Genomic biomarkers in prostate cancer.

Prostate cancer is the most common non-cutaneous cancer among men in the United States. In the last decade there has been a rapid expansion in the field of biomarker assays for diagnosis, prognosis, and treatment prediction in prostate cancer. The evidence base for these assays is rapidly evolving. With several commercial assays available at each stage of the disease, deciding which genomic assays are appropriate for which patients can be nuanced for physicians. In an effort to help guide these decisions in clinical practice, we aim to give an update on the current status of the biomarker field of prostate cancer

Interaction of acetate, glucose and growth conditions on glyconeogenesis and isocitrate lyase activity in tetrahymena

1. 1. Incubation of shaken cultures for 3 hr with acetate had little effect on the level of isocitrate lyase or the capacity for glyconeogenesis.2. 2. Maintenance of cultures under static conditions for the same period led to an eight to tenfold increase in the enzyme and to a greatly enhanced ability to convert acetate to glycogen.3. 3. Glucose prevented most of the increase in enzyme and led to a complete loss of the capacity for glyconeogenesis.4. 4. Starved cells from non-shaken suspensions developed an increased capacity for glyconeogenesis, and the presence of acetate further increased this capacity.5. 5. Cells from suspensions shaken with acetate had a much lower capacity.6. 6. It is concluded that in Tetrahymena growth conditions are much more important than acetate in the regulation of glyconeogenesis and the synthesis of isocitrate lyase.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33334/1/0000731.pd

Development of a High Throughput Method for Screening of Clean-Label Mold Inhibitors in Cheddar Cheese

Mold growth on cheddar-style cheese, though not a food safety issue, causes significant loss to the industry due to consumer rejection. For this reason, it is common for at-risk products, such as cheese shreds, to be coated with the mold inhibitor natamycin. While highly effective at extending shelf-life, preferences for clean-labels and organic foods is driving renewed interest in alternative mold inhibitors for the dairy industry. The purpose of this study was to develop a high-throughput method and use this to quantify mold grow on a cheese-mimicking matrix as a means to screen candidate clean-label inhibitors. In order to evaluate mold-growth at this scale, we adopted image-analysis using freely available ImageJ software (NIH) and the “read plate” plug-in, wherein changes in mold growth are measured using the lightness/darkness of pixels as a proxy for growth. Sensitivity of mold-growth detection was enhanced by incorporating methylene-blue dye into the cheese-mimicking agar. In order to better apply results to the food science industry, the “Growthcurver” package from R statistical software was used to calculate lag time, the time-point at which the mold has reached 50% maximum growth. This metric allowed us to compare delays in growth to the control and quickly assess inhibitor efficacy. To demonstrate the power of this approach, using a cheese-based agar, over eighty 96-well micro-titer cheese agar plates were prepared for inhibitor screening across the three proof of concept studies. Final results yielded analysis of 7,200 samples against varying concentrations of 7 inhibitors and combinations thereof. The results confirm the efficacy of natamycin, while alternative inhibitors caused less pronounced growth delays even at relatively high rates of application. Thyme oil and chitosan showed the greatest potential as alternative mold inhibitors. Thyme oil caused a delay in growth beyond the length of the experiment (168 hrs) for 5 of the 10 mold isolates. Chitosan showed a similar delay for 7 of the molds tested. Future work should focus on analysis of additional inhibitor combinations and incorporate sensory analysis to evaluate their applicability for the dairy industry

Master equation approach to DNA-breathing in heteropolymer DNA

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure

Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites

The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in S. cerevisiae is qualitatively consistent with a `barrier nucleosome model', in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model, with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to ~1000 bp to each side.Comment: includes supporting materia

Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.Comment: 7 pages, 4 figure

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4\nu-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA, in single molecule fluorescence experiments.Comment: 24 pages, 11 figures; substantially extended version of cond-mat/0610752; v2: minor text changes, virtually identical to the published versio