Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions

An original experimental method of direct molecular fishing has been developed for identification of potential partners of protein–protein and protein–peptide interactions. It is based on combination of surface plasmon resonance technology (SPR), size exclusion and affinity chromatography and mass spectrometric identification of proteins (LC-MS/MS). Previously, we demonstrated applicability of this method for protein interactomics using experimental model system, as well as in the pilot study in the frame of the Human Proteome Project (HPP). In the present paper, this method was successfully applied to identify possible molecular partners of 7 target proteins encoded by genes of 18 chromosome (also in the frame of the HPP). Fishing on the affinity sorbents with immobilized target proteins as ligands was carried out using total lysate of human liver tissue as well as pooled sets of fractions (individual for each bait-protein) obtained by means of a combination of size exclusion chromatography and SPR analysis for the presence of potential prey-proteins in each fraction. As a result we obtained lists of possible molecular partners of all 7 proteins and performed a comparative evaluation of direct fishing specificity for these target proteins. Direct molecular fishing was also successfully used for search of potential protein partners interacting with different isoforms of amyloid-beta peptide, playing a key role in the development of Alzheimer’s disease. The synthetic peptides that are analogues of the metal-binding domain isoforms of beta-amyloid were used as molecular baits and the fishing was performed in various fractions of immortalized human neural cells. As a result, 13 potential partner proteins were identified in the cytosol fraction of the cells by fishing on amyloid-beta peptide (1-16).     

Natural fishing experiments in marine reserves 1983–1993: community and trophic responses

 This study examined the effect of fishing on the density, biomass, species richness and overall structure of the reef fish community at two islands (Sumilon and Apo) in the Philippines from 1983 to 1993. A series of natural fishing experiments over this period involving marine reserves were monitored at each island, where estimates of fishing intensity and selectivity were available. Fishing intensity (15% and 25% of biomass removed per year at Sumilon and Apo, respectively) was high enough to affect total community biomass, but not density, significantly. Species richness was not affected significantly by fishing, except at Sumilon reserve. The fishery was relatively non-selective with most families/trophic groups caught roughly in proportion to their contribution to community biomass. Thus fishing did not alter the relative abundance of the major families/trophic groups significantly, except during a period of use of explosives and drive nets in the Sumilon reserve. At the level of family/trophic group the community displayed strong resilience of structure. There was little evidence of secondary effects e.g. declines in abundance of large predators resulting in measurable increases in abundance of their prey. This resilience of the community to the effects of fishing most likely results from three important community attributes (open nature of the component populations, likely maintenance of upstream recruitment supply and apparent lack of any obvious “keystone” species or families) and one important characteristic of the fishery (relatively non-selective with respect to the components of the community). Accepted: 30 June 1998     

Non-native fish in aquaculture and sport fishing in Brazil: economic benefits versus risks to fish diversity in the upper River Paraná Basin

Brazil has a highly diverse freshwater fish fauna and their freshwaters provide valuable provisioning ecosystem services in aquaculture and sport angling, especially in the developed regions in the south. Non-native fish now comprise a substantial proportion of the total aquaculture production and value, contributing at least $US 250?million in 2008 (63% of the total value of freshwater fish aquaculture) according to the Fish and Agriculture Organisation. Much of this aquaculture activity is centred in Central and Southern Brazil, such as impounded sections of the upper River Paraná. The non-native fishes used tend to feed at relatively low trophic levels, with the most prominently species being Cyprinus carpio and Oreochromis niloticus. Ecological risk assessment suggests these species are potentially highly invasive and deleterious to the native fish diversity of invaded water bodies. Fishes introduced for the creation of sport fisheries tend feed higher trophic levels through piscivory, such as the peacock basses (Cichla species) from Amazonia. Their introductions have generally resulted in establishment and invasion, which tends to be followed by significant and rapid declines in native fish diversity as a consequence of increased predation pressure. Thus, whilst non-native fish in the upper Paraná River support provisioning ecosystem services of substantial economic value, the principal species used represent high risks to fish diversity and conservation. It is recommended local management should concentrate on reducing these risks through use of more appropriate species in these ecosystem services, with these decisions derived using risk assessment and precautionary principles.     

Profits and social performance of small-scale fishing in the Upper Paraná River floodplain (Brazil).

