Potentiation of Nitric Oxide-induced Apoptosis in P53-/- Vascular Smooth Muscle Cells

American Journal of Physiology. Cell Physiology. Mar, 2002  |  Pubmed ID: 11832348

The functional role of p53 in nitric oxide (NO)-mediated vascular smooth muscle cell (VSMC) apoptosis remains unknown. In this study, VSMC from p53-/- and p53+/+ murine aortas were exposed to exogenous or endogenous sources of NO. Unexpectedly, p53-/- VSMC were much more sensitive to the proapoptotic effects of NO than were p53+/+ VSMC. Furthermore, this paradox appeared to be specific to NO, because other proapoptotic agents did not demonstrate this differential effect on p53-/- cells. NO-induced apoptosis in p53-/- VSMC occurred independently of cGMP generation. However, mitogen-activated protein kinase (MAPK) pathways appeared to play a significant role. Treatment of the p53-/- VSMC with S-nitroso-N-acetylpenicillamine resulted in a marked activation of p38 MAPK and, to a lesser extent, of c-Jun NH(2)-terminal kinase, mitogen-activated protein kinase kinase (MEK) 1/2, and p42/44 (extracellular signal-regulated kinase, ERK). Furthermore, basal activity of the MEK-p42/44 (ERK) pathway was increased in the p53+/+ VSMC. Inhibition of p38 MAPK with SB-203580 or of MEK1/2 with PD-98059 blocked NO-induced apoptosis. Therefore, p53 may protect VSMC against NO-mediated apoptosis, in part, through differential regulation of MAPK pathways.

Novel Role of Vitamin K in Preventing Oxidative Injury to Developing Oligodendrocytes and Neurons

The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Jul, 2003  |  Pubmed ID: 12843286

Oxidative stress is believed to be the cause of cell death in multiple disorders of the brain, including perinatal hypoxia/ischemia. Glutamate, cystine deprivation, homocysteic acid, and the glutathione synthesis inhibitor buthionine sulfoximine all cause oxidative injury to immature neurons and oligodendrocytes by depleting intracellular glutathione. Although vitamin K is not a classical antioxidant, we report here the novel finding that vitamin K1 and K2 (menaquinone-4) potently inhibit glutathione depletion-mediated oxidative cell death in primary cultures of oligodendrocyte precursors and immature fetal cortical neurons with EC50 values of 30 nm and 2 nm, respectively. The mechanism by which vitamin K blocks oxidative injury is independent of its only known biological function as a cofactor for gamma-glutamylcarboxylase, an enzyme responsible for posttranslational modification of specific proteins. Neither oligodendrocytes nor neurons possess significant vitamin K-dependent carboxylase or epoxidase activity. Furthermore, the vitamin K antagonists warfarin and dicoumarol and the direct carboxylase inhibitor 2-chloro-vitamin K1 have no effect on the protective function of vitamin K against oxidative injury. Vitamin K does not prevent the depletion of intracellular glutathione caused by cystine deprivation but completely blocks free radical accumulation and cell death. The protective and potent efficacy of this naturally occurring vitamin, with no established clinical side effects, suggests a potential therapeutic application in preventing oxidative damage to undifferentiated oligodendrocytes in perinatal hypoxic/ischemic brain injury.

Plasmid DNA Encoding Antigens of Infectious Bursal Disease Viruses Induce Protective Immune Responses in Chickens: Factors Influencing Efficacy

Virus Research. Dec, 2003  |  Pubmed ID: 14609631

The complete polyprotein (VP2/4/3) and VP2 genes of two infectious bursal disease viruses (IBDVs) (one attenuated strain JD1 and one virulent strain ZJ2000) were amplified by long and accurate polymerase chain reaction (LA-PCR), cloned, sequenced and inserted into plasmids pCI and pcDNA3 under the control of human cytomegalovirus (hCMV) immediate early enhancer and promoter. A series of DNA vaccine preparations were made using liposome as the adjuvant to examine their immunogenicity. Although VP2 is the main protective immunogen of IBDV, DNA encoding VP2 initiated a very low level of neutralizing antibody and only protected chickens from clinical outbreak and morality, but not bursal damage. In contrast, DNA encoding VP2/4/3 induced neutralizing antibody and satisfactory protection against virulent IBDV. Recombinant plasmids encoding the polyprotein gene of strain ZJ2000 were more efficient at inducing an immune response than that of strain JD1. Polyprotein expressed by the pCI vector induced better immune response than that expressed by the pcDNA3. Delivery of DNA through intramuscular and/or intradermal routes elicited much higher protective responses than that of oral and eyedrop routes. Most of the chickens vaccinated with high doses of DNA were protected from challenge. Additionally, the immune response to the DNA vaccine was significantly enhanced by a liposome adjuvant. These results indicate that the source of the target genes (from different IBDV strains), the eukaryotic expression vector, the adjuvant, the delivery route and the dosage might play a role of varying degree in influencing the efficacy of the DNA vaccine against IBDV.

School-based Obesity Screening in Rural Appalachia

Preventive Medicine. Dec, 2003  |  Pubmed ID: 14636788

Although identification of obesity during childhood is strongly recommended for the prevention of adult disease, access to obesity screening for children is almost exclusively through physicians' office visits. We examined the feasibility and utility of conducting a school-based obesity and cardiovascular disease (CVD) risk factor screening program in a rural Appalachian population.

Guideline Interaction: a Study of Interactions Among Drug-disease Contraindication Rules

AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium. 2003  |  Pubmed ID: 14728406

To study the interactions among the drug-disease contraindiction guidelines in a real clinical setting by using clinical databases.

An Oligosaccharide at the C-terminus of the F-specific Domain in the Stalk of the Human Parainfluenza Virus 3 Hemagglutinin-neuraminidase Modulates Fusion

Virus Research. Feb, 2004  |  Pubmed ID: 14749183

The promotion of membrane fusion by the fusion (F) protein of human parainfluenza virus 3 (hPIV3) is dependent on a virus-specific contribution from the hemagglutinin-neuraminidase (HN) protein. By evaluation of chimeric hPIV3-Newcastle disease virus (NDV) HN proteins, we have previously shown that hPIV3-F-specificity is determined by a domain that extends from the middle of the membrane anchor to the 82nd residue in the ectodomain [Virology 209, (1995) 457; Arch. Virol. 13 (1997) 115]. If the corresponding NDV-derived residues replace the two C-terminal residues in this domain, no fusion is detected. However, these substitutions restore a glycosylation site present in NDV HN, but not in hPIV3 HN. Deletion of this site from a nested set of chimeras with hPIV3-derived N-terminal portions of decreasing length partially restores fusion, suggesting that an oligosaccharide near the top of hPIV3 HN stalk modulates fusion. In addition, further mutational analyses show that a chimera with only 125 N-terminal hPIV3-derived residues (72 in the stalk) actually promotes fusion more efficiently than the wt protein. These findings localize the C-terminus of the F-specific domain in hPIV3 HN a full 10 residues closer to the membrane than previously shown.

Glutathione Peroxidase-catalase Cooperativity is Required for Resistance to Hydrogen Peroxide by Mature Rat Oligodendrocytes

The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Feb, 2004  |  Pubmed ID: 14973232

Oxidative mechanisms of injury are important in many neurological disorders, including hypoxic-ischemic brain damage. Cerebral palsy after preterm birth is hypothesized to be caused by hypoxic-ischemic injury of developing oligodendrocytes (OLs). Here we examined the developmental sensitivity of OLs to exogenous hydrogen peroxide (H2O2) with stage-specific rat oligodendrocyte cultures. We found that H2O2 itself or that generated by glucose oxidase was more toxic to developing than to mature OLs. Mature OLs were able to degrade H2O2 faster than developing OLs, suggesting that higher antioxidant enzyme activity might be the basis for their resistance. Catalase expression and activity were relatively constant during oligodendrocyte maturation, whereas glutathione peroxidase (GPx) was upregulated with a twofold to threefold increase in its expression and activity. Thus, it appeared that the developmental change in resistance to H2O2 was caused by modulation of GPx but not by catalase expression. To test the relative roles of catalase and GPx in the setting of oxidative stress, we measured enzyme activity in cells exposed to H2O2 and found that H2O2 induced a decrease in catalase activity in developing but not in mature OLs. Inhibition of GPx by mercaptosuccinate led to an increase in the vulnerability of mature OLs to H2O2 as well as a reduction in catalase activity. Finally, H2O2-dependent inactivation of catalase in developing OLs was prevented by the GPx mimic ebselen. These data provide evidence for a key role for GPx-catalase cooperativity in the resistance of mature OLs to H2O2-induced cell death.

Mutated Form of the Newcastle Disease Virus Hemagglutinin-neuraminidase Interacts with the Homologous Fusion Protein Despite Deficiencies in Both Receptor Recognition and Fusion Promotion

Journal of Virology. May, 2004  |  Pubmed ID: 15113911

The Newcastle disease virus (NDV) hemagglutinin-neuraminidase (HN) protein mediates attachment to cellular receptors. The fusion (F) protein promotes viral entry and spread. However, fusion is dependent on a virus-specific interaction between the two proteins that can be detected at the cell surface by a coimmunoprecipitation assay. A point mutation of I175E in the neuraminidase (NA) active site converts the HN of the Australia-Victoria isolate of the virus to a form that can interact with the F protein despite negligible receptor recognition and fusion-promoting activities. Thus, I175E-HN could represent a fusion intermediate in which HN and F are associated and primed for the promotion of fusion. Both the attachment and fusion-promoting activities of this mutant HN protein can be rescued either by NA activity contributed by another HN protein or by a set of four substitutions at the dimer interface. These substitutions were identified by the evaluation of chimeras composed of segments from HN proteins derived from two different NDV strains. These findings suggest that the I175E substitution converts HN to an F-interactive form, but it is one for which receptor binding is still required for fusion promotion. The data also indicate that the integrity of the HN dimer interface is critical to its receptor recognition activity.

Developmental Up-regulation of MnSOD in Rat Oligodendrocytes Confers Protection Against Oxidative Injury

The European Journal of Neuroscience. Jul, 2004  |  Pubmed ID: 15245476

Periventricular leukomalacia, the predominant pathological lesion underlying cerebral palsy in premature infants, is thought to be the result of hypoxic-ischemic injury to the cerebral white matter. The main cell type injured is the developing oligodendrocyte (OL), which has been shown to be more sensitive than mature OLs to both excitotoxic and oxidative mechanisms of injury. A maturation dependence of OL vulnerability to cystine deprivation-induced glutathione depletion has been previously demonstrated in culture. We hypothesized that mitochondria could be involved in this toxicity by generating superoxide and that increased superoxide dismutase (SOD) activity in mature OLs may account for their greater resistance. Cystine deprivation toxicity was found to be associated with mitochondrial dysfunction and intracellular superoxide accumulation in developing OLs. CuZnSOD protein expression and enzyme activity was similar along the OL lineage. In contrast, MnSOD was up-regulated in mature OLs, as manifested by a 53% increase in its expression and a four-fold increase in its activity. Overexpressing MnSOD in developing OLs was associated with a protective effect on mitochondrial membrane potential and a decrease in cell death induced by mild cystine deprivation. The greater challenge presented by total cystine deprivation was resistant to MnSOD overexpression and appeared to be related to hydrogen peroxide toxicity. These data suggest a primary involvement of superoxide in glutathione depletion toxicity in developing OLs, and suggest an important role for MnSOD in the resistance observed in mature OLs.

Fifty-year Trends in Serial Body Mass Index During Adolescence in Girls: the Fels Longitudinal Study

The American Journal of Clinical Nutrition. Aug, 2004  |  Pubmed ID: 15277168

A decline in the age at menarche was recently reported for US girls. Although it is possible that this recent drop stems from the concurrent increase in childhood obesity, few longitudinal studies of growth and development have been undertaken to specifically address the temporal relation between growth, adiposity, and the age at menarche.

Nitric Oxide-induced Cell Death in Developing Oligodendrocytes is Associated with Mitochondrial Dysfunction and Apoptosis-inducing Factor Translocation

The European Journal of Neuroscience. Oct, 2004  |  Pubmed ID: 15379992

Reactive nitrogen species are thought to be involved in both hypoxic-ischemic and cytokine-induced brain injury, including periventricular leukomalacia (PVL), the major pathological substrate of cerebral palsy in premature infants. PVL appears to be the result of perinatal inflammatory events and hypoxic-ischemic injury to the cerebral white matter. The chronic disturbance of myelination resulting from PVL suggests that developing oligodendrocytes (OLs) are involved in its pathogenesis. We hypothesized that nitric oxide (NO) could participate in the pathogenesis of PVL through a toxic effect on developing OLs. Using primary cultures of highly enriched OLs we found that NO is toxic to developing OLs (O4+, O1-, MBP-), with an EC50 value of 236 +/- 125 microm of DETANOnoate. Peroxynitrite formation does not appear to be involved in NO toxicity in developing OLs, as determined by the failure of peroxynitrite scavengers as well as superoxide dismutase overexpression to prevent NO-induced toxicity. Similarly, several pathways involving PARP, excitotoxicity, guanylyl cyclase and caspase activation were not related to NO toxicity to developing OLs. NO toxicity to OLs resulted in ATP depletion and loss of mitochondrial membrane potential (DeltaPsi) in developing OLs. Apoptosis-inducing factor (AIF) has been shown to be involved in caspase-independent cell death, and we found that AIF translocated from mitochondria into the nucleus upon NO exposure. In conclusion, we suggest that the vulnerability of developing OLs to NO involves mitochondrial dysfunction and translocation of AIF from mitochondria to nuclei.

12-Lipoxygenase Plays a Key Role in Cell Death Caused by Glutathione Depletion and Arachidonic Acid in Rat Oligodendrocytes

The European Journal of Neuroscience. Oct, 2004  |  Pubmed ID: 15450084

Oxidative injury to premyelinating oligodendrocytes (preOLs) in developing white matter has been implicated in the pathogenesis of periventricular leukomalacia, the lesion underlying most cases of cerebral palsy in premature infants. In this study, we investigated the pathways of OL death induced by intracellular glutathione (GSH) depletion. We found that the lipoxygenase (LOX) inhibitors AA-861 and BMD-122 (N-benzyl-N-hydroxy-5-phenylpentamide; BHPP), but not the cyclooxygenase (COX) inhibitor indomethacin, fully protected the cells from GSH depletion caused by cystine deprivation. Arachidonic acid (AA), the substrate for 12-LOX, potentiated the toxicity of mild cystine deprivation and at higher concentration was itself toxic. This toxicity was also blocked by 12-LOX inhibitors. Consistent with a role for 12-LOX in the cell death pathway, 12-LOX activity increased following cystine deprivation in OLs. Blocking 12-LOX with AA-861 effectively inhibited the accumulation of reactive oxygen species (ROS) induced by cystine deprivation. These data suggest that, in OLs, intracellular GSH depletion leads to activation of 12-LOX, ROS accumulation and cell death. Mature OLs were more resistant than preOLs to cystine deprivation. The difference in sensitivity was not due to a difference in 12-LOX activity but rather appeared to be related to the presence of stronger antioxidant defense mechanisms in mature OLs. These results suggest that 12-LOX activation plays a key role in oxidative stress-induced OL death.

