A modular approach to the ECVAM principles on test validity

The European Centre for the Validation of Alternative Methods (ECVAM) proposes to make the validation process more flexible, while maintaining its high standards. The various aspects of validation are broken down into independent modules, and the information necessary to complete each module is defined. The data required to assess test validity in an independent peer review, not the process, are thus emphasised. Once the information to satisfy all the modules is complete, the test can enter the peer-review process. In this way, the between-laboratory variability and predictive capacity of a test can be assessed independently. Thinking in terms of validity principles will broaden the applicability of the validation process to a variety of tests and procedures, including the generation of new tests, new technologies (for example, genomics, proteomics), computer-based models (for example, quantitative structure-activity relationship models), and expert systems. This proposal also aims to take into account existing information, defining this as retrospective validation, in contrast to a prospective validation study, which has been the predominant approach to date. This will permit the assessment of test validity by completing the missing information via the relevant validation procedure: prospective validation, retrospective validation, catch-up validation, or a combination of these procedures.     

Do viscous forces affect survival of marine fish larvae? Revisiting the ‘safe harbour’ hypothesis

Aquatic organisms physically interact with the water that surrounds them, and this interaction is fundamental in shaping many aspects of their biology. General characteristics of the hydrodynamic interactions between organisms and the flow around them can be captured by the dimensionless Reynolds number (Re), depicting the ratio between inertial and viscous forces operating on the organism. The characteristic flow regime of larval fish that cruise at slow speeds is a regime of low Re, where viscous forces dominate. In this study, we experimentally test the ‘safe harbour’ hypothesis, which proposes that increasing larval body size facilitates an ‘escape’ from the detrimental effects of low Re. Larval gilthead seabream (Sparus aurata) were reared during early ontogeny under artificially manipulated water viscosities to expose larvae to low Re regimes. Larval survival decreased significantly with increasing water viscosity, and increased with increasing standard length. Surviving larvae exceeded the mean length of mortalities by ~1 mm, on average. Our findings provide direct experimental support for the ‘safe harbour’ hypothesis, indicating that marine larvae incur a fitness cost when operating under low Re conditions. Moreover, the results highlight the need to recognize the hydrodynamic environment when considering the a-biotic characteristics that may influence organismal performance and fitness.     

Membrane-associated heparan sulfate proteoglycans are involved in the recognition of cellular targets by NKp30 and NKp46

Lysis of virus-infected and tumor cells by NK cells is mediated via natural cytotoxicity receptors (NCRs). We have recently shown that the NKp44 and NKp46 NCRs, but not the NKp30, recognize viral hemagglutinins. In this study we explored the nature of the cellular ligands recognized by the NKp30 and NKp46 NCRs. We demonstrate that target cell surface heparan sulfate proteoglycans (HSPGs) are recognized by NKp30 and NKp46 and that 6-O-sulfation and N-acetylation state of the glucose building unit affect this recognition and lysis by NK cells. Tumor cells expressing cell surface heparanase, CHO cells lacking membranal heparan sulfate and glypican-1-suppressed pancreatic cancer cells manifest reduced recognition by NKp30 and NKp46 and are lysed to a lesser extent by NK cells. Our results are the first clue for the identity of the ligands for NKp30 and NKp46. Whether the ligands are particular HSPGs, unusual heparan sulfate epitopes, or a complex of HSPGs and either other protein or lipid moieties remains to be further explored.     

Structure of the school of sock-eyed salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Apuka River (the Northeastern Kamchatka)

Results of study of sock-eyed salmon Oncorhynchus nerka from the Apuka River—the largest river of the northeast of Kamchatka—inflowing Olyutorskii Bay of the Bering Sea are presented. It is established that the school of the Apuka River is represented by the early-run sock-eyed salmon that spawns in Lake Vatyg-Gytkhyn located in the lower part of the basin and by individuals of the later run that spawn in the upper reaches of the river. Early-run sock-eyed salmon appears in the river with signs of spawning changes and a high value of gonadosomatic index (GSI). Late-run sock-eyed salmon migrates to the river without signs of spawning changes and with a relatively low GSI. The age composition of spawners of the early- and late-run sock-eyed salmon is different.     

