Novel hybrid method for the evaluation of parameters contributing in determination of protein structural classes

Due to the increasing gap between structure-determined and sequenced proteins, prediction of protein structural classes has been an important problem. It is very important to use efficient sequential parameters for developing class predictors because of the close sequence-structure relationship. The multinomial logistic regression model was used for the first time to evaluate the contribution of sequence parameters in determining the protein structural class. An in-house program generated parameters including single amino acid and all dipeptide composition frequencies. Then, the most effective parameters were selected by a multinomial logistic regression. Selected variables in the multinomial logistic model were Valine among single amino acid composition frequencies and Ala-Gly, Cys-Arg, Asp-Cys, Glu-Tyr, Gly-Glu, His-Tyr, Lys-Lys, Leu-Asp, Leu-Arg, Pro-Cys, Gln-Met, Gln-Thr, Ser-Trp, Val-Asn and Trp-Asn among dipeptide composition frequencies. Also a neural network model was constructed and fed by the parameters selected by multinomial logistic regression to build a hybrid predictor. In this study, self-consistency and jackknife tests on a database constructed by Zhou [1998. An intriguing controversy over protein structural class prediction. J. Protein Chem. 17(8), 729-738] containing 498 proteins are used to verify the performance of this hybrid method, and are compared with some of prior works. The results showed that our two-stage hybrid model approach is very promising and may play a complementary role to the existing powerful approaches.     

Status of Haemaphysalis tick infestation in domestic ruminants in Iran

The geographical distribution and ecological preferences of Haemaphysalis in domestic animals in Iran were studied 4 times a year from April 2003 to March 2005. A total of 1,622 ixodid tick specimens were collected from 3 different zones. Among them, 108 (6.7%) Haemaphysalis ticks, consisting of 6 species, were identified; H. punctata (3.4%), H. parva (0.5%), H. sulcata (0.6%), H. choldokovskyi (1.7%), H. concinna (0.06%) and Haemaphysalis sp. (0.6%). H. punctata was the most abundant species, whereas H. concinna was the rarest species collected in humid and sub-humid zones on cattle, sheep and goats. H. choldokovskyi was principally collected from sheep and goats grazed in cold mountainous areas. The infested areas consisted of Caspian Sea (Guilan, Mazandaran, Golestan, and central provinces), mountainous (Azarbaiejan, Ardebil, Kohgilouyeh, and Kordestan) and semi-dessert (Khorasan, Semnan, Kerman, Sistan, and Baluchestan) zones. The Caspian Sea zone (23.6%) was the most highly infested region. The results show that various species of Haemaphysalis ticks infest domestic ruminants in Iran and each tick species show characteristic geographical distributions.     

Epigenetic changes in gastric cancer induction by Helicobacter pylori

Epigenetic disorder mechanisms are one of the causes of cancer. The most important of these changes is the DNA methylation, which leads to the spread of Helicobacter pylori and inflammatory processes followed by induction of DNA methylation disorder. Mutations and epigenetic changes are the two main agents of neoplasia. Epithelial cells infection by H. pylori associated with activating several intracellular pathways including: MAPK, NF-κB, Wnt/β-catenin, and PI3K are affects a variety of cells and caused to an increase in the production of inflammatory cytokines, changes in apoptosis, proliferation, differentiation, and ultimately leads to the transformation of epithelial cells into oncogenic. The arose of free radicals impose the DNA cytosine methylation, and NO can increase the activity of DNA methyltransferase. H. pylori infection causes an environment that mediates inflammation and signaling pathways that probably caused to stomach tumorigenicity. The main processes that change by decreasing or increasing the expression of various microRNAs expressions include immune responses, apoptosis, cell cycle, and autophagy. In this review will be describe a probably H. pylori roles in infection and mechanisms that have contribution in epigenetic changes in the promoter of genes.     

