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Variable Part (variable + part)
Selected AbstractsThe colonization of Europe by the freshwater crustacean Asellus aquaticus (Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivityMOLECULAR ECOLOGY, Issue 14 2005R. VEROVNIK Abstract Recent continental-scale phylogeographic studies have demonstrated that not all freshwater fauna colonized Europe from the classic Mediterranean peninsular refugia, and that northern or central parts of the continent were occupied before, and remained inhabited throughout the Pleistocene. The colonization history of the ubiquitous aquatic isopod crustacean Asellus aquaticus was assessed using mitochondrial COI and a variable part of nuclear 28S rDNA sequences. Phylogeographic analysis of the former suggested that dispersion proceeded possibly during late Miocene from the western part of the Pannonian basin. Several areas colonized from here have served as secondary refugia and/or origins of dispersion, well before the beginning of the Pleistocene. Postglacial large-scale range expansion was coupled with numerous separate local dispersions from different refugial areas. Connectivity of the freshwater habitat has played an important role in shaping the current distribution of genetic diversity, which was highest in large rivers. The importance of hydrographic connections for the maintenance of genetic contact was underscored by a discordant pattern of mtDNA and nuclear rDNA differentiation. Individuals from all over Europe, differing in their mtDNA to a level normally found between species or even genera (maximal within population nucleotide divergence reached 0.16 ± 0.018), shared the same 28S rRNA gene sequence. Only populations from hydrographically isolated karst water systems in the northwestern Dinaric Karst had distinct 28S sequences. Here isolation seemed to be strong enough to prevent homogenization of the rRNA gene family, whereas across the rest of Europe genetic contact was sufficient for concerted evolution to act. [source] A feed is only as good as its ingredients , a review of ingredient evaluation strategies for aquaculture feedsAQUACULTURE NUTRITION, Issue 1 2007B.D. GLENCROSS Abstract The evaluation of feed ingredients is crucial to nutritional research and feed development for aquaculture species. In evaluating ingredients for use in aquaculture feeds, there are several important knowledge components that should be understood to enable the judicious use of a particular ingredient in feed formulation. This includes information on (1) ingredient digestibilities, (2) ingredient palatability and (3) nutrient utilization and interference. Diet design, feeding strategy, faecal collection method and method of calculation all have important implications on the determination of the digestible value of nutrients from any ingredient. There are several ways in which palatability of ingredients can be assessed, usually based on variable inclusion levels of the ingredient in question in a reference diet and feeding of those diets under an apparent satietal or self-regulating feeding regimes. However, the design of the diets, the parameters of assessment and the feeding regime can all be subject to variation depending on subtleties of the experimental design. Clearly, issues relating to feed intake are the key performance criteria in palatability assessments, and it is important that such experiments maintain sufficient stringency to allow some self-discrimination of the test feeds by the fish. The ability of fish to use nutrients from the test ingredient, or defining factors that interfere with that process, is perhaps the most complex and variable part of the ingredient evaluation process. It is crucial to discriminate effects on feed intake from effects on utilization of nutrients from ingredients (for growth and other metabolic processes). To allow an increased focus on nutrient utilization by the animals, there are several experimental strategies that can be adopted, which are based on variations in diet design and feeding regime used. Other issues such as ingredient functionality, influence on immune status and effects on organoleptic qualities are also important consideration in determining the value of ingredients in aquaculture feed formulations. A key aspect to note is the need to design all experiments with sufficient experimental capacity to detect significant effects. [source] Best domain for an elliptic problem in cartesian coordinates by means of shape-measureASIAN JOURNAL OF CONTROL, Issue 5 2009Alireza Fakharzadeh Jahromi Abstract In (ZAA J. Anal. Appl., Vol. 16, No. 1, pp. 143,155) we introduced a method to determine the optimal domains for elliptic optimal-shape design problems in polar coordinates. However, the same problem in cartesian coordinates, which are more applicable, is found to be much harder, therefore we had to develop a new approach for these designs. Herein, the unknown domain is divided into a fixed and a variable part and the optimal pair of the domain and its optimal control, is characterized in two stages. Firstly, the optimal control for the each given domain is determined by changing the problem into a measure-theoretical one, replacing this with an infinite dimensional linear programming problem and approximating schemes; then the nearly optimal control function is characterized. Therefore a function that offers the optimal value of the objective function for a given domain, is defined. In the second stage, by applying a standard optimization method, the global minimizer pair will be obtained. Some numerical examples are also given. Copyright © 2009 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society [source] Structure of a yellow lupin pathogenesis-related PR-10 protein belonging to a novel subclassACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2005Oliwia Pasternak Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varies in different plant organs. The PR-10 proteins are encoded by multigene families, have a weight of about 17,kDa and are found in the cytosol. In yellow lupin, nine different homologues have been identified and divided into two subclasses, LlPR-10.1 and LlPR-10.2. Within each subclass the sequence identity is about 75,91%, while across the subclasses it is only 59,60%. Here, the crystal structure of a yellow lupin PR-10 protein from the second subclass, LlPR-10.2A, is presented. The structure was solved by molecular replacement and refined to R = 0.205 using 1.9,Å resolution data. The general fold of LlPR-10.2A resembles that of the other PR-10 proteins and consists of a long C-terminal ,-helix surrounded by a seven-stranded antiparallel ,-sheet, with two shorter ,-helices located between strands ,1 and ,2. The most variable part of the structure, the C-terminal helix, is strongly kinked towards the ,-sheet core in both LlPR-10.2A molecules present in the asymmetric unit. This unexpected feature reduces the size of the hydrophobic cavity observed in other PR-10 proteins that is reported to be the ligand-binding site. As in other PR-10 structures, a surface loop located near the entrance to the cavity shows very high structural conservation and stability despite the high glycine content in its sequence. [source] Molecular epidemiology of hepatitis A in St. Petersburg, Russia, 1997,2003JOURNAL OF MEDICAL VIROLOGY, Issue 6 2007Irja Davidkin Abstract The molecular epidemiology of hepatitis A virus (HAV) strains circulating in the St. Petersburg and Karelia regions was studied during 1997,2003. Hepatitis A virus RNA was isolated from both clinical samples (stools or sera) and environmental samples (sewage water). RT-PCR was carried out using different primer pairs from the VP1/2A and VP1 genomic regions, the variable parts of the HAV genome. PCR products were sequenced and 306 nucleotides from the VP1/2A and 332 nucleotides from the VP1 region were used for phylogenetic analysis. The results show that the IA subtype was the most common during the follow-up period: >90% of the isolated HAV strains belonged to that subtype. The HAV strains found in intravenous drug users belonged to subtypes IA and IIIA. Only one out of a total of 88 sequenced strains was of the IB subtype. The subtypes IB and IIIA were found only in 2001,2003, which suggests that new strains were introduced into the endemic situation. The results indicate the usefulness of molecular epidemiological methods in studying changes in the circulating HAV strains and in tracing transmission routes. J. Med. Virol. 79: 657,662, 2007. © 2007 Wiley-Liss, Inc. [source] | ||||||||||