Hepatitis C virus genotypes in patients with chronic hepatitis C infection in southern Iran from 2016 to 2019

Hepatitis C is a liver disease caused by the hepatitis C virus (HCV). The treatment of HCV infection has become more complicated due to various genotypes and subtypes of HCV. The treatment of HCV has made significant advances with direct-acting antivirals. However, for the choice of medicine or the combination of drugs for hepatitis C, it is imperative to detect and discriminate the crucial HCV genotypes. The main objective of this study was to determine the pattern of circulating HCV genotypes in southern Iran, from 2016 until 2019. The other aim of the study was to determine possible associations of patients’ risk factors with HCV genotypes. A total of 803 serum samples were collected in 4 years (2016–2019) from patients with HCV antibody positive results. A total of 728 serum samples were HCV-RNA positive. The prevalence of HCV genotypes was detected using the genotype-specific RT-PCR test for serum samples obtained from 615 patients. The HCV genotype 1 (G1) was the most prevalent (48.8%) genotype in the area, with G1a, G1b, and mixed G1a/b representing 38.4%, 10.1%, and 0.3%, respectively. Genotype 3a was the next most prevalent (47.2%). Mixed genotypes 1a/3a were detected in 22 (3.6%) and finally G4 was found in 3 (0.5%) patients. The other HCV genotypes were not detected in any patient. Genotype 1 (1a and 1b alone, 1a/1b and 1a/3a coinfections) is the most prevalent HCV genotype in southern Iran. HCV G1 shows a significantly higher rate in people under 40 years old.     

The effect of carbon source supplementation on the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by Cupriavidus necator

The objective of the present study was to investigate the ability of Cupriavidus necator to produce poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) on various carbon sources in batch cultivation. These results show that C. necator produces poly-3-hydroxybutyrate from single carbon sources. The highest poly-3-hydroxybutyrate (P3HB) content was achieved at growth on fructose in the exponential growth phase. The maximum yield of the P3HV content was obtained when fructose was mixed with acetate. The highest content P3HB-co-3HV was also achieved by C. necator when we supplied C-excess and N- and P-normal conditions. These results indicate that C. necator accumulates high polyhydroxyalkanoates (PHA) content by depleting these elements in the culture medium. Nitrogen and phosphorus limitation has no significant effect on the PHA production, whereas C-excess leads to an increase in PHA formation of up to 92% PHAs of cell dry weight after growth on 5 g/L acetate and 40 g/L fructose.     

Modeling of crude oil biodegradation using two phase partitioning bioreactor

In this work, crude oil biodegradation has been optimized in a solid‐liquid two phase partitioning bioreactor (TPPB) by applying a response surface methodology based d ‐optimal design. Three key factors including phase ratio, substrate concentration in solid organic phase, and sodium chloride concentration in aqueous phase were taken as independent variables, while the efficiency of the biodegradation of absorbed crude oil on polymer beads was considered to be the dependent variable. Commercial thermoplastic polyurethane (Desmopan®) was used as the solid phase in the TPPB. The designed experiments were carried out batch wise using a mixed acclimatized bacterial consortium. Optimum combinations of key factors with a statistically significant cubic model were used to maximize biodegradation in the TPPB. The validity of the model was successfully verified by the good agreement between the model‐predicted and experimental results. When applying the optimum parameters, gas chromatography‐mass spectrometry showed a significant reduction in n‐alkanes and low molecular weight polycyclic aromatic hydrocarbons. This consequently highlights the practical applicability of TPPB in crude oil biodegradation. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:797–805, 2014     

The regulatory role of heparin on c-Met signaling in hepatocellular carcinoma cells