Enhancement of the Immunogenicity of DNA Vaccine Against Infectious Bursal Disease Virus by Co-delivery with Plasmid Encoding Chicken Interleukin 2

Virology. Nov, 2004  |  Pubmed ID: 15476877

The immunoregulatory activity of a nonmammalian interleukin 2 (IL-2), chicken IL-2 (chIL-2), was investigated using a DNA vaccine against infectious bursal disease virus (IBDV) as a model. Coadministration of a plasmid encoding the VP2 gene of IBDV (pCI-VP2) and a plasmid encoding chicken IL-2 gene (pCI-chIL-2) enhances bursal protection against both the homologous IBDV strain ZJ2000 and the heterologous strain BC6/85 compared to administration of pCI-VP2 alone. Vaccination with pCI-VP2 alone induces low bursal protection against ZJ2000 and only protects chickens from clinical outbreaks and mortality, but not from bursal damage caused by BC6/85. Co-administration of the plasmid encoding the polyprotein gene of IBDV (pCI-VP2/4/3) and pCI-chIL-2 provides complete protection (15/15) against ZJ2000 and satisfactory protection (13/15) against BC6/85. In contrast, only 10 out of 15 chickens and 6 out of 15 chickens were protected against ZJ2000 and BC6/85, respectively, using the pCI-VP2/4/3 vaccination alone. A significant increase in the IBDV-specific neutralizing antibody response was also observed in chickens that received pCI-VP2/4/3 plus pCI-chIL-2 as compared with those that received the pCI-VP2/4/3 vaccination alone. By administrating different amounts of plasmid DNA, we confirmed that the pCI-chIL-2, but not the backbone plasmid pCI, contributes to increased immunoprotection of DNA vaccine against IBDV. These results strongly indicate that the efficacy of avian DNA vaccine can be modulated by co-administration of a plasmid encoding chIL-2.

Peroxynitrite-induced Neuronal Apoptosis is Mediated by Intracellular Zinc Release and 12-lipoxygenase Activation

The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. Nov, 2004  |  Pubmed ID: 15564577

Peroxynitrite toxicity is a major cause of neuronal injury in stroke and neurodegenerative disorders. The mechanisms underlying the neurotoxicity induced by peroxynitrite are still unclear. In this study, we observed that TPEN [N,N,N',N'-tetrakis (2-pyridylmethyl)ethylenediamine], a zinc chelator, protected against neurotoxicity induced by exogenous as well as endogenous (coadministration of NMDA and a nitric oxide donor, diethylenetriamine NONOate) peroxynitrite. Two different approaches to detecting intracellular zinc release demonstrated the liberation of zinc from intracellular stores by peroxynitrite. In addition, we found that peroxynitrite toxicity was blocked by inhibitors of 12-lipoxygenase (12-LOX), p38 mitogen-activated protein kinase (MAPK), and caspase-3 and was associated with mitochondrial membrane depolarization. Inhibition of 12-LOX blocked the activation of p38 MAPK and caspase-3. Zinc itself induced the activation of 12-LOX, generation of reactive oxygen species (ROS), and activation of p38 MAPK and caspase-3. These data suggest a cell death pathway triggered by peroxynitrite in which intracellular zinc release leads to activation of 12-LOX, ROS accumulation, p38 activation, and caspase-3 activation. Therefore, therapies aimed at maintaining intracellular zinc homeostasis or blocking activation of 12-LOX may provide a novel avenue for the treatment of inflammation, stroke, and neurodegenerative diseases in which the formation of peroxynitrite is thought to be one of the important causes of cell death.

Decreased Dependence on Receptor Recognition for the Fusion Promotion Activity of L289A-mutated Newcastle Disease Virus Fusion Protein Correlates with a Monoclonal Antibody-detected Conformational Change

Journal of Virology. Jan, 2005  |  Pubmed ID: 15613345

It has been shown that the L289A-mutated Newcastle disease virus (NDV) fusion (F) protein gains the ability to promote fusion of Cos-7 cells independent of the viral hemagglutinin-neuraminidase (HN) protein and exhibits a 50% enhancement in HN-dependent fusion over wild-type (wt) F protein. Here, we show that HN-independent fusion by L289A-F is not exhibited in BHK cells or in several other cell lines. However, similar to the results in Cos-7 cells, the mutated protein plus HN does promote 50 to 70% more fusion above wt levels in all of the cell lines tested. L289A-F protein exhibits the same specificity as the wt F protein for the homologous HN protein, as well as NDV-human parainfluenza virus 3 HN chimeras. The mutated F protein promotes fusion more effectively than the wt when it is coexpressed with either the chimeras or HN proteins deficient in receptor recognition activity. In addition, its fusogenic activity is significantly more resistant to removal of sialic acid on target cells. These findings are consistent with the demonstration that L289A-F interacts more efficiently with wt and mutated HN proteins than does wt F by a cell surface coimmunoprecipitation assay. Taken together, these findings indicate that L289A-F promotes fusion by a mechanism analogous to that of the wt protein with respect to the HN-F interaction but is less dependent on the attachment activity of HN. The phenotype of the mutated F protein correlates with a conformational change in the protein detectable by two different monoclonal antibodies. This conformational change may reflect a destabilization of F structure induced by the L289A substitution, which may in turn indicate a lower energy requirement for fusion activation.

Peroxynitrite Generated by Inducible Nitric Oxide Synthase and NADPH Oxidase Mediates Microglial Toxicity to Oligodendrocytes

Proceedings of the National Academy of Sciences of the United States of America. Jul, 2005  |  Pubmed ID: 15998743

Reactive microglia in the CNS have been implicated in the pathogenesis of white matter disorders, such as periventricular leukomalacia and multiple sclerosis. However, the mechanism by which activated microglia kill oligodendrocytes (OLs) remains elusive. Here we show that lipopolysaccharide (LPS)-induced death of developing OLs is caused by microglia-derived peroxynitrite, the reaction product of nitric oxide (NO) and superoxide anion. Blocking peroxynitrite formation with nitric oxide synthase inhibitors, superoxide dismutase mimics, or a decomposition catalyst abrogated the cytotoxicity. Only microglia, but not OLs, expressed inducible NO synthase (iNOS) after LPS challenge; microglia from iNOS knockout mice were not cytotoxic upon activation. The molecular source for superoxide was identified as the superoxide-generating enzyme NADPH oxidase. The oxidase was activated upon LPS exposure, and its inhibition prevented microglial toxicity toward OLs. Furthermore, microglia isolated from mice deficient in the catalytic component of the oxidase, gp91(phox), failed to induce cell death. Our results reveal a role for NADPH oxidase in LPS-induced OL death and suggest that peroxynitrite produced by iNOS and NADPH oxidase in activated microglia may play an important role in the pathogenesis of white matter disorders.

Monoclonal Antibody Routinely Used to Identify Avirulent Strains of Newcastle Disease Virus Binds to an Epitope at the Carboxy Terminus of the Hemagglutinin-neuraminidase Protein and Recognizes Individual Mesogenic and Velogenic Strains

Journal of Clinical Microbiology. Aug, 2005  |  Pubmed ID: 16081986

Newcastle disease virus (NDV) strains are classified as having high (velogenic), intermediate (mesogenic), or low (lentogenic) pathogenesis and virulence in chickens. Recent studies have established that the hemagglutinin-neuraminidase (HN) protein plays an important role in viral tropism and virulence. A monoclonal antibody (AVS-I) has previously been shown to be specific for lentogenic strains of NDV (Srinivasappa et al., Avian Dis. 30:562-567, 1986) and is routinely used to identify these strains. We have used competition antibody binding assays with a previously characterized panel of monoclonal antibodies, binding to chimeric HN proteins, and the characterization of an escape mutant to localize the binding site of AVS-I to the extreme carboxy terminus of the protein. In addition, we have shown that AVS-I does recognize at least one mesogenic strain and one velogenic strain of the virus, calling into question the potential of this antibody as a diagnostic reagent for avirulent NDV strains.

Amino Acid Residues Within Conserved Domain VI of the Vesicular Stomatitis Virus Large Polymerase Protein Essential for MRNA Cap Methyltransferase Activity

Journal of Virology. Nov, 2005  |  Pubmed ID: 16227259

During mRNA synthesis, the polymerase of vesicular stomatitis virus (VSV) copies the genomic RNA to produce five capped and polyadenylated mRNAs with the 5'-terminal structure 7mGpppA(m)pApCpApGpNpNpApUpCp. The 5' mRNA processing events are poorly understood but presumably require triphosphatase, guanylyltransferase, [guanine-N-7]- and [ribose-2'-O]-methyltransferase (MTase) activities. Consistent with a role in mRNA methylation, conserved domain VI of the 241-kDa large (L) polymerase protein shares sequence homology with a bacterial [ribose-2'-O]-MTase, FtsJ/RrmJ. In this report, we generated six L gene mutations to test this homology. Individual substitutions to the predicted MTase active-site residues K1651, D1762, K1795, and E1833 yielded viruses with pinpoint plaque morphologies and 10- to 1,000-fold replication defects in single-step growth assays. Consistent with these defects, viral RNA and protein synthesis was diminished. In contrast, alteration of residue G1674 predicted to bind the methyl donor S-adenosylmethionine did not significantly perturb viral growth and gene expression. Analysis of the mRNA cap structure revealed that alterations to the predicted active site residues decreased [guanine-N-7]- and [ribose-2'-O]-MTase activity below the limit of detection of our assay. In contrast, the alanine substitution at G1674 had no apparent consequence. These data show that the predicted MTase active-site residues K1651, D1762, K1795, and E1833 within domain VI of the VSV L protein are essential for mRNA cap methylation. A model of mRNA processing consistent with these data is presented.

Partitioning Knowledge Bases Between Advanced Notification and Clinical Decision Support Systems

AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium. 2005  |  Pubmed ID: 16779188

Due to the varying rates of change of ephemeral administrative and enduring clinical knowledge in decision support systems (DSSs), the functional partition of knowledge base (KB) components can lead to more efficient and cost-effective system implementation and maintenance. Our prototype loosely couples a clinical event monitor developed by Columbia University Medical Center (CUMC) with a secure notification service proxy developed by IBM Research to form a novel and complex clinical event communication service.

Epidemiology of Hepatitis B, C, D and G Viruses and Cytokine Levels Among Intravenous Drug Users

Journal of Huazhong University of Science and Technology. Medical Sciences = Hua Zhong Ke Ji Da Xue Xue Bao. Yi Xue Ying De Wen Ban = Huazhong Keji Daxue Xuebao. Yixue Yingdewen Ban. 2006  |  Pubmed ID: 16850752

To investigate the features of various hepatitis virus infection in intravenous drug users (IVDU), we conducted an epidemiological survey of hepatitis viruses including hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV) and hepatitis G virus (HGV) in IVDU. The correlation of TH lymphocyte cytokine and hepatitis virus infection was examined. A study population of 406 IVDU consisted of 383 males and 23 females. HBV-DNA and HCV-RNA were detected by fluorescence quantitative polymerase chain reaction. HBsAg, HBeAg, anti-HBc, anti-HCV, HDV-Ag and anti-HGV were assayed by ELISA. The levels of cytokines of TH1 and TH2 were measured by ELISA. The similar indices taken from 102 healthy persons served as controls. The infection rate of each virus among IVDU was 36.45 % for HBV, 69.7 % for HCV, 2.22 % for HDV, and 1.97 % for HGV, respectively. The co-infection rate of HBV and HCV was detected in 113 of 406 (27.83 %). In contrast, among controls, the infection rate was 17.65 % for HBV and 0 % for the other hepatitis viruses. The levels of PHA-induced cytokines (IFN-gamma and IL-4) and the level of serum IL-2 were obviously decreased in IVDU. On the other hand, the level of serum IL-4 was increased. The IFN-gamma level was continuously decreased when the IVDU was infected with HBV/HCV. In conclusion, HBV and HCV infection were common in this population of IVDU and they had led to a high incidence of impaired TH1 cytokine levels.

Genetic Reassortment of Infectious Bursal Disease Virus in Nature

Biochemical and Biophysical Research Communications. Nov, 2006  |  Pubmed ID: 17010936

Infectious bursal disease virus (IBDV), a double-stranded RNA virus, is a member of the Birnaviridae family. Four pathotypes of IBDV, attenuated, virulent, antigenic variant, and very virulent (vvIBDV), have been identified. We isolated and characterized the genomic reassortant IBDV strain ZJ2000 from severe field outbreaks in commercial flocks. Full-length genomic sequence analysis showed that ZJ2000 is a natural genetic reassortant virus with segments A and B derived from attenuated and very virulent strains of IBDV, respectively. ZJ2000 exhibited delayed replication kinetics as compared to attenuated strains. However, ZJ2000 was pathogenic to specific pathogen free (SPF) chickens and chicken embryos. Similar to a standard virulent IBDV strain, ZJ2000 caused 26.7% mortality, 100% morbidity, and severe bursal lesions at both gross and histopathological levels. Taken together, our data provide direct evidence for genetic reassortment of IBDV in nature, which may play an important role in the evolution, virulence, and host range of IBDV. Our data also suggest that VP2 is not the sole determinant of IBDV virulence, and that the RNA-dependent RNA polymerase protein, VP1, may play an important role in IBDV virulence. The discovery of reassortant viruses in nature suggests an additional risk of using live IBDV vaccines, which could act as genetic donors for genome reassortment.

Integration of Curated Databases to Identify Genotype-phenotype Associations

BMC Genomics. 2006  |  Pubmed ID: 17038185

The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype) and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs).

An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits

PLoS Computational Biology. Nov, 2006  |  Pubmed ID: 17112314

With mounting availability of genomic and phenotypic databases, data integration and mining become increasingly challenging. While efforts have been put forward to analyze prokaryotic phenotypes, current computational technologies either lack high throughput capacity for genomic scale analysis, or are limited in their capability to integrate and mine data across different scales of biology. Consequently, simultaneous analysis of associations among genomes, phenotypes, and gene functions is prohibited. Here, we developed a high throughput computational approach, and demonstrated for the first time the feasibility of integrating large quantities of prokaryotic phenotypes along with genomic datasets for mining across multiple scales of biology (protein domains, pathways, molecular functions, and cellular processes). Applying this method over 59 fully sequenced prokaryotic species, we identified genetic basis and molecular mechanisms underlying the phenotypes in bacteria. We identified 3,711 significant correlations between 1,499 distinct Pfam and 63 phenotypes, with 2,650 correlations and 1,061 anti-correlations. Manual evaluation of a random sample of these significant correlations showed a minimal precision of 30% (95% confidence interval: 20%-42%; n = 50). We stratified the most significant 478 predictions and subjected 100 to manual evaluation, of which 60 were corroborated in the literature. We furthermore unveiled 10 significant correlations between phenotypes and KEGG pathways, eight of which were corroborated in the evaluation, and 309 significant correlations between phenotypes and 166 GO concepts evaluated using a random sample (minimal precision = 72%; 95% confidence interval: 60%-80%; n = 50). Additionally, we conducted a novel large-scale phenomic visualization analysis to provide insight into the modular nature of common molecular mechanisms spanning multiple biological scales and reused by related phenotypes (metaphenotypes). We propose that this method elucidates which classes of molecular mechanisms are associated with phenotypes or metaphenotypes and holds promise in facilitating a computable systems biology approach to genomic and biomedical research.

