Pollution and water quality control of the River Tejo. Report on a visit to Portugal, Sep 27th - October 10th, 1987

Fundamental changes in the management of water resources in Portugal are now evolving. Five regional organisations termed Administracaos de Regiao Hidrographic (ARH), will be created to manage water resources within their respective geographical areas. These areas will be catchment based. As a fore-runner to the implementation of the five ARH's a foundation project has been established within the Direcao-Geral do Recursos Naturais to examine the practical implications of the new system. This project has been divided into a number of sub-projects and complementary projects to include the Tejo complementary project. The Tejo complementary project is the focus of this report. The report is to advise on the role of biology in the proposed ARH, to establish priorities for biological studies within the present Projecto de Gestao Integrada dos Recursos Hidricos da Bacia Hidrografica do Rio Tejo (PGIRH/T) and to assist with the planning of laboratory facilities for biology at the new PGIRH/T laboratory at Alges, Lisboa.

Estudo estrutural do pênis de fetos humanos normais e anencéfalos no segundo trimestre de gestação

A anecencefalia é o Defeito do Tubo Neural (DTN) mais severo em fetos humanos. Há uma demanda crescente para reposição tissular em doenças crônicas e cirurgias reconstrutoras. Tecidos fetais têm sido utilizados como substitutos para órgãos sólidos. Comparar a estrutura e morfologia do corpo cavernoso e corpo esponjoso de pênis de fetos humanos anencéfalos e de controle a fim de propor um novo modelo para estudos biológicos e transplantes teciduais. Foram estudados 11 pênis de fetos de controle de 14 a 23 Semanas Pós Concepção (SPC), e cinco pênis de fetos anencéfalos de 18 a 22 SPC. Os órgãos foram removidos e processados pelas técnicas histo e imunohistoquímicas rotineiras. A análise do tecido conjuntivo, células musculares lisas e fibras elásticas foram realizadas em lâminas dos espécimes. Os dados foram expressos em Densidade de àrea (Da) utilizando-se um software de processamento digital. As médias foram comparadas utilizando-se o Teste - T não pareado e quando aplicável, a regressão linear simples foi utilizada. Foi considerada significância estatística se p<0,05. O septo intercavernoso encontrava-se presente em todas as amostras. Não foram observadas diferenças da Da do tecido colágeno e musculatura lisa dos pênis de fetos anencéfalos quando comparados aos normais. A regressão linear simples sugere que durante o desenvolvimento humano há um aumen2to gradual do tecido colágeno (R2=0,45) e uma diminuição da musculatura lisa (R =0,62) no corpo cavernoso de ambos os grupos. A elastina encontrava-se presente apenas em fetos a partir da 20 SPC. Não houve diferença na estrutura da genitália entre fetos normais e enencéfalos. Apresença da elastina em fetos a partir da 20 SPC é um dado objetivo da manutenção da capacidade de ereção nestes grupos. A histo e imunohistoquímica sugerem que o desenvolvimento do pênis destes fetos encontra-se inalterado. Futuros estudos deverão ser realizados com o objetivo de avaliar fetos anencéfalos como um potencial grupo de doadores teciduais e um adequado modelo para estudos biológicos.

Análise da citotoxicidade do extrato do fruto de juçara (Euterpe oleracea Mart.) do Maranhão em células malignas humanas

