Serum Concentrations of Myostatin and Myostatin-Interacting Proteins do not differ between young and Scarcopenic elderly men

Peer reviewedPostprin

Meeting report : 1st international functional metagenomics workshop May 7–8, 2012, St. Jacobs, Ontario, Canada

This report summarizes the events of the 1st International Functional Metagenomics Workshop. The workshop was held on May 7 and 8 in St. Jacobs, Ontario, Canada and was focused on building a core international functional metagenomics community, exploring strategic research areas, and identifying opportunities for future collaboration and funding. The workshop was initiated by researchers at the University of Waterloo with support from the Ontario Genomics Institute (OGI), Natural Sciences and Engineering Research Council of Canada (NSERC) and the University of Waterloo

High quality and quantity Genome-wide germline genotypes from FFPE normal tissue

<p>Abstract</p> <p>Background</p> <p>Although collections of formalin fixed paraffin embedded (FFPE) samples exist, sometimes representing decades of stored samples, they have not typically been utilized to their full potential. Normal tissue from such samples would be extremely valuable for generation of genotype data for individuals who cannot otherwise provide a DNA sample.</p> <p>Findings</p> <p>We extracted DNA from normal tissue identified in FFPE tissue blocks from prostate surgery and obtained complete genome wide genotype data for over 500,000 SNP markers for these samples, and for DNA extracted from whole blood for 2 of the cases, for comparison.</p> <p>Four of the five FFPE samples of varying age and amount of tissue had identifiable normal tissue. We obtained good quality genotype data for between 89 and 99% of all SNP markers for the 4 samples from FFPE. Concordance rates of over 99% were observed for the 2 samples with DNA from both FFPE and from whole blood.</p> <p>Conclusions</p> <p>DNA extracted from normal FFPE tissue provides excellent quality and quantity genome-wide genotyping data representing germline DNA, sufficient for both linkage and association analyses. This allows genetic analysis of informative individuals who are no longer available for sampling in genetic studies.</p

Axonal transport deficit in a KIF5A–/– mouse model

Hereditary spastic paraplegia (HSP) is a neurodegenerative disorder preferentially affecting the longest corticospinal axons. More than 40 HSP genetic loci have been identified, among them SPG10, an autosomal dominant HSP caused by point mutations in the neuronal kinesin heavy chain protein KIF5A. Constitutive KIF5A knockout (KIF5A–/–) mice die early after birth. In these mice, lungs were unexpanded, and cell bodies of lower motor neurons in the spinal cord swollen, but the pathomechanism remained unclear. To gain insights into the pathophysiology, we characterized survival, outgrowth, and function in primary motor and sensory neuron cultures from KIF5A–/– mice. Absence of KIF5A reduced survival in motor neurons, but not in sensory neurons. Outgrowth of axons and dendrites was remarkably diminished in KIF5A–/– motor neurons. The number of axonal branches was reduced, whereas the number of dendrites was not altered. In KIF5A–/– sensory neurons, neurite outgrowth was decreased but the number of neurites remained unchanged. In motor neurons maximum and average velocity of mitochondrial transport was reduced both in anterograde and retrograde direction. Our results point out a role of KIF5A in process outgrowth and axonal transport of mitochondria, affecting motor neurons more severely than sensory neurons. This gives pathophysiological insights into KIF5A associated HSP, and matches the clinical findings of predominant degeneration of the longest axons of the corticospinal tract

Event-by-event fluctuations of the kaon to pion ratio in central Pb+Pb collisions at 158 GeV per Nucleon

We present the first measurement of fluctuations from event to event in the production of strange particles in collisions of heavy nuclei. The ratio of charged kaons to charged pions is determined for individual central Pb+Pb collisions. After accounting for the fluctuations due to detector resolution and finite number statistics we derive an upper limit on genuine non-statistical fluctuations, perhaps related to a first or second order QCD phase transition. Such fluctuations are shown to be very small.Comment: 4 pages, 2 figure

Baryon Stopping and Charged Particle Distributions in Central Pb+Pb Collisions at 158 GeV per Nucleon

Net proton and negative hadron spectra for central \PbPb collisions at 158 GeV per nucleon at the CERN SPS were measured and compared to spectra from lighter systems. Net baryon distributions were derived from those of net protons, utilizing model calculations of isospin contributions as well as data and model calculations of strange baryon distributions. Stopping (rapidity shift with respect to the beam) and mean transverse momentum \meanpt of net baryons increase with system size. The rapidity density of negative hadrons scales with the number of participant nucleons for nuclear collisions, whereas their \meanpt is independent of system size. The \meanpt dependence upon particle mass and system size is consistent with larger transverse flow velocity at midrapidity for \PbPb compared to \SS central collisions.Comment: This version accepted for publication in PRL. 4 pages, 3 figures. Typos corrected, some paragraphs expanded in response to referee comments, to better explain details of analysi

Experimental Study of the Shortest Reset Word of Random Automata

In this paper we describe an approach to finding the shortest reset word of a finite synchronizing automaton by using a SAT solver. We use this approach to perform an experimental study of the length of the shortest reset word of a finite synchronizing automaton. The largest automata we considered had 100 states. The results of the experiments allow us to formulate a hypothesis that the length of the shortest reset word of a random finite automaton with $n$ states and 2 input letters with high probability is sublinear with respect to $n$ and can be estimated as $1.95 n^{0.55}.

Two-proton correlations from 158 AGeV Pb+Pb central collisions

The two-proton correlation function at midrapidity from Pb+Pb central collisions at 158 AGeV has been measured by the NA49 experiment. The results are compared to model predictions from static thermal Gaussian proton source distributions and transport models RQMD and VENUS. An effective proton source size is determined by minimizing CHI-square/ndf between the correlation functions of the data and those calculated for the Gaussian sources, yielding 3.85 +-0.15(stat.) +0.60-0.25(syst.) fm. Both the RQMD and the VENUS model are consistent with the data within the error in the correlation peak region.Comment: RevTeX style, 6 pages, 4 figures, 1 table. More discussion are added about the structure on the tail of the correlation function. The systematic error is revised. To appear in Phys. Lett.

Event-by-event fluctuations of average transverse momentum in central Pb+Pb collisions at 158 GeV per nucleon

We present first data on event-by-event fluctuations in the average transverse momentum of charged particles produced in Pb+Pb collisions at the CERN SPS. This measurement provides previously unavailable information allowing sensitive tests of microscopic and thermodynamic collision models and to search for fluctuations expected to occur in the vicinity of the predicted QCD phase transition. We find that the observed variance of the event-by-event average transverse momentum is consistent with independent particle production modified by the known two-particle correlations due to quantum statistics and final state interactions and folded with the resolution of the NA49 apparatus. For two specific models of non-statistical fluctuations in transverse momentum limits are derived in terms of fluctuation amplitude. We show that a significant part of the parameter space for a model of isospin fluctuations predicted as a consequence of chiral symmetry restoration in a non-equilibrium scenario is excluded by our measurement.Comment: 6 pages, 2 figures, submitted to Phys. Lett.