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NADPH Oxidase Limits Innate Immune Responses in the Lungs in Mice

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Chronic granulomatous disease (CGD), an inherited disorder of the NADPH oxidase in which phagocytes are defective in generating superoxide anion and downstream reactive oxidant intermediates (ROIs), is characterized by recurrent bacterial and fungal infections and by excessive inflammation (e.g., inflammatory bowel disease). The mechanisms by which NADPH oxidase regulates inflammation are not well understood.

Methodology/Principal Findings

We found that NADPH oxidase restrains inflammation by modulating redox-sensitive innate immune pathways. When challenged with either intratracheal zymosan or LPS, NADPH oxidase-deficient p47^phox−/− mice and gp91^phox-deficient mice developed exaggerated and progressive lung inflammation, augmented NF-κB activation, and elevated downstream pro-inflammatory cytokines (TNF-α, IL-17, and G-CSF) compared to wildtype mice. Replacement of functional NADPH oxidase in bone marrow-derived cells restored the normal lung inflammatory response. Studies in vivo and in isolated macrophages demonstrated that in the absence of functional NADPH oxidase, zymosan failed to activate Nrf2, a key redox-sensitive anti-inflammatory regulator. The triterpenoid, CDDO-Im, activated Nrf2 independently of NADPH oxidase and reduced zymosan-induced lung inflammation in CGD mice. Consistent with these findings, zymosan-treated peripheral blood mononuclear cells from X-linked CGD patients showed impaired Nrf2 activity and increased NF-κB activation.

Conclusions/Significance

These studies support a model in which NADPH oxidase-dependent, redox-mediated signaling is critical for termination of lung inflammation and suggest new potential therapeutic targets for CGD.

The Suppression of Immune System Disorders by Passive Attrition

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Exposure to infectious diseases has an unexpected benefit of inhibiting autoimmune diseases and allergies. This is one of many fundamental fitness tradeoffs associated with immune system architecture. The immune system attacks pathogens, but also may (inappropriately) attack the host. Exposure to pathogens can suppress the deleterious response, at the price of illness and the decay of immunity to previous diseases. This “hygiene hypothesis” has been associated with several possible underlying biological mechanisms. This study focuses on physiological constraints that lead to competition for survival between immune system cell types. Competition maintains a relatively constant total number of cells within each niche. The constraint implies that adding cells conferring new immunity requires loss (passive attrition) of some cells conferring previous immunities. We consider passive attrition as a mechanism to prevent the initial proliferation of autoreactive cells, thus preventing autoimmune disease. We see that this protection is a general property of homeostatic regulation and we look specifically at both the IL-15 and IL-7 regulated niches to make quantitative predictions using a mathematical model. This mathematical model yields insight into the dynamics of the “Hygiene Hypothesis,” and makes quantitative predictions for experiments testing the ability of passive attrition to suppress immune system disorders. The model also makes a prediction of an anti-correlation between prevalence of immune system disorders and passive attrition rates.

Modulation of Hepatocarcinoma Cell Morphology and Activity by Parylene-C Coating on PDMS

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

The ability to understand and locally control the morphogenesis of mammalian cells is a fundamental objective of cell and developmental biology as well as tissue engineering research. We present parylene-C (ParC) deposited on polydimethylsiloxane (PDMS) as a new substratum for in vitro advanced cell culture in the case of Human Hepatocarcinoma (HepG2) cells.

Principal Findings

Our findings establish that the intrinsic properties of ParC-coated PDMS (ParC/PDMS) influence and modulate initial extracellular matrix (ECM; here, type-I collagen) surface architecture, as compared to non-coated PDMS substratum. Morphological changes induced by the presence of ParC on PDMS were shown to directly affect liver cell metabolic activity and the expression of transmembrane receptors implicated in cell adhesion and cell-cell interaction. These changes were characterized by atomic force microscopy (AFM), which elucidated differences in HepG2 cell adhesion, spreading, and reorganization into two- or three-dimensional structures by neosynthesis of ECM components. Local modulation of cell aggregation was successfully performed using ParC/PDMS micropatterns constructed by simple microfabrication.

Conclusion/Significance

We demonstrated for the first time the modulation of HepG2 cells’ behavior in relation to the intrinsic physical properties of PDMS and ParC, enabling the local modulation of cell spreading in a 2D or 3D manner by simple microfabrication techniques. This work will provide promising insights into the development of cell-based platforms that have many applications in the field of in vitro liver tissue engineering, pharmacology and therapeutics.

Genetic Variations in HSPA8 Gene Associated with Coronary Heart Disease Risk in a Chinese Population

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

There is ample evidence that Hsp70 takes part in the progress of coronary heart disease (CHD). This implies that genetic variants of Hsp70 genes such as HSPA8 (HSC70) gene might contribute to the development of CHD. The present study aimed to investigate whether certain genetic variants of HSPA8 gene are associated with CHD in Han Chinese people.

Methodology/Principal Findings

A total of 2006 subjects (1003 CHD cases and 1003 age- and sex- matched healthy controls) were recruited. Genetic variants in the HSPA8 gene were identified by sequencing of the gene in 60 unrelated Chinese. Four tag single nucleotide polymorphisms (tagSNPs) (rs2236659, rs2276077, rs10892958, and rs1461496) were selected and genotyped. The function of the significant SNP was evaluated using luciferase reporter assays in two cell lines. By sequencing the promoter and all exons and introns of the HSPA8 gene, 23 genetic variants were identified. One promoter SNP rs2236659 was associated with susceptibility to CHD. Carriers of the “C” allele of rs2236659 had decreased CHD risk with odds ratio (OR) of 0.78 (95% CI: 0.62, 0.98; P = 0.033) after adjustment for conventional risk factors. Haplotype analyses indicated that haplotype GCGC contributed to a lower CHD risk (OR = 0.78, 95% CI: 0.65, 0.93; P = 0.006) compared with the common haplotype AGGT. In a transfection assay, the C allele of rs2236659 showed a 37–40% increase in luciferase expression of the reporter gene luciferase in endothelial and non-endothelial cells compared with the T allele.

Conclusions/Significance

These findings suggest that genetic variants in HSPA8 gene (especially promoter SNP rs2236659) contribute to the CHD susceptibility by affecting its expression level.

Wolbachia Age-Sex-Specific Density in Aedes albopictus: A Host Evolutionary Response to Cytoplasmic Incompatibility?

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Wolbachia bacteria have invaded many arthropod species by inducing Cytoplasmic Incompatibility (CI). These symbionts represent fascinating objects of study for evolutionary biologists, but also powerful potential biocontrol agents. Here, we assess the density dynamics of Wolbachia infections in males and females of the mosquito Aedes albopitcus, an important vector of human pathogens, and interpret the results within an evolutionary framework.

Methodology/Principal Findings

Wolbachia densities were measured in natural populations and in age controlled mosquitoes using quantitative PCR. We show that the density dynamics of the wAlbA Wolbachia strain infecting Aedes albopictus drastically differ between males and females, with a very rapid decay of infection in males only.

Conclusions/Significance

Theory predicts that Wolbachia and its hosts should cooperate to improve the transmission of infection to offspring, because only infected eggs are protected from the effects of CI. However, incompatible matings effectively lower the fertility of infected males, so that selection acting on the host genome should tend to reduce the expression of CI in males, for example, by reducing infection density in males before sexual maturation. The rapid decay of one Wolbachia infection in Aedes albopictus males, but not in females, is consistent with this prediction. We suggest that the commonly observed reduction in CI intensity with male age reflects a similar evolutionary process. Our results also highlight the importance of monitoring infection density dynamics in both males and females to assess the efficiency of Wolbachia-based control strategies.

Activation of PPARβ/δ Causes a Psoriasis-Like Skin Disease In Vivo

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Psoriasis is one of the most frequent skin diseases world-wide. The disease impacts enormously on affected patients and poses a huge financial burden on health care providers. Several lines of evidence suggest that the nuclear hormone receptor peroxisome proliferator activator (PPAR) β/δ, known to regulate epithelial differentiation and wound healing, contributes to psoriasis pathogenesis. It is unclear, however, whether activation of PPARβ/δ is sufficient to trigger psoriasis-like changes in vivo.

Methodology/Principal Findings

Using immunohistochemistry, we define the distribution of PPARβ/δ in the skin lesions of psoriasis. By expression profiling, we confirm that PPARβ/δ is overexpressed in the vast majority of psoriasis patients. We further establish a transgenic model allowing inducible activation of PPARβ/δ in murine epidermis mimicking its distribution in psoriasis lesions. Upon activation of PPARβ/δ, transgenic mice sustain an inflammatory skin disease strikingly similar to psoriasis, featuring hyperproliferation of keratinocytes, dendritic cell accumulation, and endothelial activation. Development of this phenotype requires the activation of the Th17 subset of T cells, shown previously to be central to psoriasis. Moreover, gene dysregulation in the transgenic mice is highly similar to that in psoriasis. Key transcriptional programs activated in psoriasis, including IL1-related signalling and cholesterol biosynthesis, are replicated in the mouse model, suggesting that PPARβ/δ regulates these transcriptional changes in psoriasis. Finally, we identify phosphorylation of STAT3 as a novel pathway activated by PPARβ/δ and show that inhibition of STAT3 phosphorylation blocks disease development.

