Disordered, stretched, and semiflexible biopolymers in two dimensions

We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system". Moreover, under a strong stretching force and for a long biopolymer, the sequence-disorder is immaterial for elasticity. Finally, the effect of sequence-disorder may depend upon the quantity considered

Decrease in hyperosmotic stress-induced corneal epithelial cell apoptosis by L-carnitine

Purpose: To characterize the osmoprotective properties of L-carnitine on human corneal epithelial cell volume and apoptosis during hyperosmotic stress. Methods: Human corneal limbal epithelial (HCLE) cells were exposed to culture medium at 300 mOsm (isotonic) or 500 mOsm (hyperosmotic) with or without L-carnitine (10 mM). Induction of apoptosis was detected by quantifying the proteolytic activity of caspase-8, caspase-9, and caspase-3/7 using caspase activity assays, the expression of tumor necrosis factor (TNF)-α with enzyme-linked immunosorbent assay, and annexin V/propidium iodide staining of HCLE cells evaluated with confocal microscopy and flow cytometry. Cell volume changes in response to hyperosmotic stress were analyzed using flow cytometry. Results: After the HCLE cells were exposed to hyperosmotic medium (500 mOsm), the percentage of shrunken cells and damaged/dead cells (stained positively for annexin V and/or propidium iodide) was six- and three-fold, respectively, higher than that under isotonic conditions (300 mOsm). This was paralleled by an increase in TNF-α concentration in media and caspase-8, -9, and -3/7 activities (six-, four-, ten-, and twelve-fold, respectively; all showing p\u3c0.001). Addi­tion of L-carnitine during hyperosmotic stress partly restored cell volume and significantly reduced the concentration of TNF-α released (p=0.005) and caspase-9 activity (p=0.0125). Addition of L-carnitine reduced the percentage of hyperosmolarity-induced damaged/dead cells to levels observed under isotonic conditions

Use of a Hybrid Adeno-Associated Viral Vector Transposon System to Deliver the Insulin Gene to Diabetic NOD Mice.

Previously, we used a lentiviral vector to deliver furin-cleavable human insulin (INS-FUR) to the livers in several animal models of diabetes using intervallic infusion in full flow occlusion (FFO), with resultant reversal of diabetes, restoration of glucose tolerance and pancreatic transdifferentiation (PT), due to the expression of beta (β)-cell transcription factors (β-TFs). The present study aimed to determine whether we could similarly reverse diabetes in the non-obese diabetic (NOD) mouse using an adeno-associated viral vector (AAV) to deliver INS-FUR ± the β-TF Pdx1 to the livers of diabetic mice. The traditional AAV8, which provides episomal expression, and the hybrid AAV8/piggyBac that results in transgene integration were used. Diabetic mice that received AAV8-INS-FUR became hypoglycaemic with abnormal intraperitoneal glucose tolerance tests (IPGTTs). Expression of β-TFs was not detected in the livers. Reversal of diabetes was not achieved in mice that received AAV8-INS-FUR and AAV8-Pdx1 and IPGTTs were abnormal. Normoglycaemia and glucose tolerance were achieved in mice that received AAV8/piggyBac-INS-FUR/FFO. Definitive evidence of PT was not observed. This is the first in vivo study using the hybrid AAV8/piggyBac system to treat Type 1 diabetes (T1D). However, further development is required before the system can be used for gene therapy of T1D

Determination of Toxic Metals in Indian Smokeless Tobacco Products

This study targets the lesser-known ingredients of smokeless tobacco products, i.e., the toxic metals, in Indian brands. The metals selected in the study included lead (Pb), cadmium (Cd), arsenic (As), copper (Cu), mercury (Hg), and selenium (Se). The differential pulse anodic stripping voltammetry (DPASV) technique was used for estimating the metals Pb, Cd, and Cu; square wave voltammetry for As; and the cold vapor atomic absorption technique for Hg. The resulting levels of the metals were compared to the daily consumption of the smokeless tobacco products. It was observed that almost 30% of gutkha brand samples exceeded the permissible levels of metals Pb and Cu, when compared to the provisional tolerable intake limits determined by the FAO/WHO. The reliability of data was assured by analyzing standard reference materials