The role of heparin as an anticoagulant is well defined; however, its role in tumorigenesis and tumor progression is not clear yet. Some studies have shown that anticoagulant treatment in cancer patients improve overall survival, however, recent clinical trials have not shown a survival benefit in cancer patients receiving heparin treatment. In our previous studies we have shown the inhibitory effects of heparin on Hepatocyte Growth Factor (HGF)-induced invasion and migration in hepatocellular carcinoma (HCC) cells. In this study, we showed the differential effects of heparin on the behaviors of HCC cells based on the presence or absence of HGF. In the absence of HGF, heparin activated HGF/c-Met signaling and promoted motility and invasion in HCC cells. Heparin treatment led to c-Met receptor dimerization and activated c-Met signaling in an HGF independent manner. Heparin-induced c-Met activation increased migration and invasion through ERK1/2, early growth response factor 1 (EGR1) and Matrix Metalloproteinases (MMP) axis. Interestingly, heparin modestly decreased the proliferation of HCC cells by inhibiting activatory phosphorylation of Akt. The inhibition of c-Met signaling reversed heparin-induced increase in motility and invasion and, proliferation inhibition. Our study provides a new perspective into the role of heparin on c-Met signaling in HCC.     

A motion-dependent distortion of retinotopy in area V4

When one element in an apparent motion sequence differs in color from the others, it is perceived as shifted along the motion trajectory. We examined whether V4 neurons encode the physical or perceived location of this "flashed" element by recording neuronal responses while monkeys viewed these stimuli. The retinotopic locus of V4 activity evoked by the flashed element shifted along the motion trajectory. The magnitude of the shift is consistent with the perceptual shift in humans viewing identical stimuli. This retinotopic distortion depended on the presence of a flashed element but was observed for both color-selective and non-color-selective neurons. The distortion was undiminished when the flashed element terminated the sequence, a condition that reduced the perceptual shift in humans. These findings are consistent with a Bayesian model of localization in which perceived location is derived from position signals optimally integrated across visual areas.     

Vesicle-associated membrane protein 7 (VAMP-7) is essential for target cell killing in a natural killer cell line

Natural killer cells recognize and induce apoptosis in foreign, transformed or virus-infected cells through the release of perforin and granzymes from secretory lysosomes. Clinically, NK-cell mediated killing is a major limitation to successful allo- and xenotransplantation. The molecular mechanisms that regulate the fusion of granzyme B-containing secretory lysosomes to the plasma membrane in activated NK cells, prior to target cell killing, are not fully understood. Using the NK cell line YT-Indy as a model, we have investigated the expression of SNAP REceptors (SNAREs), both target (t-) and vesicular (v-) SNAREs, and their function in granzyme B-mediated target cell killing. Our data showed that YT-Indy cells express VAMP-7 and SNAP-23, but not VAMP-2. VAMP-7 was associated with granzyme B-containing lysosomal granules. Using VAMP-7 small interfering RNA (siRNA), we successfully knocked down the expression of VAMP-7 protein in YT-Indy to less than 10% of untreated cells in 24 h. VAMP7-deficient YT-Indy cells activated via co-culture with Jurkat cells released <1 ng/mL of granzyme B, compared to 1.5-2.5 μg/mL from controls. Using Jurkat cells as targets, we showed a 7-fold reduction in NK cell-mediated killing by VAMP-7 deficient YT-Indy cells. Our results show that VAMP-7 is a crucial component of granzyme B release and target cell killing in the NK cell line YT-Indy. Thus, targeting VAMP-7 expression specifically with siRNA, following transplantation, may be a viable strategy for preventing NK cell-mediated transplant rejection, in vivo.     

A Color Hierarchy for Automatic Target Selection

Visual processing of color starts at the cones in the retina and continues through ventral stream visual areas, called the parvocellular pathway. Motion processing also starts in the retina but continues through dorsal stream visual areas, called the magnocellular system. Color and motion processing are functionally and anatomically discrete. Previously, motion processing areas MT and MST have been shown to have no color selectivity to a moving stimulus; the neurons were colorblind whenever color was presented along with motion. This occurs when the stimuli are luminance-defined versus the background and is considered achromatic motion processing. Is motion processing independent of color processing? We find that motion processing is intrinsically modulated by color. Color modulated smooth pursuit eye movements produced upon saccading to an aperture containing a surface of coherently moving dots upon a black background. Furthermore, when two surfaces that differed in color were present, one surface was automatically selected based upon a color hierarchy. The strength of that selection depended upon the distance between the two colors in color space. A quantifiable color hierarchy for automatic target selection has wide-ranging implications from sports to advertising to human-computer interfaces.     

