'98 Escherichia coli SWISS-2DPAGE database update

The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman "sequence tag" approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.     

Direction coding using a tactile chair

This laboratory study examined the possibility of using a car seat instrumented with a tactile display to communicate directional information to a driver. A car seat fitted with an 8 × 8 matrix of vibrators embedded in the seat pan was used to code eight different directions. Localization response time and angular accuracy were examined as a function of stimulus direction, presence of a tactile attention cue, temporal pattern, stimulus layout, age, and gender. The mean absolute angular error was 23°, and both localization accuracy and response times were superior for the back left, backward, and back right directions. Of the various temporal pattern/attention cue combinations examined, results favored the relatively fast patterns consisting of vibration bursts of 125 or 250 ms without a centrally located attention cue over 500 ms bursts that were preceded by an attention cue. Observed age and gender effects were relatively modest, suggesting that using tactile cueing to communicate direction is effective across a wide range of users. In addition, the tactile stimulus was detected by more than 90% of the participants under surprise trial conditions. Overall, these results indicate that the tactile chair provides a promising and robust method of providing directional information.     

A linear translation from CTL* to the first-order modal μ -calculus

The modal μ-calculus is a very expressive temporal logic. In particular, logics such as LTL, CTL and CTL* can be translated into the modal μ-calculus, although existing translations of LTL and CTL* are at least exponential in size. We show that an existing simple first-order extension of the modal μ-calculus allows for a linear translation from LTL. Furthermore, we show that solving the translated formulae is as efficient as the best known methods to solve LTL formulae directly.     

Proteomic analysis of the response of the human neutrophil-like cell line NB-4 after exposure to anthrax lethal toxin

We used 2‐D DIGE to analyze the early response of NB‐4 cells, a human promyelotic leukemia cell line, exposed to lethal toxin from Bacillus anthracis at the proteome level. After a 2 h exposure, cells were still viable and 43% of spots (n = 1042) showed a significant change in protein level. We identified 59 spots whose expression had changed significantly, and these reflected cytoskeleton damage, mitochondrial lysis and endoplasmic reticulum stress. Actin filament assembly was disrupted as evidenced by an increase in both actin subunits and phosphorylated cofilin, whilst levels of tropomyosin, tropomodulin and actin related protein 2/3 complex subunit decreased. Lower levels of ATP synthase subunits and mitochondrial inner membrane protein were identified as markers of mitochondrial lysis. Levels of various stress response proteins rose and, uniquely, levels of Ca²⁺ binding proteins such as translationally controlled tumor protein rose and hippocalcin‐like protein 1 decreased. This response may have mitigated effects brought about by mitochondrial lysis and endoplasmic reticulum stress, and delayed or prevented apoptosis in NB‐4 cells. These results resemble findings of similar proteomics studies in murine macrophages, although quantitative differences were observed.     

Enhanced Solar‐to‐Hydrogen Generation with Broadband Epsilon‐Near‐Zero Nanostructured Photocatalysts

The direct conversion of solar energy into fuels or feedstock is an attractive approach to address increasing demand of renewable energy sources. Photocatalytic systems relying on the direct photoexcitation of metals have been explored to this end, a strategy that exploits the decay of plasmonic resonances into hot carriers. An efficient hot carrier generation and collection requires, ideally, their generation to be enclosed within few tens of nanometers at the metal interface, but it is challenging to achieve this across the broadband solar spectrum. Here the authors demonstrate a new photocatalyst for hydrogen evolution based on metal epsilon‐near‐zero metamaterials. The authors have designed these to achieve broadband strong light confinement at the metal interface across the entire solar spectrum. Using electron energy loss spectroscopy, the authors prove that hot carriers are generated in a broadband fashion within 10 nm in this system. The resulting photocatalyst achieves a hydrogen production rate of 9.5 µmol h^?1 cm^?2 that exceeds, by a factor of 3.2, that of the best previously reported plasmonic‐based photocatalysts for the dissociation of H₂ with 50 h stable operation.     

Nothing good ever happens after midnight: Observed exposure and alcohol use during weekend nights among young male drivers carrying passengers in a late licensing country

