Call number: LD2668 .T4 1986 F87 / Master of Science / Biology

Emerging influenza viruses continue to challenge public health. The problem is public health science professionals have been battling emerging human influenza diseases with tactile and reactionary methods because there is a lack of knowledge and data at the human-animal interface. This research was a baseline study of the proportion of influenza A virus (IAV) in urban and rural communities in California. The population was artificial recirculating water ponds in the geographic locations of rural and urban Californian communities. Surface water samples [N = 182] were collected from artificial recirculating ponds in California. Positivity for IAV was verified by real time RT-PCR, MDCK cells for virus infectivity, nucleotide sequencing of the RNA genome, and phylogenic analysis of IAV H5N1 strains. The proportion of IAV in rural and urban ponds favored the greater burden of IAV in urban ponds over rural ponds. The presence of waterfowl and IAV M gene sequence positivity were found not to be significantly related. The geochemical properties--pH, salinity, and water temperature at time of collection--were not predictors of IAV infectivity. This baseline research study validated these water ponds as resource sites for IAV surveillance and monitoring. The social change implications of this study can be recognized at the national and international levels, to the population level, and to the individual level by providing geospatial analysis and spatial-temporal data for IAV surveillance, initiating biosecurity measures to protect poultry industries in the United States and Brazil, and contributing to the current IAV strain library. Contributions to the IAV strain library may be used to develop vaccines against human pandemics.

The aim of this study is to improve our understanding of the ecology, spatiotemporal patterns, and risk of infectious pathogens of migratory waterfowl, using the blue-winged teal (Anas discors, BWTE), as a model. From 2007-2010, 1,869 BWTE were sampled in the prairie provinces (Alberta, Saskatchewan and Manitoba, Canada) to examine infection status and/or evidence of previous exposure to avian influenza virus (AIV), West Nile virus (WNV), and avian paramyxovirus-1 (APMV-1), in relation to host demographic variables (age, sex, body condition, exposure to other pathogens), other ecological variables such as local waterfowl breeding population density and local pond density, and year. The probability of AIV infection depended on an interaction between age and AIV antibody status. Hatch year birds with antibodies to AIV were more likely to be infected, suggesting an antibody response to an active infection. After hatch year birds with antibodies to AIV were less likely to be infected, suggesting immunity resulting from previous exposure. AIV infection was positively associated with local BWTE density, supporting the hypothesis of density dependent transmission. Exposure to WNV and APMV-1 were also associated with age and year. Furthermore, the probability of WNV exposure was positively associated with local pond density rather than host population density, likely because ponds provide suitable breeding habitat for mosquitoes, the primary vectors for transmission. We also investigated large-scale spatiotemporal trends in apparent prevalence of AIV across Canada and the United States throughout the year, using data from national avian influenza surveillance programs in Canada and the US in 2007-2010. Our analyses revealed that age, sex, year of sampling, flyway, latitude, and season (categorized by stages of the BWTE annual life cycle) were all important variables in predicting probability of AIV infection. There was an interaction between age and season. During late summer staging (August) and fall migration (September-October), hatch year birds were more likely to be infected than after hatch year birds, however there was no difference between age categories for the remainder of the year (winter, spring migration, and breeding season). Probability of infection increased non-linearly with latitude, and was highest in summer, corresponding to the beginning of fall migration when densities of birds and the proportion of susceptible hatch year birds in the population are highest. Birds in the Pacific, Central and Mississippi flyways were significantly more likely to be infected compared to those in the Atlantic flyway. Observed trends in seasonal, annual, and geographic patterns of AIV infection in BWTE across Canada and the US were primarily driven by the dynamics of AIV infection in hatch year birds. Our results demonstrate demographic as well as seasonal, latitudinal and flyway trends across Canada and the US. This research provided further evidence for the role of wild dabbling ducks, particularly BWTE, in the maintenance and ecology of AIV. This improved understanding of the role of BWTE as natural hosts, and the geographic, demographic and temporal variables that affect infection and transmission parameters, moves us closer to deciphering the overall ecology of the virus and its transmission and transportation pathways at the individual, population and continental levels. This knowledge, in turn, will permit development of better tools to predict and perhaps to prevent possible outbreaks in domestic animals as well as in humans.

