, and early Macronaria, and might thus be a retained plesiomorphy, with the loss of these bones being synapomorphic for Titanosauriformes and possibly Rebbachisauridae. The new material allows to test previous hypotheses of diplodocid phylogeny. In order to do so, any type specimen previously proposed to belong to Diplodocidae was included in the study, as are relatively complete referred specimens, in order to increase the degree of overlapping material. For specimens subsequently suggested to be non-diplodocid sauropods, their hypothesized sister taxa were included as outgroups. The current phylogenetic analysis thus includes 76 operational taxonomic units, 45 of which belong to Diplodocidae. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses done within sauropod dinosaurs. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Basing on a newly developed numerical approach to reduce subjectivity in the decision of specific or generic separation, species that have historically been included into well-known genera like Apatosaurus or Diplodocus, were detected to be actually generically different. Thereby, the famous genus Brontosaurus is resuscitated, and evidence further suggests that also Elosaurus parvus (previously referred to Apatosaurus) or ‘Diplodocus’ hayi represent unique genera. The study increases our knowledge about individual variation, and helps to decide how to score multi-species genera. Such a specimen-based phylogenetic analysis thus proves a valuable tool to validate historic species in sauropods, and in paleontology as a whole.