Identification of components of the Sigma B Regulon in Listeria monocytogenes that contribute to acid and salt tolerance

Sigma B (σB) is an alternative sigma factor that controls the transcriptional response to stress in Listeria monocytogenes and is also known to play a role in the virulence of this human pathogen. In the present study we investigated the impact of a sigB deletion on the proteome of L. monocytogenes grown in a chemically defined medium both in the presence and in the absence of osmotic stress (0.5 M NaCl). Two new phenotypes associated with the sigB deletion were identified using this medium. (i) Unexpectedly, the strain with the ΔsigB deletion was found to grow faster than the parent strain in the growth medium, but only when 0.5 M NaCl was present. This phenomenon was independent of the carbon source provided in the medium. (ii) The ΔsigB mutant was found to have unusual Gram staining properties compared to the parent, suggesting that σB contributes to the maintenance of an intact cell wall. A proteomic analysis was performed by two-dimensional gel electrophoresis, using cells growing in the exponential and stationary phases. Overall, 11 proteins were found to be differentially expressed in the wild type and the ΔsigB mutant; 10 of these proteins were expressed at lower levels in the mutant, and 1 was overexpressed in the mutant. All 11 proteins were identified by tandem mass spectrometry, and putative functions were assigned based on homology to proteins from other bacteria. Five proteins had putative functions related to carbon utilization (Lmo0539, Lmo0783, Lmo0913, Lmo1830, and Lmo2696), while three proteins were similar to proteins whose functions are unknown but that are known to be stress inducible (Lmo0796, Lmo2391, and Lmo2748). To gain further insight into the role of σB in L. monocytogenes, we deleted the genes encoding four of the proteins, lmo0796, lmo0913, lmo2391, and lmo2748. Phenotypic characterization of the mutants revealed that Lmo2748 plays a role in osmotolerance, while Lmo0796, Lmo0913, and Lmo2391 were all implicated in acid stress tolerance to various degrees. Invasion assays performed with Caco-2 cells indicated that none of the four genes was required for mammalian cell invasion. Microscopic analysis suggested that loss of Lmo2748 might contribute to the cell wall defect observed in the ΔsigB mutant. Overall, this study highlighted two new phenotypes associated with the loss of σB. It also demonstrated clear roles for σB in both osmotic and low-pH stress tolerance and identified specific components of the σB regulon that contribute to the responses observed.

Proteomic analyses of a Listeria monocytogenes mutant lacking σB identify new components of the σB regulon and highlight a role for σB in the utilization of glycerol

In Listeria monocytogenes the alternative sigma factor σB plays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the σB regulon in L. monocytogenes 10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic ΔsigB deletion strain were compared. Overall, this study identified 38 proteins whose expression was σB dependent; 17 of these proteins were found to require the presence of σB for full expression, while 21 were expressed at a higher level in the ΔsigB mutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for σB in the general stress response and highlighted a probable role for σB in metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of σB in glycerol metabolism. Five newly identified members of the σB regulon were shown to be under direct regulation of σB using reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four σB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified σB-dependent genes, as well as proteomic analyses, σB was shown to play a major role in the stationary phase of growth in complex media.

Estimated intake of dietary phytoestrogens in Australian women and evaluation of correlates of phytoestrogen intake