Waterfowl are known to be capable of influencing wetland ecology in a number of ways, sometimes to the detriment of other species that also inhabit this type of environment. Western Golden Bay including Farewell Spit is one of the largest areas of intertidal sand flat habitat in New Zealand and supports a wide array of species including internationally important populations of bar-tailed godwits (Limosa lapponica) and red knot (Calidris canutus). These species, particularly red knot, have declined in number over the last the 25 years at this site. Another numerous species at this site, the black swan (Cygnus atratus), has been suggested as a possible contributor to the observed decline in wader numbers through their impact on the habitat. This thesis presents the findings of a research project on the role of black swans in the tidal seagrass (Zostera muelleri) ecosystem in western Golden Bay carried out between October 2007 and October 2008. In an effort create a clear picture of what role the black swans play in this environment the project focused on four major aspects of swan-ecosystem interactions. The first of these looked at the activity patterns of black swan. This showed the swans’ activity is largely dictated by the tidal cycle with foraging occurring during the intertidal period when the seagrass is accessible while roosting is mostly confined to around high and low tides. The second part of the project explored the influence black swans have on the tidal seagrass landscape through their foraging habits. This showed that while swan foraging occurs across the tide flats it is concentrated on denser patches, on both small (meters) and large (hectares) scales. Experimental grubbings showed that the grubbing activity of swans is capable of forming and expanding bare sand patches within seagrass beds and that these bare patches can persist for at least two months. The third part of the project focused on the direct impacts of swan foraging on the seagrass and associated benthic invertebrates. Exclusion plots showed that at some sites swan foraging can significantly reduce Zostera biomass and invertebrate biodiversity. The final aspect examined was the role of swan in biomass and nutrient cycling. A faecal deposition survey showed swans consume 23.40 g DW ha-1 day-1 of Zostera. The average intake rate was 27.25 g DW ha-1 day-1. Nutrient analysis of seagrass 4 showed that shoot material has significantly higher N, P, Ca and fibre than rhizome and that rhizome has significantly more soluble carbohydrates than shoots. On the basis of the swans’ direct and/or indirect influences on Zostera muelleri beds and the associated invertebrate fauna, swans could arguably be considered to be a major ecosystem engineer in the intertidal sandflats of Golden Bay.

Submitted by Cássia Santos (cassia.bcufg@gmail.com) on 2016-10-13T11:49:58Z No. of bitstreams: 2 Dissertação - Ana Maria de Souza Almeida - 2014.pdf: 1577589 bytes, checksum: e516be5588e40ed18ce2aa223a3be386 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2016-10-14T19:56:45Z (GMT) No. of bitstreams: 2 Dissertação - Ana Maria de Souza Almeida - 2014.pdf: 1577589 bytes, checksum: e516be5588e40ed18ce2aa223a3be386 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-10-14T19:56:45Z (GMT). No. of bitstreams: 2 Dissertação - Ana Maria de Souza Almeida - 2014.pdf: 1577589 bytes, checksum: e516be5588e40ed18ce2aa223a3be386 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-08-07 / Duck is the most important species of waterfowl reared in Brazil, however, there are no studies about the risk of duck eggs in the food chain. The main objective of this study was to outline the main characteristics of waterfowl farms, integrating the risk factors associated with E. coli infection in birds and humans, verify the presence of E.coli in 38 and 25 dozen of duck eggs from markets and subsistence farms in Federal District and Goiás State, determining the pathogenic profile and the antimicrobial resistance profile. Each dozen eggs accounted for three samples: a sample pool of eggshell, pool of albumen and a pool of yolk, totaling samples.The information obtained by questionnaires applied during the visit to the farms revealed no vaccination program, or supply of balanced feed for ducks were employed. Duck were reared with chicken and the contact between the animals occurred since incubation. Through bacteriology, we isolated and identified E.coli in 17.10% (97/567) of samples of duck eggs. In PCR for the detection of the virulence genes papC, tsh, and eae and of the resistance gene iss, of 97 positives samples to E. coli, 35 samples were positive for virulence genes, 31.8% (14/44) came from farms and 39.6% (21/53) from markets. The search of genes in E.coli isolates revealed 15.4% positive to papaC, (15/97) , 21.6% (21/97) positive to tsh, 17.5% (17/97) positive to iss, and 2% (2/97) positive to eae .It conclusion, there are pathogenic strains for both birds and humans, circulating in anseriformes eggs. The investigation of antimicrobial resistance combined with the research of virulence and resistance genes in E. coli isolates obtained from eggs of ducks is an important tool to determine the risk these birds may bring to both poultry health and of public health. / O pato é a espécie de aves aquáticas mais criada no Brasil, porém não existem estudos aprofundados a respeito do risco dos ovos de patas na cadeia alimentar. O objetivo deste trabalho foi delinear as principais características das criações integrando os fatores de risco associados a infecção de Escherichia coli em aves e humanos, investigar a presença dessa bactéria em 38 e 25 dúzias de ovos de patas procedentes de feiras livres e propriedades de subsistência no Distrito Federal e estado de Goiás, determinando seu perfil patogênico e perfil de resistência aos antimicrobianos. Cada dúzia de ovos correspondeu a três amostras: uma amostra de pool casca, uma de pool de albúmen e uma de pool gema, totalizando 567 amostras. Mediante as informações obtidas pelos questionários aplicados durante a visita nas propriedades de subsistência, observou-se que não existem programas de vacinação, nem fornecimento de ração balanceada para os patos, a criação geralmente é consorciada com galinhas e o contato entre os mesmos ocorria desde a incubação. Obteve-se, pela bacteriologia o isolamento e identificação de E.coli em 17,10% (97/567) de amostras de ovos de patas. Na PCR para detecção dos genes de virulência papC, tsh e eae, e de resistência o gene iss, das 97 amostras positivas para E.coli, 35 amostras possuiam genes de virulência, 31,8% (14/44) delas eram de propriedades de subsistência e 39,6% (21/53) de feiras livres. Em meio aos genes pesquisados nos isolados de E.coli foram positivos 15,46% (15/97) para papC, 21,65% para tsh, 17,52% para iss, 2,06% para eae. Conclui-se que existem cepas patogênicas tanto para aves quanto para humanos, circulantes em ovos de anseriformes. A investigação de resistência aos antimicrobianos aliada à pesquisa dos genes de virulência e de resistência em isolados de E.coli obtidos de ovos de patos é importante ferramenta para determinação de risco, tanto para sanidade avícola quanto para saúde pública, que essas aves podem exercer.