Conclusions

Activation of PPARβ/δ in the epidermis is sufficient to trigger inflammatory changes, immune activation, and signalling, and gene dysregulation characteristic of psoriasis.

GSK3 Influences Social Preference and Anxiety-Related Behaviors during Social Interaction in a Mouse Model of Fragile X Syndrome and Autism

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Nearly 1% of children in the United States exhibit autism spectrum disorders, but causes and treatments remain to be identified. Mice with deletion of the fragile X mental retardation 1 (Fmr1) gene are used to model autism because loss of Fmr1 gene function causes Fragile X Syndrome (FXS) and many people with FXS exhibit autistic-like behaviors. Glycogen synthase kinase-3 (GSK3) is hyperactive in brains of Fmr1 knockout mice, and inhibition of GSK3 by lithium administration ameliorates some behavioral impairment in these mice. We extended our studies of this association by testing whether GSK3 contributes to socialization behaviors. This used two mouse models with disrupted regulation of GSK3, Fmr1 knockout mice and GSK3 knockin mice, in which inhibitory serines of the two isoforms of GSK3, GSK3α and GSK3β, are mutated to alanines, leaving GSK3 fully active.

Methodology/Principal Findings

To assess sociability, test mice were introduced to a restrained stimulus mouse (S1) for 10 min, followed by introduction of a second restrained stimulus mouse (S2) for 10 min, which assesses social preference. Fmr1 knockout and GSK3 knockin mice displayed no deficit in sociability with the S1 mouse, but unlike wild-type mice neither demonstrated social preference for the novel S2 mouse. Fmr1 knockout mice displayed more anxiety-related behaviors during social interaction (grooming, rearing, and digging) than wild-type mice, which was ameliorated by inhibition of GSK3 with chronic lithium treatment.

Conclusions/Significance

These results indicate that impaired inhibitory regulation of GSK3 in Fmr1 knockout mice may contribute to some socialization deficits and that lithium treatment can ameliorate certain socialization impairments. As discussed in the present work, these results suggest a role for GSK3 in social behaviors and implicate inhibition of GSK3 as a potential therapeutic.

Exploring Eye Movements in Patients with Glaucoma When Viewing a Driving Scene

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Glaucoma is a progressive eye disease and a leading cause of visual disability. Automated assessment of the visual field determines the different stages in the disease process: it would be desirable to link these measurements taken in the clinic with patient’s actual function, or establish if patients compensate for their restricted field of view when performing everyday tasks. Hence, this study investigated eye movements in glaucomatous patients when viewing driving scenes in a hazard perception test (HPT).

Methodology/Principal Findings

The HPT is a component of the UK driving licence test consisting of a series of short film clips of various traffic scenes viewed from the driver’s perspective each containing hazardous situations that require the camera car to change direction or slow down. Data from nine glaucomatous patients with binocular visual field defects and ten age-matched control subjects were considered (all experienced drivers). Each subject viewed 26 different films with eye movements simultaneously monitored by an eye tracker. Computer software was purpose written to pre-process the data, co-register it to the film clips and to quantify eye movements and point-of-regard (using a dynamic bivariate contour ellipse analysis). On average, and across all HPT films, patients exhibited different eye movement characteristics to controls making, for example, significantly more saccades (P<0.001; 95% confidence interval for mean increase: 9.2 to 22.4%). Whilst the average region of ‘point-of-regard’ of the patients did not differ significantly from the controls, there were revealing cases where patients failed to see a hazard in relation to their binocular visual field defect.

Conclusions/Significance

Characteristics of eye movement patterns in patients with bilateral glaucoma can differ significantly from age-matched controls when viewing a traffic scene. Further studies of eye movements made by glaucomatous patients could provide useful information about the definition of the visual field component required for fitness to drive.

Non-Invasive Bleaching of the Human Lens by Femtosecond Laser Photolysis

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Globally, cataract is the leading cause of blindness and impaired vision. Cataract surgery is an attractive treatment option but it remains unavailable in sufficient quantity for the vast majority of the world population living in areas without access to specialized health care. Reducing blindness from cataract requires solutions that can be applied outside operating theatres. Cataract is a protein conformational disease characterized by accumulation of light absorbing, fluorescent and scattering protein aggregates. The aim of the study was to investigate whether these compounds were susceptible to photobleaching by a non-invasive procedure and whether this would lead to optical rejuvenation of the lens.

Methodology/Principal Findings

Nine human donor lenses were treated with an 800 nm infra-red femtosecond pulsed laser in a treatment zone measuring 1×1×0.52 mm. After laser treatment the age-induced yellow discoloration of the lens was markedly reduced and the transmission of light was increased corresponding to an optical rejuvenation of 3 to 7 years.

Conclusions/Significance

The results demonstrate that the age-induced yellowing of the human lens can be bleached by a non-invasive procedure based on femtosecond laser photolysis. Cataract is a disease associated with old age. At the current technological stage, lens aging is delayed but with a treatment covering the entire lens volume complete optical rejuvenation is expected. Thus, femtosecond photolysis has the potential clinical value of replacing invasive cataract surgery by a non-invasive treatment modality that can be placed in mobile units, thus breaking down many of the barriers impeding access to treatment in remote and poor regions of the world.

Human Breast Cancer Cell Lines Co-Express Neuronal, Epithelial, and Melanocytic Differentiation Markers In Vitro and In Vivo

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Differentiation programs are aberrant in cancer cells allowing them to express differentiation markers in addition to their tissue of origin. In the present study, we demonstrate the multi-lineage differentiation potential of breast cancer cell lines to express multiple neuronal/glial lineage-specific markers as well as mammary epithelial and melanocytic-specific markers. Multilineage expression was detected in luminal (MCF-7 and SKBR3) and basal (MDA-MB-231) types of human breast cancer cell lines. We also observed comparable co-expression of these three cell lineage markers in MDA-MB-435 cells in vitro, in MDA-MB-435 primary tumors derived from parental and single cell clones and in lung metastases in vivo. Furthermore, ectoderm multi-lineage transdifferentiation was also found in human melanoma (Ul-MeL) and glioblastoma cell lines (U87 and D54). These observations indicate that aberrant multi-lineage transdifferentiation or lineage infidelity may be a wide spread phenomenon in cancer.

N-Octanoyl Dopamine, a Non-Hemodyanic Dopamine Derivative, for Cell Protection during Hypothermic Organ Preservation

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Although donor dopamine treatment reduces the requirement for post transplantation dialysis in renal transplant recipients, implementation of dopamine in donor management is hampered by its hemodynamic side-effects. Therefore novel dopamine derivatives lacking any hemodynamic actions and yet are more efficacious in protecting tissue from cold preservation injury are warranted. We hypothesized that variation of the molecular structure would yield more efficacious compounds avoid of any hemodynamic effects.

Methodology/Principal Findings

To this end, we assessed protection against cold preservation injury in HUVEC by the attenuation of lactate dehydrogenase (LDH) release. Modification of dopamine by an alkanoyl group increased cellular uptake and significantly improved efficacy of protection. Further variation revealed that only compounds bearing two hydroxy groups in ortho or para position at the benzene nucleus, i.e. strong reductants, were protective. However, other reducing agents like N-acetyl cysteine and ascorbate, or NADPH oxidase inhibition did not prevent cellular injury following cold storage. Unlike dopamine, a prototypic novel compound caused no hemodynamic side-effects.

Conclusions/Significance

In conclusion, we demonstrate that protection against cold preservation injury by catecholamines is exclusively governed by strong reducing capacity and sufficient lipophilicity. The novel dopamine derivatives might be of clinical relevance in donor pre-conditioning as they are completely devoid of hemodynamic action, their increased cellular uptake would reduce time of treatment and therefore also may have a potential use for non-heart beating donors.

A Novel Analytical Framework for Dissecting the Genetic Architecture of Behavioral Symptoms in Neuropsychiatric Disorders

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

For diagnosis of neuropsychiatric disorders, a categorical classification system is often utilized as a simple way for conceptualizing an often complex clinical picture. This approach provides an unsatisfactory model of mental illness, since in practice patients do not conform to these prototypical diagnostic categories. Family studies show notable familial co-aggregation between schizophrenia and bipolar illness and between schizoaffective disorders and both bipolar disorder and schizophrenia, revealing that mental illness does not conform to such categorical models and is likely to follow a continuum encompassing a spectrum of behavioral symptoms.

Results and Methodology

We introduce an analytic framework to dissect the phenotypic heterogeneity present in complex psychiatric disorders based on the conceptual paradigm of a continuum of psychosis. The approach identifies subgroups of behavioral symptoms that are likely to be phenotypically and genetically homogenous. We have evaluated this approach through analysis of simulated data with simulated behavioral traits and predisposing genetic factors. We also apply this approach to a psychiatric dataset of a genome scan for schizophrenia for which extensive behavioral information was collected for each individual patient and their families. With this approach, we identified significant evidence for linkage among depressed individuals with two distinct symptom profiles, that is individuals with sleep disturbance symptoms with linkage on chromosome 2q13 and also a mutually exclusive group of individuals with symptoms of concentration problems with linkage on chromosome 2q35. In addition we identified a subset of individuals with schizophrenia defined by language disturbances with linkage to chromosome 2p25.1 and a group of patients with a phenotype intermediate between those of schizophrenia and schizoaffective disorder with linkage to chromosome 2p21.

