Trace metals -- a potential threat to our fishing industry

Trace metals constitute a major form of water pollutant that can adversely affect fish production. The potentially toxic metals have been identified as lead, zinc, copper, arsenic, antimony, mercury beryllium, barium, cadmium, chromium, nickel, selenium among others. Preliminary laboratory studies have been directed to the determination of traces of lead in the aquatic biota and its toxicity. There are indications that the levels reported in effluents from some of the industries may be above the tolerant limits of local fish species and organisms that make up their food. Metal pollution could become a serious problem to freshwater fisheries in the future as a result of increasing urbanization and industrialization, unless efforts are made to prevent it

Commercial production of natural freshwater fish food

A review is made of some of the methods that can be used for mass cultivation of natural fish food and the types of organisms that are cultured, which include various algae and zooplankton. Some examples are given of successful case histories in the mass cultivation of natural fish food in order to stimulate the interest of Nigerian scientists on research activities of live fish food for use by fish farmers in the country

Commercial pond fish culture using waste water

Waste water from some National Electric Power Authority (NEPA) housing units in Nigeria was fed to a 0.4 ha pond which was stocked with 2,200 Sarotherodon galilaeus fingerlings with a mean weight of about 36.0gm and 1000 Cyprinus carpio fingerlings with a mean weight of 10gm. This yielded after 10 months, over 2300 kg of harvestable fish plus over 20,000 Sarotherodon galilaeus fingerlings. The growth rate of C. carpio was not very encouraging possibly because of the type of plankton that colonised the pond. The S. galilaeus became stunted because of overpopulation as there were no carnivores to control their excessive breeding. The physico-chemical parameters were favourable for the growth of fish food organisms

The influence of some environmental variables on the apparent abundance of skipjack tuna, Katsuwonus pelamis, in the Eastern Pacific Ocean

