Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (Pacific Southwest): Northern anchovy

Three genetically distinct groups: British Columbia to northern California, Southern California to the northern Baja peninsula, and central and southern Baja California. (PDF contains 21 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.

Monitoring fish populations in Lower Lough Erne, Northern Ireland: applicability of current methods and implications for future monitoring under the EC Water Framework Directive

The proposed EC Water Framework Directive (WFD) will require member states to monitor both biotic and abiotic components of lake environments. With adoption of the WFD some measurement of fish populations will also be required. This paper describes work carried out since 1971, and particularly since 1991, on the status of fish populations in Lower Lough Erne, Northern Ireland, with an emphasis on defining change over time due to human impacts on the lake. This offers a reasonable starting point from which to develop a monitoring programme suitable for the needs of the WFD in this lake. The implications for as yet unmonitored fish populations in lakes are also determined.

A preliminary classification of lake types in Northern Ireland

The EC Water Framework Directive (WFD) introduces the concept of the ecological status of surface waters. The WFD requires that water bodies within an ecoregion are divided into waterbody "types" or "ecotypes". The waterbody type is determined by physico-chemical descriptors. A group of representatives from two government environmental agencies (Environment and Heritage Service and the Industrial Research and Technology Unit) and the two universities (Queen's University Belfast and the University of Ulster) in Northern Ireland, has been established to develop methods for measuring the ecological status of lakes, for the purposes of the WFD. The work here is that contributing to the first objective classification into waterbody types.

Creation of temporary ponds for amphibians in northern and central Europe

More than 4000 ponds have been created or restored in Denmark since 1985 as part of a large-scale pond-digging programme to protect endangered amphibians in particular and pond flora and fauna in general. Most ponds are created on private land with public financing. The programme was triggered by, among other factors, a drastic decline in amphibian populations in Denmark between 1940 and 1980. However, in recent years there has been an increased awareness in Denmark that temporary ponds are important for the conservation of some of the most rare amphibian species, such as fire-bellied toad Bombina bombina, natterjack toad Bufo calamita and green toad Bufo viridis. Other rare species such as moor frog Rana arvalis and European tree frog Hyla arborea also benefit from temporary ponds. The last 15 years of work on the conservation of endangered species and their habitats has resulted in a last-minute rescue and a subsequent growth in the size of most Danish populations of fire-bellied toad and green toad; some populations of the relatively more common natterjack toad have also increased. The creation of temporary ponds plays an important role in the success of these three species. The creation of ponds to help restore viable populations of the most rare amphibians has not been easy. To study the conditions that may need to be created, Danish herpetologists searched for areas with temporary ponds that had good water quality, natural hydrological conditions and a management regime influenced by traditional agricultural methods. The paper gives an overview of pond creation and restoration projects in Denmark and Poland and their significance for amphibian diversity.

A new synoptic survey of Northern Ireland lakes: sampling from the air

Northern Ireland has approximately 1670 lakes, which cover 4.4% of the land surface. However, most of the water area is accounted for by the large lakes such as Lough Neagh (385 km2) and Lower Lough Erne (109.5 km ). The majority of lakes are less than 100 hectares in area. They tend to be distributed towards the south and west of the Province, where extensive drumlin swarms are rich in small waterbodies. In 1988-1991, 610 of the 708 lakes between one and 100 hectares were sampled by the Northern Ireland Lake Survey. The objective was to assess their conservation status based on their aquatic macrophyte flora, but in addition to extensive plant surveys, the water of each lake was analysed for a range of chemical variables. This article reports on a full-scale survey carried out in early March 2002. The survey was taken with help of two helicopters. The authorise summarise the results of the chemical analysis of the survey.

