An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Optical and Electronic Properties of Conjugated Polymer -Nanocluster Semiconductor Hybrid Systems

Conjugated polymers are intensively pursued as candidate materials for emission and detection devices with the optical range of interest determined by the chemical structure. On the other hand the optical range for emission and detection can also be tuned by size selection in semiconductor nanoclusters. The mechanisms for charge generation and separation upon optical excitation, and light emission are different for these systems. Hybrid systems based on these different class of materials reveal interesting electronic and optical properties and add further insight into the individual characteristics of the different components. Multilayer structures and blends of these materials on different substrates were prepared for absorption, photocurrent (Iph), photoluminescence (PL) and electroluminscence (EL) studies. Polymers chosen were derivatives of polythiophene (PT) and polyparaphenylenevinylene (PPV) along with nanoclusters of cadmium sulphide of average size 4.4 nm (CdS-44). The photocurrent spectral response in these systems followed the absorption response around the band edges for each of the components and revealed additional features, which depended on bias voltage, thickness of the layers and interfacial effects. The current-voltage curves showed multi-component features with emission varying for different regimes of voltage. The emission spectral response revealed additive features and is discussed in terms of excitonic mechanisms.

Community-based Natural Resource Management: Issues and Cases from South Asia

Community-based natural resource management (CBNRM) is the joint management of natural resources by a community based on a community strategy, through a participatory mechanism involving all legitimate stakeholders. The approach is community-based in that the communities managing the resources have the legal rights, the local institutions and the economic incentives to take substantial responsibility for sustained use of these resources. This implies that the community plays an active role in the management of natural resources, not because it asserts sole ownership over them, but because it can claim participation in their management and benefits for practical and technical reasons1–4. This approach emerged as the dominant conservation concept in the late 1970s and early 1980s, of the disillusionment with the developmental state. Governments across South and South East Asia, Africa and Latin America have adopted and implemented CBNRM in various ways, viz. through sectoral programmes such as forestry, irrigation or wildlife management, multisectoral programmes such as watershed development and efforts towards political devolution. In India, the principle of decentralization through ‘gram swaraj’ was introduced by Mahatma Gandhi. The 73rd and 74th constitution amendments in 1992 gave impetus to the decentralized planning at panchayat levels through the creation of a statutory three-level local self-government structure5,6. The strength of this book is that it includes chapters by CBNRM advocates based on six seemingly innovative initiatives being implemented by nongovernmental organizations (NGOs) in ecologically vulnerable regions of South Asia: two in the Himalayas (watershed development programme in Lingmutechhu, Bhuthan and Thalisain tehsil, Paudi Grahwal District, Uttarakhand), three in semi-arid parts of western India (watershed development in Hivre Bazar, Maharashtra and Nathugadh village, Gujarat and water-harvesting structures in Gopalapura, Rajasthan) and one in the flood-plains of the Brahmaputra–Jamuna (Char land, Galibanda and Jamalpur districts, Bangladesh). Watersheds in semi-arid regions fall in the low-rainfall region (500–700 mm) and suffer the vagaries of drought 2–3 years in every five-year cycle. In all these locations, the major occupation is agriculture, most of which is rainfed or dry. The other two cases (in Uttarakhand) fall in the Himalayan region (temperate/sub-temperate climate), which has witnessed extensive deforestation in the last century and is now considered as one of the most vulnerable locations in South Asia. Terraced agriculture is being practised in these locations for a long time. The last case (Gono Chetona) falls in the Brahmaputra–Jamuna charlands which are the most ecologically vulnerable regions in the sub-continent with constantly changing landscape. Agriculture and livestock rearing are the main occupations, and there is substantial seasonal emigration for wage labour by the adult males. River erosion and floods force the people to adopt a semi-migratory lifestyle. The book attempts to analyse the potential as well as limitations of NGOdriven CBNRM endeavours across agroclimatic regions of South Asia with emphasis on four intrinsically linked normative concerns, namely sustainability, livelihood enhancement, equity and demographic decentralization in chapters 2–7. Comparative analysis of these case studies done in chapter 8, highlights the issues that require further research while portraying the strengths and limits of NGO-driven CBNRM. In