Peripheral genotype-phenotype correlations in Asian Indians with type 2 diabetes mellitus

OBJECTIVE

A genome-wide scan of gene expression in leucocytes in Asian Indians with type 2 diabetes was performed and correlated with their known phenotype.

METHODS

Microarray gene profiling of 13,474 sequence-verified, non-redundant human cDNAs was done to study leukocyte gene expression in Asian Indians with type 2 diabetes (DM: n=3) and matched controls (n=3).

RESULTS

Significant differential expression (fold change <0.3 or >3) was noted for 897 genes in DM vs. controls. The 147 known genes in this category belonged to following broad functional groups (%): enzyme (32), nucleic acid binding (22), ligand binding or carrier (10), signal transducer (9), transporter (7), structural protein (6), cell adhesion (3), tumor suppressor (3), transcription factor binding (2), enzyme inhibitor (2), chaperone (2), cell cycle regulator (1), and defense/immunity protein (1). The 20 genes with at least a 3-fold change, annotated with known phenotypic associations in the current gene databank (phenotype association, fold change) were aspartoacylase (Canavan disease, 9.96), growth hormone receptor (Laron dwarfism, idiopathic short stature, 8.25), lipoprotein lipase (familial chylomicronemia syndrome, lipoprotein lipase deficiency, 8.00), vitamin D (1,25- dihydroxyvitamin D3) receptor (involutional osteoporosis, vitamin D resistant rickets, 7.94), intercellular adhesion molecule 1 human rhinovirus receptor (cerebral malaria susceptibility, 7.16), peroxisomal membrane protein 3 35-kDa (Refsum disease, infantile form, Zellweger syndrome-3, 6.00), Bardet-Biedl syndrome 2 (Bardet-Biedl syndrome, 5.87), ribosomal protein S19 (Diamond Blackfan anemia, 5.85), apolipoprotein C-III (hypertriglyceridemia, 5.44), argininosuccinate lyase (argininosuccinicaciduria, 5.22), myosin VA (Griscelli syndrome-type pigmentary dilution with mental retardation, 4.92), lysozyme (renal amyloidosis, 4.17), SAM domain, SH3 domain and nuclear localisation signals 1 (Cherubism, 4.12 ), von Hippel-Lindau syndrome (hemangioblastoma, cerebellar, somatic, von Hippel-Lindau syndrome, 3.94), early-onset breast cancer 1 (BRCA1, papillary serous carcinoma of the peritoneum, 3.73), UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase (inclusion body myopathy, autosomal recessive, sialuria, 3.53), apolipoprotein A-I (amyloidosis, 3 or more types, hypoalphalipoproteinemia, 3.29), midline 1 Opitz/BBB syndrome (Opitz G syndrome, type I, 3.28), ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide (familial hemiplegic migraine, 3.05). Canavan disease, Zellweger syndrome, infantile Refsum disease, Griscelli syndrome, cherubism, breast cancer, peritoneal papillary serous carcinoma, Opitz G/BBB syndrome, and familial hemiplegic migraine (FHM) are phenotypes not previously reported in association with type 2 DM, but whose underlying genes were up-regulated in this peripheral genome scan of Asian Indians.

CONCLUSION

Rare and/or previously unknown phenotypes linked to known genes with significant differential expression in type 2 DM are reported. Further testing of heterogeneity in diabetes phenotype syndromes may reveal common pathogenic mechanisms and potential candidate genes responsible for type 2 DM.