ENGLISH: The abundance of skipjack larvae in the central and western Pacific approximately doubled for every 1°C increase in sea-surface temperature (SST) from 23°C to a maximum of about 29°C, and then usually decreased with further increases in SST. Skipjack larvae are scarce in the eastern Pacific Ocean (EPO), so most skipjack recruits and adults in this area are believed to have originated in the central and, possibly, the western Pacific. The catch per unit of effort (CPUE), in short tons per day's fishing, and the catch rate, in number of fish per day's fishing, are estimates of apparent abundance in a fishery. The logarithm of the annual CPUE for skipjack for international baitboats in the EPO for the 1934-1960 period was positively correlated with SST in the spawning area in the central Pacific 18 months earlier (r2 0.31), during the July-June period when most of the recruits in each cohort were presumed to have been spawned. Adequate data for other environmental variables were not available for testing with the baitboat data. The other environmental variables available and selected for testing for correlation with estimates of skipjack abundance for purse seiners for the 1961-1984 period and the reasons for their selection are as follows. 1)Wind-mixing index (WMI). The degree of mixing in the upper layers of the ocean is proportional to the cube of the wind speed, called WMI. The degree of mixing in the spawning areas of the central and the western Pacific may affect the concentration of organisms that skipjack larvae feed upon, thereby influencing their survival, and ultimately determining cohort strength and the number of recruits to the eastern Pacific fishery. 2) SST in the fishing areas at the time of fishing (SST). The CPUE for yellowfin tuna has been shown to be inversely related to SST in the fishing areas, and there are indications that skipjack CPUE is lower during EI Nino events when SST is higher than normal. 3) North-south SST gradient across the thermal front off the Gulf of Guayaquil. This is a measure of the degree of upwelling and nutrient enrichment of the upper waters south of the front and ultimately of the production of food for tunas. 4) Speed of the North Equatorial Countercurrent (NECC). Young skipjack may migrate from the central Pacific to the EPO in the eastward flowing NECC; if so, the number of recruits might be affected by variations in the speed of the current. The logarithm of the annual catch rate of skipjack recruits by international purse seiners in the EPO for the 1961-1984 period was positively correlated with SST in the spawning area of the central Pacific 18 months earlier (r2 = 0.21),and inversely correlated with WMI in the spawning area 18 months earlier (r2 0.46). The logarithm of CPUE for purse seiners in the area off the Gulf of Guayaquil was not correlated with SST in the spawning area 18 months earlier, but was inversely correlated with WMI in the spawning area 18 months earlier (r2 = 0.19), and inversely correlated with the north-south SST gradient in the fishing area at the time of fishing (r2 0.32). Neither of these estimates of apparent abundance from purse seiners were correlated with SST in the fishing areas, or with the speed of the NECC at earlier times. SPANISH: La abundancia de larvas de barrilete en el Pacífico central y occidental se multiplicó por dos, aproximadamente, por cada aumento de 1°Cen la temperatura de la superficie del mar (TSM) entre 23°C y un máximo de unos 29°C, y luego generalmente disminuyó con más aumentos en la TSM. Las larvas de barrilete son escasas en el Océano Pacífico oriental (OPO), y por lo tanto se cree que la mayoría de los reclutas y adultos en esta zona surgieron del Pacífico central, y posiblemente también del Pacífico occidental. La captura por unidad de esfuerzo (CPUE), en toneladas cortas por día de pesca, y la tasa de captura, en número de peces por día de pesca, son estimaciones de la abundancia aparente en una pesquería. El logaritmo de la CPUE anual de barrilete lograda por barcos de carnada en el OPO en el período 1934-1960 se correlacionó positivamente con la TSM en la zona de desove en el Pacífico central de 18 meses antes (r2 = 0.31), durante el período de junio-julio en el cual se cree que nació la mayoría de los reclutas en cada cohorte. No se dispuso de datos suficientes sobre otras variables ambientales para comprobarlos con los datos de los barcos de carnada. Las demás variables ambientales disponibles y seleccionadas para someterlas a pruebas de correlación con las estimaciones de la abundancia del barrilete de barcos cerqueros en el período 1961-1984, y las razones por su selección, son las siguientes: 1) Indice de mezcla por el viento (IMV). El grado de mezcla en las capas superiores del océano es proporcional al cubo de la velocidad del viento, llamado IMV. Es posible que el grado de mezcla en las zonas de desove del Pacífico central y occidental afecte la concentración de los organismos que alimentan a las larvas del barrilete, afectando así la supervivencia de éstas, y finalmente determinando el tamaño de las cohortes y el número de reclutas a la pesquería del OPO. 2) TSM en la zona de pesca al realizarse la pesca (TSM). Se ha mostrado que la relación de la CPUE del atún aleta amarilla a la TSM en la zona de pesca es inversa, y existen indicaciones que la CPUE de barrilete es inferior durante eventos del Niño, cuando las TSM son superiores a lo normal. 3) Gradiente norte-sur de las TSM a través del frente térmico frente al Golfo de Guayaquil. Esto es una medida del grado de afloramiento y enriquecimiento nutritivo del nivel superior de las aguas al sur de dicho frente, y finalmente de la producción de alimento para los atunes. 4) La velocidad de la Contracorriente Ecuatorial del Norte (CCEN). Es posible que los bariletes juveniles migren del Pacífico central al Pacífico oriental en la CCEN, que fluye hacia el este; de ser así, es posible que la cantidad de reclutas se vea afectada por variaciones en la velocidad de la corriente. El logaritmo de la tasa anual de captura de reclutas de barrilete por cerqueros de varias banderas en el OPO en el período 1961-1964 estuvo correlacionado de forma positiva con las TSM en la zona de desove del Pacífico central de 18meses antes (r2 0.21),y de forma inversa con el IMV de la zona de desove de 18 meses antes (r2 0.46). El logaritmo de la CPUE de los cerqueros en la zona frente al Golfo de Guayaquil no estuvo correlacionado con las TSM en la zona de desove de 18 meses antes, pero sí estuvo correlacionado de forma inversa con el IMV en la zona de desove de 18 meses antes (r2 0.19),y con el gradiente norte-sur de las TSM en la zona de pesca al realizarse la pesca (r2 0.32). Ninguna de estas estimaciones de abundancia aparente provenientes de barcos cerqueros estuvo correlacionada con las TSM en las zonas de pesca o con la velocidad de la CCEN en épocas anteriores. (PDF contains 140 pages.)

Herbicidan control of water hyacinth at Ere, Ogun State: implications for fish production

A brief account is given of a pilot demonstration of the chemical control of water hyacinth (Eichhornia crassipes) at Ere (a channel) in Nigeria using the herbicide glyphosphate. Results suggest that there was an increase in the nutrient content of the channel after herbicide application. This implied an upsurge of available food for fish and other aquatic organisms within the channel after the herbicide application. The decaying water hyacinth mass which sinks into the medium is likely to boost nutrient content, promoting the growth of fish and other aquatic animals. It is concluded that herbicidal control of water hyacinth is possible, especially under specialists' management with the conservation of fish and other non-target aquatic organisms alongside improved fish production

