Reconstitution of a Minimal DNA Replicase From Pseudomonas Aeruginosa and Stimulation by Non-Cognate Auxiliary Factors

DNA polymerase III holoenzyme is responsible for chromosomal replication in bacteria. The components and functions of Escherichia coli DNA polymerase III holoenzyme have been studied extensively. Here, we report the reconstitution of replicase activity by essential components of DNA polymerase holoenzyme from the pathogen Pseudomonas aeruginosa. We have expressed and purified the processivity factor (β), single-stranded DNA-binding protein, a complex containing the polymerase (α) and exonuclease (ϵ) subunits, and the essential components of the DnaX complex (τ3δδ′). Efficient primer elongation requires the presence of αϵ, β, and τ3δδ′. Pseudomonas aeruginosa αϵ can substitute completely for E. coli polymerase III in E. coli holoenzyme reconstitution assays. Pseudomonas β and τ3δδ′ exhibit a 10-fold lower activity relative to their E. coli counterparts in E. coli holoenzyme reconstitution assays. Although the Pseudomonas counterpart to the E. coli ψ subunit was not apparent in sequence similarity searches, addition of purified E. coli χ and ψ (components of the DnaX complex) increases the apparent specific activity of the Pseudomonas τ3δδ′ complex ∼10-fold and enables the reconstituted enzyme to function better under physiological salt conditions

Discovery and Characterization of the Cryptic Psi Subunit of the Pseudomonad DNA Replicase

We previously reconstituted a minimal DNA replicase from Pseudomonas aeruginosa consisting of α and ϵ (polymerase and editing nuclease), β (processivity factor), and the essential τ, δ, and δ′ components of the clamp loader complex (Jarvis, T., Beaudry, A., Bullard, J., Janjic, N., and McHenry, C. (2005) J. Biol. Chem. 280, 7890-7900). In Escherichia coli DNA polymerase III holoenzyme, χ and Ψ are tightly associated clamp loader accessory subunits. The addition of E. coli χΨ to the minimal P. aeruginosa replicase stimulated its activity, suggesting the existence of χ and Ψ counterparts in P. aeruginosa. The P. aeruginosa χ subunit was recognizable from sequence similarity, but Ψ was not. Here we report purification of an endogenous replication complex from P. aeruginosa. Identification of the components led to the discovery of the cryptic Ψ subunit, encoded by holD. P. aeruginosa χ and Ψ were co-expressed and purified as a 1:1 complex. P. aeruginosa χΨ increased the specific activity of τ3δδ′ 25-fold and enabled the holoenzyme to function under physiological salt conditions. A synergistic effect between χΨ and single-stranded DNA binding protein was observed. Sequence similarity to P. aeruginosa Ψ allowed us to identify Ψ subunits from several other Pseudomonads and to predict probable translational start sites for this protein family. This represents the first identification of a highly divergent branch of the Ψ family and confirms the existence of Ψ in several organisms in which Ψ was not identifiable based on sequence similarity alone

Accelerating and Retarding Anomalous Diffusion

In this paper Gaussian models of retarded and accelerated anomalous diffusion are considered. Stochastic differential equations of fractional order driven by single or multiple fractional Gaussian noise terms are introduced to describe retarding and accelerating subdiffusion and superdiffusion. Short and long time asymptotic limits of the mean squared displacement of the stochastic processes associated with the solutions of these equations are studied. Specific cases of these equations are shown to provide possible descriptions of retarding or accelerating anomalous diffusion.Comment: 18 page, 1 figur

Evaluation of Pyridoacridine Alkaloids in a Zebrafish Phenotypic Assay

Three new minor components, the pyridoacridine alkaloids 1-hydroxy-deoxyamphimedine (1), 3-hydroxy-deoxyamphimedine (2), debromopetrosamine (3), and three known compounds, amphimedine (4), neoamphimedine (5) and deoxyamphimedine (6), have been isolated from the sponge Xestospongia cf. carbonaria, collected in Palau. Structures were assigned on the basis of extensive 1D and 2D NMR studies as well as analysis by HRESIMS. Compounds 1–6 were evaluated in a zebrafish phenotype-based assay. Amphimedine (4) was the only compound that caused a phenotype in zebrafish embryos at 30 μM. No phenotype other than death was observed for compounds 1–3, 5, 6

