The Fisheries for Mangrove Cockles,Anadaraspp., from Mexico to Peru, With Descriptions of Their Habitats and Biology, the Fishermen’s Lives, and the Effects of Shrimp Farming

This paper provides the first description of the mangrove cockle, Anadara spp., fisheries throughout their Latin American range along the Pacific coast from Mexico to Peru. Two species, A. tuberculosa and A. grandis, are found over the entire range, while A. similis occurs from El Salvador to Peru. Anadara tuberculosa is by far the most abundant, while A. grandis has declined in abundance during recent decades. Anadara tuberculosa and A. similis occur in level mud sediments in mangrove swamps, comprised mostly of Rhizophora mangle, which line the main-lands and islands of lagoons, whereas A. grandis inhabits intertidal mud flats along the edges of the same mangrove swamps. All harvested cockles are sexually mature. Gametogenesis of the three species occurs year round, and juvenile cockles grow rap-idly. Cockle densities at sizes at least 16–42 mm long ranged from 7 to 24/m2 in Mexico. Macrofaunal associates of cockles include crustaceans, gastropods, and finfishes. The mangrove swamps are in nearly pristine condition in every country except Honduras, Ecuador, and Peru, where shrimp farms constructed in the 1980’s and 1990’s have destroyed some mangrove zones. In addition, Hurricane Mitch destroyed some Honduran mangrove swamps in 1998. About 15,000 fishermen, including men, women, and children, harvest the cockles. Ecuador has the largest tabulated number of fishermen, 5,055, while Peru has the fewest, 75. Colombia has a large number, perhaps exceeding that in Ecuador, but a detailed census of them has never been made. The fishermen are poor and live a meager existence; they do not earn sufficient money to purchase adequate food to allow their full health and growth potential. They travel almost daily from their villages to the harvesting areas in wooden canoes and fiberglass boats at low tide when they can walk into the mangrove swamps to harvest cockles for about 4 h. Harvest rates, which vary among countries owing to differences in cockle abundances, range from about 50 cockles/fisherman/day in El Salvador and Honduras to 500–1,000/ fisherman/day in Mexico. The fishermen return to their villages and sell the cockles to dealers, who sell them mainly whole to market outlets within their countries, but there is some exporting to adjacent countries. An important food in most countries, the cockles are eaten in seviche, raw on the half-shell, and cooked with rice. The cockles are under heavy harvesting pressure, except in Mexico, but stocks are not yet being depleted because they are harvested at sizes which have already spawned. Also some spawning stocks lie within dense mangrove stands which the fishermen cannot reach. Consumers fortunately desire the largest cockles, spurning the smallest. Cockles are important to the people, and efforts to reduce the harvests to prevent overfishing would lead to severe economic suffering in the fishing communities. Pro-grams to conserve and improve cockle habitats may be the most judicious actions to take. Preserving the mangrove swamps intact, increasing their sizes where possible, and controlling cockle predators would lead to an increase in cockle abundance and harvests. Fishes that prey on juvenile cockles might be seined along the edges of swamps before the tide rises and they swim into the swamps to feed. Transplanting mangrove seedlings to suitable areas might increase the size of those habitats. The numbers of fishermen may increase in the future, because most adults now have several children. If new fishermen are tempted to harvest small, immature cockles and stocks are not increased, minimum size rules for harvestable cockles could be implemented and enforced to ensure adequate spawning.

Understanding the Market for Charter and Headboat Fishing Services

Published and unpublished research findings regarding charter and headboat fishing customers from 11 studies were reviewed to provide a marketing data base for operators and to guide further research efforts. Generally, charter/headboat fishing is a male-oriented activity. Customers were between 30 and 55 years of age. Although both groups of anglers considered themselves to be experienced, charterboat anglers had fished for more years. Charter anglers fished more often with their families and headboat anglers more often with their friends. Charterboat anglers reported higher incomes than headboat anglers. Relaxation, having fun, and escaping from daily pressures were generally more important to both groups of anglers than motives relative to catching fish. Most anglers indicated that the skills and performance of the captain and crew contributed heavily to the overall evaluation of their fishing experience. Anglers were more heavily influenced to choose a particular captain or boat by informal advertising methods (i.e., word-of-mouth recommendations, reputation, and visits to the marina) than formal methods (i.e., advertisements, brochures, radio, and television). Charter anglers relied more on word-of-mouth recommendations and headboat customers were more influenced by previous experiences. Implications for further research are discussed.

