Thesis (M.S.)--State University of New York at Binghamton, Biology Department, 2006. / Includes bibliographical references.

M.Sc. (Zoology) / The alien fish parasite Argulus japonicus Thiele, 1900 has been introduced to the African subcontinent via exotic fish species. This parasite is now found widely distributed throughout the Transvaal and has assumed near epidemic proportions among fish in the Vaal River system. . Aspects of the reproduction of this parasite were studied. Infected fish from the Vaal River system were maintained in the laboratory in order to establish a stock of A. japonicus. These infected fish, together with Cyprinus carpio Linn. ,1785 from fishponds in Lydenburg, were maintained in a 2125 cubic meter culture tank. This culture of A. japonicus was maintained for more than a year from which specimens were used for experimental work and scanning electron microscopy (SEM). The morphology and anatomy of the sexual organs of both the adult male and female parasites were described. A. japonicus males have thoracic appendages which are functional during copulation. A peg is present on the pre-axial margin of the basis of the fourth thoracic limb and a socket occurs on the dorsal post-axial side of the coxa of the third thoracic limb. The conventional concept concerning copulation is that during copulation the above structures are used only as a clasping mechanism. The peg fits firmly into the socket, keeping the limbs of the male in position, while clasping dorsally round the last thoracic limbs of the female...

M.Sc. (Zoology) / Please refer to full text to view abstract

Dusky kob, Argyrosomus japonicus and spotted grunter, Pomadasys commersonnii occur off South Africa’s southern and eastern seaboard. They are the preferred target species for both shore and estuarine anglers. In order to sustain the billion rand recreational angling industry, healthy fish populations are of the utmost importance. However, A. japonicus is currently overexploited, with the species’ spawner biomass estimated at 1-4.5% of pristine levels. Pomadasys commersonnii spawner biomass is estimated at 40% of pristine levels, thus indicating that the species is not overexploited. For effective management of our marine resources, information about the population size, structure, dynamics and population history of individual species is needed. Genetic data can make a valuable contribution to a holistic stock determination, approach, as powerful tools in unraveling population history. Genetic variation gives a reflection of the evolutionary differences within and between populations and allows for indirect assessment of population connectivity and gene flow levels. The mitochondrial DNA (mtDNA) control region is a useful marker in population studies, due to its high substitution rate. The haploid nature of the mtDNA, maternal inheritance and the absence of recombination, means that the signal obtained from genetic drift is stronger than that for nuclear loci. For this reason the mtDNA control region was analysed for 133 juvenile A. japonicus and 139 P. commersonnii samples from four localities along their South African distribution, to determine the genetic diversity and differentiation among the coastal regions. Juvenile A. japonicus are resident around their natal estuaries until they reach sexual maturity. This residency of juveniles makes them ideal candidates to give a reflection of A japonicus population dynamics, especially to determine if any isolation-by-distance exists along the coast. In the case of P. commersonnii, both juveniles and adults were analysed, since adults are resident around their natal estuaries when not undertaking spawning migrations. High levels of genetic diversity were found in both A. japonicus and P. commersonnii, comparable to that observed in other marine fish species. No significant population differentiation results were obtained, possibly due to the small sample sizes collected or to lack of resolution in the marker. In A. japonicus, where spawning is known to occur off KwaZulu-Natal and off the southern Cape coast, possible isolation-by-distance was detected. This indicates that the adult A. japonicus population probably does not consist of one freely intermixing unit, but rather of geographically separated spawning units. For P. commersonnii, where spawning has only been recorded off the KwaZulu-Natal coast, no population differentiation was observed, indicating that the different regions along the South African coast are highly connected. In conclusion, through future analysis of larger sample sizes, preferably from single cohorts, some of the noise will be reduced and more conclusive answers with respect to female gene flow could be provided. In the case of A. japonicus the use of microsatellite markers which are better at detecting fine-scale differentiation and provide estimates of total gene flow, will be informative. At a broader geographic scale, it will be important to assess differentiation among Dusky kob populations from throughout the Western and Eastern Indian Ocean. As far as P. commersonnii is concerned, it is recommended that a comparison be undertaken to determine the relationship; of the South African population to that found along the Mozambican coast. / Dissertation (MSc (Genetics))--University of Pretoria, 2005. / Genetics / unrestricted