A juçara, Euterpe oleracea Mart., fruta indígena da Amazônia Legal, é rica em fitoquímicos com atividades anti-oxidante, antiinflamatória e anti-câncer. Este estudo tem por objetivo analisar os efeitos do extrato hidroalcoólico da casca, caroço e fruto total da juçara em diferentes linhagens de células malignas humana. Os frutos foram coletados no Parque da Juçara, localizado no Maracanã, município de São Luís, seguida da confecção da excicata que se mantém registrada no Herbário Rosa Mochel do Núcleo de Estudos Biológicos da Universidade Estadual do Maranhão. Os extratos hidroalcoólicos da casca, caroço e fruto total foram extraidos no Laboratório de Farmacologia e Psicobiologia da UERJ. As linhagens celulares utilizadas nos ensaios foram MCF-7 (adenocarcinoma de mama), CACO-2 e HT-20 (adenocarcinoma colo retal) e adenocarcinoma na mama (MDA-MB-468). As linhagens foram tratadas com 10, 20 e 40g/mL dos extratos por 24 e 48 horas e feitas às análises. Células MCF-7 controle apresentaram núcleo proeminente com nucléolos evidentes. Após tratamento com o extrato hidroalcoólico da casca da juçara, as células mostraram morfologia arredondada com retração do citoplasma. O ensaio de viabilidade com MTT ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide)) demonstrou uma redução na viabilidade das células. Após 48 horas, o tratamento das células com 20g/mL do extrato da casca reduziu a viabilidade sendo que o efeito citotóxico do tratamento com 40g/mL do extrato da casca foi potencializado. Células tratadas com 10g/mL do extrato do caroço de juçara apresentavam-se arredondadas com consequente redução no volume celular. A concentração 20g/mL de extrato hidroalcoólico do caroço, causou severa redução no volume das células e ocasionou o surgimento de vacúolos intracelulares. O mesmo foi observado após tratamento com 40g/mL. O tratamento com 40g/mL do extrato hidroalcoólico do fruto total, modificou drasticamente a morfologia das células MCF-7 causando vacuolização e aparente lise com perda do conteúdo citoplasmático e o ensaio da viabilidade com MTT demonstrou redução na viabilidade das células MCF-7 tratadas com 20 e 40g/mL após 24 horas de tratamento. Análises por MET (Microscopia Eletrônica de Transmissão) demonstraram o surgimento de vesículas autofágicas, cuja comprovação deu-se com a identificação da expressão da proteína LC3BII na membrana do autofagossoma pela técnica de Western Blotting. Mediante o demonstrado pelos experimentos, com as linhagens MCF-7 e MDA-MB-468, confirma-se que as frações isoladas do extrato do caroço da juçara, promove modificações celulares indicativas de autofagia a partir de 10g/mL, em 24 horas. O núcleo permaneceu íntegro, não apresentando características de núcleo apoptótico. Os dados são conclusivos para ocorrência de morte celular por autofagia em linhagem celulares de carcinoma de mama MCF-7 quando tratadas com extrato hidroalcoólico da casca, caroço e fruto total da juçara do Maranhão, agente quimiopreventivo no câncer de mama estrogênio-dependente.

Os recursos de algas marinhas de importáncia económica na República popular de Moçambique com especial referéncia para Euchema (Florideae) em Cabo Delgado

Composition, abundance and environmental characteristics of the sea-weed resources of Mozambique were investigated along the whole Mozambican sea shore between May, 1979 and November, 1980. The limits of distribution of tropical algae were identified and located close to parallel 21 degree 00'S. Important concentrations of sea-weeds were found in the southern region, but only the Euchema resource in the coast of Cabo Delgado looked promising for commercial exploitation. Biological studies of Euchema were undertaken, the results of which permit the recommendation of a strategy for immediate harvesting which could yield 400-500 tons annually. Further proposals for the culture of sea-weeds are also included.

Fishery and biology of Penaeid prawns at Harnaii, Mahatashtra

Penaeid prawn fishery at Harnaii in Ratnagiri District of Maharashtra was investigated during fishing seasons of 2002-03 and 2003-04 from mechanized (MLD) and hand operated trawlers (HT). During the two years, MLD contributed 86% and HT 14% to the average annual penaeid prawn catch of 2,242 t. The catch showed two peaks, a major during October-December and a minor during April-May in both the gears but abundance of the individual species differed. P. stylifera, Metapenaeopsis affinis, Solenocera crassicornis, Metapenaeopsis brevicornis, P. merguiensis and Metapenaeopsis dobsoni mainly constituted the fishery and their species composition, seasonal abundance, annual size distribution and monthly mean size were investigated. Biological studies on food, size at maturity, spawning period, sex-ratio and juvenile abundance were carried out to explain temporal abundance of the species in the fishery. Among the species P. stylifera, M. affinis and S. crassicornis exhibited distinct seasonality with two spawning peaks, one in pre-monsoon and the other in post monsoon period to produce two discrete broods while P. merguiensis despite two spawning peaks exhibited a single dominant brood. M. brevicornis showed monsoon and post-monsoon spawning while M. dobsoni showed only post-monsoon spawning. Migrations between nearshore and offshore waters resulted in mixing of the broods and they remained inseparable in the catch.