Invertebrate communities in northern Lake Victoria, with reference to their potential for fishery production

The zooplankton and macrobenthic communities of Lake Victoria were sampled by lift net and Ponar grab, respectively. The zooplankton comprised copepods and cladocerans, rotifers and aquatic insect larvae. Most taxa exhibited wide distribution in the lake, with the exception of rotifers which were rare in deep offshore waters. The main components in the macro-benthos were chaoborid and chironomid larvae and molluscs. Caridina nilotica (Roux) and other groups were rare in the samples. Zooplankton density ranged from 100000 or more to 4 million ind. m2 and increased from the shallow inshore to deep offshore waters. Numerical dominance of cyclopoids and nauplius larvae was a common feature at all stations sampled. Most macrobenthic taxa were also widely distributed, although chaoborid and chironomid larvae were rare in the samples. Rastrineobola argentea (Pellegrin) and larval Lates niloticus (L.) ate mainly cyclopoid copepods, while cichlids showed a strong preference for adult insects. High ecological stability of the cyclopoids, and the zooplankton community in general, despite radical ecosystem changes in recent years, coupled with what appears to be high predation pressure, offers good prospects for the pelagic fishery in the lake.

Reproductive biology of Rastrineobola argentea (Pellegrin) in the northern waters of Lake Victoria

Size at first maturity, breeding periods and condition factor were determined for the small pelagic cyprinid Rastrineobola argentea (Pellegrin) in the Jinja waters of Lake Victoria in 1996-1997. Females showed a reduced size at maturity compared to ten years earlier when exploitation of the species was minimal. The males, however, have changed little. Although the species breeds throughout the year, two breeding peaks were observed during the drier months of August and December-January. Minimal breeding was observed in the rainy months of April-May and October-November. Fish from the open water station at Bugaia showed a higher proportion of breeding individuals than those from inshore areas. The mean monthly condition factor of fish from Napoleon Gulf confirmed breeding peaks obtained from examination of gonad development.

Species composition and relative abundance of zooplanktivorous haplochromines in the northern portion of Lake Victoria (Uganda)

Recent surveys have indicated an increase in haplochromine biomass recorded from the bottom trawl and in the beam trawl. The haplochromines recovering in the offshore waters belong to three species in the zooplanktivorous trophic group: Yssichromis laparogramma (Greenwood and Gee), Yssichromis fusiformis (Greenwood and Gee) and Astatotilapia lacrimosa (Boulenger). In this paper, the species composition and relative abundance of the zooplanktivorous haplochromines recorded from the bottom and frame trawl surveys in the various parts of the Ugandan waters of Lake Victoria are discussed.

Study and comparison of four forest structures on Mt. Chortiatis (northern Greece)

EL proyecto estudia y analiza la estructura de cuatro bosques en el monte Chortiatis, Grecia.

Metallogenic Provinces of the Southwestern United States and Northern Mexico

Some of the metallogenic provinces of the southwestern United States and northern Mexico are defined by the geographic distribution of trace elements in the primary sulfide minerals chalcopyrite and sphalerite. The elements investigated include antimony, arsenic, bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, molybdenum, nickel, silver, tellurium, thallium, and tin. Of these elements, cobalt, gallium, germanium, indium, nickel, silver, and tin exhibit the best defined geographic distribution.

The data indicate that chalcopyrite is the preferred host for tin and perhaps molybdenum; sphalerite is the preferred host for cadmium, gallium, germanium, indium, and manganese; galena is the preferred host for antimony, bismuth, silver, tellurium, and thallium; and pyrite is the preferred host for cobalt, nickel, and perhaps arsenic. With respect to the two minerals chalcopyrite and sphalerite, antimony, arsenic, molybdenum, nickel, silver, and tin prefer chalcopyrite; and bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, and thallium prefer sphalerite. This distribution probably is the result of the interaction of several factors, among which are these: the various radii of the elements, the association due to chemical similarities of the major and trace elements, and the degree of ionic versus covalent and metallic character of the metal-sulfur bonds in chalcopyrite and sphalerite. The type of deposit, according to a temperature classification, appears to be of minor importance in determining the trace element content of chalcopyrite and sphalerite.