Metas de socialização e práticas educativas de mães de crianças com câncer: um estudo comparativo com mães de crianças sem diagnóstico de doença

Sistemas parentais são construídos através das interações no cotidiano dos pais com seus filhos e com base nos padrões culturais vigentes, dentro de um perfil socioeconômico e da história de vida dos indivíduos. Importantes componentes dos sistemas parentais são as metas de socialização e as práticas educativas. As metas de socialização se referem a como os pais desejam que seus filhos sejam no futuro, àquilo que eles esperam que sua criação ajude a promover em seus filhos. Já as práticas educativas são as práticas de comunicar à criança a forma correta com que se espera que ela se comporte. A revisão bibliográfica evidencia que as metas de socialização e práticas educativas são afetadas pelo ambiente cultural dos cuidadores e por variáveis socioeconômicas, mas não há estudos a respeito de possíveis impactos causados por situações de vida particularmente difíceis. A presente dissertação se propôs a examinar as metas de socialização e práticas educativas de mães cujos filhos estão em tratamento oncológico, contrastando-as com as de mães de crianças saudáveis. Nesse sentido, o objetivo estabelecido foi o de investigar se havia particularidades nas metas de socialização e formas de cuidado de mães com filhos que tenham câncer devido à situação específica vivida de um tratamento oncológico. Hipotetizou-se que a vivência da experiência do câncer e a inserção em uma instituição de tratamento, no caso, o Instituto Nacional do Câncer (INCA), teriam impacto no sistema de cuidados e metas parentais. Participaram deste estudo 20 mães de crianças de três a cinco anos que estavam em tratamento oncológico no INCA e 20 mães de crianças na mesma faixa etária sem problemas de saúde diagnosticados. Todas assinaram o Termo de Consentimento Livre e Esclarecido. Foram aplicados os formulários "Dados de identificação" e "Dados sociodemográficos", e o Questionário de Metas de Socialização. Foi também realizada com as mães uma entrevista semiestruturada, com questões abertas que buscaram investigar práticas educativas. A análise de dados contemplou uma parte de análises quantitativas em que os dados foram tratados descritivamente (médias, percentuais etc.) e empregados testes não-paramétricos para comparação entre os grupos de mães. Análises qualitativas, voltadas para as respostas ao questionário de metas de socialização e à entrevista sobre práticas de cuidado educativas foram realizadas através do método de análise de conteúdo temático-categorial. Encontrou-se que as metas de socialização das mães de crianças em tratamento oncológico apresentaram diferenças em relação às das mães de crianças sem diagnóstico de doença, refletindo uma tendência mais individualista. Também foram encontradas diferenças entre os dois grupos nas ações para atingir as metas, sendo visto um uso menor da estratégia educar e orientar por parte do grupo das mães de crianças em tratamento no INCA, refletindo uma tendência mais pragmática. Quanto às práticas educativas não foram encontradas diferenças significativas entre os dois grupos. Espera-se que esse estudo traga contribuições para a formulação de programas de intervenção, para pais e cuidadores, através da melhor compreensão das metas e práticas maternas utilizadas nesta situação particular e de grande dificuldade para as crianças e suas famílias

Strandings as indicators of marine mammal biodiversity and human interactions off the coast of North Carolina

