Reversal of the ΔdegP Phenotypes by a Novel rpoE Allele of Escherichia coli

RseA sequesters RpoE (σE) to the inner membrane of Escherichia coli when envelope stress is low. Elevated envelope stress triggers RseA cleavage by the sequential action of two membrane proteases, DegS and RseP, releasing σE to activate an envelope stress reducing pathway. Revertants of a ΔdegP ΔbamB strain, which fails to grow at 37°C due to high envelope stress, harbored mutations in the rseA and rpoE genes. Null and missense rseA mutations constitutively hyper-activated the σE regulon and significantly reduced the major outer membrane protein (OMP) levels. In contrast, a novel rpoE allele, rpoE3, resulting from the partial duplication of the rpoE gene, increased σE levels greater than that seen in the rseA mutant background but did not reduce OMP levels. A σE-dependent RybB::LacZ construct showed only a weak activation of the σE pathway by rpoE3. Despite this, rpoE3 fully reversed the growth and envelope vesiculation phenotypes of ΔdegP. Interestingly, rpoE3 also brought down the modestly activated Cpx envelope stress pathway in the ΔdegP strain to the wild type level, showing the complementary nature of the σE and Cpx pathways. Through employing a labile mutant periplasmic protein, AcrAL222Q, it was determined that the rpoE3 mutation overcomes the ΔdegP phenotypes, in part, by activating a σE-dependent proteolytic pathway. Our data suggest that a reduction in the OMP levels is not intrinsic to the σE-mediated mechanism of lowering envelope stress. They also suggest that under extreme envelope stress, a tight homeostasis loop between RseA and σE may partly be responsible for cell death, and this loop can be broken by mutations that either lower RseA activity or increase σE levels

A prosodically controlled word and nonword repetition task for 2- to 4- year-olds: Evidence from typically developing children

An association has been found between nonword repetition and language skills in school-aged children with both typical and atypical language development (Dollaghan & Campbell, 1998; Ellis Weismer et al., 2000; Gathercole & Baddeley, 1990; Montgomery, 2002). This raises the possibility that younger children’s repetition performance may be predictive of later language deficits. In order to investigate this possibility, it is important to establish that elicited repetition with very young children is both feasible and informative. To this end, a repetition task was designed and carried out with 66 children aged 2-4. The task consisted of 18 words and 18 matched nonwords that were systematically manipulated for length and prosodic structure. In addition, an assessment of receptive vocabulary was administered. The repetition task elicited high levels of response. Total scores as well as word and nonword scores were sensitive to age. Lexical status and item length affected performance regardless of age: words were repeated more accurately than nonwords, and one-syllable items were repeated more accurately than two-syllable items, which were in turn repeated more accurately than three-syllable items. The effect of prosodic structure was also significant. Whole syllable errors were almost exclusive to unstressed syllables, with those preceding stress being most vulnerable. Performance on the repetition task was significantly correlated with performance on the receptive vocabulary test. Since this repetition task was effective in eliciting responses from most of the 2 to 4-year-old participants, tapped developmental change in their repetition skills, and revealed patterns in their performance, it has the potential to identify deficits in very early repetition skills that may be indicative of wider language difficulties

Protein Aggregation on Metal Oxides Governs Catalytic Activity and Cellular Uptake.

Engineering of catalytically active inorganic nanomaterials holds promising prospects for biomedicine. Catalytically active metal oxides show applications in enhancing wound healing but have also been employed to induce cell death in photodynamic or radiation therapy. Upon introduction into a biological system, nanomaterials are exposed to complex fluids, causing interaction and adsorption of ions and proteins. While protein corona formation on nanomaterials is acknowledged, its modulation of nanomaterial catalytic efficacy is less understood. In this study, proteomic analyses and nano-analytic methodologies quantify and characterize adsorbed proteins, correlating this protein layer with metal oxide catalytic activity in vitro and in vivo. The protein corona comprises up to 280 different proteins, constituting up to 38% by weight. Enhanced complement factors and other opsonins on nanocatalyst surfaces lead to their uptake into macrophages when applied topically, localizing >99% of the nanomaterials in tissue-resident macrophages. Initially, the formation of the protein corona significantly reduces the nanocatalysts' activity, but this activity can be partially recovered in endosomal conditions due to the proteolytic degradation of the corona. Overall, the research reveals the complex relationship between physisorbed proteins and the catalytic characteristics of specific metal oxide nanoparticles, providing design parameters for optimizing nanocatalysts in complex biological environments

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Reviews and syntheses : Turning the challenges of partitioning ecosystem evaporation and transpiration into opportunities

Evaporation (E) and transpiration (T) respond differently to ongoing changes in climate, atmospheric composition, and land use. It is difficult to partition ecosystem-scale evapotranspiration (ET) measurements into E and T, which makes it difficult to validate satellite data and land surface models. Here, we review current progress in partitioning E and T and provide a prospectus for how to improve theory and observations going forward. Recent advancements in analytical techniques create new opportunities for partitioning E and T at the ecosystem scale, but their assumptions have yet to be fully tested. For example, many approaches to partition E and T rely on the notion that plant canopy conductance and ecosystem water use efficiency exhibit optimal responses to atmospheric vapor pressure deficit (D). We use observations from 240 eddy covariance flux towers to demonstrate that optimal ecosystem response to D is a reasonable assumption, in agreement with recent studies, but more analysis is necessary to determine the conditions for which this assumption holds. Another critical assumption for many partitioning approaches is that ET can be approximated as T during ideal transpiring conditions, which has been challenged by observational studies. We demonstrate that T can exceed 95% of ET from certain ecosystems, but other ecosystems do not appear to reach this value, which suggests that this assumption is ecosystem-dependent with implications for partitioning. It is important to further improve approaches for partitioning E and T, yet few multi-method comparisons have been undertaken to date. Advances in our understanding of carbon-water coupling at the stomatal, leaf, and canopy level open new perspectives on how to quantify T via its strong coupling with photosynthesis. Photosynthesis can be constrained at the ecosystem and global scales with emerging data sources including solar-induced fluorescence, carbonyl sulfide flux measurements, thermography, and more. Such comparisons would improve our mechanistic understanding of ecosystem water fluxes and provide the observations necessary to validate remote sensing algorithms and land surface models to understand the changing global water cycle.Peer reviewe

