A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.

BACKGROUND: In the human genome, the transcription factors (TFs) and transcription factor-binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single-nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them. METHODS: A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA). RESULTS: In 6 out of 18 TFBSs in the following genes COL1A1, Hb cá´ª, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis. CONCLUSION: Our preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.

Staging of colorectal cancer using serum metabolomics with 1HNMR Spectroscopy.

OBJECTIVES: Determination of stages of colon cancer is done by biopsy usually after surgery. Metabolomics is the study of all the metabolites using LC-MS and 1HNMR spectroscopy with chemometric techniques. The stages of colon cancer were detected from patients' sera using 1HNMR. MATERIALS AND METHODS: Five ml blood was collected from 16 confirmed patients referred for colonoscopy. One group of eight patients were diagnosed with stage 0 to I colon cancer and the second group of 8 patients with II-IV stage colon cancer. Sera were sent for 1HNMR. The differentiating metabolites were identified using HMDB and the metabolic cycles from Metaboanalyst. RESULTS: Six metabolites of which pyridoxine levels lowered, and glycine, cholesterol, taurocholic acid, cholesteryl ester and deoxyinosine increased. CONCLUSION: The different stages of cancer were identified by the main metabolic cycles such as primary bile acid biosynthesis, purine and vitamin B metabolic pathways and the glutathione cycle.

Serum Metabolomic Profiling of Sulphur Mustard-Exposed Individuals Using (1)H Nuclear Magnetic Resonance Spectroscopy.

Sulphur mustard is an alkylating agent that reacts with different cellular components, causing acute and delayed complications that may remain for decades after exposure. This study aimed to identify differentially expressed metabolites between mustard-exposed individuals suffering from chronic complications compared with unexposed individuals as the control group. Serum samples were obtained from 15 mustard-exposed individuals and 15 apparently healthy unexposed individuals. Metabolomic profiling was performed using (1)H nuclear magnetic resonance spectroscopy, and analyses were carried out using Chenomex and MATLAB softwares. Metabolites were identified using Human Metabolome Database, and the main metabolic pathways were identified using MetaboAnalyst software. Chemometric analysis of serum samples identified 11 differentially expressed metabolites between mustard-exposed and unexposed groups. The main pathways that were influenced by sulphur mustard exposure were related to vitamin B6 (down-regulation), bile acid (up-regulation) and tryptophan (down-regulation) metabolism. Metabolism of vitamin B6, bile acids and tryptophan are the most severely impaired pathways in individuals suffering from chronic mustard-induced complications. These findings may find implications in the monitoring of exposed patients and identification of new therapeutic approaches.

Effect of trinitroglycerin therapy on serum zinc and copper levels and liver enzyme activities in BALB/c mice infected with Leishmania major MRHO/IR/75/ER.

OBJECTIVES: To evaluate the effect of trinitroglycerin (TNG) as nitric oxide donor agent on serum copper (Cu) and zinc (Zn) levels and liver enzymes in BALB/c mice infected with Leishmania major (L. major) MRHO/IR/75/ER. MATERIALS AND METHODS: Inbred female mice were divided into three groups: healthy group (uninfected naive mice), control group (infected with L. major), and test group (L. major infected mice treated with TNG). TNG (200 µg/µl) was inoculated subcutaneously into the mice of the test group. Serum Cu and Zn levels and liver enzymes activities were then evaluated by atomic absorption spectrophometer and colorimetric methods, respectively. RESULTS: Serum Cu levels were significantly higher in the test group than in the control and naive groups (P-value <0.05), while Zn levels were higher in the test group than in the control group with no significant difference. Serum glutamicoxaloacetic transaminase concentrations in the test group were significantly lower than those in other groups (P-value <0.05), while serum glutamate pyruvic transaminase concentrations were significantly higher in test compared with those in other groups (P-value <0.05). Moreover, alkaline phosphatase in the control and test groups were significantly lower than that in the naive group (P-value <0.05). CONCLUSION: TNG treatment increased Zn and Cu levels and thus increased resistance to Leishmania because of the role of Zn and Cu; therefore, TNG therapy will be useful for treating cutaneous leishmania. In addition, the decrease of serum glutamicoxaloacetic transaminase activity can be an index of therapeutic process of TNG.