Synthesis and Crystal Structures of Multidimensional Coordination Polymers Based on W/Cu/S Clusters with Flexible Imidazole Ligands

Inorganic Chemistry. Dec, 2006  |  Pubmed ID: 17140222

Reactions of [WES3]2- (E = S, O) with CuX (X = NCS, CN, I) in the presence of bix (bix = 1,4-bis(imidazole-1-ylmethyl)benzene) in DMF or CH3CN resulted in the formation of two novel 2D --> 3D interpenetrating coordination polymers [S2W2S6Cu4(bix)2]n (1) and {[WS4Cu4(NCS)2(bix)3].CH3CN}n (2), a noninterpenetrating 3D polymer {[WS4Cu2(bix)].DMF}n (3), and two 2D sheet polymers [WS4Cu3(CN)(bix)]n (4) and {[OWS3Cu3(bix)2][I].DMF.2H2O}n (5), depending on the reaction temperature and the reagents used. Compound 1 contains a hexagonal prism of W2Cu4S6 cluster core, which serves as a 4-connecting node to link equivalent nodes via bix ligands, forming a 2D (4,4) net. In 2, a WCu4S4 core, which also acts as a 4-connecting node, connects the neighboring nodes either through single or double bix bridges, affording a different 2D (4,4) sheet. Inclined interpenetration occurs between two stacks of 2D sheets in the total structure of 1, while 2 involves a parallel interpenetration between the adjacent layers, both creating a 3D network. Compounds 1 and 2 represent the first examples of interpenetrating (4,4) frameworks with clusters as nodes and bidentate pyridyl-based ligands as linkers. Unlike 1 and 2, compound 3 has a noninterpenetrating 3D network, which is composed of the inorganic 1D (WS4Cu2)n chains linked by cis and trans bix ligands. Compound 4 features an inorganic 1D (WS4Cu3)n chain structure, which is linked by CN groups and bix ligands to form an infinite 2D network. Compound 5 is a 2D layer polymer with large inner cavities.

Intracellular Zinc Release and ERK Phosphorylation Are Required Upstream of 12-lipoxygenase Activation in Peroxynitrite Toxicity to Mature Rat Oligodendrocytes

The Journal of Biological Chemistry. Apr, 2006  |  Pubmed ID: 16431921

Peroxynitrite toxicity has been implicated in the pathogenesis of white matter injury. The mechanisms of peroxynitrite toxicity to oligodendrocytes (OLs), the major cell type of the white matter, are unknown. Using primary cultures of mature OLs that express myelin basic protein, we found that 3-morpholinosydnonimine, a peroxynitrite generator, caused toxicity to OLs. N,N,N',N'-tetrakis (2-pyridylmethyl)ethylenediamine, a zinc chelator, completely blocked peroxynitrite-induced toxicity. Use of FluoZin-3, a specific fluorescence zinc indicator, demonstrated the liberation of zinc from intracellular stores by peroxynitrite. Peroxynitrite caused the sequential activation of extracellular signal-regulated kinase 42/44 (ERK42/44), 12-lipoxygenase, and generation of reactive oxygen species, which were all dependent upon the intracellular release of zinc. The same cell death pathway was also activated when exogenous zinc was used. These results suggest that in addition to preventing the formation of peroxynitrite, useful strategies in preventing disease progression in pathologies in which peroxynitrite toxicity plays a critical role might include maintaining intracellular zinc homeostasis, blocking phosphorylation of ERK42/44, inhibiting activation of 12-lipoxygenase, and eliminating the accumulation of reactive oxygen species.

22q11.2 Deletion Mosaicism in Patients with Conotruncal Heart Defects

Birth Defects Research. Part A, Clinical and Molecular Teratology. Apr, 2006  |  Pubmed ID: 16575883

Some patients with conotruncal heart defects (CTDs) have a chromosome 22q11.2 deletion, but we do not know whether patients with CTDs who are missing the peripheral blood-cell chromosome 22q11.2 deletion are also missing the 22q11.2 deletion in myocardial cells, and whether patients with the 22q11.2 deletion can show a different 22q11.2 deletion in peripheral blood cells and myocardial cells due to a postzygotic mutation during the embryonic period.

A Unique Strategy for MRNA Cap Methylation Used by Vesicular Stomatitis Virus

Proceedings of the National Academy of Sciences of the United States of America. May, 2006  |  Pubmed ID: 16709677

Nonsegmented negative-sense (nsNS) RNA viruses typically replicate within the host cell cytoplasm and do not have access to the host mRNA capping machinery. These viruses have evolved a unique mechanism for mRNA cap formation in that the guanylyltransferase transfers GDP rather than GMP onto the 5' end of the RNA. Working with vesicular stomatitis virus (VSV), a prototype nsNS RNA virus, we now provide genetic and biochemical evidence that its mRNA cap methylase activities are also unique. Using recombinant VSV, we determined the function in mRNA cap methylation of a predicted binding site in the polymerase for the methyl donor, S-adenosyl-l-methionine. We found that amino acid substitutions to this site disrupted methylation at the guanine-N-7 (G-N-7) position or at both the G-N-7 and ribose-2'-O (2'-O) positions of the mRNA cap. These studies provide genetic evidence that the two methylase activities share an S-adenosyl-l-methionine-binding site and show that, in contrast to other cap methylation reactions, methylation of the G-N-7 position is not required for 2'-O methylation. These findings suggest that VSV evolved an unusual strategy of mRNA cap methylation that may be shared by other nsNS RNA viruses.

Oral DNA Vaccination with the Polyprotein Gene of Infectious Bursal Disease Virus (IBDV) Delivered by the Attenuated Salmonella Elicits Protective Immune Responses in Chickens

Vaccine. Aug, 2006  |  Pubmed ID: 16769159

Our previous study showed that vaccination with plasmid DNA containing infectious bursal disease virus (IBDV) gene which encodes complete polyprotein (VP2/4/3) induced protective immune responses. In this study, we examined the efficacy of an oral DNA vaccine carrying the IBDV polyprotein antigen delivered by attenuated Salmonella enterica sv. Typhimurium (S. typhimurium). The recombinant plasmid pCI-VP2/4/3 was transformed by electroporation into an attenuated S.typhimurium Strain (Dam Phop) (designated hereafter as SV/pCI-VP2/4/3). The IBDV polyprotein gene was expressed in chicken embryo fibroblast (CEF) cells infected with strain SV/pCI-VP2/4/3, as shown by gene-specific RT-PCR and Western blot. Oral immunization of 7-day-old specific-pathogen-free (SPF) chickens with SV/pCI-VP2/4/3 elicited specific humoral responses as measured by ELISA. Vaccination with the strain SV/pCI-VP2/4/3 at 10(9) CFU per chicken offered 11/15 (73%) protection of the chickens against virulent IBDV challenge. Our results have implications in the development of DNA vaccines against avian viral diseases by bacteria-vectored oral delivery system.

Chemical Characteristics and Source Implications of Petroleum Hydrocarbon Contaminants in the Sediments Near Major Drainage Outfalls Along the Coastal of Laizhou Bay, Bohai Sea, China

Environmental Monitoring and Assessment. Feb, 2007  |  Pubmed ID: 17219246

The associated industrial and urban developments are located to a large extent along the Laizhou Bay, Bohai Sea coastal and raw sewage is often discharged into near shore waters with little treatment. To find out chemical characteristics and pollution source of the petroleum related contaminations in sediments near the major drainage outfalls located in the coastal, in this study, 10 surface sediment samples were collected during June. Sediment samples were extracted by organic solvents, separated by silica gel column chromatography and the concentrations and the profiles of n-alkane, biomarker and PAH in sediments were analyzed by gas chromatography-mass selective detector (GC-MSD). The use of several molecular markers and related indexes derived for n-alkane and PAHs has been proposed for assessing the relative contributions to the environment of hydrocarbon sources. As a result, n-alkanes reflect that the sea area of paper mill (Station ZZ08) is dominated by vascular plant. DY petroleum oil field and outer shore of the paper mill (Station ZZ02) have some degrees of petroleum related hydrocarbon contamination. Whereas the contamination of the sea area of TH River may be ascribed to different sources such as territorial non-point pollution source, domestic sewages, and stormwater runoff. Judged by their PAH ratios, the sediments near the paper mill (Station ZZ02) and the outer station of the oil field (Staion TH2) were pyrolytic. The estuary of Tiao River including the inner Station THX, TH10 and TH05 are petrogenic. The marine sediment near DY drainage outfall may have a mixture source of PAH both pyrolytic and petrogenic.

Vesicular Stomatitis Viruses Resistant to the Methylase Inhibitor Sinefungin Upregulate RNA Synthesis and Reveal Mutations That Affect MRNA Cap Methylation

Journal of Virology. Apr, 2007  |  Pubmed ID: 17301155

Sinefungin (SIN), a natural S-adenosyl-L-methionine analog produced by Streptomyces griseolus, is a potent inhibitor of methyltransferases. We evaluated the effect of SIN on replication of vesicular stomatitis virus (VSV), a prototype of the nonsegmented negative-strand RNA viruses. The 241-kDa large polymerase (L) protein of VSV methylates viral mRNA cap structures at the guanine-N-7 (G-N-7) and ribose-2'-O (2'-O) positions. By performing transcription reactions in vitro, we show that both methylations are inhibited by SIN and that methylation was more sensitive at the G-N-7 than at 2'-O position. We further show that SIN inhibited growth of VSV in cell culture, reducing viral yield by 50-fold and diminishing plaque size. We isolated eight mutants that were resistant to SIN as judged by their growth characteristics. The SIN-resistant (SINR) viruses contained mutations in the L gene, the promoter for L gene expression provided by the conserved sequence elements of the G-L gene junction and the M gene. Five mutations resulted in amino acid substitutions to conserved regions II/III and VI of the L protein. For each mutant, we examined viral gene expression in cells and cap methylation in vitro. SINR mutants upregulated RNA synthesis in the presence of SIN, which may be responsible for their resistance. We also found that some SINR viruses with L gene mutations were defective in cap methylation in vitro, yet their methylases were less sensitive to SIN inhibition than those of the wild-type parent. These studies show that the VSV methylases are inhibited by SIN, and they define new regions of L protein that affect cap methylation. These studies also provide experimental evidence that inhibition of cap methylases is a potential strategy for development of antiviral therapeutics against nonsegmented negative-strand RNA viruses.

Determination of Formaldehyde in Squid by High-performance Liquid Chromatography

Asia Pacific Journal of Clinical Nutrition. 2007  |  Pubmed ID: 17392090

Great attention has been paid to volatile toxic aldehydes like formaldehyde in aquatic products. In order to investigate content of formaldehyde in squid and squid products, a high-performance liquid chromatography (HPLC) method was developed for determination of formaldehyde. Based on steam distillation and 2,4-dinitrophenylhydrazine derivatization, formaldehyde was analysis by HPLC using ODS-C18 column at UV detector (355 nm). Detection limit was 8.92 microg/L in standard solution and 0.18 mg/kg in sample, and recovery was 83.09-103.20%. By this method, the formaldehyde content of squid muscle and viscera, dried squid thread and boiled squid were determined. The results showed that variable formaldehyde levels were observed among four species squid, which was generally far higher in viscera than in muscle of frozen squid. And cooking accelerated the formaldehyde production of squids. The study indicated that the HPLC method, with a better selectivity, precision and accuracy, was available to determine the formaldehyde in squid products with satisfactory results. Formaldehyde level in muscle and products of squid exceeded the formaldehyde limit by the Ministry of Agriculture in China.

Regional Brain Strains and Role of Falx in Lateral Impact-induced Head Rotational Acceleration

Biomedical Sciences Instrumentation. 2007  |  Pubmed ID: 17487052

The objective of the present investigation is to determine localized brains strains in lateral impact using finite element modeling and evaluate the role of the falx. A two-dimensional finite element model was developed and validated with experimental data from literature. Motions and strains from the stress analysis matched well with experimental results. A parametric study was conducted by introducing flexible falx in the finite element model. For the model with the rigid falx, high strains were concentrated in the corpus callosum, whereas for the model with the flexible falx, high strains extended into the cerebral vertex. These preliminary findings indicate that the flexibility of falx has an effect on regional brain strains in lateral impact.

Evaluation of High-throughput Functional Categorization of Human Disease Genes

BMC Bioinformatics. 2007  |  Pubmed ID: 17493290

Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classifications of human diseases genes using Gene Ontology. In this study, we evaluate automated classifications of well-defined human disease genes using their Gene Ontology annotations and compared them to a gold standard. This gold standard was independently conceived by Valle's research group, and contains 923 human disease genes organized in 14 categories of protein function.

Isolation and Culture of Rat and Mouse Oligodendrocyte Precursor Cells

Nature Protocols. 2007  |  Pubmed ID: 17546009

The ability to isolate oligodendroglial precursor cells (OPCs) provides a powerful means to characterize their differentiation, properties and potential for myelin repair. Although much knowledge is available for isolation of OPCs from the rat central nervous system, preparation and maintenance of mouse OPCs has been until recently a challenge owing to difficulties in obtaining a sufficient quantity of purified OPCs. Here, we describe protocols to prepare highly enriched rat OPCs and nearly homogenous mouse OPCs. The mouse method generates predominantly OPCs from cortical neural progenitor cells as clonal aggregates called "oligospheres" by taking advantage of molecular genetic tools. Isolated OPCs can be further differentiated into oligodendrocytes. Collectively, we describe simple and efficient methods for the preparation and in vitro maintenance of enriched OPCs from rats and mice. Isolation and culture of a large, homogenous population of rodent OPCs should significantly facilitate studies on OPC lineage progression and their utility in myelin repair after injury.

Information Theory Applied to the Sparse Gene Ontology Annotation Network to Predict Novel Gene Function

Bioinformatics (Oxford, England). Jul, 2007  |  Pubmed ID: 17646340

Despite advances in the gene annotation process, the functions of a large portion of gene products remain insufficiently characterized. In addition, the in silico prediction of novel Gene Ontology (GO) annotations for partially characterized gene functions or processes is highly dependent on reverse genetic or functional genomic approaches. To our knowledge, no prediction method has been demonstrated to be highly accurate for sparsely annotated GO terms (those associated to fewer than 10 genes).