O gênero Aspergillus tem se destacado na produção de enzimas de aplicação industrial, destacando-se dentre estas, as amilases, capazes de hidrolisar as ligações -glicosídicas do amido. As amilases são usadas nos processos industriais para a produção de etanol, glicose e xarope de frutose, além da indústria têxtil, de papéis e detergentes. Neste contexto, este trabalho visou a prospecção de fungos filamentosos para a produção de amilase e a padronização das condições de cultura do Aspergillus japonicus. A otimização das condições de reação da amilase produzida pelo fungo, a purificação, caracterização e teste de diferentes concentrações de íons na atividade enzima pura, a determinação do conteúdo de carboidratos, das constantes cinéticas e análise dos aminoácidos que compõem a glucoamilase purificada e a aplicação da amilase bruta produzida pelo fungo A. japonicus no processo de branqueamento do papel reciclado. Os resultados do screening de fungos filamentosos bons produtores de enzimas amilolíticas evidenciaram dois fungos com alta produção de amilase, os quais foram identificados como Aspergillus parasiticus e Aspergillus japonicus. Os estudos prosseguiram com o A. japonicus como fungo selecionado. Este fungo mostrou melhor produção enzimática no meio de cultura KHANNA e máxima produção amilolítica após 4 dias de crescimento em condições estáticas obtendo uma atividade de 44.65 (± 0.49) U/mL. O pH ideal do meio de cultivo foi de 5,5 e a temperatura ótima de 25°C. As melhores fontes de carbono para a produção enzimática foram o amido de batata e a maltose, respectivamente, e o melhor resíduo de alimento foi a casca e bagaço de laranja. Após a caracterização das condições de cultivo do fungo, vieram as caracterizações dos parâmetros físico-químicos da amilase. A temperatura e pH ótimo de ensaio enzimático foram padronizados sendo, respectivamente, 50C e 5,5. A amilase manteve a sua atividade em torno de 90% de 30º a 50ºC após uma hora de incubação, aproximadamente 95% de sua atividade nos pH de 4,0 a 6,0 e 50% nos pH de 6,5 à 9,0 após uma hora de incubação. Os produtos da hidrólise da amilase mostraram a formação apenas de glicose, na cromatografia de placa delgada de silica, podendo-se supor que esta enzima trata-se de uma glucoamilase, o que foi comprovado por experimentos subsequentes. A enzima bruta foi submetida a eluição em DEAE-cellulose e uma glucoamilase com massa molecular de 72 kDa foi purificada conforme determinado por SDS-PAGE. A temperatura ótima desta glucoamilase purificada foi de 65°C e o pH foi de 5.0. A enzima também demonstrou alta estabilidade a diferentes temperaturas e pH, assim como, uma grande quantidade de produtos gerados quando usada a amilopectina como substrato de reação. A glucoamilase mostrou uma alta ativação na presença de 10 mM de MnCl2, KCl, Pb(C2H3O2)2.3H2O, and 2-mercaptoetanol e um valor de Km de 0,59 mg/mL, Vmáx de 308,01 U/mg e Kcat de 369,58 (s-1). A quantidade de carboidratos que compõem a estrutura da enzima bruta e purificada foram quantificados sendo de 15% e 5,5%, respectivamente. A enzima pura teve seus aminoácidos identificados por análise comparativa com outros gêneros e espécies de fungos produtores de glucoamilase, a enzima também apresentou identidade com o domínio de ligação ao amido existente no fungo Neosartorya fischeri NRRL 181. Quando a glucoamilase bruta foi aplicada no processo de biobranqueamento do papel reciclado impresso por tinta ao jato, a enzima apresentou uma média de 23,34% de aumento da alvura relativa quando comparada ao controle, já na polpa de papel de revista a enzima levou a uma média de 23,89% de aumento na alvura relativa. Os resultados apresentados abrem a possibilidade da utilização destas enzimas no biobranqueamento de polpa de celulose, para a produção e reciclagem de papel pelas indústrias. / The genus Aspergillus has been highlighted in the production of enzymes for industrial application, standing out among these, amylases, capable of hydrolyzing the ?-glycosidic linkages of starch. Amylases are used in industrial processes for the production of ethanol, glucose and fructose syrup, in addition to textiles, detergents and paper. In this context, this work aimed the prospecting of filamentous fungi to produce amylase and the standardization of Aspergillus japonicus culture conditions. The optimization of reaction conditions for amylase produced by the fungus, purification, characterization and testing different concentrations of ions in pure enzyme activity, determining the carbohydrate content, the kinetic constants, analysis of the amino acids that comprise the purified glucoamylase and the application of crude amylase in the bleaching process of the recycled paper. The results of the screening of filamentous fungi that produced good levels of amylolytic enzymes showed two fungi with high production of amylase, which were identified as Aspergillus parasiticus and Aspergillus japonicus. The studies continued with A. japonicus as selected fungus. This strain showed the best enzyme production in the culture medium Khanna and maximum amilolytic production after 4 days of growth under static conditions obtaining an activity of 44.65 (± 0:49) U/ml. The optimum pH of the medium was 5.5 and the optimum temperature of 25°C. The best carbon sources for the enzyme production were potato starch and maltose, respectively, and the best food residue was orange peel and bagasse. After the characterization of fungal culture conditions, came the characterization of physical and chemical parameters of amylase. The temperature and optimum pH of enzyme assay were standardized being, respectively, 5.5 and 50°C. Amylase retained its activity around 90% at 30 to 50°C after one hour of incubation, approximately 95% of its activity in the pH range of 4.0 to 6.0 and 50% in pH range of 6.5 to 9.0 after an hour of incubation. Amylase hydrolysis products showed only the formation of glucose, in thin layer chromatography on silica, and it can be assumed that it is a glucoamylase, which was confirmed by subsequent experiments. The crude enzyme was subjected to elution through DEAE-cellulose and a glucoamylase showing a molecular weight of 72 kDa as determined by SDS-PAGE was purified. The optimum temperature of this purified glucoamylase was 65°C and the pH was 5.0. The enzyme also showed high stability at different temperatures and pH, as well as a large amount of products generated when used as a reaction substrate the amylopectin. Glucoamylase showed a high activation in the presence of 10 mM de MnCl2, KCl, Pb(C2H3O2)2.3H2O, and 2-mercaptoethanol and a Km value of 0.59 mg/mL, Vmax of 308.01 U/mg and Kcat of 369.58 (s-1). The amount of carbohydrates that compose the structure of crude and purified enzyme were measured at 15% and 5.5%, respectively. The pure enzyme had its amino acids identified by comparison with other genera and species of fungi producers of glucoamylase, the enzyme also showed identity with the existing starch binding domain in Neosartorya fischeri NRRL 181 fungus. When the crude glucoamylase was applied in biobleaching process of the recycled paper printed by the ink jet, the enzyme showed an average of 23.34% increase in relative brightness as compared to control, in the journal paper pulp has led to the enzyme an average of 23.89% increase in the relative brightness. The results presented here open the possibility of using these enzymes in pulp biobleaching pulp for the production and recycling of paper by industry.