The adjacency of 2 marine biogeographic regions off Cape Hatteras, North Carolina (NC), and the proximity of the Gulf Stream result in a high biodiversity of species from northern and southern provinces and from coastal and pelagic habitats. We examined spatiotemporal patterns of marine mammal strandings and evidence of human interaction for these strandings along NC shorelines and evaluated whether the spatiotemporal patterns and species diversity of the stranded animals reflected published records of populations in NC waters. During the period of 1997–2008, 1847 stranded animals were documented from 1777 reported events. These animals represented 9 families and 34 species that ranged from tropical delphinids to pagophilic seals. This biodiversity is higher than levels observed in other regions. Most strandings were of coastal bottlenose dolphins (Tursiops truncatus) (56%), harbor porpoises (Phocoena phocoena) (14%), and harbor seals (Phoca vitulina) (4%). Overall, strandings of northern species peaked in spring. Bottlenose dolphin strandings peaked in spring and fall. Almost half of the strandings, including southern delphinids, occurred north of Cape Hatteras, on only 30% of NC’s coastline. Most stranded animals that were positive for human interaction showed evidence of having been entangled in fishing gear, particularly bottlenose dolphins, harbor porpoises, short-finned pilot whales (Globicephala macrorhynchus), harbor seals, and humpback whales (Megaptera novaeangliae). Spatiotemporal patterns of bottlenose dolphin strandings were similar to ocean gillnet fishing effort. Biodiversity of the animals stranded on the beaches reflected biodiversity in the waters off NC, albeit not always proportional to the relative abundance of species (e.g., Kogia species). Changes in the spatiotemporal patterns of strandings can serve as indicators of underlying changes due to anthropogenic or naturally occurring events in the source populations.

Quantitative and qualitative assessment of plankton: some ecological aspect and water quality parameters of the river Meghna, Bangladesh

Investigation on the seasonal distribution and abundance of various major taxa of phyto and zooplankton and the corresponding physico-chemical characteristics were carried out in four selected stations between the latitude 22°35.494N N-23°23.987 N and longitude 90°35.793 E- 90°49.061 E of the Meghna river system, Bangladesh. Drop count method was followed for the qualitative and quantitative analysis of both phyto- and zooplankton. A total of 41 phytoplankton genera belonging to 17 families and 13 zooplankton genera belonging to 11 families were recorded. Zooplankton growth cycle was noticeably less (3.0%) than the phytoplankton abundance almost throughout the study period. Quantity of plankton registered to increase chronologically from the upper to lower stretches of the river. During summer investigation the load of phytoplankton was recorded maximum (11,300-51,850 No/1). Ratio-wise quantitative difference between zoo- and phytoplankton in composition of the total standing crop fluctuated between 1.0:5.5 and 1:1037. Among the phytoplanktonic groups, Chlorophyceae was found to be dominating (95.0%) in all sampling stations. Protococcus, a single genus of Chlorophyceae played a unique role during summer, contributing the highest density of about 74.0%. The pattern of qualitative and quantitative difference of plankton standing crop in different sampling sites can be attributed to the existing physico-chemical characteristics, mainly water temperature, pH and hardness.

Vegetation structure and faunal composition of Wathurana wetland ecosystem Tebuwana, Kalutara, Sri Lanka

A study was conducted in Tebuwana Wathurana Wetland ecosystem to understand its vegetation structure and faunal composition in order to assess its conservation needs. As there are no published records on the flora and fauna of Wathurana Wetlands in Tebuwana, it is necessary to understand the ecological and other relevant features in order to develop strategies to conserve this wetland. These objectives were pursued by surveying the vegetation of the wetland and by identifying fish and bird species present. A total of 66 species of flora and 61 species of fauna were identified in the survey. Of the 27 fish species recorded from the Tebuwana Wetland, 9 species were endemic and 17 species belonged to the indigenous category. With regard to the flora in the wetlands, the dominant families were Rubaceae, Fabaceae and Arecaceae. The 66 species belonged to 39 families and 61 genera while 12 species were endemic and 4 species were considered highly threatened. These flora were found in four layers. Of the 22 species of birds recorded, two species were endemic. This study revealed that these Wathurana Wetlands have a high species diversity but that they face many threats including encroachments, extraction of forest products mainly as timber, land filling, mining and occurrence of invasive species. It is essential to minimize the exploitation of natural resources from this wetland in the future and in particular to mark the boundary, conduct awareness programmes and continue research.

