Stretching short sequences of DNA with constant force axial optical tweezers

Single-molecule techniques for stretching DNA of contour lengths less than a kilobase are fraught with experimental difficulties. However, many interesting biological events such as histone binding and protein-mediated looping of DNA, occur on this length scale. In recent years, the mechanical properties of DNA have been shown to play a significant role in fundamental cellular processes like the packaging of DNA into compact nucleosomes and chromatin fibers. Clearly, it is then important to understand the mechanical properties of short stretches of DNA. In this paper, we provide a practical guide to a single-molecule optical tweezing technique that we have developed to study the mechanical behavior of DNA with contour lengths as short as a few hundred basepairs. The major hurdle in stretching short segments of DNA is that conventional optical tweezers are generally designed to apply force in a direction lateral to the stage (see Fig. 1). In this geometry, the angle between the bead and the coverslip, to which the DNA is tethered, becomes very steep for submicron length DNA. The axial position must now be accounted for, which can be a challenge, and, since the extension drags the microsphere closer to the coverslip, steric effects are enhanced. Furthermore, as a result of the asymmetry of the microspheres, lateral extensions will generate varying levels of torque due to rotation of the microsphere within the optical trap since the direction of the reactive force changes during the extension. Alternate methods for stretching submicron DNA run up against their own unique hurdles. For instance, a dual-beam optical trap is limited to stretching DNA of around a wavelength, at which point interference effects between the two traps and from light scattering between the microspheres begin to pose a significant problem. Replacing one of the traps with a micropipette would most likely suffer from similar challenges. While one could directly use the axial potential to stretch the DNA, an active feedback scheme would be needed to apply a constant force and the bandwidth of this will be quite limited, especially at low forces. We circumvent these fundamental problems by directly pulling the DNA away from the coverslip by using a constant force axial optical tweezers. This is achieved by trapping the bead in a linear region of the optical potential, where the optical force is constant-the strength of which can be tuned by adjusting the laser power. Trapping within the linear region also serves as an all optical force-clamp on the DNA that extends for nearly 350 nm in the axial direction. We simultaneously compensate for thermal and mechanical drift by finely adjusting the position of the stage so that a reference microsphere stuck to the coverslip remains at the same position and focus, allowing for a virtually limitless observation period.     

Host selection and responses to forest fragmentation in acorn weevils: inferences from dynamic occupancy models

Prior studies on species‐specific responses to habitat alteration have demonstrated that niche breadth is positively associated with patch occupancy rates in landscapes fragmented by agriculture. However, these studies generally have focused on vertebrates and relied upon data collected at a single point in time, neglecting dynamic processes that could alter inferences. We studied the effects of host selection and forest fragmentation on population dynamics of acorn weevils Curculio, the primary insect seed predators of oaks in North America. Detection/non‐detection data were collected from 174 red and white oaks in 19 forested fragments from 2005–2008. We used dynamic multi‐season site‐occupancy models within a Bayesian framework to explore variation in patch (tree‐level) occupancy dynamics of three species of weevils that vary in their specialization, i.e. their relative selection of red and white oak as hosts: C. pardalis (white oak specialist), C. sulcatulus (generalist) and C. proboscideus (generalist). Contrary to expectations, the specialist exhibited greater estimated rates of occupancy than generalists. However, red oak trees occupied by the white oak specialist appeared to function as sink populations maintained by frequent colonization following local extinction. Specialists also exhibited greater relative variation in occupancy and relative abundance on their host trees among years. Generalists exhibited lower local extinction and colonization rates than the specialist. Occupancy and vital rates of weevils on a host tree increased with acorn production and were significantly influenced by neighborhood forest density. Our results suggest that across much of their range in the eastern United States acorn weevils exist in fragmented, temporally dynamic landscapes, with generalists occurring on a lower proportion of usable trees but buffered by access to more suitable patches and greater patch‐specific survival. More generally, our results demonstrate that estimates of specialization derived from occupancy data may be misleading in the absence of patch‐specific information on vital rates.     