RNA interference (RNAi) is a conserved pathway that plays key roles in heterochromatin formation, gene regulation and genome surveillance across a wide range of eukaryotes. One of the most utilised model organisms for studying the RNAi pathway is the fission yeast Schizosaccharomyces pombe. However, this species is somewhat atypical, in that it has not retained the ancestral role for RNAi in the silencing of mobile genetic elements. In contrast, the related fission yeast S. japonicus has a large and diverse retrotransposon complement that appears to give rise to abundant siRNAs. For this reason, we believe that S. japonicus may be a more suitable model for studying the role of RNAi in silencing mobile genetic elements, a function that is conserved in many higher eukaryotes. Functional analysis of the S. japonicus RNAi pathway proved more challenging than expected, as it was generally not possible to recover strains bearing deletions of core RNAi components (Ago1/Clr4/Rdp1/Arb1/Arb2). This suggests that a functional RNAi pathway may be required for viability in S. japonicus, unlike in S. pombe. However, disruption mutants were isolated for the sole Dicer ribonuclease Dcr1, at very low frequency. Analysis of these mutants revealed that disruption of Dcr1 impaired the generation of retrotransposon derived siRNAs, and caused de-repression of retroelement transcript accumulation and mobilisation in an element dependent manner. Surprisingly however, Dcr1 appeared dispensable for the maintenance of H3K9me2 at transposons, suggesting that, in contrast to S. pombe, silencing may occur principally at the post-transcriptional level. It is also possible that the isolated Dcr1 mutants represent rare survivors that are viable due to the presence of suppressor mutations elsewhere in the genome. I utilised my genome wide RNA sequencing data to help improve the annotation of the S. japonicus genome, with a specific focus on the retrotransposon complement. From this, I identified 12 new families of LTR retrotransposon, which increased the annotated retrotransposon complement by around 40% in S. japonicus. Finally, I characterised the integrative preference of the S. japonicus retrotransposon Tj1, and found that it shares characteristics associated with the S. cerevisiae retrotransposons Ty1 and Ty3, mostly integrating upstream of RNA PolIII transcribed tRNA genes. The findings of this work highlight some potentially key differences in the way the RNAi pathway functions across the fission yeast clade, both in terms of its importance for viability and its mode of action. The work undertaken here also contributes to the establishment of S. japonicus as a model for the study of RNA interference and genome regulation.

