The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

The basics and advances of immunomodulators and antigen presentation: a key to development of potent memory response against pathogens

Introduction: Immunomodulators are agents, which can modulate the immune response to specific antigens, while causing least toxicity to the host system. Being part of the modern vaccine formulations, these compounds have contributed remarkably to the field of therapeutics. Despite the successful record maintained by these agents, the requirement of novel immunomodulators keeps increasing due to the increasing severity of diseases. Hence, research regarding the same holds great importance. Areas covered: In this review, we discuss the role of immunomodulators in improving performance of various vaccines used for counteracting most threatening infectious diseases, mechanisms behind their action and criteria for development of novel immunomodulators. Expert opinion: Understanding the molecular mechanisms underlying immune response is a prerequisite for development of effective therapeutics as these are often exploited by pathogens for their own propagation. Keeping this in mind, the present research in the field of immunotherapy focuses on developing immunomodulators that would not only enhance the protection against pathogen, but also generate a long-term memory response. With the introduction of advanced formulations including combination of different kinds of immunomodulators, one can expect tremendous success in near future.

Efficacious Gene Silencing in Serum and Significant Apoptotic Activity Induction by Survivin Downregulation Mediated by New Cationic Gemini Tocopheryl Lipids

Nonviral gene delivery offers cationic liposomes as promising instruments for the delivery of double-stranded RNA (ds RNA) molecules for successful sequence-specific gene silencing (RNA interference). The efficient delivery of siRNA (small interfering RNA) to cells while avoiding unexpected side effects is an important prerequisite for the exploitation of the power of this excellent tool. We present here six new tocopherol based cationic gemini lipids, which induce substantial gene knockdown without any obvious cytotoxicity. All the efficient coliposomal formulations derived from each of these geminis and a helper lipid, dioleoylphosphatidylethanolamine (DOPE), were well characterized using physical methods such as atomic force microscopy (AFM) and dynamic light scattering (DLS). Zeta potential measurements were conducted to estimate the surface charge of these formulations. Flow cytometric analysis showed that the optimized coliposomal formulations could transfect anti-GFP siRNA efficiently in three different GFP expressing cell lines, viz., HEK 293T, HeLa, and Caco-2, significantly better than a potent commercial standard Lipofectamine 2000 (L2K) both in the absence and in the presence of serum (FBS). Notably, the knockdown activity of coliposomes of gemini lipids was not affected even in the presence of serum (10% and 50% FBS) while it dropped down for L2K significantly. Observations under a fluorescence microscope, RT-PCR, and Western blot analysis substantiated the flow cytometry results. The efficient cellular entry of labeled siRNA in GFP expressing cells as evidenced from confocal microscopy put forward these gemini lipids among the potent lipidic carriers for siRNA. The efficient transfection capabilities were also profiled in a more relevant fashion while performing siRNA transfections against survivin (an anti-apoptotic protein) which induced substantial apoptosis. Furthermore, the survivin downregulation improved the therapeutic efficacy levels of an anticancer drug, doxorubicin, significantly. In short, the new tocopherol based gemini lipids appear to be highly promising for achieving siRNA mediated gene knockdown in various cell lines.

Males and females of the social wasp Ropalidia marginata do not differ in their cuticular hydrocarbon profiles and do not seem to use any long-distance volatile mate attraction cues

Sex pheromones are vital in communication between individuals belonging to opposite sexes and form an integral part of the reproductive biology of various species. Among insects, sexual dimorphism in CHCs has been reported from diverse taxa spanning seven different orders, and thereby CHCs have been implicated as sex pheromones. Because males and females of the primitively eusocial wasp Ropalidia marginata touch each other with their antennae during mating, before engaging in sperm transfer, a sex pheromone that is perceived via contact chemosensation through the antennae can possibly exist in this species. Since CHCs have been implied as sex pheromones in various insects (including hymenopterans), and since sexual dimorphism of CHCs should be an obligatory prerequisite for them to act as sex pheromones, we investigated whether males and females of R. marginata differ in their CHC profiles. We found only nonvolatile CHCs, and our results show absence of sexual dimorphism in CHCs, suggesting that CHCs do not function as sex pheromone in this species. A behavioral assay failed to show presence of mate attraction at a distance, thereby showing the absence of volatile long-distance mate attraction cues (that may originate from sources other than and in addition to CHCs).