Small scale fishing profits in two communities in the Upper Paraná River floodplain (Porto Rico - PRI and Porto S?o José - PSJ villages) are assessed based on interviews carried out with professional fishermen. There is a high illiteracy level in both PRI (50%) and PSJ (44.5%). The main contributions to income are "vessel costs" and "fish consumption" by the family. Specific tackle (such as cevadeira) and gear used for fishing close to dams make the gear costs higher at PSJ, emphasising the heterogeneity of the activity. The majority of fishermen in both villages have income complementation activities associated with tourism, because floodplain fishing is not a profitable occupation with any poverty alleviation capacity. Since the ecosystem is seriously disrupted, nowadays fishers are vulnerable to high oscillations in costs and income due to uncertainty in catches aggravated by flood control of the dams.     

When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs

Bottom trawls are a globally used fishing gear that physically disturb the seabed and kill non-target organisms, including those that are food for the targeted fish species. There are indications that ensuing changes to the benthic invertebrate community may increase the availability of food and promote growth and even fisheries yield of target fish species. If and how this occurs is the subject of ongoing debate, with evidence both in favour and against. We model the effects of trawling on a simple ecosystem of benthivorous fish and two food populations (benthos), susceptible and resistant to trawling. We show that the ecosystem response to trawling depends on whether the abundance of benthos is top-down or bottom-up controlled. Fishing may result in higher fish abundance, higher (maximum sustainable) yield and increased persistence of fish when the benthos which is the best-quality fish food is also more resistant to trawling. These positive effects occur in bottom-up controlled systems and systems with limited impact of fish feeding on benthos, resembling bottom-up control. Fishing leads to lower yields and fish persistence in all configurations where susceptible benthos are more profitable prey. Our results highlight the importance of mechanistic ecosystem knowledge as a requirement for successful management.     

Farming,fishing, and fire in the history of the upper Río Negro region of Venezuela

Studies of Río Negro subsistence farming and fishing activities are used to estimate the human carrying capacity for the region and the likely pattern of human land-use during prehistory. Ceramic evidence suggests human presence in the region more than 3000 years ago. Traditional farming is labor intensive and relatively unproductive. Nevertheless, farmers achieve an energy return of 15.21, and produce 2600 kcal per work hour. Fish are the major protein source, but fish catch per unit of effort and fish yield per hectare of floodplain are very low; fishermen are probably exploiting local fish resources very close to their limit. The low human population density would suggest that the Río Negro forest has been relatively undisturbed. Nevertheless, charcoal is widespread and abundant in forest soils. This charcoal is probably from anthropogenic or natural wildfires. These results suggest a much more complex history for Amazonia than previously thought.K. Clark is a free-lance biologist residing in Lima, Peru     

Repositioning drugs for inflammatory disease – fishing for new anti-inflammatory agents

Inflammation is an important and appropriate host response to infection or injury. However, dysregulation of this response, with resulting persistent or inappropriate inflammation, underlies a broad range of pathological processes, from inflammatory dermatoses to type 2 diabetes and cancer. As such, identifying new drugs to suppress inflammation is an area of intense interest. Despite notable successes, there still exists an unmet need for new effective therapeutic approaches to treat inflammation. Traditional drug discovery, including structure-based drug design, have largely fallen short of satisfying this unmet need. With faster development times and reduced safety and pharmacokinetic uncertainty, drug repositioning – the process of finding new uses for existing drugs – is emerging as an alternative strategy to traditional drug design that promises an improved risk-reward trade-off. Using a zebrafish in vivo neutrophil migration assay, we undertook a drug repositioning screen to identify unknown anti-inflammatory activities for known drugs. By interrogating a library of 1280 approved drugs for their ability to suppress the recruitment of neutrophils to tail fin injury, we identified a number of drugs with significant anti-inflammatory activity that have not previously been characterized as general anti-inflammatories. Importantly, we reveal that the ten most potent repositioned drugs from our zebrafish screen displayed conserved anti-inflammatory activity in a mouse model of skin inflammation (atopic dermatitis). This study provides compelling evidence that exploiting the zebrafish as an in vivo drug repositioning platform holds promise as a strategy to reveal new anti-inflammatory activities for existing drugs.KEY WORDS: Drug repositioning, Zebrafish, Inflammation, Neutrophil, Atopic dermatitis, Immunity     

What’s in a hearth? Seeds and fruits from the Neolithic fishing and fowling camp at Bergschenhoek,The Netherlands,in a wider context

This paper presents new results from the Early Neolithic Dutch wetland site of Bergschenhoek (ca. 4200 cal b.c., Swifterbant Culture), which are compared with finds from similar features and sites. The data indicate the presence of predominantly eutrophic, nutrient-rich reed and forb vegetation and suggest the preparation of meals consisting of fish and fruits. The finds from the hearth, dominated by uncarbonised remains of wetland taxa, form a remarkable part of the find assemblage. Therefore, the discussion concerns assemblages, deposition processes and interpretations of uncarbonised and carbonised finds from hearths at comparable, contemporary sites. The wide variation of macroremains assemblages of hearths indicates that plant deposition in hearths is understood only partly and remains a topic for further research.     

