Genetic diagnosis of cancer by fuzzy-rough gene selection and the complementary hierarchical fuzzy classifier

Gene expression data have extremely high dimensionality with respect to traditional classifiers which causes not to be used efficiently. In this paper a Fuzzy-Rough Gene Selection and Complementary Hierarchical Fuzzy classifier (FRGS-CHF) to classify the gene expression data as a new methodology is proposed. First, some relevant genes are selected using fuzzy-rough attribute selection method. After removing redundant genes, a new complementary hierarchical fuzzy classifier is proposed. The complementary learning mechanism refers to positive and negative learning which are found in the human brain hippocampus. FRGS-CHF is made-up of two parallel hierarchical fuzzy systems; the first is trained with positive samples whilst the other is treated with negative samples. In contrast to many other methods such as statistical or neural networks, FRGS-CHF provides greater interpretability. It does not rely on the assumption of underlying data distribution. Using complementary and hierarchical approaches, the proposed method exploits the lateral inhibition between output classes and considers the problem as a multidimensional problem. Benchmarked datasets are used to demonstrate the validity and advantages of the proposed method over the other existing methods in terms of the accuracy, better transparency, time efficiency together with fewer fuzzy rules and parameters.     

The rat NK cell receptors Ly49s4 and Ly49i4 recognize nonclassical MHC-I molecules on Listeria monocytogenes-infected macrophages

Ly49 receptors in rodents, like KIRs in humans, regulate NK cell activity. Although inhibitory Ly49 receptors clearly recognize MHC-I molecules, ligands for the activating Ly49 receptors are less well defined. Here, we show that the activating Ly49s4 and the inhibitory Ly49i4 receptors recognize nonclassical MHC-I molecules on the rat macrophage cell line R2 (RT1(d)). Listeria infection of R2 macrophages led to increased expression of classical and nonclassical MHC-I molecules. Coincubation of these infected cells with reporter cells expressing Ly49i4 or Ly49s4 increased the reporter cell responses. These responses were blocked by mAb OX18 (anti-MHC-I) and AAS1 (anti-nonclassical MHC-I). IFN-γ treatment of normal R2 cells also increased the MHC-I expression and enhanced the reporter cell responses. These results suggest that activating and inhibitory Ly49 receptors monitor MHC-I expression on Listeria-infected cells.     

Transplantation of retrovirally transduced bone marrow prevents autoimmune disease in aged mice by peripheral tolerance mechanisms

Transplantation of bone marrow (BM) engineered to express self-antigen has been shown to protect 100% of young mice from myelin oligodendrocyte glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE), with thymic clonal deletion as a tolerance mechanism. Here, we asked whether aged mice can also be tolerised following transplantation with self-antigen-engineered BM and whether castration-induced thymus regrowth can enhance this outcomes. Then, 50% of aged mice were protected from EAE regardless of castration-induced thymus regrowth. EAE-free and diseased mice demonstrated MOG-specific lymphocyte proliferation and antibody production regardless of castration-induced thymus regrowth, consistent with lack of intrathymic deletion of self-antigen-reactive T cells. Although low chimerism levels (?相似文献   

Antihyperglycemic and antihyperlipidemic effect of Rumex patientia seed preparation in streptozotocin-diabetic rats

Background and objective:Rumex patientia (RP) could exert beneficial health effects to ameliorate metabolic diseases. The effect of subchronic feeding of RP seeds was evaluated on serum glucose and lipid profile in streptozotocin (STZ)-diabetic rats. Methods: Wistar rats were divided into control, RP-treated control, diabetic, glibenclamide-treated diabetic, and RP-treated diabetic groups. For induction of diabetes, streptozotcin was administered at a dose of 60 mg/kg. Meanwhile, RP-treated groups received RP seed powder mixed with standard pelleted food at a weight ratio of 6% for 4 weeks. Serum glucose and lipid levels were determined before the study and at 2nd and 4th weeks after the study in addition to the oxidative stress markers in hepatic tissue. Results: Serum glucose was significantly lower in RP-treated diabetic rats at 2nd and 4th weeks as compared to untreated diabetics (p < 0.05 and p < 0.01, respectively). Serum total cholesterol and triglyceride levels did not show significant reductions in RP-treated diabetic rats as compared to untreated diabetics. Serum HDL-cholesterol, however, significantly increased (p < 0.05) and LDL-cholesterol showed a significant reduction (p < 0.05) in RP-treated diabetic rats as compared to untreated diabetics (p < 0.05). RP also attenuated the increased malondialdehyde (MDA) content and reduced activity of superoxide dismutase (SOD) in hepatic tissue. Conclusion: Subchronic treatment of diabetic rats with RP could lessen the abnormal changes in blood glucose level and to improve lipid profile regarding HDL- and LDL-cholesterol in part due to its attenuation of lipid peroxidation in hepatic tissue.     