Survey of biosystematic and sexual reproductive physiology in Holothuroidea on Hormozgan Province

Sea cucumbers belong to phylum Echinodermata, order Holothuroidea are an abundant and diverse group of Invertebrates, with over 1400 species occuring from the intertidal to the deepest oceanic trenches. Sea cucumbers are important components of the food chain in temperate and coral reef ecosystems and they play an important role as deposite feeders and suspension feeders. Rapid decline in populations may have serious consequences for the survival of other species that are part of the same complex food web,as the eggs, larve and juveniles constitute an important food source for the other marine species including crustaceans, fish and mollusks. In addition sea cucumbers are often called the earthworms of the sea, because they are responsible for the extensive shifting and mixing of the substrate, and recycling of detrital matter. Sea cucumbers consume and grind sediment and organic material into finer particles , turning over the top layers of sediment in lagoons , reefs and other habitats and allowing the penetration of oxygen. While the taxonomy of the holothurian families is generally well known , the distinction of similar species is difficult. There are relatively few holothurian taxonomist.Most sea cucumber species can be identified by Holothurin taxonomists by using the calcareous skeletal ossicles found in the body wall. In this study , at first a sea cucumber from Kish island in Persian gulf has recognized. Individuals collected from west and east extend far away into north and south of coral reefs by diving. I have checked them morphologically and anatomically.Then with key to the orders of the Holothuroidea, They belong to the Aspidochirotida with key to the families of Aspidochirotida, they were in Stichopodidae families and with key to the genus of Stchopodidae, they were Stichopus. Then ossicles were extracted at National Museum of Natural History, by Dr David Pawson. The ossicles were measured on a transect across a slide prepared from the mid-dorsal region of each specimen.The one we have in the shallow waters of Kish island, is Stichopus hermanni, a massive holothurian, body broad, considerably flattened ventraly ,the dorsal side slightly arched and the lateral sides almost vertical; body wall fairy thick and soft ; mouth subterminal; anus central; tentacles usually 20 in number of length and leaf shaped. Numerous ossicles consisting of table with large discs having usually 7 to 15 peripheral holes, but often irregular or incomplete and spire of moderate height ending in a group of spinelets, rosettes of variable development, and c-shaped rods. Color (exept papillae)partly remained after preservation in alcohol which is found at the depth of 4 to 8 meters, on coral reef. Furthermore, the sexual reproductive cycle was described using standard methods. Gonads were removed and transferred to Bouin's fixative for four weeks and then processed according to standard embedding technique. To prevent the loss of tubule contents during embedding, the tubule sections, were cut well beyond the segment selected for sectioning. For each individual, six sections, each section with 5µm diameter by microtome were cut from tubules. These sections were first placed on gelatin coated slides (the gelatin was heated to 42°c) and then transferred to the oven at 37°c for one hour. This technique usually prevents the fragil tubules from breaking and the loss of gametes. The slides were stained with Eosin and Hematoxylin, and good resolution of the various cell types achieved.A second series of slides was stained with the Periodic Acid Schiff(PAS) to identify polysaccharides(glycogen). Monthly sampling was occurred.The sexual reproductive cycle was defined through the combined use of these criteria: Monthly percentages of the gonad stages for each sex, the monthly gonad index (GI) , given as the ratio of the wet gonad weight (G) to the dray weight (DW)and the monthly percentage of individuals that undetermined sex. The gonad consists of two tufts of tubules on which saccules develop. Gonadal development was classified into five stages: post spawning, recovery, growth, advanced growth, and mature stage that were adapted from the earlier studies of holothurians. Histological preparations showed that the sex of larger individuals could be identified by the presence of oogonia and young oocytes in females, and spermatogonic stages in males.The mean diameter of the tubules and gonadal mass follow annual cycles, increasing from late winter through spring, and dropping abruptly after spawning in the summer. Gametogenesis is generally a prolongate process and begins in March. By summer the ovarian tubules contain oocytes with diameter of 120-240 pm and the testicular tubules contain an abundance of spermatozoa (diameter 5-6 gm ).Following spawning the predominant activity within the spent tubules is phagocytosis of the residual gamets.The active phase of gametogenesis (March to July), coincides with an increasing photoperiod regim, and an accelerated gametogenesis occurs in July when temperature is high. Throughout the year, the gonad of Stichopus hermanni is larger in males than in females, and this is due to the number of tubules in the testis rather than to tubules length or diameter.

