Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes.

A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is ∼21% of all analysed sequences of the genome. The Type I and Type II error rates were estimated as 11% and 30%, respectively. Similar results were obtained for the genomes of Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Rattus norvegicus and Xenopus tropicalis. Also, the developed algorithm was tested on 17 bacterial genomes. We compared our results with the previously obtained data on the search for potential reading frameshifts in these genomes. This study discussed the possibility that the reading frameshift seems like a relatively frequently encountered mutation; and this mutation could participate in the creation of new genes and proteins.

[Developing the Mathematical Method in order to Search for Latent Periodicity in Protein Amino Acid Sequences with Deletions and Insertions].

A mathematical method was developed in order to search for latent periodicity in protein amino acid and other symbolical sequences using the dynamic programming and random matrixes. The method permits detection of the latent periodicity with insertions and deletions in the previously unknown positions. The developed method was applied to search for the periodicity in the amino acid sequences of some proteins and the periodicity in EUR/USD exchange rate since 2001. The presence of the long period length with insertions and deletions in amino acid sequences was shown. The period length of 7 amino acids was found in proteins containing supercoiled areas (coiled coil), the period length of 6 and 5 and more amino acids was also demonstrated. The existence of the period length of 6 and 7 days as well as 24 and 25 hours in the analyzed financial time series, which can be detected with insertions and deletions only, is revealed. The reasons of the occurence of the latent periodicity with insertions and deletions in the amino acid sequences and financial time series are discussed.

IL-1ß/HMGB1 complexes promote The PGE2 biosynthesis pathway in synovial fibroblasts.

PGE2 is a potent lipid mediator of pain and oedema found elevated in RA. Microsomal prostaglandin E synthase-1 (mPGES-1) is a terminal enzyme of the PGE2 pathway inducible by proinflammatory cytokines. mPGES-1 is markedly upregulated in RA synovial tissue despite antirheumatic treatments, suggesting that multiple inflammatory stimuli contribute to its induction. High-mobility group box chromosomal protein 1 (HMGB1) is known to induce inflammation both by direct interaction with TLR4 and by enhancement of other proinflammatory molecules signalling, through complex formation. The high expression of extracellular HMGB1 within the inflamed synovium, implies its pro-arthritogenic role in RA. We aimed to investigate the effects of IL-1ß/HMGB1 complexes on mPGES-1 and other enzymes of the PGE2 pathway in synovial fibroblasts (SFs) from patients with arthritis. Furthermore, we studied the effect of COX-2 inhibition and IL-1RI antagonism on prostanoid and cytokine production by SFs. Stimulation of SFs with HMGB1 in complex with suboptimal amounts of IL-1ß significantly increased mPGES-1 and COX-2 expressions as well as PGE2 production, as compared to treatment with HMGB1 or IL-1ß alone. Furthermore, NS-398 reduced the production of IL-6 and IL-8, thus indicating that IL-1ß/HMGB1 complexes modulate cytokine production in part through prostanoid synthesis. Treatment with IL-1RA completely abolished the induced PGE2 and cytokine production, suggesting an effect mediated through IL-1RI. IL-1ß/HMGB1 complexes promote the induction of mPGES-1, COX-2 and PGE2 in SF. The amplification of the PGE2 biosynthesis pathway by HMGB1 might constitute an important pathogenic mechanism perpetuating inflammatory and destructive activities in rheumatoid arthritis.

[Immunobiologically active compounds from skin].

This paper describes physiochemical and biological properties of 3 immunologically active compounds extracted by acetone from porcine skin. High pressure gel chromatography confirmed their heterogeneity. RP-HPLC of compound 2 (C2 or K-activin) also characterizes it as a heterogeneous entity. It was shown to inhibit proliferation of cultured fibroblasts from human fetuses and exhibit weak activity in general anaphylactic reaction (anaphylactic shock) and skin anaphylactic reaction. A summary of data on immunologically active compounds are presented with special emphasis laid on acetone-extractable K-activin.

Effects of immunosuppressive treatment on microsomal prostaglandin E synthase 1 and cyclooxygenases expression in muscle tissue of patients with polymyositis or dermatomyositis.