Discovery of Protein Interaction Networks Shared by Diseases

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2007  |  Pubmed ID: 17992746

The study of protein-protein interactions is essential to define the molecular networks that contribute to maintain homeostasis of an organism's body functions. Disruptions in protein interaction networks have been shown to result in diseases in both humans and animals. Monogenic diseases disrupting biochemical pathways such as hereditary coagulopathies (e.g. hemophilia), provided a deep insight in the biochemical pathways of acquired coagulopathies of complex diseases. Indeed, a variety of complex liver diseases can lead to decreased synthesis of the same set of coagulation factors as in hemophilia. Similarly, more complex diseases such as different cancers have been shown to result from malfunctions of common proteins pathways. In order to discover, in high throughput, the molecular underpinnings of poorly characterized diseases, we present a statistical method to identify shared protein interaction network(s) between diseases. Integrating (i) a protein interaction network with (ii) disease to protein relationships derived from mining Gene Ontology annotations and the biomedical literature with natural language understanding (PhenoGO), we identified protein-protein interactions that were associated with pairs of diseases and calculated the statistical significance of the occurrence of interactions in the protein interaction knowledgebase. Significant correlations between diseases and shared protein networks were identified and evaluated in this study, demonstrating the high precision of the approach and correct non-trivial predictions, signifying the potential for discovery. In conclusion, we demonstrate that the associations between diseases are directly correlated to their underlying protein-protein interaction networks, possibly providing insight into the underlying molecular mechanisms of phenotypes and biological processes disrupted in related diseases.

Monitoring the Function and Use of a Clinical Decision Support System

AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium. 2007  |  Pubmed ID: 18694002

The continuous monitoring of systems that provide healthcare functions is essential to ensuring their constant operation, optimal performance, and value to providers. Log files are rich resources for studying the various aspects of systems including their function and use. Here, we describe the types of log files, applications of results from their analysis, and creation of a monitoring tool for the Vigilens Health Monitor (an operational clinical decision support system at New York-Presbyterian Hospital).

Robust Informatics Methods for Accurate Diagnosis Using Highly Multiplexed Virus Arrays

AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium. 2007  |  Pubmed ID: 18694137

To address the limitations of traditional pathogen detection methodologies in clinical diagnosis, scientists have developed oligonucleotide microarrays. However, pathogen array interpretation remains challenging because of false positive probes. We conceived a novel computational method to interpret these arrays. In an evaluation using clinical samples, our method was compared to five others. Though most methods showed high specificity and sensitivity, only the proposed method showed significant advantages in positive predictive value (2-60 fold increase).

Information-theoretic Classification of SNOMED Improves the Organization of Context-sensitive Excerpts from Cochrane Reviews

AMIA ... Annual Symposium Proceedings / AMIA Symposium. AMIA Symposium. 2007  |  Pubmed ID: 18694197

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

Effects of Various Temperatures and PH Values on the Extraction Yield of Phenolics from Litchi Fruit Pericarp Tissue and the Antioxidant Activity of the Extracted Anthocyanins

International Journal of Molecular Sciences. Jun, 2008  |  Pubmed ID: 19325806

Litchi fruit pericarp tissue is considered an important source of dietary phenolics. This study consisted of two experiments. The first was conducted to examine the effects of various extraction temperatures (30, 40, 50, 60, 70 and 80 degrees C) and pH values (2, 3, 4, 5 and 6) on the extraction yield of phenolics from litchi fruit pericarp. Extraction was most efficient at pH 4.0, while an extraction temperature of 60 degrees C was the best in terms of the combined extraction yield of phenolics and the stability of the extracted litchi anthocyanins. The second experiment was carried out to further evaluate the effects of various temperatures (25, 35, 45, 55 and 65 degrees C) and pH values (1, 3, 5 and 7) on the total antioxidant ability and scavenging activities of DPPH radicals, hydroxyl radical and superoxide anion of the extracted anthocyanins. The results indicated that use of 45-60 degrees C or pH 3-4 exhibited a relatively high antioxidant activity. The study will help improve extraction yield of phenolics from litchi fruit pericarp and promote better utilization of the extracted litchi anthocyanins as antioxidants.

A Conserved Motif in Region V of the Large Polymerase Proteins of Nonsegmented Negative-sense RNA Viruses That is Essential for MRNA Capping

Journal of Virology. Jan, 2008  |  Pubmed ID: 18003731

Nonsegmented negative-sense (NNS) RNA viruses cap their mRNA by an unconventional mechanism. Specifically, 5' monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. This polyribonucleotidyltransferase activity contrasts with all other capping reactions, which are catalyzed by an RNA triphosphatase and guanylyltransferase. In these reactions, a 5' diphosphate mRNA is capped by transfer of GMP via a covalent enzyme-GMP intermediate. RNA guanylyltransferases typically have a KxDG motif in which the lysine forms this covalent intermediate. Consistent with the distinct mechanism of capping employed by NNS RNA viruses, such a motif is absent from L. To determine the residues of L protein required for capping, we reconstituted the capping reaction of the prototype NNS RNA virus, vesicular stomatitis virus, from highly purified components. Using a panel of L proteins with single-amino-acid substitutions to residues universally conserved among NNS RNA virus L proteins, we define a new motif, GxxT[n]HR, present within conserved region V of L protein that is essential for this unconventional mechanism of mRNA cap formation.

Comparison of Incisions and Outcomes for Closure of Ventricular Septal Defects

The Annals of Thoracic Surgery. Jan, 2008  |  Pubmed ID: 18154810

Repair of ventricular septal defects (VSD) through a shorter right lateral thoracotomy has evolved for 10 years. However, outcomes of this surgery and patients' health-related quality of life have not been evaluated so far.

Tumor Necrosis Factor Alpha Mediates Lipopolysaccharide-induced Microglial Toxicity to Developing Oligodendrocytes when Astrocytes Are Present

The Journal of Neuroscience : the Official Journal of the Society for Neuroscience. May, 2008  |  Pubmed ID: 18480288

Reactive microglia and astrocytes are present in lesions of white matter disorders, such as periventricular leukomalacia and multiple sclerosis. However, it is not clear whether they are actively involved in the pathogenesis of these disorders. Previous studies demonstrated that microglia, but not astrocytes, are required for lipopolysaccharide (LPS)-induced selective killing of developing oligodendrocytes (preOLs) and that the toxicity is mediated by microglia-derived peroxynitrite. Here we report that, when astrocytes are present, the LPS-induced, microglia-dependent toxicity to preOLs is no longer mediated by peroxynitrite but instead by a mechanism dependent on tumor necrosis factor-alpha (TNFalpha) signaling. Blocking peroxynitrite formation with nitric oxide synthase (NOS) inhibitors or a decomposition catalyst did not prevent LPS-induced loss of preOLs in mixed glial cultures. PreOLs were highly vulnerable to peroxynitrite; however, the presence of astrocytes prevented the toxicity. Whereas LPS failed to kill preOLs in cocultures of microglia and preOLs deficient in inducible NOS (iNOS) or gp91(phox), the catalytic subunit of the superoxide-generating NADPH oxidase, LPS caused a similar degree of preOL death in mixed glial cultures of wild-type, iNOS-/-, and gp91(phox-/-) mice. TNFalpha neutralizing antibody inhibited LPS toxicity, and addition of TNFalpha induced selective preOL injury in mixed glial cultures. Furthermore, disrupting the genes encoding TNFalpha or its receptors TNFR1/2 completely abolished the deleterious effect of LPS. Our results reveal that TNFalpha signaling, rather than peroxynitrite, is essential in LPS-triggered preOL death in an environment containing all major glial cell types and underscore the importance of intercellular communication in determining the mechanism underlying inflammatory preOL death.

Influence of Angular Acceleration-deceleration Pulse Shapes on Regional Brain Strains

Journal of Biomechanics. Jul, 2008  |  Pubmed ID: 18556004

Recognizing the association of angular loading with brain injuries and inconsistency in previous studies in the application of the biphasic loads to animal, physical, and experimental models, the present study examined the role of the acceleration-deceleration pulse shapes on region-specific strains. An experimentally validated two-dimensional finite element model representing the adult male human head was used. The model simulated the skull and falx as a linear elastic material, cerebrospinal fluid as a hydrodynamic material, and cerebrum as a linear viscoelastic material. The angular loading matrix consisted coronal plane rotation about a center of rotation that was acceleration-only (4.5 ms duration, 7.8 krad/s/s peak), deceleration-only (20 ms, 1.4 krad/s/s peak), acceleration-deceleration, and deceleration-acceleration pulses. Both biphasic pulses had peaks separated by intervals ranging from 0 to 25 ms. Principal strains were determined at the corpus callosum, base of the postcentral sulcus, and cerebral cortex of the parietal lobe. The cerebrum was divided into 17 regions and peak values of average maximum principal strains were determined. In all simulations, the corpus callosum responded with the highest strains. Strains were the least under all simulations in the lower parietal lobes. In all regions peak strains were the same for both monophase pulses suggesting that the angular velocity may be a better metric than peak acceleration or deceleration. In contrast, for the biphasic pulse, peak strains were region- and pulse-shape specific. Peak values were lower in both biphasic pulses when there was no time separation between the pulses than the corresponding monophase pulse. Increasing separation time intervals increased strains, albeit non-uniformly. Acceleration followed by deceleration pulse produced greater strains in all regions than the other form of biphasic pulse. Thus, pulse shape appears to have an effect on regional strains in the brain.

Microfluidic Compartmentalized Co-culture Platform for CNS Axon Myelination Research

Biomedical Microdevices. Dec, 2009  |  Pubmed ID: 19554452

This paper presents a circular microfluidic compartmentalized co-culture platform that can be used for central nervous system (CNS) axon myelination research. The microfluidic platform is composed of a soma compartment and an axon/glia compartment connected through arrays of axon-guiding microchannels. Myelin-producing glia, oligodendrocytes (OLs), placed in the axon/glia compartment, interact with only axons but not with neuronal somata confined to the soma compartment, reminiscent to in vivo situation where many axon fibres are myelinated by OLs at distance away from neuronal cell bodies. Primary forebrain neurons from embryonic day 16-18 rats were cultured inside the soma compartment for two weeks to allow them to mature and form extensive axon networks. OL progenitors, isolated from postnatal day 1-2 rat brains, were then added to the axon/glia compartment and co-cultured with neurons for an additional two weeks. The microdevice showed fluidic isolation between the two compartments and successfully isolated neuronal cell bodies and dendrites from axons growing through the arrays of axon-guiding microchannels into the axon/glia compartment. The circular co-culture device developed here showed excellent cell loading characteristics where significant numbers of cells were positioned near the axon-guiding microchannels. This significantly increased the probability of axons crossing these microchannels as demonstrated by the more than 51 % of the area of the axon/glia compartment covered with axons two weeks after cell seeding. OL progenitors co-cultured with axons inside the axon/glia compartment successfully differentiated into mature OLs. These results indicate that this device can be used as an excellent in vitro co-culture platform for studying localized axon-glia interaction and signalling.

Integration of Neuroimaging and Microarray Datasets Through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

Cancer Informatics. Jun, 2009  |  Pubmed ID: 20495688

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT(R)). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames and allowed for complex queries such as "List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes". Precision of the NLP-derived coding of the unstructured phenotypes in each dataset was 88% (n=50), and precision of the semantic mapping between these terms across datasets was 98% (n=100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets.

Effect of Prebiotic Xylooligosaccharides on Growth Performances and Digestive Enzyme Activities of Allogynogenetic Crucian Carp (Carassius Auratus Gibelio)

Fish Physiology and Biochemistry. Aug, 2009  |  Pubmed ID: 18704733

The effect of prebiotic xylooligosaccharides (XOS) on the growth performance and digestive enzyme activities of the allogynogenetic crucian carp, Carassius auratus gibelio, was investigated. XOS was added to fish basal semi-purified diets at three concentrations by dry feed weight: diet 1, 50 mg kg(-1); diet 2, 100 mg kg(-1); diet 3, 200 mg kg(-1), respectively. Twelve aquaria (n = 20) with three replicates for each treatment group (diets 1-3) and control treated without XOS were used. Weights of all collected carp from each aquarium were determined at the initial phase and at the end of the experiment, and the carp survival was also determined by counting the individuals in each aquarium. After 45 days, there were significant differences (P < 0.05) in the relative gain rate (RGR), and daily weight gain (DWG) of diets 1-3 were compared with the control. However, the survival rate was not affected (P > 0.05) by the dietary treatments. For enzymatic analysis, dissection produced a crude mixture of intestine and hepatopancreas of each segment to measure. The protease activity in the intestine and hepatopancreas content of fish in diet 2 (487.37 +/- 20.58 U g(-1) and 20.52 +/- 1.93 U g(-1)) were significantly different (P < 0.05) from that in the control (428.13 +/- 23.26 U g(-1) and 12.81 +/- 1.52 U g(-1)) and diet 3 (428.00 +/- 23.78 U g(-1) and 14.04 +/- 1.59 U g(-1)). Amylase activity in the intestine was significantly higher for diet 2 compared to diet 1 and the control. As for amylase in the hepatopancreas, assays showed higher activity in diet 2 (P < 0.05) compared to the rest.

Duchesnea Phenolic Fraction Inhibits in Vitro and in Vivo Growth of Cervical Cancer Through Induction of Apoptosis and Cell Cycle Arrest

Experimental Biology and Medicine (Maywood, N.J.). Jan, 2009  |  Pubmed ID: 19064947

Duchesnea indica (Andr.) Focke has been commonly used to treat cancer in Asian countries for centuries, and recently has been shown to possess anticancer properties in vitro and in vivo. But the underlying mechanism of the anticancer action is unclear, especially in in vivo studies. In this study, we investigated the anticancer effect and associated mechanisms of Duchesnea phenolic fraction (DPF) on cervical cancer in vitro and in vivo. Our results showed that DPF significantly inhibited cervical cancer cell proliferation in dose- and time-dependent manners. DPF induced apoptosis as determined by AO/EB staining, DNA fragmentation and flow cytometry. Some apoptosis correlated proteins were altered following DPF treatment. Bax was up-regulated while Bcl-2 was down-regulated, and the expression ratio of Bax/Bcl-2 was increased. These resulted in the translocation of Bax to mitochondria, the release of cytochrome c from the mitochondria to the cytosol and caspase-3 activation. Concurrently, DPF provoked S phase arrest along with significant down-regulation of S phase-associated proteins, such as cyclin A, cyclin E, cyclin D1 and cdk2. Transplanted U14 cervical cancer mouse model was used to evaluate the antitumor effect of DPF in vivo. Compared with control, DPF treatment markedly prolonged survival of tumor-bearing mice and dose-dependently reduced the tumor weight. DPF could induce apoptosis in tumor tissues as evidenced by increased TUNEL-positive cells, activation of caspase-3, up-regulation of Bax and down-regulation of Bcl-2. In addition, DPF significantly decreased the expression of cell proliferation markers PCNA and ki67 in tumors. All together, these data sustain our contention that DPF has anticancer properties and merits further investigation as a potential therapeutic agent.

