Cis-trans interactions of cell surface receptors: biological roles and structural basis.

Cell surface receptors bind ligands expressed on other cells (in trans) in order to communicate with neighboring cells. However, an increasing number of cell surface receptors are found to also interact with ligands expressed on the same cell (in cis). These observations raise questions regarding the biological role of such cis interactions. Specifically, it is important to know whether cis and trans binding have distinct functional effects and, if so, how a single cell discriminates between interactions in cis versus trans. Further, what are the structural features that allow certain cell surface receptors to engage ligand both on the same as well as on an apposed cell membrane? Here, we summarize known examples of receptors that display cis-trans binding and discuss the emerging diversity of biological roles played by these unconventional two-way interactions, along with their structural basis.

Fine speckle contrast in InGaAs/InP systems: Influence of layer thickness, missmatch, and growing temperature

This work is focused on the study of the fine speckle contrast present in planar view observations of matched and mismatched InGaAs layers grown by molecular beam epitaxy on InP substrates. Our results provide experimental evidence of the evolution of this fine structure with the mismatch, layer thickness, and growth temperature. The correlation of the influence of all these parameters on the appearance of the contrast modulation points to the development of the fine structure during the growth. Moreover, as growth proceeds, this structure shows a dynamic behavior which depends on the intrinsic layer substrate stress.

Athermal character of structural phase transitions

The significance of thermal fluctuations in nucleation in structural first-order phase transitions has been examined. The prototypical case of martensitic transitions has been experimentally investigated by means of acoustic emission techniques. We propose a model based on the mean first-passage time to account for the experimental observations. Our study provides a unified framework to establish the conditions for isothermal and athermal transitions to be observed.

Expression, purification, and structural insights for the human uric acid transporter, GLUT9, using the Xenopus laevis oocytes system.

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies.

Structural Analysis of Aggregate Blends Using the SHRP Gyratory Compactor, MLR-95-8, 1996

The Iowa Department of Transportation (IDOT) received a Strategic Highway Research Program (SHRP) gyratory compactor in December 1994. Since then IDOT has been studying the ability of the compactor to analyze fundamental properties of aggregates such as shape, texture, and gradation by studying the volumetrics of the aggregate blends under a standard load using the SHRP gyratory compactor. This method of analyzing the volumetrics of aggregate blends is similar to SHRP's fine aggregate angularity procedure, which analyzes void levels in noncompacted aggregate blends, which in turn can be used to evaluate the texture or shape of aggregates, what SHRP refers to as angularity. Research is showing that by splitting the aggregate blend on the 2.36-mm (#8) sieve and analyzing the volumetrics or angularity of the separated blend, important fundamental properties can be determined. Most important is structure (the degree and location of aggregate interlock). In addition, analysis of the volumes of the coarse and fine portions can predict the voids in the mineral aggregate and the desired asphalt content. By predicting these properties, it can be determined whether the combined aggregate blend, when mixed with asphalt cement, will produce a mix with structural adequacy to carry the designed traffic load.

Structural Characterization of UHPC Waffle Bridge Deck and Connections, TR-614, 2014

The AASHTO strategic plan in 2005 for bridge engineering identified extending the service life of bridges and accelerating bridge construction as two of the grand challenges in bridge engineering. These challenges have the objective of producing safer and more economical bridges at a faster rate with a minimum service life of 75 years and reduced maintenance cost to serve the country’s infrastructure needs. Previous studies have shown that a prefabricated full-depth precast concrete deck system is an innovative technique that accelerates the rehabilitation process of a bridge deck, extending its service life with reduced user delays and community disruptions and lowering its life-cycle costs. Previous use of ultra-high performance concrete (UHPC) for bridge applications in the United States has been considered to be efficient and economical because of its superior structural characteristics and durability properties. Full-depth UHPC waffle deck panel systems have been developed over the past three years in Europe and the United States. Subsequently, a single span, 60-ft long and 33-ft wide prototype bridge with full-depth prefabricated UHPC waffle deck panels has been designed and built for a replacement bridge in Wapello County, Iowa. The structural performance characteristics and the constructability of the UHPC waffle deck system and its critical connections were studied through an experimental program at the structural laboratory of Iowa State University (ISU). Two prefabricated full-depth UHPC waffle deck (8 feet by 9 feet 9 inches by 8 inches) panels were connected to 24-ft long precast girders, and the system was tested under service, fatigue, overload, and ultimate loads. Three months after the completion of the bridge with waffle deck system, it was load tested under live loads in February 2012. The measured strain and deflection values were within the acceptable limits, validating the structural performance of the bridge deck. Based on the laboratory test results, observations, field testing of the prototype bridge, and experience gained from the sequence of construction events such as panel fabrication and casting of transverse and longitudinal joints, a prefabricated UHPC waffle deck system is found to be a viable option to achieve the goals of the AASHTO strategic plan.

