Determination of the pK for the acid-induced denaturation of ferrocytochrome c

Optical absorption spectroscopy was used to characterize the acid-induced conformational transition of horse heart ferrocytochrome c in the presence of urea. By using linear extrapolation to zero denaturant concentration, an apparent pK value for denaturation was found to be 0.86 +/- 0.07 at 25 degrees C. Visible absorption spectra in the presence of high urea concentration indicate that the dominant population is a high-spin, five-coordinate form under acidic conditions. Ferricytochrome c, used as a model reference system, shows a linear dependence of pK values versus urea concentration in the range from 0 to 4.1 M. Our data also indicate that even at a pH below 2 the iron-sulfur bond in ferrocytochrome c is present.     

Conformation, stability, and active-site cysteine titrations of Escherichia coli D26A thioredoxin probed by Raman spectroscopy.

The active-site cysteines (Cys 32 and Cys 35) of Escherichia coli thioredoxin are oxidized to a disulfide bridge when the protein mediates substrate reduction. In reduced thioredoxin, Cys 32 and Cys 35 are characterized by abnormally low pKa values. A conserved side chain, Asp 26, which is sterically accessible to the active site, is also essential to oxidoreductase activity. pKa values governing cysteine thiol-thiolate equilibria in the mutant thioredoxin, D26A, have been determined by direct Raman spectrophotometric measurement of sulfhydryl ionizations. The results indicate that, in D26A thioredoxin, both sulfhydryls titrate with apparent pKa values of 7.5+/-0.2, close to values measured previously for wild-type thioredoxin. Sulfhydryl Raman markers of D26A and wild-type thioredoxin also exhibit similar band shapes, consistent with minimal differences in respective cysteine side-chain conformations and sulfhydryl interactions. The results imply that neither the Cys 32 nor Cys 35 SH donor is hydrogen bonded directly to Asp 26 in the wild-type protein. Additionally, the thioredoxin main-chain conformation is largely conserved with D26A mutation. Conversely, the mutation perturbs Raman bands diagnostic of tryptophan (Trp 28 and Trp 31) orientations and leads to differences in their pH dependencies, implying local conformational differences near the active site. We conclude that, although the carboxyl side chain of Asp 26 neither interacts directly with active-site cysteines nor is responsible for their abnormally low pKa values, the aspartate side chain may play a role in determining the conformation of the enzyme active site.     

Geno viewer, a SAM/BAM viewer tool

The ever evolving Next Generation Sequencing technology is calling for new and innovative ways of data processing and visualization. Following a detailed survey of the current needs of researchers and service providers, the authors have developed GenoViewer: a highly user-friendly, easy-to-operate SAM/BAM viewer and aligner tool. GenoViewer enables fast and efficient NGS assembly browsing, analysis and read mapping. It is highly customized, making it suitable for a wide range of NGS related tasks. Due to its relatively simple architecture, it is easy to add specialised visualization functionalities, facilitating further customised data analysis. The software's source code is freely available; it is open for project and task-specific modifications. AVAILABILITY: The database is available for free at http://www.genoviewer.com/     

Quantitative analysis of mRNA expression levels and DNA methylation profiles of three neighboring genes: FUS1, NPRL2/G21 and RASSF1A in non-small cell lung cancer patients

Background

Tumor suppressor gene (TSG) inactivation plays a crucial role in carcinogenesis. FUS1, NPRL2/G21 and RASSF1A are TSGs from LUCA region at 3p21.3, a critical chromosomal region in lung cancer development. The aim of the study was to analyze and compare the expression levels of these 3 TSGs in NSCLC, as well as in macroscopically unchanged lung tissue surrounding the primary lesion, and to look for the possible epigenetic mechanism of TSG inactivation via gene promoter methylation.

Methods

Expression levels of 3 TSGs and 2 DNA methyltransferases, DNMT1 and DNMT3B, were assessed using real-time PCR method (qPCR) in 59 primary non-small cell lung tumors and the matched macroscopically unchanged lung tissue samples. Promoter methylation status of TSGs was analyzed using methylation-specific PCRs (MSP method) and Methylation Index (MI) value was calculated for each gene.

Results

The expression of all three TSGs were significantly different between NSCLC subtypes: RASSF1A and FUS1 expression levels were significantly lower in squamous cell carcinoma (SCC), and NPRL2/G21 in adenocarcinoma (AC). RASSF1A showed significantly lower expression in tumors vs macroscopically unchanged lung tissues. Methylation frequency was 38–76 %, depending on the gene. The highest MI value was found for RASSF1A (52 %) and the lowest for NPRL2/G21 (5 %). The simultaneous decreased expression and methylation of at least one RASSF1A allele was observed in 71 % tumor samples. Inverse correlation between gene expression and promoter methylation was found for FUS1 (rs = −0.41) in SCC subtype. Expression levels of DNMTs were significantly increased in 75–92 % NSCLCs and were significantly higher in tumors than in normal lung tissue. However, no correlation between mRNA expression levels of DNMTs and DNA methylation status of the studied TSGs was found.

Conclusions

The results indicate the potential role of the studied TSGs in the differentiation of NSCLC histopathological subtypes. The significant differences in RASSF1A expression levels between NSCLC and macroscopically unchanged lung tissue highlight its possible diagnostic role in lung cancer in situ recognition. High percentage of lung tumor samples with simultaneous RASSF1A decreased expression and gene promoter methylation indicates its epigenetic silencing. However, DNMT overexpression doesn’t seem to be a critical determinate of its promoter hypermethylation.     

