New insights into small molecules inhibitors and protein-protein interactions of VirB8 : a critical conserved component of the type IV secretion system.

Les systèmes bactériens de sécrétion de type IV (T4SS) sont constitués d’un ensemble de 8 à 12 protéines conservées. Ces dernières sont utilisées lors de la translocation de protéines, la translocation de complexes ADN-protéines mais aussi pour le transport de ces derniers au travers de la membrane cellulaire. Les T4SS, en tant que facteurs de virulence pour beaucoup de pathogènes comme Brucella suis, sont donc d’excellents modèles cibles pour le développement de médicaments d’antivirulence. Ces médicaments, en privant le pathogène de son facteur essentiel de virulence : le T4SS, constituent une alternative ou encore une amélioration des traitements antibiotiques utilisés actuellement. VirB8, un facteur d’assemblage conservé dans le T4SS, forme des dimères qui sont importants pour la fonction des T4SS dans ces pathogènes. De par ses interactions multiples, VirB8 est un excellent modèle pour l’analyse des facteurs d’assemblage mais aussi en tant que cible de médicaments qui empêcheraient son interaction avec d’autres protéines et qui, in fine, désarmeraient les bactéries en les privant de leur fonctions essentielles de virulence. À ce jour, nous savons qu’il existe un équilibre monomère-dimère et un processus d’homodimerization de VirB8 dont l’importance est vitale pour la fonctionnement biologique des T4SSs. En se basant sur des essais quantitatifs d’interaction, nous avons identifié (i) des sites potentiels d’interaction avec d’autres protéines VirB du T4SS mais aussi (ii) isolé des petites molécules inhibitrices afin de tester la fonction protéique de VirB8. Afin de déterminer les acides aminés importants pour l’hétérodimérization de VirB8 avec VirB10, nous avons effectué des expériences de mutagenèse aléatoire, de phage display et d’arrimage moléculaire in silico. Ces expériences ont démontré l’importance de trois acides aminés localisés sur le feuillet β : R160, S162, T164 et I165. Ces derniers seraient importants pour l’association de VirB8 avec VirB10 étant donné que leur mutagenèse entraine une diminution de la formation du complexe VirB8-VirB10. L’objectif actuel de notre projet de recherche est de pouvoir mieux comprendre mais aussi d’évaluer le rôle de VirB8 dans l’assemblage du T4SS. Grace à un méthode de criblage adaptée à partir de la structure de VirB8, nous avons pu identifié une petite molécule inhibitrice BAR-068, qui aurait un rôle prometteur dans l’inhibition du T4SS. Nous avons utilisé la spectroscopie par fluorescence, l’essai à deux hybrides, le cross-linking et la cristallographie afin de déterminer le mécanisme d'interaction existant entre VirB8 et BAR-068. Ces travaux pourraient permettre de nombreuses avancées, notamment en termes de compréhension des mécanismes d’inhibition du T4SS. Notre objectif ultime est de pouvoir caractériser la séquence d’évènements essentiels à l’assemblage et au fonctionnement du T4SS. De manière globale, notre projet de recherche permettrait de révéler les grands principes d’assemblage des protéines membranaires, les processus de sécrétion de protéines chez les bactéries mais aussi de proposer une nouvelle stratégie lors du développement de drogues antimicrobiennes.

Studies on the Vertical Structure of Horizontal Wind Variability in the Surface Boundary Layer Over Sriharikota

The present study on the vertical structure of horizontal wind variability in the surface boundary layer over Sriharikota. Based on clock wind speed and direction measuring meteorological tower facility from seven levels in the 100 m layer. The study on wind variability and elliptical approximation of wind hodographs investigated for this tropical coastal station established that Sriharikota is of meso-scale weather entity. Wind variability ratio increases from lower levels to upper levels. In South West monsoon months the station is of high ratio values and it gets affected with meso-scale weather features like thunderstorms. Average total shears are observed greater values than scalar shears. Scalar shears are high in the lowest shear levels compared to upper levels. Semi diurnal types of oscillation in average total shears are found in south west monsoon months. During cyclonic storm passage it is observed that there can be significant difference in mean wind speed from 10 m to 100 m level, but it is not so for peak wind speeds. The variations in wind variability ratio in different months is clearly depicted its strong link to define meso-scale or synoptic –scale forcing domination for this station. Meso-scale forcing is characterized by diurnal wind variability and synoptic- scale forcing by interdiurnal wind variability.

