Water Confined in Cylindrical Pores: A Molecular Dynamics Study

Molecular dynamics simulations of water confined in two hydrophilic cylindrical pores—PH and PL—that differ in their silanol surface concentration (7.6 and 3.0 nm⁻², respectively) have been performed at 300 K. A strong interaction of interfacial water molecules with the pore was systematically found and gives rise to a layering effect, a significant distortion of both the hydrogen bond network (HBN) and the tetrahedral structure of these water molecules, and a corresponding subdiffusive mean square displacement along the main axis of the pores. By contrast, water molecules in the inner part of both pores were found to behave similarly to bulk water. The HBN and the tetrahedral configuration of water were more gradually distorted in the PL pore given the larger heterogeneity and rugosity of the surface, and the number of water–pore hydrogen bonds did not scale linearly with the silanol surface concentration of the pores, in part because of the close proximity between silanols in the PH pore. With the PL pore, the dynamic slowing down of water was found consistent with the experiment, suggesting that it provides a better model for the cylindrical MCM-41 mesopores. The structural and dynamical properties of water vary little with the silica force field.     

Defining obesity cut-off points for migrant South Asians

Background

Body mass index (BMI) and waist circumference (WC) are used to define cardiovascular and type 2 diabetes risk. We aimed to derive appropriate BMI and WC obesity cut-off points in a migrant South Asian population.

Methods

4688 White Europeans and 1333 South Asians resident in the UK aged 40–75 years inclusive were screened for type 2 diabetes. Principal components analysis was used to derive a glycaemia, lipid, and a blood pressure factor. Regression models for each factor, adjusted for age and stratified by sex, were used to identify BMI and WC cut-off points in South Asians that correspond to those defined for White Europeans.

Findings

For South Asian males, derived BMI obesity cut-off points equivalent to 30.0 kg/m² in White Europeans were 22.6 kg/m² (95% Confidence Interval (95% CI) 20.7 kg/m² to 24.5 kg/m²) for the glycaemia factor, 26.0 kg/m² (95% CI 24.7 kg/m² to 27.3 kg/m²) for the lipid factor, and 28.4 kg/m² (95% CI 26.5 kg/m² to 30.4 kg/m²) for the blood pressure factor. For WC, derived cut-off points for South Asian males equivalent to 102 cm in White Europeans were 83.8 cm (95% CI 79.3 cm to 88.2 cm) for the glycaemia factor, 91.4 cm (95% CI 86.9 cm to 95.8 cm) for the lipid factor, and 99.3 cm (95% CI 93.3 cm to 105.2 cm) for the blood pressure factor. Lower ethnicity cut-off points were seen for females for both BMI and WC.

Conclusions

Substantially lower obesity cut-off points are needed in South Asians to detect an equivalent level of dysglycemia and dyslipidemia as observed in White Europeans. South Asian ethnicity could be considered as a similar level of risk as obesity (in White Europeans) for the development of type 2 diabetes.     

Enhanced Cytoprotective Effects of the Inhibitor of Apoptosis Protein Cellular IAP1 through Stabilization with TRAF2

