• 제어로봇시스템학회논문지
• /
• 제12권10호
• /
• pp.1044-1049
• /
• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Journal of Microbiology and Biotechnology
• /
• 제18권5호
• /
• pp.908-912
• /
• 2008

To achieve a higher succinic acid productivity and evaluate the industrial applicability, this study used Mannheimia succiniciproducens LPK7 (knock-out: ldhA, pflB, pta-ackA), which was recently designed to enhance the productivity of succinic acid and reduce by-product secretion. Anaerobic continuous fermentation of Mannheimia succiniciproducens LPK7 was carried out at different glucose feed concentrations and dilution rates. After extensive fermentation experiments, a succinic acid yield and productivity of 0.38 mol/mol and 1.77 g/l/h, respectively, were achieved with a glucose feed concentration of 18.0 g/l and $0.2\;h^{-1}$ dilution rate. A similar amount of succinic acid production was also produced in batch culture experiments. Therefore, these optimal conditions can be industrially applied for the continuous production of succinic acid. To examine the quantitative balance of the metabolism, a flux distribution analysis was also performed using the metabolic network model of glycolysis and the pentose phosphate pathway.

• Journal of Microbiology and Biotechnology
• /
• 제27권9호
• /
• pp.1681-1691
• /
• 2017

This study investigated the effect of proline addition on the salt tolerance of Tetragenococcus halophilus. Salt stress led to the accumulation of intracellular proline in T. halophilus. When 0.5 g/l proline was added to hyperhaline medium, the biomass increased 34.6% (12% NaCl) and 27.7% (18% NaCl) compared with the control (without proline addition), respectively. A metabolomic approach was employed to reveal the cellular metabolic responses and protective mechanisms of proline upon salt stress. The results showed that both the cellular membrane fatty acid composition and metabolite profiling responded by increasing unsaturated and cyclopropane fatty acid proportions, as well as accumulating some specific intracellular metabolites (environmental stress protector). Higher contents of intermediates involved in glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway were observed in the cells supplemented with proline. In addition, addition of proline resulted in increased concentrations of many organic osmolytes, including glutamate, alanine, citrulline, N-acetyl-tryptophan, and mannitol, which may be beneficial for osmotic homeostasis. Taken together, results in this study suggested that proline plays a protective role in improving the salt tolerance of T. halophilus by regulating the related metabolic pathways.

• Asian-Australasian Journal of Animal Sciences
• /
• 제13권6호
• /
• pp.748-756
• /
• 2000

Effects of xanthine (X), xanthine oxidase (XO), and catalase (C), $H_2O_2$, and carbohydrates on sperm capacitation, acrosome reaction, and fertilizing ability in vitro were examined. Glucose alone, but not fructose, supported the maximum rate of sperm capacitation and acrosome reaction. However, in the combination of X, XO, and C (XXOC) or $H_2O_2$, fructose alone also supported maximum capacitation, acrosome reaction, and fertilization. Either insufficient or excessive amounts of $H_2O_2$ decreased sperm capacitation and the acrosome reaction. In order to understand how glucose generates $H_2O_2$ or other reactive oxygen species in sperm cells, 6-aminonicotinamide, an inhibitor of the pentose-phosphate pathway (PPP), and apocynin, an inhibitor of NADPH oxidase, were added to sperm suspensions in glucose-containing medium. Results appeared that sperm capacitation, acrosome reaction, and fertilization were consequently inhibited by either one of these compounds. These inhibitory effects were nullified by addition of XXOC. These results support the hypothesis that glucose, in addition to being a substrate for glycolysis, facilitates sperm capacitation and the acrosome reaction by generating reactive oxygen species through G-6-P dehydrogenase and NADPH oxidase.