Molecular networks perturbed in a developmental animal model of brain injury

Methylazoxymethanol (MAM) is widely used as a developmental neurotoxin and exposure to its glucoside (i.e., cycasin) is associated with the prototypical neurological disorder western Pacific ALS/PDC. However, the specific molecular targets that play a key role in MAM-induced brain injury remain unclear. To reveal potential molecular networks targeted by MAM in the developing nervous system, we examined characteristic phenotypic changes (DNA damage, cytoarchitecture) induced by MAM and their correlation with gene expression differences using microarray assays (27,648 genes). Three day-old postnatal C57BL/6 mice (PND3) received a single injection of MAM and the cerebellum and cerebral cortex of PND4, 8, 15, and 22 mice were analyzed. DNA damage was detected in both the cerebellum (N7-mGua, TUNEL labeling) and cerebral cortex (N7-mGua) of PND4 mice, but progressive disruption of the cytoarchitecture was restricted to the cerebellum. A majority (>75%) of the genes affected (cerebellum 636 genes, cortex 1080 genes) by MAM were developmentally regulated, with a predominant response early (PND4) in the cerebellum and delayed (PND8 and 15) in the cerebral cortex. The genes and pathways (e.g., proteasome) affected by MAM in the cerebellum are distinct from cortex. The genes perturbed in the cerebellum reflect critical cellular processes such as development (17%), cell cycle (7%), protein metabolism (12%), and transcriptional regulation (9%) that could contribute to the observed cytoarchitectural disruption of the cerebellum. This study demonstrates for the first time that specific genes and molecular networks are affected by MAM during CNS development. Further investigation of these targets will help to understand how disruption of these developmental programs could contribute to chronic brain injury or neurodegenerative disease.

Development of a global stochastic model relating the distribution of individual cell and population physiological states

Our ability to predict the lag (lambda) prior to growth of foodborne pathogens is limited by our lack of understanding of the physiological changes taking place in the individual cell during the adaptation process. Theoretical models have been developed to describe the stochastic nature of individual cells, and probability distributions have been used to assign hypothetical values of the physiological state to individual cells (p(i)). The aim of this study is to develop a polynomial model which will link distributions of p(i) values to the physiological state of the population (h(0)), and thus to the lambda. Risk analysis software was used to simulate values of p(i) for populations of cells drawn from lognormal distributions with parameters alpha and beta, and growth curves were simulated using a modified continuous-discrete-continuous (CDC) model. Values for h(0) were then obtained for each growth curve by fitting with the heterogeneous population model (HPM). Multiple regression analysis was used to develop a polynomial function which described the subsequent h(0) value as a function of alpha and beta (R(2)=0.9957). Outputs from simulations using the polynomial model agree well with results from related stochastic models, and suggest that distributions can accurately describe the physiological state of cell populations.

Thomson scattering measurements of heat flux from ion-acoustic waves in laser-produced aluminum plasmas

Thomson scattering (TS) measurements are performed at different locations in a laser-produced aluminum plasma. Variations of the separation, wavelength shift, and asymmetric distribution of the two ion-acoustic waves are investigated from their spectral-time-resolved TS images. Detailed information on the space-time evolution of the plasma parameters is obtained. Electron distribution and variation of the heat flux in the plasma are also obtained for a steep temperature gradient.

Age-dependence of urinary normal and modified nucleosides in childhood as determined by reversed-phase high-performance liquid chromatography

Modified nucleosides have been characterized as tumor markers for a number of malignant diseases. In order to use these markers in children, the age-dependence of the nucleoside levels in healthy children has to be established and taken into account in diagnostic decisions. In this study, the levels of 12 normal and modified nucleosides in urine of 166 healthy children and adolescents with an age between 1 day and 19 years are determined by reversed-phase HPLC, and age-dependent reference ranges are defined. The urinary nucleoside concentrations are related to the creatinine concentrations, which allows the use of randomly collected urine samples. All nucleoside levels in urine of children decrease with age, most pronounced during the first 4 years of life, and the age-dependence of the reference values of the individual nucleosides can be approximated by a mathematical function y = b(0) + b(1) (1/x) with the regression coefficients b(0) and b(1,) the nucleoside levels y and the age x between 1 year and 19 years. In the very young children, the shifts in the nucleoside concentrations are more differentiated. Starting with low levels on the first day of life, the concentrations of all studied nucleosides rise up to an age of 1-2 months, when they reach their absolute maximum for all age periods, and then decrease.