Three Component Mannich Reaction and 1,5-Benzodiazepine Synthesis Catalyzed by a Tetranitrile-Silver Complex

This manuscript describes the first example of silver ion complex of a dendritic tetranitrile ligand catalyzed one-pot three component Mannich reaction and 1,5-benzodiazepine synthesis. The catalyst can be separated from the products by a change in the solvent. The catalyst is reusable.

Studies on the Characteristics of Vertical Circulation and Equatorial Waves using Indian MST Radar

The aim of the present study is to understand the characteristics and properties of different wave modes and the vertical circulation pattern in the troposphere and lower stratosphere over Indian region using data obtained from the Indian Mesosphere-Stratosphere Troposphere (MST) radar, National Center for Environmental Prediction/National Centres of Atmospheric Research (NCEP/NCAR) reanalysed data and radiosonde observations.Studies on the vertical motion in monsoon Hadley circulation are carried out and the results are discussed . From the analysis of MST radar data, an overall picture of vertical motion of air over Indian region is explained and noted that there exists sinking motion both during winter and summer. Besides, the study shows that there is an anomalous northerly wind in the troposphere over the southern peninsular region during southwest monsoon season.The outcome of the study on intrusion of mid-latitude upper tropospheric trough and associated synoptic-scale vertical velocity over the tropical Indian latitudes are reported and discussed . It shows that there is interaction between north Indian latitudes and tropical easterly region, when there is an eastward movement of Western Disturbance across the country. It explains the strengthening of westerlies and a change of winter westerlies into easterlies in the tropical troposphere and lower stratosphere. The divergence field computed over the MST radar station shows intensification in the downward motion in association with the synoptic systems of the northwest Indian region.

Studies on Metallocene Polyolefin and Polyvinyl Chloride for Blood and Blood Component Storage Applications

Plasticized poly(vinyl chloride) (pPVC), although a major player in the medical field, is at present facing lot of criticism due to some of its limitations like the leaching out of the toxic plasticizer, di ethylhexyl phthalate (DEHP) to the medium and the emission of an environmental pollutant,dioxin gas,at the time of the post use disposal of PVC Products by incineration. Due to these reasons, efforts are on to reduce the use of pPVC considerably in the medical field and to find viable alternative materials. The present study has been undertaken in this context to find a suitable material for the manufacture of medical aids in place of pPVC. The main focus of this study has been to find out a non-DEHP material as plasticizer for pPVC and another suitable material for the complete repalcement of pPVC for blood/ blood component storage applications.Two approaches have been undertaken for this purpose-(1)the controversial plasticizer, DEHP has been partially replaced by polymeric plasticizers(2) an alternative material, namely, metallocene polyolefin (mPO) has been used and suitably modified to match the properties of flexible PVC used for blood and blood component storage applications.

Investigations on nanosecond laser produced plasma in air from the multi-component material YBa2Cu3O7

The laser produced plasma from the multi-component target YBa2CU3O7 was analyzed using Michelson interferometry and time resolved emission spectroscopy. The interaction of 10 ns pulses of 1.06 mum radiation from a Q-switched Nd:YAG laser at laser power densities ranging from 0.55 GW cm-2 to 1.5 GW cm-2 has been studied. Time resolved spectral measurements of the plasma evolution show distinct features at different points in its temporal history. For a time duration of less than 55 ns after the laser pulse (for a typical laser power density of 0.8 GW cm-2, the emission spectrum is dominated by black-body radiation. During cooling after 55 ns the spectral emission consists mainly of neutral and ionic species. Line averaged electron densities were deduced from interferometric line intensity measurements at various laser power densities. Plasma electron densities are of the order of 1017 cm-3 and the plasma temperature at the core region is about 1 eV. The measurement of plasma emission line intensities of various ions inside the plasma gave evidence of multiphoton ionization of the elements constituting the target at low laser power densities. At higher laser power densities the ionization mechanism is collision dominated. For elements such as nitrogen present outside the target, ionization is due to collisions only.