Biochemical association between essential trace elements and susceptibility to Leishmania major in BALB/c and C57BL/6 mice

Several enzymes that contribute to immune system responses require zinc and copper as trace elements for their activity. We examined zinc and copper levels in two susceptible Balb/c mouse lines and resistant C57bl/6 mice infected with Leishmania major MRHO/IR/75/ER, a prevalent strain that causes cutaneous leishmaniasis in Iran. Serum Zn and Cu were determined by flame atomic absorption spectrophotometry. Higher Cu levels were found in infected C57bl/6 mice and higher Zn levels were found in infected Balb/c mice. Also, Cu/Zn ratios were increased in both the Balb/c and the C57bl/6 mice. We conclude that concentrations of essential trace elements vary during cutaneous leishmaniasis infection and that this variation is associated with susceptibility/resistance to Leishmania major in Balb/c and C57bl/6 mice. We detected Zn deficiency in the plasma of infected Balb/c mice; possibly, therapeutic administration of Zn would be useful for treating this form of leishmaniasis. Increases in Cu level might increase resistance to leishmaniasis. Based on our findings, the Cu/Zn ratio could be a useful marker for the pathophysiology of leishmaniasis.

Sequence diversity of the C-terminal region of Plasmodium falciparum merozoite surface protein 1 in southern Iran.

The C-terminal region of the merozoite surface protein 1 (MSP-1) of Plasmodium falciparum is a strong vaccine candidate as it is associated with immunity to the parasite. This corresponds approximately to the conserved 17th block of the gene and is composed of two EGF- like domains. These domains exhibit only four single amino acid substitutions which show several potential variants in this region of the gene. As the variations might be important for a regional vaccine design, a study was carried out to determine the variations present in P. falciparum isolates from southern Iran. Besides the usual E-T-S-R-L and the Q-K-N-G-F types, we found Q-T-S-R-L, E-K-N-G-F, E-T-S-G-L, Z-T-S-G-L and Z-T-S-R-L types, where Z was E or Q signifying the presence of mixed clones in single isolates.

Biochemical association between essential trace elements and susceptibility to Leishmania major in BALB/c and C57BL/6 mice.

Several enzymes that contribute to immune system responses require zinc and copper as trace elements for their activity. We examined zinc and copper levels in two susceptible Balb/c mouse lines and resistant C57bl/6 mice infected with Leishmania major MRHO/IR/75/ER, a prevalent strain that causes cutaneous leishmaniasis in Iran. Serum Zn and Cu were determined by flame atomic absorption spectrophotometry. Higher Cu levels were found in infected C57bl/6 mice and higher Zn levels were found in infected Balb/c mice. Also, Cu/Zn ratios were increased in both the Balb/c and the C57bl/6 mice. We conclude that concentrations of essential trace elements vary during cutaneous leishmaniasis infection and that this variation is associated with susceptibility/resistance to Leishmania major in Balb/c and C57bl/6 mice. We detected Zn deficiency in the plasma of infected Balb/c mice; possibly, therapeutic administration of Zn would be useful for treating this form of leishmaniasis. Increases in Cu level might increase resistance to leishmaniasis. Based on our findings, the Cu/Zn ratio could be a useful marker for the pathophysiology of leishmaniasis.

Pro12Ala polymorphism of the peroxisome proliferator-activated receptor-gamma2 (PPARgamma-2) gene is associated with greater insulin sensitivity and decreased risk of type 2 diabetes in an Iranian population.

BACKGROUND: The Pro12Ala polymorphism of the peroxisome proliferator-activated receptor-gamma2 (PPARgamma-2) gene has been variably associated with insulin resistance, obesity and type 2 diabetes in several populations. However, this association has not been studied in Iranian subjects and we hypothesized that this variation might be associated with insulin resistance, type 2 diabetes and related metabolic traits in this population. METHODS: The Pro12Ala genotypes were determined by PCR-restriction fragment length polymorphism in 696 unrelated subjects including 412 non-diabetic controls and 284 type 2 diabetic patients. RESULTS: The frequency of the Ala allele was 9.4% and 5.9% in controls and type 2 diabetic subjects, respectively [adjusted odds ratio (OR) 0.457, p=0.005]. The Ala allele did not show a significant effect on anthropometric and biochemical parameters in the type 2 diabetic group, whereas in non-diabetic subjects, carriers of the Ala allele had significantly lower fasting insulin (p=0.007) and homeostasis model assessment of insulin resistance (HOMA-IR) (p=0.009) levels compared to Pro/Pro subjects. Multivariate logistic regression analysis showed that Pro12Ala polymorphism was an independent determinant of type 2 diabetes in this population. CONCLUSIONS: Our results for a sample of Iranian type 2 diabetes cases and controls provide evidence that the Pro/Ala genotype of the PPARgamma-2 gene is associated with insulin sensitivity and may also have protective role against type 2 diabetes.