Application of a virological tracer method for the assessment of pathogen removal by physicochemical treatment and chemical disinfection

Coxsackie B3 (CoxB3) virus was used as a virological tracer for an assessment of the efficiency of pathogen removal by several typical physicochemical treatment and chemical disinfection processes, such as coagulation-filtration, ultra-filtration, and disinfection using chlorine and ozone, with regard to the pathogenic quality of the treated domestic wastewater for reuse purposes. The CoxB3 virus was seeded to sterilized secondary effluent to make a raw water of known pathogenic level. After applying the raw water to each treatment or disinfection process, the residual virus in the finished water was concentrated, and virus assay was carried out by the Tissue Culture Infectious Dose technique. TCID50 was used as an indicative parameter of CoxB3 virus in the raw and treated water. Parallel experiments were also conducted to evaluate the effectiveness of each process for the removal of coliform bacteria. It was noticed from the experiment that both coagulation-filtration and ultrafiltration could achieve substantial removal of TCID50 at about the same level (2-log removal). However, the effect of the two processes on the removal of coliform bacteria was much different: 2-log removal by coagulation-filtration and 4 to 5-log removal by ultrafiltration. The TCID50 removal correlates more closely with the removal of turbidity than that of coliform bacteria. Chlorine was found to be effective in coliform removal but almost had no effect on TCID50. As ozone was applied, a high removal of both coliform bacteria and TCID50 could be obtained.

Patterns of seizures, hippocampal injury and neurogenesis in three models of status epilepticus in galanin receptor type 1 (GalR1) knockout mice

The neuropeptide galanin exhibits anticonvulsant effects in experimental epilepsy. Two galanin receptor subtypes, GalR1 and GalR2, are present in the brain. We examined the role of GalR1 in seizures by studying the susceptibility of GalR1 knockout (KO) mice to status epilepticus (SE) and accompanying neuronal injury. SE was induced in GalR1 KO and wild type (WT) mice by Li-pilocarpine, 60 min electrical perforant path stimulation (PPS), or systemic kainic acid (KA). Seizures were analyzed using Harmonie software. Cell injury was examined by FluoroJade B- and terminal deoxynucleotidyl transferase-mediated uridine triphosphate nick end labeling; neurogenesis was studied using bromodeoxyuridine labeling. Compared with WT littermates, GalR1 KO showed more severe seizures, more profound injury to the CA1 pyramidal cell layer, as well as injury to hilar interneurons and dentate granule cells upon Li-pilocarpine administration. PPS led to more severe seizures in KO, as compared with WT mice. No difference in the extent of neuronal degeneration was observed between the mice of two genotypes in CA1 pyramidal cell layer; however, in contrast to WT, GalR1 KO developed mild injury to hilar interneurons on the side of PPS. KA-induced seizures did not differ between GalR1 KO and WT animals, and led to no injury to the hippocampus in either of experimental group. No differences were found between KO and WT mice in both basal and seizure-induced neuronal progenitor proliferation in all seizure types. Li-pilocarpine led to more extensive glia proliferation in GalR1 KO than in WT, and in both mouse types in two other SE models. In conclusion, GalR1 mediate galanin protection from seizures and seizure-induced hippocampal injury in Li-pilocarpine and PPS models of limbic SE, but not under conditions of KA-induced seizures. The results justify the development and use of GalR1 agonists in the treatment of certain forms of epilepsy.

The novel molecule porcine OSR1 up-regulated expression on porcine endothelial cell by human peripheral blood mononuclear cell activation

INTRODUCTION

Clinical xenotransplantation is being considered to overcome the shortage of human organ donors. In our previous studies, using human-anti-porcine xenogeneic mixed mononuclear cell-endothelial cell cultures with the suppression subtractive hybridization method, we obtained a subtracted cDNA library that included about 300 clones corresponding to up-regulated genes. One porcine sequence showed 81% identity with the human oxidative-stress responsive 1 (OSR1) molecule. The objective of this study was to confirm the gene up-regulation and obtain the full-length sequences.

METHODS

The full-length gene was cloned through the technique of rapid amplification of cDNA ends (RACE). The other methods included bioinformatics analysis and RT-PCR.

RESULTS

RT-PCR confirmed that the gene was up-regulated upon the interactions of human peripheral blood mononuclear cells (PBMCs) and porcine endothelial cells. By SMART RACE technique, we obtained the full-length cDNA of porcine OSR1. The gene is 4333 bp. The open-read frame of 1590 bp encodes 529 amino acid residues. GenBank accession number is AY271356. The gene shows 92.8% nucleotide identity and 95.5% amino acid identity with human OSR1.

