A fast model of voltage-dependent NMDA receptors

NMDA receptors are among the crucial elements of central nervous system models. Recent studies show that both conductance and kinetics of these receptors are changing voltage-dependently in some parts of the brain. Therefore, several models have been introduced to simulate their current. However, on the one hand, kinetic models—which are able to simulate these voltage-dependent phenomena—are computationally expensive for modeling of large neural networks. On the other hand, classic exponential models, which are computationally less expensive, are not able to simulate the voltage-dependency of these receptors, accurately. In this study, we have modified these classic models to endow them with the voltage-dependent conductance and time constants. Temperature sensitivity and desensitization of these receptors are also taken into account. We show that, it is possible to simulate the most important physiological aspects of NMDA receptor’s behavior using only three to four differential equations, which is significantly smaller than the previous kinetic models. Consequently, it seems that our model is both fast and physiologically plausible and therefore is a suitable candidate for the modeling of large neural networks.     

Elevational gradient and vegetation‐environmental relationships in the central Hyrcanian forests of northern Iran

Tertiary‐relict Hyrcanian (Caspian) forest along the shores of the southern Caspian Sea is a center of biodiversity. Still, there is little information on plant diversity patterns in this area. This study evaluated plant diversity, variation in life forms, and geographical distribution of the zonal vegetation types and their relationships with environmental variables, in the educational and experimental forest of Kheyrudkenar, an important protected area in the central Hyrcanian forest of northern Iran. For this purpose, 226 vegetation plots of 400 m² were laid out along two altitudinal transects from the lowlands (100 m a.s.l.) to the timberline (2000 m a.s.l.). Four vegetation types were identified using modified TWINSPAN, indirect and direct gradient analyses. Species‐related (species diversity indices, life form and phytogeographical elements) and environmental variables (climate, topographic and soil variables) were calculated and subjected to one‐way ANOVA among the vegetation types. Both constrained (CCA) and unconstrained (DCA) ordination analyses showed an almost identical variation of the floristic composition along their axes and demonstrated that there are two main gradients in the Hyrcanian forest. Elevation together with annual precipitation and mean annual temperature were the most important factors controlling the floristic composition in the area. Topographic features such as slope inclination and heat index were found to be important within an elevation zone/vegetation type. Soil physical and chemical properties were of secondary importance for the separation of the vegetation types. This knowledge will be useful for forest management and conservation practices in the Hyrcanian area with its distinct and unique flora and vegetation.     

QTL mapping of complex binary traits in an advanced intercross line

An advanced intercross line (AIL) is an easier and more cost-effective approach compared to recombinant inbred lines for fine mapping of quantitative trait loci (QTL) identified by F(2) designs. In an AIL, a complex binary trait can be mapped through analysis of either continuously distributed proxy traits for the liability of the binary trait or the liability itself, the latter presenting the greater statistical challenge. In another work, we successfully applied both approaches in an AIL to fine map previously identified QTL underlying anatomical parameters of the cardiac inter-atrial septum including patent foramen ovale. Here, we describe the statistical methods that we used to analyse complex binary traits in our AIL design. This is achieved using a likelihood-based method, with the expectation-maximisation algorithm allowing use of standard logistic regression methods for model fitting.     

Apoptotic Effect of Melittin Purified from Iranian Honey Bee Venom on Human Cervical Cancer HeLa Cell Line

Melittin, an amphipathic 26-residue peptide, is the main component of honey bee venom. Studies have been demonstrated that melittin has an inhibitory effect on proliferation of cancer cells. However, the precise mechanism of action is not completely understood. In the present study we have shown that purified melittin from Iranian honey bee venom shows anti-cancer effects on human cervical cancer cell line through induction of apoptosis. The venom was collected from Iranian honey bee (Apis mellifera meda) and melittin isolated using reversed phase HPLC. Biological activity of melittin was analyzed by hemolytic test on human red blood cells. In order to investigate whether melittin inhibits proliferation of cervical cancer cells, the viability of the melittin treated HeLa cell line was measured via MTT assay. Finally, cell death analysis was performed using Propidum iodide and Annexin V-FITC dual staining. The results showed that the half hemolytic concentration (HD50) induced by mellitin was 0.5 µg/ml in free FBS solution. IC50 obtained after 12 h at 1.8 µg/ml by MTT assay. According to flow cytometric analysis, melittin induced apoptosis at concentrations more than 1 µg/ml. These results suggest that melittin induces apoptotic cell death in cervical cancerous cells as observed by flow cytometric assay. It is concluded that melittin could be regarded as a potential candidate in future studies to discovery of new anticancer agents.     

Stereological and gene expression examinations on the combined effects of photobiomodulation and curcumin on wound healing in type one diabetic rats

We examined the effects of photobiomodulation (PBM) independently and combined with curcumin on stereological parameters and basic fibroblast growth factor (bFGF), hypoxia-inducible factor-1α (HIF-1α), and stromal cell-derived factor-1α (SDF-1α) gene expressions in an excisional wound model of rats with type one diabetes mellitus (T1DM). T1DM was induced by an injection of streptozotocin (STZ) in each of the 90 male Wistar rats. One round excision was generated in the skin on the back of each of the 108 rats. The rats were divided into six groups (n = 18 per group): control (diabetic), untreated group; vehicle (diabetic) group, which received sesame oil; PBM (diabetic) group; curcumin (diabetic) group; PBM + curcumin (diabetic) group; and a healthy control group. On days 4, 7, and 15, we conducted both stereological and quantitative real-time PCR (qRT-PCR) analyses. The PBM and PBM + curcumin groups had significantly better inflammatory response modulation in terms of macrophages (P < .01), neutrophils (P < .001), and increased fibroblast values compared with the other groups at day 4 (P < .001), day 7 (P < .01), and day 15 (P < .001). PBM treatment resulted in increased bFGF gene expression on days 4 (P < .001) and 7 (P < .001), and SDF-1α gene expression on day 4 (P < .001). The curcumin group had increased bFGF (P < .001) expression on day 4. Both the PBM and PBM + curcumin groups significantly increased wound healing by modulation of the inflammatory response, and increased fibroblast values and angiogenesis. The PBM group increased bFGF and SDF-1α according to stereological and gene expression analyses compared with the other groups. The PBM and PBM + curcumin groups significantly increased the skin injury repair process to more rapidly reach the proliferation phase of the wound healing in T1DM rats.     