Multiple Avirulence Loci and Allele-Specific Effector Recognition Control the Pm3 Race-Specific Resistance of Wheat to Powdery Mildew

In cereals, several mildew resistance genes occur as large allelic series; for example, in wheat (Triticum aestivum and Triticum turgidum), 17 functional Pm3 alleles confer agronomically important race-specific resistance to powdery mildew (Blumeria graminis). The molecular basis of race specificity has been characterized in wheat, but little is known about the corresponding avirulence genes in powdery mildew. Here, we dissected the genetics of avirulence for six Pm3 alleles and found that three major Avr loci affect avirulence, with a common locus_1 involved in all AvrPm3-Pm3 interactions. We cloned the effector gene AvrPm3^a2/f2 from locus_2, which is recognized by the Pm3a and Pm3f alleles. Induction of a Pm3 allele-dependent hypersensitive response in transient assays in Nicotiana benthamiana and in wheat demonstrated specificity. Gene expression analysis of Bcg1 (encoded by locus_1) and AvrPm3 ^a2/f2 revealed significant differences between isolates, indicating that in addition to protein polymorphisms, expression levels play a role in avirulence. We propose a model for race specificity involving three components: an allele-specific avirulence effector, a resistance gene allele, and a pathogen-encoded suppressor of avirulence. Thus, whereas a genetically simple allelic series controls specificity in the plant host, recognition on the pathogen side is more complex, allowing flexible evolutionary responses and adaptation to resistance genes.     

Biological Properties of the Phosphorus-Mobilizing Bacillus subtilis Strain IMV V-7023

Biological characteristics of a new phosphate-mobilizing bacillus strain are reported. Species-level identification of the strain was performed according to morphological, cultural, and biochemical characteristics and the sequence of the 16S rRNA gene. The strain was identified as Bacillus subtilis IMV V-7023 and displayed a very high ability to mobilize phosphorus from its sparingly soluble inorganic and organic compounds and the capability of synthesizing biologically active substances; in addition, the strain essentially suppressed the growth of phytopathogenic bacteria, micromycetes, and agents causing various diseases of vegetable, cereal, leguminous, and other plants. The strain Bacillus subtilis IMV V-7023 is promising for developing bacterial preparations for crop production.     

The determinants of species richness of a relatively young coral-reef ichthyofauna

Aim Unique topographic features left the Red Sea and its north‐eastern extension into the Gulf of Aqaba practically devoid of coral‐reef‐based organisms during the last glacial maximum. The current ichthyofauna in these two ‘regions’ thus represents the product of relatively recent colonization by species found in the Arabian Sea, which adjoins the Red Sea at its southern tip. We used this system to test why some marine species seemingly fail to extend their geographic range, thereby generating spatial heterogeneity in biodiversity. Location The Arabian Sea, Red Sea, and the Gulf of Aqaba. Methods A list of coral‐reef‐associated fish species, belonging to the 10 most speciose families, was compiled for each region using published sources. The data were analysed (major axis regression, randomization tests) for taxonomic and body‐size‐dependent biases in colonization probabilities. A simple probabilistic model was used to examine the potential contribution of local (within‐region) extinctions to determining species composition in the Red Sea. Results Of the 462 reef‐associated species that inhabit the Arabian Sea, 69% have crossed successfully into the Red Sea; of these, 55% have crossed into the Gulf of Aqaba. A species’ probability of being found in either ‘target’ was independent of presumed innate differences, i.e. ecological correlates of taxonomic affiliation and body size. Similarly, local extinctions were found unlikely to have been of consequence over the past several thousand years. Main conclusions Present‐day differences in the species richness of reef‐associated fish species among the Arabian Sea, Red Sea and Gulf of Aqaba appear to be the product of external, non‐selective constraints on colonization. The random nature of the colonization process is suggestive of ecological redundancy among coral‐reef fish species. Importantly, the study places a time frame on the processes that determine spatial patterns of biodiversity in reef fish.