Thesis (M.Sc. (Ichthyology & Fisheries Science)) - Rhodes University, 2008.

O gênero Aspergillus tem se destacado na produção de enzimas de aplicação industrial, destacando-se dentre estas, as amilases, capazes de hidrolisar as ligações -glicosídicas do amido. As amilases são usadas nos processos industriais para a produção de etanol, glicose e xarope de frutose, além da indústria têxtil, de papéis e detergentes. Neste contexto, este trabalho visou a prospecção de fungos filamentosos para a produção de amilase e a padronização das condições de cultura do Aspergillus japonicus. A otimização das condições de reação da amilase produzida pelo fungo, a purificação, caracterização e teste de diferentes concentrações de íons na atividade enzima pura, a determinação do conteúdo de carboidratos, das constantes cinéticas e análise dos aminoácidos que compõem a glucoamilase purificada e a aplicação da amilase bruta produzida pelo fungo A. japonicus no processo de branqueamento do papel reciclado. Os resultados do screening de fungos filamentosos bons produtores de enzimas amilolíticas evidenciaram dois fungos com alta produção de amilase, os quais foram identificados como Aspergillus parasiticus e Aspergillus japonicus. Os estudos prosseguiram com o A. japonicus como fungo selecionado. Este fungo mostrou melhor produção enzimática no meio de cultura KHANNA e máxima produção amilolítica após 4 dias de crescimento em condições estáticas obtendo uma atividade de 44.65 (± 0.49) U/mL. O pH ideal do meio de cultivo foi de 5,5 e a temperatura ótima de 25°C. As melhores fontes de carbono para a produção enzimática foram o amido de batata e a maltose, respectivamente, e o melhor resíduo de alimento foi a casca e bagaço de laranja. Após a caracterização das condições de cultivo do fungo, vieram as caracterizações dos parâmetros físico-químicos da amilase. A temperatura e pH ótimo de ensaio enzimático foram padronizados sendo, respectivamente, 50C e 5,5. A amilase manteve a sua atividade em torno de 90% de 30º a 50ºC após uma hora de incubação, aproximadamente 95% de sua atividade nos pH de 4,0 a 6,0 e 50% nos pH de 6,5 à 9,0 após uma hora de incubação. Os produtos da hidrólise da amilase mostraram a formação apenas de glicose, na cromatografia de placa delgada de silica, podendo-se supor que esta enzima trata-se de uma glucoamilase, o que foi comprovado por experimentos subsequentes. A enzima bruta foi submetida a eluição em DEAE-cellulose e uma glucoamilase com massa molecular de 72 kDa foi purificada conforme determinado por SDS-PAGE. A temperatura ótima desta glucoamilase purificada foi de 65°C e o pH foi de 5.0. A enzima também demonstrou alta estabilidade a diferentes temperaturas e pH, assim como, uma grande quantidade de produtos gerados quando usada a amilopectina como substrato de reação. A glucoamilase mostrou uma alta ativação na presença de 10 mM de MnCl2, KCl, Pb(C2H3O2)2.3H2O, and 2-mercaptoetanol e um valor de Km de 0,59 mg/mL, Vmáx de 308,01 U/mg e Kcat de 369,58 (s-1). A quantidade de carboidratos que compõem a estrutura da enzima bruta e purificada foram quantificados sendo de 15% e 5,5%, respectivamente. A enzima pura teve seus aminoácidos identificados por análise comparativa com outros gêneros e espécies de fungos produtores de glucoamilase, a enzima também apresentou identidade com o domínio de ligação ao amido existente no fungo Neosartorya fischeri NRRL 181. Quando a glucoamilase bruta foi aplicada no processo de biobranqueamento do papel reciclado impresso por tinta ao jato, a enzima apresentou uma média de 23,34% de aumento da alvura relativa quando comparada ao controle, já na polpa de papel de revista a enzima levou a uma média de 23,89% de aumento na alvura relativa. Os resultados apresentados abrem a possibilidade da utilização destas enzimas no biobranqueamento de polpa de celulose, para a produção e reciclagem de papel pelas indústrias. / The genus Aspergillus has been highlighted in the production of enzymes for industrial application, standing out among these, amylases, capable of hydrolyzing the ?-glycosidic linkages of starch. Amylases are used in industrial processes for the production of ethanol, glucose and fructose syrup, in addition to textiles, detergents and paper. In this context, this work aimed the prospecting of filamentous fungi to produce amylase and the standardization of Aspergillus japonicus culture conditions. The optimization of reaction conditions for amylase produced by the fungus, purification, characterization and testing different concentrations of ions in pure enzyme activity, determining the carbohydrate content, the kinetic constants, analysis of the amino acids that comprise the purified glucoamylase and the application of crude amylase in the bleaching process of the recycled paper. The results of the screening of filamentous fungi that produced good levels of amylolytic enzymes showed two fungi with high production of amylase, which were identified as Aspergillus parasiticus and Aspergillus japonicus. The studies continued with A. japonicus as selected fungus. This strain showed the best enzyme production in the culture medium Khanna and maximum amilolytic production after 4 days of growth under static conditions obtaining an activity of 44.65 (± 0:49) U/ml. The optimum pH of the medium was 5.5 and the optimum temperature of 25°C. The best carbon sources for the enzyme production were potato starch and maltose, respectively, and the best food residue was orange peel and bagasse. After the characterization of fungal culture conditions, came the characterization of physical and chemical parameters of amylase. The temperature and optimum pH of enzyme assay were standardized being, respectively, 5.5 and 50°C. Amylase retained its activity around 90% at 30 to 50°C after one hour of incubation, approximately 95% of its activity in the pH range of 4.0 to 6.0 and 50% in pH range of 6.5 to 9.0 after an hour of incubation. Amylase hydrolysis products showed only the formation of glucose, in thin layer chromatography on silica, and it can be assumed that it is a glucoamylase, which was confirmed by subsequent experiments. The crude enzyme was subjected to elution through DEAE-cellulose and a glucoamylase showing a molecular weight of 72 kDa as determined by SDS-PAGE was purified. The optimum temperature of this purified glucoamylase was 65°C and the pH was 5.0. The enzyme also showed high stability at different temperatures and pH, as well as a large amount of products generated when used as a reaction substrate the amylopectin. Glucoamylase showed a high activation in the presence of 10 mM de MnCl2, KCl, Pb(C2H3O2)2.3H2O, and 2-mercaptoethanol and a Km value of 0.59 mg/mL, Vmax of 308.01 U/mg and Kcat of 369.58 (s-1). The amount of carbohydrates that compose the structure of crude and purified enzyme were measured at 15% and 5.5%, respectively. The pure enzyme had its amino acids identified by comparison with other genera and species of fungi producers of glucoamylase, the enzyme also showed identity with the existing starch binding domain in Neosartorya fischeri NRRL 181 fungus. When the crude glucoamylase was applied in biobleaching process of the recycled paper printed by the ink jet, the enzyme showed an average of 23.34% increase in relative brightness as compared to control, in the journal paper pulp has led to the enzyme an average of 23.89% increase in the relative brightness. The results presented here open the possibility of using these enzymes in pulp biobleaching pulp for the production and recycling of paper by industry.