Structural analysis of Turtle Mountain: Origin and influence of fractures in the development of rock slope failures

Large slope failures in fractured rocks are often controlled by the combination of pre-existing tectonic fracturing and brittle failure propagation in the intact rock mass during the pre-failure phase. This study focuses on the influence of fold-related fractures and of post-folding fractures on slope instabilities with emphasis on Turtle Mountain, located in SW Alberta (Canada). The structural features of Turtle Mountain, especially to the south of the 1903 Frank Slide, were investigated using a high-resolution digital elevation model combined with a detailed field survey. These investigations allowed the identification of six main discontinuity sets influencing the slope instability and surface morphology. According to the different deformation phases affecting the area, the potential origin of the detected fractures was assessed. Three discontinuity sets are correlated with the folding phase and the others with post-folding movements. In order to characterize the rock mass quality in the different portions of the Turtle Mountain anticline, the geological strength index (GSI) has been estimated. The GSI results show a decrease in rock mass quality approaching the fold hinge area due to higher fracture persistence and higher weathering. These observations allow us to propose a model for the potential failure mechanisms related to fold structures.

Hepatitis C virus RNA replication requires a conserved structural motif within the transmembrane domain of the NS5B RNA-dependent RNA polymerase.

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B), the viral RNA-dependent RNA polymerase (RdRp), is a tail-anchored protein with a highly conserved C-terminal transmembrane domain (TMD) that is required for the assembly of a functional replication complex. Here, we report that the TMD of the HCV RdRp can be functionally replaced by a newly identified analogous membrane anchor of the GB virus B (GBV-B) NS5B RdRp. Replicons with a chimeric RdRp consisting of the HCV catalytic domain and the GBV-B membrane anchor replicated with reduced efficiency. Compensatory amino acid changes at defined positions within the TMD improved the replication efficiency of these chimeras. These observations highlight a conserved structural motif within the TMD of the HCV NS5B RdRp that is required for RNA replication.

Structural changes induced by daily music listening in the recovering brain after middle cerebral artery stroke: a voxel-based morphometry study

Music is a highly complex and versatile stimulus for the brain that engages many temporal, frontal, parietal, cerebellar, and subcortical areas involved in auditory, cognitive, emotional, and motor processing. Regular musical activities have been shown to effectively enhance the structure and function of many brain areas, making music a potential tool also in neurological rehabilitation. In our previous randomized controlled study, we found that listening to music on a daily basis can improve cognitive recovery and improve mood after an acute middle cerebral artery stroke. Extending this study, a voxel-based morphometry (VBM) analysis utilizing cost function masking was performed on the acute and 6-month post-stroke stage structural magnetic resonance imaging data of the patients (n = 49) who either listened to their favorite music [music group (MG), n = 16] or verbal material [audio book group (ABG), n = 18] or did not receive any listening material [control group (CG), n = 15] during the 6-month recovery period. Although all groups showed significant gray matter volume (GMV) increases from the acute to the 6-month stage, there was a specific network of frontal areas [left and right superior frontal gyrus (SFG), right medial SFG] and limbic areas [left ventral/subgenual anterior cingulate cortex (SACC) and right ventral striatum (VS)] in patients with left hemisphere damage in which the GMV increases were larger in the MG than in the ABG and in the CG. Moreover, the GM reorganization in the frontal areas correlated with enhanced recovery of verbal memory, focused attention, and language skills, whereas the GM reorganization in the SACC correlated with reduced negative mood. This study adds on previous results, showing that music listening after stroke not only enhances behavioral recovery, but also induces fine-grained neuroanatomical changes in the recovering brain.