Identification and distribution of cartilaginous fishes of the Persian Gulf (Bushehr Province waters)

Class Condrichthyes consist of two sub-classes: Holocehali and. Elasmobranchii, the second one are more divers and has more importance. Selachimorpha (sharkes) and Batidoidimorpha (rays and skates) are two super-order of Elasmobranchii, which they have crucial role in ecological balance in marine ecosystmes. Except few cases, most of sharks and rays (rays and skates) are not well identified, so a lot of works need to be done in this regards. The area of study is located between 49°, 35' and 52°, 33' E and between 27°, 21' and 30°, 02' N in depth of 7 to 78 in. Study were conducted diuring August 1998, September 1999. Samples were taken during 3 sea cruises from 70 bottom trawl net. All sharks and batoid fishes were identified based on biometric specifications (weight, total, length and sexuality for both group and extra biometric specifications, disc width, disc length, and tail length only for, batoid fishes). The 1140 specimens of batoid fishes identified belonged to 6 families, and 18 species. 3 new species were identified, they are Himantura sp.1 and Himantura sp.2 belonged to Dasyatidae family and Rhinobatos sp. belonged to Rhinobatidae Familiy. It needs more works and more adaquate ducuments for cl.earfing scientific names of these species. The 275 specimens of sharks identified belonged to 6 families and 10 species. Chiloscyllium sp. belonged to Hemiscylliidae, family as a new species was identified.

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Gynogenesis and sex determination in large-scale loach Paramisgurnus dabryanus (Sauvage)

Gynogenesis was induced using heterologous sperms in large-scale loach, Paramisgurnus dabryanus (Sauvage), in which a ZW/ZZ sex determination was previously proposed. Three microsatellite loci were used to monitor exclusive maternal inheritance of gynogenetic progenies. The results showed that high percentages of meiogynogens were produced at 4 min post-fertilization and mitogynogens were produced at 18 min post-fertilization by heat shocks, while meiotic gynogenesis was induced by cold shocks within a wide period and high heterozygosity was even observed in gynogens produced at 24 min post-fertilization. The sex ratios of the F, progenies in three gynogenetic families were significantly deviated from 1: 1 expectation with a female bias in two families and a male bias in one family (P < 0.05), and the other four gynogenetic families showed approximate 1:1 sex ratios. Moreover, the self-mating between gynogenetic F, progenies and mating between gynogenetic F, progenies and normal individuals produced all-female progenies or identical proportions of females and males. The data of sex ratios generally confirmed that the sex determination in large-scale loach was determined by the putative ZW/ZZ system, and the possible reasons causing the biased sex ratios are discussed.

Composition, Abundance, and Diversity of the Peracarida on Different Vegetation Types in the Qi'ao-Dan'gan Island Mangrove Nature Reserve on Qi'ao Island in the Pearl River Estuary, China

Chang-Fu Wang, Xian-Qiu Ren, and Run-Lin Xu (2010) Composition, abundance, and diversity of the Peracarida on different vegetation types in the Qi'ao-Dan'gan Island Mangrove Nature Reserve on Qi'ao Island in the Pearl River estuary, China. Zoological Studies 49(5): 608-615. Almost nothing is known about the Peracarida in the Pearl River estuary. This is the 1st report to study the composition, abundance, and diversity of the Peracarida in the Qi'ao-Dan'gan I. Mangrove Nature Reserve on Qi'ao I., in the Pearl River estuary, southern China. Bimonthly samplings were carried out in 3 representative vegetation types (mangrove arbor, emergent plants, and seaweed) for 2 yr. Using a Peterson grab, 1940 individuals (id.) were collected in total, including 11 species of 6 genera, 5 families, and 3 orders (Amphipoda, Isopoda, and Tanaidacean). Discapseudes mackiei Bamber 1997 was the dominant species with the highest density of 1,432 incl./m(2). The effect of temperature on the abundance of Peracarida was significant (p < 0.01), and the optimum temperature was 22-23 degrees C in both the mangrove arbor and seaweed. The results showed that the abundance of the Peracarida was higher in the mangrove arbor, while the diversity, especially Amphipoda diversity, was higher in the seaweed. In contrast, emergent plants provided no suitable habitats for the Peracarida. http://zoolstud.sinica.edu.tw/Journals/49.5/608.pdf

