Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence

Background: Serovars of Salmonella enterica, namely Typhi and Typhimurium, reportedly, are the bacterial pathogens causing systemic infections like gastroenteritis and typhoid fever. To elucidate the role and importance in such infection, the proteins of the Type III secretion system of Salmonella pathogenicity islands and two component signal transduction systems, have been mainly focused. However, the most indispensable of these virulent ones and their hierarchical role has not yet been studied extensively. Results: We have adopted a theoretical approach to build an interactome comprising the proteins from the Salmonella pathogeneicity islands (SPI) and two component signal transduction systems. This interactome was then analyzed by using network parameters like centrality and k-core measures. An initial step to capture the fingerprint of the core network resulted in a set of proteins which are involved in the process of invasion and colonization, thereby becoming more important in the process of infection. These proteins pertained to the Inv, Org, Prg, Sip, Spa, Ssa and Sse operons along with chaperone protein SicA. Amongst them, SicA was figured out to be the most indispensable protein from different network parametric analyses. Subsequently, the gene expression levels of all these theoretically identified important proteins were confirmed by microarray data analysis. Finally, we have proposed a hierarchy of the proteins involved in the total infection process. This theoretical approach is the first of its kind to figure out potential virulence determinants encoded by SPI for therapeutic targets for enteric infection. Conclusions: A set of responsible virulent proteins was identified and the expression level of their genes was validated by using independent, published microarray data. The result was a targeted set of proteins that could serve as sensitive predictors and form the foundation for a series of trials in the wet-lab setting. Understanding these regulatory and virulent proteins would provide insight into conditions which are encountered by this intracellular enteric pathogen during the course of infection. This would further contribute in identifying novel targets for antimicrobial agents. (C) 2014 Elsevier Ltd. All rights reserved.

Forgotten records of Chrysopelea taprobanica Smith, 1943 (Squamata: Colubridae) from India

The colubrid snake Chrysopelea taprobanica Smith, 1943 was described from a holotype from Kanthali (= Kantalai) and paratypes from Kurunegala, both localities in Sri Lanka (formerly Ceylon) (Smith 1943). Since its description, literature pertaining to Sri Lankan snake fauna considered this taxon to be endemic to the island (Taylor 1950, Deraniyagala 1955, de Silva 1980, de Silva 1990, Somaweera 2004, Somaweera 2006, de Silva 2009, Pyron et al. 2013). In addition, earlier efforts on the Indian peninsula (e.g. Das 1994, 1997, Das 2003, Whitaker & Captain 2004, Aengals et al. 2012) and global data compilations (e.g. Wallach et al. 2014, Uetz & Hošek 2015) did not identify any record from mainland India until Guptha et al. (2015) recorded a specimen (voucher BLT 076 housed at Bio-Lab of Seshachalam Hills, Tirupathi, India) in the dry deciduous forest of Chamala, Seshachalam Biosphere Reserve in Andhra Pradesh, India in November 2013. Guptha et al. (2015) further mentioned an individual previously photographed in 2000 at Rishi Valley, Andhra Pradesh, but with no voucher specimen collected. Guptha’s record, assumed to be the first confirmed record of C. taprobanica in India, is noteworthy as it results in a large range extension, from northern Sri Lanka to eastern India with an Euclidean distance of over 400 km, as well as a change of status, i.e., species not endemic to Sri Lanka. However, at least three little-known previous records of this species from India evaded most literature and were overlooked by the researchers including ourselves.

Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005-1013. (c) 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Enhancement Mechanism of Fluorescence Intensity in Presence of Plasmonic Nanoparticles

The emission intensity of fluorophore molecule may change in presence of strong plasmon field induced by nanoparticles. The enhancement intensity is optimized through selective clustering or functionalization of nanoparticles in closed vicinity of fluorophore. Our study is aimed at understanding the enhancement mechanism of fluorescence intensity in presence of gold nanoparticles to utilize it in molecular sensing and in situ imaging in the microfluidic lab-on-chip device. Related phenomena are studied in situ in a microfluidic channel via fluorescence imaging. Detailed analysis is carried out to understand the possible mechanism of enhancement of fluorescence due to nanoparticles. In the present experimental study we show that SYTO9 fluorescence intensity increased in presence of Au nanoparticles of similar to 20 nm diameter. The fluorescence intensity is 20 time more compared to that in absence of Au nanoparticles. The enhancement of fluorescence intensity is attributed to the plasmonic resonance of Au nanoparticle at around the fluorescence emission wavelength. Underlying fundamental mechanism via dipole interaction model is explored for quantitative correlation of plasmonic enhancement properties.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