Modulation of Buckling Dynamics in Nanoparticle Laden Droplets Using External Heating

Dynamics of contact free (levitated) drying of nanofluid droplets is ubiquitous in many application domains ranging from spray drying to pharmaceutics. Controlling the final morphology (macro to micro scales) of the dried out sample poses some serious challenges. Evaporation of solvent and agglomeration of particles leads to porous shell formation in acoustically levitated nanosilica droplets. The capillary pressure due to evaporation across the menisci at the nanoscale pores causes buckling of the shell which leads to ring and bowl shaped final structures. Acoustics plays a crucial role in flattening of droplets which is a prerequisite for initiation of buckling in the shell: Introduction of mixed nanocolloids (sodium dodecyl sulfate + nanosilica) reduces evaporation rate, disrupts formation of porous shell, and enhances mechanical strength of the shell, all of which restricts the process of buckling. Although buckling is completely arrested in such surfactant added droplets, controlled external heating using laser enhances evaporation through the pores in the shell due to thermally induced structural changes and rearrangement of SDS aggregates which reinitializes buckling in such droplets, Furthermore, inclusion of anilinium hydrochloride into the nanoparticle laden droplets produces ions which adsorb and modify the morphology of sodium dodecyl sulfate crystals and reinitializes buckling in the shell (irrespective of external heating conditions). The kinetics of buckling is determined by the combined effect of morphology of the colloidal particles, particle/aggregate diffusion rate within the droplet, and the rate of evaporation of water. The buckling dynamics leads to cavity formation which grows subsequently to yield final structures with drastically different morphological features. The cavity growth is controlled by evaporation through the nanoscate pores and exhibits a universal trend irrespective of heating rate and nanoparticle type.

A dynamic view of the spread and intracellular distribution of Salmonella enterica.

The events that determine the dynamics of proliferation, spread and distribution of microbial pathogens within their hosts are surprisingly heterogeneous and poorly understood. We contend that understanding these phenomena at a sophisticated level with the help of mathematical models is a prerequisite for the development of truly novel, targeted preventative measures and drug regimes. We describe here recent studies of Salmonella enterica infections in mice which suggest that bacteria resist the antimicrobial environment inside host cells and spread to new sites, where infection foci develop, and thus avoid local escalation of the adaptive immune response. We further describe implications for our understanding of the pathogenic mechanism inside the host.

Damage evaluation and damage localization of rock

Knowledge of damage accumulation and corresponding failure evolution are prerequisite for effective maintenance of civil engineering so as to avoid disaster. Based on statistical mesoscopic damage mechanics, it was revealed that there are three stages in the process of deformation, damage and failure of multiscale heterogeneous elastic-brittle medium. These are uniformly distributed damage, localized damage and catastrophic failure. In order to identify the transitions from scattering damage to macroscopically localized one, a condition for damage localization was given. The experiments of rock under uniaxial compression with the aid of observations of acoustic emission and speckle correlation do support the concept of localization. This provides a potential approach to properly evaluate damage accumulation in practice. In addition, it is found in the experiments that catastrophic failure displays critical sensitivity. This gives a helpful clue to the prediction of catastrophic failure. (C) 2004 Elsevier Ltd. All rights reserved.

Finding space to mental health : promoting mental health in adolescents (12 to 14 year olds): preliminary results of the intervention's effectiveness