Which Factors Affect the Success or Failure of Eradication Campaigns against Alien Species?

Although issues related to the management of invasive alien species are receiving increasing attention, little is known about which factors affect the likelihood of success of management measures. We applied two data mining techniques, classification trees and boosted trees, to identify factors that relate to the success of management campaigns aimed at eradicating invasive alien invertebrates, plants and plant pathogens. We assembled a dataset of 173 different eradication campaigns against 94 species worldwide, about a half of which (50.9%) were successful. Eradications in man-made habitats, greenhouses in particular, were more likely to succeed than those in (semi-)natural habitats. In man-made habitats the probability of success was generally high in Australasia, while in Europe and the Americas it was higher for local infestations that are easier to deal with, and for international campaigns that are likely to profit from cross-border cooperation. In (semi-) natural habitats, eradication campaigns were more likely to succeed for plants introduced as an ornamental and escaped from cultivation prior to invasion. Averaging out all other factors in boosted trees, pathogens, bacteria and viruses were most, and fungi the least likely to be eradicated; for plants and invertebrates the probability was intermediate. Our analysis indicates that initiating the campaign before the extent of infestation reaches the critical threshold, starting to eradicate within the first four years since the problem has been noticed, paying special attention to species introduced by the cultivation pathway, and applying sanitary measures can substantially increase the probability of eradication success. Our investigations also revealed that information on socioeconomic factors, which are often considered to be crucial for eradication success, is rarely available, and thus their relative importance cannot be evaluated. Future campaigns should carefully document socioeconomic factors to enable tests of their importance.     

Effect of Blue Light on Endogenous Isopentenyladenine and Endoreduplication during Photomorphogenesis and De-Etiolation of Tomato (Solanum lycopersicum L.) Seedlings

Light is one of the most important factor influencing plant growth and development all through their life cycle. One of the well-known light-regulated processes is de-etiolation, i.e. the switch from skotomorphogenesis to photomorphogenesis. The hormones cytokinins (CKs) play an important role during the establishment of photomorphogenesis as exogenous CKs induced photomorphogenesis of dark-grown seedlings. Most of the studies are conducted on the plant model Arabidopsis, but no or few information are available for important crop species, such as tomato (Solanum lycopersicum L.). In our study, we analyzed for the first time the endogenous CKs content in tomato hypocotyls during skotomorphogenesis, photomorphogenesis and de-etiolation. For this purpose, two tomato genotypes were used: cv. Rutgers (wild-type; WT) and its corresponding mutant (7B-1) affected in its responses to blue light (BL). Using physiological and molecular approaches, we identified that the skotomorphogenesis is characterized by an endoreduplication-mediated cell expansion, which is inhibited upon BL exposure as seen by the accumulation of trancripts encoding CycD3, key regulators of the cell cycle. Our study showed for the first time that iP (isopentenyladenine) is the CK accumulated in the tomato hypocotyl upon BL exposure, suggesting its specific role in photomorphogenesis. This result was supported by physiological experiments and gene expression data. We propose a common model to explain the role and the relationship between CKs, namely iP, and endoreduplication during de-etiolation and photomorphogenesis.     

Distribution of HSV-1 IgG antibodies by two methods comparing in Turkish atopic children

Herpes Simplex Virus Type 1 (HSV-1) is a ubiquitous pathogen. Other than known diseases, HSV-1 may have an important role in the pathogenesis of atopy by causing immortality of th2 cells. From June 1st to July 31st 2006, seventy five blood samples were collected from atopic children referred to the allergy clinic of the hospital. The bloods samples were used to detect HSV-1 IgG antibodies by Enzyme-Linked Immunosorbent Assay and Virus Neutralization Test. HSV-1 IgG antibody seroprevalence in atopic children was found high, 62.6% by Enzyme-Linked Immunosorbent Assay and 57.3% by Virus Neutralization Test. Thus Virus Neutralization Test sensitivity was 92.15% and specificity was 100% regarding to the Enzyme-Linked Immunosorbent Assay technic. Although Enzyme-Linked Immunosorbent Assay was more sensitive than Virus Neutralization Test, there was no significant difference between two technics (p > 0.05) in detecting HSV-1 IgG antibodies in serum.     

A new species of Onychopterochelius Blüthgen (Hymenoptera: Vespidae: Eumeninae) from Turkey

Onychopterocheilus sarikamisensis sp. n. is described and illustrated from eastern Turkey. The species is related to O. hellenicus (Morawitz, 1885) but differs by the shape of the clypeus and antennae, and by the pale colouration of the maculations.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A3E75353-EC16-458F-908FAB9240E8016B     

Lipid spirals in Bacillus subtilis and their role in cell division

The fluid mosaic model of membrane structure has been revised in recent years as it has become evident that domains of different lipid composition are present in eukaryotic and prokaryotic cells. Using membrane binding fluorescent dyes, we demonstrate the presence of lipid spirals extending along the long axis of cells of the rod-shaped bacterium Bacillus subtilis. These spiral structures are absent from cells in which the synthesis of phosphatidylglycerol is disrupted, suggesting an enrichment in anionic phospholipids. Green fluorescent protein fusions of the cell division protein MinD also form spiral structures and these were shown by fluorescence resonance energy transfer to be coincident with the lipid spirals. These data indicate a higher level of membrane lipid organization than previously observed and a primary role for lipid spirals in determining the site of cell division in bacterial cells.