Growth of eight Pacific abalone families at three temperatures

Growth rates, measured as shell length and body weight daily growth, were studied in the eight families of Pacific abalone, Haliotis discus hannai Ino, reared at 12, 16 and 20 degrees C for 40 d respectively. The results show that J(1)Rh family grew the best at 12 degrees C, with growth rates of (32.88 +/- 4.66) mu m/d and (5.24 +/- 1.84) mg/d. C(1)Jm family had the highest growth rates of (58.00 +/- 2.00) mu m/d and (9.71 +/- 1.21) mg/d at 16 degrees C. J(1)Jm family ranked the first at 20 degrees C, with growth rates of (66.00 +/- 1.76) mu m/d and (10.99 +/- 0.34) mg/d. RjRh family had the slowest growth rates at all three temperatures. Shell length growth rates were 18.25, 33.00 and 43.13 mu m/d respectively, while body weight growth rates were 2.47, 2.56 and 4.75 mg/d respectively. Both temperature and family had significant effect on growth rates (P<0.05). At 16 and 20 degrees C, maternal effects on growth rates were not significant (P>0.05), but paternal effects on growth rates were significant (P<0.05). Results of this study indicate genetic difference among the families and importance of selecting male breeders in the commercial hatchery.

中小学生欺负行为及其主要影响因素研究

The present paper studied the school bullying and the primary impact factors, for understanding the nature of bullying, and providing measures and references to the elimination and controlling of school bullying. Primarily with methods of questionnaires and psychometrics, combined with case study and interviews, the following findings were found: in Chinese culture, bullying is a behavior intentionally causing harm to the weaker or weakers. There were 5 types of bullying-physical, social exclusion, threat, breakage and verbal. In Chinese schools the occurrence of bullying had regular patterns. The factor that impact children's bullying behavior was personality traits, interpersonal techniques, family atmosphere, education and upbringing styles. In personality traits, bullies tended to be more extroversive, impulsive, obstinate, obdurate and lack of sympathy. Victims tended to be more introversive, self-restrained, lack of confidence, lonely, anxious and depressive. Both of them expressed more mental problem tendencies than normal children did. When confronted with interpersonal conflicts, they used little problem solving strategies. Bullies had more extroverted emotional responses, and victims had more social support strategies. In the light of family influence, bullies were relatively superior in family's social economic conditions. But their parents had little time and energy spent on them. They tended to be punitive, and had indulgent, reject or despotic upbringing styles. The role of victim might be related to the disadvantage of family's social economic status. Their parents had the tendency of spoiling and overindulgence. The research concluded that in different cultures the connotation of bullying was not homogenous. The occurrence of school bullying had regular patterns. Bullying behavior was primarily influenced by the personality traits of both bullies and victims, the coping strategies of interpersonal conflicts, family's social economic status, parents' basic emotional attitudes, ways of educating, punitive tendencies and school atmosphere. The occurrence of bullying behavior was the result of the combined process of past experience, behavior habits, personality traits, cognitive evaluation, certain evocative clues and the environment conditions. It reminded that quality education and mental health education in schools was essential. Strengthening basic social skill training in school, creating positive family atmosphere, having more communications between schools and families and implementing strict regulations against bullying was essential to interfere and eliminate the school bullying.

O autoconceito de crianças e pré-adolescentes com e sem história de maus-tratos numa amostra de 90 participantes

Dissertação de Mestrado apresentada à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Psicologia, especialização em Psicologia da Educação e Intervenção Comunitária.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.