Probing the QCD Critical Point with Higher Moments of Net-proton Multiplicity Distributions

Higher moments of event-by-event net-proton multiplicity distributions are applied to search for the QCD critical point in the heavy ion collisions. It has been demonstrated that higher moments as well as moment products are sensitive to the correlation length and directly connected to the thermodynamic susceptibilities computed in the Lattice QCD and Hadron Resonance Gas (HRG) model. In this paper, we will present measurements for kurtosis ($\kappa$), skewness ($S$) and variance ($\sigma^{2}$) of net-proton multiplicity distributions at the mid-rapidity ($|y|<0.5$) and $0.4<p_{T}<0.8$ GeV/$c$ for Au+Au collisions at $\sqrt{s_{NN}}$=19.6, 39, 62.4, 130 and 200 GeV, Cu+Cu collisions at $\sqrt{s_{NN}}$=22.4, 62.4 and 200 GeV, d+Au collisions at $\sqrt{s_{NN}}$=200 GeV and p+p collisions at $\sqrt{s_{NN}}$=62.4 and 200 GeV. The moment products $\kappa \sigma^{2}$ and $S \sigma$ of net-proton distributions, which are related to volume independent baryon number susceptibility ratio, are compared to the Lattice QCD and HRG model calculations. The $\kappa \sigma^{2}$ and $S \sigma$ of net-proton distributions are consistent with Lattice QCD and HRG model calculations at high energy, which support the thermalization of the colliding system. Deviations of $\kappa \sigma^{2}$ and $S \sigma$ for the Au+Au collisions at low energies from HRG model calculations are also observed.Comment: 10 pages, 8 figures, Proceedings of 27th Winter Workshon on Nuclear Dynamics. Feb. 6-13 (2011

Template-dependent multiple displacement amplification for profiling human circulating RNA

Multiple displacement amplification (MDA) is widely used in whole-genome/transcriptome amplification. However, template-independent amplification (TIA) in MDA is a commonly observed phenomenon, particularly when using high concentrations of random hexamer primers and extended incubation times. Here, we demonstrate that the use of random pentamer primers with 5´ ends blocked by a C18 spacer results in MDA solely in a template-dependent manner, a technique we have named tdMDA. Together with an optimized procedure for the removal of residual genomic DNA during RNA extraction, tdMDA was used to profile circulating RNA from 0.2 mL of patient sera. In comparison to regular MDA, tdMDA demonstrated a lack of quantifiable DNA amplification in the negative control, a remarkable reduction of unmapped reads from Illumina sequencing (7 ± 10.9% versus 58.6 ± 39%, P = 0.006), and increased mapping rates of the serum transcriptome (26.9 ± 7.9% versus 5.8 ± 8.2%, P = 3.8 × 10-4). Transcriptome profiles could be used to separate patients with chronic hepatitis C virus (HCV) infection from those with HCV-associated hepatocellular carcinoma (HCC). We conclude that tdMDA should facilitate RNA-based liquid biopsy, as well as other genome studies with biological specimens having ultralow amounts of genetic material. </jats:p

The diversity of microbial aldo/keto reductases from Escherichia coli K12

The genome of Escherichia coli K12 contains 9 open reading frames encoding aldo/keto reductases (AKRs) that are differentially regulated and sequence diverse. A significant amount of data is available for the E. coli AKRs through the availability of gene knockouts and gene expression studies, which adds to the biochemical and kinetic data. This together with the availability of crystal structures for nearly half of the E. coli AKRs and homologues of several others provides an opportunity to look at the diversity of these representative bacterial AKRs. Based around the common AKR fold of (β/α)8 barrel with two additional α-helices, the E. coli AKRs have a loop structure that is more diverse than their mammalian counterparts, creating a variety of active site architectures. Nearly half of the AKRs are expected to be monomeric, but there are examples of dimeric, trimeric and octameric enzymes, as well as diversity in specificity for NAD as well as NADP as a cofactor. However in functional assignments and characterisation of enzyme activities there is a paucity of data when compared to the mammalian AKR enzymes