Opposing Effects of Inhibiting Cap Addition and Cap Methylation on Polyadenylation During Vesicular Stomatitis Virus MRNA Synthesis

Journal of Virology. Feb, 2009  |  Pubmed ID: 19073725

The multifunctional large (L) polymerase protein of vesicular stomatitis virus (VSV) contains enzymatic activities essential for RNA synthesis, including mRNA cap addition and polyadenylation. We previously mapped amino acid residues G1154, T1157, H1227, and R1228, present within conserved region V (CRV) of L, as essential for mRNA cap addition. Here we show that alanine substitutions to these residues also affect 3'-end formation. Specifically, the cap-defective polymerases produced truncated transcripts that contained A-rich sequences at their 3' termini and predominantly terminated within the first 500 nucleotides (nt) of the N gene. To examine how the cap-defective polymerases respond to an authentic VSV termination and reinitiation signal present at each gene junction, we reconstituted RNA synthesis using templates that contained genes inserted (I) at the leader-N gene junction. The I genes ranged in size from 382 to 1,098 nt and were typically transcribed into full-length uncapped transcripts. In addition to lacking a cap structure, the full-length I transcripts synthesized by the cap-defective polymerases lacked an authentic polyadenylate tail and instead contained 0 to 24 A residues. Moreover, the cap-defective polymerases were also unable to copy efficiently the downstream gene. Thus, single amino acid substitutions in CRV of L protein that inhibit cap addition also inhibit polyadenylation and sequential transcription of the genome. In contrast, an amino acid substitution, K1651A, in CRVI of L protein that completely inhibits cap methylation results in the hyperpolyadenylation of mRNA. This work reveals that inhibiting cap addition and cap methylation have opposing effects on polyadenylation during VSV mRNA synthesis and provides evidence in support of a link between correct 5' cap formation and 3' polyadenylation.

Robust Methods for Accurate Diagnosis Using Pan-microbiological Oligonucleotide Microarrays

BMC Bioinformatics. 2009  |  Pubmed ID: 19208186

To address the limitations of traditional virus and pathogen detection methodologies in clinical diagnosis, scientists have developed high-throughput oligonucleotide microarrays to rapidly identify infectious agents. However, objectively identifying pathogens from the complex hybridization patterns of these massively multiplexed arrays remains challenging.

PhenoGO: an Integrated Resource for the Multiscale Mining of Clinical and Biological Data

BMC Bioinformatics. 2009  |  Pubmed ID: 19208196

The evolving complexity of genome-scale experiments has increasingly centralized the role of a highly computable, accurate, and comprehensive resource spanning multiple biological scales and viewpoints. To provide a resource to meet this need, we have significantly extended the PhenoGO database with gene-disease specific annotations and included an additional ten species. This a computationally-derived resource is primarily intended to provide phenotypic context (cell type, tissue, organ, and disease) for mining existing associations between gene products and GO terms specified in the Gene Ontology Databases Automated natural language processing (BioMedLEE) and computational ontology (PhenOS) methods were used to derive these relationships from the literature, expanding the database with information from ten additional species to include over 600,000 phenotypic contexts spanning eleven species from five GO annotation databases. A comprehensive evaluation evaluating the mappings (n = 300) found precision (positive predictive value) at 85%, and recall (sensitivity) at 76%. Phenotypes are encoded in general purpose ontologies such as Cell Ontology, the Unified Medical Language System, and in specialized ontologies such as the Mouse Anatomy and the Mammalian Phenotype Ontology. A web portal has also been developed, allowing for advanced filtering and querying of the database as well as download of the entire dataset http://www.phenogo.org.

Vitamin K Prevents Oxidative Cell Death by Inhibiting Activation of 12-lipoxygenase in Developing Oligodendrocytes

Journal of Neuroscience Research. Jul, 2009  |  Pubmed ID: 19235890

Oxidative mechanisms of injury are important in many neurological disorders. Developing oligodendrocytes (pre-OLs) are particularly sensitive to oxidative stress-mediated injury. We previously demonstrated a novel function of phylloquinone (vitamin K(1)) and menaquinone 4 (MK-4; a major form of vitamin K2) in protecting pre-OLs and immature neurons against glutathione depletion-induced oxidative damage (Li et al. [ 2003] J. Neurosci. 23:5816-5826). Here we report that vitamin K at nanomolar concentrations prevents arachidonic acid-induced oxidative injury to pre-OLs through blocking the activation of 12-lipoxygenase (12-LOX). Arachidonic acid metabolism is a potential source for reactive oxygen species (ROS) generation during ischemia and reperfusion. Exposure of pre-OLs to arachidonic acid resulted in oxidative cell death in a concentration-dependent manner. Administration of vitamin K (K(1) and MK-4) completely prevented the toxicity. Consistent with our previous findings, inhibitors of 12-LOX abolished ROS production and cell death, indicating that activation of 12-LOX is a key event in arachidonic acid-induced pre-OL death. Vitamin K(1) and MK-4 significantly blocked 12-LOX activation and prevented ROS accumulation in pre-OLs challenged with arachidonic acid. However, vitamin K itself did not directly inhibit 12-LOX enzymatic activity when assayed with purified 12-LOX in vitro. These results suggest that vitamin K, or likely its metabolites, acts upstream of activation of 12-LOX in pre-OLs. In summary, our data indicate that vitamin K prevents oxidative cell death by blocking activation of 12-LOX and ROS generation.

Ribose 2'-O Methylation of the Vesicular Stomatitis Virus MRNA Cap Precedes and Facilitates Subsequent Guanine-N-7 Methylation by the Large Polymerase Protein

Journal of Virology. Nov, 2009  |  Pubmed ID: 19710136

During conventional mRNA cap formation, two separate methyltransferases sequentially modify the cap structure, first at the guanine-N-7 (G-N-7) position and subsequently at the ribose 2'-O position. For vesicular stomatitis virus (VSV), a prototype of the nonsegmented negative-strand RNA viruses, the two methylase activities share a binding site for the methyl donor S-adenosyl-l-methionine and are inhibited by individual amino acid substitutions within the C-terminal domain of the large (L) polymerase protein. This led to the suggestion that a single methylase domain functions for both 2'-O and G-N-7 methylations. Here we report a trans-methylation assay that recapitulates both ribose 2'-O and G-N-7 modifications by using purified recombinant L and in vitro-synthesized RNA. Using this assay, we demonstrate that VSV L typically modifies the 2'-O position of the cap prior to the G-N-7 position and that G-N-7 methylation is diminished by pre-2'-O methylation of the substrate RNA. Amino acid substitutions in the C terminus of L that prevent all cap methylation in recombinant VSV (rVSV) partially retain the ability to G-N-7 methylate a pre-2'-O-methylated RNA, therefore uncoupling the effect of substitutions in the C terminus of the L protein on the two methylations. In addition, we show that the 2'-O and G-N-7 methylase activities act specifically on RNA substrates that contain the conserved elements of a VSV mRNA start at the 5' terminus. This study provides new mechanistic insights into the mRNA cap methylase activities of VSV L, demonstrates that 2'-O methylation precedes and facilitates subsequent G-N-7 methylation, and reveals an RNA sequence and length requirement for the two methylase activities. We propose a model of regulation of the activity of the C terminus of L protein in 2'-O and G-N-7 methylation of the cap structure.

Inhibition of Peroxynitrite-mediated DNA Strand Cleavage and Hydroxyl Radical Formation by Aspirin at Pharmacologically Relevant Concentrations: Implications for Cancer Intervention

Biochemical and Biophysical Research Communications. Dec, 2009  |  Pubmed ID: 19785994

Epidemiological studies have suggested that the long-term use of aspirin is associated with a decreased incidence of human malignancies, especially colorectal cancer. Since accumulating evidence indicates that peroxynitrite is critically involved in multistage carcinogenesis, this study was undertaken to investigate the ability of aspirin to inhibit peroxynitrite-mediated DNA damage. Peroxynitrite and its generator 3-morpholinosydnonimine (SIN-1) were used to cause DNA strand breaks in phiX-174 plasmid DNA. We demonstrated that the presence of aspirin at concentrations (0.25-2mM) compatible with amounts in plasma during chronic anti-inflammatory therapy resulted in a significant inhibition of DNA cleavage induced by both peroxynitrite and SIN-1. Moreover, the consumption of oxygen caused by 250 microM SIN-1 was found to be decreased in the presence of aspirin, indicating that aspirin might affect the auto-oxidation of SIN-1. Furthermore, EPR spectroscopy using 5,5-dimethylpyrroline-N-oxide (DMPO) as a spin trap demonstrated the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from authentic peroxynitrite, and that aspirin at 0.25-2mM potently diminished the radical adduct formation in a concentration-dependent manner. Taken together, these results demonstrate for the first time that aspirin at pharmacologically relevant concentrations can inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. These results may have implications for cancer intervention by aspirin.

The Oligodendrocyte-specific G Protein-coupled Receptor GPR17 is a Cell-intrinsic Timer of Myelination

Nature Neuroscience. Nov, 2009  |  Pubmed ID: 19838178

The basic helix-loop-helix transcription factor Olig1 promotes oligodendrocyte maturation and is required for myelin repair. We characterized an Olig1-regulated G protein-coupled receptor, GPR17, whose function is to oppose the action of Olig1. Gpr17 was restricted to oligodendrocyte lineage cells, but was downregulated during the peak period of myelination and in adulthood. Transgenic mice with sustained Gpr17 expression in oligodendrocytes exhibited stereotypic features of myelinating disorders in the CNS. Gpr17 overexpression inhibited oligodendrocyte differentiation and maturation both in vivo and in vitro. Conversely, Gpr17 knockout mice showed early onset of oligodendrocyte myelination. The opposing action of Gpr17 on oligodendrocyte maturation reflects, at least partially, upregulation and nuclear translocation of the potent oligodendrocyte differentiation inhibitors ID2/4. Collectively, these findings suggest that GPR17 orchestrates the transition between immature and myelinating oligodendrocytes via an ID protein-mediated negative regulation and may serve as a potential therapeutic target for CNS myelin repair.

[Isolation and Identification of Cholesterol-reducing Lactic Acid Bacteria from Indigenously Fermented Pickles and Dried-sausage]

Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica. Nov, 2009  |  Pubmed ID: 20112670

To obtain cholesterol-reducing lactic acid bacteria (LAB), we isolated and identified strains of LAB from indigenously fermented pickles and dried-sausage.

[Effect of Ultra High Pressure Treatment on Vibrio Parahaemolyticus]

Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica. Nov, 2009  |  Pubmed ID: 20112678

We explored the mechanism of the microbial inactivation by high hydrostatic pressure.

Integration of Neuroimaging and Microarray Datasets Through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

Summit on Translational Bioinformatics. 2009  |  Pubmed ID: 21347176

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledgebased phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO and Neuronames and allowed for complex queries such as "List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes". Precision of the NLP-derived coding of the unstructured phenotypes in each datasets was 88% (n=50), and precision of the semantic mapping between these terms across datasets was 98% (n=100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets.

A Broad-spectrum Antiviral Targeting Entry of Enveloped Viruses

Proceedings of the National Academy of Sciences of the United States of America. Feb, 2010  |  Pubmed ID: 20133606

We describe an antiviral small molecule, LJ001, effective against numerous enveloped viruses including Influenza A, filoviruses, poxviruses, arenaviruses, bunyaviruses, paramyxoviruses, flaviviruses, and HIV-1. In sharp contrast, the compound had no effect on the infection of nonenveloped viruses. In vitro and in vivo assays showed no overt toxicity. LJ001 specifically intercalated into viral membranes, irreversibly inactivated virions while leaving functionally intact envelope proteins, and inhibited viral entry at a step after virus binding but before virus-cell fusion. LJ001 pretreatment also prevented virus-induced mortality from Ebola and Rift Valley fever viruses. Structure-activity relationship analyses of LJ001, a rhodanine derivative, implicated both the polar and nonpolar ends of LJ001 in its antiviral activity. LJ001 specifically inhibited virus-cell but not cell-cell fusion, and further studies with lipid biosynthesis inhibitors indicated that LJ001 exploits the therapeutic window that exists between static viral membranes and biogenic cellular membranes with reparative capacity. In sum, our data reveal a class of broad-spectrum antivirals effective against enveloped viruses that target the viral lipid membrane and compromises its ability to mediate virus-cell fusion.

Cellulose Conversion to Isosorbide in Molten Salt Hydrate Media

ChemSusChem. Mar, 2010  |  Pubmed ID: 20186909

Protein Interaction Network Underpins Concordant Prognosis Among Heterogeneous Breast Cancer Signatures

Journal of Biomedical Informatics. Jun, 2010  |  Pubmed ID: 20350617

Characterizing the biomolecular systems' properties underpinning prognosis signatures derived from gene expression profiles remains a key clinical and biological challenge. In breast cancer, while different "poor-prognosis" sets of genes have predicted patient survival outcome equally well in independent cohorts, these prognostic signatures have surprisingly little genetic overlap. We examine 10 such published expression-based signatures that are predictors or distinct breast cancer phenotypes, uncover their mechanistic interconnectivity through a protein-protein interaction network, and introduce a novel cross-"gene expression signature" analysis method using (i) domain knowledge to constrain multiple comparisons in a mechanistically relevant single-gene network interactions and (ii) scale-free permutation re-sampling to statistically control for hubness (SPAN - Single Protein Analysis of Network with constant node degree per protein). At adjusted p-values<5%, 54-genes thus identified have a significantly greater connectivity than those through meticulous permutation re-sampling of the context-constrained network. More importantly, eight of 10 genetically non-overlapping signatures are connected through well-established mechanisms of breast cancer oncogenesis and progression. Gene Ontology enrichment studies demonstrate common markers of cell cycle regulation. Kaplan-Meier analysis of three independent historical gene expression sets confirms this network-signature's inherent ability to identify "poor outcome" in ER(+) patients without the requirement of machine learning. We provide a novel demonstration that genetically distinct prognosis signatures, developed from independent clinical datasets, occupy overlapping prognostic space of breast cancer via shared mechanisms that are mediated by genetically different yet mechanistically comparable interactions among proteins of differentially expressed genes in the signatures. This is the first study employing a networks' approach to aggregate established gene expression signatures in order to develop a phenotype/pathway-based cancer roadmap with the potential for (i) novel drug development applications and for (ii) facilitating the clinical deployment of prognostic gene signatures with improved mechanistic understanding of biological processes and functions associated with gene expression changes. http://www.lussierlab.org/publication/networksignature/.

