The "school trap": a mechanism promoting large-amplitude out-of-phase population oscillations of small pelagic fish species

Small coastal pelagic marine fishes often form mixed schools containing two or more species. Individuals of a less abundant species, which are entrained in schools that are dominated numerically by a more abundant species, may be adversely impacted. This may help to account for an observed pattern of strong alternations in dominance between sardines and anchovies in a number of regions of the world's oceans.     

Greenhouse gas buildup, sardines, submarine eruptions and the possibility of abrupt degradation of intense marine upwelling ecosystems

Widespread hypoxia and massive eruptions of noxious, radiatively active gases currently characterize the world's strongest eastern ocean upwelling zone. Theory, modelling results and observations suggest that the world's coastal upwelling zones will undergo progressive intensification in response to greenhouse gas buildup. This presents the prospect of progressive development of similarly degraded marine ecosystems in additional regions and of a contributing feedback loop involving associated additions to the global buildup rate of greenhouse gases, resulting further increases in upwelling intensity, creation of additional sources of greenhouse gas emissions, and so on. Abundant sardine stocks might be a mitigating factor opposing the process.     

Diffprot - software for non-parametric statistical analysis of differential proteomics data

Mass spectrometry-based global proteomics experiments generate large sets of data that can be converted into useful information only with an appropriate statistical approach. We present Diffprot - a software tool for statistical analysis of MS-derived quantitative data. With implemented resampling-based statistical test and local variance estimate, Diffprot allows to draw significant results from small scale experiments and effectively eliminates false positive results. To demonstrate the advantages of this software, we performed two spike-in tests with complex biological matrices, one label-free and one based on iTRAQ quantification; in addition, we performed an iTRAQ experiment on bacterial samples. In the spike-in tests, protein ratios were estimated and were in good agreement with theoretical values; statistical significance was assigned to spiked proteins and single or no false positive results were obtained with Diffprot. We compared the performance of Diffprot with other statistical tests - widely used t-test and non-parametric Wilcoxon test. In contrast to Diffprot, both generated many false positive hits in the spike-in experiment. This proved the superiority of the resampling-based method in terms of specificity, making Diffprot a rational choice for small scale high-throughput experiments, when the need to control the false positive rate is particularly pressing.     

Urine proteome of autosomal dominant polycystic kidney disease patients

Background

Autosomal dominant polycystic kidney disease (ADPKD) is responsible for 10% of cases of the end stage renal disease. Early diagnosis, especially of potential fast progressors would be of benefit for efficient planning of therapy. Urine excreted proteome has become a promising field of the search for marker patterns of renal diseases including ADPKD. Up to now however, only the low molecular weight fraction of ADPKD proteomic fingerprint was studied. The aim of our study was to characterize the higher molecular weight fraction of urinary proteome of ADPKD population in comparison to healthy controls as a part of a general effort aiming at exhaustive characterization of human urine proteome in health and disease, preceding establishment of clinically useful disease marker panel.

Results

We have analyzed the protein composition of urine retentate (>10 kDa cutoff) from 30 ADPKD patients and an appropriate healthy control group by means of a gel-free relative quantitation of a set of more than 1400 proteins. We have identified an ADPKD-characteristic footprint of 155 proteins significantly up- or downrepresented in the urine of ADPKD patients. We have found changes in proteins of complement system, apolipoproteins, serpins, several growth factors in addition to known collagens and extracellular matrix components. For a subset of these proteins we have confirmed the results using an alternative analytical technique.

Conclusions

Obtained results provide basis for further characterization of pathomechanism underlying the observed differences and establishing the proteomic prognostic marker panel.     

Structural studies of Alzheimer's disease Abeta peptide oligomers

Amyloid beta peptide is recognized as the main constituent of the extracellular amyloid plaques, the major neuropathological hallmark of Alzheimer's disease. Abeta is a small peptide constitutively expressed in normal cells, not toxic in the monomeric form but aggregated Abeta is assumed to be the main if not the only factor causing Alzheimer's disease. Interestingly, the new reports suggest neurotoxicity of soluble Abeta oligomers rather than amyloid fibrils. Because of the fact that fibrils were thought to be the main toxic species in AD, early structural studies focused on fibrils themselves and Abeta monomers, as their building blocks while there is practically no data on oligomer structure and mechanism of neurotoxicity. Using a model peptide spanning residues 10–30 of Abeta, obtained by overexpression in bacteria, we have employed mass spectrometry of noncovalent complexes and disulfide rearrangement assay to gain new insight into structure and dynamics of a prenucleation step of Abeta peptide oligomerisation.     