Acute toxicity of atrazine to Oreochromis niloticus fingerlings

Acute toxicity of atrazine to Oreochromis niloticus was undertaken to find the lethal concentration (LC) 50 of atrazine using fingerlings. Different concentrations were prepared in mg/L. There were six different concentrations with a control and each treatment was replicated three times. A total number of twenty-one aquaria were used. The highest concentration was 30mg/L. Ten test organisms were used in each aquarium. At 24, 48, 72 and 96 hours there were LC 50 of 15.6mg/L, 14mg/L, 11mg/L and 9.4, respectively. At 24, 48, 72 and 96 hours there were mean survivals of 49.0%, 34.3%, 28.6% and 28.1%, respectively

Isotopic proxies for microbial and environmental change : insights hydrogen isotopes and the Ediacaran Khufai Formation

Microbes have profoundly influenced the Earth’s environments through time. Records of these interactions come primarily from the development and implementation of proxies that relate known modern processes to chemical signatures in the sedimentary record. This thesis is presented in two parts, focusing first on novel proxy development in the modern and second on interpretation of past environments using well-established methods. Part 1, presented in two chapters, builds on previous observations that different microbial metabolisms produce vastly different lipid hydrogen isotopic compositions. Chapter 1 evaluates the potential environmental expression of metabolism-based fractionation differences by exploiting the natural microbial community gradients in hydrothermal springs. We find a very large range in isotopic composition that can be demonstrably linked to the microbial source(s) of the fatty acids at each sample site. In Chapter 2, anaerobic culturing techniques are used to evaluate the hydrogen isotopic fractionations produced by anaerobic microbial metabolisms. Although the observed fractionation patterns are similar to those reported for aerobic cultures for some organisms, others show large differences. Part 2 changes focus from the modern to the ancient and uses classical stratigraphic methods combined with isotope stratigraphy to interpret microbial and environmental changes during the latest Precambrian Era. Chapter 3 presents a detailed characterization of the facies, parasequence development, and stratigraphic architecture of the Ediacaran Khufai Formation. Chapter 4 presents measurements of carbon, oxygen, and sulfur isotopic ratios in stratigraphic context. Large oscillations in the isotopic composition of sulfate constrain the size of the marine sulfate reservoir and suggest incorporation of an enriched isotopic source. Because this data was measured in stratigraphic context, we can assert with confidence that these isotopic shifts are not related to stratigraphic surfaces or facies type but instead reflect the evolution of the ocean through time. This data integrates into the chemostratigraphic global record and contributes to the emerging picture of changing marine chemistry during the latest Precambrian Era.

Some ecological roles of Hippopotamus (Hippopotamus amphibious Linn. 1758) in fish production: possibilities for integrated fish-cum Agric production system

The common hippopotamus (Hippopotamus amphibious Linn. 1758) contributes to the productivity of aquatic systems where it lives. This paper reviews ecological roles of the hippo in this regard. Desk review of available literature information complemented with field observations were employed in the data collection. The ecological roles of the common hippopotamus being presented draw examples from East, West, Central and South African sub regions. The nutritional importance of the amphibious hippopotamus to rural communities was highlighted. In Southern Ethiopia, the Bodi, Bacha and Mura tribes eat hippo meat and this has led to severe hunting consequences on the wild populations of the animal. The important relationships between the hippopotamus and fish were presented. Hippopotamuses usually defecate in water and their excrements enrich the nutrients in the water resulting in favourable conditions for large fish populations. Some fish, including Labeo spp. were observed to feed on the micro-organisms and algae that grow on the skin of the hippotamus. A strong case was made for hippo-cum-fish integrated farm development in Nigeria based on ecological relationships so observed between the amphibious mammals and fish. This is one of the meeting points of fisheries and wildlife management that should be exploited for the benefits of the teeming Nigerian population