Enhancing absorptive capacity in a non-research and development. An action research approach to converting individual observations into organisational awareness

The ability to recognize potential knowledge and convert it into business opportunities is one of the key factors of renewal in uncertain environments. This thesis examines absorptive capacity in the context of non-research and development innovation, with a primary focus on the social interaction that facilitates the absorption of knowledge. It proposes that everyone is and should be entitled to take part in the social interaction that shapes individual observations into innovations. Both innovation and absorptive capacity have been traditionally related to research and development departments and institutions. These innovations need to be adopted and adapted by others. This so-called waterfall model of innovations is only one aspect of new knowledge generation and innovation. In addition to this Science–Technology–Innovation perspective, more attention has been recently paid to the Doing–Using–Interacting mode of generating new knowledge and innovations. The amount of literature on absorptive capacity is vast, yet the concept is reified. The greater part of the literature links absorptive capacity to research and development departments. Some publications have focused on the nature of absorptive capacity in practice and the role of social interaction in enhancing it. Recent literature on absorptive capacity calls for studies that shed light on the relationship between individual absorptive capacity and organisational absorptive capacity. There has also been a call to examine absorptive capacity in non-research and development environments. Drawing on the literature on employee-driven innovation and social capital, this thesis looks at how individual observations and ideas are converted into something that an organisation can use. The critical phases of absorptive capacity, during which the ideas of individuals are incorporated into a group context, are assimilation and transformation. These two phases are seen as complementary: whereas assimilation is the application of easy-to-accept knowledge, transformation challenges the current way of thinking. The two require distinct kinds of social interaction and practices. The results of this study can been crystallised thus: “Enhancing absorptive capacity in practicebased non-research and development context is to organise the optimal circumstances for social interaction. Every individual is a potential source of signals leading to innovations. The individual, thus, recognises opportunities and acquires signals. Through the social interaction processes of assimilation and transformation, these signals are processed into the organisation’s reality and language. The conditions of creative social capital facilitate the interplay between assimilation and transformation. An organisation that strives for employee-driven innovation gains the benefits of a broader surface for opportunity recognition and faster absorption.” If organisations and managers become more aware of the benefits of enhancing absorptive capacity in practice, they have reason to assign resources to those practices that facilitate the creation of absorptive capacity. By recognising the underlying social mechanisms and structural features that lead either to assimilation or transformation, it is easier to balance between renewal and effective operations.

Genesis and Evolution of Brittle Structures In Southwestern Finland and Western South Africa. Insights into Fault Reactivation, Fluid Flow and Structural Maturity in Precambrian Cratons