Hivre Bazar, the post-watershed intervention scenario is such that farmers often grow three crops in a year – kharif bajra, rabi jowar and summer vegetable crops. Productivity has increased in the dry lands due to improvement in soil moisture levels. The revival of johads in Gopalpura has led to the proliferation of wheat and increased productivity. In Lingmuteychhu, productivity gains have also arisen, but more due to the introduction of both local and high-yielding, new varieties as opposed to increased water availability. In the case of Gono Chetona, improvements have come due to diversification of agriculture; for example, the promotion of vegetable gardens. CBNRM interventions in most cases have also led to new avenues of employment and income generation. The synthesis shows that CBNRM efforts have made significant contributions to livelihood enhancement and only limited gains in terms of collective action for sustainable and equitable access to benefits and continuing resource use, and in terms of democratic decentralization, contrary to the objectives of the programme. Livelihood benefits include improvements in availability of livelihood support resources (fuelwood, fodder, drinking water), increased productivity (including diversification of cropping pattern) in agriculture and allied activities, and new sources of livelihood. However, NGO-driven CBNRM has not met its goal of providing ‘alternative’ forms of ‘development’ due to impediments of state policy, short-sighted vision of implementers and confrontation with the socio-ecological reality of the region, which almost always are that of fragmented communities (or communities in flux) with unequal dependence and access to land and other natural resources along with great gender imbalances. Appalling, however, is the general absence of recognition of the importance of and the will to explore practical ways to bring about equitable resource transfer or benefit-sharing and the consequent innovations in this respect that are evident in the pioneering community initiatives such as pani panchayat, etc. Pertaining to the gains on the ecological sustainability front, Hivre Bazar and Thalisain initiatives through active participation of villagers have made significant regeneration of the water table within the village, and mechanisms such as ban on number of bore wells, the regulation of cropping pattern, restrictions on felling of trees and free grazing to ensure that in the future, the groundwater is neither over-exploited nor its recharge capability impaired. Nevertheless, the longterm sustainability of the interventions in the case of Ghoga and Gopalpura initiatives as the focus has been mostly on regeneration of resources, and less on regulating the use of regenerated resources. Further, in Lingmuteychhu and Gono Chetona, the interventions are mainly household-based and the focus has been less explicit on ecological components. The studies demonstrate the livelihood benefits to all of the interventions and significant variation in achievements with reference to sustainability, equity and democratic decentralization depending on the level and extent of community participation apart from the vision of implementers, strategy (or nature of intervention shaped by the question of community formation), the centrality of community formation and also the State policy. Case studies show that the influence of State policy is multi-faceted and often contradictory in nature. This necessitates NGOs to engage with the State in a much more purposeful way than in an ‘autonomous space’. Thus the role of NGOs in CBNRM is complementary, wherein they provide innovative experiments that the State can learn. This helps in achieving the goals of CBNRM through democratic decentralization. The book addresses the vital issues related to natural resource management and interests of the community. Key topics discussed throughout the book are still at the centre of the current debate. This compilation consists of well-written chapters based on rigorous synthesis of CBNRM case studies, which will serve as good references for students, researchers and practitioners in the years to come.

Physics-Based Band Gap Model for Relaxed and Strained 100] Silicon Nanowires

In this paper, we propose a physics-based simplified analytical model of the energy band gap and electron effective mass in a relaxed and strained rectangular 100] silicon nanowires (SiNWs). Our proposed formulation is based on the effective mass approximation for the nondegenerate two-band model and 4 x 4 Luttinger Hamiltonian for energy dispersion relation of conduction band electrons and the valence band heavy and light holes, respectively. Using this, we demonstrate the effect of the uniaxial strain applied along 100]-direction and a biaxial strain, which is assumed to be decomposed from a hydrostatic deformation along 001] followed by a uniaxial one along the 100]-direction, respectively, on both the band gap and the transport and subband electron effective masses in SiNW. Our analytical model is in good agreement with the extracted data using the extended-Huckel-method-based numerical simulations over a wide range of device dimensions and applied strain.