Studies on taxonomy and ecology of Mysidacea from the EEZ of India

Members of the order Mysidacea are important component in marine and estuarine plankton inhabiting all regions of the oceans. There are many brackish water species and few species occur in fresh water, some have become adapted to the specialized environments of caves and wells. They are omnivores, responsible for remineralisation of a substantial portion of the detritus in the water column. They form an important link in the food chain (between microbial producers and secondary consumers) and therefore play a major role in the cycling of energy within the aquatic ecosystem. In tropical and subtropical waters, swarms of mysids are exploited commercially and marketed as preserved cooked food. Mysids have been used in fish farming as live feed resource. They are also excellent experimental organism, extremely useful in the studies of potential impact of various pollutants in the aquatic environment. Mysids are also used in wood pulp effluent plants.Considering the significant role of mysids in the productivity of tropical and coastal ecosystems,the present study has been undertaken to extend our knowledge on the systematics, species composition, distribution,abundance and ecology of mysid fauna of the Indian EEZ and adjoining areas. The present study therefore will undoubtedly fumish valuable information on Mysidacea of the Indian waters.

Integer filling facfor phases and isospin in vertical diatomic artificial molecules

Integer filling factor phases of many-electron vertically coupled diatomic artificial quantum dot molecules are investigated for different values of the interdot coupling. The experimental results are analyzed within local-spin density functional theory for which we have determined a simple lateral confining potential law that can be scaled for the different coupling regimes, and Hartree-Fock theory. Maximum density droplets composed of electrons in both bonding and antibonding or just bonding states are revealed, and interesting isospin-flip physics appears for weak interdot coupling when the systematic depopulation of antibonding states leads to changes in isospin.

Studies on the horizontal and vertical distribution of clouds and their impact on energetics of the Atmosphere over the Indian Region

Motivation for the present study is to improve the scienti c understanding on the prominent gap areas in the average three-dimensional distribution of clouds and their impact on the energetics of the earth-atmosphere system. This study is focused on the Indian subcontinent and the surrounding oceans bound within the latitude-longitude bands of 30 S to 30 N and 30 E to 110 E. Main objectives of this study are to : (i) estimate the monthly and seasonal mean vertical distributions of clouds and their spatial variations (which provide the monthly and seasonal mean 3-dimensional distributions of clouds) using multi-year satellite data and investigate their association with the general circulation of the atmosphere, (ii) investigate the characteristics of the `pool of inhibited cloudiness' that appear over the southwest Bay of Bengal during the Asian summer monsoon season (revealed by the 3-dimensional distribution of clouds) and identify the potential mechanisms for its genesis, (iii) investigate the role of SST and atmospheric thermo-dynamical parameters in regulating the vertical development and distribution of clouds, (iv) investigate the vertical distribution of tropical cirrus clouds and their descending nature using lidar observations at Thiruvananthapuram (8.5 N, 77 E), a tropical coastal station at the southwest Peninsular India, and (v) assessment of the impact of clouds on the energetics of the earth-atmosphere system, by estimating the regional seasonal mean cloud radiative forcing at top-of-the-atmosphere (TOA) and latent heating of the atmosphere by precipitating clouds using satellite data

An Efficient Multi-component Synthesis of 6-Amino-3-methyl-4-Aryl-2,4- dihydropyrano[2,3-c]Pyrazole-5-carbonitriles

