V-ATPase B1-subunit promoter drives expression of EGFP in intercalated cells of kidney, clear cells of epididymis and airway cells of lung in transgenic mice

Inward rectifier K⁺ channels (Kir) are a significant determinant of endothelial cell (EC) membrane potential, which plays an important role in endothelium-dependent vasodilatation. In the present study, several complementary strategies were applied to determine the Kir2 subunit composition of human aortic endothelial cells (HAECs). Expression levels of Kir2.1, Kir2.2, and Kir2.4 mRNA were similar, whereas Kir2.3 mRNA expression was significantly weaker. Western blot analysis showed clear Kir2.1 and Kir2.2 protein expression, but Kir2.3 protein was undetectable. Functional analysis of endothelial inward rectifier K⁺ current (I_K) demonstrated that 1) I_K current sensitivity to Ba²⁺ and pH were consistent with currents determined using Kir2.1 and Kir2.2 but not Kir2.3 and Kir2.4, and 2) unitary conductance distributions showed two prominent peaks corresponding to known unitary conductances of Kir2.1 and Kir2.2 channels with a ratio of 4:6. When HAECs were transfected with dominant-negative (dn)Kir2.x mutants, endogenous current was reduced 50% by dnKir2.1 and 85% by dnKir2.2, whereas no significant effect was observed with dnKir2.3 or dnKir2.4. These studies suggest that Kir2.2 and Kir2.1 are primary determinants of endogenous K⁺ conductance in HAECs under resting conditions and that Kir2.2 provides the dominant conductance in these cells. potassium channels; inward rectifier potassium channel     

Urinary Benzene Biomarkers and DNA Methylation in Bulgarian Petrochemical Workers: Study Findings and Comparison of Linear and Beta Regression Models

Chronic occupational exposure to benzene is associated with an increased risk of hematological malignancies such as acute myeloid leukemia (AML), but the underlying mechanisms are still unclear. The main objective of this study was to investigate the association between benzene exposure and DNA methylation, both in repeated elements and candidate genes, in a population of 158 Bulgarian petrochemical workers and 50 unexposed office workers. Exposure assessment included personal monitoring of airborne benzene at work and urinary biomarkers of benzene metabolism (S-phenylmercapturic acid [SPMA] and trans,trans-muconic acid [t,t-MA]) at the end of the work-shift. The median levels of airborne benzene, SPMA and t,t-MA in workers were 0.46 ppm, 15.5 µg/L and 711 µg/L respectively, and exposure levels were significantly lower in the controls. Repeated-element DNA methylation was measured in Alu and LINE-1, and gene-specific methylation in MAGE and p15. DNA methylation levels were not significantly different between exposed workers and controls (P>0.05). Both ordinary least squares (OLS) and beta-regression models were used to estimate benzene-methylation associations. Beta-regression showed better model specification, as reflected in improved coefficient of determination (pseudo R²) and Akaike’s information criterion (AIC). In beta-regression, we found statistically significant reductions in LINE-1 (−0.15%, P<0.01) and p15 (−0.096%, P<0.01) mean methylation levels with each interquartile range (IQR) increase in SPMA. This study showed statistically significant but weak associations of LINE-1 and p15 hypomethylation with SPMA in Bulgarian petrochemical workers. We showed that beta-regression is more appropriate than OLS regression for fitting methylation data.     

From taxonomic literature to cybertaxonomic content

In the ubiquitin-proteasome system, a subset of ubiquitylated proteins requires the AAA+ ATPase p97 (also known as VCP or Cdc48) for extraction from membranes or protein complexes before delivery to the proteasome for degradation. Diverse ubiquitin adapters are known to link p97 to its client proteins, but two recent papers on the adapter protein UBXD7, including one by Bandau et al. in BMC Biology, suggest that rather than simply linking p97 to ubiquitylated proteins, this adapter may be essential to coordinate ubiquitylation and p97-mediated extraction of the proteasome substrate. These findings add to growing indications of richly diverse roles of adapters in p97-mediated signaling functions. See research article: http://www.biomedcentral.com/1741-7007/10/36     

Growth-Regulating Activity of Three 4-Hydroxycoumarin Derivatives on Inoculated Soybean Plants

Three 4-hydroxycoumarin derivatives (ethyl 2-[(4-hydroxy-2-oxo-2H-chromen-3-yl)(4-hydroxyphenyl)methyl]-3-oxobutanoate (SS-14), ethyl 2-[(4-hydroxy-2-oxo-2H-chromen-3-yl)(3-nitrophenyl)methyl]-3-oxobutanoate (SS-21), and 2-[(3,4,5-trimethoxyphenyl)(4-hydroxy-2-oxo-2H-chromen-3-yl)methyl]-3-oxobutanoate (T-2)] were tested for growth-regulating activity on nitrogen-fixing soybean plants in different concentrations: 10⁻⁵, 10⁻⁴, and 10⁻³ M. They revealed growth-regulating activity in a concentration-dependent manner. The most powerful suppression effect of T-2 on shoot and root fresh and dry biomass accumulation, length of roots, and height of plants was found. Shoot fresh biomass was suppressed in an equal extent at 10⁻³ M of the three compounds but the order of inhibition regarding the three applied concentrations was T2 > SS-14 ≈ SS-21. The compound SS-14 inhibited nodule number and nodule biomass mainly at the highest applied concentration, 10⁻³ M. The highest inhibition of nitrogenase activity was established at the three applied concentrations of the compound SS-14.     