The bedrock of old crystalline cratons is characteristically saturated with brittle structures formed during successive superimposed episodes of deformation and under varying stress regimes. As a result, the crust effectively deforms through the reactivation of pre-existing structures rather than by through the activation, or generation, of new ones, and is said to be in a state of 'structural maturity'. By combining data from Olkiluoto Island, southwestern Finland, which has been investigated as the potential site of a deep geological repository for high-level nuclear waste, with observations from southern Sweden, it can be concluded that the southern part of the Svecofennian shield had already attained structural maturity during the Mesoproterozoic era. This indicates that the phase of activation of the crust, i.e. the time interval during which new fractures were generated, was brief in comparison to the subsequent reactivation phase. Structural maturity of the bedrock was also attained relatively rapidly in Namaqualand, western South Africa, after the formation of first brittle structures during Neoproterozoic time. Subsequent brittle deformation in Namaqualand was controlled by the reactivation of pre-existing strike-slip faults.In such settings, seismic events are likely to occur through reactivation of pre-existing zones that are favourably oriented with respect to prevailing stresses. In Namaqualand, this is shown for present day seismicity by slip tendency analysis, and at Olkiluoto, for a Neoproterozoic earthquake reactivating a Mesoproterozoic fault. By combining detailed field observations with the results of paleostress inversions and relative and absolute time constraints, seven distinctm superimposed paleostress regimes have been recognized in the Olkiluoto region. From oldest to youngest these are: (1) NW-SE to NNW-SSE transpression, which prevailed soon after 1.75 Ga, when the crust had sufficiently cooled down to allow brittle deformation to occur. During this phase conjugate NNW-SSE and NE-SW striking strike-slip faults were active simultaneous with reactivation of SE-dipping low-angle shear zones and foliation planes. This was followed by (2) N-S to NE-SW transpression, which caused partial reactivation of structures formed in the first event; (3) NW-SE extension during the Gothian orogeny and at the time of rapakivi magmatism and intrusion of diabase dikes; (4) NE-SW transtension that occurred between 1.60 and 1.30 Ga and which also formed the NW-SE-trending Satakunta graben located some 20 km north of Olkiluoto. Greisen-type veins also formed during this phase. (5) NE-SW compression that postdates both the formation of the 1.56 Ga rapakivi granites and 1.27 Ga olivine diabases of the region; (6) E-W transpression during the early stages of the Mesoproterozoic Sveconorwegian orogeny and which also predated (7) almost coaxial E-W extension attributed to the collapse of the Sveconorwegian orogeny. The kinematic analysis of fracture systems in crystalline bedrock also provides a robust framework for evaluating fluid-rock interaction in the brittle regime; this is essential in assessment of bedrock integrity for numerous geo-engineering applications, including groundwater management, transient or permanent CO2 storage and site investigations for permanent waste disposal. Investigations at Olkiluoto revealed that fluid flow along fractures is coupled with low normal tractions due to in-situ stresses and thus deviates from the generally accepted critically stressed fracture concept, where fluid flow is concentrated on fractures on the verge of failure. The difference is linked to the shallow conditions of Olkiluoto - due to the low differential stresses inherent at shallow depths, fracture activation and fluid flow is controlled by dilation due to low normal tractions. At deeper settings, however, fluid flow is controlled by fracture criticality caused by large differential stress, which drives shear deformation instead of dilation.

Studies on the Effect of High Energy Ball Milling On the Structural, Electrical and Magnetic Properties of Some Normal Spinets in the Ultrafine Regime

The present work is an attempt to understand the characteristics of high energy ball milling on the structural, electrical and magnetic properties of some normal spinets in the ultra fine regime, Magnetism and magnetic materials have been a fascinating subject for the mankind ever since the discovery of lodestone. Since then, man has been applying this principle of magnetism to build devices for various applications. Magnetism can be classified broadly into five categories. They are diamagnetic, paramagnetic, ferromagnetic antiferromagnetic and ferrimagnetic. Of these, ferro and ferri magnetic materials assume great commercial importance due to their unique properties like appropriate magnetic characteristics, high resistivity and low eddy current losses. The emergence of nanoscience and nanotechnology during the last decade had its impact in the field of magnetism and magnetic materials too. Now, it is common knowledge that materials synthesized in the nanoregime exhibit novel and superlative properties with respect to their coarser sized counterparts in the micron regime. These studies reveal that dielectric properties can be varied appreciably by high-energy ball milling in nanosized zinc ferrites produced by coprecipitation method. A semi conducting behaviour was observed in these materials with the Oxygen vacancies acting as the main charge carrier for conduction, which was produced at the time of coprecipitation and milling. Thus through this study, it was possible to successfully investigate the finite size effects on the structural, electrical and magnetic properties of normal spinels in the ultra fine regime