Aspects of the biology of the Lake Tanganyika sardine, Limnothrissa miodon (Boulenger), in Lake Kariba

Juveniles of limnothrissa miodon (Boulenger) were introduced into the man-made Lake Kariba in 1967-1968. Thirty months of night-fishing for this species from Sinazongwe, near the centre of the Kariba North bank, from 1971 to 1974 are described. Biological studies were carried out on samples of the catch during most of these months. Limnological studies were carried out over a period of four months in 1973. Limnothrissa is breeding successfully and its number have greatly increased. It has reached an equilibrium level of population size at a lower density than that of Lake Tanganyika sardines, but nevertheless is an important factor in the ecology of Lake Kariba. The growth rate, size at maturity and maximum size are all less than those of Lake Tanganyika Limnothrissa. A marked disruption in the orderly progression of length frequency modes occurs in September, for which the present body of evidence cannot supply an explanation.

Badania spektroskopowe, strukturalna i aktywność przeciwdrobnoustrojowa nowych soli kwasu lasalowego z aminami

Wydział Chemii

Design, synthesis and development of novel indolocarbazole derivatives as potential anti-cancer agents

This thesis describes work carried out on the design of new routes to a range of bisindolylmaleimide and indolo[2,3-a]carbazole analogs, and investigation of their potential as successful anti-cancer agents. Following initial investigation of classical routes to indolo[2,3-a]pyrrolo[3,4-c]carbazole aglycons, a new strategy employing base-mediated condensation of thiourea and guanidine with a bisindolyl β-ketoester intermediate afforded novel 5,6-bisindolylpyrimidin-4(3H)-ones in moderate yields. Chemical diversity within this H-bonding scaffold was then studied by substitution with a panel of biologically relevant electrophiles, and by reductive desulfurisation. Optimisation of difficult heterogeneous literature conditions for oxidative desulfurisation of thiouracils was also accomplished, enabling a mild route to a novel 5,6-bisindolyluracil pharmacophore to be developed within this work. The oxidative cyclisation of selected acyclic bisindolyl systems to form a new planar class of indolo[2,3-a]pyrimido[5,4-c]carbazoles was also investigated. Successful conditions for this transformation, as well as the limitations currently prevailing for this approach are discussed. Synthesis of 3,4-bisindolyl-5-aminopyrazole as a potential isostere of bisindolylmaleimide agents was encountered, along with a comprehensive derivatisation study, in order to probe the chemical space for potential protein backbone H-bonding interactions. Synthesis of a related 3,4-arylindolyl-5-aminopyrazole series was also undertaken, based on identification of potent kinase inhibition within a closely related heterocyclic template. Following synthesis of approximately 50 novel compounds with a diversity of H-bonding enzyme-interacting potential within these classes, biological studies confirmed that significant topo II inhibition was present for 9 lead compounds, in previously unseen pyrazolo[1,5-a]pyrimidine, indolo[2,3-c]carbazole and branched S,N-disubstituted thiouracil derivative series. NCI-60 cancer cell line growth inhibition data for 6 representative compounds also revealed interesting selectivity differences between each compound class, while a new pyrimido[5,4-c]carbazole agent strongly inhibited cancer cell division at 10 µM, with appreciable cytotoxic activity observed across several tumour types.

Coccolithophore bloom detection in the north east Atlantic using SeaWiFS: Algorithm description, application and sensitivity analysis

Coccolithophores are the largest source of calcium carbonate in the oceans and are considered to play an important role in oceanic carbon cycles. Current methods to detect the presence of coccolithophore blooms from Earth observation data often produce high numbers of false positives in shelf seas and coastal zones due to the spectral similarity between coccolithophores and other suspended particulates. Current methods are therefore unable to characterise the bloom events in shelf seas and coastal zones, despite the importance of these phytoplankton in the global carbon cycle. A novel approach to detect the presence of coccolithophore blooms from Earth observation data is presented. The method builds upon previous optical work and uses a statistical framework to combine spectral, spatial and temporal information to produce maps of coccolithophore bloom extent. Validation and verification results for an area of the north east Atlantic are presented using an in situ database (N = 432) and all available SeaWiFS data for 2003 and 2004. Verification results show that the approach produces a temporal seasonal signal consistent with biological studies of these phytoplankton. Validation using the in situ coccolithophore cell count database shows a high correct recognition rate of 80% and a low false-positive rate of 0.14 (in comparison to 63% and 0.34 respectively for the established, purely spectral approach). To guide its broader use, a full sensitivity analysis for the algorithm parameters is presented.