Resumen: La salud mental y el bienestar son fundamentales para nuestra capacidad colectiva y individual como seres humanos de pensar, de exteriorizar los sentimientos, de establecer y mantener relaciones, para estudiar, para perseguir las actividades de ocio, para tomar decisiones diarias y para disfrutar de una vida plena. Una adolescencia saludable es un prerrequisito para una vida adulta saludable. Sin embargo, la realidad actual presenta un panorama preocupante. La formación del capital mental individual y colectivo - especialmente en las primeras etapas de la vida - está siendo retenida por una serie de riesgos evitables para la salud mental (World Health Organization [WHO], 2013). Los adolescentes del sur de Europa (región que ha sido más severamente afectada por la crisis financiera; e.g., Portugal) son señalados como un grupo extremadamente vulnerable, ya que su salud mental fácilmente podría ser influenciada por las dificultades económicas de sus padres y la escasez de solidaridad social (European Parliament, 2012). La promoción de la salud mental de los adolescentes es considerada como una preocupación fundamental (WHO, 2005a, 2013). En este ámbito, las intervenciones centradas en la promoción de la literacía de la salud mental han revelado importantes ventajas en la prevención, reconocimiento, intervención precoz y la reducción del estigma (Pinfold, Stuart, Thornicroft & Arboleda-Florez, 2005; Pinfold, Toulmin, Thornicroft, Huxley, Farmer & Graham, 2003; Schulze, Richter-Werling, Matschinger & Angermeyer, 2003; Stuart, 2006). En consonancia con los marcos de promoción de la salud mentales propuestos por la Organización Mundial de la Salud (2005a), tenemos que involucrar a jóvenes en los ambientes donde interactúan (Burns, 2011). Las escuelas son implícitamente uno de los locales más importantes para la promoción de la salud mental de los adolescentes (Barry, Clarke, Jenkins & Patel, 2013; WHO, 2001). El proyecto “Abrir Espacio para la Salud Mental – Promoción de la salud mental en adolescentes (12-14 años)” tiene como objetivo incrementar literacía de la salud mental en los jóvenes. En el primer año se ha desarrollado un instrumento de evaluación - Mental Health Literacy questionnaire (MHLq) - y la intervención para la promoción de la salud mental. La intervención consiste en 2 sesiones, 90 minutos cada una, implementadas con intervalo de una semana. Siguen una metodología interactiva, utilizando dinámicas de grupo, videos, música y discusión. El estudio de la eficacia de la intervención se lleva a cabo mediante un análisis pre y pos-test con el MHLq, utilizando un grupo experimental y un grupo de control. Este artículo presenta los resultados preliminares de la eficacia de la intervención de promoción de la salud mental en una muestra de 100 adolescentes portugueses (12-14 años). El pos-test mostró un incremento de los niveles de conocimientos de salud mental y estrategias de autoayuda. Los resultados sugieren que la intervención desarrollada parece ser adecuada al objetivo propuesto y refuerzan la creencia de que intervenciones escolares, sistemáticas y sostenibles, para la promoción de la salud mental con jóvenes, es un enfoque prometedor para la promoción de la literacía de la salud mental (Schulze et al., 2003; Rickwood et al., 2005; Corrigan et al., 2007; WHO, 2010).

Internal resonance of an L-shaped beam with a limit stop .1. Free vibration

Real-life structures often possess piecewise stiffness because of clearances or interference between subassemblies. Such an aspect can alter a system's fundamental free vibration response and leads to complex mode interaction. The free vibration behaviour of an L-shaped beam with a limit stop is analyzed by using the frequency response function and the incremental harmonic balance method. The presence of multiple internal resonances, which involve interactions among the first five modes and are extremely complex, have been discovered by including higher harmonics in the analysis. The results show that mode interaction may occur if the higher harmonics of a vibration mode are close to the natural frequency of a higher mode. The conditions for the existence of internal resonance are explored, and it is shown that a prerequisite is the presence of bifurcation points in the form of intersecting backbone curves. A method to compute such intersections by using only one harmonic in the free vibration solution is proposed. (C) 1996 Academic Press Limited

Initial development of microdamage under impact loading

In this paper, the initial development of microdamage in material subjected to impulsive loading was investigated experimentally and analytically with controllable short-load duration. Based on a general solution to the statistical evolution of a one-dimensional system of ideal microcracks, a prerequisite to experimental investigation of nucleation of microcracks was derived. By counting the number of microcracks, the distribution of nucleation of microcracks was studied. The law of the nucleation rate of microcracks can be expressed as a separable function of stress and cracksize. It is roughly linear dependence on loading stress. The normalized number density of microcracks is in agreement with that of a second-phase particle.