OBJECTIVES: To investigate the expression of microsomal prostaglandin E (PGE) synthase 1 (mPGES-1) and cyclooxygenase (COX) in muscle biopsies from patients with polymyositis or dermatomyositis before and after conventional immunosuppressive treatment. METHODS: mPGES-1 and COX expression was evaluated by immunohistochemistry in muscle tissue from healthy individuals and from patients with polymyositis or dermatomyositis before and after conventional immunosuppressive treatment. The number of inflammatory cell infiltrates, T lymphocytes and macrophages was estimated before and after treatment. To localise the mPGES-1 expression double immunofluorescence was performed with antibodies against mPGES-1, CD3, CD68, CD163 and a fibroblast marker. A functional index was used to assess muscle function. RESULTS: In patients with myositis, mPGES-1, COX-2 and COX-1 expression was significantly higher compared to healthy individuals and associated with inflammatory cells. Double immunofluorescence demonstrated a predominant expression of mPGES-1 in macrophages. Conventional immunosuppressive treatment resulted in improved but still lower muscle function than normal. A decreased number of CD68-positive macrophages and reduced COX-2 expression in muscle tissue was also seen. By contrast, following the same treatment no significant changes were observed in muscle tissue regarding number of infiltrates, T lymphocytes, CD163-positive macrophages or mPGES-1 protein levels. CONCLUSIONS: Increased expression of mPGES-1, COX-1 and COX-2 at protein level was observed in muscle tissue from patients with myositis compared to healthy individuals. Conventional immunosuppressive treatment led to a significant downregulation of COX-2 in myositis muscle tissue. However, the expression of mPGES-1 and COX-1 remained unchanged indicating a role of these enzymes in the chronicity of these diseases.

[The problems and perspectives of schoolchildren's health promotion at the municipal level].

The paper gives the results of studies aimed at evaluating the efficiency of the interdepartmental interaction system in schoolchildren's health promotion at the municipal level and at substantiating the recommendations for its optimization in case of the Leninsky District (Yekaterinburg). A package of measures, such as to develop the network of health-promotion schools, to assist in introducing effective health-saving technologies, to upgrade the personnel's competence in health culture, and to develop monitoring systems is proposed.

Perinatal essential fatty acid deficiency influences body weight and bone parameters in adult male rats.

Fetal and postnatal nutrition have long-term effects on the risk for development of diseases late in life in humans and animals. The aim of the present study was to investigate the effect of dietary deficiency of essential fatty acids (EFA) in the perinatal period on later body weight and bone mass. During late gestation and throughout lactation, rats were fed a control or an EFA-deficient (EFAD) diet. At 3 weeks of age the offspring were weaned onto an ordinary chow and followed until adult age. The mean body weight of adult rats receiving the EFAD diet during the perinatal period was significantly increased from 12 weeks of age compared to the controls (P<0.05). Analysis by peripheral quantitative computerized tomography (pQCT) at 44 weeks of age showed that the trabecular volumetric bone mineral density (BMD) of the femur was significantly decreased (P<0.05) but the cortical bone mineral content, cortical area, and cortical thickness were increased (P<0.05) in the EFAD group of rats. The length of the femur was not affected. In conclusion, neonatal EFA deficiency was in adult rats associated with increased body weight and significant changes in both cortical and trabecular bone. The results indicate that regulatory mechanisms related to bone mass seemed to be programmed by EFA in the perinatal period. The nature of this modulation needs to be identified.

Dietary n-6:n-3 fatty acid ratio in the perinatal period affects bone parameters in adult female rats.