Multi-component reactions are effective in building complex molecules in a single step in a minimum amount of time and with facile isolation procedures; they have high economy1–7 and thus have become a powerful synthetic strategy in recent years.8–10 The multicomponent protocols are even more attractive when carried out in aqueous medium. Water offers several benefits, including control over exothermicity, and the isolation of products can be carried out by single phase separation technique. Pyranopyrazoles are a biologically important class of heterocyclic compounds and in particular dihydropyrano[2,3-c]pyrazoles play an essential role in promoting biological activity and represent an interesting template in medicinal chemistry. Heterocyclic compounds bearing the 4-H pyran unit have received much attention in recent years as they constitute important precursors for promising drugs.11–13 Pyrano[2,3-c]pyrazoles exhibit analgesic,14 anti-cancer,15 anti-microbial and anti-inflammatory16 activity. Furthermore dihydropyrano[2,3-c]pyrazoles show molluscidal activity17,18 and are used in a screening kit for Chk 1 kinase inhibitor activity.19,20 They also find applications as pharmaceutical ingredients and bio-degradable agrochemicals.21–29 Junek and Aigner30 first reported the synthesis of pyrano[2,3-c]pyrazole derivatives from 3-methyl-1-phenylpyrazolin-5-one and tetracyanoethylene in the presence of triethylamine. Subsequently, a number of synthetic approaches such as the use of triethylamine,31 piperazine,32 piperidine,33 N-methylmorpholine in ethanol,34 microwave irradiation,35,36 solvent-free conditions,37–39 cyclodextrins (CDs),40 different bases in water,41 γ -alumina,42 and l-proline43 have been reported for the synthesis of 6-amino-4-alkyl/aryl-3-methyl- 2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitriles. Recently, tetraethylammonium bromide (TEABr) has emerged as mild, water-tolerant, eco-friendly and inexpensive catalyst. To the best of our knowledge, quaternary ammonium salts, more specifically TEABr, have notbeen used as catalysts for the synthesis of pyrano[2,3-c]pyrazoles, and we decided to investigate the application of TEABr as a catalyst for the synthesis of a series of pyrazole-fused pyran derivatives via multi-component reactions

Spectral clustering independent component analysis for tissue classification from brain MRI

A spectral angle based feature extraction method, Spectral Clustering Independent Component Analysis (SC-ICA), is proposed in this work to improve the brain tissue classification from Magnetic Resonance Images (MRI). SC-ICA provides equal priority to global and local features; thereby it tries to resolve the inefficiency of conventional approaches in abnormal tissue extraction. First, input multispectral MRI is divided into different clusters by a spectral distance based clustering. Then, Independent Component Analysis (ICA) is applied on the clustered data, in conjunction with Support Vector Machines (SVM) for brain tissue analysis. Normal and abnormal datasets, consisting of real and synthetic T1-weighted, T2-weighted and proton density/fluid-attenuated inversion recovery images, were used to evaluate the performance of the new method. Comparative analysis with ICA based SVM and other conventional classifiers established the stability and efficiency of SC-ICA based classification, especially in reproduction of small abnormalities. Clinical abnormal case analysis demonstrated it through the highest Tanimoto Index/accuracy values, 0.75/98.8%, observed against ICA based SVM results, 0.17/96.1%, for reproduced lesions. Experimental results recommend the proposed method as a promising approach in clinical and pathological studies of brain diseases

Brain Tissue Classification from Multispectral MRI by Wavelet based Principal Component Analysis

In this paper, we propose a multispectral analysis system using wavelet based Principal Component Analysis (PCA), to improve the brain tissue classification from MRI images. Global transforms like PCA often neglects significant small abnormality details, while dealing with a massive amount of multispectral data. In order to resolve this issue, input dataset is expanded by detail coefficients from multisignal wavelet analysis. Then, PCA is applied on the new dataset to perform feature analysis. Finally, an unsupervised classification with Fuzzy C-Means clustering algorithm is used to measure the improvement in reproducibility and accuracy of the results. A detailed comparative analysis of classified tissues with those from conventional PCA is also carried out. Proposed method yielded good improvement in classification of small abnormalities with high sensitivity/accuracy values, 98.9/98.3, for clinical analysis. Experimental results from synthetic and clinical data recommend the new method as a promising approach in brain tissue analysis.