An overview of historical changes in the fishing gear and practices of pelagic longliners,with particular reference to Japan’s Pacific fleet

We identify changes in pelagic longline fishing gear and practices that need to be accounted for in stock assessments. Pelagic longline fishers have continuously modified their fishing gear and practices to improve fishing power and catchability, which has altered the relationship between catch rates and abundance. Advances in technology resulted in the introduction of many electronic devices to assist in navigation, communication and finding target species. The development of synthetic materials allowed improvements to lines and hooks that increased the probability of hooking target species and landing them. Other changes increased fishing power by improving searching efficiency (e.g., satellite imagery) or the time spent on fishing grounds (e.g., freezers). The number of hooks deployed in daily longlining operations has steadily increased since 1950. However, mean soak time did not change significantly because faster longline retrieval and deployment speeds balanced the increased hook numbers. There has been a shift from having all baits available at dawn, to having more available at dusk and at night. In the 1970s, several longline fleets began to exploit a much greater depth range, resulting in increased catchability for deep-dwelling species (e.g., bigeye tuna, Thunnus obesus) and reduced catchability for epipelagic species like blue marlin (Makaira nigricans). Research has been mostly limited to the effects of longline depth on the catchability of target species. Recent experiments have quantified the effects of bycatch mitigation measures on fishing power and catchability. Progressive improvements in expertise and technological improvements in the gear will also affect fishing power, but are particularly difficult to quantify.     

Small marine pelagic fish and the threat of fishing; are they endangered?

Evidence of the collapse and recovery of major marine fisheries for pelagic fish species is reviewed, distinguishing the influence of fishing compared with natural (environmental) effects. In one only of the best documented cases (Icelandic spring-spawning herring) has the stock failed to reappear, after 20 years. Several others, e.g. California sardine, have persisted at 1/000th or possibly less of their peak size for some years before beginning to recover. Fishing has been the main cause of collapse in most but not all cases, due initially to the escalation of catchability as stock size decreases–a phenomenon characteristic of fisheries for pelagic species due to their shoaling habit, ease of detection and vulnerability to modern fishing methods. It is concluded that although the threat of fishing to the continuity of the species is remote, excessive depletion (although avoidable by firm and timely management) is potentially able to cause temporary disappearance of local stock and disruption of the ecosystem.     

Spatial patterns in impacts of fishing on temperate rocky reefs: Are fish abundance and mean size related to proximity to fisher access points?

Effects of fishing on marine communities are becoming increasingly evident, yet little is known of the spatial extent of impacts, particularly for multiple impacts distributed over broad scales. We tested the common perception that commercial and recreational fishing on inshore temperate reefs generate spatial impacts that diminish with distance from fisher access points. We collected data on harvested and non-harvested reef species using underwater visual censuses at 133 shallow rocky reef sites around Tasmania and tested for relationships between assemblage and species level indices of fishing impacts and distance to the nearest boat launching ramp. Slopes of size spectra of fish communities tended to decrease with distance from the nearest boat ramp, with this relationship apparently resulting from low numbers of large fish (> 30 cm TL) and a greater number of smaller fish (< 15 cm TL) at sites closest to access points. At the species level, relationships were evident either in the abundance of legal individuals or the mean size of harvested species with distance to the nearest boat ramp, except for rock lobster. Patterns for rock lobster differed when areas in which commercial or recreational fisheries dominated were considered separately from the statewide analysis. A pattern of increasing numbers of legal lobsters with increasing distance from boat ramps was observed, but only in the areas in which the recreational fishery dominated. Observed relationships in all species were consistent with greater fishing impacts at sites closest to boat ramps, with the exception of exploited wrasses. Banded morwong, which are subject to a live export fishery, appeared to be most affected by proximity to boat ramps. Conversely, no relationships were found between the abundance or size of the most frequently occurring non-harvested species and distance to boat ramps.These results support the hypothesis that greater fishing impacts occur at more accessible sites over the entire Tasmanian coastline. The variability of results among individual species are likely, at least in part, to be related to differences in fisheries characteristics such as vessel size and range, as well as the suitability of our methods for detecting impacts. The potential of such a pattern in fishing impacts to be evident in other locations will thus likely depend on characteristics of the particular fishes and fisheries.     

Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (silver birch and hybrid aspen), dwarf shrubs (bilberry), and both monocotyledonous (regal lily) and dicotyledonous (Saint John's wort, round-leaved sundew, and tobacco) herbaceous plants. Buffers developed for DNA extraction were successfully used in addition to manufacturer's extraction kits. The quality of RNA was appropriate for many applications, but the quality of DNA was not always sufficient for polymerase chain reaction (PCR) amplification. However, we could strikingly improve the quality by eliminating the adherent compounds during the extraction or later in the PCR phase. Our results show that the use of the procedure could be extended to diverse plant species. This procedure is especially suitable for small sample sizes and for simultaneous processing of many samples enabling large-scale plant applications in population genetics, or in the screening of putative transgenic plants.     

First record of Buller’s Albatross (Thalassarche bulleri) from a fishing vessel in the south-western Atlantic Ocean off Southern Patagonia (Argentina)

Buller’s Albatross, Thalassarche bulleri, is a New Zealand breeding endemic that is frequently observed in the subtropical and sub-Antarctic South Pacific Ocean between Australia and Peru. However, in the South Atlantic Ocean, it is a vagrant, as information on its presence in this region is limited to only a few sightings. Here, we report a new record of T. bulleri in the south-western Atlantic Ocean off Argentina (55°06′13″S, 66°06′44″W) while investigating interactions between commercial fisheries and seabirds. This record provides new information about the distribution of this albatross species and its relation with fisheries outside of its regular range.     

The poor health of deep-water species in the context of fishing activity and a warming climate: will populations of Molva species rebuild or collapse?

Many deep-water fish populations, being K-selected species, have little resilience to overexploitation and may be at serious risk of depletion as a consequence. Sea warming represents an additional threat. In this study, the condition, or health, of several populations of common ling (Molva molva), blue ling (Molva dypterygia) and Mediterranean or Spanish ling (Molva macrophthalma) inhabiting different areas in the North Atlantic and the Mediterranean was evaluated, to shed light on the challenges these deep-water species are facing in the context of fishing activity and a warming climate. The data on the condition of Molva populations which are analysed here have been complemented with data on abundance and, for the southernmost species (Mediterranean ling), with two other health indicators (parasitism and hepato-somatic index). Despite some exceptions (e.g., common ling in Icelandic waters), this study shows that the condition of many populations of Molva species in the northeastern Atlantic and the Mediterranean Sea has worsened, a trend which, in recent decades, has usually been found to be accompanied by a decline in their abundance. In addition, the poor health status of most populations of common ling, blue ling and Mediterranean ling considered in this analysis points to a lower sustainability of these populations in the future. Overall, the health status and abundance of Molva populations in the northeastern Atlantic and the Mediterranean suggest that only some populations located in the North Atlantic may be able to rebuild, whereas the populations in southern North Atlantic and the Mediterranean, which are probably most at risk from sea warming, are facing serious difficulties in doing so. In the context of fisheries and global warming, this study's results strongly indicate that management bodies need to consider the health status of many of the populations of Molva species, particularly in southern European waters, before implementing their decisions.     

Strategic procurement of fish by the pumé: A South American “fishing culture”

Information is presented on fishing effort, efficiency, techniques, and catch composition for Pumé men, women, and children along with a conceptual model of fishing as a food procurement strategy. The Pumé are a native lowland South American group living in the topical savanna region of southwestern Venezuela characterized by seasonal flooding. Results are discussed in relation to the Pumé environmental and social situation, and briefly compared with results from other lowland South American groups.     

The effects of fishing on the diversity,biomass and trophic structure of Seychelles’ reef fish communities

A fishery independent underwater visual census technique was used to assess the effects of fishing on the diversity, biomass and trophic structure of the diurnally active non-cryptic reef-associated fish communities of the Seychelles. One hundred and thirty four species associated with three significantly different types of reef habitat were censused at one unfished ground and in six fishing grounds subject to different fishing intensity and the biomass of several species targeted by the fishery. The diversity of families containing target species (lutjanidae, lethrinidae) was significantly higher at unfished and lightly fished sites as was the total biomass of the fish community and the biomass of piscivorous, piscivorous/invertebrate feeding and herbivorous trophic groups. However, there was no indication that the biomass of non-target species increased in response to the removal of their predators by fishing. The findings of this study are significant for fishery managers because they suggest that the intensive differential cropping of top predators will not necessarily lead to increases in the biomass and productivity of their prey.