Production of Pine Resjn Balsams for Microscopical and Optical Uses

The authors describe a method of obtaining balsam from the crude resin of Yugoslav pines. The quality and the refraction of those balsams are very favorable and they may be used instead of Canada balsam and cedar oil for microscopic work and in some cases for the optical industry. When placed in the above mentioned balsams, histological preparations dyed with very sensitive colors remained unaltered. The authors are of the opinion that the best of all is Balsamum Pini peuce. The balsams of Pinus halpensis, Pinus leucodermis, Pinus nigrae and Pinus silvestris are very similar in their properties to the balsam of Pinus peuce. Tables are given to show: some physical properties of these balsams; the yield obtained in preparing them; their composition in respect to resin and turpentine.     

Aldosterone stimulates vacuolar H(+)-ATPase activity in renal acid-secretory intercalated cells mainly via a protein kinase C-dependent pathway

Urinary acidification in the collecting duct is mediated by the activity of H(+)-ATPases and is stimulated by various factors including angiotensin II and aldosterone. Classically, aldosterone effects are mediated via the mineralocorticoid receptor. Recently, we demonstrated a nongenomic stimulatory effect of aldosterone on H(+)-ATPase activity in acid-secretory intercalated cells of isolated mouse outer medullary collecting ducts (OMCD). Here we investigated the intracellular signaling cascade mediating this stimulatory effect. Aldosterone stimulated H(+)-ATPase activity in isolated mouse and human OMCDs. This effect was blocked by suramin, a general G protein inhibitor, and GP-2A, a specific G(αq) inhibitor, whereas pertussis toxin was without effect. Inhibition of phospholipase C with U-73122, chelation of intracellular Ca(2+) with BAPTA, and blockade of protein kinase C prevented the stimulation of H(+)-ATPases. Stimulation of PKC by DOG mimicked the effect of aldosterone on H(+)-ATPase activity. Similarly, aldosterone and DOG induced a rapid translocation of H(+)-ATPases to the luminal side of OMCD cells in vivo. In addition, PD098059, an inhibitor of ERK1/2 activation, blocked the aldosterone and DOG effects. Inhibition of PKA with H89 or KT2750 prevented and incubation with 8-bromoadenosine-cAMP mildly increased H(+)-ATPase activity. Thus, the nongenomic modulation of H(+)-ATPase activity in OMCD-intercalated cells by aldosterone involves several intracellular pathways and may be mediated by a G(αq) protein-coupled receptor and PKC. PKA and cAMP appear to have a modulatory effect. The rapid nongenomic action of aldosterone may participate in the regulation of H(+)-ATPase activity and contribute to final urinary acidification.     

XML schemas and mark-up practices of taxonomic literature

We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.     

The production of a new extracellular putative long-chain saturated polyester by smooth variants of Mycobacterium vaccae interferes with Th1-cytokine production

Mycobacterium vaccae is of major pharmaceutical interest as an immunotherapeutic agent. Although M. vaccae 15483 ATCC(T) strain displays smooth and rough colonial morphologies on solid culture media, it is not known in which conditions M. vaccae switches from one colonial morphotype to the other or whether there are biological differences, especially immunological, between them. We have found that the change from a smooth to rough stable variant occurs spontaneously at 30 degrees C. The analysis of the composition of the cell wall in both variants showed that the smooth morphotype presents an extracellular material that has never previously been described and was identified as a long-chain saturated polyester that, interestingly, is not produced by the rough morphotype. Our results also indicate that this compound could be implicated in the spreading ability of smooth colonies. Proliferation, IFN-gamma and IL-12(p40) production by splenocyte cultures was significantly higher in mice immunised with the rough variant compared with those immunised with the smooth one. This latter finding suggests that the different colonial morphology of M. vaccae may affect the immunomodulatory effects induced from M. vaccae preparations.     

Probing differentially expressed genes against a microarray database for in silico suppressor/enhancer and inhibitor/activator screens

High-density oligonucleotide arrays are widely used for analysis of gene expression on a genomic scale, but the generated data remain largely inaccessible for comparative analysis purposes. Similarity searches in databases with differentially expressed gene (DEG) lists may be used to assign potential functions to new genes and to identify potential chemical inhibitors/activators and genetic suppressors/enhancers. Although this is a very promising concept, it requires the compatibility and validity of the DEG lists to be significantly improved. Using Arabidopsis and human datasets, we have developed guidelines for the performance of similarity searches against databases that collect microarray data. We found that, in comparison with many other methods, a rank-product analysis achieves a higher degree of inter- and intra-laboratory consistency of DEG lists, and is advantageous for assessing similarities and differences between them. To support this concept, we developed a tool called MASTA (microarray overlap search tool and analysis), and re-analyzed over 600 Arabidopsis microarray expression datasets. This revealed that large-scale searches produce reliable intersections between DEG lists that prove to be useful for genetic analysis, thus aiding in the characterization of cellular and molecular mechanisms. We show that this approach can be used to discover unexpected connections and to illuminate unanticipated interactions between individual genes.