Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait

When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice.     

Quantitative Trait Locus Analysis Implicates CD4+/CD44high Memory T Cells in the Pathogenesis of Murine Autoimmune Pancreatitis

The mouse strain MRL/MpJ is prone to spontaneously develop autoimmune pancreatitis (AIP). To elucidate the genetic control towards the development of the phenotype and to characterize contributions of immunocompetent cell types, MRL/MpJ mice were interbred with three additional strains (BXD2/TYJ, NZM2410/J, CAST/EIJ) for four generations in an advanced intercross line. Cellular phenotypes were determined by flow cytometric quantification of splenic leukocytes and complemented by the histopathological evaluation of pancreatic lesions. An Illumina SNP array was used for genotyping. QTL analyses were performed with the R implementation of HAPPY. Out of 41 leukocyte subpopulations (B cells, T cells and dendritic cells), only three were significantly associated with AIP: While CD4⁺/CD44^high memory T cells and CD4⁺/CD69⁺ T helper (Th) cells correlated positively with the disease, the cytotoxic T cell phenotype CD8⁺/CD44^low showed a negative correlation. A QTL for AIP on chromosome 2 overlapped with QTLs for CD4⁺/CD44^high and CD8⁺/CD44^high memory T cells, FoxP3⁺/CD4⁺ and FoxP3⁺/CD8⁺ regulatory T cells (Tregs), and CD8⁺/CD69⁺ cytotoxic T cells. On chromosome 6, overlapping QTLs for AIP and CD4⁺/IL17⁺ Th17 cells and again FoxP3⁺/CD8⁺ Tregs were observed. In conclusion, CD4⁺/CD44^high memory T cells are the only leukocyte subtype that could be linked to AIP both by correlation studies and from observed overlapping QTL. The potential role of this cell type in the pathogenesis of AIP warrants further investigations.     

Crystal structure of inositol 1-phosphate synthase from Mycobacterium tuberculosis,a key enzyme in phosphatidylinositol synthesis

Phosphatidylinositol (PI) is essential for Mycobacterium tuberculosis viability and the enzymes involved in the PI biosynthetic pathway are potential antimycobacterial agents for which little structural information is available. The rate-limiting step in the pathway is the production of (L)-myo-inositol 1-phosphate from (D)-glucose 6-phosphate, a complex reaction catalyzed by the enzyme inositol 1-phosphate synthase. We have determined the crystal structure of this enzyme from Mycobacterium tuberculosis (tbINO) at 1.95 A resolution, bound to the cofactor NAD+. The active site is located within a deep cleft at the junction between two domains. The unexpected presence of a zinc ion here suggests a mechanistic difference from the eukaryotic inositol synthases, which are stimulated by monovalent cations, that may be exploitable in developing selective inhibitors of tbINO.     

Anti-Helicobacter pylori activities of six Iranian plants

BACKGROUND: Helicobacter pylori is the major worldwide cause of bacterial gastrointestinal infections in adults and children. Antibiotic therapy and a combination of two or three drugs have been widely used to eradicate these infections. However, development of drug resistance in bacteria calls for new sources of drugs, and plants seem to be a logical source of new antibacterial compounds. METHODS: The anti-H. pylori activities of six native Iranian plants (Glycyrrhiza aspera, Juglans regia, Ligustrum vulgare, Thymus kotschyanus, Trachyspermum copticum and Xanthium brasilicum) and seven antibiotics were determined against 70 clinical isolates from children using the disk susceptibility assay. Minimum inhibitory concentrations were also measured for the biologically active extracts. One extract with the best anti-H. pylori activity was fractionated by silica gel and thin layer chromatography and the active compounds were identified by hydrogen nuclear magnetic resonance ((1)HNMR) spectroscopy. RESULTS: All plant extracts showed anti-H. pylori activity by the disk sensitivity method, but the most active extracts were those from X. brasilicum and T. copticum. In fact, the anti-H. pylori activities of the two extracts were superior to the disk antibiotic susceptibility profile. Minimum inhibitory concentrations were within the range of 31.25-250 micro g/ml. Fractionation and chemical identification of the extract from X. brasilicum showed the presence of two substances, a flavonoid and a xanthanolide. CONCLUSIONS: Due to the rise in antibiotic resistance, new sources of anti-H. pylori drugs are needed. The use of medicinal plants and/or their chemical components may have potential benefit in eradicating such problems.     

Evaluating the mechanism underlying antitumor effect of interleukin 27 on B cells of chronic lymphocytic leukemia patients

Chronic lymphocyte leukemia (CLL) is a B-cell malignancy resisted to apoptosis. Recently, some studies indicated that cytokines such as interleukin 27 (IL-27) can reduce B-cell proliferation. The aim of this study is to evaluate the mechanism underlying the proapoptotic effect of IL-27 on B cells of patients with CLL in comparison with B cells of normal subjects. The effect of IL-27 on the antitumor activity of natural killer (NK) and T cells was also evaluated. Peripheral blood mononuclear cells (PBMCs) were isolated from 35 patients with CLL and 15 normal subjects. B cells and PBMCs were cocultured with IL-27 and B cells apoptosis to evaluate proliferation. Both messenger RNA and protein expression of IL-27 and IL-27 receptor were determined using flow cytometry and real-time polymerase chain reaction analysis. To evaluate the apoptotic effect of IL-27 on B cells of patients with CLL, Annexin V-FITC and 7-AAD (BioLegend) fluorescent dyes were used. In addition, the IL-27 effect on activation of T cell and NK cell was determined by determining CD96 molecule expression. IL-27 and IL-27 receptor expression in patients with CLL was significantly lower than that of normal subjects (p < .05). IL-27 enhanced apoptosis of B cells in patients with CLL (p < .05) but this effect was not significantly observed in B cells of normal subjects (p > .05). Consequently, IL-27 reduced the proliferation of B cells and enhanced NK cell activity (p < .05). IL-27, through inducing apoptosis, can exert an inhibitory effect on cancer B cells of CLL patients with minimal effect on normal B cells.     