Network Modeling Identifies Molecular Functions Targeted by MiR-204 to Suppress Head and Neck Tumor Metastasis

PLoS Computational Biology. Apr, 2010  |  Pubmed ID: 20369013

Due to the large number of putative microRNA gene targets predicted by sequence-alignment databases and the relative low accuracy of such predictions which are conducted independently of biological context by design, systematic experimental identification and validation of every functional microRNA target is currently challenging. Consequently, biological studies have yet to identify, on a genome scale, key regulatory networks perturbed by altered microRNA functions in the context of cancer. In this report, we demonstrate for the first time how phenotypic knowledge of inheritable cancer traits and of risk factor loci can be utilized jointly with gene expression analysis to efficiently prioritize deregulated microRNAs for biological characterization. Using this approach we characterize miR-204 as a tumor suppressor microRNA and uncover previously unknown connections between microRNA regulation, network topology, and expression dynamics. Specifically, we validate 18 gene targets of miR-204 that show elevated mRNA expression and are enriched in biological processes associated with tumor progression in squamous cell carcinoma of the head and neck (HNSCC). We further demonstrate the enrichment of bottleneckness, a key molecular network topology, among miR-204 gene targets. Restoration of miR-204 function in HNSCC cell lines inhibits the expression of its functionally related gene targets, leads to the reduced adhesion, migration and invasion in vitro and attenuates experimental lung metastasis in vivo. As importantly, our investigation also provides experimental evidence linking the function of microRNAs that are located in the cancer-associated genomic regions (CAGRs) to the observed predisposition to human cancers. Specifically, we show miR-204 may serve as a tumor suppressor gene at the 9q21.1-22.3 CAGR locus, a well established risk factor locus in head and neck cancers for which tumor suppressor genes have not been identified. This new strategy that integrates expression profiling, genetics and novel computational biology approaches provides for improved efficiency in characterization and modeling of microRNA functions in cancer as compared to the state of art and is applicable to the investigation of microRNA functions in other biological processes and diseases.

Chelating and Radical Scavenging Activities of Soy Protein Hydrolysates Prepared from Microbial Proteases and Their Effect on Meat Lipid Peroxidation

Bioresource Technology. Apr, 2010  |  Pubmed ID: 20015640

Three commercial microbial proteases, neutral protease from Bacillus subtilis (NP), validase from Aspergillus oryze (Val), and alkaline protease from Bacillus licheniformis (AP), were investigated for producing antioxidant hydrolysates from soy protein. The resulting hydrolysates were fractioned by sequential ultrafiltration and their antioxidant properties were examined. All the 12 hydrolysate fractions showed noticeable oxygen radical absorbance capacity (ORAC) but significantly varied from 23.8 to 83.8 micromol Trolox equivalents (TE)/g. The hydrolysates also possessed significantly different 1,1-diphenyl-2-picrylhydrazyl (DPPH()) scavenging activities and transition metal chelating activities. Three fractions with strong antioxidant activities, NP-F1, Val-F1, and AP-F3, were incorporated into ground beef to determine their dose-response on lipid peroxidation during 15-day storage. AP-F3 and NP-F1 but not Val-F1 significantly reduced meat lipid peroxidation by 20.1% and 12.9%, respectively. Our results suggested that the commercial microbial proteases such as B. subtilis and B. licheniformis could be used to produce effective antioxidant hydrolysates from food proteins.

Micro-macro Hybrid Soft-lithography Master (MMHSM) Fabrication for Lab-on-a-chip Applications

Biomedical Microdevices. Apr, 2010  |  Pubmed ID: 20049640

We present a novel micro-macro hybrid soft-lithography master (MMHSM) fabrication technique where microdevices having both microscale and macroscale features can be replicated with a single soft-lithography step. A poly(methyl methacrylate) (PMMA) master having macroscale structures was first created by a bench-top milling machine. An imprinting master mold having microscale structures was then imprinted on the PMMA surface through a hot-embossing process to obtain a PMMA master mold. A poly(dimethylsiloxane) (PDMS) master was then replicated from this PMMA master through a standard soft-lithography process. This process allowed both microscale (height: 3-20 microm, width: 20-500 microm) and macroscale (height: 3.5 mm, width: 1.2-7 mm) structures to co-exist on the PDMS master mold, from which final PDMS devices could be easily stamped out in large quantities. Microfluidic structures requiring macroscale dimensions in height, such as reservoirs or fluidic tubing interconnects, could be directly built into PDMS microfluidic devices without the typically used manual punching process. This significantly reduced alignment errors and time required for such manual fabrication steps. In this paper, we successfully demonstrated the utility of this novel hybrid fabrication method by fabricating a PDMS microfluidic device with 40 built-in fluidic interfaces and a PDMS multi-compartment neuron co-culture platform, where millimeter-scale compartments are connected via arrays of 20 microm wide and 200 microm long microfluidic channels. The resulting structures were characterized for the integrity of the transferred pattern sizes and the surface roughness using scanning electron microscopy and optical profilometry.

In Vitro and in Vivo Activities of a New Lead Compound I2906 Against Mycobacterium Tuberculosis

Pharmacology. 2010  |  Pubmed ID: 20530976

Due to the long duration of treatment and the emergence of multidrug-resistant strains, new antitubercular agents are urgently needed. I2906, as a novel lead, was screened and tested for efficacy in vitro and in vivo.

Rapid Separation and Characterization of Active Flavonolignans of Silybum Marianum by Ultra-performance Liquid Chromatography Coupled with Electrospray Tandem Mass Spectrometry

Journal of Pharmaceutical and Biomedical Analysis. Dec, 2010  |  Pubmed ID: 20674209

Ultra-performance liquid chromatography (UPLC) interfaced with the electrospray ionization (ESI) tandem mass spectrometer (MS(n)) was developed for the simultaneous determination of silychristins A (1) and B (2), silydianin (3), silybins A (4) and B (5), and isosilybins A (6) and B (7), major bioactive flavonolignans in silymarin, a herbal remedy derived from the milk thistle Silybum marianum. In this study, the seven major active flavonolignans including the diastereomers 1/2, 4/5, and 6/7 were completely separated using UPLC with an ACQUITY UPLC C(18) column and a MeOH/water/formic acid mobile phase system. The collision-induced dissociation (CID) MS(n) spectra of these flavonolignans were studied systematically using ESI-MS. The results with the present methodology show that UPLC-MS(n) can be useful for general screening of active natural products from plant extracts and for the specific quality control of silymarin.

RIP1 Kinase Mediates Arachidonic Acid-induced Oxidative Death of Oligodendrocyte Precursors

International Journal of Physiology, Pathophysiology and Pharmacology. 2010  |  Pubmed ID: 20706550

Oxidative damage is implicated in many neurological disorders including ischemic cerebral white matter injury. Oligodendrocyte precursors (preOLs) are intrinsically highly susceptible to various forms of oxidative stress. Here we report the identification of RIP1 kinase as a signaling molecule that mediates arachidonic acid- and glu-tathione depletion-induced oxidative death of preOLs. Blockade of RIP1 kinase activity with the specific allosteric inhibitor, necrostatin-1, rescued preOLs from arachidonic acid, cystine deprivation, and buthionine sulfoximine, but not hydrogen peroxide, induced necrosis. Arachidonic acid triggered robust production of reactive oxygen species (ROS) and sustained activation of the JNK pathway in preOLs, whereas inhibition of JNK significantly prevented cell death. Treatment of cells with necrostatin-1 efficiently abolished arachidonic acid-induced ROS production and JNK activation, indicating that RIP1 kinase activation is an upstream event. This study provides the first evidence that RIP1 kinase may play an active role in arachidonic acid- and glutathione depletion-mediated oxidative damage and suggests the therapeutic potential of necrostatin-1 in protecting undifferentiated OLs against oxidative injury.

Antioxidant Rich Grape Pomace Extract Suppresses Postprandial Hyperglycemia in Diabetic Mice by Specifically Inhibiting Alpha-glucosidase

Nutrition & Metabolism. 2010  |  Pubmed ID: 20799969

Postprandial hyperglycemia is an early defect of type 2 diabetes and one of primary anti-diabetic targets. Treatment of postprandial hyperglycemia can be achieved by inhibiting intestinal α-glucosidase, the key enzyme for oligosaccharide digestion and further glucose absorption. Grape pomace is winemaking byproduct rich in bioactive food compounds such as phenolic antioxidants. This study evaluated the anti-diabetic potential of two specific grape pomace extracts by determining their antioxidant and anti-postprandial hyperglycemic activities in vitro and in vivo.

Identification of Aromatic Amino Acid Residues in Conserved Region VI of the Large Polymerase of Vesicular Stomatitis Virus is Essential for Both Guanine-N-7 and Ribose 2'-O Methyltransferases

Virology. Dec, 2010  |  Pubmed ID: 20961592

Non-segmented negative-sense RNA viruses possess a unique mechanism for mRNA cap methylation. For vesicular stomatitis virus, conserved region VI in the large (L) polymerase protein catalyzes both guanine-N-7 (G-N-7) and ribose 2'-O (2'-O) methyltransferases, and the two methylases share a binding site for the methyl donor S-adenosyl-l-methionine. Unlike conventional mRNA cap methylation, the 2'-O methylation of VSV precedes subsequent G-N-7 methylation. In this study, we found that individual alanine substitutions in two conserved aromatic residues (Y1650 and F1691) in region VI of L protein abolished both G-N-7 and 2'-O methylation. However, replacement of one aromatic residue with another aromatic residue did not significantly affect the methyltransferase activities. Our studies provide genetic and biochemical evidence that conserved aromatic residues in region VI of L protein essential for both G-N-7 and 2'-O methylations. In combination with the structural prediction, our results suggest that these aromatic residues may participate in RNA recognition.

NMR Characterization for Polysaccharide Moiety of a Glycopeptide

Fitoterapia. Mar, 2010  |  Pubmed ID: 19686815

Ganoderma lucidum is a traditional medicinal herb used to treat various diseases in China and Southeast Asia for thousands of years. An aqueous glycopeptide, LZ-B-1, was prepared by successive chromatography and exhibited an immunostimulating potential. To better understand the mechanism of bioactivity for this compound, the polysaccharide moiety of glycopeptide LZ-B-1 was studied by NMR spectroscopy. The results indicated that the polysaccharide moiety had a backbone of 1,6-disubstituted-alpha-galactopyranosyl, 1,2,6-trisubstituted-alpha-galactopyranosyl, 1,3-disubstituted-beta-glucopyranosyl and 1,4,6-trisubstituted-beta-glucopyranosyl residues. The branches were mainly composed of 1-substituted-beta-glucopyranosyl and 1-substituted-alpha-fucopyranosyl residues.

Kinase Inhibition-related Adverse Events Predicted from in Vitro Kinome and Clinical Trial Data

Journal of Biomedical Informatics. Jun, 2010  |  Pubmed ID: 20434586

Kinase inhibition is an increasingly popular strategy for pharmacotherapy of human diseases. Although many of these agents have been described as "targeted therapy", they will typically inhibit multiple kinases with varying potency. Pre-clinical model testing has not predicted the numerous significant toxicities identified during clinical development. The purpose of this study was to develop a bioinformatics-based method to predict specific adverse events (AEs) in humans associated with the inhibition of particular kinase targets (KTs).

Optimisation of Lactic Acid Fermentation for Improved Vinegar Flavour During Rosy Vinegar Brewing

Journal of the Science of Food and Agriculture. Jun, 2010  |  Pubmed ID: 20474052

Rosy vinegar is a well-known traditional Chinese product whose flavour is affected by its lactic acid content. In this study, Lactobacillus bacteria were employed to increase the content of lactic acid during the ethanol fermentation stage.

[Comparative Study of Effect of Magnolia Officinalis and M. Officinalis Var. Biloba on Gastrointestinal Motility Dysfunction]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Oct, 2010  |  Pubmed ID: 21174779

To compare the effect of Magnolia officinalis and M. officinalis var. biloba on gastrointestinal motility dysfunction.

Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine

AMIA Summits on Translational Science Proceedings AMIA Summit on Translational Science. 2010  |  Pubmed ID: 21347135

The ability to adequately and efficiently integrate unstructured, heterogeneous datasets, which are incumbent to systems biology and medicine, is one of the primary limitations to their comprehensive analysis. Natural language processing (NLP) and biomedical ontologies are automated methods for capturing, standardizing and integrating information across diverse sources, including narrative text. We have utilized the BioMedLEE NLP system to extract and encode, using standard ontologies (e.g., Cell Type Ontology, Mammalian Phenotype, Gene Ontology), biomolecular mechanisms and clinical phenotypes from the scientific literature. We subsequently applied semantic processing techniques to the structured BioMedLEE output to determine the relationships between these biomolecular and clinical phenotype concepts. We conducted an evaluation that shows an average precision and recall of BioMedLEE with respect to annotating phrases comprised of cell type, anatomy/disease, and gene/protein concepts were 86% and 78%, respectively. The precision of the asserted phenotype-molecular relationships was 75%.

Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology

AMIA Summits on Translational Science Proceedings AMIA Summit on Translational Science. 2010  |  Pubmed ID: 21347143

A key challenge for genome-wide association studies (GWAS) is to understand how single nucleotide polymorphisms (SNPs) mechanistically underpin complex diseases. While this challenge has been addressed partially by Gene Ontology (GO) enrichment of large list of host genes of SNPs prioritized in GWAS, these enrichment have not been formally evaluated. Here, we develop a novel computational approach anchored in information theoretic similarity, by systematically mining lists of host genes of SNPs prioritized in three adult-onset diabetes mellitus GWAS. The "gold-standard" is based on GO associated with 20 published diabetes SNPs' host genes and on our own evaluation. We computationally identify 69 similarity-predicted GO independently validated in all three GWAS (FDR<5%), enriched with those of the gold-standard (odds ratio=5.89, P=4.81e-05), and these terms can be organized by similarity criteria into 11 groupings termed "biomolecular systems". Six biomolecular systems were corroborated by the gold-standard and the remaining five were previously uncharacterized. http://lussierlab.org/publications/ITS-GWAS.

Inactivation of a Human Norovirus Surrogate by High-pressure Processing: Effectiveness, Mechanism, and Potential Application in the Fresh Produce Industry

Applied and Environmental Microbiology. Mar, 2011  |  Pubmed ID: 21193662

Fresh produce is often a high-risk food for norovirus contamination because it can become contaminated at both preharvest and postharvest stages and it undergoes minimal or no processing. Currently, there is no effective method to eliminate the viruses from fresh produce. This study systematically investigated the effectiveness of high-pressure processing (HPP) on inactivating murine norovirus (MNV-1), a surrogate for human norovirus, in aqueous medium and fresh produce. We demonstrated that MNV-1 was effectively inactivated by HPP. More than a 5-log-PFU/g reduction was achieved in all tested fresh produce when it was pressurized at 400 MPa for 2 min at 4°C. We found that pressure, pH, temperature, and food matrix affected the virus survival in foods. MNV-1 was more effectively inactivated at 4°C than at 20°C in both medium and fresh produce. MNV-1 was also more sensitive to HPP at neutral pH than at acidic pH. We further demonstrated that disruption of viral capsid structure, but not degradation of viral genomic RNA, is the primary mechanism of virus inactivation by HPP. However, HPP does not degrade viral capsid protein, and the pressurized capsid protein was still antigenic. Overall, HPP had a variable effect on the sensorial quality of fresh produce, depending on the pressure level and type of product. Taken together, HPP effectively inactivated a human norovirus surrogate in fresh produce with a minimal impact on food quality and thus can provide a novel intervention for processing fruits intended for frozen storage and related products such as purees, sauces, and juices.

