Heterogeneous surface expression of EspA translocon filaments by Escherichia coli O157:H7 is controlled at the posttranscriptional level

Type III secretion systems of enteric bacteria enable translocation of effector proteins into host cells. Secreted proteins of verotoxigenic Escherichia coli O157 strains include components of a translocation apparatus, EspA, -B, and -D, as well as "effectors" such as the translocated intimin receptor (Tir) and the mitochondrion-associated protein (Map). This research has investigated the regulation of LEE4 translocon proteins, in particular EspA. EspA filaments could not be detected on the bacterial cell surface when E. coli O157:H7 was cultured in M9 minimal medium but were expressed from only a proportion of the bacterial population when cultured in minimal essential medium modified with 25 mM HEPES. The highest proportions of EspA-filamented bacteria were detected in late exponential phase, after which filaments were lost rapidly from the bacterial cell surface. Our previous research had shown that human and bovine E. coli O157:H7 strains exhibit marked differences in EspD secretion levels. Here it is demonstrated that the proportion of the bacterial population expressing EspA filaments was associated with the level of EspD secretion. The ability of individual bacteria to express EspA filaments was not controlled at the level of LEE1-4 operon transcription, as demonstrated by using both beta-galactosidase and green fluorescent protein (GFP) promoter fusions. All bacteria, whether expressing EspA filaments or not, showed equivalent levels of GFP expression when LEEI-4 translational fusions were used. Despite this, the LEE4-espADB mRNA was more abundant from populations with a high proportion of nonsecreting bacteria (low secretors) than from populations with a high proportion of secreting and therefore filamented bacteria (high secretors). This research demonstrates that while specific environmental conditions are required to induce LEEI-4 expression, a further checkpoint exists before EspA filaments are produced on the bacterial surface and secretion of effector proteins occurs. This checkpoint in E. coli O157:H7 translocon expression is controlled by a posttranscriptional mechanism acting on LEE4-espADB mRNA. The heterogeneity in EspA filamentation could arise from phase-variable expression of regulators that control this posttranscriptional mechanism.

Homogeneous and heterogeneous distributed classification for pocket data mining

Pocket Data Mining (PDM) describes the full process of analysing data streams in mobile ad hoc distributed environments. Advances in mobile devices like smart phones and tablet computers have made it possible for a wide range of applications to run in such an environment. In this paper, we propose the adoption of data stream classification techniques for PDM. Evident by a thorough experimental study, it has been proved that running heterogeneous/different, or homogeneous/similar data stream classification techniques over vertically partitioned data (data partitioned according to the feature space) results in comparable performance to batch and centralised learning techniques.

What have dendritic cells ever done for adjuvant design? Cellular and molecular methods for the rational development of vaccine adjuvants

Our new molecular understanding of immune priming states that dendritic cell activation is absolutely pivotal for expansion and differentiation of naïve T lymphocytes, and it follows that understanding DC activation is essential to understand and design vaccine adjuvants. This chapter describes how dendritic cells can be used as a core tool to provide detailed quantitative and predictive immunomics information about how adjuvants function. The role of distinct antigen, costimulation, and differentiation signals from activated DC in priming is explained. Four categories of input signals which control DC activation – direct pathogen detection, sensing of injury or cell death, indirect activation via endogenous proinflammatory mediators, and feedback from activated T cells – are compared and contrasted. Practical methods for studying adjuvants using DC are summarised and the importance of DC subset choice, simulating T cell feedback, and use of knockout cells is highlighted. Finally, five case studies are examined that illustrate the benefit of DC activation analysis for understanding vaccine adjuvant function.