The role of dietary phytoestrogens in health has been of continued interest and debate, but available data on the distribution of intake in the Australian diet is scarce. Therefore, we aimed to estimate phytoestrogen consumption in Australian women, describe the pattern of intake and identify correlates of high phytoestrogen intake. Study participants were 2078 control women (18-79 y) from two population-based case-control studies on gyneacological cancers (2002-2007). Dietary information was obtained using a 135-item semiquantitative FFQ and intakes of isoflavones, lignans, enterolignans and coumestans, including their individual components, were estimated using a database of phytoestrogen content in food developed in the UK. Median total intake (energy-adjusted) of phytoestrogens was 1.29 mg/d, of isoflavones 611 μg/d, of lignans 639 μg/d, of enterolignans 21μg/d and of coumestrol 8 μg/d. Both isoflavone and lignan intake were strongly skewed towards higher values and positively correlated with age. Women consumed on average 2 serves of soy foods/week. Compared to low phytoestrogen consumers (≤1.29 mg/d, median split), high phytoestrogen consumers (>1.29 mg/d) were slightly older, less likely to be smokers, had a higher educational and physical activity level, lower BMI, lower intake of dietary fat, and higher intake of fibre, selected micronutrient and soy food (all p<0.03). The daily intake of phytoestrogens in Australian women with predominantly Caucasian ethnicity is approximately 1 mg, similar to other Western populations, but considerably lower than among Asian women. However, those with a relatively high phytoestrogen diet seem to have healthier lifestyle and more favourable dietary profile compared to others.

Intakes and sources of isoflavones, lignans, enterolignans, coumestrol and soya-containing foods in the Norfolk arm of the European Prospective Investigation into Cancer and Nutrition (EPIC-Norfolk), from 7-day food diaries, using a newly updated database

Objective: A phytoestrogen-rich diet has been suggested to protect against a variety of common diseases but UK intake data on phytoestrogens or their food sources is sparse. This study aims to estimate the average intake of isoflavones, lignans, enterolignans and coumestrol from 7-day food diaries (7dFD), and to provide data on total isoflavone, lignan and phytoestrogen consumption by food group. Design: Development of a food composition database for twelve phytoestrogens and analysis of soya food and phytoestrogen consumption in a population-based study. Setting: Men and women, aged 40-79 years from the general population participating in EPIC-Norfolk between 1993 and 1997, with nutrient and food data from 7dFD. Subjects: A subset of 20 437 participants. Results: The median daily phytoestrogen intake for men was 1.20mg (interquartile range (IQR) 0.93-1.54 mg; mean 1.50 mg, SD 1.50 mg) and 0.89 mg for women (IQR 0.71-1.14 mg; mean 1.20 mg, SD 1.70 mg). In soya-consumers (SC), median daily intakes were higher: 2.86 mg in men (IQR – 1.30-7.27mg; mean 5.05 mg, SD 5.03 mg) and 3.14 mg in women (IQR – 1.09-7.33mg; mean 5.40 mg, SD 6.09 mg). In both men and women, bread made the greatest contribution to phytoestrogen intake – 40.7% and 35.7% respectively. In SC men and women, vegetable dishes and soya/goat’s/sheep’s milks were the main contributors – 42.6% and 18.9% in men and 38.8% and 29.1% in women, respectively. Conclusions: The ability to estimate phytoestrogen intake in Western populations more accurately will aid investigations into their suggested effects on health.

Effect on components of the intestinal microflora and plasma neuropeptide levels of feeding Lactobacillus delbrueckii, Bifidobacterium lactis, and inulin to adult and elderly rats

The aim of this study was to compare the effects of the mixture of Lactobacillus delbrueckii subsp. rhamnosus strain GG, Bifidobacterium lactis Bb12, and inulin on intestinal populations of lactobacilli, bifidobacteria, and enterobacteria in adult and elderly rats fed the same (in quality and quantity) diet. The portal plasma levels of two neuropeptides, neuropeptide Y (NPY) and peptide YY (PYY), were also evaluated to assess the physiological consequences of the synbiotic treatment for the gastrointestinal (GI) tracts of rats of different ages. Adult (n = 24) and elderly (n = 24) male rats were fed the AIN-93 M maintenance diet. After 2 weeks of adaptation, the diet of 12 rats of each age group was supplemented with 8% inulin and with strains GG and Bb12 to provide 2.2 x 10(9) CFU of each strain g(-1) of the diet. Blood and different regions of the GI tract were sampled from all rats after 21 days of the treatment. Treatment with the mixture of strain GG, strain BB12, and inulin induced significantly different changes in the numbers of lactobacilli, bifidobacteria, and enterobacteria of the stomach, small intestine, cecum, and colon microflora. Moreover, the GG, BB12, and inulin mixture increased the concentrations of NPY and PYY for adult rats. For the elderly animals, the PYY concentration was not changed, while the NPY concentration was decreased by treatment with the GG, BB12, and inulin mixture. The results of the present study indicate that the physiological status of the GI tract, and not just diet, has a major role in the regulation of important groups of the GI bacteria community, since even the outcome of the dietary modification with synbiotics depends on the ages of the animals.