INDIAN AND ANTARCTIC BRYOZOANS - TAXONOMY AND OBSERVATIONS ON TOXICOLOGY

This thesis embodies findings on a taxonomical investigation of a group of lower marine invertebrates belonging to the category coelomata. Bryozoans are well known both in fossil and recent taxonomical history. They comprise of about 5,000 living and 16000 fossil species. Bryozoans are well known for their taxonomic abundance and structural diversity,representing the various ecological niches ranging from the intertidal to the abyssal benthic. At a time when global marine biological diversity has become a concern of not only to the scientists but also to the policy makers,an understanding of species diversity and abundance are cardinal aspects of biological studies. Geological time scales which is known that by Pre-Cambrian, marine invertebrate diversity reach the maximum and this diversity has become more comprehensive as time advanced. Taxonomists a vanishing species of scientists have become more concerned in discerning patterns of species diversity. The basic tool for this is identification fo animals. with this idea in mind a detailed study of taxonomy of bryozoan was undertaken . The major part of this thesis is devoted to describe various species of bryozoans with detailed description and ecotypical variations.The pattern of distribution and abundance which are important aspects of animal groups have also been documented. Possible effects of heavy metal contamination on the tolerance and growth of bryozoans, a few species of which have been eliminated from the chronically polluted areas of Cochin backwaters have also been documented.

A structural investigation relating to the pozzolanic activity of rice husk ashes

Various factors determine the applicability of rice husk ash (RHA) as a pozzolanic material. The amount and accessibility of reactive sites is thought to be a key factor. A structural study of RHA samples in relation to their reactivity has been performed; Silica in RHA formed by burning rice husk in a laboratory furnace under continuous supply of air have been characterized as a function of incineration temperature, time and cooling regime. The characterization methods included chemical analyses, conductivity measurements, microscopic analysis, X-ray diffraction (XRD) and 29Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR). In line with earlier observations, the analyses show that the highest amounts of amorphous silica occur in samples burnt in the range of 500 °C–700 °C. The 29Si NMR data allow direct identification of the reactive silanol sites in the RHA samples. De-convolution of the NMR spectra clearly shows that the quickly cooled RHA resulting from burning rice husk for 12 h at 500 °C has the highest amount of silanol groups. This sample also induced the largest drop in conductivity when added to a saturated calcium hydroxide solution giving an indication of its reactivity towards lime. Therefore, this RHA is the favorable sample to be used as pozzolanic cement additive

Coupled simulations of the Indian monsoon intraseasonal oscillation using a fine-resolution mixed-layer ocean model

The intraseasonal variability (ISV) of the Indian summer monsoon is dominated by a 30–50 day oscillation between “active” and “break” events of enhanced and reduced rainfall over the subcontinent, respectively. These organized convective events form in the equatorial Indian Ocean and propagate north to India. Atmosphere–ocean coupled processes are thought to play a key role the intensity and propagation of these events. A high-resolution, coupled atmosphere–mixed-layer-oceanmodel is assembled: HadKPP. HadKPP comprises the Hadley Centre Atmospheric Model (HadAM3) and the K Profile Parameterization (KPP) mixed-layer ocean model. Following studies that upper-ocean vertical resolution and sub-diurnal coupling frequencies improve the simulation of ISV in SSTs, KPP is run at 1 m vertical resolution near the surface; the atmosphere and ocean are coupled every three hours. HadKPP accurately simulates the 30–50 day ISV in rainfall and SSTs over India and the Bay of Bengal, respectively, but suffers from low ISV on the equator. This is due to the HadAM3 convection scheme producing limited ISV in surface fluxes. HadKPP demonstrates little of the observed northward propagation of intraseasonal events, producing instead a standing oscillation. The lack of equatorial ISV in convection in HadAM3 constrains the ability of KPP to produce equatorial SST anomalies, which further weakens the ISV of convection. It is concluded that while atmosphere–ocean interactions are undoubtedly essential to an accurate simulation of ISV, they are not a panacea for model deficiencies. In regions where the atmospheric forcing is adequate, such as the Bay of Bengal, KPP produces SST anomalies that are comparable to the Tropical Rainfall Measuring Mission Microwave Imager (TMI) SST analyses in both their magnitude and their timing with respect to rainfall anomalies over India. HadKPP also displays a much-improved phase relationship between rainfall and SSTs over a HadAM3 ensemble forced by observed SSTs, when both are compared to observations. Coupling to mixed-layer models such as KPP has the potential to improve operational predictions of ISV, particularly when the persistence time of SST anomalies is shorter than the forecast lead time.