• Journal of Veterinary Science
• /
• 제23권5호
• /
• pp.76.1-76.14
• /
• 2022

Background: Clinical dexamethasone (DEX) treatment or stress in bovines results in extensive physiological changes with prominent hyperglycemia and neutrophils dysfunction. Objectives: To elucidate the effects of DEX treatment in vivo on cellular energy status and the underlying mechanism in circulating neutrophils. Methods: We selected eight-month-old male bovines and injected DEX for 3 consecutive days (1 time/d). The levels of glucose, total protein (TP), total cholesterol (TC), and the proinflammatory cytokines interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α in blood were examined, and we then detected glycogen and adenosine triphosphate (ATP) content, phosphofructosekinase-1 (PFK1) and glucose-6-phosphate dehydrogenase (G6PDH) activity, glucose transporter (GLUT)1, GLUT4, sodium/glucose cotransporter (SGLT)1 and citrate synthase (CS) protein expression and autophagy levels in circulating neutrophils. Results: DEX injection markedly increased blood glucose, TP and TC levels, the Ca²⁺/P⁵⁺ ratio and the neutrophil/lymphocyte ratio and significantly decreased blood IL-1β, IL-6 and TNF-α levels. Particularly in neutrophils, DEX injection inhibited p65-NFκB activation and elevated glycogen and ATP contents and SGLT1, GLUT1 and GR expression while inhibiting PFK1 activity, enhancing G6PDH activity and CS expression and lowering cell autophagy levels. Conclusions: DEX induced neutrophils glucose uptake by enhancing SGLT1 and GLUT1 expression and the transformation of energy metabolism from glycolysis to pentose phosphate pathway (PPP)-tricarboxylic acid (TCA) cycle. This finding gives us a new perspective on deeper understanding of clinical anti-inflammatory effects of DEX on bovine.

• BMB Reports
• /
• 제51권9호
• /
• pp.462-467
• /
• 2018

A previous study of ours indicated that Drosophila flightless-1 controls lipid metabolism, and that there is an accumulation of triglycerides in flightless-1 (fliI)-mutant flies, where this mutation triggers metabolic stress and an obesity phenotype. Here, with the aim of characterizing the function of FliI in metabolism, we analyzed the levels of gene expression and metabolites in fliI-mutant flies. The levels of enzymes related to glycolysis, lipogenesis, and the pentose phosphate pathway increased in fliI mutants; this result is consistent with the levels of metabolites corresponding to a metabolic pathway. Moreover, high-throughput RNA sequencing revealed that Drosophila FliI regulates the expression of genes related to biological processes such as chromosome organization, carbohydrate metabolism, and immune reactions. These results showed that Drosophila FliI regulates the expression of metabolic genes, and that dysregulation of the transcription controlled by FliI gives rise to metabolic stress and problems in the development and physiology of Drosophila.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권9호
• /
• pp.3691-3696
• /
• 2015

Background: Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards. Materials and Methods: In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS. Results: Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways. Conclusions: The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.

• Journal of Plant Biology
• /
• 제12권2호
• /
• pp.7-14
• /
• 1969

Dunaliella tertiolecta did not show any increase in respiration rate when supplied with glucose, glycerol, sucrose, L-alanine, acetate, pyruvate and succinate. This was in contrast to Chlorella pyrenoidosa, which, under identical conditions, showed significant increase when supplied with glucose or acetate but not with the other compounds. Production of 14CO2 from added 14C-glucose in D. tertiolecta was lower than the other 14C-labelled substrates: L-alinine, glycerol, succinate, but higher than 14C-sucrose addition. And it was also lower than C. pyrenoidosa experiments which was added 14C-glucose as a substrate. Light reduced amounts of labelled carbon dioxide from 14C-glucose or 14C-acetate and increased incorporation of 14C from the substrates to cell materials in either D. tertiolecta or C. pyrenoidosa. The contribution of 14C from 14C-glucose to 14CO2 in cell-free system of D. tertiolecta were much higher than in whole cell suspension. It was contrast to C. pyrenoidosa which were showed reduction of 14CO2 production in cell-free systems than whole cell suspensions. When cell-free systems of D. tertiolecta and C. pyrenoidosa were supplied with ATP, NAD, NADP or/and hexokinase, it was remarkably increased production of 14CO2 from the substrates than the control. It was concluded that the low ability of D. tertiolecta to metabolize glucose were caused by the impermeability of the cell membrane to glucose and were not due to deficiencies of enzyme systems concerning glucose metabolism. In the cell-free systems, it seemed to be more active pentose phosphate pathway than glycolytic pathway in D. tertiolecta.

