System of distributed storage and analysis of genomic information

A distributed computing system is developed to search and analyze genetic databases using parallel computing technologies. Queries are processed by a local network PC cluster. A universal task and data exchange format is developed for effective query processing. A multilevel hierarchic task batching procedure is elaborated to generate multiple subtasks and distribute them over cluster units under dynamic priority levels and with dynamic distribution of replicated source data subbases. Primary source data preparation and generation of annotation word indices are used to significantly reduce query processing time.     

Mice with targeted disruption of spermidine/spermine N1-acetyltransferase gene maintain nearly normal tissue polyamine homeostasis but show signs of insulin resistance upon aging

The N(1)-acetylation of spermidine or spermine by spermidine/spermine N(1)-acetyltransferase (SSAT) is the ratecontrolling enzymatic step in the polyamine catabolism. We have now generated SSAT knockout (SSAT-KO) mice, which confirmed our earlier results with SSATdeficient embryonic stem (ES) cells showing only slightly affected polyamine homeostasis, mainly manifested as an elevated molar ratio of spermidine to spermine in most tissues indicating the indispensability of SSAT for the spermidine backconversion.Contrary to SSAT deficient ES cells, polyamine pools in SSAT-KO mice remained almost unchanged in response to N(1),N(11)-diethylnorspermine (DENSPM) treatment compared to a significant reduction of the polyamine pools in the wild-type animals and ES cells. Furthermore, SSATKO mice were more sensitive to the toxicity exerted by DENSPM in comparison with wild-type mice. The latter finding indicates that inducible SSAT plays an essential role in vivo in DENSPM treatmentevoked polyamine depletion, but a controversial role in toxicity of DENSPM. Surprisingly, liver polyamine pools were depleted similarly in wild-type and SSAT-KO mice in response to carbon tetrachloride treatment. Further characterization of SSAT knockout mice revealed insulin resistance at old age which supported the role of polyamine catabolism in glucose metabolism detected earlier with our SSAT overexpressing mice displaying enhanced basal metabolic rate, high insulin sensitivity and improved glucose tolerance. Therefore SSAT knockout mice might serve as a novel mouse model for type 2 diabetes.     

Low-intensity tensile loading increases intratendinous glucose uptake in the Achilles tendon.

The metabolic activity of tendinous tissues has traditionally been considered to be of limited magnitude. However, recent studies have suggested that glucose uptake increases in the force-transmitting tissues as a response to contractile loading, which in turn indicates an elevated tissue metabolism. The purpose of the present study was to investigate whether such a mechanism could be observed for the human Achilles tendon following tensile loading. Six subjects participated in the study. Unilateral Achilles tendon loading was applied by 25-min intermittent voluntary plantar flexor contractions. A radioactive tracer ([18F]-2-fluoro-2-deoxy-D-glucose) was administered during muscle action, and glucose uptake was measured by use of PET. Regions of interest were defined on the PET images corresponding to the cross section of Achilles tendon at two longitudinally separated sites (insertion and free tendon). Glucose uptake index was determined within respective regions of interest for the active and resting leg. Tendon force during voluntary contractions was approximately 13% of maximal voluntary contraction force. Tendon loading induced an elevated glucose uptake index compared with that of the contralateral resting tendon in the region of tendon insertion (0.13 +/- 0.05 vs. 0.09 +/- 0.02; P < 0.05) and at the free tendon (0.12 +/- 0.01 vs. 0.08 +/- 0.02; P < 0.05). The present data suggest that tissue metabolism is elevated in the human Achilles tendon in response to low-intensity loading.     

Lymph node status as a guide to selection of available prognostic markers in breast cancer: the clinical practice of the future?

Prognosticators evaluating survival in breast cancer vary in significance in respect to lymph node status. Studies have shown e.g. that HER2/neu immunohistochemistry or HER2/neu gene amplification analysis do perform well as prognosticators in lymph node positive (LN +) patients but are less valuable in lymph node negative (LN -) patients. We collected data from different studies and tried to evaluate the relative significance of different prognosticators in LN+/LN- patient groups. In LN+ patients HER2/neu and E-cadherin immunohistochemistry were the statistically most significant prognosticators followed by proliferation associated features (mitotic counts by SMI (standardised mitotic index) or MAI (mitotic activity index), or S-phase fraction). Bcl-2 immunohistochemistry was also significant but p53 and cystatin A had no significance as prognosticators. In LN- patients proliferation associated prognosticators (SMI, MAI, Ki-67 index, PCNA immunohistochemistry, S-phase fraction) are especially valuable and also Cathepsin D, cystatin A, and p53 are significant, but HER2/neu or bcl-2, or E-cadherin less significant or without significance. We find that in studies evaluating single prognosticators one should distinguish between prognosticators suitable for LN+ and LN- patients. This will allow the choice of best prognosticators in evaluating the prospects of the patient. The distinction between LN+ and LN- patients in this respect may also be of special value in therapeutic decisions.     