Made available in DSpace on 2016-08-18T17:23:43Z (GMT). No. of bitstreams: 1 Dissertacao Daniel Rocha.pdf: 2551995 bytes, checksum: 65ba8cf188c0a50be02f159bd8286406 (MD5) Previous issue date: 2014-02-20 / Assessment of compliance of the Program Monitoring Migratory Birds (PMMB) during deployment pier in San Luis - MA, through documents obtained from the entrepreneur and the environmental agency. It was shown in this study that several PMMB guidelines were not followed and the results showed different patterns of the studies of other authors for the same region. Therefore, the PMMB was not completed as proposed and the results of monitoring may have been committed in this sense is not possible to define the dynamics of interference in birds studied by the project. / Avaliação do cumprimento do Programa de Monitoramento de Aves Migratórias (PMAM) durante a implantação de píer em São Luís MA, por meio de documentos obtidos junto ao empreendedor e ao órgão ambiental. Foi evidenciado nessa pesquisa que várias diretrizes do PMAM não foram seguidas e que os resultados mostraram padrões diferentes dos estudos de outros autores, para a mesma região. Portanto, o PMAM não foi cumprido conforme proposto e os resultados dos monitoramentos podem ter ficado comprometidos, nesse sentido não é possível definir a interferência na dinâmica das aves estudadas por parte do empreendimento.

M. Tech. (Department of Biotechnology, Faculty of Applied and Computer Science), Vaal University of Technology. / Influenza-A virus is a single stranded negative sense RNA virus that is a member of a Orthomyxoviridae group. The virus is diverse and consists of 16 haemagglutinin (H) and 9 neuraminidase (N) glycoproteins subtypes that form a serotype. Avian influenza virus (AIV) has been detected in more than 100 bird species from 26 different families, although Anseriformes and Charadriiformes are considered the natural hosts of the virus. A 12-month study was conducted at the African Pride Irene Country Club lodge in Pretoria where the prevalence of AIV was monitored in a community of wild birds. The African Pride Irene Country Club lodge houses a population of wild bird species such as Egyptian geese (Alopochen aegytptiaca), Yellow-billed duck (Anas undulata), Red knobbed coot (Fulica cristata), African sacred ibis (Threskiornis aethiopicus) and Hadeda ibis (Bostrycha hagedash). A total of 3674 faecal samples were collected over a period of 12 months and screened for AIV group using the Matrix gene (M-gene) real time reverse-transcriptase PCR (rRT-PCR). Positive samples were submitted for virus isolation in embryonated chicken eggs. In addition, the RNAs were screened using H5 and H7 subtype specific rRT-PCR and a conventional universal RCR assay that targets the HA gene was also used. Polymerase Chain Reaction (PCR) products were requenced using Sanger sequencing and the viral isolates were subjected to Next Generation sequencing (NGS). Twenty percent of the samples tested positive for the AIV group and four virus subtypes were identified. One virus isolate was identified through NGS as H3N6; two through conventional PCR and Sanger sequencing as H9Nx and H6Nx. Of the twenty percent samples that tested positive for AIV 98% were identified as H7Nx by subtype specific through rRT-PCR. The highest frequency of AIV positive samples was detected between the months of January and February 2017 (20%), with smaller peaks detected in february and March 2016 (0.3%). Lower peaks were also detected between the months July and November 2016 (0.1%), respectively. A high prevalence of AIV was detected in the late summer months with a frequency of 65% positive, although a low prevalence was also detected in the autumn (0.6%) winter (0.6%) and spring 0.08%). Thus, the study provides a valuable insight into the seasonal prevalence of AIV in a heterogeneous wild duck population in Gauteng Province.