Insight into the Evaporation Dynamics of a Pair of Sessile Droplets on a Hydrophobic Substrate

In this work, we have demonstrated three unique regimes in the evaporation lifecycle of a pair of sessile droplets placed in variable proximity on a hydrophobic substrate. For small separation distance, the droplets undergo asymmetric spatiotemporal,evaporation leading to contact angle hysteresis and suppressed vaporization. The reduced evaporation has been attributed quantitatively to the existence of a constrained vapor-rich dome between the two droplets. However, a dynamic decrease in the droplet radius due to solvent removal marks a return to symmetry in terms of evaporation and contact angle. We have described the variation in evaporation flux using a universal correction factor. We have also demonstrated the existence of a critical separation distance beyond which the droplets in the, droplet pair do not affect each other. The results are crucial to a plethora of applications ranging from surface patterning to lab-on-a-chip devices.

In-situ flexural OPV measurements on flexible glass substrate

In-situ dark and light IV characteristics of inverted P3HT-PCBM devices on flexible glass substrates were measured while bending. Bending set up was simple and home built with servo controlled 2 parallel plate movements. ITO was sputter coated onto the thin flexible glass sheets of 25mmx25mm size in the lab. OPV devices were fabricated inside the glove box and conversion efficiency measured was about 2.8%. Bending of the device substrates and simultaneous PV measurements were carried out in ambient conditions. It was observed that the J(SC) and efficiency increased until the substrate breaking point but the V-OC and fill factor remained unchanged.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

A finite element method for cracked components of structures

In this paper, a method is developed for determining the effective stiffness of the cracked component. The stiffness matrix of the cracked component is integrated into the global stiffness matrix of the finite element model of the global platform for the FE calculation of the structure in any environmental conditions. The stiffness matrix equation of the cracked component is derived by use of the finite variation principle and fracture mechanics. The equivalent parameters defining the element that simulates the cracked component are mathematically presented, and can be easily used for the FE calculation of large scale cracked structures together with any finite element program. The theories developed are validated by both lab tests and numerical calculations, and applied to the evaluation of crack effect on the strength of a fixed platform and a self-elevating drilling rig.

Evaluation of manufacturing techniques for a minifluidics demonstrator system

A multi-disciplinary team based at Heriot-Watt University and other Universities has been set up to tackle the design and manufacturing of lab-on-a-chip for industries as one of the demonstrators of the EPSRC Grand Challenge project "3D-Mintegration". The team focuses on the analysis of foetal genetic material extracted from maternal blood as a smart alternative to invasive prenatal testing such as amniocentesis. The first module of the microsystem envisaged achieves a separation of blood cells from plasma. This system permits the testing of different manufacturing techniques.

Manejo de malezas bajo dos sistemas de labranza en cultivo de soya (Glycine max (L.) Merril)

El presente trabajo fue realizado en el Centro Experimental del Algodón, en el ciclo agrícola 1989-1990 con el objetivo de estudiar la influencia del control químico y la Labranza Minina y Convencional en las poblaciones de malezas, durante el primer ciclo del cultivo de soya. Se utilizó un diseño de Bloque Completos al Azar non tres tratamientos y cuatro repeticiones. Se realizaron recuentos de malezas a los 15, 30 y 45 días después de la emergencia del cultivo. Se tomaron datos de individuos/especie y biomasa seca de malezas en un metro cuadrado. Al final se midió el rendimiento del cultivo en Kg/ha Los Tratamientos fueron: Tratamiento (Lab. Min; Lab. Min; Lab. Conv.) N. Común (Paraguat; Glifosto; Imazaquin + Pendimentalin) N. Comercial (Gramoxone; Roundup; Scepter + Prowl) Dosis (1/ha) (2.13; 4.26; 0.99+1.42) En el estudio se encontró que el mejor tratamiento fue donde se utilizó Labranza Convencional y control de malezas ron Scepter y Prowl.

