Estimating the food consumption of fishes: one step in linking a species with its ecosystem

Details are given of a new software package MAXIMS which may be used to estimate the daily food consumption of fish. The software estimates the feeding times, the rates of ingestion and evacuation and related parameters. Two applications of the program are described. The first pertains to anchovy (Engraulis ringens ) with one feeding period per day, and the second one to juvenile cod (Gadus morhua ), which feed during dawn and dusk.

Exploring the use of neural networks for biomass forecasts in the Peruvian upwelling ecosystem

A pilot study was conducted to study the ability of an artificial neural network to predict the biomass of Peruvian anchoveta Engraulis ringens, given time series of earlier biomasses, and of environmental parameters (ocenographic data and predator abundances). Acceptable predictions of three months or more appear feasible after thorough scrutiny of the input data set.

Structure-function analysis of USP1: insights into the role of Ser313 phosphorylation site and the effect of cancer-associated mutations on autocleavage

Background: In complex with its cofactor UAF1, the USP1 deubiquitinase plays an important role in cellular processes related to cancer, including the response to DNA damage. The USP1/UAF1 complex is emerging as a novel target in cancer therapy, but several aspects of its function and regulation remain to be further clarified. These include the role of the serine 313 phosphorylation site, the relative contribution of different USP1 sequence motifs to UAF1 binding, and the potential effect of cancer-associated mutations on USP1 regulation by autocleavage. Methods: We have generated a large set of USP1 structural variants, including a catalytically inactive form (C90S), non-phosphorylatable (S313A) and phosphomimetic (S313D) mutants, deletion mutants lacking potential UAF1 binding sites, a mutant (GG/AA) unable to undergo autocleavage at the well-characterized G670/G671 diglycine motif, and four USP1 mutants identified in tumor samples that cluster around this cleavage site (G667A, L669P, K673T and A676T). Using cell-based assays, we have determined the ability of these mutants to bind UAF1, to reverse DNA damage-induced monoubiquitination of PCNA, and to undergo autocleavage. Results: A non-phosphorylatable S313A mutant of USP1 retained the ability to bind UAF1 and to reverse PCNA ubiquitination in cell-based assays. Regardless of the presence of a phosphomimetic S313D mutation, deletion of USP1 fragment 420-520 disrupted UAF1 binding, as determined using a nuclear relocation assay. The UAF1 binding site in a second UAF1-interacting DUB, USP46, was mapped to a region homologous to USP1(420-520). Regarding USP1 autocleavage, co-expression of the C90S and GG/AA mutants did not result in cleavage, while the cancer-associated mutation L669P was found to reduce cleavage efficiency. Conclusions: USP1 phosphorylation at S313 is not critical for PCNA deubiquitination, neither for binding to UAF1 in a cellular environment. In this context, USP1 amino acid motif 420-520 is necessary and sufficient for UAF1 binding. This motif, and a homologous amino acid segment that mediates USP46 binding to UAF1, map to the Fingers sub-domain of these DUBs. On the other hand, our results support the view that USP1 autocleavage may occur in cis, and can be altered by a cancer-associated mutation.

On the way to management of west Sumatra's coastal ecosystem

Various impacts on the coast of the Indonesian province of West Sumatra are presented together with activities and achievements to address them, e.g. public awareness, public relations and capacity building, including the establishment of a marine protected area.

Rice-fish-vegetable integrated farming: towards a sustainable ecosystem

An outline is given of procedures to take in order to adopt an integrated rice-fish-vegetable farming system in India. Vegetables, which are cultivated in the dikes of the system, may include Luffa acutangula, Vigna unguiculata and Phaseolus vulgaris . When the water depth of the field rises to 30-40 cm, fish fingerlings (Puntius javanicus, Cyprinus carpio and Labeo rohita ) and prawn juveniles (Macrobranchium rosenbergii ) may be stocked. The advantages of such a system are listed and include year round employment opportunities for the farm family and improved farm family income and nutrition.

Food conversion efficiency and the von Bertalanffy growth function 1: a modification of Pauly's model

A simple modification of Pauly's model for relating food conversion efficiency (K sub(1)) and body weight is proposed. The key parameter is an index to how efficiently food can be absorbed; the other parameter is related to the surface-limiting growth, an important component of von Bertalanff's and Pauly's theories of fish growth.

Food conversion efficiency and the von Bertalanffy growth function. Part II and conclusion: Extension of the new model to the generalized von Bertalanffy growth function

The simple model relating food conversion efficiency (K sub(1)) to body weight derived from the theoretical concepts behind von Bertalanffy's growth model, is extended here in the context of Pauly's generalization of that model. The exponent, which was fixed to 1/3 in the simple model, is in the extended model equivalent to 1-d, with d being the weight exponent of the anabolism term in Pauly's growth model. This makes the model applicable to fish for which the assumptions of the original (special) version of von Bertalanffy's growth model are violated.