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

BACKGROUND: All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events. RESULTS: Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. CONCLUSIONS: The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/

Effect of dates of planting and spacing on growth and yield characteristics of ginger (Zingiber officinale Ros.) var. IISR Mahima

A field trial was carried out with an objective to determine the optimum date of rhizome planting and spacing to obtain good growth and yield of ginger var. ‘IISR Mahima’ at Dapoli (Maharashtra). The experiment was laid out in split plot design with planting dates as main plot treatments (15th April, 1st May, 15th May, 30th May and 15th June) and intra row spacing as sub plot treatments (25 cm × 15 cm, 25 cm × 25 cm and 25 cm × 35 cm) in three replications. It is evident from the results that dates of planting had significant effect on almost all the characters under study. Planting of rhizomes on 15th April showed better growth, yield and yield attributing characters. Among spacing levels, the closer spacing of 25 cm × 15 cm recorded significantly higher plant height, green and dry ginger yield. The interaction treatments showed significant effect for most of the characters except for number of days required for sprouting, per cent sprouting and finger characters. Among the various treatment combinations planting on 15th April and 25 cm × 15 cm spacing exhibited higher plant height, yield of green (40.16 t ha-1) and dry ginger (8.58 t ha-1). Planting after 15th May with wider spacing 25 cm × 35 cm resulted in lower yield. &nbsp

Complex Effective Path: A Semi-Classical Probe of Quantum Effects

We discuss the notion of an effective, average, quantum mechanical path which is a solution of the dynamical equations obtained by extremizing the quantum effective action. Since the effective action can, in general, be complex, the effective path will also, in general, be complex. The imaginary part of the effective action is known to be related to the probability of particle creation by an external source and hence we expect the imaginary part of the effective path also to contain information about particle creation. We try to identify such features using simple examples including that of effective path through the black hole horizon leading to thermal radiation. Implications of this approach are discussed.Comment: 20 pages; no figures; to appear in Phys.Rev.

Green's function for the Relativistic Coulomb System via Sum Over Perturbation Series

We evaluate the Green's function of the D-dimensional relativistic Coulomb system via sum over perturbation series which is obtained by expanding the exponential containing the potential term $V({\bf x)}$ in the path integral into a power series. The energy spectra and wave functions are extracted from the resulting amplitude.Comment: 13 pages, ReVTeX, no figure

Effect of dates of planting on growth, yield and quality of ginger (Zingiber officinale Roscoe)

The trial was carried out during 2008–09 to study the ideal date of planting and spacing to obtain better growth, yield and quality of ginger crop var. ‘IISR Mahima’. The experiment was laid out in Split Plot Design with dates of planting as main plot treatment (15th April, 1st May, 15th May, 30th May and 15th June) and three treatments of spacing as sub plot treatment (35 cm × 25 cm, 25 cm × 25 cm and 15 cm × 25 cm) with three replications. The observations were recorded on dry recovery (%), harvest index, oil and crude fibre content. Dates of planting had significant effect on all the characters studied. April 15th planting showed better oil content. Among spacings, the spacing of 35 cm × 25 cm gave highest dry recovery. The closer spacing of 15 cm × 25 cm recorded higher harvest index. It was observed that spacing had no significant effect on quality attributes viz., oil and crude fibre content. The treatment combination of 15th April planting and 35 cm × 25 cm spacing exhibited higher dry recovery. The treatment combination of 15th April planting and 15 cm × 25 cm spacing showed maximum harvest index. Economics of interactions revealed maximum net returns of Rs. 559,690.1 ha-1 with benefit cost (B:C) ratio of 2.67 for the treatment combination of 15th April planting and 15 cm × 25 cm spacing. &nbsp