Dysregulation of REST-regulated coding and non-coding RNAs in a cellular model of Huntington's disease

Huntingtin (Htt) protein interacts with many transcriptional regulators, with widespread disruption to the transcriptome in Huntington's disease (HD) brought about by altered interactions with the mutant Htt (muHtt) protein. Repressor Element-1 Silencing Transcription Factor (REST) is a repressor whose association with Htt in the cytoplasm is disrupted in HD, leading to increased nuclear REST and concomitant repression of several neuronal-specific genes, including brain-derived neurotrophic factor (Bdnf). Here, we explored a wide set of HD dysregulated genes to identify direct REST targets whose expression is altered in a cellular model of HD but that can be rescued by knock-down of REST activity. We found many direct REST target genes encoding proteins important for nervous system development, including a cohort involved in synaptic transmission, at least two of which can be rescued at the protein level by REST knock-down. We also identified several microRNAs (miRNAs) whose aberrant repression is directly mediated by REST, including miR-137, which has not previously been shown to be a direct REST target in mouse. These data provide evidence of the contribution of inappropriate REST-mediated transcriptional repression to the widespread changes in coding and non-coding gene expression in a cellular model of HD that may affect normal neuronal function and survival.

Rescue of gene expression by modified REST decoy oligonucleotides in a cellular model of Huntington's disease

Transcriptional dysfunction is a prominent hallmark of Huntington's disease (HD). Several transcription factors have been implicated in the aetiology of HD progression and one of the most prominent is repressor element 1 (RE1) silencing transcription factor (REST). REST is a global repressor of neuronal gene expression and in the presence of mutant Huntingtin increased nuclear REST levels lead to elevated RE1 occupancy and a concomitant increase in target gene repression, including brain-derived neurotrophic factor. It is of great interest to devise strategies to reverse transcriptional dysregulation caused by increased nuclear REST and determine the consequences in HD. Thus far, such strategies have involved RNAi or mutant REST constructs. Decoys are double-stranded oligodeoxynucleotides corresponding to the DNA-binding element of a transcription factor and act to sequester it, thereby abrogating its transcriptional activity. Here, we report the use of a novel decoy strategy to rescue REST target gene expression in a cellular model of HD. We show that delivery of the decoy in cells expressing mutant Huntingtin leads to its specific interaction with REST, a reduction in REST occupancy of RE1s and rescue of target gene expression, including Bdnf. These data point to an alternative strategy for rebalancing the transcriptional dysregulation in HD.

Transcriptional dysregulation of coding and non-coding genes in cellular models of Huntington's disease

HD (Huntington's disease) is a late onset heritable neurodegenerative disorder that is characterized by neuronal dysfunction and death, particularly in the cerebral cortex and medium spiny neurons of the striatum. This is followed by progressive chorea, dementia and emotional dysfunction, eventually resulting in death. HD is caused by an expanded CAG repeat in the first exon of the HD gene that results in an abnormally elongated polyQ (polyglutamine) tract in its protein product, Htt (Huntingtin). Wild-type Htt is largely cytoplasmic; however, in HD, proteolytic N-terminal fragments of Htt form insoluble deposits in both the cytoplasm and nucleus, provoking the idea that mutHtt (mutant Htt) causes transcriptional dysfunction. While a number of specific transcription factors and co-factors have been proposed as mediators of mutHtt toxicity, the causal relationship between these Htt/transcription factor interactions and HD pathology remains unknown. Previous work has highlighted REST [RE1 (repressor element 1)-silencing transcription factor] as one such transcription factor. REST is a master regulator of neuronal genes, repressing their expression. Many of its direct target genes are known or suspected to have a role in HD pathogenesis, including BDNF (brain-derived neurotrophic factor). Recent evidence has also shown that REST regulates transcription of regulatory miRNAs (microRNAs), many of which are known to regulate neuronal gene expression and are dysregulated in HD. Thus repression of miRNAs constitutes a second, indirect mechanism by which REST can alter the neuronal transcriptome in HD. We will describe the evidence that disruption to the REST regulon brought about by a loss of interaction between REST and mutHtt may be a key contributory factor in the widespread dysregulation of gene expression in HD.