Components of olive oil and chemoprevention of colorectal cancer

Olive oil contains a vast range of substances such as monounsaturated free fatty acids (e.g., oleic acid), hydrocarbon squalene, tocopherols, aroma components, and phenolic compounds. Higher consumption of olive oil is considered the hallmark of the traditional Mediterranean diet, which has been associated with low incidence and prevalence of cancer, including colorectal cancer. The anticancer properties of olive oil have been attributed to its high levels of monounsaturated fatty acids, squalene, tocopherols, and phenolic compounds. Nevertheless, there is a growing interest in studying the role of olive oil phenolics in carcinogenesis. This review aims to provide an overview of the relationship between olive oil phenolics and colorectal cancer, in particular summarizing the epidemiologic, in vitro, cellular, and animal studies on antioxidant and anticarcinogenic effects of olive oil phenolics.

An extratropical cyclone database: A tool for illustrating cyclone structure and evolution characteristics

Extratropical cyclone lifecycles have been studied extensively with the aim of understanding the dynamical mechanisms involved in their development. Previous work has often been based on subjective analysis of individual case studies. Such case studies have contributed heavily to the generation of conceptual models of extratropical cyclones that provide a framework for understanding the dynamical evolution of cyclones. These conceptual models are widely used in educational meteorology courses throughout the world to illustrate the basic structure and evolution of extratropical cyclones. This article presents a database of extratropical cyclone composites which highlight the average structure and evolution of 20 years of extratropical cyclones, as opposed to individual case studies. The composite fields are achieved by combining a database containing cyclone tracks from the ERA-Interim reanalysis (1989-2009, 6 hourly) with the full 3D ERA-Interim reanalysis fields. Vertical and horizontal composites of cyclone structure for cyclones generated in the Atlantic and Pacific regions identifying features such as the relative positions of cold, warm and occluded fronts and their associated wind and cloud patterns are shown. In addition the evolution of cyclonic flows such as the warm and cold conveyor belts and dry intrusion are illustrated. A webpage containing an archive of the composited data is freely available for educational purposes.

Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray

We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S. enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.

The data-mining of studies database 'HHdbIV'

This article clarifies what was done with the sub-7-man positions in data-mining Harold van der Heijden's 'HHdbIV' database of chess studies prior to its publication. It emphasises that only positions in the main lines of studies were examined and that the information about uniqueness of move was not incorporated in HHdbIV. There is some reflection on the separate technical and artistic dimensions of study evaluation.

Developing new components for variable flow distribution system modelling in TRNSYS

This study attempts to fill the existing gap in the simulation of variable flow distribution systems through developing new pressure governing components. These components are able to capture the actual ever-changing system performance curve in variable flow distribution systems together with the prediction of controversial issues such as starving, over-flow and the lack of controllability on the flow rate of different branches in a hydronic system. The performance of the proposed components is verified using a case study under design and off-design circumstances. Full integration of the new components within the TRNSYS simulation package is another advantage of this study, which makes it more applicable for designers in both the design and commissioning of hydronic systems.