Habitat enhancing marine structures: Creating habitat in urban waters

Although maritime regions support a large portion of the world’s human population, their value as habitat for other species is overlooked. Urban structures that are built in the marine environment are not designed or managed for the habitat they provide, and are built without considering the communities of marine organisms that could colonize them (Clynick et al., 2008). However, the urban waterfront may be capable of supporting a significant proportion of regional aquatic biodiversity (Duffy-Anderson et al., 2003). While urban shorelines will never return to their original condition, some scientists think that the habitat quality of urban waterfronts could be significantly improved through further research and some design modifications, and that many opportunities exist to make these modifications (Russel et al., 1983, Goff, 2008). Habitat enhancing marine structures (or HEMS) are a potentially promising approach to address the impact of cities on marine organisms including habitat fragmentation and degradation. HEMS are a type of habitat improvement project that are ecologically engineered to improve the habitat quality of urban marine structures such as bulkheads and docks for marine organisms. More specifically, HEMS attempt to improve or enhance the physical habitat that organisms depend on for survival in the inter- and sub-tidal waterfronts of densely populated areas. HEMS projects are targeted at areas where human-made structures cannot be significantly altered or removed. While these techniques can be used in suburban or rural areas restoration or removal is preferred in these settings, and HEMS are resorted to only if removal of the human-made structure is not an option. Recent research supports the use of HEMS projects. Researchers have examined the communities found on urban structures including docks, bulkheads, and breakwaters. Complete community shifts have been observed where the natural shoreline was sandy, silty, or muddy. There is also evidence of declines in community composition, ecosystem functioning, and increases in non-native species abundances in assemblages on urban marine structures. Researchers have identified two key differences between these substrates including the slope (seawalls are vertical; rocky shores contain multiple slopes) and microhabitat availability (seawalls have very little; rocky shores contain many different types). In response, researchers have suggested designing and building seawalls with gentler slopes or a combination of horizontal and vertical surfaces. Researchers have also suggested incorporating microhabitat, including cavities designed to retain water during low tide, crevices, and other analogous features (Chapman, 2003; Moreira et al., 2006) (PDF contains 4 pages)

Single-cell analysis of the physiology of mechanosensation in bacteria

Escherichia coli is one of the best studied living organisms and a model system for many biophysical investigations. Despite countless discoveries of the details of its physiology, we still lack a holistic understanding of how these bacteria react to changes in their environment. One of the most important examples is their response to osmotic shock. One of the mechanistic elements protecting cell integrity upon exposure to sudden changes of osmolarity is the presence of mechanosensitive channels in the cell membrane. These channels are believed to act as tension release valves protecting the inner membrane from rupturing. This thesis presents an experimental study of various aspects of mechanosensation in bacteria. We examine cell survival after osmotic shock and how the number of MscL (Mechanosensitive channel of Large conductance) channels expressed in a cell influences its physiology. We developed an assay that allows real-time monitoring of the rate of the osmotic challenge and direct observation of cell morphology during and after the exposure to osmolarity change. The work described in this thesis introduces tools that can be used to quantitatively determine at the single-cell level the number of expressed proteins (in this case MscL channels) as a function of, e.g., growth conditions. The improvement in our quantitative description of mechanosensation in bacteria allows us to address many, so far unsolved, problems, like the minimal number of channels needed for survival, and can begin to paint a clearer picture of why there are so many distinct types of mechanosensitive channels.

Protecting a threatened coastal fish species through regional collaboration

Rainbow smelt (Osmerus mordax) are small anadromous fish that live in nearshore coastal waters during much of the year and migrate to tidal rivers to spawn during the spring. They are a key prey species in marine food webs, as they are consumed by larger organisms such as striped bass, bluefish, and seabirds. In addition, smelt are valued culturally and economically, as they support important recreational and commercial fisheries. The Atlantic Coast range of rainbow smelt has been contracting in recent decades. Historically, populations extended from the Delaware River to eastern Labrador and the Gulf of St. Lawrence (Buckley 1989). More recent observations indicate that rainbow smelt spawning populations have been extirpated south of Long Island Sound, and evidence of spawning activity is extremely limited between Long Island and Cape Cod, MA. In the Gulf of Maine region, spawning runs are still observed, but monitoring surveys as well as commercial and recreational catches indicate that these populations have also declined (e.g., Chase and Childs 2001). Many diverse factors could drive the recently noted declines in rainbow smelt populations, including spawning habitat conditions, fish health, marine environmental conditions, and fishing pressure. Few studies have assessed any of these potential threats or their joint implications. In 2004, the National Marine Fisheries Service (NMFS) listed rainbow smelt as a species of concern. Subsequently, the states of Maine, New Hampshire, and Massachusetts were awarded a grant through NMFS’s Proactive Conservation Program to gather new information on the status of rainbow smelt, identify factors that affect spawning populations, and develop a multi-state conservation program. This paper provides an overview of this collaborative project, highlighting key biological monitoring and threats assessment research that is being conducted throughout the Gulf of Maine. (PDF contains 4 pages)

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Proteomic analysis of the Cdc48/Ubx network identifies a role for Ubx2 in the regulation of lipid biosynthesis

Cdc48/p97 is an essential, highly abundant hexameric member of the AAA (ATPase associated with various cellular activities) family. It has been linked to a variety of processes throughout the cell but it is best known for its role in the ubiquitin proteasome pathway. In this system it is believed that Cdc48 behaves as a segregase, transducing the chemical energy of ATP hydrolysis into mechanical force to separate ubiquitin-conjugated proteins from their tightly-bound partners.