PUFA and their metabolites are important regulators of bone formation and resorption. The effect of PUFA on bone growth may be especially striking during the perinatal period. The aim of the present study was to investigate the effect of diets with different n-6:n-3 fatty acid (FA) ratios during the perinatal period on bone parameters in the adult offspring. During late gestation and throughout lactation, rat dams were fed an isoenergetic diet containing 70 g linseed oil (n-3 diet), soyabean oil (n-6+n-3 diet) or sunflower-seed oil (n-6 diet) per kg with n-6:n-3 FA ratios of 0.4, 9 and 216, respectively. The offspring were weaned onto an ordinary chow and followed until 30 weeks of age. Bone parameters were analysed using peripheral quantitative computerised tomography and dual-energy X-ray absorptiometry. Femur length and cortical cross-sectional bone area and bone mineral content were significantly higher in the n-6+n-3 group than in the other groups. Cortical bone thickness in the n-6+n-3 group was increased compared with the n-3 group, but most cortical bone parameters did not differ between the n-3 and n-6 groups. The results suggest that regulatory mechanisms were influenced by the n-6:n-3 FA ratio early in life and not compensated for by the introduction of an ordinary diet after weaning.

The ratio of n-6 to n-3 fatty acids in maternal diet influences the induction of neonatal immunological tolerance to ovalbumin.

Prevalence of allergy is increasing in many countries and might be related to changed environmental factors, such as dietary fatty acids (FA). The present study investigates whether dietary ratio of n-6 to n-3 FA influences the induction of immunological tolerance to ovalbumin (OA) in neonatal rats. During late gestation and throughout lactation Sprague-Dawley rats were fed a diet containing 7% linseed oil (n-3 diet), sunflower oil (n-6 diet) or soybean oil (n-6/n-3 diet). At 10-16 days of age the rat offspring were subsequently exposed, or not, to OA via the milk. The offspring were weaned onto the same diets as the mothers and immunized with OA and the bystander antigen human serum albumin (HSA). In the offspring on the n-3 diet exposure to OA via the milk resulted in lower delayed type hypersensitivity reaction (DTH) and antibody responses against both OA and HSA, compared to those in the offspring not exposed to OA, indicating the induction of oral tolerance. In the offspring on the n-6 diet, the exposure to OA led to depressed specific immune responses against only OA, not HSA. In the offspring on the n-6/n-3 diet oral exposure to OA did not influence immune responses against OA, or HSA. The results indicate that the dietary ratio of n-6/n-3 FA is important for the induction of neonatal oral tolerance. Thus nonoptimal feeding may have effects on the development of immunological tolerance to dietary antigen ingested by the mother. The ratio of n-6/n-3 FA in the diet may be considered in the context of increased prevalence of allergy.

Expression of microsomal prostaglandin E synthase 1 in rheumatoid arthritis synovium.

OBJECTIVE: Microsomal prostaglandin E synthase 1 (mPGES-1) catalyzes the formation of PGE(2) from cyclooxygenase-derived PGH(2). Microsomal PGES-1 is induced by proinflammatory cytokines and is strongly linked to conditions that result in high PGE(2) biosynthesis. PGE(2) contributes to the pathogenesis of rheumatoid arthritis (RA), acting as a mediator of inflammation and promoting bone destruction. Induction of mPGES-1 in rheumatoid synoviocytes by proinflammatory cytokines has been demonstrated in vitro, indicating an important role in RA pathogenesis. Recent studies using mPGES-1-deficient mice demonstrated the importance of this gene in chronic inflammation. The aim of this study was to investigate the expression and localization of mPGES-1 in synovial biopsy specimens obtained from patients with RA. METHODS: Synovial tissue samples from 24 patients with RA were obtained, and immunohistologic analysis was performed using polyclonal antibodies against mPGES-1. Double immunofluorescence staining was performed with antibodies to CD3, CD19, CD20, CD68, CD163, and prolyl 4-hydroxylase. RESULTS: Intracellular mPGES-1 staining was observed in synovial membranes from all of the RA patients studied. Specifically, strong expression of mPGES-1 was detected in synovial lining cells. In sublining mononuclear and fibroblast-like cells, the extent of mPGES-1 staining was less than that in the synovial lining cells. In some patients, positive staining was observed in endothelial cells. With the double immunofluorescence technique, mPGES-1 production was detected in synovial macrophages and fibroblasts, while mPGES-1 expression was not observed in lymphocytes. CONCLUSION: The demonstration of mPGES-1 expression in synovial tissues from patients with RA suggests a role for mPGES-1 in the RA disease process. Microsomal PGES-1 might be a potential new target for treatment strategies to control PGE(2) synthesis in patients with RA, without the systemic side effects associated with cyclooxygenase inhibitors.