The Nonlinear Phenomena Of Thin Polydimethylsiloxane (Pdms) Films In Electrowetting

Electrowetting (EW) is an effective way to manipulate small volume liquid in micro- and nano-devices, for it can improve its wettability. Since the late 1990s, electrowetting-on-dielectric (EWOD) has been used widely in bio-MEMS, lab-on-a-chip, etc. Polydimethlsiloxane (PDMS) is extensively utilized as base materials in the fabrication of biomedical micro- and nano-devices. The properties of thin PDMS films used as dielectric layer in EW are studied in this paper. The experimental results show that the thin PDMS films exhibit good properties in EWOD. As to PDMS films with different thicknesses, a threshold voltage and a hysteresis were observed in the EIWOD experiments.

Role Of Vertical Component Of Surface Tension Of The Droplet On The Elastic Deformation Of Pdms Membrane

Poly(dimethylsiloxane) (PDMS) has been widely used in lab-on-a-chip and micro- total analysis systems (mu-TAS), thus wetting and electrowetting behaviors of PDMS are of great importance in these devices. PDMS is a kind of soft polymer material, so the elastic deformation of PDMS membrane by a droplet cannot be neglected due to the vertical component of the interfacial tension between the liquid and vapor, and this vertical component of liquid-vapor surface tension is also balanced by the stress distribution within the PDMS membrane. Such elastic deformation and stress distribution not only affect the exact measurement of contact angle, but also have influence on the micro-fluidic behavior of the devices. Using ANSYS code, we simulated numerically the elastic deformation and stress distribution of PDMS membrane on a rigid substrate due to the liquid-vapor surface tension. It is found that the vertical elastic deformation of the PDMS membrane is on the order of several tens of nanometers due to the application of a droplet with a diameter of 2.31 mm, which is no longer negligible for lab-on-a-chip and mu-TAS. The vertical elastic deformation increases with the thickness of the PDMS membrane, and there exists a saturated membrane thickness, regarded as a semi-infinite membrane thickness, and the vertical elastic deformation reaches a limiting value when the membrane thickness is equal to or thicker than such saturated thickness. (C) Koninklijke Brill NV, Leiden, 2008.

Do experimental subjects favor their friends?

Ideally we would like subjects of experiments to be perfect strangers so that the situation they face at the lab is not just part of a long run interaction. Unfortunately, it is not easy to reach those conditions and experimenters try to mitigate any effects from those out-of-the-lab relationships by, for instance, randomly matching subjects. However, even if this type of procedure is used, there is a positive probability that a subject may face a friend or an acquaintance. We find evidence that social proximity between subjects is irrelevant to experiment results in dictator games. Thus, although ideal conditions are not met, relations between subjects do not contaminate the results of experiments.

Chemical recycling of municipal packaging waste by pyrolysis

[EN]The present doctoral thesis centers on studying pyrolysis as a chemical recycling technique for rejected packaging waste fractions coming from separation and sorting plants. The pyrolysis experiments have been carried out in a lab-scale installation equipped with a 3.5 L semi-batch reactor and a condensation and collection system for the liquids and gases generated. In the present thesis, an experimental study on the conventional pyrolysis process applied to the aforementioned waste fractions has been conducted, as well as the study of non-conventional or advanced pyrolysis processes such as catalytic and stepwise pyrolysis. The study of the operating parameters has been carried out using a mixed plastics simulated sample, the composition of which is similar to that found in real fractions, and subsequently the optimized process has been applied to real packaging waste. An exhaustive characterization of the solids, liquids and gases obtained in the process has been made after each experiment and their potential uses have been established. Finally, an empirical model that will predict the pyrolysis yields (% organic liquid, % aqueous liquid, % gases, % char, % inorganic solid) as a function of the composition of the initial sample has been developed. As a result of the experimental work done, the requirements have been established for an industrial packaging waste pyrolysis plant that aims to be sufficiently versatile as to generate useful products regardless of the nature of the raw material.