One-port de-embedding technique for the quasi-optical characterization of integrated components

We describe a one-port de-embedding technique suitable for the quasi-optical characterization of terahertz integrated components at frequencies beyond the operational range of most vector network analyzers. This technique is also suitable when the manufacturing of precision terminations to sufficiently fine tolerances for the application of a TRL de-embedding technique is not possible. The technique is based on vector reflection measurements of a series of easily realizable test pieces. A theoretical analysis is presented for the precision of the technique when implemented using a quasi-optical null-balanced bridge reflectometer. The analysis takes into account quantization effects in the linear and angular encoders associated with the balancing procedure, as well as source power and detector noise equivalent power. The precision in measuring waveguide characteristic impedance and attenuation using this de-embedding technique is further analyzed after taking into account changes in the power coupled due to axial, rotational, and lateral alignment errors between the device under test and the instruments' test port. The analysis is based on the propagation of errors after assuming imperfect coupling of two fundamental Gaussian beams. The required precision in repositioning the samples at the instruments' test-port is discussed. Quasi-optical measurements using the de-embedding process for a WR-8 adjustable precision short at 125 GHz are presented. The de-embedding methodology may be extended to allow the determination of S-parameters of arbitrary two-port junctions. The measurement technique proposed should prove most useful above 325 GHz where there is a lack of measurement standards.

Ozone database in support of CMIP5 simulations: results and corresponding radiative forcing

A continuous tropospheric and stratospheric vertically resolved ozone time series, from 1850 to 2099, has been generated to be used as forcing in global climate models that do not include interactive chemistry. A multiple linear regression analysis of SAGE I+II satellite observations and polar ozonesonde measurements is used for the stratospheric zonal mean dataset during the well-observed period from 1979 to 2009. In addition to terms describing the mean annual cycle, the regression includes terms representing equivalent effective stratospheric chlorine (EESC) and the 11-yr solar cycle variability. The EESC regression fit coefficients, together with pre-1979 EESC values, are used to extrapolate the stratospheric ozone time series backward to 1850. While a similar procedure could be used to extrapolate into the future, coupled chemistry climate model (CCM) simulations indicate that future stratospheric ozone abundances are likely to be significantly affected by climate change, and capturing such effects through a regression model approach is not feasible. Therefore, the stratospheric ozone dataset is extended into the future (merged in 2009) with multimodel mean projections from 13 CCMs that performed a simulation until 2099 under the SRES (Special Report on Emission Scenarios) A1B greenhouse gas scenario and the A1 adjusted halogen scenario in the second round of the Chemistry-Climate Model Validation (CCMVal-2) Activity. The stratospheric zonal mean ozone time series is merged with a three-dimensional tropospheric data set extracted from simulations of the past by two CCMs (CAM3.5 and GISSPUCCINI)and of the future by one CCM (CAM3.5). The future tropospheric ozone time series continues the historical CAM3.5 simulation until 2099 following the four different Representative Concentration Pathways (RCPs). Generally good agreement is found between the historical segment of the ozone database and satellite observations, although it should be noted that total column ozone is overestimated in the southern polar latitudes during spring and tropospheric column ozone is slightly underestimated. Vertical profiles of tropospheric ozone are broadly consistent with ozonesondes and in-situ measurements, with some deviations in regions of biomass burning. The tropospheric ozone radiative forcing (RF) from the 1850s to the 2000s is 0.23Wm−2, lower than previous results. The lower value is mainly due to (i) a smaller increase in biomass burning emissions; (ii) a larger influence of stratospheric ozone depletion on upper tropospheric ozone at high southern latitudes; and possibly (iii) a larger influence of clouds (which act to reduce the net forcing) compared to previous radiative forcing calculations. Over the same period, decreases in stratospheric ozone, mainly at high latitudes, produce a RF of −0.08Wm−2, which is more negative than the central Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) value of −0.05Wm−2, but which is within the stated range of −0.15 to +0.05Wm−2. The more negative value is explained by the fact that the regression model simulates significant ozone depletion prior to 1979, in line with the increase in EESC and as confirmed by CCMs, while the AR4 assumed no change in stratospheric RF prior to 1979. A negative RF of similar magnitude persists into the future, although its location shifts from high latitudes to the tropics. This shift is due to increases in polar stratospheric ozone, but decreases in tropical lower stratospheric ozone, related to a strengthening of the Brewer-Dobson circulation, particularly through the latter half of the 21st century. Differences in trends in tropospheric ozone among the four RCPs are mainly driven by different methane concentrations, resulting in a range of tropospheric ozone RFs between 0.4 and 0.1Wm−2 by 2100. The ozone dataset described here has been released for the Coupled Model Intercomparison Project (CMIP5) model simulations in netCDF Climate and Forecast (CF) Metadata Convention at the PCMDI website (http://cmip-pcmdi.llnl.gov/).