In vitro sensitivity of Blastocystis hominis to garlic, ginger, white cumin, and black pepper used in diet

To determine the growth pattern and in vitro susceptibility of Blastocystis hominis to metronidazole (MTZ), garlic, ginger, white cumin, and black pepper. Stool specimens were collected from 16 irritable bowel syndrome (IBS) and 10 controls between July–November 2010. Stool microscopy and culture for B. hominis was performed. Drug susceptibility assays was done using 0.01 and 0.1 mg/ml of MTZ, garlic, ginger, white cumin, and black pepper. Effect was assessed on B. hominis culture after 48 h. Stool DNA was extracted using stool DNA extraction kit (Qiagen) and polymerase chain reaction (PCR) done using subtype-specific sequence-tagged-site primers. B. hominis genotype 3 and coinfection of 1 and 3 tended to grow well in culture compared to isolated type 1 infection. Exposed to MTZ at a concentration of 0.01 mg/ml, 38% (6/16) B. hominis from IBS did not grow in culture compared to 100% (10/10) of B. hominis from control (p = 0.001). When they were exposed to MTZ at 0.1 mg/ml, 56% (9/16) B. hominis from IBS did not grow in cultures compared to 100% (10/10) from control (p = 0.01). Forty-four percent (7/16) B. hominis from IBS did not grow in culture compared to 100% (10/10) B. hominis from control when exposed to garlic at a concentration of 0.01 mg/ml (p = 0.003) and following exposure to garlic at 0.1 mg/ml, 38% (6/16) B. hominis from IBS did not grow in cultures compared to 100% (10/10) from control (p = 0.001). B. hominis isolates from IBS had a cell count of 6,625 at a MTZ concentration of 0.01 mg/ml that reduced to 1,250 as MTZ concentration was increased to 0.1 mg/ml (p = 0.08). B. hominis from IBS with a mean cell count of 3 × 10⁵ at baseline decreased to 1 × 10⁴ when exposed to garlic at 0.01 mg/ml (p < 0.001) and to 1 × 10³ (p < 0.001) when garlic was 0.1 mg/ml. B. hominis from IBS cell count decreased to 1 × 10⁵ when exposed to white cumin at 0.01 mg/ml (p = 0.01) and to 1 × 10⁵ (p < 0.001) when white cumin was 0.1 mg/ml. Exposed to black pepper at 0.1 mg/ml, cell count of B. hominis from IBS decreased to 1 × 10⁵ (p = 0.01). B. hominis from IBS decreased to 1.3 × 10⁵ exposed to ginger at 0.01 mg/ml (p = 0.001). B. hominis isolates were mostly genotypes 3, type 1 and 3 coinfection, and non-typeable B. hominis isolates. B. hominis isolates from IBS mostly genotype 1 demonstrated an increased sensitivity to garlic at 0.01 mg/ml with a B. hominis cell count of 3,714 compared to 6,142 when exposed to 0.01 mg/ml of MTZ. However, this sensitivity did not increase as garlic concentration was increased to 0.1 mg/ml, for B. hominis cell count was 6,000 compared to 1,428 as MTZ was increased to 0.1 mg/ml.     