Spectroscopic studies of the effects of glycation of human serum albumin on L-Trp binding

Modification of proteins by nonenzymatic glycation is one of the underlying factors that contribute to the development of the complications of diabetes. Human serum albumin (HSA) is one of the major targets of interaction with glucose through the Maillard reaction. The effects of 1 and 5 mg/ml glucose concentrations, which are consistent with blood glucose levels found in diabetic patients, on human serum albumin were studied by circular dichroism and fluorescence spectroscopy in sodium phosphate buffer, pH 7.4. Partial denaturation and changes in the structural integrity of HSA are caused by glycation at lower (1 mg/ml) and higher (5 mg/ml) concentrations of glucose. To study the relationship between structure and function, we investigated the interaction of L-tryptophan (L-Trp) with glycated and non-glycated HSA. The results showed that L-Trp, as the only free amino acid that substantially binds to HSA, has a lower affinity for the glycated form (especially at low concentrations of glucose) than for non-glycated HSA.     

Sub-second adsorptive fast Fourier transform coulometric technique as a novel method for the determination of nanomolar concentrations of sodium valproate in its pharmaceutical preparation in flowing solution systems

In this work, a novel electrochemical technique has been developed for determination of nanomolar concentration of sodium valproate in flow-injection systems. The detection was done by adsorptive fast Fourier transform coulometric (AFFTC), in which the potential waveform consists of potential steps for cleaning, accumulation, and a potential ramp that was continuously applied on an Au disk microelectrode. Moreover, a special computer program is introduced based on numerical method, for calculation of the analyte signal (which is the partial and total charge exchanges at the electrode surface) and noise reduction. The optimum parameters were: pH value of 2.0, scan rate value of 40 Vs(-1), accumulation potential of 200 mV and accumulation time of 0.3 s. Detection limit of the method for sodium valproate was 9.0x10(-9) M. The relative standard deviation of the method at 1.3x10(-7) M was 2.0% for 10 runs.     

Probiotics importance and their immunomodulatory properties

Mammalian intestine contains a large diversity of commensal microbiota, which is far more than the number of host cells. Probiotics play an insecure and protective role against the colonization of intestinal pathogenic microbes and increase mucosal integrity by stimulating epithelial cells. Probiotics have innate capabilities in many ways, including receptor antagonism, receptor expression, binding and expression of adapter proteins, expression of negative regulatory signal molecules, induction of microRNAs, endotoxin tolerance, and ultimately secretion of immunomodulatory proteins, lipids, and metabolites to modulate the immune system. Probiotic bacteria can affect homeostasis, inflammation, and immunopathology through direct or indirect effects on signaling pathways as immunosuppressant or activators. Probiotics suppress inflammation by inhibiting various signaling pathways such as the nuclear factor-κB (NF-κβ) pathway, possibly related to alterations in mitogen-activated protein kinases and pattern recognition receptors pathways. Probiotics can also inhibit the binding of lipopolysaccharides to the CD14 receptor, thereby reducing the overall activation of NF-κβ and producing proinflammatory cytokines. Some effects of modulation by probiotics include cytokine production by epithelial cells, increased mucin secretion, increased activity of phagocytosis, and activation of T and natural killer T cells, stimulation of immunoglobulin A production and decreased T cell proliferation. Intestinal microbiota has a major impact on the systemic immune system. Specific microbiota controls the differentiation of cells in lamina propria, in which Th17 cells secrete interleukin 17. The presence of Th17 and Treg cells in the small intestine is associated with intestinal microbiota, with the preferential Treg differentiation and the absence of Th17 cells, possibly reflecting alterations in the lamina propria cytokines and the intestinal gut microbiota.     

Complete Genome Sequence of Cronobacter sakazakii Bacteriophage vB_CsaM_GAP161

Cronobacter sakazakii is an opportunistic pathogen that causes infant meningitis and is often associated with milk-based infant formula. We have fully sequenced the genome of a newly isolated lytic C. sakazakii myovirus, vB_CsaM_GAP161, briefly named GAP161. It consists of 178,193 bp and has a G+C content of 44.5%. A total of 277 genes, including 275 open reading frames and two tRNA-encoding genes, were identified. This phage is closely related to coliphages RB16 and RB43 and Klebsiella pneumoniae phage KP15.     

Netrin-1 protects the SH-SY5Y cells against amyloid beta neurotoxicity through NF-κB/Nrf2 dependent mechanism

Molecular Biology Reports - Many evidence confirms that amyloid beta 1–42 fragment (Aβ1–42) causes neuroinflammation, oxidative stress, and cell death, which are related to...