Delicate balance of electrostatic interactions and disulfide bridges in thermostability of firefly luciferase

The wild type Photinus pyralis luciferase does not have any disulfide bridge. Disulfide bridges are determinant in inherent stability of protein at moderate temperatures. Meanwhile, arginin is responsible for thermostability at higher temperatures. In this study, by concomitant introduction of disulfide bridge and a surface arginin in a mutant (A296C-A326C/I232R), the contribution of disulfide bridge introduction and surface hydrophilic residue on activity and global stability of P. pyralis luciferase is investigated. In addition to the mentioned mutant; I232R, A296C-A326C and wild type luciferases are characterized. Though addition of Arg caused stability against proteolysis but in combination with disulfide bridge resulted in decreased thermal stability compared to A296C-A326C mutant. In spite of long distance of two different mutations (A296C-A326C and I232R) from each other in the three-dimensional structure, combination of their effects on the stability of luciferase was not cumulative.     

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

We have characterized the conformational ensembles of polyglutamine peptides of various lengths (ranging from to ), both with and without the presence of a C-terminal polyproline hexapeptide. For this, we used state-of-the-art molecular dynamics simulations combined with a novel statistical analysis to characterize the various properties of the backbone dihedral angles and secondary structural motifs of the glutamine residues. For (i.e., just above the pathological length for Huntington''s disease), the equilibrium conformations of the monomer consist primarily of disordered, compact structures with non-negligible -helical and turn content. We also observed a relatively small population of extended structures suitable for forming aggregates including - and -strands, and - and -hairpins. Most importantly, for we find that there exists a long-range correlation (ranging for at least residues) among the backbone dihedral angles of the Q residues. For polyglutamine peptides below the pathological length, the population of the extended strands and hairpins is considerably smaller, and the correlations are short-range (at most residues apart). Adding a C-terminal hexaproline to suppresses both the population of these rare motifs and the long-range correlation of the dihedral angles. We argue that the long-range correlation of the polyglutamine homopeptide, along with the presence of these rare motifs, could be responsible for its aggregation phenomena.     

The role of microRNAs in 5-FU resistance of colorectal cancer: Possible mechanisms

Colorectal cancer (CRC) is one of the most common cancers globally. Despite recent advances in therapeutic approaches, this cancer continues to have a poor prognosis, particularly when diagnosed late. 5-Fluorouracil (5-FU) has been commonly prescribed for patients with CRC, but resistance to 5-FU is one of the main reasons for failure in the treatment of this condition. Recently, microRNAs (miRNAs) have been established as a means of modifying the signaling pathways involved in initiation and progression of CRC and their role as oncogene or tumor suppressor have been investigated in various studies. Moreover, miRNAs through various mechanisms play an important role in inducing tumor resistance or sensitivity to anticancer drugs. Detecting and targeting these mechanisms may be a new therapeutic approach. This review summarizes the current knowledge about the potential roles of miRNAs in 5-FU resistance, with particular emphasis on molecular mechanism involved.     

Inhibitory effects of deferasirox on the structure and function of bovine liver catalase: a spectroscopic and theoretical study

Deferasirox (DFX), as an oral chelator, is used for treatment of transfusional iron overload. In this study, we have investigated the effects of DFX as an iron chelator, on the function and structure of bovine liver catalase (BLC) by different spectroscopic methods of UV–visible, fluorescence, and circular dichroism (CD) at two temperatures of 25 and 37 °C. In vitro kinetic studies showed that DFX can inhibit the enzymatic activity in a competitive manner. K _I value was calculated 39 nM according to the Lineweaver–Burk plot indicating a high rate of inhibition of the enzyme. Intrinsic fluorescence data showed that increasing the drug concentrations leads to a significant decrease in the intrinsic emission of the enzyme indicating a significant change in the three-dimensional environment around the chromophores of the enzyme structure. By analyzing the fluorescence quenching data, it was found that the BLC has two binding sites for DFX and the values of binding constant at 25 and 37 °C were calculated 1.7 × 10⁷ and 3 × 10⁷ M^?1, respectively. The static type of quenching mechanism is involved in the quenching of intrinsic emission of enzyme. The thermodynamic data suggest that hydrophobic interactions play a major role in the binding reaction. UV–vis spectroscopy results represented the changes in tryptophan (Trp) absorption and Soret band spectra, which indicated changes in Trp and heme group position caused by the drug binding. Also, CD data represented that high concentrations of DFX lead to a significant decreasing in the content of β-sheet and random coil accompanied an increasing in α-helical content of the protein. The molecular docking results indicate that docking may be an appropriate method for prediction and confirmation of experimental results and also useful for determining the binding mechanism of proteins and drugs. According to above results, it can be concluded that the DFX can chelate the Fe(III) on the enzyme active site leading to changes in the function and structure of catalase which can be considered as a side effect of this drug and consequently has an important role in hepatic complications and fibrosis.