Genetic association of Glutathione peroxidase-1 (GPx-1) and NAD(P)H:Quinone Oxidoreductase 1(NQO1) variants and their association of CAD in patients with type-2 diabetes

Coronary artery disease (CAD) is a major health concern and the leading cause of death in individuals with type-2 diabetes mellitus (T2DM). Glutathione peroxidase-1 (GPx-1) and NAD(P)H: quinone oxidoreductase (NQO1) are known for its broad range of detoxification. The role of functional variants of these genes in the development of various disorders is proven. Hereby, we investigated the possible role of these variants in the development of CAD in T2DM patients of South Indian population. In this case-control study, a total of 539 patients (T2DM = 241; T2DM-CAD = 298) and 285 controls were included. The C198T GPx-1 and C609T NQO1 single-nucleotide polymorphisms were analyzed by PCR-RFLP. Further, these genotypes were correlated with blood lipid profile. Regression analysis showed that GPx1-C/T genotype is associated with a 1.35-fold increase (95% CI = 1.000-1.824; P = 0.048) and GPx1-T/T genotype is associated with a 1.76-fold increase (95% CI = 1.011 to 3.066; P = 0.046) to the T2DM development. Increased odds ratio showed that NQO1-T/T genotype had a higher occurrence of CAD in diabetic patients with CAD (95% CI = 1.003-2.674, P = 0.049) than T2DM patients without CAD. The level of triglycerides alone showed significant increase for GPx-1-C/T and -T/T genotypes in Tukey's Post hoc analysis (177.1 ± 19.2 vs. 184 ± 23.5; P = 0.039 and 177.1 ± 19.2 vs. 190 ± 22.4; P = 0.006) among the patients with T2DM-CAD. Our work concludes that GPx-1 variants might contribute to the development of diabetes and both GPx-1 and NQO1 variants confirm the association of CAD in people with T2DM of South Indian population.     

Segregation of calcium signalling mechanisms in magnocellular neurones and terminals

Every cell or neuronal type utilizes its own specific organization of its Ca(2+) homeostasis depending on its specific function and its physiological needs. The magnocellular neurones, with their somata situated in the supraoptic and paraventricular nuclei of the hypothalamus and their nerve terminals populating the posterior hypophysis (neural lobe) are a typical and classical example of a neuroendocrine system, and an important experimental model for attempting to understand the characteristics of the neuronal organization of Ca(2+) homeostasis. The magnocellular neurones synthesize, in a cell specific manner, two neurohormones: arginine-vasopressin (AVP) and oxytocin (OT), which can be released, in a strict Ca(2+)-dependent manner, both at the axonal terminals, in the neural lobe, and at the somatodendritic level. The two types of neurones show also distinct type of bioelectrical activity, associated with specific secretory patterns. In these neurones, the Ca(2+) homeostatic pathways such as the Na(+)/Ca(2+) exchanger (NCX), the endoplasmic reticulum (ER) Ca(2+) pump, the plasmalemmal Ca(2+) pump (PMCA) and the mitochondria are acting in a complementary fashion in clearing Ca(2+) loads that follow neuronal stimulation. The somatodendritic AVP and OT release closely correlates with intracellular Ca(2+) dynamics. More importantly, the ER Ca(2+) stores play a major role in Ca(2+) homeostatic mechanism in identified OT neurones. The balance between the Ca(2+) homeostatic systems that are in the supraoptic neurones differ from those active in the terminals, in which mainly Ca(2+) extrusion through the Ca(2+) pump in the plasma membrane and uptake by mitochondria are active. In both AVP and OT nerve terminals, no functional ER Ca(2+) stores can be evidenced experimentally. We conclude that the physiological significance of the complexity of Ca(2+) homeostatic mechanisms in the somatodendritic region of supraoptic neurones and their terminals can be multifaceted, attributable, in major part, to their specialized electrical activity and Ca(2+)-dependent neurohormone release.     