[The informational concept of searching for periodicity in symbol sequences]. / Informatsionnaia kontseptsiia poiska periodichnosti v simvol'nykh posledovatel'nostiakh.

Method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequences. The informational decomposition is calculated without conversion of a symbol sequence into the numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.

[Presence of MIR-elements in the complete nucleotide sequence of human chromosome 22]. / Prisutstvie MIR-lementov v polnoi nukleotidnoi posledovatel'nosti khromosmy 22 cheloveka.

The location of mammalian interspersed repeats (MIRs) and their density have been determined in the complete nucleotide sequence of human chromosome 22. The approach developed by us has allowed detection of 9675 MIRs at a statistically significant level, which by 15% exceeds the MIR number revealed by all previous approaches. It has been demonstrated that a considerable amount of MIRs missed by the algorithms applied earlier occurs in known DNA sequences of the human genome. The study of the MIR density revealed substantial irregularity of their distribution along the chromosome. The data on the MIRs thus found and the computer program searching for diverged sequences are available by E-mail: katrin2@mail.ru or katrin22@mtu-net.ru.

Maternal essential fatty acid deficiency depresses serum leptin levels in suckling rat pups.

Dietary lipid quantity and quality have recently been shown to affect serum leptin levels in adult rats. Moreover, suckling pups from dams fed a high fat diet had increased serum leptin levels. The aim of the present study was to analyze the influence of essential fatty acid (EFA) deficiency on serum leptin levels in dams and their pups during the suckling period. For the last 10 days of gestation and throughout lactation, pregnant rats were fed a control or an EFA-deficient (EFAD) diet. The levels of leptin and EFA in the serum of the dams and pups were analyzed 1, 2, and 3 weeks after delivery. In parallel, serum levels of glucose and corticosterone were analyzed in the pups. Low serum leptin levels were found in the control lactating dams during the entire lactation period compared with the age-matched nonlactating animals. The leptin concentrations in the lactating dams fed the EFAD diet were lower compared with those fed the control diet. The serum leptin levels of suckling pups from dams on the EFAD diet were markedly decreased compared with controls (P < 0.05). The reduced serum leptin levels could not be explained by nutritional restriction as evaluated by serum levels of glucose and corticosterone. These results indicate the importance of the EFA composition of the maternal diet for serum leptin levels in both dams and pups. EFA deficiency in lactating dams may cause long-term effects on the pups through dysregulation of leptin and leptin-dependent functions. -- Korotkova, M., B. Gabrielsson, L. A. Hanson, and B. Strandvik. Maternal essential fatty acid deficiency depresses serum leptin levels in suckling rat pups. J. Lipid Res. 2001. 42: 359--365.

Essential fatty acid deficiency affects the fatty acid composition of the rat small intestinal and colonic mucosa differently.

The intestinal mucosal fatty acid (FA) composition was investigated in Sprague-Dawley rats after 7 and 23 weeks on an isocaloric diet with qualitatively different essential fatty acid (EFA) composition. For comparison, serum and red blood cell (RBC) membranes were investigated in parallel. The molar percentage of most FAs differed significantly between serum and RBC membranes both in controls and rats fed an EFA deficient (EFAD) diet. The influence of the EFA diet was similar on serum and RBC membrane phospholipids except for arachidonic acid (AA) which was more markedly decreased in serum than in RBC membranes. The FA composition was similar in ileal and colonic mucosa, markedly differing from the jejunal mucosa, in which the AA concentration was lower (13.0+/-0.8 versus 16.8+/-0.5 and 15. 7+/-2.8 mol%) and the linoleic acid (LA) concentration higher (34. 0+/-1.6 versus 17.8+/-1.3 and 15.5+/-2.8 mol%, respectively). The EFAD diet induced a more than five-fold decrease in the jejunal and ileal concentration of LA from 33.9+/-1.6 to 6.0+/-1.5 mol% and 17. 8+/-1.3 to 2.1+/-0.7 mol%, respectively. AA decreased more in the ileal and colonic mucosa than in the jejunum. The changes in the FA composition of the intestinal compartments after EFAD diet were different from that in serum and RBC membranes, and did not further change after 23 weeks compared to 7 weeks after introduction of the diet. The study shows that dietary influences are tissue specific and serum or RBC membranes do not mirror local changes in any of the different intestinal segments.

