"Unknown genome" proteomics: a new NADP-dependent epimerase/dehydratase revealed by N-terminal sequencing, inverted PCR, and high resolution mass spectrometry

We present here a new approach that enabled the identification of a new protein from a bacterial strain with unknown genomic background using a combination of inverted PCR with degenerate primers derived from N-terminal protein sequences and high resolution peptide mass determination of proteolytic digests from two-dimensional electrophoretic separation. Proteins of the sulfate-reducing bacterium Desulfotignum phosphitoxidans specifically induced in the presence of phosphite were separated by two-dimensional gel electrophoresis as a series of apparent soluble and membrane-bound isoforms with molecular masses of approximately 35 kDa. Inverted PCR based on N-terminal sequences and high resolution peptide mass fingerprinting by Fourier transform-ion cyclotron resonance mass spectrometry provided the identification of a new NAD(P) epimerase/dehydratase by specific assignment of peptide masses to a single ORF, excluding other possible ORF candidates. The protein identification was ascertained by chromatographic separation and sequencing of internal proteolytic peptides. Metal ion affinity isolation of tryptic peptides and high resolution mass spectrometry provided the identification of five phosphorylations identified in the domains 23-47 and 91-118 of the protein. In agreement with the phosphorylations identified, direct molecular weight determination of the soluble protein eluted from the two-dimensional gels by mass spectrometry provided a molecular mass of 35,400 Da, which is consistent with an average degree of three phosphorylations.     

On Quality Control Measures in Genome-Wide Association Studies: A Test to Assess the Genotyping Quality of Individual Probands in Family-Based Association Studies and an Application to the HapMap Data

Allele transmissions in pedigrees provide a natural way of evaluating the genotyping quality of a particular proband in a family-based, genome-wide association study. We propose a transmission test that is based on this feature and that can be used for quality control filtering of genome-wide genotype data for individual probands. The test has one degree of freedom and assesses the average genotyping error rate of the genotyped SNPs for a particular proband. As we show in simulation studies, the test is sufficiently powerful to identify probands with an unreliable genotyping quality that cannot be detected with standard quality control filters. This feature of the test is further exemplified by an application to the third release of the HapMap data. The test is ideally suited as the final layer of quality control filters in the cleaning process of genome-wide association studies. It identifies probands with insufficient genotyping quality that were not removed by standard quality control filtering.     

Mollusc assemblages of the Pontian and Dacian deposits from the Topolog-Arge? area (southern Carpathian foredeep - Romania)

A better understanding of Mediterranean-Paratethys water-exchange during the Messinian Salinity Crisis has since long been hampered by the absence of a reliable time frame for the Paratethys. High-resolution magnetostratigraphic studies on the sedimentary sequences of the eastern and southern Carpathian foredeep recently resulted in an accurate chronology for the Mio-Pliocene deposits of the Dacic Basin of Romania. This allowed a straightforward correlation of the Pontian and Dacian stages to the geological time scale, which revived earlier discussions on Mediterranean-Paratethys connectivity. Here, we present Pontian and Dacian mollusc assemblages of the Getic Depression (Topolog-Arge? area, southern Carpathians) of Romania, which are incorporated in a magnetostratigraphic time frame. They indicate that a hiatus - comprising the Early Pontian - is present in the stratigraphic successions, which could be related to a base level drop of the Paratethys water column or to more local tectonic processes. The mollusc assemblages furthermore show a gradual transition at the Pontian/Dacian boundary, which is magnetostratigraphically dated at ∼4.9 Ma. This is significantly later (by more than 400 kyrs) than the Mio-Pliocene boundary in the Mediterranean sequences.     

Adjuvant properties of bacterial product cantastim

Aluminum compounds have been used as adjuvants in practical vaccination for more than 60 years to induce an early, an efficient and a long lasting protective immunity. Nowadays they are the most widely used adjuvants in both veterinary and human vaccines. Unfortunately these adjuvants do not only cause undesirable side effects, but often induce T-helper type 2 (Th2)-biased responses. In this study we investigated the ability of the bacterial product CANTASTIM (CS) to augment the immune responses to a model antigen, tetanus toxoid (TT). Immunization of mice with TT+CS elicited higher anti-TT IgG antibody levels as compared to mice that received TT alone. Moreover, treatment with TT+CS resulted in a lower IgG1/IgG2a ratio and a stronger in vitro IFN-gamma synthesis by splenocytes and T cells cocultured with macrophages. These data suggest that CS can be used to enhance the magnitude of the immune response and to skew it towards the Th1 type.     