Diagnostic Dilemma in a Patient with Jaundice: How to Differentiate between Autoimmune Pancreatitis, Primary Sclerosing Cholangitis and Pancreas Carcinoma

A 68-year-old male patient was referred to our institution in May 2011 for a suspected tumor in the pancreatic head with consecutive jaundice. Using magnetic resonance imaging, further differentiation between chronic inflammation and a malignant process was not possible with certainty. Apart from cholestasis, laboratory studies showed increased values for CA 19-9 to 532 U/ml (normal <37 U/ml) and hypergammaglobulinemia (immunoglobulin G, IgG) of 19.3% (normal 8.0–15.8%) with an elevation of the IgG4 subtype to 2,350 mg/l (normal 52–1,250 mg/l). Endoscopic retrograde cholangiopancreatography revealed a prominent stenosis of the distal ductus hepaticus communis caused by pancreatic head swelling and also a bihilar stenosis of the main hepatic bile ducts. Cytology demonstrated inflammatory cells without evidence of malignancy. Under suspicion of autoimmune pancreatitis with IgG4-associated cholangitis, immunosuppressive therapy with steroids and azathioprine was started. Follow-up endoscopic retrograde cholangiopancreatography after 3 months displayed regressive development of the diverse stenoses. Jaundice had disappeared and blood values had returned to normal ranges. Moreover, no tumor of the pancreatic head was present in the magnetic resonance control images. Due to clinical and radiological similarities but a consecutive completely different prognosis and therapy, it is of fundamental importance to differentiate between pancreatic cancer and autoimmune pancreatitis. Especially, determination of serum IgG4 levels and associated bile duct lesions induced by inflammation should clarify the diagnosis of autoimmune pancreatitis and legitimate immunosuppressive therapy

Primitive computations in speech processing

Previous research suggests that artificial-language learners exposed to quasi-continuous speech can learn that the first and the last syllables of words have to belong to distinct classes (e.g., Endress & Bonatti, 2007; Peña, Bonatti, Nespor, & Mehler, 2002). The mechanisms of these generalizations, however, are debated. Here we show that participants learn such generalizations only when the crucial syllables are in edge positions (i.e., the first and the last), but not when they are in medial positions (i.e., the second and the fourth in pentasyllabic items). In contrast to the generalizations, participants readily perform statistical analyses also in word middles. In analogy to sequential memory, we suggest that participants extract the generalizations using a simple but specific mechanism that encodes the positions of syllables that occur in edges. Simultaneously, they use another mechanism to track the syllable distribution in the speech streams. In contrast to previous accounts, this model explains why the generalizations are faster than the statistical computations, require additional cues, and break down under different conditions, and why they can be performed at all. We also show that that similar edge-based mechanisms may explain many results in artificial-grammar learning and also various linguistic observations

All-In-One: Advanced preparation of Human Parenchymal and Non-Parenchymal Liver Cells

BACKGROUND & AIMS: Liver cells are key players in innate immunity. Thus, studying primary isolated liver cells is necessary for determining their role in liver physiology and pathophysiology. In particular, the quantity and quality of isolated cells are crucial to their function. Our aim was to isolate a large quantity of high-quality human parenchymal and non-parenchymal cells from a single liver specimen. METHODS: Hepatocytes, Kupffer cells, liver sinusoidal endothelial cells, and stellate cells were isolated from liver tissues by collagenase perfusion in combination with low-speed centrifugation, density gradient centrifugation, and magnetic-activated cell sorting. The purity and functionality of cultured cell populations were controlled by determining their morphology, discriminative cell marker expression, and functional activity. RESULTS: Cell preparation yielded the following cell counts per gram of liver tissue: 2.0+/-0.4x107 hepatocytes, 1.8+/-0.5x106 Kupffer cells, 4.3+/-1.9x105 liver sinusoidal endothelial cells, and 3.2+/-0.5x105 stellate cells. Hepatocytes were identified by albumin (95.5+/-1.7%) and exhibited time-dependent activity of cytochrome P450 enzymes. Kupffer cells expressed CD68 (94.5+/-1.2%) and exhibited phagocytic activity, as determined with 1mum latex beads. Endothelial cells were CD146+ (97.8+/-1.1%) and exhibited efficient uptake of acetylated low-density lipoprotein. Hepatic stellate cells were identified by the expression of alpha-smooth muscle actin (97.1+/-1.5%). These cells further exhibited retinol (vitamin A)-mediated autofluorescence. CONCLUSIONS: Our isolation procedure for primary parenchymal and non-parenchymal liver cells resulted in cell populations of high purity and quality, with retained physiological functionality in vitro. Thus, this system may provide a valuable tool for determining liver function and disease