CONCLUSION

We obtained the full-length cDNA of porcine OSR1. It was up-regulated on porcine endothelial cells following activation by human PBMCs. We succeeded in constructing a pcDNA-pOSR1 recombinant eukaryotic cell expression vector, the function of which is the subject as our ongoing work.

Nitric oxide is significantly reduced in ex vivo porcine arteries during reverse flow because of increased superoxide production

Oscillatory and negative flows occur normally in the cardiovascular system, which predispose those regions to atherosclerosis. Nitric oxide (NO) production increases in proportion to the magnitude of flow and is known to be athero-protective. What is not known, however, is the effect of flow reversal on NO concentration ([NO]). The hypothesis of the present study is that [NO] is reduced in reverse flow. An additional hypothesis is that the reduction in [NO] is mediated through an increase in superoxide production during flow reversal. These hypotheses were tested in an ex vivo preparation of porcine elastic and muscular arteries. The flow of a physiological solution through the vessels was regulated in the forward and reverse direction and the effluent was assayed for nitrite levels using a combination of a diazo coupling method and high performance liquid chromatography. Our results show that [NO] is significantly reduced during reverse flow. Furthermore, addition of tempol (superoxide dismutase-mimetic) which is a superoxide scavenger returns the [NO] during reverse flow to mirror those of forward flow. These results have important implications since the action of superoxide is implicated in many cardiovascular diseases, and the present finding suggests that flow reversal should be added to the list.

Prolongation of skin allograft survival by combined feeding of donor spleen cells and cyclosporine in mice

BACKGROUND

Oral immune tolerance is a method for inducing donor-specific immunotolerance and prolonging graft survival.

OBJECTIVES

We studied the effect of feeding donor spleen cells in combination with cyclosporine (CsA) on skin allograft survival in mice.

METHODS

Tail skins from BALB/c (H-2d) female mice were transplanted onto C57BL/6 (H-2b) female mice. The animals were divided into four groups, each with eight mice: group I, untreated controls; group II, treated with spleen cells; group III, treated with CsA; and group IV, treated with spleen cells and CsA. All grafts were inspected daily. Rejection was diagnosed when the graft loss was >80% to 90%. The immune responses of C57BL/6 toward donor mice were examined by delayed-type hypersensitivity (DTH).

RESULTS

Survival times of allogeneic skin grafts in groups I, II, III, and IV were 9.9 +/- 0.6, 13.1 +/- 0.6, 14.7 +/- 0.9, and 20.0 +/- 0.7 days, respectively. When compared with group I, the survival times of groups II, III, and IV were prolonged significantly (P < .01). The survival time for group IV was prolonged significantly compared with groups II and III (P < .01). The DTH responses of group IV were decreased significantly in contrast to groups II and III (P < .01).

CONCLUSIONS

Feeding donor spleen cells prolonged the survival of skin allografts in mice; combination with CsA led to further prolongation of skin allograft survival.

Modeling cellular processes with variational Bayesian cooperative vector quantizer

Gene expression of a cell is controlled by sophisticated cellular processes. The capability of inferring the states of these cellular processes would provide insight into the mechanism of gene expression control system. In this paper, we propose and investigate the cooperative vector quantizer (CVQ) model for analysis of microarray data. The CVQ model could be capable of decomposing observed microarray data into many different regulatory subprocesses. To make the CVQ analysis tractable we develop and apply variational approximations. Bayesian model selection is employed in the model, so that the optimal number processes is determined purely from observed micro-array data. We test the model and algorithms on two datasets: (1) simulated gene-expression data and (2) real-world yeast cell-cycle microarray data. The results illustrate the ability of the CVQ approach to recover and characterize regulatory gene expression subprocesses, indicating a potential for advanced gene expression data analysis.