Composition and permeability of syncytiotrophoblast plasma membranes in pregnancies complicated by intrauterine growth restriction.

The objective of this study was to determine placental membrane permeabilities to water, urea and mannitol in intrauterine growth restriction (IUGR) and compare them to normal gestational age matched controls. Further, we wished to investigate whether potential changes in permeability were related to changes in membrane fluidity, cholesterol or phospholipid fatty acid content of the membranes. Syncytiotrophoblast microvillous (MVM) and basal membranes (BM) were isolated from normal and IUGR placentas at term. Passive permeability to water, urea, and mannitol showed no significant alterations in IUGR compared to controls. Cholesterol content in BM, but not in MVM, was lower in placentas from pregnancies complicated by IUGR. However, membrane fluidity did not change in these pregnancies. The phospholipid fatty acid composition of the plasma membranes isolated from all placentas showed a predominance of unsaturated fatty acid species in the BM and saturated species in the MVM. In the MVM from IUGR, mead acid (20:3), behenic acid (22:0) and nervonic acid (24:1) constituted higher percentages of the total when compared to normally grown controls. In the BM from IUGR, mead acid (20:3) was increased relative to the total phospholipid fatty acid content. In conclusion, the syncytiotrophoblast membranes exhibit only minor changes in passive permeability and composition when the pregnancy is complicated by IUGR.

Latent sequence periodicity of some oncogenes and DNA-binding protein genes.

A method of latent periodicity search is developed. We use mutual information to reveal the latent periodicity of mRNA sequences. The latent periodicity of an mRNA sequence is a periodicity with a low level of similarity between any two periods inside the mRNA sequence. The mutual information between an artificial numerical sequence and an mRNA sequence is calculated. The length of the artificial sequence period is varied from 2 to 150. The high level of the mutual information between artificial and mRNA sequences allows us to find any type of latent periodicity of mRNA sequence. The latent periodicity of many mRNA coding regions has been found. For example, the retinoblastoma gene of HSRBS clone contains a region with a latent period equal to 45 bases. The A-RAF oncogene of HSARAFIR clone contains a region with a latent period equal to 84 bases. Integrated sequences for the regions with latent periodicity are determined. The potential significance of latent periodicity is discussed.

Enlarged similarity of nucleic acid sequences.

The concept of nucleic acid sequence base alternations is presented. The number of base alterations for the sequences of different length is established. The definition of "enlarged similarity" of nucleic acids sequences on the basis of sequence base alterations is introduced. Mutual information between sequences is used as a quantitative measure of enlarged similarity for two compared sequences. The method of mutual information calculation is developed considering the correlation of bases in compared sequences. The definitions of correlated similarity and evolution similarity between compared sequences are given. Results of the use of enlarged similarity approach for DNA sequences analysis are discussed.

Latent periodicity of DNA sequences from some human gene regions.

The mutual information is used to reveal of DNA sequences latent periodicity. Latent periodicity of DNA sequence is periodic. ity with low level of homology between any two periods inside DNA sequence. The mutual information between artificial numerical sequence and DNA sequence is calculated. The length of artificial sequence period is changed from 2 to 250. High level of mutual information between artificial and DNA sequences allows to find any type of latent periodicity of DNA sequence. The latent periodicity of some DNA coding regions is considered. For example, 24 exon of Apo B-100 gene from HSAP821 clone contains latent period 84 bases long. The IGF-I receptor gene from HSIGFIRR clone contains the region with latent period 57 bases long. Possible significance of latent periodicity is discussed.