Submerged aquatic vegetation (SAV) is an important source of food for waterfowl. Effects of waterfowl grazing on SAV has foremost been studied in freshwater and agricultural ecosystems. This study used drone-based remote sensing to identify waterfowl grazing patterns and quantify the effect their grazing has on SAV in shallow coastal areas in Västerbotten County. Six subareas containing a total of 27 bays were studied in detail. Grazed areas were delimited by polygons in GIS. Using GIS, layers containing water depth, wave exposure and biotope were added to polygons and mean-values were calculated. Field data containing types of SAV were noted in grazed areas and compiled by number of observations. Data was tested in a regression analysis and a X2-test. Results revealed no connection between water depth and wave exposure in regard to the proportion of grazed area. Grazing was identified in 20 out 27 bays and in 41 out of 126 drone images. Field data containing charophytes often overlapped with polygons for grazed areas, but a more systematic collection of data is needed to conclude whether the presence of charophytes is crucial for the choice of grazing area. Shallow coastal areas can have a great variance in SAV species composition from year to year due to ice scraping during winter and yearly land raise. Continuous studies of these areas are therefore needed in order to conclude if changes in SAV species composition is due to abiotic factors or grazing from waterfowl.

Hundreds of wetland bird species use ricelands annually in the Gulf Coast Prairie region of Louisiana and Texas. Much of the original ecosystem was transformed for rice and other crops, cattle ranching, flood control, and other human uses. Flooded production and idled ricelands provide critical foraging habitat for breeding, migrating, and wintering wetland birds. Ricelands in coastal Louisiana and Texas provide approximately 42% of the estimated habitat carrying capacity for wintering waterfowl in this region. In 2010, the Deepwater Horizon oil spill in the Gulf of Mexico prompted enactment of the Migratory Bird Habitat Initiative (MBHI) by USDA Natural Resources Conservation Service. The MBHI provided avian habitat, including flooded ricelands, inland from oil impacted areas. My objectives were to: 1) estimate and model variation in biomass of waste rice and natural seeds as potential waterfowl forage in Gulf Coast Prairie ricelands, 2) estimate and model variation in wetland bird use of ricelands, and 3) conduct sensitivity analyses of bioenergetics models by varying foraging thresholds and true metabolizable energy (TME) values. A growing season of ~270 days allows Gulf Coast rice producers to grow two rice crops (i.e., the second termed ratoon). Waste rice was greatest in production fields with harvested and standing ratoon crops, and natural seed biomass was greatest in idled fields with standing vegetation. Wetland bird species richness and waterbird abundance were greatest in shallowly flooded (1–15 cm) ricelands with sparse vertical vegetation (1–20 cm), and duck abundance was greatest in shallow–intermediately (1–30 cm) flooded ricelands with short vegetation (1–15 cm). Shallowly flooded rice fields containing harvested or standing ratoon crops, and shallowly flooded idled fields with standing vegetation provided abundant potential foods for waterfowl and waterbirds. Bioenergetics models indicated that planners in the Gulf Coast Prairie region may be underestimating riceland habitat requirements for waterfowl by 10,000 ha. Models were most sensitive to changes in seed biomass estimates, and less sensitive to changes in foraging thresholds and TME values. Collectively, these results will facilitate conservation partners to refine models for conserving habitats for waterfowl and other waterbirds in the Gulf Coast Prairie.

Rice not collected by harvesters and natural seeds are important foods for waterfowl. Estimation of abundance of these seeds is necessary for calculating waterfowl habitat conservation needs in the Louisiana Chenier Plain (LCP) and Texas Mid-Coast (TMC). My objectives were to quantify dry mass of rice and other seeds from August-November 2010, and estimate waterbird abundances on farmed and idle ricelands in these regions from December 2010-March 2011. Rice abundance in farmed ricelands ranged from 159.7 kg/ha (CV = 66.6%) to 1,014.0 kg/ha (CV = 8.3%). Natural seed abundance in idle ricelands ranged from 99.7 kg/ha (CV = 32.9%) to 957.4 kg/ha (CV = 17.2%). Greatest waterbird densities occurred in shallowly flooded (i.e., ¡Ü30 cm) disked ricelands (mean = 7.35 waterbirds/ha, 90%; CI = 2.37-19.70). Ratoon, disked, and shallowly flooded ricelands are important habitat for non-breeding waterbirds but variable estimates of seed and waterbird abundances warrant continuation of this study.