Monte Carlo Simulations indicate that Chromati: Nanostructure is accessible by Light Microscopy

A long controversy exists about the structure of chromatin. Theoretically, this structure could be resolved by scattering experiments if one determines the scattering function - or equivalently the pair distribution function - of the nucleosomes. Unfortunately, scattering experiments with live cells are very difficult and limited to only a couple of nucleosomes

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei

The fractal globule as a model of chromatin architecture in the cell

The fractal globule is a compact polymer state that emerges during polymer condensation as a result of topological constraints which prevent one region of the chain from passing across another one. This long-lived intermediate state was introduced in 1988 (Grosberg et al. 1988) and has not been observed in experiments or simulations until recently (Lieberman-Aiden et al. 2009). Recent characterization of human chromatin using a novel chromosome conformational capture technique brought the fractal globule into the spotlight as a structural model of human chromosome on the scale of up to 10 Mb (Lieberman-Aiden et al. 2009). Here, we present the concept of the fractal globule, comparing it to other states of a polymer and focusing on its properties relevant for the biophysics of chromatin. We then discuss properties of the fractal globule that make it an attractive model for chromatin organization inside a cell. Next, we connect the fractal globule to recent studies that emphasize topological constraints as a primary factor driving formation of chromosomal territories. We discuss how theoretical predictions, made on the basis of the fractal globule model, can be tested experimentally. Finally, we discuss whether fractal globule architecture can be relevant for chromatin packing in other organisms such as yeast and bacteria

Identification of an autoantibody panel to separate lung cancer from smokers and nonsmokers

<p>Abstract</p> <p>Background</p> <p>Sera from lung cancer patients contain autoantibodies that react with tumor associated antigens (TAAs) that reflect genetic over-expression, mutation, or other anomalies of cell cycle, growth, signaling, and metabolism pathways.</p> <p>Methods</p> <p>We performed immunoassays to detect autoantibodies to ten tumor associated antigens (TAAs) selected on the basis of previous studies showing that they had preferential specificity for certain cancers. Sera examined were from lung cancer patients (22); smokers with ground-glass opacities (GGOs) (46), benign solid nodules (55), or normal CTs (35); and normal non-smokers (36). Logistic regression models based on the antibody biomarker levels among the high risk and lung cancer groups were developed to identify the combinations of biomarkers that predict lung cancer in these cohorts.</p> <p>Results</p> <p>Statistically significant differences in the distributions of each of the biomarkers were identified among all five groups. Using Receiver Operating Characteristic (ROC) curves based on age, c-myc, Cyclin A, Cyclin B1, Cyclin D1, CDK2, and survivin, we obtained a sensitivity = 81% and specificity = 97% for the classification of cancer vs smokers(no nodules, solid nodules, or GGO) and correctly predicted 31/36 healthy controls as noncancer.</p> <p>Conclusion</p> <p>A pattern of autoantibody reactivity to TAAs may distinguish patients with lung cancer versus smokers with normal CTs, stable solid nodules, ground glass opacities, or normal healthy never smokers.</p

Average crossing number of Gaussian and equilateral chains with and without excluded volume

We study the influence of excluded volume interactions on the behaviour of the mean average crossing number (mACN) for random off-lattice walks. We investigated Gaussian and equilateral off-lattice random walks with and without ellipsoidal excluded volume up to chain lengths of N=1500 and equilateral random walks on a cubic lattice up to N=20000. We find that the excluded volume interactions have a strong influence on the behaviour of the local crossing number 〈 a(l 1,l 2) 〉 at very short distances but only a weak one at large distances. This behaviour is the basis of the proof in [ Y. Diao et al., Math. Gen. 36, 11561 (2003); Y. Diao and C. Ernst, Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences] for the dependence of the mean average crossing number on the chain length N. We show that the data is compatible with an Nln(N)-bahaviour for the mACN, even in the case with excluded volume. Copyright EDP Sciences/Società Italiana di Fisica/Springer-Verlag 200861.82.Pv Polymers, organic compounds,

Voltage transient analysis as a generic tool for solar junction characterization

Surface photovoltage transients on solar junctions have often been associated with carrier lifetime in the literature. However, the carrier decay in a junction is not governed by a first order carrier decay, but resulting from a differential capacitance interacting with a differential conductivity. This phenomenon is well known as the Kane-Swanson formalism in an engineering context where the carrier density transient is measured by photoconductance with a microwave or infrared beam. In this work, we solve the same differential equations numerically to model the carrier decay in the large signal domain extending over five orders of carrier density. Since the surface voltage is linked to the carrier density by a logarithmic relation, we express the carrier decay as surface photovoltage transients. We show how from photovoltage transients, the same information as from photoconductance can be drawn. To demonstrate the method as a generic tool, it is applied to four types of solar cells, two monocrystalline silicon cells, a Perovskite solar cell, a transition metal oxide/silicon hybrid junction, and a CIGS solar cell. Acquiring photovoltage transients by Kelvin force microscopy allows working on partial junctions without top contact, speeding up research of future photovoltaic materials. Furthermore, parameters may be mapped with a better lateral resolution compared to microwave photoconductance

Asset allocation and liquidity breakdowns: what if your broker does not answer the phone?

Illiquidity, Blackout period, Portfolio decision, Efficiency loss, Rare disasters, 91B28, 93E20, G11,