CaMKII-γ mediates phosphorylation of BAD at Ser170 to regulate cytokine-dependent survival and proliferation

Phosphorylation of the BH3 (Bcl-2 homology domain 3)-only protein BAD (Bcl-2/Bcl-X(L)-antagonist, causing cell death) can either directly disrupt its association with the pro-survival proteins Bcl-X(L) and/or Bcl-2, or cause association of BAD with 14-3-3 proteins. In the present study, we further characterize phosphorylation of BAD at Ser170, a unique site with unclear function. We provide further evidence that mutation of Ser170 to a phospho-mimetic aspartic acid residue (S170D) can have a profound inhibitory effect on the pro-apoptosis function of BAD. Furthermore, mutated BAD with an alanine substitution inhibited cell proliferation, slowing progression specifically through S-phase. We identify the kinase responsible for phosphorylation at this site as CaMKII-γ (γ isoform of Ca2+/calmodulin-dependent kinase II), but not the other three isoforms of CaMKII, revealing an extraordinary specificity among these closely related kinases. Furthermore, cytokine treatment increased BAD-Ser170-directed CaMKII-γ activity and phosphorylation of CaMKII-γ at an activating site, and CaMKII activity directed to the BAD-Ser170 site was elevated during S-phase. Treating cells with a selective inhibitor of CaMKII caused apoptosis in cells expressing BAD, but not in cells expressing the BAD-S170D mutant. The present study provides support for BAD-Ser170 phosphorylation playing a key role not only in regulating BAD's pro-apoptotic activity, but also in cell proliferation.     

Effects of supercritical fluid CO<Subscript>2</Subscript> and 25 kGy gamma irradiation on the initial mechanical properties and histological appearance of tendon allograft

Tendon allografts, when autograft options are limited or when obtaining an autograft is not aligned with the patients’ best interest, play an important role in tendon and ligament reconstruction. To minimize the risk of infectious disease transmission tissue banks perform screening tests and the allografts cleaned are sterilized. The current study examines and compares the initial mechanical properties and histological appearance of supercritical CO₂ (SCCO₂)-treated and gamma-irradiated porcine extensor tendons. Thirty intact porcine forelimb extensor tendons randomized equally into three groups: control group, gamma-irradiation group, and SCCO₂-treated group. Once treated, histological assessment and histomorphologic measurements were made on the histological sections obtained from each tendon while stiffness and ultimate failure loads were evaluated from tensile testing. Histological evaluation of gamma-irradiated tendons showed significant disruption to the hierarchical morphology of the fascicle bundles, which was not evident in SCCO₂-treated specimens. Histomorphologic measurements showed a significant increase for measured dead space (void) between tendon fibrils of the gamma-irradiated group comparing to both control and SCCO₂ treated groups (p?<?0.01). There was a significant reduction in the ultimate failure load for tendons treated by gamma-irradiation compared to the control group (p?<?0.05). No statistically significant difference was detected between control and SCCO₂-treated tendons in the ultimate failure load. Stiffness values were not significantly different between three-study groups. This study suggests that while gamma-irradiation has a deleterious effect on mechanical properties of tendon tissue, SCCO₂ does not alter the biomechanical properties and the histological structure of porcine extensor tendons.     

Detection of organics using porphyrin embedded nanoporous organosilicas

Molecularly imprinted polymers and silica have been studied as receptor binding site mimics for use in a wide range of separation, catalysis, and detection applications employing transduction mechanisms including conductometric, amperometric, and capacitance. Porphyrins are also well known as sensor components due to the extreme sensitivity of their spectrophotometric characteristics to changes in their immediate environment. We have developed periodic mesoporous organosilicas (PMO) which incorporate a porphyrin into the material for use as an optical indicator of target binding. This material combines the stability, selectivity, and high density of binding sites characteristic of the molecularly imprinted PMO with the sensitivity and selectivity of the porphyrin. We demonstrate binding of p-nitrophenol, p-cresol, 2,4,6-trinitrotoluene, and RDX by the porphyrin-embedded PMOs with selective adsorption of TNT over the other analytes. In addition, the binding of each of the organics by the PMO results in unique changes in the spectrophotometric characteristics of the incorporated porphyrin. These changes can be observed by visual inspection or through the use of fluorescence spectra collected in 96-well format.