Similar to other countries, also in the Netherlands young male drivers (ages between 18 and 24 years) are overrepresented in crashes during weekend nights, thereby fatally injuring one or more of their passengers. This overrepresentation may be due to two contributing factors: (a) a higher exposure-to-risk because of dangerous trip condition, and (b) a higher tendency to take risks. Studies on these factors, mostly carried out in jurisdictions where youngsters are licensed at an earlier age than in Europe, suggest a strong –often negative– influence from peer-aged passengers. Given that in adolescence susceptibility to peer pressure reduces with age, these findings may not be applicable to late licensing countries, such as in Europe. In the Netherlands –a late licensing country– youngsters are licensed after the age of 18 years, followed by a 5 year probation period with a legal alcohol limit of 0.2 g/L. Further, designated driver schemes are in place since 2001, alcohol limits are enforced by random breath testing schemes, and no passenger and night time restrictions are in force. Against this background, we examined the incidence of dangerous trip conditions and risk taking among young male drivers and compared those with a reference group with a low passenger fatality rate. To that end, data on trip conditions and risk behavior were obtained from a data base on 18,608 randomly selected drivers during weekend nights in 2010, between 22:00 and 06:00. This data base held information for each randomly selected on breath alcohol concentration (BAC), license status, driver characteristics (age and gender), number of passengers, time of night, and level of urbanization. Binary logistic regression analysis confirmed the overrepresentation of young male drivers in traffic, carrying more frequently passengers than the reference group, especially after midnight. Urbanization level was not a modifying factor, but ‘time of night’ was, with riskier conditions after midnight in terms of: (a) a higher young male driver presence, (b) young male drivers carrying more frequently multiple passengers and (c) a higher prevalence of illegal BACs. After midnight, no evidence was found for a protective effect of the presence of one passenger on alcohol use. Of the young male drivers, 5% were over the legal limit and 3 in 5 young males who were over the limit carried passengers. However, the indicative result that young male drivers with multiple passengers were less likely to have been drinking than solo drivers or drivers with just one passenger, is suggestive of a protective effect of multiple passengers. These results may guide preventive strategies, including police enforcement and designated driver programmes.     

Zafirlukast Induces VHL- and HIF-2α-Dependent Oxidative Cell Death in 786-O Clear Cell Renal Carcinoma Cells

Mutations in the Von Hippel–Lindau (VHL) gene are the driving force in many forms of clear cell renal cell carcinoma (ccRCC) and promote hypoxia-inducible factor (HIF)-dependent tumor proliferation, metastasis and angiogenesis. Despite the progress that has already been made, ccRCC generally remain resistant to conventional therapies and ccRCC patients suffer from metastasis and acquired resistance, highlighting the need for novel therapeutic options. Cysteinyl leukotriene receptor 1 (CysLTR1) antagonists, like zafirlukast, are administered in bronchial asthma to control eicosanoid signaling. Intriguingly, long-term use of zafirlukast decreases cancer risk and leukotriene receptor antagonists inhibit tumor growth, but the mechanisms still remain unexplored. Therefore, we aim to understand the mechanisms of zafirlukast-mediated cell death in ccRCC cells. We show that zafirlukast induces VHL-dependent and TNFα-independent non-apoptotic and non-necroptotic cell death in ccRCC cells. Cell death triggered by zafirlukast could be rescued with antioxidants and the PARP-1 inhibitor Olaparib, and additionally relies on HIF-2α. Finally, MG-132-mediated proteasome inhibition sensitized VHL wild-type cells to zafirlukast-induced cell death and inhibition of HIF-2α rescued zafirlukast- and MG-132-triggered cell death. Together, these results highlight the importance of VHL, HIF and proteasomal degradation in zafirlukast-induced oxidative cell death with potentially novel therapeutic implications for ccRCC.     

Flow-Induced Failure of Cable-Tied Blocks

An experimental study of flow-induced failure of cable-tied blocks is presented. The particular failure mechanism studied is overturning and rolling up of the leading edge of a cable-tied block mat. Individual blocks were investigated also. The block size, flow depth, and block (mat) protrusion above the surrounding bed were systematically varied. The results are presented in terms of the critical dimensionless shear stress θc for block (mat) failure. A relationship between θc, block size and block protrusion, and flow depth is given.     

Genome-Wide Investigation of Multifocal and Unifocal Prostate Cancer—Are They Genetically Different?

Prostate cancer is widely observed to be biologically heterogeneous. Its heterogeneity is manifested histologically as multifocal prostate cancer, which is observed more frequently than unifocal prostate cancer. The clinical and prognostic significance of either focal cancer type is not fully established. To investigate prostate cancer heterogeneity, the genetic profiles of multifocal and unifocal prostate cancers were compared. Here, we report observations deduced from tumor-tumor comparison of copy number alteration data of both focal categories. Forty-one fresh frozen prostate cancer foci from 14 multifocal prostate cancers and eight unifocal prostate cancers were subjected to copy number variation analysis with the Affymetrix SNP 6.0 microarray tool. With the investigated cases, tumors obtained from a single prostate exhibited different genetic profiles of variable degrees. Further comparison identified no distinct genetic pattern or signatures specific to multifocal or unifocal prostate cancer. Our findings suggest that samples obtained from multiple sites of a single unifocal prostate cancer show as much genetic heterogeneity and variability as separate tumors obtained from a single multifocal prostate cancer.