A preliminary investigation of large single crystals of sphalerite and chalcopyrite indicates that the distribution within a single crystal of some elements such as cadmium in sphalerite and indium and silver in chalcopyrite is relatively uniform, whereas the distribution of some other elements such as cobalt and manganese in sphalerite is somewhat less uniform and the distribution of tin in sphalerite is extremely erratic. The variations in trace element content probably are due largely to variations in the composition of the fluids during the growth of the crystals, but the erratic behavior of tin in sphalerite perhaps is related to the presence of numerous cavities and inclusions in the crystal studied.

Maps of the geographic distribution of trace elements in chalcopyrite and sphalerite exhibit three main belts of greater than average trace element content, which are called the Eastern, Central, and Western belts. These belts are consistent in trend and position with a beltlike distribution of copper, gold, lead, zinc, silver, and tungsten deposits and with most of the major tectonic features. However, there appear to be no definite time relationships, for as many as four metallogenic epochs, from Precambrian to late Tertiary, are represented by ore deposits within the Central belt.

The evidence suggests that the beltlike features have a deep seated origin, perhaps in the sub-crust or outer parts of the mantle, and that the deposits within each belt might be genetically related through a beltlike compositional heterogeneity in the source regions of the ores. Hence, the belts are regarded as metallogenic provinces.

Progressive Decrease in the Potential Usefulness of Meningococcal Serogroup B Vaccine (4CMenB, Bexsero (R)) in Gipuzkoa, Northern Spain

The effectiveness of a vaccine is determined not only by the immunogenicity of its components, but especially by how widely it covers the disease-causing strains circulating in a given region. Because vaccine coverage varies over time, this study aimed to detect possible changes that could affect vaccine protection during a specific period in a southern European region. The 4CMenB vaccine is licensed for use in Europe, Canada, and Australia and is mainly directed against Neisseria meningitidis serogroup B. This vaccine contains four main immunogenic components: three recombinant proteins, FHbp, Nhba and NadA, and an outer membrane vesicle [PorA P1.4]. The allelic distribution of FHbp, Nhba, NadA, and PorA antigens in 82 invasive isolates (B and non-B serogroups) isolated from January 2008 to December 2013 were analyzed. 4CMenB was likely protective against 61.8% and 50% of serogroup B and non-B meningococci, respectively, in the entire period, but between 2012 and 2013, the predicted protection fell below 45% (42.1% for serogroup B isolates). The observed decreasing trend in the predicted protection during the 6 years of the study (X-2 for trend = 4.68, p=0.03) coincided with a progressive decrease of several clonal complexes (e. g., cc11, cc32 and cc41/44), which had one or more antigens against which the vaccine would offer protection.

Final Evaluation Memorandum: Strategies for Resolving Low Dissolved Oxygen and Methylmercury Events in Northern Suisun Marsh