Conclusions

The findings presented are novel and demonstrate the efficacy of this approach in detection of genes underlying such complex human disorders as schizophrenia and depression.

Cytoprotective Effect of the Elongation Factor-2 Kinase-Mediated Autophagy in Breast Cancer Cells Subjected to Growth Factor Inhibition

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Autophagy is a highly conserved and regulated cellular process employed by living cells to degrade proteins and organelles as a response to metabolic stress. We have previously reported that eukaryotic elongation factor-2 kinase (eEF-2 kinase, also known as Ca²⁺/calmodulin-dependent protein kinase III) can positively modulate autophagy and negatively regulate protein synthesis. The purpose of the current study was to determine the role of the eEF-2 kinase-regulated autophagy in the response of breast cancer cells to inhibitors of growth factor signaling.

Methodology/Principal Findings

We found that nutrient depletion or growth factor inhibitors activated autophagy in human breast cancer cells, and the increased activity of autophagy was associated with a decrease in cellular ATP and an increase in activities of AMP kinase and eEF-2 kinase. Silencing of eEF-2 kinase relieved the inhibition of protein synthesis, led to a greater reduction of cellular ATP, and blunted autophagic response. We further showed that suppression of eEF-2 kinase-regulated autophagy impeded cell growth in serum/nutrient-deprived cultures and handicapped cell survival, and enhanced the efficacy of the growth factor inhibitors such as trastuzumab, gefitinib, and lapatinib.

Conclusion/Significance

The results of this study provide new evidence that activation of eEF-2 kinase-mediated autophagy plays a protective role for cancer cells under metabolic stress conditions, and that targeting autophagic survival may represent a novel approach to enhancing the effectiveness of growth factor inhibitors.

In Vivo Accumulation of Helicobacter pylori Products, NOD1, Ubiquitinated Proteins and Proteasome in a Novel Cytoplasmic Structure

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Cell internalization and intracellular fate of H. pylori products/virulence factors in vivo by human gastric epithelium, the main target of H. pylori-induced pathologies (i.e., peptic ulcer and cancer), are still largely unknown. Investigating gastric endoscopic biopsies from dyspeptic patients by means of ultrastructural immunocytochemistry, here we show that, in human superficial-foveolar epithelium and its metaplastic or dysplastic foci, H. pylori virulence factors accumulated in a discrete cytoplasmic structure characterized by 13-nm-thick cylindrical particles of regular punctate-linear substructure resembling the proteasome complex in size and structure. Inside this particle-rich cytoplasmic structure (PaCS) we observed colocalization of VacA, CagA, urease and outer membrane proteins with NOD1 receptor, ubiquitin-activating enzyme E1, polyubiquitinated proteins, proteasome components and potentially oncogenic proteins like SHP2 and ERKs in human gastric epithelium. By means of electron and confocal microscopy, we demonstrate that the in vivo findings were reproduced in vitro by incubating human epithelial cell lines with H. pylori products/virulence factors. PaCSs differed from VacA-induced vacuoles, phagosomes, aggresomes or related bodies. Our data suggest that PaCS is a novel, proteasome-enriched structure arising in ribosome-rich cytoplasm at sites of H. pylori products accumulation. As a site of selective concentration of bacterial virulence factors, the ubiquitin-proteasome system and interactive proteins, PaCS is likely to modulate immune-inflammatory and proliferative responses of the gastric epithelium of potential pathologic relevance.

Molecular Evolution of Human H1N1 and H3N2 Influenza A Virus in Thailand, 2006–2009

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Annual seasonal influenza outbreaks are associated with high morbidity and mortality.

Objective

To index and document evolutionary changes among influenza A H1N1 and H3N2 viruses isolated from Thailand during 2006–2009, using complete genome sequences.

Methods

Nasopharyngeal aspirates were collected from patients diagnosed with respiratory illness in Thailand during 2006–2009. All samples were screened for Influenza A virus. A total of 13 H1N1 and 21 H3N2 were confirmed and whole genome sequenced for the evolutionary analysis using standard phylogenetic approaches.

Results

Phylogenetic analysis of HA revealed a clear diversification of seasonal from vaccine strain lineages. H3N2 seasonal clusters were closely related to the WHO recommended vaccine strains in each season. Most H1N1 isolates could be differentiated into 3 lineages. The A/Brisbane/59/2007 lineage, a vaccine strain for H1N1 since 2008, is closely related with the H1N1 subtypes circulating in 2009. HA sequences were conserved at the receptor-binding site. Amino acid variations in the antigenic site resulted in a possible N-linked glycosylation motif. Recent H3N2 isolates had higher genetic variations compared to H1N1 isolates. Most substitutions in the NP protein were clustered in the T-cell recognition domains.

Conclusion

In this study we performed evolutionary genetic analysis of influenza A viruses in Thailand between 2006–2009. Although the current vaccine strain is efficient for controlling the circulating outbreak subtypes, surveillance is necessary to provide unambiguous information on emergent viruses. In summary, the findings of this study contribute the understanding of evolution in influenza A viruses in humans and is useful for routine surveillance and vaccine strain selection.

A at Single Nucleotide Polymorphism-358 Is Required for G at -420 to Confer the Highest Plasma Resistin in the General Japanese Population

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Insulin resistance is a feature of type 2 diabetes. Resistin, secreted from adipocytes, causes insulin resistance in mice. We previously reported that the G/G genotype of single nucleotide polymorphism (SNP) at −420 (rs1862513) in the human resistin gene (RETN) increased susceptibility to type 2 diabetes by enhancing its promoter activity. Plasma resistin was highest in Japanese subjects with G/G genotype, followed by C/G, and C/C. In this study, we cross-sectionally analyzed plasma resistin and SNPs in the RETN region in 2,019 community-dwelling Japanese subjects. Plasma resistin was associated with SNP-638 (rs34861192), SNP-537 (rs34124816), SNP-420, SNP-358 (rs3219175), SNP+299 (rs3745367), and SNP+1263 (rs3745369) (P<10⁻¹³ in all cases). SNP-638, SNP -420, SNP-358, and SNP+157 were in the same linkage disequilibrium (LD) block. SNP-358 and SNP-638 were nearly in complete LD (r² = 0.98), and were tightly correlated with SNP-420 (r² = 0.50, and 0.51, respectively). The correlation between either SNP-358 (or SNP-638) or SNP-420 and plasma resistin appeared to be strong (risk alleles for high plasma resistin; A at SNP-358, r² = 0.5224, P = 4.94×10⁻³²⁴; G at SNP-420, r² = 0.2616, P = 1.71×10⁻¹³³). In haplotypes determined by SNP-420 and SNP-358, the estimated frequencies for C-G, G-A, and G-G were 0.6700, 0.2005, and 0.1284, respectively, and C-A was rare (0.0011), suggesting that subjects with A at −358, generally had G at −420. This G-A haplotype conferred the highest plasma resistin (8.24 ng/ml difference/allele compared to C-G, P<0.0001). In THP-1 cells, the RETN promoter with the G-A haplotype showed the highest activity. Nuclear proteins specifically recognized one base difference at SNP-358, but not at SNP-638. Therefore, A at -358 is required for G at −420 to confer the highest plasma resistin in the general Japanese population. In Caucasians, the association between SNP-420 and plasma resistin is not strong, and A at −358 may not exist, suggesting that SNP-358 could explain this ethnic difference.

A Monomeric Variant of Insulin Degrading Enzyme (IDE) Loses Its Regulatory Properties

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Background

Insulin degrading enzyme (IDE) is a key enzyme in the metabolism of both insulin and amyloid beta peptides. IDE is unique in that it is subject to allosteric activation which is hypothesized to occur through an oligomeric structuture.

Methodology/Principal Findings

IDE is known to exist as an equilibrium mixture of monomers, dimers, and higher oligomers, with the dimer being the predominant form. Based on the crystal structure of IDE we deleted the putative dimer interface in the C-terminal region, which resulted in a monomeric variant. Monomeric IDE retained enzymatic activity, however instead of the allosteric behavior seen with wild type enzyme it displayed Michaelis-Menten kinetic behavior. With the substrate Abz-GGFLRKHGQ-EDDnp, monomeric IDE retained ~25% of the wild type activity. In contrast with the larger peptide substrates β-endorphin and amyloid β peptide 1–40, monomeric IDE retained only 1 to 0.25% of wild type activity. Unlike wild type IDE neither bradykinin nor dynorphin B-9 activated the monomeric variant of the enzyme. Similarly, monomeric IDE was not activated by polyphosphates under conditions in which the activity of wild type enzyme was increased more than 50 fold.

Conclusions/Significance

These findings serve to establish the dimer interface in IDE and demonstrate the requirement for an oligomeric form of the enzyme for its regulatory properties. The data support a mechanism where the binding of activators to oligomeric IDE induces a conformational change that cannot occur in the monomeric variant. Since a conformational change from a closed to a more open structure is likely the rate-determining step in the IDE reaction, the subunit induced conformational change likely shifts the structure of the oligomeric enzyme to a more open conformation.