Porohyperviscoelastic model simultaneously predicts parenchymal fluid pressure and reaction force in perfused liver

Porohyperviscoelastic (PHVE) modeling gives a simplified continuum approximation of pore fluid behavior within the parenchyma of liver tissue. This modeling approach is particularly applicable to tissue engineering of artificial livers, where the inherent complexity of the engineered scaffolds prevents the use of computational fluid dynamics. The objectives of this study were to simultaneously predict the experimental parenchymal fluid pressure (PFP) and compression response in a PHVE liver model. The model PFP matched the experimental measurements (318?Pa) to within 1.5%. Linear regression of both phases of compression, ramp, and hold, demonstrated a strong correlation between the model and the experimental reaction force (p<0.5). The ability of this PVE model to accurately predict both fluid and solid behavior is important due to the highly vascularized nature of liver tissue and the mechanosensitivity of liver cells to solid matrix and fluid flow properties.     

Generation of anti-c-met single domain antibody fragment based on human stable frameworks

The size reduction is an important issue in the biomedical application of antibody and single domain antibody fragment is recognized as very attractive tool. However, it is very time-consuming and laborious to generate the fragment antibody with targeted binding function. Here, we investigated the possibility to prepare single domain antibody (sdAb) by a simple grafting method based on stable human consensus framework sequences. The complementarity determining region sequences in V_H domain of anti-c-Met scFv from rabbit were grafted with the human V_H3 consensus framework sequences, which generated the anti-c-Met single domain antibody showing almost same binding activity to its scFv form. The generated single domain antibody could be produced as functional form in oxidizing cytoplasm of E. coli, but produced as inactive form in reducing cytoplasm. The structural analysis of the homology models gave us the insight on the stability of the single domain antibody. In this report, we have demonstrated that the very stable human consensus framework sequence can be used for the generation of active anti-c-Met sdAb via complementarity determining regions grafting. We expect that this kind of grafting method for the generation of sdAb may provide us with the opportunities to prepare sdAbs based on the known antibody sequences.     

Entomopathogenicity of endophytic <Emphasis Type="Italic">Serratia marcescens</Emphasis> strain SRM against larvae of <Emphasis Type="Italic">Helicoverpa armigera</Emphasis> (Noctuidae: Lepidoptera)

An endophytic Serratia marcescens strain SRM (MTCC 8708) isolated from the flowers of summer squash was found to be entomopathogenic against the larvae of Helicoverpa armigera. Natural epizootic of this bacterial strain on the larvae collected from summer squash flowers ranged from 19.9 to 72.3%. Under laboratory conditions, a dose of 6 × 10¹⁰ c.f.u./ml diet induced 66.3% mortality of first instar H. armigera larvae. Similarly all other growth and development parameters of the insect were severely retarded in a dose-dependent manner. The bacterium invaded the entire alimentary canal and haemolymph with successful replacement of all other gut-associated microflora. There was a great reduction in midgut proteinase activity due to inhibition of five major proteinase isozymes by S. marcescens infection. Further, a synergistic interaction between chitinases isolated from this strain and Bacillus thuringiensis Cry1Ac toxin was observed. The present findings suggest that this plant-associated S. marcescens strain SRM could be suitably exploited for the management of H. armigera.     

Isolation and characterization of rat liver nuclear glucocorticoid receptor

The rat liver nuclear glucocorticoid receptor has a molecular weight of 90 000. Using antibody bound to the stationary matrix, the cytosol and nuclear glucocorticoid receptors from rat liver were purified. The translocation of glucocorticoid receptor from rat liver cytosol into the nucleus was studied using immunoaffinity chromatography. Immediately after the intraperitoneal injection of rats with the hormone, the receptor translocation started and was complete within 10 min. The 90 000 dalton nuclear receptor component is identical to the 90 000 dalton cytosol component. They have identical molecular weights in the same gel electrophoresis system and produce identical peptide fragments after digestion with Staphyolococcal aureus V8 protease. The receptor component enriched by immunoaffinity chromatography from cytosol of adrenalectomised rats contained mainly a 45 000 dalton component.