Staging of colorectal cancer using serum metabolomics with 1HNMR Spectroscopy

Objective(s): 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

{4,4′-Dichloro-2,2′-[2,2-dimethylpropane-1,3-diylbis(nitrilomethanylylidene)]diphenolato}copper(II)

In the title Schiff base complex, [Cu(C19H18Cl2N2O2)], the CuII ion is coordinated in a distorted square-planar environment by two N atoms and two O atoms of the tetradentate ligand. The dihedral angle between the benzene rings is 36.86 (14)°. In the crystal, molecules are linked into inversion dimers by pairs of weak C—H...O hydrogen bonds. In addition, π–π [centroid–centroid distance = 3.7279 (16) Å] and weak C—H...π interactions are observed

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

Abstract 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 ḉᴪ, 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

2-((Z)-{3-[(Z)-(2-Hydroxy-5-methylbenzylidene)amino]-2,2-dimethylpropyl}iminomethyl)-4-methylphenol

In the title compound, C21H26N2O2, the dihedral angle between the two benzene rings is 73.47 (16)°. Strong intramolecular O—H...N hydrogen bonds generate S(6) ring motifs. The substituted benzene rings are twisted around the central quaternary C atom in opposite directions, making a vault geometry

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