Biological activities of lipopolysaccharides from Pectinatus cerevisiophilus

Abstract A procedure is described in which the protein crystals produced by Bacillus thuringiensis var. israelensis were solubilized in 50 mM NaOH with 10 mM EDTA at pH 11.7. This solubilization procedure gave protein gel profiles identical with those for intact crystals while maintaining full biological activity in the form of erythrocyte lysis capability. Crystals with and without protease activity were equally toxic to Aedes aegypti larvae.     

Stream Vulnerability to Widespread and Emergent Stressors: A Focus on Unconventional Oil and Gas

Multiple stressors threaten stream physical and biological quality, including elevated nutrients and other contaminants, riparian and in-stream habitat degradation and altered natural flow regime. Unconventional oil and gas (UOG) development is one emerging stressor that spans the U.S. UOG development could alter stream sedimentation, riparian extent and composition, in-stream flow, and water quality. We developed indices to describe the watershed sensitivity and exposure to natural and anthropogenic disturbances and computed a vulnerability index from these two scores across stream catchments in six productive shale plays. We predicted that catchment vulnerability scores would vary across plays due to climatic, geologic and anthropogenic differences. Across-shale averages supported this prediction revealing differences in catchment sensitivity, exposure, and vulnerability scores that resulted from different natural and anthropogenic environmental conditions. For example, semi-arid Western shale play catchments (Mowry, Hilliard, and Bakken) tended to be more sensitive to stressors due to low annual average precipitation and extensive grassland. Catchments in the Barnett and Marcellus-Utica were naturally sensitive from more erosive soils and steeper catchment slopes, but these catchments also experienced areas with greater UOG densities and urbanization. Our analysis suggested Fayetteville and Barnett catchments were vulnerable due to existing anthropogenic exposure. However, all shale plays had catchments that spanned a wide vulnerability gradient. Our results identify vulnerable catchments that can help prioritize stream protection and monitoring efforts. Resource managers can also use these findings to guide local development activities to help reduce possible environmental effects.     

Lipid environment modulates the development of acute tolerance to ethanol in Caenorhabditis elegans

The development of tolerance to a drug at the level of the neuron reflects a homeostatic mechanism by which neurons respond to perturbations of their function by external stimuli. Acute functional tolerance (AFT) to ethanol is a fast compensatory response that develops within a single drug session and normalizes neuronal function despite the continued presence of the drug. We performed a genetic screen to identify genes required for the development of acute functional tolerance to ethanol in the nematode C. elegans. We identified mutations affecting multiple genes in a genetic pathway known to regulate levels of triacylglycerols (TAGs) via the lipase LIPS-7, indicating that there is an important role for TAGs in the development of tolerance. Genetic manipulation of lips-7 expression, up or down, produced opposing effects on ethanol sensitivity and on the rate of development of AFT. Further, decreasing cholesterol levels through environmental manipulation mirrored the effects of decreased TAG levels. Finally, we found that genetic alterations in the levels of the TAG lipase LIPS-7 can modify the phenotype of gain-of-function mutations in the ethanol-inducible ion channel SLO-1, the voltage- and calcium-sensitive BK channel. This study demonstrates that the lipid milieu modulates neuronal responses to ethanol that include initial sensitivity and the development of acute tolerance. These results lend new insight into studies of alcohol dependence, and suggest a model in which TAG levels are important for the development of AFT through alterations of the action of ethanol on membrane proteins.     

HIV impairs TNF-alpha mediated macrophage apoptotic response to Mycobacterium tuberculosis

The factors that contribute to the exceptionally high incidence of Mycobacterium tuberculosis (MTb) disease in HIV(+) persons are poorly understood. Macrophage apoptosis represents a critical innate host cell response to control MTb infection and limit disease. In the current study, virulent live or irradiated MTb (iMTbRv) induced apoptosis of differentiated human U937 macrophages in vitro, in part dependent on TNF-alpha. In contrast, apoptosis of differentiated HIV(+) human U1 macrophages (HIV(+) U937 subclone) was markedly reduced in response to iMTbRv and associated with significantly reduced TNF-alpha release, whereas apoptosis and TNF-alpha release were intact to TLR-independent stimuli. Furthermore, reduced macrophage apoptosis and TNF-alpha release were independent of MTb phagocytosis. Whereas surface expression of macrophage TLR2 and TLR4 was preserved, IL-1 receptor associated kinase-1 phosphorylation and NF-kappaB nuclear translocation were reduced in HIV(+) U1 macrophages in response to iMTbRv. These findings were confirmed using clinically relevant human alveolar macrophages (AM) from healthy persons and asymptomatic HIV(+) persons at clinical risk for MTb infection. Furthermore, in vitro HIV infection of AM from healthy persons reduced both TNF-alpha release and AM apoptosis in response to iMTbRv. These data identify an intrinsic specific defect in a critical macrophage cellular response to MTb that may contribute to disease pathogenesis in HIV(+) persons.     

Characterization of an Fe(2+)-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii

The first step in the biosynthesis of pterins in bacteria and plants is the conversion of GTP to 7,8-dihydro-d-neopterin triphosphate catalyzed by GTP cyclohydrolase I (GTPCHI). Although GTP has been shown to be a precursor of pterins in archaea, homologues of GTPCHI have not been identified in most archaeal genomes. Here we report the identification of a new GTP cyclohydrolase that converts GTP to 7,8-dihydro-d-neopterin 2',3'-cyclic phosphate, the first intermediate in methanopterin biosynthesis in methanogenic archaea. The enzyme from Methanocaldococcus jannaschii is designated MptA to indicate that it catalyzes the first step in the biosynthesis of methanopterin. MptA is the archetype of a new class of GTP cyclohydrolases that catalyzes a series of reactions most similar to that seen with GTPCHI but unique in that the cyclic phosphate is the product. MptA was found to require Fe2+ for activity. Mutation of conserved histidine residues H200N, H293N, and H295N, expected to be involved in Fe2+ binding, resulted in reduced enzymatic activity but no reduction in the amount of bound iron.     

