Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing

BACKGROUND: Mass spectrometry based proteomics result in huge amounts of data that has to be processed in real time in order to efficiently feed identification algorithms and to easily integrate in automated environments. We present wiff2dta, a tool created to convert MS/MS data obtained using Applied Biosystem's QStar and QTrap 2000 and 4000 series. RESULTS: Comparing the performance of wiff2dta with the standard tools, we find wiff2dta being the fastest solution for extracting spectrum data from ABIs raw file format. wiff2dta is at least 10% faster than the standard tools. It is also capable of batch processing and can be easily integrated in high throughput environments. The program is freely available via , and is also available from Applied Biosystems. CONCLUSIONS: wiff2dta offers the possibility to run as stand-alone application or within a batch process as command-line tool integrated in automation and high-throughput environments. It is more efficient than the state-of-the-art tools provided

Efficient generation of neural stem cell-like cells from adult human bone marrow stromal cells

Clonogenic neural stem cells (NSCs) are self-renewing cells that maintain the capacity to differentiate into brain-specific cell types, and may also replace or repair diseased brain tissue. NSCs can be directly isolated from fetal or adult nervous tissue, or derived from embryonic stem cells. Here, we describe the efficient conversion of human adult bone marrow stromal cells (hMSC) into a neural stem cell-like population (hmNSC, for human marrow-derived NSC-like cells). These cells grow in neurosphere-like structures, express high levels of early neuroectodermal markers, such as the proneural genes NeuroD1, Neurog2, MSl1 as well as otx1 and nestin, but lose the characteristics of mesodermal stromal cells. In the presence of selected growth factors, hmNSCs can be differentiated into the three main neural phenotypes: astroglia, oligodendroglia and neurons. Clonal analysis demonstrates that individual hmNSCs are multipotent and retain the capacity to generate both glia and neurons. Our cell culture system provides a powerful tool for investigating the molecular mechanisms of neural differentiation in adult human NSCs. hmNSCs may therefore ultimately help to treat acute and chronic neurodegenerative diseases

The ZZ' kinetic mixing in the light of the recent direct and indirect dark matter searches

Several constructions, of stringy origins or not, generate abelian gauge extensions of the Standard Model (SM). Even if the particles of the SM are not charged under this extra $U'(1)$, one cannot avoid the presence of a kinetic mixing between $U'(1)$ and the hypercharge $U_Y(1)$. In this work, we constraint drastically this kinetic mixing, taking into account the recent experimental data from accelerator physics, direct detection and indirect detection of dark matter. We show that the region respecting WMAP and experimental constraints is now very narrowed along the pole line where $M_{Z_D}\simeq 2 m_{DM}$, $Z_D$ being the gauge boson associated to the extra $U'(1)$.Comment: 9 pages, 3 figures, final version to appear in JCA

Tests of the fundamental symmetries in eta meson decays

Patterns of chiral symmetry violation and tests of the conservation of the fundamental C, P and CP symmetries are key physics issues in studies of the pi0, eta and eta' meson decays. These tests include searches for rare or forbidden decays and searches for asymmetries among the decay products in the not-so-rare decays. Some examples for the rare decays are eta-->2pi, eta-->4pi0 (CP tests), decays into an odd number of photons (e.g., eta-->3g) and the decay eta-->pi0e+e- (C tests). The experimental studies of the pi0, eta and eta' meson decays are carried out at four European accelerator research facilities: KLOE/KLOE-2 at DAFNE (Frascati), Crystal Ball at MAMI (Mainz), WASA at COSY (J\"ulich), Crystal Barrel at ELSA (Bonn).Comment: 9 pages, 2 figures, proceedings of Symposium on Prospects in the Physics of Discrete Symmetries, DISCRETE 2010, 6 - 11 December, Rome; v2: added reference

Uromodulin is expressed in renal primary cilia and UMOD mutations result in decreased ciliary uromodulin expression

Uromodulin (UMOD) mutations are responsible for three autosomal dominant tubulo-interstitial nephropathies including medullary cystic kidney disease type 2 (MCKD2), familial juvenile hyperuricemic nephropathy and glomerulocystic kidney disease. Symptoms include renal salt wasting, hyperuricemia, gout, hypertension and end-stage renal disease. MCKD is part of the ‘nephronophthisis-MCKD complex', a group of cystic kidney diseases. Both disorders have an indistinguishable histology and renal cysts are observed in either. For most genes mutated in cystic kidney disease, their proteins are expressed in the primary cilia/basal body complex. We identified seven novel UMOD mutations and were interested if UMOD protein was expressed in the primary renal cilia of human renal biopsies and if mutant UMOD would show a different expression pattern compared with that seen in control individuals. We demonstrate that UMOD is expressed in the primary cilia of renal tubules, using immunofluorescent studies in human kidney biopsy samples. The number of UMOD-positive primary cilia in UMOD patients is significantly decreased when compared with control samples. Additional immunofluorescence studies confirm ciliary expression of UMOD in cell culture. Ciliary expression of UMOD is also confirmed by electron microscopy. UMOD localization at the mitotic spindle poles and colocalization with other ciliary proteins such as nephrocystin-1 and kinesin family member 3A is demonstrated. Our data add UMOD to the group of proteins expressed in primary cilia, where mutations of the gene lead to cystic kidney diseas

Relic Neutralino Densities and Detection Rates with Nonuniversal Gaugino Masses

We extend previous analyses on the interplay between nonuniversalities in the gaugino mass sector and the thermal relic densities of LSP neutralinos, in particular to the case of moderate to large tan beta. We introduce a set of parameters that generalizes the standard unified scenario to cover the complete allowed parameter space in the gaugino mass sector. We discuss the physical significance of the cosmologically preferred degree of degeneracy between charginos and the LSP and study the effect this degree of degeneracy has on the prospects for direct detection of relic neutralinos in the next round of dark matter detection experiments. Lastly, we compare the fine tuning required to achieve a satisfactory relic density with the case of universal gaugino masses, as in minimal supergravity, and find it to be of a similar magnitude. The sensitivity of quantifiable measures of fine-tuning on such factors as the gluino mass and top and bottom masses is also examined.Comment: Uses RevTeX; 14 pages, 16 figure