Suggested Binding Mechanism of the HIV-gp120 to its CD4 Receptor

The molecular recognition and attachment of the CD4 molecule and the HIV envelope glycoprotein (gp120) might be described as a consecutive three-step molecular recognition process. 1. (a) Long range interaction: electrostatic pre-orientation, 2. (b) short range interaction: electronic attachment followed by a ‘Locking-in’ (via aromatic ring orientation) and 3. (c) internal interaction (induced fit): conformational readjustment of the protein molecules. On the basis of the preliminary investigations (X-ray structures of CD4 and biological studies of CD4 and gp120 point mutants) we described a computational model. This approach consists of empirical calculations as well as ab initio level of quantum chemistry. The conformational analysis of the wild type and mutant CD4 molecules was supported by molecular mechanics and dynamics (Amber force field). The latter analysis involves the application of a novel method, the Amino Acid Conformation Assignment of Proteins (ACAP) software, developed for the notation of secondary protein structures. According to the cardinal role of the electrostatic factors during this interaction, several ab initio investigations were performed for better understanding of the recognition process on submolecular level. Using the above mentioned computational model, we could interpret the basic behaviours and predict some additional features of CD4-gp120 interaction, in spite of the missing gp120 X-ray structure.

New tools for chemical modification of proteins

Tese de doutoramento, Farmácia (Química Farmacêutica e Terapêutica), Universidade de Lisboa, Faculdade de Farmácia, 2014

On the applicability of mathematics : philosophical and historical perspectives

The present thesis is a contribution to the debate on the applicability of mathematics; it examines the interplay between mathematics and the world, using historical case studies. The first part of the thesis consists of four small case studies. In chapter 1, I criticize "ante rem structuralism", proposed by Stewart Shapiro, by showing that his so-called "finite cardinal structures" are in conflict with mathematical practice. In chapter 2, I discuss Leonhard Euler's solution to the Königsberg bridges problem. I propose interpreting Euler's solution both as an explanation within mathematics and as a scientific explanation. I put the insights from the historical case to work against recent philosophical accounts of the Königsberg case. In chapter 3, I analyze the predator-prey model, proposed by Lotka and Volterra. I extract some interesting philosophical lessons from Volterra's original account of the model, such as: Volterra's remarks on mathematical methodology; the relation between mathematics and idealization in the construction of the model; some relevant details in the derivation of the Third Law, and; notions of intervention that are motivated by one of Volterra's main mathematical tools, phase spaces. In chapter 4, I discuss scientific and mathematical attempts to explain the structure of the bee's honeycomb. In the first part, I discuss a candidate explanation, based on the mathematical Honeycomb Conjecture, presented in Lyon and Colyvan (2008). I argue that this explanation is not scientifically adequate. In the second part, I discuss other mathematical, physical and biological studies that could contribute to an explanation of the bee's honeycomb. The upshot is that most of the relevant mathematics is not yet sufficiently understood, and there is also an ongoing debate as to the biological details of the construction of the bee's honeycomb. The second part of the thesis is a bigger case study from physics: the genesis of GR. Chapter 5 is a short introduction to the history, physics and mathematics that is relevant to the genesis of general relativity (GR). Chapter 6 discusses the historical question as to what Marcel Grossmann contributed to the genesis of GR. I will examine the so-called "Entwurf" paper, an important joint publication by Einstein and Grossmann, containing the first tensorial formulation of GR. By comparing Grossmann's part with the mathematical theories he used, we can gain a better understanding of what is involved in the first steps of assimilating a mathematical theory to a physical question. In chapter 7, I introduce, and discuss, a recent account of the applicability of mathematics to the world, the Inferential Conception (IC), proposed by Bueno and Colyvan (2011). I give a short exposition of the IC, offer some critical remarks on the account, discuss potential philosophical objections, and I propose some extensions of the IC. In chapter 8, I put the Inferential Conception (IC) to work in the historical case study: the genesis of GR. I analyze three historical episodes, using the conceptual apparatus provided by the IC. In episode one, I investigate how the starting point of the application process, the "assumed structure", is chosen. Then I analyze two small application cycles that led to revisions of the initial assumed structure. In episode two, I examine how the application of "new" mathematics - the application of the Absolute Differential Calculus (ADC) to gravitational theory - meshes with the IC. In episode three, I take a closer look at two of Einstein's failed attempts to find a suitable differential operator for the field equations, and apply the conceptual tools provided by the IC so as to better understand why he erroneously rejected both the Ricci tensor and the November tensor in the Zurich Notebook.