Vesicular Stomatitis Virus As a Vector to Deliver Virus-like Particles of Human Norovirus: a New Vaccine Candidate Against an Important Noncultivable Virus

Journal of Virology. Mar, 2011  |  Pubmed ID: 21228240

Human norovirus (HuNoV) is a major causative agent of food-borne gastroenteritis worldwide. Currently, there are no vaccines or effective therapeutic interventions for this virus. Development of an attenuated vaccine for HuNoV has been hampered by the inability to grow the virus in cell culture. Thus, a vector-based vaccine may be ideal. In this study, we constructed a recombinant vesicular stomatitis virus (rVSV-VP1) expressing VP1, the major capsid protein of HuNoV. Expression of the capsid protein by VSV resulted in the formation of HuNoV virus-like particles (VLPs) that are morphologically and antigenically similar to native virions. Recombinant rVSV-VP1 was attenuated in cultured mammalian cells as well as in mice. Mice inoculated with a single dose of rVSV-VP1 through intranasal and oral routes stimulated a significantly stronger humoral and cellular immune response than baculovirus-expressed VLP vaccination. Moreover, we demonstrated that mice inoculated with rVSV-VP1 triggered a comparable level of fecal and vaginal IgA antibody. Taken together, the VSV recombinant system not only provides a new approach to generate HuNoV VLPs in vitro but also a new avenue for the development of vectored vaccines against norovirus and other noncultivable viruses.

Effects of Chitosan Nanoparticles on Survival, Growth and Meat Quality of Tilapia, Oreochromis Nilotica

Nanotoxicology. Sep, 2011  |  Pubmed ID: 21039183

To evaluate the effect of dietary chitosan and chitosan nanoparticles on survival rate, growth performance and meat quality of tilapia (Oreochromis nilotica) under laboratory conditions, fish were fed with these compounds both at 5.0 g kg(-1) of diet for a period of 60 days. The addition of chitosan nanoparticles (T-2) significantly improved (P < 0.05) final weight, daily weight gain (DWG) and feed conversion ratio (FCR) compared to fish fed chitosan containing diet (T-1) and basal diet (control). However, there were no significant differences in final weight, DWG and FCR between T-1 and control. As for crude fat, the lowest content (P < 0.05) was found in T-2. In addition, a significant increase (P < 0.05) in inosinic acid content was found in T-2 compared with T-1 and control. These results indicate that dietary chitosan nanoparticles supplementation improved the growth performance and meat quality status of tilapia.

Astrocytes Promote TNF-mediated Toxicity to Oligodendrocyte Precursors

Journal of Neurochemistry. Jan, 2011  |  Pubmed ID: 21044081

Neuroinflammation and increased production of tumor necrosis factor (TNF) in the CNS have been implicated in many neurological diseases including white matter disorders periventricular leukomalacia and multiple sclerosis. However, the exact role of TNF in these diseases and how it mediates oligodendrocyte injury remain unclear. Previously, we demonstrated that lipopolysaccharide (LPS) selectively kills oligodendrocyte precursors (preOLs) in a non-cell autonomous fashion through the induction of TNF in mixed glial cultures. Here, we report that activation of oligodendroglial, but not astroglial and microglial, TNFR1 is required for LPS toxicity, and that astrocytes promote TNF-mediated preOL death through a cell contact-dependent mechanism. Microglia were the sole source for TNF production in LPS-treated mixed glial cultures. Ablation of TNFR1 in mixed glia completely prevented LPS-induced death of preOLs. TNFR1-expressing preOLs were similarly susceptible to LPS treatment when seeded into wildtype and TNFR1(-/-) mixed glial cultures, demonstrating a requirement for oligodendroglial TNFR1 in the cell death. Although exogenous TNF failed to cause significant cell death in enriched preOL cultures, it became cytotoxic when preOLs were in contact with astrocytes. Collectively, our results demonstrate oligodendroglial TNFR1 in mediating inflammatory destruction of preOLs and suggest a previously unrecognized role for astrocytes in promoting TNF toxicity to preOLs.

Induction of Apoptosis in Human Colon Carcinoma COLO 205 Cells by the Recombinant α Subunit of C-phycocyanin

Biotechnology Letters. Mar, 2011  |  Pubmed ID: 21072562

The α-subunit of C-phycocyanin (CpcA) was expressed in Escherichia coli and purified. The recombinant CpcA inhibited the growth of human colon carcinoma COLO 205 cells. Typical apoptotic morphological characteristics, such as chromatin condensation and nuclear fragmentation, were observed in CpcA-treated COLO 205 cells by fluorescence microscopy and transmission electron microscopy. Moreover, the apoptotic process was associated with the Bax/Bcl-2 ratio up-regulation, mitochondrial membrane depolarization, cytochrome c release, and caspase-9 activation. These findings indicate that CpcA induced the death of COLO 205 cells through the intrinsic apoptotic pathway.

Expression of β-defensin-3 in Lungs of Immunocompetent Rats with Methicillin-resistant Staphylococcus Aureus Ventilator-associated Pneumonia

The Journal of Surgical Research. Aug, 2011  |  Pubmed ID: 20400114

Despite the rising incidence and high rate of treatment failure of ventilator-associated pneumonia (VAP) due to methicillin-resistant Staphylococcus aureus (MRSA), to date there has been no rat model specifically designed for antimicrobial evaluation. β-Defensin-3 Acronym for β-defensin-3 is correct as (BD-3) is an antimicrobial peptide and mainly expresses in the gastrointestinal and respiratory tract. It demonstrates a broad spectrum of potent antimicrobial activity against many potentially pathogenic microbes, including multi-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Therefore, the authors hypothesized that the expression of BD-3 might change in lungs of rats with MRSA VAP, and this change might play an important role in the pathogenesis of VAP.

GO-Module: Functional Synthesis and Improved Interpretation of Gene Ontology Patterns

Bioinformatics (Oxford, England). May, 2011  |  Pubmed ID: 21421553

GO-Module is a web-accessible synthesis and visualization tool developed for end-user biologists to greatly simplify the interpretation of prioritized Gene Ontology (GO) terms. GO-Module radically reduces the complexity of raw GO results into compact biomodules in two distinct ways, by (i) constructing biomodules from significant GO terms based on hierarchical knowledge, and (ii) refining the GO terms in each biomodule to contain only true positive results. Altogether, the features (biomodules) of GO-Module outputs are better organized and on average four times smaller than the input GO terms list (P = 0.0005, n = 16). AVAILABILITY: http://lussierlab.org/GO-Module.

Inactivation of a Human Norovirus Surrogate, Human Norovirus Virus-like Particles, and Vesicular Stomatitis Virus by Gamma Irradiation

Applied and Environmental Microbiology. May, 2011  |  Pubmed ID: 21441330

Gamma irradiation is a nonthermal processing technology that has been used for the preservation of a variety of food products. This technology has been shown to effectively inactivate bacterial pathogens. Currently, the FDA has approved doses of up to 4.0 kGy to control food-borne pathogens in fresh iceberg lettuce and spinach. However, whether this dose range effectively inactivates food-borne viruses is less understood. We have performed a systematic study on the inactivation of a human norovirus surrogate (murine norovirus 1 [MNV-1]), human norovirus virus-like particles (VLPs), and vesicular stomatitis virus (VSV) by gamma irradiation. We demonstrated that MNV-1 and human norovirus VLPs were resistant to gamma irradiation. For MNV-1, only a 1.7- to 2.4-log virus reduction in fresh produce at the dose of 5.6 kGy was observed. However, VSV was more susceptible to gamma irradiation, and a 3.3-log virus reduction at a dose of 5.6 kGy in Dulbecco's modified Eagle medium (DMEM) was achieved. We further demonstrated that gamma irradiation disrupted virion structure and degraded viral proteins and genomic RNA, which resulted in virus inactivation. Using human norovirus VLPs as a model, we provide the first evidence that the capsid of human norovirus has stability similar to that of MNV-1 after exposure to gamma irradiation. Overall, our results suggest that viruses are much more resistant to irradiation than bacterial pathogens. Although gamma irradiation used to eliminate the virus contaminants in fresh produce by the FDA-approved irradiation dose limits seems impractical, this technology may be practical to inactivate viruses for other purposes, such as sterilization of medical equipment.

Effect of Tea Polyphenols on Microbiological and Biochemical Quality of Collichthys Fish Ball

Journal of the Science of Food and Agriculture. Jul, 2011  |  Pubmed ID: 21445875

Tea polyphenols (TP), as the most active constituents of tea, are considered natural food additives. This study examined the preservative properties of TP for Collichthys fish ball in well storage. Vacuum-packed Collichthys fish balls were treated with 0, 0.1, 0.15, 0.20, 0.25, and 0.30 g kg(-1) TP and stored at 0 °C for 17 days.

[Attenuation Effects of Compatible Medicines on Arsenical and Lead Toxicity of Badu Shengji San]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Aug, 2011  |  Pubmed ID: 22066453

Badu Shengji San(BDSJS) is a traditional Chinese medicine (TCM) used for drawing out toxin, eliminating suppuration and promoting granulation. Toxic minerals such as arsenic and lead are the two most important components of BDSJS. Previous hypothesis indicated that according to the compatibility theory of TCM, the toxicity of the entire BDSJS was weaker than that of arsenic and lead, respectively. In the present study, SD rats with injured skin were treated with distilled water and different composition of BDSJS (complete formulations, compatible herbs, mineral medicine containing arsenic and lead, mineral medicine containing arsenic and mineral medicine containing lead) once a day for consecutive 2 weeks. Kidney coefficient and urinary beta-N-acetyl glucosidase (NAG) were used as the indicators of renal toxicity and the content of malondiadehyde (MDA), superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), glutathione (GSH) and metallothionein (MT) in the renal tissue were measured. Our data showed that kidney coefficient, the severity of renal pathological lesion and MT level in the kidney of the entire BDSJS group decreased significantly compared with arsenic and lead group. Additionally, the NAG content of the entire BDSJS group had the decreased trend. The kidney CuZn-SOD level of the entire BDSJS group had the increased trend, but the MDA, GSH-PX, GSH level had no obvious difference. Our results suggested that compatible herbs in BDSJS relieved renal injury induced by arsenic and lead, and the attenuation mechanism may be related to MT and CuZn-SOD, but not to MDA, GSH-PX and GSH directly.

Complete Transposition of the Atrioventricular Valves Associated with Left Ventricular Apical Hypoplasia

Circulation. Nov, 2011  |  Pubmed ID: 22105200

Enhanced Removal of a Human Norovirus Surrogate from Fresh Vegetables and Fruits by a Combination of Surfactants and Sanitizers

Applied and Environmental Microbiology. Jul, 2011  |  Pubmed ID: 21622782

Fruits and vegetables are major vehicles for transmission of food-borne enteric viruses since they are easily contaminated at pre- and postharvest stages and they undergo little or no processing. However, commonly used sanitizers are relatively ineffective for removing human norovirus surrogates from fresh produce. In this study, we systematically evaluated the effectiveness of surfactants on removal of a human norovirus surrogate, murine norovirus 1 (MNV-1), from fresh produce. We showed that a panel of surfactants, including sodium dodecyl sulfate (SDS), Nonidet P-40 (NP-40), Triton X-100, and polysorbates, significantly enhanced the removal of viruses from fresh fruits and vegetables. While tap water alone and chlorine solution (200 ppm) gave only <1.2-log reductions in virus titer in all fresh produce, a solution containing 50 ppm of surfactant was able to achieve a 3-log reduction in virus titer in strawberries and an approximately 2-log reduction in virus titer in lettuce, cabbage, and raspberries. Moreover, a reduction of approximately 3 logs was observed in all the tested fresh produce after sanitization with a solution containing a combination of 50 ppm of each surfactant and 200 ppm of chlorine. Taken together, our results demonstrate that the combination of a surfactant with a commonly used sanitizer enhanced the efficiency in removing viruses from fresh produce by approximately 100 times. Since SDS is an FDA-approved food additive and polysorbates are recognized by the FDA as GRAS (generally recognized as safe) products, implementation of this novel sanitization strategy would be a feasible approach for efficient reduction of the virus load in fresh produce.

Protein-network Modeling of Prostate Cancer Gene Signatures Reveals Essential Pathways in Disease Recurrence

Journal of the American Medical Informatics Association : JAMIA. Jul-Aug, 2011  |  Pubmed ID: 21672909

Uncovering the dominant molecular deregulation among the multitude of pathways implicated in aggressive prostate cancer is essential to intelligently developing targeted therapies. Paradoxically, published prostate cancer gene expression signatures of poor prognosis share little overlap and thus do not reveal shared mechanisms. The authors hypothesize that, by analyzing gene signatures with quantitative models of protein-protein interactions, key pathways will be elucidated and shown to be shared.

Electron-beam Inactivation of a Norovirus Surrogate in Fresh Produce and Model Systems

Journal of Food Protection. Jul, 2011  |  Pubmed ID: 21740718

Norovirus remains the leading cause of foodborne illness, but there is no effective intervention to eliminate viral contaminants in fresh produce. Murine norovirus 1 (MNV-1) was inoculated in either 100 ml of liquid or 100 g of food. The inactivation of MNV-1 by electron-beam (e-beam), or high-energy electrons, at varying doses was measured in model systems (phosphate-buffered saline [PBS], Dulbecco's modified Eagle's medium [DMEM]) or from fresh foods (shredded cabbage, diced strawberries). E-beam was applied at a current of 1.5 mA, with doses of 0, 2, 4, 6, 8, 10, and 12 kGy. The surviving viral titer was determined by plaque assays in RAW 264.7 cells. In PBS and DMEM, e-beam at 0 and 2 kGy provided less than a 1-log reduction of virus. At doses of 4, 6, 8, 10, and 12 kGy, viral inactivation in PBS ranged from 2.37 to 6.40 log, while in DMEM inactivation ranged from 1.40 to 3.59 log. Irradiation of inoculated cabbage showed up to a 1-log reduction at 4 kGy, and less than a 3-log reduction at 12 kGy. On strawberries, less than a 1-log reduction occurred at doses up to 6 kGy, with a maximum reduction of 2.21 log at 12 kGy. These results suggest that a food matrix might provide increased survival for viruses. In foods, noroviruses are difficult to inactivate because of the protective effect of the food matrix, their small sizes, and their highly stable viral capsid.

Myricetin Affords Protection Against Peroxynitrite-mediated DNA Damage and Hydroxyl Radical Formation

Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association. Sep, 2011  |  Pubmed ID: 21741426

Peroxynitrite has been extensively implicated in the pathogenesis of various forms of neurodegenerative disorders via its cytotoxic effects, this study was undertaken to investigate whether the neuroprotective effect of myricetin is associated with inhibition of peroxynitrite-mediated DNA damage, a critical event leading to peroxynitrite elicited cytotoxicity. We observed that peroxynitrite can cause DNA damage in ϕX-174 plasmid DNA and rat primary astrocytes. The presence of myricetin at physiological concentration was found to significantly inhibit DNA strand breakage induced by both peroxynitrite and its generator 3-morpholinosydnonimine (SIN-1). Moreover, the consumption of oxygen caused by SIN-1 was found to be decreased in the presence of myricetin, indicating that myricetin might affect the auto-oxidation of SIN-1. Furthermore, EPR spectroscopy demonstrated that the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from peroxynitrite, and that myricetin inhibited the adduct signal in a concentration-dependent manner. Taken together, these results demonstrate for the first time that myricetin can inhibit peroxynitrite-mediated DNA damage and hydroxyl radical formation.