Inhibitor of apoptosis (IAP) proteins are key regulators of intracellular signaling that interact with tumor necrosis factor (TNF) receptor superfamily members as well as proapoptotic molecules such as Smac/DIABLO and caspases. Whereas the X-linked IAP is an established caspase inhibitor, the protective mechanisms utilized by the cellular IAP (c-IAP) proteins are less clear because c-IAPs bind to but do not inhibit the enzymatic activities of caspases. In this study, c-IAPs are shown to be highly unstable molecules that undergo autoubiquitination. The autoubiquitination of c-IAP1 is blocked upon coexpression with TNF receptor-associated factor (TRAF) 2, and this is achieved by inhibition of the E3 ubiquitin ligase activity intrinsic to the RING of c-IAP1. Consistent with these observations, loss of TRAF2 results in a decrease in c-IAP1 levels. Stabilized c-IAP1 was found to sequester and prevent Smac/DIABLO from antagonizing X-linked IAP and protect against cell death. Therefore, this study describes an intriguing cytoprotective mechanism utilized by c-IAP1 and provides critical insight into how IAP proteins function to alter the apoptotic threshold.The inhibitors of apoptosis (IAPs)² are an evolutionarily conserved gene family described originally as encoding cell death inhibitors. IAP proteins have subsequently been found to participate in a variety of additional intracellular signaling processes (1), and it has become evident that IAP proteins are versatile molecules playing numerous distinct roles within the cell. Although a more complete understanding of these additional functions for IAP proteins is emerging, the distinct mechanisms utilized by some IAP proteins to function in their originally defined roles as cell death inhibitors remain unclear.Members of the IAP family are characterized by the presence of 1–3 tandem repeats of an ∼70-residue baculovirus IAP repeat domain (2). The baculovirus IAP repeat domains of many IAP proteins have been shown to be the region within IAP proteins that associates with caspases and other proapoptotic molecules (3, 4). IAP proteins have remarkably different apoptotic inhibitory abilities. For example, X-linked IAP (XIAP) is a highly potent cell death inhibitor (5) and is thought to be the only mammalian IAP protein that directly inhibits the enzymatic activities of caspases (2–4, 6). Although cellular IAP1 and -2 (c-IAP1 and c-IAP2) are anti-apoptotic proteins that can bind to caspase-7 and -9, they do not inhibit the enzymatic activities of these caspases (2, 6).Many IAP proteins, including c-IAP1 and c-IAP2, contain a carboxyl-terminal RING domain that can function as an E3 ubiquitin ligase (7). The E3 ubiquitin ligase activity of the RING domain in c-IAP1 and c-IAP2 was previously shown to negatively regulate the apoptotic inhibitory properties of c-IAP proteins and to promote autoubiquitination and degradation of c-IAP1 (8, 9), thus hindering attempts to define the cellular properties of this protein.A specialized property of the c-IAP proteins is their involvement in tumor necrosis family (TNF) signaling (10–12). Both c-IAP1 and c-IAP2 were discovered in a biochemical screen for factors associated with the type 2 TNF receptor. This association was found to be indirect and bridged by interactions with TNF receptor-associated factors (TRAFs), most notably TRAF1 and TRAF2 (11). Though the consequences of the association between TRAF2 and c-IAP1 on TNF-mediated signaling have been investigated (12), less is known about the functional significance of the association between TRAF2 and c-IAP1 on cell death inhibition. Because both c-IAP1 and TRAF2 possess E3 ubiquitin ligase activity in their respective RING domains, it seemed that the association between these molecules might impact the protective properties of c-IAP1 and alter the apoptotic threshold.In this study, the role of TRAF2 in c-IAP1 stability and how the association of TRAF2 with c-IAP1 affects the apoptotic inhibitory properties of c-IAP1 were examined. The presence of TRAF2 greatly enhanced the stability of c-IAP1, and these data suggest that the interaction between TRAF2 and c-IAP1 inhibits the E3 ubiquitin ligase activity intrinsic to the RING domain of c-IAP1. Using stabilized c-IAP1, the anti-apoptotic activity of c-IAP1 was characterized, and it was found that c-IAP1 suppresses apoptosis to a degree comparable with XIAP. Furthermore, we show that c-IAP1 functions to prevent the IAP antagonist, Smac/DIABLO (13, 14), from interfering with XIAP inhibition of caspases. Together, this study demonstrates that although c-IAP1 does not directly inhibit caspase activity, stabilized c-IAP1 can sequester Smac/DIABLO, prevent Smac/DIABLO from antagonizing XIAP, and inhibit cell death.     

RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase in human cells reveals requirements for de novo initiation and protein-protein interaction

Brome mosaic virus (BMV) is a model positive-strand RNA virus whose replication has been studied in a number of surrogate hosts. In transiently transfected human cells, the BMV polymerase 2a activated signaling by the innate immune receptor RIG-I, which recognizes de novo-initiated non-self-RNAs. Active-site mutations in 2a abolished RIG-I activation, and coexpression of the BMV 1a protein stimulated 2a activity. Mutations previously shown to abolish 1a and 2a interaction prevented the 1a-dependent enhancement of 2a activity. New insights into 1a-2a interaction include the findings that helicase active site of 1a is required to enhance 2a polymerase activity and that negatively charged amino acid residues between positions 110 and 120 of 2a contribute to interaction with the 1a helicase-like domain but not to the intrinsic polymerase activity. Confocal fluorescence microscopy revealed that the BMV 1a and 2a colocalized to perinuclear region in human cells. However, no perinuclear spherule-like structures were detected in human cells by immunoelectron microscopy. Sequencing of the RNAs coimmunoprecipitated with RIG-I revealed that the 2a-synthesized short RNAs are derived from the message used to translate 2a. That is, 2a exhibits a strong cis preference for BMV RNA2. Strikingly, the 2a RNA products had initiation sequences (5'-GUAAA-3') identical to those from the 5' sequence of the BMV genomic RNA2 and RNA3. These results show that the BMV 2a polymerase does not require other BMV proteins to initiate RNA synthesis but that the 1a helicase domain, and likely helicase activity, can affect RNA synthesis by 2a.     

Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains

Epidemiological studies of Pierce's disease (PD) can be confounded by a lack of taxonomic detail on the bacterial causative agent, Xylella fastidiosa (Xf). PD in grape is caused by strains of Xylella fastidiosa subsp. fastidiosa, but is not caused by other subspecies of Xf that typically colonize plants other than grape. Detection assays using ELISA and qPCR are effective at detecting and quantifying Xf presence or absence, but offer no information on Xf subspecies or strain identity. Surveying insects or host plants for Xf by current ELISA or qPCR methods provides only presence/absence and quantity information for any and all Xf subspecies, potentially leading to false assessments of disease threat. This study uses a series of adjacent-hybridizing DNA melt analysis probes that are capable of efficiently discriminating Xf subspecies and strain relationships in rapid real-time PCR reactions.     

BrpA is involved in regulation of cell envelope stress responses in Streptococcus mutans

Previous studies have shown that BrpA plays a major role in acid and oxidative stress tolerance and biofilm formation by Streptococcus mutans. Mutant strains lacking BrpA also display increased autolysis and decreased viability, suggesting a role for BrpA in cell envelope integrity. In this study, we examined the impact of BrpA deficiency on cell envelope stresses induced by envelope-active antimicrobials. Compared to the wild-type strain UA159, the BrpA-deficient mutant (TW14D) was significantly more susceptible to antimicrobial agents, especially lipid II inhibitors. Several genes involved in peptidoglycan synthesis were identified by DNA microarray analysis as downregulated in TW14D. Luciferase reporter gene fusion assays also revealed that expression of brpA is regulated in response to environmental conditions and stresses induced by exposure to subinhibitory concentrations of cell envelope antimicrobials. In a Galleria mellonella (wax worm) model, BrpA deficiency was shown to diminish the virulence of S. mutans OMZ175, which, unlike S. mutans UA159, efficiently kills the worms. Collectively, these results suggest that BrpA plays a role in the regulation of cell envelope integrity and that deficiency of BrpA adversely affects the fitness and diminishes the virulence of OMZ175, a highly invasive strain of S. mutans.     

IVIAT: a novel method to identify microbial genes expressed specifically during human infections

In vivo induced antigen technology (IVIAT) is a novel technology that can quickly and easily identify in vivo induced genes in human infections, without the use of animal models. This technology is expected to facilitate the discovery of new targets for vaccines, antimicrobials and diagnostic strategies in a wide range of microbial pathogens.