Analysis of the variability of auditory brainstem response components through linear regression

(ABR) is of fundamental importance to the investiga- tion of the auditory system behavior, though its in- terpretation has a subjective nature because of the manual process employed in its study and the clinical experience required for its analysis. When analyzing the ABR, clinicians are often interested in the identi- fication of ABR signal components referred to as Jewett waves. In particular, the detection and study of the time when these waves occur (i.e., the wave la- tency) is a practical tool for the diagnosis of disorders affecting the auditory system. In this context, the aim of this research is to compare ABR manual/visual analysis provided by different examiners. Methods: The ABR data were collected from 10 normal-hearing subjects (5 men and 5 women, from 20 to 52 years). A total of 160 data samples were analyzed and a pair- wise comparison between four distinct examiners was executed. We carried out a statistical study aiming to identify significant differences between assessments provided by the examiners. For this, we used Linear Regression in conjunction with Bootstrap, as a me- thod for evaluating the relation between the responses given by the examiners. Results: The analysis sug- gests agreement among examiners however reveals differences between assessments of the variability of the waves. We quantified the magnitude of the ob- tained wave latency differences and 18% of the inves- tigated waves presented substantial differences (large and moderate) and of these 3.79% were considered not acceptable for the clinical practice. Conclusions: Our results characterize the variability of the manual analysis of ABR data and the necessity of establishing unified standards and protocols for the analysis of these data. These results may also contribute to the validation and development of automatic systems that are employed in the early diagnosis of hearing loss.

Credit and liquidity components of corporate CDS spreads

This paper investigates the role of credit and liquidity factors in explaining corporate CDS price changes during normal and crisis periods. We find that liquidity risk is more important than firm-specific credit risk regardless of market conditions. Moreover, in the period prior to the recent “Great Recession” credit risk plays no role in explaining CDS price changes. The dominance of liquidity effects casts serious doubts on the relevance of CDS price changes as an indicator of default risk dynamics. Our results show how multiple liquidity factors including firm specific and aggregate liquidity proxies as well as an asymmetric information measure are critical determinants of CDS price variations. In particular, the impact of informed traders on the CDS price increases when markets are characterised by higher uncertainty, which supports concerns of insider trading during the crisis.

Dissociating between object affordances and spatial compatibility effects using early response components

Perception and action are tightly linked: objects may be perceived not only in terms of visual features, but also in terms of possibilities for action. Previous studies showed that when a centrally located object has a salient graspable feature (e.g., a handle), it facilitates motor responses corresponding with the feature's position. However, such so-called affordance effects have been criticized as resulting from spatial compatibility effects, due to the visual asymmetry created by the graspable feature, irrespective of any affordances. In order to dissociate between affordance and spatial compatibility effects, we asked participants to perform a simple reaction-time task to typically graspable and non-graspable objects with similar visual features (e.g., lollipop and stop sign). Responses were measured using either electromyography (EMG) on proximal arm muscles during reaching-like movements, or with finger key-presses. In both EMG and button press measurements, participants responded faster when the object was either presented in the same location as the responding hand, or was affordable, resulting in significant and independent spatial compatibility and affordance effects, but no interaction. Furthermore, while the spatial compatibility effect was present from the earliest stages of movement preparation and throughout the different stages of movement execution, the affordance effect was restricted to the early stages of movement execution. Finally, we tested a small group of unilateral arm amputees using EMG, and found residual spatial compatibility but no affordance, suggesting that spatial compatibility effects do not necessarily rely on individuals’ available affordances. Our results show dissociation between affordance and spatial compatibility effects, and suggest that rather than evoking the specific motor action most suitable for interaction with the viewed object, graspable objects prompt the motor system in a general, body-part independent fashion