Asymptotic expansions for the structural wavenumbers of isotropic and orthotropic fluid-filled circular cylindrical shells in the intermediate frequency range

We consider wavenumbers in in vacuo and fluid-filled isotropic and orthotropic shells. Using the Donnell-Mushtari (DM) theory we find compact and elegant asymptotic expansions for the wavenumbers in the intermediate frequency range, i.e., around the ring frequency. This frequency range corresponds to the frequencies where there is a rapid change in the values of bending wavenumbers and is found to exist in isotropic and orthotropic shells (in vacua and fluid-filled) for low circumferential orders n only. The same is first identified using the n=0 mode of an orthotropic shell. Following this, using the expression for the intermediate frequency, asymptotic expansions are found for other cases. Here, in order to get compact expansions we consider slight orthotropy (epsilon << 1) and light fluid loading (mu << 1). Thus, the orthotropy parameter epsilon and the fluid loading parameter mu are used as asymptotic parameters along with the non-dimensional thickness parameter beta. The methodology can be extended to any order of epsilon, only the expansions become unwieldy. The expansions are matched with the numerical solutions of the corresponding dispersion relation. The match is found to be good.

In vitro/In vivo assessment and mechanisms of toxicity of bioceramic materials and its wear particulates

With the progress in modern technological research, novel biomaterials are being largely developed for various biomedical applications. Over the past two decades, most of the research focuses on the development of a new generation of bioceramics as substitutes for hard tissue replacement. In reference to their application in different anatomical locations of a patient, newly developed bioceramic materials can potentially induce a toxic/harmful effect to the host tissues. Therefore, prior to clinical testing, relevant biochemical screening assays are to be performed at the cellular and molecular level, to address the issues of biocompatibility and long term performance of the implants. Along with testing strategies in the bulk material toxicity, a detailed evaluation should also be conducted to determine the toxicity of the wear products of the potential bioceramics. This is important as the bioceramics are intended to be implanted in patients with longer life expectancy and notwithstanding, the material will eventually release finer (mostly nanosized) sized debris particles due to continuous wear at articulating surfaces in the hostile corrosive environment of the human body. The wear particulates generated from a biocompatible bioceramic may act in a different way, inducing early/late aseptic loosening at the implant site, resulting in osteolysis and inflammation. Hence, a study on the chronic effects of the wear particulates, in terms of local and systemic toxicity becomes the major criteria in the toxicity evaluation of implantable bioceramics. In this broad perspective, this article summarizes some of the currently used techniques and knowledge in assessing the in vitro and in vivo cytotoxicity and genotoxicity of bioceramic implant materials. It also addresses the need to conduct a broad evaluation before claiming the biocompatibility and clinical feasibility of any new biomaterial. This review also emphasizes some of the case studies based on the experimental designs that are currently followed and its importance in the context of clinical applications.

TRANSIENT NATURAL CONVECTION FLOW IN A RECTANGULAR CAVITY FILLED WITH A POROUS MATERIAL WITH LOCALIZED HEATING FROM BELOW AND THERMAL STRATIFICATION

The transient natural convection flow with thermal stratification in a rectangular cavity filled with fluid saturated porous medium obeying Darcy's law has been studied. Prior to the time t* = 0, the flow in the cavity is assumed to be motionless and all four walls of the cavity are at the same constant temperature. At time t* = 0, the temperatures of the vertical walls are suddenly increased which vary linearly with the distance y and at the same time on the bottom wall an isothermal heat source is placed centrally. This sudden change in the wall temperatures gives rise to unsteadiness in the problem. The horizontal temperature difference induces and sustains a buoyancy driven flow in the cavity which is then controlled by the vertical temperature difference. The partial differential equations governing the transient natural convection flow have been solved numerically. The local and average Nusselt numbers decrease rapidly in a small time interval after the start of the impulsive change in the wall temperatures and the steady state is reached quickly. The time required to reach the steady state depends on the Rayleigh number and the thermal stratification parameter.

Study of motion around a static black hole in Einstein and Lovelock gravity

We study motion around a static Einstein and pure Lovelock black hole in higher dimensions. It is known that in higher dimensions bound orbits exist only for a pure Lovelock black hole in all even dimensions, D = 2N + 2, where N is the degree of Lovelock polynomial action. In particular, we compute periastron shift and light bending, and the latter is given by one of the transverse spatial components of the Riemann curvature tensor. We also consider the pseudo-Newtonian potentials and Kruskal coordinates.