Critical current anisotropy in high temperature superconductors

After nearly 15 years of research effort, High Temperature Superconductors (HTS) are finding a wide range of practical applications. A clear understanding of the factors controlling the current carrying capacity of these materials is a prerequisite to their successful technological development. The critical current density (Jc) in HTS is directly dependent on the structure and pinning of the Flux Line Lattice (FLL) in these materials. This thesis presents an investigation of the Jc anisotropy in HTS. The use of thin films grown on off c-axis (vicinal) substrates allowed the effect of current directions outside the cuprate planes to be studied. With this experimental geometry Berghuis, et al. (Phys. Rev. Lett. 79, 12, pg. 2332) observed a striking flux channelling effect in vicinal YBa2Cu3O7-δ (YBCO) films. By confirming, and extending, this observation, it is demonstrated that this is an intrinsic effect. The results obtained, appear to fit well with the predictions of a field angle dependent cross-over from a three dimensional rectilinear FLL to a kinked lattice of strings and pancakes. The pinning force density for movement of strings inside the cuprate planes is considerably less than that on vortex pancake elements. When the FLL is entirely string-like this reduced pinning leads to the observed channelling minima. It is observed that anti-phase boundaries enhance the Jc in vicinal YBCO films by strongly pinning vortex strings. The effect on the FLL structure cross-over of increasing anisotropy has been elucidated using de-oxygenated vicinal YBCO films. Intriguingly, the counter intuitive prediction that the range of applied field angle for which the kinked lattice is fully developed reduces with increasing anisotropy, appears to be confirmed. Although vortex channelling cannot be observed in c-axis YBCO films, the pinning force density for vortex string channelling has been extracted by observing string dragging. By studying the effect of rotating the applied field at a constant angle to the cuprate planes, it is possible to observe the cross-over into the string pancake regime in c-axis films. In the 3D region, the observed behaviour is well explained by the anisotropic Ginzburg-Landau model. Measurements were also made on thin films of the much more anisotropic Bi 2Sr2CaCu2O8+x material, grown on vicinal substrates. The absence of any flux channelling effect and clear adherence to the expected Kes-Law behaviour in the observed Jc characteristics does not provide evidence for the existence of the predicted ‘crossing lattice’ in Bi 2Sr2CaCu2O8+x .

The role of oceanography in fisheries resources exploitation

The 800 km coastline of Nigeria is a huge gateway to a supply of food and raw materials. But while immense fishery resource is perceived by many, its full exploitation is obstructed by how little is understood of the ocean processes necessary for effective utilisation. Much basic oceanographic research is needed as a prerequisite to evolving successful strategies for full application of Nigeria's marine fisheries resources

Kurzinformation zum EU - Projekt: "Mechanisms influencing long term trends in reproductive success and recruitment of Baltic cod : implications for fisheries management"

In July 1994 an internationally coordinated and EU financed multidisciplinary research project about Baltic cod recruitment was started. The primary goals are to identify and describe dominant biotic and abiotic processes affecting the developmental success of early stages and the maturation of cod in the Central Baltic, to incorporate these processes into recruitment models in order to enhance prediction of future stock fluctuations due to environmental pertubations, species interactions and fisheries management directives as a prerequisite for an integrated fish stock assessment in the Central Baltic and to evaluate the feasibility and possible effects of stock enhancement programs on stock and recruitment and providing the biological basis for assessing their economic value.

The Demand for Environmental Quality in Driving Transitions to Low Polluting Energy Sources

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基于统计光学的无透镜鬼成像数值模拟与实验验证

作为量子信息领域分支的鬼成像,由于物体的像将出现在不包含物体的光路上的特点,使得这一领域的研究引人入胜。一度认为,只有基于纠缠态双光子的纠缠光源,才能实现鬼成像;但近年来的研究表明,经典热光场也能实现这一过程。从经典统计光学入手,建立了热光场的数值模型,模拟符合热光特性的光场变化、光场传播、以及物体透射函数对热光场的调制,进而从光强度起伏的关联函数中,分别重现振幅型物体和纯相位型物体的傅里叶变换图像;通过与真实实验结果的对比,表明基于统计光学原理的该数值模型所预测的实验结果,与真实的实验结果完全一致。