Hypoxia Inactivates the VHL Tumor Suppressor through PIASy-Mediated SUMO Modification

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

The hypoxic microenvironment contributes to embryonic development and tumor progression through stabilization of the potent transcriptional factor HIFα. In normoxia, the tumor suppressor protein VHL acts as an E3 ubiquitin ligase to target HIFα for proteolytic destruction. Increasing evidence shows that VHL is a multifunctional adaptor involved in inhibition of HIFα-dependent and independent cellular processes. However, the molecular effect of hypoxic stress on VHL functions remains elusive. Here we report that PIASy, a SUMO E3 ligase upregulated in hypoxia, interacts with VHL and induces VHL SUMOylation on lysine residue 171. Moreover, PIASy-mediated SUMO1 modification induces VHL oligomerization and abrogates its inhibitory function on tumor cell growth, migration and clonogenicity. Knockdown of PIASy by small interfering RNA leads to reduction of VHL oligomerization and increases HIF1α degradation. These findings reveal a unique molecular strategy for inactivation of VHL under hypoxic stress.

Inefficient Complement System Clearance of Trypanosoma cruzi Metacyclic Trypomastigotes Enables Resistant Strains to Invade Eukaryotic Cells

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

The complement system is the main arm of the vertebrate innate immune system against pathogen infection. For the protozoan Trypanosoma cruzi, the causative agent of Chagas disease, subverting the complement system and invading the host cells is crucial to succeed in infection. However, little attention has focused on whether the complement system can effectively control T. cruzi infection. To address this question, we decided to analyse: 1) which complement pathways are activated by T. cruzi using strains isolated from different hosts, 2) the capacity of these strains to resist the complement-mediated killing at nearly physiological conditions, and 3) whether the complement system could limit or control T. cruzi invasion of eukaryotic cells. The complement activating molecules C1q, C3, mannan-binding lectin and ficolins bound to all strains analysed; however, C3b and C4b deposition assays revealed that T. cruzi activates mainly the lectin and alternative complement pathways in non-immune human serum. Strikingly, we detected that metacyclic trypomastigotes of some T. cruzi strains were highly susceptible to complement-mediated killing in non-immune serum, while other strains were resistant. Furthermore, the rate of parasite invasion in eukaryotic cells was decreased by non-immune serum. Altogether, these results establish that the complement system recognizes T. cruzi metacyclic trypomastigotes, resulting in killing of susceptible strains. The complement system, therefore, acts as a physiological barrier which resistant strains have to evade for successful host infection.

Transformation of Environmental Bacillus subtilis Isolates by Transiently Inducing Genetic Competence

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Domesticated laboratory strains of Bacillus subtilis readily take up and integrate exogenous DNA. In contrast, “wild” ancestors or Bacillus strains recently isolated from the environment can only be genetically modified by phage transduction, electroporation or protoplast transformation. Such methods are laborious, have a variable yield or cannot efficiently be used to alter chromosomal DNA. A major disadvantage of using laboratory strains is that they have often lost, or do not display ecologically relevant physiologies such as the ability to form biofilms. Here we present a method that allows genetic transformation by natural competence in several environmental isolates of B. subtilis. Competence in these strains was established by expressing the B. subtilis competence transcription factor ComK from an IPTG-inducible promoter construct present on an unstable plasmid. This transiently activates expression of the genes required for DNA uptake and recombination in the host strain. After transformation, the comK encoding plasmid is lost easily because of its intrinsic instability and the transformed strain returns to its wild state. Using this method, we have successfully generated mutants and introduced foreign DNA into a number of environmental isolates and also B. subtilis strain NCIB3610, which is widely used to study biofilm formation. Application of the same method to strains of B. licheniformis was unsuccessful. The efficient and rapid approach described here may facilitate genetic studies in a wider array of environmental B. subtilis strains.

Aptamer Antagonists of Myelin-Derived Inhibitors Promote Axon Growth

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Myelin of the adult central nervous system (CNS) is one of the major sources of inhibitors of axon regeneration following injury. The three known myelin-derived inhibitors (Nogo, MAG, and OMgp) bind with high affinity to the Nogo-66 receptor (NgR) on axons and limit neurite outgrowth. Here we show that RNA aptamers can be generated that bind with high affinity to NgR, compete with myelin-derived inhibitors for binding to NgR, and promote axon elongation of neurons in vitro even in the presence of these inhibitors. Aptamers may have key advantages over protein antagonists, including low immunogenicity and the possibility of ready modification during chemical synthesis for stability, signaling, or immobilization. This first demonstration that aptamers can directly influence neuronal function suggests that aptamers may prove useful for not only healing spinal cord and other neuronal damage, but may be more generally useful as neuromodulators.

Grip Force Is Part of the Semantic Representation of Manual Action Verbs

Nicolas Guex et al. — Tue, 16 Mar 2010 07:00:00 +0000

Motor actions and action verbs activate similar cortical brain regions. A functional interference can be taken as evidence that there is a parallel treatment of these two types of information and would argue for the biological grounding of language in action. A novel approach examining the relationship between language and grip force is presented. With eyes closed and arm extended, subjects listened to words relating (verbs) or not relating (nouns) to a manual action while holding a cylinder with an integrated force sensor. There was a change in grip force when subjects heard verbs that related to manual action. Grip force increased from about 100 ms following the verb presentation, peaked at 380 ms and fell abruptly after 400 ms, signalling a possible inhibition of the motor simulation evoked by these words. These observations reveal the intimate relationship that exists between language and grasp and show that it is possible to elucidate online new aspects of sensorimotor interaction.

Lack of linguistic support for Proto-Uto-Aztecan at 8900 BP [Letter]

Brown, C. H. — Mon, 15 Mar 2010 23:01:21 +0000

New evidence for a Mesoamerican homeland for Proto-Uto-Aztecan [Letter]

Hill, J. H. — Mon, 15 Mar 2010 23:01:21 +0000

Reply to Hill and Brown: Maize and Uto-Aztecan cultural history [Letter]

Mon, 15 Mar 2010 22:09:24 +0000

Correction for Lindqvist et al., Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear [Correction]

Mon, 15 Mar 2010 20:44:34 +0000

A neural substrate in the human hippocampus for linking successive events [Neuroscience]

Paz, R., Gelbard-Sagiv, H., Mukamel, R., Harel, M., Malach, R., Fried, I. — Mon, 15 Mar 2010 20:44:34 +0000

Memory formation requires the placement of experienced events in the same order in which they appeared. A large body of…

The future of social experimenting [Commentary]

Helbing, D., Yu, W. — Mon, 15 Mar 2010 20:44:33 +0000

A new Lower Pleistocene archeological site in Europe (Vallparadis, Barcelona, Spain) [Anthropology]

Mon, 15 Mar 2010 20:44:33 +0000

Here we report the discovery of a new late Lower Pleistocene site named Vallparadís (Barcelona, Spain) that produced a rich…

Notch signaling drives IL-22 secretion in CD4+ T cells by stimulating the aryl hydrocarbon receptor [Immunology]

Mon, 15 Mar 2010 20:44:33 +0000

CD4⁺ helper T (Th) cells differentiate toward distinct effector cell lineages characterized by their distinct cytokine expression patterns and functions….

Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people [Medical_Sciences]

Mon, 15 Mar 2010 20:44:32 +0000

Malaria therapy, experimental, and epidemiological studies have shown that erythrocyte Duffy blood group-negative people, largely of African ancestry, are resistant…

Induction of TGF-{beta}1 and TGF-{beta}1-dependent predominant Th17 differentiation by group A streptococcal infection [Immunology]

Mon, 15 Mar 2010 20:44:32 +0000

Recurrent group A Streptococcus (GAS) tonsillitis and associated autoimmune diseases indicate that the immune response to this organism can be…

Genomic definition of multiple ex vivo regulatory T cell subphenotypes [Immunology]

Mon, 15 Mar 2010 20:44:31 +0000

Regulatory T (Treg) cells that express the Foxp3 transcription factor are essential for lymphoid homeostasis and immune tolerance to self….