Alzheimer's disease Abeta peptide fragment 10-30 forms a spectrum of metastable oligomers with marked preference for N to N and C to C monomer termini proximity

Oligomers of Abeta peptide have been indicated recently as a possible main causative agent of Alzheimer's disease. However, information concerning their structural properties is very limited. Here Abeta oligomers are studied by non-covalent complexes mass spectrometry and disulfide rearrangement. As a model molecule, an Abeta fragment spanning residues 10-30 (Abeta10-30) has been used. This model peptide is known to contain the core region responsible for Abeta aggregation to fibrils. Non-covalent complexes mass spectrometry indicates that, at neutral pH, monomers are accompanied by oligomers up to hexamers of gradually decreasing population. H-2H exchange studies and direct monomer exchange rate measurements with the use of 15N labeled peptides and mass spectrometry show a fast exchange of monomeric units between oligomers. Disulfide exchange studies of cysteine tagged Abeta10-30 and its mutant show proximity of N-N and C-C termini of monomers in oligomers. The presented data underscore a dynamic character for pre-nucleation forms of Abeta, however, with a marked tendency for parallel strand orientation in oligomers.     

The Capricorn Eddy: a prominent driver of the ecology and future of the southern Great Barrier Reef

This study focuses on a mesoscale eddy feature, the ‘Capricorn Eddy’, that typically forms within an indentation of the continental shelf in the southern GBR system. Satellite data at moderate resolution (1 km) are used to examine relevant mesoscale and sub-mesoscale sea surface dynamics. Available in situ measurements and model data are used to validate the satellite observations and to specify the nature of the processes occurring within the water column itself. The characteristic features are identified and physical theory employed to develop an understanding of associated processes. In particular, the effect of the eddy in raising cooler, nutrient-enriched oceanic subsurface water and transporting it to the reef zone, and eventually into the lagoon, is shown. This study demonstrates that the linkages between large-scale oceanography and the meso- and sub-mesoscale patterns are crucial to determining biologic responses on the scale of reef communities and may be key to understanding climate change impacts at the relevant spatial scales.     

Postradiation life span of mice in relation to the modifying action of leukemic cells administered

Leukemic cells administered to X-irradiated mice modify the radiobiological effect to a degree that depends on the radiation dose, bone marrow transplantation, the quantity and quality of leukemic cells, and the time of their administration.     

Issues of ecosystem-based management of forage fisheries in “open” non-stationary ecosystems: the example of the sardine fishery in the Gulf of California

The Gulf of California system presents major challenges to the still developing frameworks for ecosystem-based management (EBM). It is very much an open system and is intermittently subject to important influxes of migratory visitors, including large pelagic predatory fishes and small pelagic forage fishes. These migrants include the more tropical species from the coastal ecosystems to the south and perhaps subtropical sardines and anchovies from the California Current upwelling system. In addition to the multi-annual ENSO-scale and what may seem to be rather erratic episodes of major population incursions, the Gulf presents nonstationary, transient aspects on a variety of longer time scales. Moreover, the removal of top predators by commercial and sport fisheries has introduced trends that must be affecting the entire ecosystem, and certainly the forage fishes that are their major prey base. In addition to size limits, fishing seasons, area closures and license limitations, the fishery is managed by an ad hoc adaptive management system, in which the fishing season can be shortened or additional areas closed to fishing if pre-season exploratory fishing surveys indicate a shortage of small pelagic fishes on the fishing grounds. Whether this system is likely to be sustainable in the long term is difficult to determine, given the potential for rapid changes in the system because of environmental changes and/or feedbacks within the food web. Thus it appears that innovative management frameworks, among other things utilizing the comparative method, may be required in order to determine defensible tradeoffs between precaution and resource utilization.