The ganglioside G(D2) induces the constitutive activation of c-Met in MDA-MB-231 breast cancer cells expressing the G(D3) synthase

We have recently established and characterized cellular clones deriving from MDA-MB-231 breast cancer cells that express the human G(D3) synthase (GD3S), the enzyme that controls the biosynthesis of b- and c-series gangliosides. The GD3S positive clones show a proliferative phenotype in the absence of serum or growth factors and an increased tumor growth in severe immunodeficient mice. This phenotype results from the constitutive activation of the receptor tyrosine kinase c-Met in spite of the absence of ligand and subsequent activation of mitogen-activated protein kinase/extracellular signal-regulated kinase and phosphoinositide 3-kinase/Akt pathways. Here, we show by mass spectrometry analysis of total glycosphingolipids that G(D3) and G(D2) are the main gangliosides expressed by the GD3S positive clones. Moreover, G(D2) colocalized with c-Met at the plasma membrane and small interfering RNA silencing of the G(M2)/G(D2) synthase efficiently reduced the expression of G(D2) as well as c-Met phosphorylation and reversed the proliferative phenotype. Competition assays using anti-G(D2) monoclonal antibodies also inhibit proliferation and c-Met phosphorylation of GD3S positive clones in serum-free conditions. Altogether, these results demonstrate the involvement of the disialoganglioside G(D2) in MDA-MB-231 cell proliferation via the constitutive activation of c-Met. The accumulation of G(D2) in c-Met expressing cells could therefore reinforce the tumorigenicity and aggressiveness of breast cancer tumors.     

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

Structural genetic variation, including copy-number variation (CNV), constitutes a substantial fraction of total genetic variability and the importance of structural genetic variants in modulating human disease is increasingly being recognized. Early successes in identifying disease-associated CNVs via a candidate gene approach mandate that future disease association studies need to include structural genetic variation. Such analyses should not rely on previously developed methodologies that were designed to evaluate single nucleotide polymorphisms (SNPs). Instead, development of novel technical, statistical, and epidemiologic methods will be necessary to optimally capture this newly-appreciated form of genetic variation in a meaningful manner.     

Experimental studies on bacterial product cantastim derived from Pseudomonas aeruginosa. VII. Activation of immune cells of healthy controls and cancer patients

CANTASTIM (CS) is a purified extract of Pseudomonas aeruginosa with beneficial effects related to enhancing the immune responses in conditions such as chronic viral and bacterial infections, immunodeficiencies and cancer immunosuppression. The aim of this study was to determine the capacity of this biological product to stimulate in vitro human leukocytes in whole blood. Blood samples from healthy donors and cancer patients were incubated with CS for 24 h and leukocytes were assessed for induction of inflammatory cytokines (TNF-alpha and IL-1beta) by ELISA and expression of early activation marker CD69 by flow-cytometry. For both groups of investigated subjects, the levels of TNF-alpha and IL-1beta in the supernatants of whole blood culture stimulated with CS were significantly higher than in unstimulated cultures, although lower than in LPS-stimulated samples. Stimulation of whole blood cultures with CS increased both the frequency and the expression of CD69 on the surface of T lymphocytes and NK cells. Importantly, this was noticed not only for healthy controls, but also for cancer patients. These data demonstrate the capacity of bacterial immunomodulator CS to activate human leukocytes of healthy subjects and cancer patients.     

A new testing strategy to identify rare variants with either risk or protective effect on disease

Rapid advances in sequencing technologies set the stage for the large-scale medical sequencing efforts to be performed in the near future, with the goal of assessing the importance of rare variants in complex diseases. The discovery of new disease susceptibility genes requires powerful statistical methods for rare variant analysis. The low frequency and the expected large number of such variants pose great difficulties for the analysis of these data. We propose here a robust and powerful testing strategy to study the role rare variants may play in affecting susceptibility to complex traits. The strategy is based on assessing whether rare variants in a genetic region collectively occur at significantly higher frequencies in cases compared with controls (or vice versa). A main feature of the proposed methodology is that, although it is an overall test assessing a possibly large number of rare variants simultaneously, the disease variants can be both protective and risk variants, with moderate decreases in statistical power when both types of variants are present. Using simulations, we show that this approach can be powerful under complex and general disease models, as well as in larger genetic regions where the proportion of disease susceptibility variants may be small. Comparisons with previously published tests on simulated data show that the proposed approach can have better power than the existing methods. An application to a recently published study on Type-1 Diabetes finds rare variants in gene IFIH1 to be protective against Type-1 Diabetes.     

Enantioanalysis of Pipecolic Acid with Stochastic and Potentiometric Microsensors

Stochastic and potentiometric microsensors based on porphyrins and polymeric surfactants such as polysodium N‐undecanoyl‐ l ‐leucylvanilate and polysodium 相似文献