Role of host protein glutaredoxin 3 in the control of transcription during bacteriophage {Phi}2954 infection [Microbiology]

Qiao, J., Qiao, X., Sun, Y., Mindich, L. — Mon, 15 Mar 2010 20:44:31 +0000

Bacteriophage 2954 contains three dsRNA genomic segments, designated L, M, and S. The RNA is located inside a core particle…

Rhythmic engagement with music in infancy [Psychological_And_Cognitive_Sciences-SS]

Zentner, M., Eerola, T. — Mon, 15 Mar 2010 20:44:31 +0000

Humans have a unique ability to coordinate their motor movements to an external auditory stimulus, as in music-induced foot tapping…

Lack of p21 expression links cell cycle control and appendage regeneration in mice [Cell_Biology]

Mon, 15 Mar 2010 20:44:30 +0000

Animals capable of regenerating multiple tissue types, organs, and appendages after injury are common yet sporadic and include some sponge,…

Cell-cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris [Microbiology]

Mon, 15 Mar 2010 20:44:30 +0000

RpfG is a paradigm for a class of widespread bacterial two-component regulators with a CheY-like receiver domain attached to a…

AtBAG7, an Arabidopsis Bcl-2-associated athanogene, resides in the endoplasmic reticulum and is involved in the unfolded protein response [Plant_Biology]

Williams, B., Kabbage, M., Britt, R., Dickman, M. B. — Mon, 15 Mar 2010 20:44:30 +0000

The Bcl-2–associated athanogene (BAG) family is an evolutionarily conserved, multifunctional group of cochaperones that perform diverse cellular functions ranging from…

Forensic identification using skin bacterial communities [Microbiology]

Fierer, N., Lauber, C. L., Zhou, N., McDonald, D., Costello, E. K., Knight, R. — Mon, 15 Mar 2010 20:44:29 +0000

Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high…

Molecular components of signal amplification in olfactory sensory cilia [Neuroscience]

Hengl, T., Kaneko, H., Dauner, K., Vocke, K., Frings, S., Mohrlen, F. — Mon, 15 Mar 2010 20:44:29 +0000

The mammalian olfactory system detects an unlimited variety of odorants with a limited set of odorant receptors. To cope with…

Mouse cystic fibrosis transmembrane conductance regulator forms cAMP-PKA-regulated apical chloride channels in cortical collecting duct [Physiology]

Lu, M., Dong, K., Egan, M. E., Giebisch, G. H., Boulpaep, E. L., Hebert, S. C. — Mon, 15 Mar 2010 20:44:29 +0000

The cystic fibrosis transmembrane conductance regulator (CFTR) is expressed in many segments of the mammalian nephron, where it may interact…

Hypothalamic and pituitary c-Jun N-terminal kinase 1 signaling coordinately regulates glucose metabolism [Neuroscience]

Mon, 15 Mar 2010 20:44:28 +0000

c-Jun N-terminal kinase (JNK) 1-dependent signaling plays a crucial role in the development of obesity-associated insulin resistance. Here we demonstrate…

Huwe1 ubiquitin ligase is essential to synchronize neuronal and glial differentiation in the developing cerebellum [Developmental_Biology]

Mon, 15 Mar 2010 20:44:28 +0000

We have generated a knockout mouse strain in which the gene coding for the ubiquitin ligase Huwe1 has been inactivated…

Increased fibrillar amyloid-{beta} burden in normal individuals with a family history of late-onset Alzheimer’s [Medical_Sciences]

Mon, 15 Mar 2010 20:44:27 +0000

Having a parent affected with late-onset Alzheimer’s disease (LOAD) is a major risk factor among cognitively normal (NL) individuals. This…

Identification of hepatoprotective flavonolignans from silymarin [Microbiology]

Mon, 15 Mar 2010 20:44:27 +0000

Silymarin, also known as milk thistle extract, inhibits hepatitis C virus (HCV) infection and also displays antioxidant, anti-inflammatory, and immunomodulatory…

Prolonged exposure of the HIV-1 gp41 membrane proximal region with L669S substitution [Medical_Sciences]

Mon, 15 Mar 2010 20:44:27 +0000

The conserved membrane-proximal external region (MPER) of HIV-1 envelope is a target for the rare broadly neutralizing 2F5, Z13, and…

Discovery of a highly synergistic anthelmintic combination that shows mutual hypersusceptibility [Medical_Sciences]

Hu, Y., Platzer, E. G., Bellier, A., Aroian, R. V. — Mon, 15 Mar 2010 20:44:26 +0000

The soil-transmitted helminths or nematodes (hookworms, whipworms, and Ascaris) are roundworms that infect more than 1 billion of the poorest…

Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of {alpha}- and PPII-helices [Microbiology]

Mon, 15 Mar 2010 20:44:25 +0000

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary…

Hypoxia converts the myogenic action of insulin-like growth factors into mitogenic action by differentially regulating multiple signaling pathways [Cell_Biology]

Ren, H., Accili, D., Duan, C. — Mon, 15 Mar 2010 20:44:25 +0000

Insulin-like growth factors (IGFs) stimulate myoblast proliferation and differentiation. It remains elusive how these mutually exclusive cellular responses are elicited…

Post-Paleozoic crinoid radiation in response to benthic predation preceded the Mesozoic marine revolution [Geology]

Mon, 15 Mar 2010 20:44:24 +0000

It has been argued that increases in predation over geological time should result in increases in defensive adaptations in prey…

Targeted deletion of {beta}III spectrin impairs synaptogenesis and generates ataxic and seizure phenotypes [Neuroscience]

Mon, 15 Mar 2010 20:44:23 +0000

The spectrin membrane skeleton controls the disposition of selected membrane channels, receptors, and transporters. In the brain βIII spectrin binds…

Src kinase regulates the integrity and function of the Golgi apparatus via activation of dynamin 2 [Cell_Biology]

Mon, 15 Mar 2010 20:44:23 +0000

The size and integrity of the Golgi apparatus is maintained via a tightly controlled regulation of membrane traffic using a…

Mitotic gene conversion events induced in G1-synchronized yeast cells by gamma rays are similar to spontaneous conversion events [Genetics]

Lee, P. S., Petes, T. D. — Mon, 15 Mar 2010 20:44:22 +0000

In a previous study, we mapped spontaneous mitotic reciprocal crossovers (RCOs) in a 120-kb interval of chromosome V of Saccharomyces…

Polymorphonuclear leukocytes mediate Staphylococcus aureus Panton-Valentine leukocidin-induced lung inflammation and injury [Microbiology]

Mon, 15 Mar 2010 20:44:22 +0000

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is epidemic in the United States, even rivaling HIV/AIDS in its public health impact. The…

Plasmacytoid dendritic cells sense hepatitis C virus-infected cells, produce interferon, and inhibit infection [Immunology]

Mon, 15 Mar 2010 20:44:21 +0000

Hepatitis C virus (HCV), a member of the Flaviviridae family, is a single-stranded positive-sense RNA virus that infects >170 million…

Dally-like core protein and its mammalian homologues mediate stimulatory and inhibitory effects on Hedgehog signal response [Developmental_Biology]

Mon, 15 Mar 2010 20:44:21 +0000

The distribution and activities of morphogenic signaling proteins such as Hedgehog (Hh) and Wingless (Wg) depend on heparan sulfate proteoglycans…

Motor output evoked by subsaccadic stimulation of primate frontal eye fields [Neuroscience]

Corneil, B. D., Elsley, J. K., Nagy, B., Cushing, S. L. — Mon, 15 Mar 2010 20:44:20 +0000

In addition to its role in shifting the line of sight, the oculomotor system is also involved in the covert…

Mechanisms of acute axonal degeneration in the optic nerve in vivo [Neuroscience]

Mon, 15 Mar 2010 20:44:20 +0000

Axonal degeneration is an initial key step in traumatic and neurodegenerative CNS disorders. We established a unique in vivo epifluorescence…

Dormancy contributes to the maintenance of microbial diversity [Ecology]

Jones, S. E., Lennon, J. T. — Mon, 15 Mar 2010 20:44:19 +0000

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible…

Overcoming status quo bias in the human brain [Psychological_And_Cognitive_Sciences-SS]

Fleming, S. M., Thomas, C. L., Dolan, R. J. — Mon, 15 Mar 2010 20:44:19 +0000

Humans often accept the status quo when faced with conflicting choice alternatives. However, it is unknown how neural pathways connecting…

Arabidopsis dynamin-related proteins DRP2B and DRP1A participate together in clathrin-coated vesicle formation during endocytosis [Plant_Biology]

Mon, 15 Mar 2010 20:44:18 +0000

Endocytosis performs a wide range of functions in animals and plants. Clathrin-coated vesicle (CCV) formation is an initial step of…

Dendritic cells control T cell tonic signaling required for responsiveness to foreign antigen [Immunology]

Mon, 15 Mar 2010 20:44:18 +0000

Dendritic cells (DCs) are key components of the adaptive immune system contributing to initiation and regulation of T cell responses….

