Simulation of coevolution in community by using the "Evolutionary Constructor" program

An original modeling tool called Evolutionary Constructor has been proposed and described. Evolutionary Constructor combines the advantages of both generalized and portrait modeling and, additionally, provides an option to modify a current model's structure. The evolution of communities comprising atrophic ring-like network with the horizontal transfer of metabolism genes occurring among the communities has been modeled and presented. It has been demonstrated that a prolonged increase in the fitness of any single population that forms part of that trophic ring-like network of antagonistic communities will eventually lead that system to becoming absolutely dependent on environmental fluctuations. This result challenges the intuitive attitudes that the higher population fitness, the more stability is given to that population. Modeling of a system comprised by symbiotic communities has revealed that horizontal transfer confers a selective advantage not only on the acceptor population (which is up to expectations) but also on the donor population. It has therefore been demonstrated that horizontal transfer can be preserved by selection along evolution even without "selfish genes". Evolutionary Constructor can handle any phenotypic trait that is controlled genetically, epigenetically, etc., which extends the applicability of this tool to various processes of information transduction among populations, provided that these processes resemble horizontal gene transfer.     

Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

Efficient systemic expression of bioactive IL-15 in mice upon delivery of optimized DNA expression plasmids

Efficient expression vectors for interleukin 15 (IL-15) were developed combining RNA/codon optimization and modification of the IL-15 native long signal peptide. These changes resulted in elevated cytoplasmic levels of the optimized mRNA and more than 100-fold improved production of secreted human IL-15 protein. Similar modifications have also led to greatly increased rhesus macaque and murine IL-15 production. Comparison of different heterologous secretory signals showed that the tissue plasminogen activator signal is most efficient for the production of extracellular IL-15. Upon intramuscular injection of the fully optimized expression vectors in mice, IL-15 was readily detected in the serum. Serum levels represented <1% of intramuscular IL-15 and were sufficient in causing some systemic effects, such as increasing the frequency of natural killer (NK) cells in the liver. Upon hydrodynamic DNA delivery in mice, very high levels of IL-15 were produced, which increased the frequency of NK cells in liver as well as in spleen and lung. These optimized expression vectors have potential applications in vaccine and immunotherapy approaches against AIDS and cancer.     

Imbalance in seminal fluid MIF indicates male infertility

Macrophage migration inhibitory factor (MIF) is a ubiquitous cytokine that functions in reproduction and plays an important role in sperm maturation and motility. Here we reveal a correlation between MIF levels in human seminal fluid and fertility status. We identify an abnormal biphasic profile of MIF in the seminal fluid of patients with impaired sperm parameters. Our findings may be of interest for the development of a diagnostic method for fertility status.     

Hatching rates of resting eggs of 'Cladocera' (Crustacea; Branchiopoda) at a tropical bay, Brazil.

The aim of this study was to determine the development time of embryos and to estimate the hatching rates of resting eggs of cladocerans found in the sediment of Guanabara Bay, Rio de Janeiro, Brazil, under experimental conditions. Eggs were sorted by species (Penilia avirostris--Sididae; Pleopis polyphemoides and Pseudevadne tergestina--Podonidae) and incubated at a temperature of 25 degrees C, salinity 35 and photoperiod 12 hours light/ 12 hours dark. Hatching rates were about 38% for Pseudevadne tergestina and 28% for Pleopis polyphemoides. Embryos of resting eggs of Penilia avirostris developed comparatively slowly (hatching after 86 days of incubation), with a hatching rate of only 5%. It was observed that development and hatching of resting eggs of marine cladocerans suggest that pulses of recruitment may exist, thus contributing to the rapid appearance and maintenance of planktonic populations of these crustaceans in Guanabara Bay.     

Proteomic analysis of the oxidative stress response in Candida albicans

An efficient oxidative stress response (OSR) is important for the facultative pathogenic yeast Candida albicans to survive within the human host. We used a large scale 2-D protein gel electrophoresis approach to analyze the stress response mechanisms of C. albicans after treatment with hydrogen peroxide and the thiol oxidizing agent, diamide. Quantitation of in vivo protein synthesis after pulse labeling of the proteins with radioactive L-[35S]-methionine resulted in characteristic proteome signatures for hydrogen peroxide and diamide with significant overlap of 21 up-regulated proteins for both stressors. Among the induced proteins were enzymes with known antioxidant functions like catalase or thioredoxin reductase and a set of oxidoreductases. 2-D gel analysis of mutants in the CAP1 gene revealed that the synthesis of 12 proteins is controlled by the oxidative stress regulator Cap1p. Stressing its importance for the C. albicans OSR, all 12 proteins were also induced after oxidative challenge by hydrogen peroxide or diamide.