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine

Six sequence variants on chromosome 9p21.3 are associated with a positive family history of myocardial infarction: a multicenter registry

<p>Abstract</p> <p>Background</p> <p>Recent genome-wide association studies have identified several genetic loci linked to coronary artery disease (CAD) and myocardial infarction (MI). The 9p21.3 locus was verified by numerous replication studies to be the first common locus for CAD and MI. In the present study, we investigated whether six single nucleotide polymorphisms (SNP) rs1333049, rs1333040, rs10757274, rs2383206, rs10757278, and rs2383207 representing the 9p21.3 locus were associated with the incidence of an acute MI in patients with the main focus on the familial aggregation of the disease.</p> <p>Methods</p> <p>The overall cohort consisted of 976 unrelated male patients presenting with an acute coronary syndrome (ACS) with ST-elevated (STEMI) as well as non-ST-elevated myocardial infarction (NSTEMI). Genotyping data of the investigated SNPs were generated and statistically analyzed in comparison to previously published findings of matchable control cohorts.</p> <p>Results</p> <p>Statistical evaluation confirmed a highly significant association of all analyzed SNP's with the occurrence of MI (p < 0.0001; OR: 1.621-2.039). When only MI patients with a positive family disposition were comprised in the analysis a much stronger association of the accordant risk alleles with incident disease was found with odds ratios up to 2.769.</p> <p>Conclusions</p> <p>The findings in the present study confirmed a strong association of the 9p21.3 locus with MI particularly in patients with a positive family history thereby, emphasizing the pathogenic relevance of this locus as a common genetic cardiovascular risk factor.</p

Protein Signature of Lung Cancer Tissues

Lung cancer remains the most common cause of cancer-related mortality. We applied a highly multiplexed proteomic technology (SOMAscan) to compare protein expression signatures of non small-cell lung cancer (NSCLC) tissues with healthy adjacent and distant tissues from surgical resections. In this first report of SOMAscan applied to tissues, we highlight 36 proteins that exhibit the largest expression differences between matched tumor and non-tumor tissues. The concentrations of twenty proteins increased and sixteen decreased in tumor tissue, thirteen of which are novel for NSCLC. NSCLC tissue biomarkers identified here overlap with a core set identified in a large serum-based NSCLC study with SOMAscan. We show that large-scale comparative analysis of protein expression can be used to develop novel histochemical probes. As expected, relative differences in protein expression are greater in tissues than in serum. The combined results from tissue and serum present the most extensive view to date of the complex changes in NSCLC protein expression and provide important implications for diagnosis and treatment

A Novel Method for Real Time Protection of DC Microgrid Using Cumulative Summation and Wavelet Transform

DC microgrid is a compact framework comprising interconnected nearby sources and loads. The renewable energy source used in DC microgrids being intermittent leads to the change in the power availability as well as the fault current levels. In such situations, detecting and clearing the faults is very important to protect the DC microgrid without compromising on fault clearing time and interruption of the load. This paper proposes a hybrid Cumulative Sum (CumSum) and Wavelet transform-based approach to detect the fault. The CumSum value raises the amplitude by averaging the fault current. Wavelet transforms obtain important fault current features by decomposing the current signal. The hybrid method of CumSum and Wavelet analysis proposed here enables the detection of the fault and differentiates the fault condition from sudden load variation. Additionally, it helps to recognize the location of the fault by the wavelet energy difference. The proposed scheme is tested with a developed ring-type low voltage DC (LVDC) microgrid hardware model under various fault conditions. The scheme is implemented using TMS320F28069 digital signal processors (DSP) of Texas Instruments. The hardware results are validated using MATLAB simulation. The proposed method performance is also compared with the existing methods used for DC microgrid protection. The outcome shows that the proposed method has a high accuracy of 98.72%, selectivity of 96.08%, and reliability of 99.01%. The execution time required by the proposed method is also less