Bone marrow stromal cells use TGF-{beta} to suppress allergic responses in a mouse model of ragweed-induced asthma [Physiology]

Mon, 15 Mar 2010 20:44:17 +0000

Bone marrow stromal cells [BMSCs; also known as mesenchymal stem cells (MSCs)] effectively suppress inflammatory responses in acute graft-versus-host disease…

Diabetes-accelerated memory dysfunction via cerebrovascular inflammation and A{beta} deposition in an Alzheimer mouse model with diabetes [Neuroscience]

Mon, 15 Mar 2010 20:44:16 +0000

Recent epidemiological studies suggest that diabetes mellitus is a strong risk factor for Alzheimer disease. However, the underlying mechanisms remain…

Restoration of visual function in P23H rhodopsin transgenic rats by gene delivery of BiP/Grp78 [Medical_Sciences]

Mon, 15 Mar 2010 20:44:16 +0000

The P23H mutation within the rhodopsin gene (RHO ) causes rhodopsin misfolding, endoplasmic reticulum (ER) stress, and activates the unfolded…

Ghrelin O-acyltransferase (GOAT) is essential for growth hormone-mediated survival of calorie-restricted mice [Medical_Sciences]

Mon, 15 Mar 2010 20:44:15 +0000

Ghrelin O-acyltransferase (GOAT) attaches octanoate to proghrelin, which is processed to ghrelin, an octanoylated peptide hormone that stimulates release of…

Allopregnanolone reverses neurogenic and cognitive deficits in mouse model of Alzheimer’s disease [Neuroscience]

Mon, 15 Mar 2010 20:44:15 +0000

Our previous analyses showed that allopregnanolone (AP) significantly increased proliferation of rodent and human neural progenitor cells in vitro. In…

Brassinosteroids control male fertility by regulating the expression of key genes involved in Arabidopsis anther and pollen development [Plant_Biology]

Ye, Q., Zhu, W., Li, L., Zhang, S., Yin, Y., Ma, H., Wang, X. — Mon, 15 Mar 2010 20:44:15 +0000

The development of anther and pollen is important for male reproduction, and this process is coordinately regulated by many external…

Vaccinia-like cytoplasmic replication of the giant Mimivirus [Microbiology]

Mutsafi, Y., Zauberman, N., Sabanay, I., Minsky, A. — Mon, 15 Mar 2010 20:44:14 +0000

Poxviruses are considered to be unique among all DNA viruses, because their infection cycle is carried out exclusively in the…

Iron enrichment stimulates toxic diatom production in high-nitrate, low-chlorophyll areas [Environmental_Sciences-BS]

Mon, 15 Mar 2010 20:44:14 +0000

Oceanic high-nitrate, low-chlorophyll environments have been highlighted for potential large-scale iron fertilizations to help mitigate global climate change. Controversy surrounds…

Ordering human CD34+CD10-CD19+ pre/pro-B-cell and CD19- common lymphoid progenitor stages in two pro-B-cell development pathways [Immunology]

Mon, 15 Mar 2010 20:44:14 +0000

Studies here respond to two long-standing questions: Are human “pre/pro-B” CD34⁺CD10^–CD19⁺ and “common lymphoid progenitor (CLP)/early-B” CD34⁺CD10⁺CD19^– alternate precursors to…

The neural code of reward anticipation in human orbitofrontal cortex [Psychological_And_Cognitive_Sciences-SS]

Kahnt, T., Heinzle, J., Park, S. Q, Haynes, J.-D. — Mon, 15 Mar 2010 20:44:13 +0000

An optimal choice among alternative behavioral options requires precise anticipatory representations of their possible outcomes. A fundamental question is how…

Locus ceruleus controls Alzheimer’s disease pathology by modulating microglial functions through norepinephrine [Neuroscience]

Mon, 15 Mar 2010 20:44:13 +0000

Locus ceruleus (LC)-supplied norepinephrine (NE) suppresses neuroinflammation in the brain. To elucidate the effect of LC degeneration and subsequent NE…

Principles of conduction and hydrophobic gating in K+ channels [Biophysics_And_Computational_Biology]

Mon, 15 Mar 2010 19:09:46 +0000

We present the first atomic-resolution observations of permeation and gating in a K⁺ channel, based on molecular dynamics simulations of…

Information dynamics shape the sexual networks of Internet-mediated prostitution [Social_Sciences]

Rocha, L. E. C., Liljeros, F., Holme, P. — Mon, 15 Mar 2010 19:09:45 +0000

Like many other social phenomena, prostitution is increasingly coordinated over the Internet. The online behavior affects the offline activity; the…

Global patterns in leaf 13C discrimination and implications for studies of past and future climate [Ecology]

Diefendorf, A. F., Mueller, K. E., Wing, Scott. L., Koch, P. L., Freeman, K. H. — Mon, 15 Mar 2010 19:09:45 +0000

Fractionation of carbon isotopes by plants during CO₂ uptake and fixation (_leaf) varies with environmental conditions, but quantitative patterns of…

The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor [Biochemistry]

Mon, 15 Mar 2010 19:09:45 +0000

The circadian rhythms exhibited in the cyanobacterium Synechococcus elongatus are generated by an oscillator comprised of the proteins KaiA, KaiB,…

Protein-assisted self-assembly of multifunctional nanoparticles [Biophysics_And_Computational_Biology]

Nikitin, M. P., Zdobnova, T. A., Lukash, S. V., Stremovskiy, O. A., Deyev, S. M. — Mon, 15 Mar 2010 19:09:44 +0000

A bioengineering method for self-assembly of multifunctional superstructures with in-advance programmable properties has been proposed. The method employs two unique…

MiDReG: A method of mining developmentally regulated genes using Boolean implications [Systems_Biology]

Mon, 15 Mar 2010 19:09:44 +0000

We present a method termed mining developmentally regulated genes (MiDReG) to predict genes whose expression is either activated or repressed…

A flavin-dependent halogenase catalyzes the chlorination step in the biosynthesis of Dictyostelium differentiation-inducing factor 1 [Biochemistry]

Neumann, C. S., Walsh, C. T., Kay, R. R. — Mon, 15 Mar 2010 19:09:43 +0000

Differentiation-inducing factor 1 (DIF-1) is a polyketide-derived morphogen which drives stalk cell formation in the developmental cycle of Dictyostelium discoideum….

L-amino acids catalyze the formation of an excess of D-glyceraldehyde, and thus of other D sugars, under credible prebiotic conditions [Biochemistry]

Breslow, R., Cheng, Z.-L. — Mon, 15 Mar 2010 19:09:43 +0000

Previous work by us, and others, has shown that the formation of amino acids on prebiotic earth with the geometric…

Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy [Biophysics_And_Computational_Biology]

Gipson, P., Mills, D. J., Wouts, R., Grininger, M., Vonck, J., Kuhlbrandt, W. — Mon, 15 Mar 2010 19:09:43 +0000

Yeast fatty acid synthase (FAS) is a 2.6-MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By…

Global classical solutions of the Boltzmann equation with long-range interactions [Mathematics]

Gressman, P. T., Strain, R. M. — Mon, 15 Mar 2010 19:09:42 +0000

This is a brief announcement of our recent proof of global existence and rapid decay to equilibrium of classical solutions…

Implications of the HIV-1 Rev dimer structure at 3.2 A resolution for multimeric binding to the Rev response element [Biochemistry]

Mon, 15 Mar 2010 19:09:42 +0000

HIV-1 Rev is a small regulatory protein that mediates the nuclear export of viral mRNAs, an essential step in the…

Cyclopentenone prostaglandin-induced unfolding and aggregation of the Parkinson disease-associated UCH-L1 [Biophysics_And_Computational_Biology]

Mon, 15 Mar 2010 19:09:41 +0000

Ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) has been implicated in Parkinson’s disease (PD) and is present in neurofibrillary tangles or Lewy…

Pandemic Dynamics and the Breakdown of Herd Immunity

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

In this note we discuss the issues involved in attempting to model pandemic dynamics. More specifically, we show how it may be possible to make projections for the ongoing H1N1 pandemic as extrapolated from knowledge of seasonal influenza. We derive first-approximation parameter estimates for the SIR model to describe seasonal influenza, and then explore the implications of the existing classical epidemiological theory for the case of a pandemic virus. In particular, we note the dramatic nonlinear increase in attack rate as a function of the percentage of susceptibles initially present in the population. This has severe consequences for the pandemic, given the general lack of immunity in the global population.

Evolutionary Constraints Acting on DDX3X Protein Potentially Interferes with Rev-Mediated Nuclear Export of HIV-1 RNA

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Differential host-pathogen interactions direct viral replication in infected cells. In HIV-1 infected cells, nuclear export of viral RNA transcripts into cellular cytoplasm is governed by interaction of HIV-1 Rev, Exportin-1 (CRM-1) and DDX3X. Knock down of DDX3X has been shown to drastically impair HIV replication. Here we show that evolutionary forces are responsible for demarking previously unidentified critical functionally important residues on the surface of DDX3X. Using computational approaches, we show that these functional residues, depending on their location, are capable of regulating ATPase and RNA helicase functions of DDX3X. The potential of these residues in designing better blockers against HIV-1 replication was also assessed. Also, using stepwise docking simulations, we could identify DDX3X-CRM-1 interface and its critical functional residues. Our data would help explain the role of DDX3X in HIV-1 Rev function with potential to design new intervention strategies against HIV-1 replication.

A Comparative Proteomic Analysis Reveals a New Bi-Lobe Protein Required for Bi-Lobe Duplication and Cell Division in Trypanosoma brucei

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

A Golgi-associated bi-lobed structure was previously found to be important for Golgi duplication and cell division in Trypanosoma brucei. To further understand its functions, comparative proteomics was performed on extracted flagellar complexes (including the flagellum and flagellum-associated structures such as the basal bodies and the bi-lobe) and purified flagella to identify new bi-lobe proteins. A leucine-rich repeats containing protein, TbLRRP1, was characterized as a new bi-lobe component. The anterior part of the TbLRRP1-labeled bi-lobe is adjacent to the single Golgi apparatus, and the posterior side is tightly associated with the flagellar pocket collar marked by TbBILBO1. Inducible depletion of TbLRRP1 by RNA interference inhibited duplication of the bi-lobe as well as the adjacent Golgi apparatus and flagellar pocket collar. Formation of a new flagellum attachment zone and subsequent cell division were also inhibited, suggesting a central role of bi-lobe in Golgi, flagellar pocket collar and flagellum attachment zone biogenesis.

