High confident protein identification from ETD and ECD spectra with a new mass list preprocessor

Comunicaciones a congreso

Segal-Bargmann-Fock modules of monogenic functions

In this paper we introduce the classical Segal-Bargmann transform starting from the basis of Hermite polynomials and extend it to Clifford algebra-valued functions. Then we apply the results to monogenic functions and prove that the Segal-Bargmann kernel corresponds to the kernel of the Fourier-Borel transform for monogenic functionals. This kernel is also the reproducing kernel for the monogenic Bargmann module.Comment: 11 page

Hilbert transforms in Clifford analysis

The Hilbert transform on the real line has applications in many fields. In particular in one–dimensional signal processing, the Hilbert operator is used to extract global as well as instantaneous characteristics, such as frequency, amplitude and phase, from real signals. The multidimensional approach to the Hilbert transform usually is a tensorial one, considering the so-called Riesz transforms in each of the cartesian variables separately. In this paper we give an overview of generalized Hilbert transforms in Euclidean space, developed within the framework of Clifford analysis. Roughly speaking, this is a function theory of higher dimensional holomorphic functions, which is particularly suited for a treatment of multidimensional phenomena since all dimensions are encompassed at once as an intrinsic feature

PT symmetry, Cartan decompositions, Lie triple systems and Krein space related Clifford algebras

Gauged PT quantum mechanics (PTQM) and corresponding Krein space setups are studied. For models with constant non-Abelian gauge potentials and extended parity inversions compact and noncompact Lie group components are analyzed via Cartan decompositions. A Lie triple structure is found and an interpretation as PT-symmetrically generalized Jaynes-Cummings model is possible with close relation to recently studied cavity QED setups with transmon states in multilevel artificial atoms. For models with Abelian gauge potentials a hidden Clifford algebra structure is found and used to obtain the fundamental symmetry of Krein space related J-selfadjoint extensions for PTQM setups with ultra-localized potentials.Comment: 11 page

Spherical harmonics and integration in superspace

In this paper the classical theory of spherical harmonics in R^m is extended to superspace using techniques from Clifford analysis. After defining a super-Laplace operator and studying some basic properties of polynomial null-solutions of this operator, a new type of integration over the supersphere is introduced by exploiting the formal equivalence with an old result of Pizzetti. This integral is then used to prove orthogonality of spherical harmonics of different degree, Green-like theorems and also an extension of the important Funk-Hecke theorem to superspace. Finally, this integration over the supersphere is used to define an integral over the whole superspace and it is proven that this is equivalent with the Berezin integral, thus providing a more sound definition of the Berezin integral.Comment: 22 pages, accepted for publication in J. Phys.

Haptoglobin phenotype is not a predictor of recurrence free survival in high-risk primary breast cancer patients

Contains fulltext : 70104tjan-heijnen.pdf (publisher's version ) (Open Access)BACKGROUND: Better breast cancer prognostication may improve selection of patients for adjuvant therapy. We conducted a retrospective follow-up study in which we investigated sera of high-risk primary breast cancer patients, to search for proteins predictive of recurrence free survival. METHODS: Two sample sets of high-risk primary breast cancer patients participating in a randomised national trial investigating the effectiveness of high-dose chemotherapy were analysed. Sera in set I (n = 63) were analysed by surface enhanced laser desorption ionisation time-of-flight mass spectrometry (SELDI-TOF MS) for biomarker finding. Initial results were validated by analysis of sample set II (n = 371), using one-dimensional gel-electrophoresis. RESULTS: In sample set I, the expression of a peak at mass-to-charge ratio 9198 (relative intensity 20), identified as haptoglobin (Hp) alpha-1 chain, was strongly associated with recurrence free survival (global Log-rank test; p = 0.0014). Haptoglobin is present in three distinct phenotypes (Hp 1-1, Hp 2-1, and Hp 2-2), of which only individuals with phenotype Hp 1-1 or Hp 2-1 express the haptoglobin alpha-1 chain. As the expression of the haptoglobin alpha-1 chain, determined by SELDI-TOF MS, corresponds to the phenotype, initial results were validated by haptoglobin phenotyping of the independent sample set II by native one-dimensional gel-electrophoresis. With the Hp 1-1 phenotype as the reference category, the univariate hazard ratio for recurrence was 0.87 (95% CI: 0.56 - 1.34, p = 0.5221) and 1.03 (95% CI: 0.65 - 1.64, p = 0.8966) for the Hp 2-1 and Hp 2-2 phenotypes, respectively, in sample set II. CONCLUSION: In contrast to our initial results, the haptoglobin phenotype was not identified as a predictor of recurrence free survival in high-risk primary breast cancer in our validation set. Our initial observation in the discovery set was probably the result of a type I error (i.e. false positive). This study illustrates the importance of validation in obtaining the true clinical applicability of a potential biomarker