US inflation expectations and heterogeneous loss functions, 1968-2010

Recent literature has suggested that macroeconomic forecasters may have asymmetric loss functions, and that there may be heterogeneity across forecasters in the degree to which they weigh under- and over-predictions. Using an individual-level analysis that exploits the Survey of Professional Forecasters respondents’ histogram forecasts, we find little evidence of asymmetric loss for the inflation forecasters

Simple method for sub-diffraction resolution imaging of cellular structures on standard confocal microscopes by three-photon absorption of quantum dots

This study describes a simple technique that improves a recently developed 3D sub-diffraction imaging method based on three-photon absorption of commercially available quantum dots. The method combines imaging of biological samples via tri-exciton generation in quantum dots with deconvolution and spectral multiplexing, resulting in a novel approach for multi-color imaging of even thick biological samples at a 1.4 to 1.9-fold better spatial resolution. This approach is realized on a conventional confocal microscope equipped with standard continuous-wave lasers. We demonstrate the potential of multi-color tri-exciton imaging of quantum dots combined with deconvolution on viral vesicles in lentivirally transduced cells as well as intermediate filaments in three-dimensional clusters of mouse-derived neural stem cells (neurospheres) and dense microtubuli arrays in myotubes formed by stacks of differentiated C2C12 myoblasts.

Emergence of spatially heterogeneous burst suppression in a neural field model of electrocortical activity

Burst suppression in the electroencephalogram (EEG) is a well-described phenomenon that occurs during deep anesthesia, as well as in a variety of congenital and acquired brain insults. Classically it is thought of as spatially synchronous, quasi-periodic bursts of high amplitude EEG separated by low amplitude activity. However, its characterization as a “global brain state” has been challenged by recent results obtained with intracranial electrocortigraphy. Not only does it appear that burst suppression activity is highly asynchronous across cortex, but also that it may occur in isolated regions of circumscribed spatial extent. Here we outline a realistic neural field model for burst suppression by adding a slow process of synaptic resource depletion and recovery, which is able to reproduce qualitatively the empirically observed features during general anesthesia at the whole cortex level. Simulations reveal heterogeneous bursting over the model cortex and complex spatiotemporal dynamics during simulated anesthetic action, and provide forward predictions of neuroimaging signals for subsequent empirical comparisons and more detailed characterization. Because burst suppression corresponds to a dynamical end-point of brain activity, theoretically accounting for its spatiotemporal emergence will vitally contribute to efforts aimed at clarifying whether a common physiological trajectory is induced by the actions of general anesthetic agents. We have taken a first step in this direction by showing that a neural field model can qualitatively match recent experimental data that indicate spatial differentiation of burst suppression activity across cortex.

Gender, race, and heterogeneous effects of epidemic malaria on human capital and income

This article investigates the impact of exposure to a serious, unusual, and unforeseen malaria epidemic in northeast Brazil in 1938–40 on subsequent human capital attainment and income. Arguing the event was exogenous, the article exploits cohort and regional heterogeneity in exposure to identify effects. Results are consistent with differential mortality rates according to gender and socioeconomic status, such that heterogeneous selection and scarring effects are observed. Analyzing by gender alone, positive (selection) effects are found for men, and mixed (positive and negative) effects for women. Allowing for heterogeneity by race, selection effects persist for men. In contrast, positive (selection) effects are observed for nonwhite women, and negative (scarring) effects for white women. Results contribute to evidence suggesting that exposure to negative environmental shocks affects human capital attainment, while also suggesting it heterogeneously affects cohort composition.

Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

Endocrine therapies target the activation of the oestrogen receptor alpha (ERα) via distinct mechanisms, but it is not clear whether breast cancer cells can adapt to treatment using drug-specific mechanisms. Here we demonstrate that resistance emerges via drug-specific epigenetic reprogramming. Resistant cells display a spectrum of phenotypical changes with invasive phenotypes evolving in lines resistant to the aromatase inhibitor (AI). Orthogonal genomics analysis of reprogrammed regulatory regions identifies individual drug-induced epigenetic states involving large topologically associating domains (TADs) and the activation of super-enhancers. AI-resistant cells activate endogenous cholesterol biosynthesis (CB) through stable epigenetic activation in vitro and in vivo. Mechanistically, CB sparks the constitutive activation of oestrogen receptors alpha (ERα) in AI-resistant cells, partly via the biosynthesis of 27-hydroxycholesterol. By targeting CB using statins, ERα binding is reduced and cell invasion is prevented. Epigenomic-led stratification can predict resistance to AI in a subset of ERα-positive patients

Cellular mechanisms of cardiac hypertrophy.