GNB3 gene C825T and ACE gene I/D polymorphisms in essential hypertension in a Kazakh genetic isolate

The Kazakh inhabitants living in Barkol pasture of northeast China belong to a genetic isolate characterized by ethnically homogeneous and a communal pastoral lifestyle. To investigate whether the polymorphisms in the G-protein beta-3 subunit (GNB3) gene and angiotensin-converting enzyme (ACE) gene are associated with essential hypertension (EH), we carried out a case-control study of 290 hypertensive subjects and 244 normotensive (NT) controls randomly selected from Kazakh populations of Barkol. A previous medical history of diabetes and hypertension, and body mass index (BMI) was recorded. Plasma glucose, triglyceride, and cholesterol were measured. The insertion/deletion (I/D) polymorphism of the ACE gene and the C825T polymorphism of the GNB3 gene were determined by the polymerase chain reaction (PCR) technique. The distributions of genotypes and alleles for the two polymorphisms did not differ significantly between the case and control populations, and odds ratio of EH related to the ACE gene D allele and GNB3 gene T allele was not significantly different from 1.0. Logistic regression analysis shows the variation at the GNB3 and ACE did not have any statistically significant synergistic effect on blood pressure (BP). Stratification of NT and untreated hypertensives according to I/D polymorphism of ACE gene and C825T polymorphism of GNB3 gene disclosed no significant difference across genotypes with respect to BMI, glucose, triglyceride, cholesterol, systolic and diastolic BP. In conclusion, the polymorphisms in the GNB3 gene and ACE gene, solely or combined, did not confer a significantly increased risk for the development of EH in the Kazakh isolate of northeast China.

The biological response of MCF7 breast cancer cells to proteosome inhibition or gamma-radiation is unrelated to the level of p53 induction

The p53 tumour suppressor is stabilised following exposure to genotoxic agents, such as gamma-radiation. Cell responses to p53 stabilisation include induction of apoptosis and/or cell cycle arrest. Several studies have suggested that gamma-radiation stabilises p53 by blocking ubiquitin mediated proteolysis. Here we have compared the biological activities of p53 stabilized following exposure to gamma-radiation or treatment with the proteosome inhibitor N-acetyl-leucinyl-leucinyl-norleucinal (ALLN) in MCF7 cells with wild type p53. Stabilisation of p53 by ALLN was reversible and was not blocked by caffeine. Although ALLN was a more effective p53 stabilising agent than gamma-radiation, ALLN was not as effective at inducing cell cycle arrest/apoptosis as gamma-radiation. Although p53 stabilised by ALLN and gamma-radiation were both able to bind DNA and activate transcription, ALLN did not increase expression of BAX, which is involved in p53-induced apoptosis. Therefore, p53 stabilised by different agents is not always biologically active to the same extent and additional alterations triggered by gamma-radiation may enable p53 to activate a subset of critical target genes, such as BAX, which are required for p53 responses.

Shear modulus of porcine coronary artery: contributions of media and adventitia

The epicardial coronary arteries experience significant torsion in the axial direction due to changes in the shape of the heart during the cardiac cycle. The objective of this study was to determine the torsional mechanical properties of the coronary arteries under various circumferential and longitudinal loadings. The coronary artery was treated as a two-layer composite vessel consisting of intima-medial and adventitial layers, and the shear modulus of each layer was determined. Eight porcine hearts were obtained at a local abattoir, and their right coronary and left anterior descending arteries were isolated and tested in vitro with a triaxial torsion machine (inflation, longitudinal stretch, and circumferential twist). After the intact vessel was tested, the adventitia was dissected away, leaving an intact media that was then tested under identical triaxial loading conditions. We proposed a biomechanical analysis to compute the shear modulus of the adventitia from the measured shear moduli of the intact vessel and the media. To validate our predictions, we used four additional hearts in which the shear modulus of the adventitia was measured after dissection of media. Our results show that the shear modulus does not depend on the shear stress or strain but varies linearly with circumferential and longitudinal stresses and in a nonlinear way with the corresponding strains. Furthermore, we found that the shear modulus of the adventitia is larger than that of the intact vessel, which is larger than the vessel media. These results may have important implications for baroreceptor sensitivity, circulation of the vasa vasorum, and coronary dissection.