The purpose of the project is to improve our understanding about best management practices that can be utilized on diked managed wetlands in Suisun Marsh for reducing the occurrence of low dissolved oxygen (DO) and high methylmercury (MeHg) events associated primarily with fall flood-up practices. Low DO events are of concern because they can lead to undue stress and even mortality of sensitive aquatic organisms. Elevated MeHg levels are of concern because MeHg is a neurotoxin that bio-magnifies up the food chain and can cause deleterious effects to higher trophic level consumers such as piscivorous fish, birds, and mammals (including humans). This study involved two years (2007-2008) of intensive field data collection at two managed wetland sites in northwest Suisun Marsh and their surrounding tidal sloughs, an area with prior documented low DO events. In addition, the study collected limited soils and water quality field data and mapped vegetation for three managed wetland sites in the central interior of Suisun Marsh, for the purpose of examining whether wetlands at other locations exhibit characteristics that could indicate potential for similar concerns. In Year 1 of the study, the objective was to identify the baseline conditions in the managed wetlands and determine which physical management conditions could be modified for Year 2 to reduce low DO and MeHg production issues most effectively. The objective of Year 2 was to evaluate the effectiveness of these modified management actions at reducing production of low DO and elevated MeHg conditions within the managed wetlands and to continue improving understanding of the underlying biogeochemical processes at play. This Final Evaluation Memorandum examined a total of 19 BMPs, 14 involving modified water management operations and the remaining five involving modified soil and vegetation management practices. Some of these BMPs were previously employed and others have not yet been tested. For each BMP this report assesses its efficacy in improving water quality conditions and potential conflicts with wetland management. It makes recommendations for further study (either feasibility assessments or field testing) and whether to consider for future use. Certain previously used BMPs were found to be important contributors to poor water quality conditions and their continued use is not recommended. Some BMPs that could improve water quality conditions appear difficult to implement in regards to compatibility with wetland management; these BMPs require further elaboration and feasibility assessment to determine whether they should be field tested. In practice for any given wetland, there is likely a combination of BMPs that would together have the greatest potential to address the low DO and high MeHg water quality concerns. Consequently, this report makes no sweeping recommendations applicable to large groups of wetlands but instead promotes a careful consideration of factors at each wetland or small groups of wetlands and from that assessment to apply the most effective suite of BMPs. This report also identifies a number of recommended future actions and studies. These recommendations are geared toward improving the process understanding of factors that promote low DO and high MeHg conditions, the extent of these problems in Suisun Marsh, the regulatory basis for the DO standards for a large estuarine marsh, the economics of BMPs, and alternative approaches to BMPs on diked managed wetlands that may address the water quality issues. The most important of these recommendations is that future BMP implementation should be carried out within the context of rigorous scientific evaluation so as to gain the maximum improvement in how to manage these water quality issues in the diked managed wetlands of Suisun Marsh.

Remote Sensing and Field Assessment of Tsunami Effects on Coastal Pond Aquaculture in Northern Sumatra

An attempt was made to conduct spatial assessment of the pattern and extent of damage to coastal aquaculture ponds along the east coast of Aceh province in Sumatra, Indonesia, resulting from the tsunami event of 26 December 2004. High-resolution satellite imagery, i.e., SPOT-5 multispectral scenes covering the 700 km stretch of the coast, acquired before and after the tsunami, were digitally enhanced and visually interpreted to delineate pockets of aquaculture ponds that were discerned to be damaged and relatively intact. Field checks were conducted at 87 sites in the four eastern coastal districts. The results indicate that SPOT-5 multispectral imagery was minimally sufficient to detect areas of damaged and relatively intact aquaculture ponds, but the 10-m spatial resolution poses limitations to evaluating the extent of pond damage. Nevertheless, the 60 km swath of the imagery makes it reasonably affordable for large-area assessment to identify pockets of severe damage for targeting more detailed assessments. The image maps produced from a mosaic of the SPOT-5 scenes can also serve as base maps for spatial planning in the challenging task of reconstruction and rehabilitation of the disrupted livelihoods of the coastal communities.

Contrasting abundance and residency patterns of two sympatric populations of transient killer whales (Orcinus orca) in the northern Gulf of Alaska

Two sympatric populations of “transient” (mammal-eating) killer whales were photo-identified over 27 years (1984–2010) in Prince William Sound and Kenai Fjords, coastal waters of the northern Gulf of Alaska (GOA). A total of 88 individuals were identified during 203 encounters with “AT1” transients (22 individuals) and 91 encounters with “GOA” transients (66 individuals). The median number of individuals identified annually was similar for both populations (AT1=7; GOA=8), but mark-recapture estimates showed the AT1 whales to have much higher fidelity to the study area, whereas the GOA whales had a higher exchange of individuals. Apparent survival estimates were generally high for both populations, but there was a significant reduction in the survival of AT1 transients after the Exxon Valdez oil spill in 1989, with an abrupt decline in estimated abundance from a high of 22 in 1989 to a low of seven whales at the end of 2010. There was no detectable decline in GOA population abundance or survival over the same period, but abundance ranged from just 6 to 18 whales annually. Resighting data from adjacent coastal waters and movement tracks from satellite tags further indicated that the GOA whales are part of a larger population with a more extensive range, whereas AT1 whales are resident to the study area.