• Asian-Australasian Journal of Animal Sciences
• /
• 제13권3호
• /
• pp.334-347
• /
• 2000

The present experiment was carried out to study the utilization of glucose in the mammary gland of crossbred Holstein cattle during feeding with different types of roughage. Sixteen first lactating crossbred Holstein cattle which comprised eight animals of two breed types, Holstein Friesian${\times}$Red Sindhi ($50{\times}50=50%$ HF) and Holstein Friesian${\times}$Red Sindhi ($87.5{\times}12.5=87.5%$ HF). They were divided into four groups of 4 animals each of the same breed. The utilization of glucose in the mammary gland was determined by measuring rates of glucose uptake and the incorporation of glucose into milk components in both groups of 50% HF and 87.5% HF animals feeding on either hay or urea treated rice straw. In early lactation, there were no significant differences of the total glucose entry rate and glucose carbon recycling among groups of crossbred animals feeding on either hay or urea treated rice straw. During lactation advance, the total glucose turnover rates and recycling of carbon glucose of crossbred HF animals feeding on urea treated rice straw were markedly higher than those of crossbred HF animals feeding on hay as roughage, whereas there were no significant changes for both groups of crossbred animals feeding on hay. The percentages and values of non-mammary glucose utilization showed an increase during lactation advance in the same group of both 50% HF and 87.5% HF animals. The percentage of glucose uptake for utilization in the synthesis of milk lactose by the mammary gland was approximately 62% for both groups of 87.5% HF and by approximately 55% for both groups of 50% HF animals feeding on either hay or urea treated rice straw. Intracellular glucose 6-phosphate metabolized via the pentose phosphate pathway accounted for the NADPH (reducing equivalent) of fatty acid synthesis in the mammary gland being higher in 87.5% HF animals during mid-lactation. A large proportion of metabolism of glucose via the Embden-Meyerhof pathway in the mammary gland was more apparent in both groups of 50% HF animals than those of 87.5 % HF animals during early and mid-lactation while it markedly increased for both groups of 87.5% HF animals during late lactation. It can be concluded that utilization of glucose in the mammary gland occurs in a different manner for 50% HF and 87.5% HF animals feeding on either hay or urea treated rice straw. The glucose utilization for biosynthetic pathways in the mammary gland of 50% HF animals is maintained in a similar pattern throughout the periods of lactation. A poorer lactation persistency in both groups of 87.5% HF animals occurs during lactation advance, which is related to a decrease in the lactose biosynthetic pathway.

• Clinical and Experimental Reproductive Medicine
• /
• 제43권4호
• /
• pp.193-198
• /
• 2016

Objective: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common human enzyme defect. G6PD plays a key role in the pentose phosphate pathway, which is a major source of nicotinamide adenine dinucleotide phosphate (NADPH). NADPH provides the reducing equivalents for oxidation-reduction reductions involved in protecting against the toxicity of reactive oxygen species such as $H_2O_2$. We hypothesized that G6PD deficiency may reduce the amount of NADPH in sperms, thereby inhibiting the detoxification of $H_2O_2$, which could potentially affect their motility and viability, resulting in an increased susceptibility to infertility. Methods: Semen samples were obtained from four males with G6PD deficiency and eight healthy males as a control. In both groups, motile sperms were isolated from the seminal fluid and incubated with 0, 10, 20, 40, 60, 80, and $120{\mu}M$ concentrations of $H_2O_2$. After 1 hour incubation at $37^{\circ}C$, sperms were evaluated for motility and viability. Results: Incubation of sperms with 10 and $20{\mu}M\;H_2O_2$ led to very little decrease in motility and viability, but motility decreased notably in both groups in 40, 60, and $80{\mu}M\;H_2O_2$, and viability decreased in both groups in 40, 60, 80, and $120{\mu}M\;H_2O_2$. However, no statistically significant differences were found between the G6PD-deficient group and controls. Conclusion: G6PD deficiency does not increase the susceptibility of sperm to oxidative stress induced by $H_2O_2$, and the reducing equivalents necessary for protection against $H_2O_2$ are most likely produced by other pathways. Therefore, G6PD deficiency cannot be considered as major risk factor for male infertility.