Association of Vitamin D Receptor Polymorphisms (FokI (Rs2228570), ApaI (Rs7975232), BsmI (Rs1544410), and TaqI (Rs731236)) with Gastric Cancer in a Kurdish Population from West of Iran

Background:The association of 1,25-dihydroxy vitamin D3 (1,25(OH)2D3) and its receptor, vitamin D receptor (VDR), with cancer types have been studied. However, there are controversial findings regarding the association of specific VDR polymorphisms with different kinds of cancers. In the current study, we investigated the association of VDR polymorphisms (Fok1 (rs2228570), ApaI (rs7975232), BsmI (rs1544410), and TaqI (rs731236)) with the risk of gastric cancer in a Kurdish population of Kermanshah in Iran for the first time. Methods:In this case-control study, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used in 99 gastric cancer patients and 100 healthy subjects as controls.Results:The frequencies of f (FokI), b (BsmI), t (TaqI), and a (ApaI) alleles were: 55.6%, 27.3%, 62.1%, and 44.95% in the patient group, respectively and 42%, 29.5%, 54.5%, and 46.0% in the control group, respectively. Analysis of the results indicated that there was a positive association between the frequency of FokI genotypes with gastric cancer risk (p= 0.021). However, no statistically significant association of BsmI, Taq1, and ApaI polymorphisms of VDR was detected in gastric patients when compared with healthy individuals.Conclusion:VDR-FokI polymorphism could increase the risk of GC development and predispose to the disease by mechanisms.Key Words: Gastric cancer, PCR-RFLP, Polymorphism, Vitamin D receptor     

Localizing confined epileptic foci in patients with an unclear focus or presumed multifocality using a component-based EEG-fMRI method

Precise localization of epileptic foci is an unavoidable prerequisite in epilepsy surgery. Simultaneous EEG-fMRI recording has recently created new horizons to locate foci in patients with epilepsy and, in comparison with single-modality methods, has yielded more promising results although it is still subject to limitations such as lack of access to information between interictal events. This study assesses its potential added value in the presurgical evaluation of patients with complex source localization. Adult candidates considered ineligible for surgery on account of an unclear focus and/or presumed multifocality on the basis of EEG underwent EEG-fMRI. Adopting a component-based approach, this study attempts to identify the neural behavior of the epileptic generators and detect the components-of-interest which will later be used as input in the GLM model, substituting the classical linear regressor. Twenty-eight sets interictal epileptiform discharges (IED) from nine patients were analyzed. In eight patients, at least one BOLD response was significant, positive and topographically related to the IEDs. These patients were rejected for surgery because of an unclear focus in four, presumed multifocality in three, and a combination of the two conditions in two. Component-based EEG-fMRI improved localization in five out of six patients with unclear foci. In patients with presumed multifocality, component-based EEG-fMRI advocated one of the foci in five patients and confirmed multifocality in one of the patients. In seven patients, component-based EEG-fMRI opened new prospects for surgery and in two of these patients, intracranial EEG supported the EEG-fMRI results. In these complex cases, component-based EEG-fMRI either improved source localization or corroborated a negative decision regarding surgical candidacy. As supported by the statistical findings, the developed EEG-fMRI method leads to a more realistic estimation of localization compared to the conventional EEG-fMRI approach, making it a tool of high value in pre-surgical evaluation of patients with refractory epilepsy. To ensure proper implementation, we have included guidelines for the application of component-based EEG-fMRI in clinical practice.     

Nanoparticles in cancer immunotherapies: An innovative strategy

Cancer has been one of the most significant causes of mortality, worldwide. Cancer immunotherapy has recently emerged as a competent, cancer-fighting clinical strategy. Nevertheless, due to the difficulty of such treatments, costs, and off-target adverse effects, the implementation of cancer immunotherapy described by the antigen-presenting cell (APC) vaccine and chimeric antigen receptor T cell therapy ex vivo in large clinical trials have been limited. Nowadays, the nanoparticles theranostic system as a promising target-based modality provides new opportunities to improve cancer immunotherapy difficulties and reduce their adverse effects. Meanwhile, the appropriate engineering of nanoparticles taking into consideration nanoparticle characteristics, such as, size, shape, and surface features, as well as the use of these physicochemical properties for suitable biological interactions, provides new possibilities for the application of nanoparticles in cancer immunotherapy. In this review article, we focus on the latest state-of-the-art nanoparticle-based antigen/adjuvant delivery vehicle strategies to professional APCs and engineering specific T lymphocyte required for improving the efficiency of tumor-specific immunotherapy.