Wavelet based Independent Component Analysis for Multispectral Brain Tissue Classification

Multispectral analysis is a promising approach in tissue classification and abnormality detection from Magnetic Resonance (MR) images. But instability in accuracy and reproducibility of the classification results from conventional techniques keeps it far from clinical applications. Recent studies proposed Independent Component Analysis (ICA) as an effective method for source signals separation from multispectral MR data. However, it often fails to extract the local features like small abnormalities, especially from dependent real data. A multisignal wavelet analysis prior to ICA is proposed in this work to resolve these issues. Best de-correlated detail coefficients are combined with input images to give better classification results. Performance improvement of the proposed method over conventional ICA is effectively demonstrated by segmentation and classification using k-means clustering. Experimental results from synthetic and real data strongly confirm the positive effect of the new method with an improved Tanimoto index/Sensitivity values, 0.884/93.605, for reproduced small white matter lesions

Air-gap based vertical cavity micro-opto-electro-mechanical Fabry-Perot filters

Mikrooptische Filter sind heutzutage in vielen Bereichen in der Telekommunikation unersetzlich. Wichtige Einsatzgebiete sind aber auch spektroskopische Systeme in der Medizin-, Prozess- und Umwelttechnik. Diese Arbeit befasst sich mit der Technologieentwicklung und Herstellung von luftspaltbasierenden, vertikal auf einem Substrat angeordneten, oberflächenmikromechanisch hergestellten Fabry-Perot-Filtern. Es werden zwei verschiedene Filtervarianten, basierend auf zwei verschiedenen Materialsystemen, ausführlich untersucht. Zum einen handelt es sich dabei um die Weiterentwicklung von kontinuierlich mikromechanisch durchstimmbaren InP / Luftspaltfiltern; zum anderen werden neuartige, kostengünstige Siliziumnitrid / Luftspaltfilter wissenschaftlich behandelt. Der Inhalt der Arbeit ist so gegliedert, dass nach einer Einleitung mit Vergleichen zu Arbeiten und Ergebnissen anderer Forschergruppen weltweit, zunächst einige theoretische Grundlagen zur Berechnung der spektralen Reflektivität und Transmission von beliebigen optischen Schichtanordnungen aufgezeigt werden. Auß erdem wird ein kurzer theoretischer Ü berblick zu wichtigen Eigenschaften von Fabry-Perot-Filtern sowie der Möglichkeit einer mikromechanischen Durchstimmbarkeit gegeben. Daran anschließ end folgt ein Kapitel, welches sich den grundlegenden technologischen Aspekten der Herstellung von luftspaltbasierenden Filtern widmet. Es wird ein Zusammenhang zu wichtigen Referenzarbeiten hergestellt, auf denen diverse Weiterentwicklungen dieser Arbeit basieren. Die beiden folgenden Kapitel erläutern dann ausführlich das Design, die Herstellung und die Charakterisierung der beiden oben erwähnten Filtervarianten. Abgesehen von der vorangehenden Epitaxie von InP / GaInAs Schichten, ist die Herstellung der InP / Luftspaltfilter komplett im Institut durchgeführt worden. Die Herstellungsschritte sind ausführlich in der Arbeit erläutert, wobei ein Schwerpunktthema das trockenchemische Ä tzen von InP sowie GaInAs, welches als Opferschichtmaterial für die Herstellung der Luftspalte genutzt wurde, behandelt. Im Verlauf der wissenschaftlichen Arbeit konnten sehr wichtige technische Verbesserungen entwickelt und eingesetzt werden, welche zu einer effizienteren technologischen Herstellung der Filter führten und in der vorliegenden Niederschrift ausführlich dokumentiert sind. Die hergestellten, für einen Einsatz in der optischen Telekommunikation entworfenen, elektrostatisch aktuierbaren Filter sind aus zwei luftspaltbasierenden Braggspiegeln aufgebaut, welche wiederum jeweils 3 InP-Schichten von (je nach Design) 357nm bzw. 367nm Dicke aufweisen. Die Filter bestehen aus im definierten Abstand parallel