Current models posit that Cdc48 is linked to its substrates through a variety of adaptor proteins, including a family of seven proteins (13 in humans) that contain a Cdc48-binding UBX domain. As such, due to the complexity of the network of adaptor proteins for which it serves as the hub, Cdc48/p97 has the potential to exert a profound influence on the ubiquitin proteasome pathway. However, the number of known substrates of Cdc48/p97 remains relatively small, and smaller still is the number of substrates that have been linked to a specific UBX domain protein. As such, the goal of this dissertation research has been to discover new substrates and better understand the functions of the Cdc48 network. With this objective in mind, we established a proteomic screen to assemble a catalog of candidate substrate/targets of the Ubx adaptor system.

Here we describe the implementation and optimization of a cutting-edge quantitative mass spectrometry method to measure relative changes in the Saccharomyces cerevisiae proteome. Utilizing this technology, and in order to better understand the breadth of function of Cdc48 and its adaptors, we then performed a global screen to identify accumulating ubiquitin conjugates in cdc48-3 and ubxΔ mutants. In this screen different ubx mutants exhibited reproducible patterns of conjugate accumulation that differed greatly from each other, pointing to various unexpected functional specializations of the individual Ubx proteins.

As validation of our mass spectrometry findings, we then examined in detail the endoplasmic-reticulum bound transcription factor Spt23, which we identified as a putative Ubx2 substrate. In these studies ubx2Δ cells were deficient in processing of Spt23 to its active p90 form, and in localizing p90 to the nucleus. Additionally, consistent with reduced processing of Spt23, ubx2Δ cells demonstrated a defect in expression of their target gene OLE1, a fatty acid desaturase. Overall, this work demonstrates the power of proteomics as a tool to identify new targets of various pathways and reveals Ubx2 as a key regulator lipid membrane biosynthesis.

Limits and tradeoffs in the control of autocatalytic systems

Despite the complexity of biological networks, we find that certain common architectures govern network structures. These architectures impose fundamental constraints on system performance and create tradeoffs that the system must balance in the face of uncertainty in the environment. This means that while a system may be optimized for a specific function through evolution, the optimal achievable state must follow these constraints. One such constraining architecture is autocatalysis, as seen in many biological networks including glycolysis and ribosomal protein synthesis. Using a minimal model, we show that ATP autocatalysis in glycolysis imposes stability and performance constraints and that the experimentally well-studied glycolytic oscillations are in fact a consequence of a tradeoff between error minimization and stability. We also show that additional complexity in the network results in increased robustness. Ribosome synthesis is also autocatalytic where ribosomes must be used to make more ribosomal proteins. When ribosomes have higher protein content, the autocatalysis is increased. We show that this autocatalysis destabilizes the system, slows down response, and also constrains the system’s performance. On a larger scale, transcriptional regulation of whole organisms also follows architectural constraints and this can be seen in the differences between bacterial and yeast transcription networks. We show that the degree distributions of bacterial transcription network follow a power law distribution while the yeast network follows an exponential distribution. We then explored the evolutionary models that have previously been proposed and show that neither the preferential linking model nor the duplication-divergence model of network evolution generates the power-law, hierarchical structure found in bacteria. However, in real biological systems, the generation of new nodes occurs through both duplication and horizontal gene transfers, and we show that a biologically reasonable combination of the two mechanisms generates the desired network.

Some potential occupational and environmental hazards associated with fish pond production in Nigeria

The paper highlights the concept of information and the significance of environmental and occupational hazards associated with pond fish production in Nigeria and discuss the possible options for the ways forward. The major raw material used in fish production system is the organic manure (cow dung, poultry droppings, porcine manure etc) that serves as substrate for heterotrophic production of bacteria and protozoa, which act as food for zooplankton and the fish. The pathogenic organisms (viruses, bacteria, protozoa's, and parasites), are noted for the potential hazard to the fish handlers and consumers. Nine species from seven genera of bacteria associated with fish diseases are found to have association with diseases of human such as typhoid fever, bacillary dysentery and other gastrointestinal tract related problems. Also the environmental contaminants in pond fish production become important because of its significance to consumers' acceptance of the fish products