[Effect of Chlorogenic Acid on Degranulation in Mast Cell RBL-2H3]

Zhongguo Zhong Yao Za Zhi = Zhongguo Zhongyao Zazhi = China Journal of Chinese Materia Medica. Apr, 2011  |  Pubmed ID: 21761734

To provide evidences for evaluating the role of chlorogenic acid (CA) on the adverse reaction of traditional Chinese medicine injection and promoting clinical rational usage of CA, the effect of CA and chlorogenic acid-HSA(CA-HSA) on the degranulation in mast cell RBL-2H3 were compared and the allergenic effect and its mechanism were investigated.

Dissecting Aneurysm of the Left Atrium with an Abnormal Left Ventricular-atrial Tunnel

Journal of the American College of Cardiology. Jul, 2011  |  Pubmed ID: 21777754

[Cholesterol-degrading by Lactobacillus Plantarum LpT1 and LpT2 in Vitro]

Wei Sheng Wu Xue Bao = Acta Microbiologica Sinica. Apr, 2011  |  Pubmed ID: 21796993

To explore the mechanism of cholesterol-degrading by Lactobacillus plantarum LpT1 and LpT2 in vitro.

Poly(I:C) Promotes TNFα/TNFR1-dependent Oligodendrocyte Death in Mixed Glial Cultures

Journal of Neuroinflammation. 2011  |  Pubmed ID: 21812954

Activation of glial cells via toll-like receptors (TLRs) and other intracellular pathogen recognition receptors promotes the release of potentially toxic acute phase reactants such as TNFα and nitric oxide into the extracellular space. As such, prolonged glial activation, as is thought to occur during a persistent viral infection of the CNS, may contribute to both neurodegeneration and demyelination. However, the effects of virus-induced glial activation on oligodendrocytes are not fully understood.

The Patency of Sequential and Individual Vein Coronary Bypass Grafts: a Systematic Review

The Annals of Thoracic Surgery. Oct, 2011  |  Pubmed ID: 21958774

Saphenous vein grafts continue to be the backbone of daily coronary revascularization practice, but controversy still exists about whether to use them as an individual or sequential graft. We undertook a systematic review and meta-analysis of cohort studies to compare the midterm or long-term patency of sequential vein coronary bypass grafts with those of vein grafts.

Lack of Correlation Between Virus Barosensitivity and the Presence of a Viral Envelope During Inactivation of Human Rotavirus, Vesicular Stomatitis Virus, and Avian Metapneumovirus by High-pressure Processing

Applied and Environmental Microbiology. Dec, 2011  |  Pubmed ID: 22003028

High-pressure processing (HPP) is a nonthermal technology that has been shown to effectively inactivate a wide range of microorganisms. However, the effectiveness of HPP on inactivation of viruses is relatively less well understood. We systematically investigated the effects of intrinsic (pH) and processing (pressure, time, and temperature) parameters on the pressure inactivation of a nonenveloped virus (human rotavirus [HRV]) and two enveloped viruses (vesicular stomatitis virus [VSV] and avian metapneumovirus [aMPV]). We demonstrated that HPP can efficiently inactivate all tested viruses under optimal conditions, although the pressure susceptibilities and the roles of temperature and pH substantially varied among these viruses regardless of the presence of a viral envelope. We found that VSV was much more stable than most food-borne viruses, whereas aMPV was highly susceptible to HPP. When viruses were held for 2 min under 350 MPa at 4°C, 1.1-log, 3.9-log, and 5.0-log virus reductions were achieved for VSV, HRV, and aMPV, respectively. Both VSV and aMPV were more susceptible to HPP at higher temperature and lower pH. In contrast, HRV was more easily inactivated at higher pH, although temperature did not have a significant impact on inactivation. Furthermore, we demonstrated that the damage of virion structure by disruption of the viral envelope and/or capsid is the primary mechanism underlying HPP-induced viral inactivation. In addition, VSV glycoprotein remained antigenic although VSV was completely inactivated. Taken together, our findings suggest that HPP is a promising technology to eliminate viral contaminants in high-risk foods, water, and other fomites.

385 C/A Polymorphism of the Fatty Acid Amide Hydrolase Gene is Associated with Metabolic Syndrome in the Chinese Han Population

Archives of Medical Science : AMS. Jun, 2011  |  Pubmed ID: 22295023

The endocannabinoid system participates in food intake, energy balance and lipid and glucose metabolism. The biological effects of cannabinoids are limited by the activation of the endocannabinoid degrading enzyme fatty acid amide hydrolase (FAAH). This study aims to analyse whether 385 C/A polymorphism of FAAH is associated with metabolic syndrome (MetS) in the Chinese Han population.

Translating Mendelian and Complex Inheritance of Alzheimer's Disease Genes for Predicting Unique Personal Genome Variants

Journal of the American Medical Informatics Association : JAMIA. Mar, 2012  |  Pubmed ID: 22319180

Objective Although trait-associated genes identified as complex versus single-gene inheritance differ substantially in odds ratio, the authors nonetheless posit that their mechanistic concordance can reveal fundamental properties of the genetic architecture, allowing the automated interpretation of unique polymorphisms within a personal genome. Materials and methods An analytical method, SPADE-gen, spanning three biological scales was developed to demonstrate the mechanistic concordance between Mendelian and complex inheritance of Alzheimer's disease (AD) genes: biological functions (BP), protein interaction modeling, and protein domain implicated in the disease-associated polymorphism. Results Among Gene Ontology (GO) biological processes (BP) enriched at a false detection rate <5% in 15 AD genes of Mendelian inheritance (Online Mendelian Inheritance in Man) and independently in those of complex inheritance (25 host genes of intragenic AD single-nucleotide polymorphisms confirmed in genome-wide association studies), 16 overlapped (empirical p=0.007) and 45 were similar (empirical p<0.009; information theory). SPAN network modeling extended the canonical pathway of AD (KEGG) with 26 new protein interactions (empirical p<0.0001). Discussion The study prioritized new AD-associated biological mechanisms and focused the analysis on previously unreported interactions associated with the biological processes of polymorphisms that affect specific protein domains within characterized AD genes and their direct interactors using (1) concordant GO-BP and (2) domain interactions within STRING protein-protein interactions corresponding to the genomic location of the AD polymorphism (eg, EPHA1, APOE, and CD2AP). Conclusion These results are in line with unique-event polymorphism theory, indicating how disease-associated polymorphisms of Mendelian or complex inheritance relate genetically to those observed as 'unique personal variants'. They also provide insight for identifying novel targets, for repositioning drugs, and for personal therapeutics.

Demyelination and Remyelination in Anatomically Distinct Regions of the Corpus Callosum Following Cuprizone Intoxication

Neuroscience Research. Jan, 2012  |  Pubmed ID: 22015947

Multiple sclerosis is a chronic demyelinating disease of the central nervous system. Spontaneous remyelination during early disease stages is thought to preserve and partially restore function. However, this process ceases in later stages despite the presence of pre-oligodendrocytes. Cuprizone-induced demyelination is a useful model with which to study the remyelination process. Previous studies have demonstrated heterogeneities in demyelination in individual animals. Here we investigated regional differences in demyelination and remyelination within the corpus callosum. C57BL/6 mice were fed 0.2% cuprizone for 5 weeks to induce demyelination. Remyelination was examined 2-5 weeks after cuprizone withdrawal. Immunohistochemistry and electron microscopy were used to quantify regional differences in demyelination, gliosis, and remyelination. We found that, while demyelination was limited in the rostral region of corpus callosum, nearly complete demyelination occurred in the caudal callosum, beginning at approximately -0.5mm from bregma. Astrogliosis and microgliosis were correlated with demyelination and differed between the rostral and caudal callosal structures. Remyelination upon cessation of cuprizone ensued at different rates with splenium remyelinating faster than dorsal hippocampal commissure. Our data show anatomical differences of cuprizone-induced demyelination and remyelination in the corpus callosum and the importance of examining specific callosal regions in myelin repair studies using this model.

Genetic Interactions Between Chromosomes 11 and 18 Contribute to Airway Hyperresponsiveness in Mice

PloS One. 2012  |  Pubmed ID: 22253740

We used two-dimensional quantitative trait locus analysis to identify interacting genetic loci that contribute to the native airway constrictor hyperresponsiveness to methacholine that characterizes A/J mice, relative to C57BL/6J mice. We quantified airway responsiveness to intravenous methacholine boluses in eighty-eight (C57BL/6J X A/J) F(2) and twenty-seven (A/J X C57BL/6J) F(2) mice as well as ten A/J mice and six C57BL/6J mice; all studies were performed in male mice. Mice were genotyped at 384 SNP markers, and from these data two-QTL analyses disclosed one pair of interacting loci on chromosomes 11 and 18; the homozygous A/J genotype at each locus constituted the genetic interaction linked to the hyperresponsive A/J phenotype. Bioinformatic network analysis of potential interactions among proteins encoded by genes in the linked regions disclosed two high priority subnetworks - Myl7, Rock1, Limk2; and Npc1, Npc1l1. Evidence in the literature supports the possibility that either or both networks could contribute to the regulation of airway constrictor responsiveness. Together, these results should stimulate evaluation of the genetic contribution of these networks in the regulation of airway responsiveness in humans.

Complex-disease Networks of Trait-associated Single-nucleotide Polymorphisms (SNPs) Unveiled by Information Theory

Journal of the American Medical Informatics Association : JAMIA. Mar, 2012  |  Pubmed ID: 22278381

Objective Thousands of complex-disease single-nucleotide polymorphisms (SNPs) have been discovered in genome-wide association studies (GWAS). However, these intragenic SNPs have not been collectively mined to unveil the genetic architecture between complex clinical traits. The authors hypothesize that biological annotations of host genes of trait-associated SNPs may reveal the biomolecular modularity across complex-disease traits and offer insights for drug repositioning. Methods Trait-to-polymorphism (SNPs) associations confirmed in GWAS were used. A novel method to quantify trait-trait similarity anchored in Gene Ontology annotations of human proteins and information theory was developed. The results were then validated with the shortest paths of physical protein interactions between biologically similar traits. Results A network was constructed consisting of 280 significant intertrait similarities among 177 disease traits, which covered 1438 well-validated disease-associated SNPs. Thirty-nine percent of intertrait connections were confirmed by curators, and the following additional studies demonstrated the validity of a proportion of the remainder. On a phenotypic trait level, higher Gene Ontology similarity between proteins correlated with smaller 'shortest distance' in protein interaction networks of complexly inherited diseases (Spearman p<2.2×10(-16)). Further, 'cancer traits' were similar to one another, as were 'metabolic syndrome traits' (Fisher's exact test p=0.001 and 3.5×10(-7), respectively). Conclusion An imputed disease network by information-anchored functional similarity from GWAS trait-associated SNPs is reported. It is also demonstrated that small shortest paths of protein interactions correlate with complex-disease function. Taken together, these findings provide the framework for investigating drug targets with unbiased functional biomolecular networks rather than worn-out single-gene and subjective canonical pathway approaches.

Single Sample Expression-anchored Mechanisms Predict Survival in Head and Neck Cancer

PLoS Computational Biology. Jan, 2012  |  Pubmed ID: 22291585

Gene expression signatures that are predictive of therapeutic response or prognosis are increasingly useful in clinical care; however, mechanistic (and intuitive) interpretation of expression arrays remains an unmet challenge. Additionally, there is surprisingly little gene overlap among distinct clinically validated expression signatures. These "causality challenges" hinder the adoption of signatures as compared to functionally well-characterized single gene biomarkers. To increase the utility of multi-gene signatures in survival studies, we developed a novel approach to generate "personal mechanism signatures" of molecular pathways and functions from gene expression arrays. FAIME, the Functional Analysis of Individual Microarray Expression, computes mechanism scores using rank-weighted gene expression of an individual sample. By comparing head and neck squamous cell carcinoma (HNSCC) samples with non-tumor control tissues, the precision and recall of deregulated FAIME-derived mechanisms of pathways and molecular functions are comparable to those produced by conventional cohort-wide methods (e.g. GSEA). The overlap of "Oncogenic FAIME Features of HNSCC" (statistically significant and differentially regulated FAIME-derived genesets representing GO functions or KEGG pathways derived from HNSCC tissue) among three distinct HNSCC datasets (pathways:46%, p<0.001) is more significant than the gene overlap (genes:4%). These Oncogenic FAIME Features of HNSCC can accurately discriminate tumors from control tissues in two additional HNSCC datasets (n = 35 and 91, F-accuracy = 100% and 97%, empirical p<0.001, area under the receiver operating characteristic curves = 99% and 92%), and stratify recurrence-free survival in patients from two independent studies (p = 0.0018 and p = 0.032, log-rank). Previous approaches depending on group assignment of individual samples before selecting features or learning a classifier are limited by design to discrete-class prediction. In contrast, FAIME calculates mechanism profiles for individual patients without requiring group assignment in validation sets. FAIME is more amenable for clinical deployment since it translates the gene-level measurements of each given sample into pathways and molecular function profiles that can be applied to analyze continuous phenotypes in clinical outcome studies (e.g. survival time, tumor volume).

Aberrant Upregulation of Astroglial Ceramide Potentiates Oligodendrocyte Injury

Brain Pathology (Zurich, Switzerland). Jan, 2012  |  Pubmed ID: 21615590

Oligodendroglial injury is a pathological hallmark of many human white matter diseases, including multiple sclerosis (MS) and periventricular leukomalacia (PVL). Critical regulatory mechanisms of oligodendroglia destruction, however, remain incompletely understood. Ceramide, a bioactive sphingolipid pivotal to sphingolipid metabolism pathways, regulates cell death in response to diverse stimuli and has been implicated in neurodegenerative disorders. We report here that ceramide accumulates in reactive astrocytes in active lesions of MS and PVL, as well as in animal models of demyelination. Serine palmitoyltransferase, the rate-limiting enzyme for ceramide de novo biosynthesis, was consistently upregulated in reactive astrocytes in the cuprizone mouse model of demyelination. Mass spectrometry confirmed the upregulation of specific ceramides during demyelination, and revealed a concomitant increase of sphingosine and a suppression of sphingosine-1-phosphate, a potent signaling molecule with key roles in cell survival and mitogenesis. Importantly, this altered sphingolipid metabolism during demyelination was restored upon active remyelination. In culture, ceramide acted synergistically with tumor necrosis factor, leading to apoptotic death of oligodendroglia in an astrocyte-dependent manner. Taken together, our findings implicate that disturbed sphingolipid pathways in reactive astrocytes may indirectly contribute to oligodendroglial injury in cerebral white matter disorders.