übereinander angeordneten Membranen, die über Verbindungsbrücken unterschiedlicher Anzahl und Länge an Haltepfosten befestigt sind. Da die mit 357nm bzw. 367nm vergleichsweise sehr dünnen Schichten freitragende Konstrukte mit bis zu 140 nm Länge bilden, aber trotzdem Positionsgenauigkeiten im nm-Bereich einhalten müssen, handelt es sich hierbei um sehr anspruchsvolle mikromechanische Bauelemente. Um den Einfluss der zahlreichen geometrischen Strukturparameter studieren zu können, wurden verschiedene laterale Filterdesigns implementiert. Mit den realisierten Filter konnte ein enorm weiter spektraler Abstimmbereich erzielt werden. Je nach lateralem Design wurden internationale Bestwerte für durchstimmbare Fabry-Perot-Filter von mehr als 140nm erreicht. Die Abstimmung konnte dabei kontinuierlich mit einer angelegten Spannung von nur wenigen Volt durchgeführt werden. Im Vergleich zu früher berichteten Ergebnissen konnten damit sowohl die Wellenlängenabstimmung als auch die dafür benötigte Abstimmungsspannung signifikant verbessert werden. Durch den hohen Brechungsindexkontrast und die geringe Schichtdicke zeigen die Filter ein vorteilhaftes, extrem weites Stopband in der Größ enordnung um 550nm. Die gewählten, sehr kurzen Kavitätslängen ermöglichen einen freien Spektralbereich des Filters welcher ebenfalls in diesen Größ enordnungen liegt, so dass ein weiter spektraler Einsatzbereich ermöglicht wird. Während der Arbeit zeigte sich, dass Verspannungen in den freitragenden InPSchichten die Funktionsweise der mikrooptischen Filter stark beeinflussen bzw. behindern. Insbesondere eine Unterätzung der Haltepfosten und die daraus resultierende Verbiegung der Ecken an denen sich die Verbindungsbrücken befinden, führte zu enormen vertikalen Membranverschiebungen, welche die Filtereigenschaften verändern. Um optimale Ergebnisse zu erreichen, muss eine weitere Verbesserung der Epitaxie erfolgen. Jedoch konnten durch den zusätzlichen Einsatz einer speziellen Schutzmaske die Unterätzung der Haltepfosten und damit starke vertikale Verformungen reduziert werden. Die aus der Verspannung resultierenden Verformungen und die Reaktion einzelner freistehender InP Schichten auf eine angelegte Gleich- oder Wechselspannung wurde detailliert untersucht. Mittels Weisslichtinterferometrie wurden lateral identische Strukturen verglichen, die aus unterschiedlich dicken InP-Schichten (357nm bzw. 1065nm) bestehen. Einen weiteren Hauptteil der Arbeit stellen Siliziumnitrid / Luftspaltfilter dar, welche auf einem neuen, im Rahmen dieser Dissertation entwickelten, technologischen Ansatz basieren. Die Filter bestehen aus zwei Braggspiegeln, die jeweils aus fünf 590nm dicken, freistehenden Siliziumnitridschichten aufgebaut sind und einem Abstand von 390nm untereinander aufweisen. Die Filter wurden auf Glassubstraten hergestellt. Der Herstellungsprozess ist jedoch auch mit vielen anderen Materialien oder Prozessen kompatibel, so dass z.B. eine Integration mit anderen Bauelemente relativ leicht möglich ist. Die Prozesse dieser ebenfalls oberflächenmikromechanisch hergestellten Filter wurden konsequent auf niedrige Herstellungskosten optimiert. Als Opferschichtmaterial wurde hier amorph abgeschiedenes Silizium verwendet. Der Herstellungsprozess beinhaltet die Abscheidung verspannungsoptimierter Schichten (Silizium und Siliziumnitrid) mittels PECVD, die laterale Strukturierung per reaktiven Ionenätzen mit den Gasen SF6 / CHF3 / Ar sowie Fotolack als Maske, die nasschemische Unterätzung der Opferschichten mittels KOH und das Kritisch-Punkt-Trocken der Proben. Die Ergebnisse der optischen Charakterisierung der Filter zeigen eine hohe Ü bereinstimmung zwischen den experimentell ermittelten Daten und den korrespondierenden theoretischen Modellrechnungen. Weisslichtinterferometermessungen der freigeätzten Strukturen zeigen ebene Filterschichten und bestätigen die hohe vertikale Positioniergenauigkeit, die mit diesem technologischen Ansatz erreicht werden kann.