Genetic polymorphism at the C-terminal domain (region III) of knob-associated histidine-rich protein (KAHRP) of Plasmodium falciparum in isolates from Iran

The knob-associated histidine-rich protein (KAHRP) plays a major role in the virulence of Plasmodium falciparum and is one of the targets for molecular therapy. The primary structure of KAHRP of P. falciparum consists of three domains (regions I–III), of which the C-terminal domain (region III) is the most polymorphic segment of this protein. One of the main obstacles is genetic diversity in designing and developing of malaria control strategies such as molecular therapy and vaccines. The primary objective of the present study was to investigate and analyze the extent of genetic polymorphism at the region III of KAHRP of P. falciparum in isolates from Iran. A fragment of the kahrp gene spanning the C-terminal domain was amplified by nested PCR from 50 P. falciparum isolates collected from two malaria endemic areas of Iran during 2009 to August 2010 and sequenced. In this study, three allelic types were observed at the C-terminal domain of KAHRP on the basis of the molecular weight of nested PCR products and the obtained sequencing data. The presence of multiple alleles of the kahrp gene indicates that several P. falciparum strains exist in the malaria endemic areas of Iran. Our findings will be valuable in the design and the development of the molecular therapeutic reagents for falciparum malaria.     

Ultrastructural and molecular characterization of Sarcocystis isolated from camel (Camelus dromedarius) in Iran

Sarcocystis cameli was first described in one-humped camels (Camelus dromedarius), and it is the only species which have so far reported in camels. Although more than 150 species of Sarcocystis were described in various animals, only a few data on camel Sarcocystis ultrastructure were published, and this report is the first for molecular information (DNA sequence and RLFP digestion pattern). The main objective of the present work is to characterize Sarcocystis isolated from camels by electron microscopy and PCR-RFLP methods. Muscle samples were taken from the fresh esophagus, diaphragm, skeletal muscles, and heart of one-humped camels (C. dromedarius) slaughtered in abattoirs of Tehran and Ghazvin provinces, Iran. The dissection and trypsin digestion techniques were applied for the detection of the cysts. The infected samples were fixed in glutaraldehyde and/or frozen at −20°C until use for ultrastructural and molecular studies, respectively. The ultrastructural and molecular studies were carried out contemporaneously. The 18S rRNA gene of the parasites was amplified by PCR. The PCR products were cloned into a pTZ57R/T and sequenced. In addition, the PCR products were digested separately with each of the four restriction enzymes for RFLP. Our results indicated that only microcysts were observed in muscle samples. The microcysts were white, elongated, spindled, and a few spiral-shaped, with mean size 260 × 75 μm which are identical with S. cameli. The ultrastructure of microcyst wall had many non-branched finger-like protrusions irregularly folded. There was a 600-bp specific band amplified after PCR with specific primers. The molecular data for camel Sarcocystis is reported for the first time in Iran and the world.     

B cells and autoimmunity

There is a growing appreciation for the role for B cells in autoimmune disorders in which inflammation is driven by T cells, in addition to the well-established role for B cells in autoimmune disorders characterized by pathogenic auto-antibodies. Current information on tolerance checkpoints in B cells, B cell depletion, BAFF blockade, regulatory B cells and clonal ignorance mediated by the SIAE/Siglec pathway will be reviewed.     

A novel function for programmed death ligand-1 regulation of angiogenesis

Programmed death ligand-1 (PD-L1) plays a critical role in T-cell regulatory function. Here, we report a newly discovered effect of PD-L1 on angiogenesis. We demonstrate that PD-L1 and its receptor CD80, but not PD-1, are expressed by primary murine lung and heart vascular endothelial cells and the miscrovascular endothelial cell line (MS1) at both the mRNA and protein levels in vitro. The inhibition of PD-L1 or CD80 expression in MS1 cells, by small-interfering RNA transfection, led to a significant up-regulation of vascular endothelial growth factor receptor 2 expression and cell proliferation levels in MS1 cells. Furthermore, MS1 cells were found to have a significantly lower proliferation and vascular endothelial growth factor receptor 2 expression levels when they were co-cultured with PD-L1-expressing normal corneal epithelial cells, as compared to MS1 cells co-cultured with PD-L1(-/-) corneal epithelial cells. In a suture-induced corneal angiogenesis model, we observed a significantly higher level of angiogenic response in PD-L1(-/-) knockout mice as compared to wild-type mice, although there was no significant difference in the expression of inflammatory cytokines (interleukin-1α, interleukin-1β, or tumor necrosis factor-α) or the infiltration of innate immune cells (neutrophils and macrophages) between the two groups. We conclude that the expression of PD-L1 in both vascular endothelial cells and corneal epithelial cells regulates corneal angiogenesis.