Bioanthropological analysis of human occipital condyles using geometric morphometric method

Sex differences are present in all parts of the body, including the skeletal system. Several methods are used to analyze the sex differences of skeleton, while more recently, a new method called geometric morphometry has been used. The aim of this study was to examine the sexual dimorphism of occipital condyles on human skulls originating from the population of Bosnia and Herzegovina using the geometric morphometric method.Material and methodsThe study was conducted on 214 human skulls of known gender from Bosnian population. For analysis of sexual dimorphism of occipital condyles, we used geometric morphometry, where all the skulls were scanned to obtain three-dimensional skull models. On the obtained models, we marked anthropometric points on occipital condyles in a Landmark Editor program from which we exported data in the form NTSYS file and analyzed it in MorphoJ program.ResultsFirst principal component PC1 describes 26.917% of total variability, the second principal component PC2 describes 20.992% of total variability, while the first eight principal components together describe 100% of total variability. The greatest variability between the male skulls and female skulls was present in the anterior-posterior diameter (length of occipital condyles). Discriminant functional analysis of the shape and size of the occipital condyles was possible with 69.50% accuracy for male skulls and with 60.27% accuracy for female skulls. The size of the occipital condyles showed a statistically significant effect on sexual determination. Discriminant functional analysis of the shape of the occipital condyles without affecting size enabled the determination of gender with with 65.96% accuracy for male skulls and with 63.01% accuracy for female skulls.ConclusionAnalysis of sexual dimorphism of occipital condyles using geometric morphometry showed statistically significant differences in the shape and size of occipital condyles between the sexes. The accuracy of sex determination based on occipital condyles was higher for male gender.     

Multiple marker abundance profiling: combining selected reaction monitoring and data‐dependent acquisition for rapid estimation of organelle abundance in subcellular samples

Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently‐used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower‐abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox ( http://suba.live ).     

Podocalyxin Is a Marker of Poor Prognosis in Pancreatic Ductal Adenocarcinoma

Aim of the Study

Podocalyxin-like 1 is a transmembrane glyco-protein whose overexpression associates in many cancers with poor prognosis and unfavorable clinicopathological characteristics. Until now, its prognostic value has never been studied in pancreatic ductal adenocarcinoma (PDAC). The aim of this study was to investigate podocalyxin expression in PDAC by a novel monoclonal antibody and a commercially available polyclonal antibody.

Patients and Materials

With tissue microarrays and immuno-histochemistry, podocalyxin expression evaluation involved 168 PDAC patients. The associa-tions of the podocalyxin tumor expression with clinicopathological variables were explored by Fisher’s exact test and the linear-by-linear test. Survival analyses were by Kaplan-Meier anal-ysis and the Cox proportional hazard model.

Results

The polyclonal antibody revealed membranous podocalyxin expression in 73 (44.0%) specimens and the monoclonal antibody was highly expressed in 36 (21.8%) cases. Membranous expression by the polyclonal antibody was associated with T classification (p=0.045) and perineural invasion (p=0.005), and high expression by the mono-clonal antibody with poor differentiation (p=0.033). High podocalyxin expression associated significantly with higher risk of death from PDAC by both the polyclonal antibody (hazard ratio (HR) = 1.62; 95% confidence interval (CI) 1.12-2.33; p=0.01) and the monoclonal antibody (HR = 2.10, 95% CI 1.38-3.20; p<0.001). The results remained significant in multivariate analysis, adjusted for age, gender, stage, lymph node ratio (≥/< 20%), and perivascular invasion (respectively as HR = 2.03; 95% CI 1.32-3.13, p=0.001; and as HR = 2.36; 95% CI 1.47-3.80, p<0.001).

Conclusion

We found podocalyxin to be an independent factor for poor prognosis in PDAC. To our knowledge, this is the first such report of its prognostic value.     

Littoral-pelagial interchange and the decomposition of dissolved organic matter in a polyhumic lake

The small, polyhumic lake, Mekkojärvi (southern Finland), is bordered by a moss vegetation zone (Warnstorfia and Sphagnum species) which provides a habitat-rich and productive environment for many planktonic and periphytic animals. Impacts of moss on the metabolism of bacterioplankton, phytoplankton and zooplankton in polyhumic water were investigated in laboratory throughflow systems. Growing Warnstorfia (together with epiphytic algae and bacteria) suppressed the production of planktonic algae but had no clear effect on leucine uptake, and hence bacterial production, or on the decomposition of humic substances. Phenol uptake and mineralization rates, however, were lower in the littoral water than in the pelagial water. Excretion of organic carbon by Warnstorfia algae or Daphnia longispina (the predominant crustacean in the pelagial water) provided only a minor contribution to bacterial production; therefore, a major contribution had to be from humic substances. A bacterial production efficiency of 31–38% could account for the microbial respiration in the water. The results indicated that bacterial, or detrital matter (originating largely from the littoral zone), could not obviate the need for algal food, and that a great deal of particulate matter in the water was poor or useless food for Daphnia. In all, the bulk of dissolved organic matter in Lake Mekkojärvi was biochemically highly recalcitrant. Our results indicate that humic substances (from watershed or littoral area) which, through bacterial degradation, enter the planktonic food web of the lake are mainly lost through respiration by microorganisms.