Thesis (M.Sc. (Ichthyology & Fisheries Science)) - Rhodes University, 2008.

The aim of this study was to investigate the dependence of selected antagonists to the abundance of Lymantria dispar. The aim of the study was to determine whether these natural enemies can affect the abundance of L. dispar. I have focused on South Moravia, where L. dispar occurs. In 2015 the Turček method reviewed a total of 3,600 trees in seven locations with the historical appearance of outbreaks of gypsy moth. Density egg clutches were extremely low, about 0.019 for each new clutch per tree, which corresponds to the latent state. On the studied locations egg clutches was collected, measured and recorded in notebooks. A load with at least one egg in each area was removed with the top 5 cm of litter and a top layer of mineral soil. The removed soil was put into pots in which were stored late instar caterpillars for the detection of E. maimaiga. The cups were inserted along with the caterpillars in the refrigerator for three days at 15°C without food. Aafter three days the caterpillars were taken away individually and placed on an artificial diet. An inspection was performed and a their mortality was monitored. The presence of E. maimaiga was examined microscopically for 325 dead caterpillars, but no pathogen was detected. In the laboratory, the individual egg clutches were placed upon a Petri dishes with filter paper and the number of eggs counted with a stereo microscope. Subsequently, the eggs were left to hatch and were analyzed for the presence of parasitoids. A total of 1 246 species of egg parasitoids Anastatus japonicus was found in six locations, taking in donations females predominated. Egg parasitism was on average around 5%. Flight activity A. japonicus was quite long and covered the period 24 May 2015 to 28 July 2015. In the absence of E. maimaiga and low egg parasitism at the studied locations we do not expect any strong influence of the studied antagonists on population density and outbreak cycle L. dispar in South Moravia.