Development of a bacteriophage-based biopesticide for fire blight

Fire blight is an economically important disease of apples and pears that is caused by the bacterium Erwinia amylovora. Control of the disease depends on limiting primaly blosson1 infection in the spring, and rapidly removing infected tissue. The possibility of using phages to control E.amylovora populations has been suggested, but previous studies have. failed to show high treatment efficacies. This work describes the development of a phage-based biopesticide that controls E. amylovora populations under field conditions, and significantly reduces the incidence of fire blight. This work reports the first use ofPantoea agglomerans, a non-pathogenic relative ofE. amylovora, as a carrier for E. amylovora.phages. Its role is to support a replicating population of these phages on blossom surfaces during the period when the flowers are most susceptible to infection. Seven phages and one carrier isolate were selected for field trials from existing collections of 56 E. amylovora phages and 249 epiphytic orchard bacteria. Selection of the . /' phages and carrier was based on characteristics relevant to the production and field perfonnance of a biopesticide: host range, genetic diversity, growth under the conditions of large-scale production, and the ability to prevent E. amylovora from infecting pear blossoms. In planta assays showed that both the phages and the carrier make significant contributions to reducirig the development of fire blight symptoms in pear blossoms. Field-scale phage production and purification methods were developed based on the growth characteristics of the phages and bacteria in liquid culture, and on the survival of phages in various liquid media. Six of twelve phage-carrier biopesticide treatments caused statistically signiflcant reductions in disease incidence during orchard trials. Multiplex real-time PCR was used to simultaneously monitor the phage, carrier, and pathogen populations over the course of selected treatments. In all cases. the observed population dynamics of the biocontrol agents and the pathogen were consistent with the success or failure of each treatment to control disease incidence. In treatments exhibiting a significantly reduced incidel1ce of fire blight, the average blossom population ofE.amylovora had been reduced to pre-experiment epiphytic levels. In successful treatments the phages grew on the P. agglomerans carrier for 2 to 3 d after treatment application. The phages then grew preferentially on the pathogen, once it was introduced into this blossom ecosystem. The efficacy of the successful phage-based treatnlents was statistically similar to that of streptomycin, which is the most effective bactericide currently available for fire blight prevention. The in planta behaviour ofE. amylovora was compared to that ofErwinia pyrifoliae, a closely related species that causes fire blight-like synlptoms on pears in southeast Asia. Duplex real-time PCR was used to monitor the population dynamics of both species on single blossonls. E. amylovora exhibited a greater competitive fitness on Bartlett pear blossoms than E. pyrifoliae. The genome ofErwinia phage Ea21-4 was sequenced and annotated. Most of the 8-4.7 kB genome is substantially different from previously described sequences, though some regions are notably similar to Salmonella phage Felix 01 . Putative functions were assigned to approximately 30% of the predicted open reading frames based on amino acid sequence comparisons and N-terminal sequencing of structural proteins.