The Neural Correlates of Visuospatial Perceptual and Oculomotor Extrapolation

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

The human visual system must perform complex visuospatial extrapolations (VSE) across space and time in order to extract shape and form from the retinal projection of a cluttered visual environment characterized by occluded surfaces and moving objects. Even if we exclude the temporal dimension, for instance when judging whether an extended finger is pointing towards one object or another, the mechanisms of VSE remain opaque. Here we investigated the neural correlates of VSE using functional magnetic resonance imaging in sixteen human observers while they judged the relative position of, or saccaded to, a (virtual) target defined by the extrapolated path of a pointer. Using whole brain and region of interest (ROI) analyses, we compared the brain activity evoked by these VSE tasks to similar control judgements or eye movements made to explicit (dot) targets that did not require extrapolation. The data show that activity in an occipitotemporal region that included the lateral occipital cortex (LOC) was significantly greater during VSE than during control tasks. A similar, though less pronounced, pattern was also evident in regions of the fronto-parietal cortex that included the frontal eye fields. However, none of the ROIs examined exhibited a significant interaction between target type (extrapolated/explicit) and response type (oculomotor/perceptual). These findings are consistent with a close association between visuoperceptual and oculomotor responses, and highlight a critical role for the LOC in the process of VSE.

Genetic Heterogeneity of Oesophageal Cancer in High-Incidence Areas of Southern and Northern China

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background and Objective

Oesophageal cancer is one of the most common and deadliest cancers worldwide. Our previous population-based study reported a high prevalence of oesophageal cancer in Chaoshan, Guangdong Province, China. Ancestors of the Chaoshan population migrated from the Taihang Mountain region of north-central China, which is another high-incidence area for oesophageal cancer. The purpose of the present study was to obtain evidence of inherited susceptibility to oesophageal cancer in the Chaoshan population, with reference to the Taihang Mountain population, with the eventual goal of molecular identification of the disease genes.

Methods

We conducted familial correlation, commingling, and complex segregation analyses of 224 families from the Chaoshan population and 403 families from the Taihang population using the FPMM program of S.A.G.E. version 5.3.0. A second analysis focused on specific families having large numbers of affected individuals or early onset of the disease.

Results

For the general population, moderate sib-sib correlation was noticed for esophageal cancer. Additionally, brother-brother correlation was even higher. Commingling analyses indicated that a three-component distribution model best accounts for the variation in age of onset of oesophageal cancer, and that a multifactorial model provides the best fit to the general population data. An autosomal dominant mode and a dominant or recessive major gene with polygenic inheritance were found to be the best models of inherited susceptibility to oesophageal cancer in some large families.

Conclusions

The current results provide evidence for inherited susceptibility to oesophageal cancer in certain high-risk groups in China, and support efforts to identify the susceptibility genes.

Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

We tested the metabolic rate hypothesis (whereby rates of mtDNA evolution are postulated to be mediated primarily by mutagenic by-products of respiration) by examining whether mass-specific metabolic rate was correlated with root-to-tip distance on a set of mtDNA trees for the springtail Cryptopygus antarcticus travei from sub-Antarctic Marion Island.

Using Bayesian analyses and a novel application of the comparative phylogenetic method, we did not find significant evidence that contemporary metabolic rates directly correlate with mutation rate (i.e., root-to-tip distance) once the underlying phylogeny is taken into account. However, we did find significant evidence that metabolic rate is dependent on the underlying mtDNA tree, or in other words, lineages with related mtDNA also have similar metabolic rates.

We anticipate that future analyses which apply this methodology to datasets with longer sequences, more taxa, or greater variability will have more power to detect a significant direct correlation between metabolic rate and mutation rate. We conclude with suggestions for future analyses that would extend the preliminary approach applied here, in particular highlighting ways to tease apart oxidative stress effects from the effects of population size and/or selection coefficients operating on the molecular evolutionary rate.

Bile Acid-Induced Arrhythmia Is Mediated by Muscarinic M2 Receptors in Neonatal Rat Cardiomyocytes

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

Intrahepatic cholestasis of pregnancy (ICP) is a common disease affecting up to 5% of pregnancies and which can cause fetal arrhythmia and sudden intrauterine death. We previously demonstrated that bile acid taurocholate (TC), which is raised in the bloodstream of ICP, can acutely alter the rate and rhythm of contraction and induce abnormal calcium destabilization in cultured neonatal rat cardiomyocytes (NRCM). Apart from their hepatic functions bile acids are ubiquitous signalling molecules with diverse systemic effects mediated by either the nuclear receptor FXR or by a recently discovered G-protein coupled receptor TGR5. We aim to investigate the mechanism of bile-acid induced arrhythmogenic effects in an in-vitro model of the fetal heart.

Methods and Results

Levels of bile acid transporters and nuclear receptor FXR were studied by quantitative real time PCR, western blot and immunostaining, which showed low levels of expression. We did not observe functional involvement of the canonical receptors FXR and TGR5. Instead, we found that TC binds to the muscarinic M₂ receptor in NRCM and serves as a partial agonist of this receptor in terms of inhibitory effect on intracellular cAMP and negative chronotropic response. Pharmacological inhibition and siRNA-knockdown of the M₂ receptor completely abolished the negative effect of TC on contraction, calcium transient amplitude and synchronisation in NRCM clusters.

Conclusion

We conclude that in NRCM the TC-induced arrhythmia is mediated by the partial agonism at the M₂ receptor. This mechanism might serve as a promising new therapeutic target for fetal arrhythmia.

Neurotrophins Regulate Bone Marrow Stromal Cell IL-6 Expression through the MAPK Pathway

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

The host’s response to infection is characterized by altered levels of neurotrophins and an influx of inflammatory cells to sites of injured tissue. Progenitor cells that give rise to the differentiated cellular mediators of inflammation are derived from bone marrow progenitor cells where their development is regulated, in part, by cues from bone marrow stromal cells (BMSC). As such, alteration of BMSC function in response to elevated systemic mediators has the potential to alter their function in biologically relevant ways, including downstream alteration of cytokine production that influences hematopoietic development.

Methodology/Principal Findings

In the current study we investigated BMSC neurotrophin receptor expression by flow cytometric analysis to determine differences in expression as well as potential to respond to NGF or BDNF. Intracellular signaling subsequent to neurotrophin stimulation of BMSC was analyzed by western blot, microarray analysis, confocal microscopy and real-time PCR. Analysis of BMSC Interleukin-6 (IL-6) expression was completed using ELISA and real-time PCR.

Conclusion

BMSC established from different individuals had distinct expression profiles of the neurotrophin receptors, TrkA, TrkB, TrkC, and p75^NTR. These receptors were functional, demonstrated by an increase in Akt-phosphorylation following BMSC exposure to recombinant NGF or BDNF. Neurotrophin stimulation of BMSC resulted in increased IL-6 gene and protein expression which required activation of ERK and p38 MAPK signaling, but was not mediated by the NFκB pathway. BMSC response to neurotrophins, including the up-regulation of IL-6, may alter their support of hematopoiesis and regulate the availability of inflammatory cells for migration to sites of injury or infection. As such, these studies are relevant to the growing appreciation of the interplay between neurotropic mediators and the regulation of hematopoiesis.

Time-Dependent c-Myc Transactomes Mapped by Array-Based Nuclear Run-On Reveal Transcriptional Modules in Human B Cells

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined “transactome”).

Methodology/Principal Findings

We developed a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO) assay using commercial microarray platforms. This strategy provides the missing component, the transactome, to fully map transcriptional networks. ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model reveals time-dependent waves of transcription, with a transactome early after c-Myc induction that does not persist at a late, steady-state phase, when genes that are regulated by c-Myc and E2F predominate. Gene set matrix analysis further uncovers functionally related groups of genes putatively regulated by waves of transcription factor motifs following Myc induction, starting with AP1 and CREB that are followed by EGR1, NFkB and STAT, and ending with E2F, Myc and ARNT/HIF motifs.

Conclusions/Significance

By coupling ANRO with previous global mapping of c-Myc binding sites by chromatin immunoprecipitation (ChIP) in P493-6 cells, we define a set of transcriptionally regulated direct c-Myc target genes and pave the way for the use of ANRO to comprehensively map any transcriptional network.

DNA Methylation as a Biomarker for Cardiovascular Disease Risk

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

Elevated serum homocysteine is associated with an increased risk of cardiovascular disease (CVD). This may reflect a reduced systemic remethylation capacity, which would be expected to cause decreased genomic DNA methylation in peripheral blood leukocytes (PBL).