OP0137 GENOME-WIDE WHOLE-BLOOD TRANSCRIPTOME PROFILING IN A LARGE EUROPEAN COHORT OF SYSTEMIC SCLEROSIS PATIENTS

Background:The analysis of annotated transcripts from genome-wide expression studies data is of paramount importance to understand the molecular phenomena underlying the occurrence of complex diseases, such as systemic sclerosis (SSc).Objectives:To perform whole-blood transcriptome and pathway analysis on whole-blood (WB) RNA collected in two cohorts of European SSc patients. Via a discovery and validation strategy we aimed at characterizing the molecular pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations.Methods:WB samples from 252 controls and 162 SSc patients were collected in RNA stabilizers. Patients were divided into a discovery (n=79; Southern Europe) and validation cohort (n=83; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the FAIME algorithm. In parallel, a immunophenotyping analysis on 28 circulating cell populations was assessed. We then tested: the presence of differentially expressed genes or pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated.Results:A total of 15224 genes and 1277 related functional pathways were available for analysis. Among these, 99 genes and 225 pathways were significant in both sets. The heatmap in figure shows the relative expression of replicated pathways and the distribution of cases and controls (red and green bars). Among the significant pathways we found a deregulation in: type-I IFN, TLR-cascade and signalling, function of the tumor suppressor p53 protein, platelet degranulation and activation. Correlation analysis showed that the count of several cell subtypes is jointly associated with RNA transcripts or FAIME scores with strong differences in relation to the geographical origin of samples; neutrophils emerged as the major determinant of gene expression in SSc-whole-blood samples.Conclusion:We discovered a set of differentially expressed genes and pathways that could be validated in two independent sets of SSc patients highlighting a number of deregulated molecular processes that have relevance for the pathogenesis of autoimmunity and SSc.Acknowledgments:This work was supported by EU/EFPIA/Innovative Medicines Initiative Joint Undertaking PRECISESADS grant No. 115565.Disclosure of Interests:Lorenzo Beretta Grant/research support from: Pfizer, Guillermo Barturen: None declared, Barbara Vigone: None declared, Chiara Bellocchi: None declared, Nicolas Hunzelmann: None declared, Ellen Delanghe: None declared, László Kovács: None declared, Ricard Cervera: None declared, Maria Gerosa: None declared, Rafaela Ortega Castro: None declared, Isabel Almeida: None declared, Divi Cornec: None declared, Carlo Chizzolini Consultant of: Boehringer Ingelheim, Roche, Jacques-Olivier Pers: None declared, Zuzanna Makowska Employee of: Bayer AG, Anne buttgereit Employee of: Bayer AG, Ralf Lesche Employee of: Bayer, Martin Kerick: None declared, Marta Alarcon-Riquelme: None declared, Javier Martin Ibanez: None declare

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry

UV (ultra-violet) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA-and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA-protein, DNA-protein, and nucleotide-protein complexes in vitro and in vivo. We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid–protein complexes and adds spatial information to the described RNA-binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor-binding domains. In vivo UV and chemical XL-MS data from E. coli cells analysed by NuXL establish a comprehensive nucleic acid–protein crosslink inventory with crosslink sites at amino acid level for more than 1500 proteins. Our new workflow combined with the dedicated NuXL search engine identified RNA crosslinks that cover most RNA-binding proteins, with DNA and RNA crosslinks detected in transcriptional repressors and activators

Glycated nail proteins as a new biomarker in management of the South Kivu Congolese diabetics

Introduction: Diagnosis and monitoring of diabetes mellitus in sub-Saharan Africa, based on blood analyses, are hampered by infrastructural and cultural reasons. The first aim of this study was to evaluate the diagnostic accuracy of glycated nail proteins for diabetes mellitus. The second aim was to compare the course of short- and long-term glycemic biomarkers after 6 months of antidiabetic treatment. These objectives should support our hypothesis that glycated nail proteins could be used as an alternative glycemic biomarker. Materials and methods: This case-control study consisted of 163 black diabetics and 67 non-diabetics of the South Kivu (Democratic Republic of Congo). Diagnostic accuracy of glycated nail proteins was evaluated using ROC curve analysis. At the start of the study, glycated nail protein concentrations were compared between diabetics and non-diabetics, using a nitro blue tetrazolium (NBT) colorimetric method. In a subgroup of 30 diabetics, concentrations of glycated nail proteins, fasting glucose (Accu-Chek® Aviva), serum fructosamine (NBT) and HbA1c (DCA-2000+®) were measured at start and after 6 months. Results: ROC analysis yielded an AUC of 0.71 (95% confidence interval (CI): 0.65-0.76) and a cut-off point of 3.83 µmol/g nail. Concentration of glycated nail proteins was significantly higher (P < 0.001) in diabetics in comparison with non-diabetics. After 6 months of antidiabetic treatment, a significant drop in the fasting glucose concentration (P = 0.017) and concentration of glycated nail proteins (P = 0.008) was observed in contrast to serum fructosamine and HbA1c. Conclusions: Measurement of glycated nail proteins could be used to diagnose and monitor diabetes mellitus in sub-Saharan Africa

Whole blood Fe isotopic signature in a sub-Saharan African population

The Fe isotopic composition of an individual's whole blood has recently been shown to be an interesting clinical indicator of Fe status. The present study aimed to evaluate the influence of several endemic characteristics of a representative population of the South Kivu province, an Fe-rich volcanic African region, on the whole blood Fe isotopic composition. Both diabetes mellitus and the ferroportin Q248H mutation are very common in Africa and are strongly associated with impairments in Fe metabolism. Fe isotopic analysis of whole blood samples was carried out using multi-collector inductively coupled plasma-mass spectrometry (after chromatographic isolation of the target element). Forty-two male subjects (between 48 and 59 years old) living in Bukavu (South Kivu) were enrolled in this study. Among the selected population, wild-type subjects and subjects presenting the ferroportin Q248H mutation (heterozygotes and homozygotes) were included. Within each group, diabetic and non-diabetic patients were considered. The whole blood delta Fe-56 value ranged from -3.09% to -2.41%. The delta Fe-56 value shows a significant negative correlation with the ferritin concentration. No correlation could be established between the whole blood delta Fe-56 value and the transferrin concentration, transferrin saturation or serum Fe concentration. The ferroportin Q248H mutation did not seem to have affected the whole blood Fe isotopic signature. The whole blood delta Fe-56 values were significantly higher in diabetic subjects than in non-diabetic subjects and showed a significant negative correlation with body mass index (BMI) values