Synthèse stéréosélective de pipéridines et activation électrophile chimiosélective d’amides en présence de dérivés de la pyridine

L’importance des produits naturels dans le développement de nouveaux médicaments est indéniable. Malheureusement, l’isolation et la purification de ces produits de leurs sources naturelles procure normalement de très faibles quantités de molécules biologiquement actives. Ce problème a grandement limité l’accès à des études biologiques approfondies et/ou à une distribution sur une grande échelle du composé actif. Par exemple, la famille des pipéridines contient plusieurs composés bioactifs isolés de sources naturelles en très faible quantité (de l’ordre du milligramme). Pour pallier à ce problème, nous avons développé trois nouvelles approches synthétiques divergentes vers des pipéridines polysubstituées contenant une séquence d’activation/désaromatisation d’un sel de pyridinium chiral et énantioenrichi. La première approche vise la synthèse de pipéridines 2,5-disubstituées par l’utilisation d’une réaction d’arylation intermoléculaire sur des 1,2,3,4-tétrahydropyridines 2-substituées. Nous avons ensuite développé une méthode de synthèse d’indolizidines et de quinolizidines par l’utilisation d’amides secondaires. Cette deuxième approche permet ainsi la synthèse formelle d’alcaloïdes non-naturels à la suite d’une addition/cyclisation diastéréosélective et régiosélective sur un intermédiaire pyridinium commun. Finalement, nous avons développé une nouvelle approche pour la synthèse de pipéridines 2,6-disubstituées par l’utilisation d’une réaction de lithiation dirigée suivie d’un couplage croisé de Negishi ou d’un parachèvement avec un réactif électrophile. Le développement de transformations chimiosélectives et versatiles est un enjeu crucial et actuel pour les chimistes organiciens. Nous avons émis l’hypothèse qu’il serait possible d’appliquer le concept de chimiosélectivité à la fonctionnalisation d’amides, un des groupements le plus souvent rencontrés dans la structure des molécules naturelles. Dans le cadre précis de cette thèse, des transformations chimiosélectives ont été réalisées sur des amides secondaires fonctionnalisés. La méthode repose sur l’activation de la fonction carbonyle par l’anhydride triflique en présence d’une base faible. Dans un premier temps, l’amide ainsi activé a été réduit sélectivement en fonction imine, aldéhyde ou amine en présence d’hydrures peu nucléophiles. Alternativement, un nucléophile carboné a été employé afin de permettre la synthèse de cétones ou des cétimines. D’autre part, en combinant un amide et un dérivé de pyridine, une réaction de cyclisation/déshydratation permet d’obtenir les d’imidazo[1,5-a]pyridines polysubstituées. De plus, nous avons brièvement appliqué ces conditions d’activation au réarrangement interrompu de type Beckmann sur des cétoximes. Une nouvelle voie synthétique pour la synthèse d’iodures d’alcyne a finalement été développée en utilisant une réaction d’homologation/élimination en un seul pot à partir de bromures benzyliques et allyliques commercialement disponibles. La présente méthode se distincte des autres méthodes disponibles dans la littérature par la simplicité des procédures réactionnelles qui ont été optimisées afin d’être applicable sur grande échelle.

INDIAN AND ANTARCTIC BRYOZOANS - TAXONOMY AND OBSERVATIONS ON TOXICOLOGY

This thesis embodies findings on a taxonomical investigation of a group of lower marine invertebrates belonging to the category coelomata. Bryozoans are well known both in fossil and recent taxonomical history. They comprise of about 5,000 living and 16000 fossil species. Bryozoans are well known for their taxonomic abundance and structural diversity,representing the various ecological niches ranging from the intertidal to the abyssal benthic. At a time when global marine biological diversity has become a concern of not only to the scientists but also to the policy makers,an understanding of species diversity and abundance are cardinal aspects of biological studies. Geological time scales which is known that by Pre-Cambrian, marine invertebrate diversity reach the maximum and this diversity has become more comprehensive as time advanced. Taxonomists a vanishing species of scientists have become more concerned in discerning patterns of species diversity. The basic tool for this is identification fo animals. with this idea in mind a detailed study of taxonomy of bryozoan was undertaken . The major part of this thesis is devoted to describe various species of bryozoans with detailed description and ecotypical variations.The pattern of distribution and abundance which are important aspects of animal groups have also been documented. Possible effects of heavy metal contamination on the tolerance and growth of bryozoans, a few species of which have been eliminated from the chronically polluted areas of Cochin backwaters have also been documented.