Methodology/Principal Findings

We examined the association between prevalence of CVD (myocardial infarction, stroke) and its predisposing conditions (hypertension, diabetes) and PBL global genomic DNA methylation as represented by ALU and Satellite 2 (AS) repetitive element DNA methylation in 286 participants of the Singapore Chinese Health Study, a population-based prospective investigation of 63,257 men and women aged 45–74 years recruited during 1993–1998. Men exhibited significantly higher global DNA methylation [geometric mean (95% confidence interval (CI)): 159 (143, 178)] than women [133 (121, 147)] (P = 0·01). Global DNA methylation was significantly elevated in men with a history of CVD or its predisposing conditions at baseline (P = 0·03) but not in women (P = 0·53). Fifty-two subjects (22 men, 30 women) who were negative for these CVD/predisposing conditions at baseline acquired one or more of these conditions by the time of their follow-up I interviews, which took place on average about 5·8 years post-enrollment. Global DNA methylation levels of the 22 incident cases in men were intermediate (AS, 177) relative to the 56 male subjects who remained free of CVD/predisposing conditions at follow-up (lowest AS, 132) and the 51 male subjects with a diagnosis of CVD or predisposing conditions reported at baseline (highest AS 184) (P for trend = 0.0008) No such association was observed in women (P = 0.91). Baseline body mass index was positively associated with AS in both men and women (P = 0·007).

Conclusions/Significance

Our findings indicate that elevated, not decreased, PBL DNA methylation is positively associated with prevalence of CVD/predisposing conditions and obesity in Singapore Chinese.

Genetic Characterization of the Influenza A Pandemic (H1N1) 2009 Virus Isolates from India

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

The Influenza A pandemic H1N1 2009 (H1N1pdm) virus appeared in India in May 2009 and thereafter outbreaks with considerable morbidity and mortality have been reported from many parts of the country. Continuous monitoring of the genetic makeup of the virus is essential to understand its evolution within the country in relation to global diversification and to track the mutations that may affect the behavior of the virus.

Methods

H1N1pdm viruses were isolated from both recovered and fatal cases representing major cities and sequenced. Phylogenetic analyses of six concatenated whole genomes and the hemagglutinin (HA) gene of seven more isolates from May-September 2009 was performed with reference to 685 whole genomes of global isolates available as of November 24, 2009. Molecular characterization of all the 8 segments was carried out for known pathogenic markers.

Results

The first isolate of May 2009 belonged to clade 5. Although clade 7 was the dominant H1N1pdm lineage in India, both clades 6 and 7 were found to be co-circulating. The neuraminidase of all the Indian isolates possessed H275, the marker for sensitivity to the neuraminidase inhibitor Oseltamivir. Some of the mutations in HA are at or in the vicinity of antigenic sites and may therefore be of possible antigenic significance. Among these a D222G mutation in the HA receptor binding domain was found in two of the eight Indian isolates obtained from fatal cases.

Conclusions

The majority of the 13 Indian isolates grouped in the globally most widely circulating H1N1pdm clade 7. Further, correlations of the mutations specific to clade 7 Indian isolates to viral fitness and adaptability in the country remains to be understood. The D222G mutation in HA from isolates of fatal cases needs to be studied for pathogenicity.

Morbid Obesity as a Risk Factor for Hospitalization and Death Due to 2009 Pandemic Influenza A(H1N1) Disease

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

Severe illness due to 2009 pandemic A(H1N1) infection has been reported among persons who are obese or morbidly obese. We assessed whether obesity is a risk factor for hospitalization and death due to 2009 pandemic influenza A(H1N1), independent of chronic medical conditions considered by the Advisory Committee on Immunization Practices (ACIP) to increase the risk of influenza-related complications.

Methodology/Principal Findings

We used a case-cohort design to compare cases of hospitalizations and deaths from 2009 pandemic A(H1N1) influenza occurring between April–July, 2009, with a cohort of the U.S. population estimated from the 2003–2006 National Health and Nutrition Examination Survey (NHANES); pregnant women and children <2 years old were excluded. For hospitalizations, we defined categories of relative weight by body mass index (BMI, kg/m²); for deaths, obesity or morbid obesity was recorded on medical charts, and death certificates. Odds ratio (OR) of being in each BMI category was determined; normal weight was the reference category. Overall, 361 hospitalizations and 233 deaths included information to determine BMI category and presence of ACIP-recognized medical conditions. Among ≥20 year olds, hospitalization was associated with being morbidly obese (BMI≥40) for individuals with ACIP-recognized chronic conditions (OR = 4.9, 95% CI 2.4–9.9) and without ACIP-recognized chronic conditions (OR = 4.7, 95%CI 1.3–17.2). Among 2–19 year olds, hospitalization was associated with being underweight (BMI≤5^th percentile) among those with (OR = 12.5, 95%CI 3.4–45.5) and without (OR = 5.5, 95%CI 1.3–22.5) ACIP-recognized chronic conditions. Death was not associated with BMI category among individuals 2–19 years old. Among individuals aged ≥20 years without ACIP-recognized chronic medical conditions death was associated with obesity (OR = 3.1, 95%CI: 1.5–6.6) and morbid obesity (OR = 7.6, 95%CI 2.1–27.9).

Conclusions/Significance

Our findings support observations that morbid obesity may be associated with hospitalization and possibly death due to 2009 pandemic H1N1 infection. These complications could be prevented by early antiviral therapy and vaccination.

FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Adhesion constitutes one of the initial stages of infection in microbial diseases and is mediated by adhesins. Hence, identification and comprehensive knowledge of adhesins and adhesin-like proteins is essential to understand adhesin mediated pathogenesis and how to exploit its therapeutic potential. However, the knowledge about fungal adhesins is rudimentary compared to that of bacterial adhesins. In addition to host cell attachment and mating, the fungal adhesins play a significant role in homotypic and xenotypic aggregation, foraging and biofilm formation. Experimental identification of fungal adhesins is labor- as well as time-intensive. In this work, we present a Support Vector Machine (SVM) based method for the prediction of fungal adhesins and adhesin-like proteins. The SVM models were trained with different compositional features, namely, amino acid, dipeptide, multiplet fractions, charge and hydrophobic compositions, as well as PSI-BLAST derived PSSM matrices. The best classifiers are based on compositional properties as well as PSSM and yield an overall accuracy of 86%. The prediction method based on best classifiers is freely accessible as a world wide web based server at http://bioinfo.icgeb.res.in/faap. This work will aid rapid and rational identification of fungal adhesins, expedite the pace of experimental characterization of novel fungal adhesins and enhance our knowledge about role of adhesins in fungal infections.

A New Statistic to Evaluate Imputation Reliability

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

As the amount of data from genome wide association studies grows dramatically, many interesting scientific questions require imputation to combine or expand datasets. However, there are two situations for which imputation has been problematic: (1) polymorphisms with low minor allele frequency (MAF), and (2) datasets where subjects are genotyped on different platforms. Traditional measures of imputation cannot effectively address these problems.

Methodology/Principal Findings

We introduce a new statistic, the imputation quality score (IQS). In order to differentiate between well-imputed and poorly-imputed single nucleotide polymorphisms (SNPs), IQS adjusts the concordance between imputed and genotyped SNPs for chance. We first evaluated IQS in relation to minor allele frequency. Using a sample of subjects genotyped on the Illumina 1 M array, we extracted those SNPs that were also on the Illumina 550 K array and imputed them to the full set of the 1 M SNPs. As expected, the average IQS value drops dramatically with a decrease in minor allele frequency, indicating that IQS appropriately adjusts for minor allele frequency. We then evaluated whether IQS can filter poorly-imputed SNPs in situations where cases and controls are genotyped on different platforms. Randomly dividing the data into “cases” and “controls”, we extracted the Illumina 550 K SNPs from the cases and imputed the remaining Illumina 1 M SNPs. The initial Q-Q plot for the test of association between cases and controls was grossly distorted (λ = 1.15) and had 4016 false positives, reflecting imputation error. After filtering out SNPs with IQS<0.9, the Q-Q plot was acceptable and there were no longer false positives. We then evaluated the robustness of IQS computed independently on the two halves of the data. In both European Americans and African Americans the correlation was >0.99 demonstrating that a database of IQS values from common imputations could be used as an effective filter to combine data genotyped on different platforms.

Conclusions/Significance

IQS effectively differentiates well-imputed and poorly-imputed SNPs. It is particularly useful for SNPs with low minor allele frequency and when datasets are genotyped on different platforms.

Anti Transglutaminase Antibodies Cause Ataxia in Mice

Nicolas Guex et al. — Mon, 15 Mar 2010 07:00:00 +0000

Background

Celiac disease (CD) is an autoimmune gastrointestinal disorder characterized by the presence of anti-transglutaminase 2 (TG2) and anti-gliadin antibodies. Amongst the neurological dysfunctions associated with CD, ataxia represents the most common one.

Methods

We analyzed by immunohistochemistry, the anti-neural reactivity of the serum from 20 CD patients. To determine the role of anti-TG2 antibodies in ataxia, two anti-TG2 single chain variable fragments (scFv), isolated from a phage-display IgA antibody library, were characterized by immunohistochemistry and ELISA, and injected in mice to study their effects on motor coordination. We found that 75% of the CD patient population without evidence of neurological involvement, has circulating anti-neural IgA and/or IgG antibodies. Two anti-TG2 scFvs, cloned from one CD patient, stained blood vessels but only one reacted with neurons. This anti-TG2 antibody showed cross reactivity with the transglutaminase isozymes TG3 and TG6. Intraventricular injection of the anti-TG2 or the anti-TG2/3/6 cross-reactive scFv provoked transient, equally intensive ataxia in mice.

Conclusion

The serum from CD patients contains anti-TG2, TG3 and TG6 antibodies that may potentially cause ataxia.