Hypertrophy of myocytes in the heart ventricles is an important adaptation that in vivo occurs in response to a requirement for increased contractile power. It involves changes at the level of gene transcription, stimulation of the rate of protein synthesis (translation), and increased assembly of myofibrils. There is mounting evidence of the involvement of reversible protein phosphorylation and dephosphorylation in most of these processes. Protein kinase C, mitogen-activated protein kinases, and transcription factors have been implicated in the modulation of the transcriptional changes. Activation of translation may also be mediated through protein phosphorylation/dephosphorylation, although this has not been clearly established in the heart. Here we provide a critical overview of the signalling pathways involved in the hypertrophic response and provide a scheme to account for many of its features.

Ungulate behavioral responses to the heterogeneous road-network of a touristic protected area in Africa

Understanding how wildlife responds to road and traffic is essential for effective conservation. Yet, not many studies have evaluated how roads influence wildlife in protected areas, particularly within the large iconic African National Parks where tourism is mainly based on sightings from motorized vehicles with the consequent development and intense use of roads. To reduce this knowledge gap, we studied the behavioral response and local spatial distribution of impala Aepyceros melampus along the heterogeneous (with variation in road surface type and traffic intensity) road-network of Kruger National Park (KNP, South Africa). We surveyed different types of roads (paved and unpaved) recording the occurrence of flight responses among sighted impala and describing their local spatial distribution (in relation to the roads). We observed relatively few flight responses (19.5% of 118 observations), suggesting impalas could be partly habituated to vehicles in KNP. In addition, impala local distribution is apparently unaffected by unpaved roads, yet animals seem to avoid the close proximity of paved roads. Overall, our results suggest a negative, albeit small, effect of traffic intensity, and of presence of pavement on roads on the behavior of impala at KNP. Future studies would be necessary to understand how roads influence other species, but our results show that even within a protected area that has been well-visited for a long time, wildlife can still be affected by roads and traffic. This result has ecological (e.g., changes in spatial distribution of fauna) and management implications (e.g., challenges of facilitating wildlife sightings while minimizing disturbance) for protected areas where touristic activities are largely based on driving.

On the parameterization of turbulent surface fluxes over heterogeneous sea ice surfaces

Turbulent surface fluxes of momentum and sensible and latent heat as well as surface temperature, air temperature, air humidity, and wind speed were measured by the German Falcon research aircraft over the marginal ice zone (MIZ) of the northern Baltic Sea and the Fram Strait. Applying the bulk formulas and the stability functions to the measurements, the roughness lengths for momentum z0, sensible heat zT, and latent heat zq were calculated. As mean values over a wide range of sea ice conditions, we obtain z0 = 5 � 10�4 m, zT = 1 � 10�8 m, and zq = 1 � 10�7 m. These correspond to the following mean values (± standard deviations) of neutral transfer coefficients reduced to 10 m height, CDN10 = (1.9 ± 0.8) � 10�3, CHN10 = (0.9 ± 0.3) � 10�3, and CEN10 = (1.0 ± 0.2) � 10�3. An average ratio of z0/zT � 104 was observed over the range of 10�6 m < z0 < 10�2 m and differs from previously published results over compact sea ice (10�1 < z0/zT < 103). Other observational results over heterogeneous sea ice do not exist. However, our z0/zT ratio approximately agrees with observations over heterogeneous land surfaces. Flux parameterizations based on commonly used roughness lengths ratios (z0 = zT = zq) overestimate the surface heat fluxes compared to our measurements by more than 100%.