Aminobisphosphonate-pretreated dendritic cells trigger successful Vγ9Vδ2 T cell amplification for immunotherapy in advanced cancer patients

Hepatocellular carcinoma (HCC) and colorectal carcinoma with hepatic metastases (mCRC) are cancers with poor prognosis and limited therapeutic options. New approaches are needed and adoptive immunotherapy with Vγ9Vδ2 T lymphocytes represents an attractive strategy. Indeed, Vγ9Vδ2 T cells were shown to exhibit efficient lytic activity against various human tumor cell lines, and in vitro Vγ9Vδ2 T expansion protocol based on single phosphoantigen stimulation could be easily performed for healthy donors. However, a low proliferative response of Vγ9Vδ2 T cells was observed in about half of the cancer patients, leading to an important limitation in the development of Vγ9Vδ2 T cell-based immunotherapy. Here, for the first time in the context of cancer patients, Vγ9Vδ2 T cell expansions were performed by co-culturing peripheral blood mononuclear cell (PBMCs) with autologous dendritic cells (DCs) pretreated with aminobisphosphonate zoledronate. For patients not responding to the conventional culture protocol, co-culture of PBMC with zoledronate-pretreated DCs induced strong cell expansion and allowed reaching a minimal rate of purity of 70% of Vγ9Vδ2 T cells. The potent immunostimulatory activity of zoledronate-treated DCs was associated with higher amount of isopentenyl pyrophosphate (IPP) in the culture and was correlated with better ability to activate Vγ9Vδ2 T cells as measured by IFN-γ production. Moreover, we demonstrated that the cytotoxic level of Vγ9Vδ2 T cells against freshly autologous tumor cells isolated from patients could be significantly increased by pretreating the tumor cells with zoledronate. Thus, this method of generating Vγ9Vδ2 T cells leads eligible for Vγ9Vδ2 T cell adoptive immunotherapy the HCC and mCRC patients.     

Antimitotic activity of new 2,6-dinitroaniline derivatives and their synergistic activity in compositions with graminicides

Shown antimicrotrubules activity of new 2,6-dinitroaniline compounds. Investigated their ability on apoptotic processes in a plant cell when used as a composition with inhibitors of acetyl-CoA carboxylase.     

Allelic polymorphism of FMR1 gene CGG-repeat region in patients with impairment of natural and stimulated ovulation

The frequency of heterozygote carriers of (risk zone, alleles of FMR1 gene (40-47 CGG-repeats) was significantly higher in group of patients with ovarian dysfunction than in control group I. The tendency for higher frequency of those alleles was observed in patients with "poor response" to superovulation induction in IVF cycles. The average number of oocytes and follicles, which was obtained after stimulation of superovulation, was significantly decreased in FMR1 gene "risk zone" alleles carriers compared to patients with normal alleles of FMR1 gene. The average general dosage of exogenous gonadotrophin, necessary for superovulation induction was significantly higher in heterozygote carriers of FMR1 gene "risk zone" alleles than in patients with normal genotype. Thereby, the FMR1 gene "risk zone" alleles can be one of the hereditary susceptibility factors of impairment nature and stimulated ovulation.     

Bioinformatic search for plant homologs of protein kinase BUB1--the keypoint of mitotic spindle assembly

Fourteen plant homologs of animal, yeast and myxomycetes spindle assembly checkpoint protein kinases were identified bioinformatically. It was shown that the closest plant homologues of the BUB1 protein kinases are unknown proteins XP_002274770.1 (CBI21878.1) from Vitis vinifera, EEC82122.1 from Oryza sativa Indica, EEE67244.1 from O. sativa Japonica, EEF44403.1 from Ricinus communis and CAL57156.1 from Ostreococcus tauri. The reconstruction and analysis of spatial structures of the EEC82122.1, EEE67244.1 and XP_002274770.1 (CBI21878.1), catalytic domains confirmed their conformity to spindle assembly checkpoint protein kinases BUB1.