Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Task-Level Robot Learning

We are investigating how to program robots so that they learn from experience. Our goal is to develop principled methods of learning that can improve a robot's performance of a wide range of dynamic tasks. We have developed task-level learning that successfully improves a robot's performance of two complex tasks, ball-throwing and juggling. With task- level learning, a robot practices a task, monitors its own performance, and uses that experience to adjust its task-level commands. This learning method serves to complement other approaches, such as model calibration, for improving robot performance.

Computational Structure of Human Language

The central thesis of this report is that human language is NP-complete. That is, the process of comprehending and producing utterances is bounded above by the class NP, and below by NP-hardness. This constructive complexity thesis has two empirical consequences. The first is to predict that a linguistic theory outside NP is unnaturally powerful. The second is to predict that a linguistic theory easier than NP-hard is descriptively inadequate. To prove the lower bound, I show that the following three subproblems of language comprehension are all NP-hard: decide whether a given sound is possible sound of a given language; disambiguate a sequence of words; and compute the antecedents of pronouns. The proofs are based directly on the empirical facts of the language user's knowledge, under an appropriate idealization. Therefore, they are invariant across linguistic theories. (For this reason, no knowledge of linguistic theory is needed to understand the proofs, only knowledge of English.) To illustrate the usefulness of the upper bound, I show that two widely-accepted analyses of the language user's knowledge (of syntactic ellipsis and phonological dependencies) lead to complexity outside of NP (PSPACE-hard and Undecidable, respectively). Next, guided by the complexity proofs, I construct alternate linguisitic analyses that are strictly superior on descriptive grounds, as well as being less complex computationally (in NP). The report also presents a new framework for linguistic theorizing, that resolves important puzzles in generative linguistics, and guides the mathematical investigation of human language.

Preliminary Observations on Program Instability

This white paper reports emerging findings at the end of Phase I of the Lean Aircraft Initiative in the Policy focus group area. Specifically, it provides details about research on program instability. Its objective is to discuss high-level findings detailing: 1) the relative contribution of different factors to a program’s overall instability; 2) the cost impact of program instability on acquisition programs; and 3) some strategies recommended by program managers for overcoming and/or mitigating the negative effects of program instability on their programs. Because this report comes as this research is underway, this is not meant to be a definitive document on the subject. Rather, is it anticipated that this research may potentially produce a number of reports on program instability-related topics. The government managers of military acquisition programs rated annual budget or production rate changes, changes in requirements, and technical difficulties as the three top contributors, respectively, to program instability. When asked to partition actual variance in their program’s planned cost and schedule to each of these factors, it was found that the combined effects of unplanned budget and requirement changes accounted for 5.2% annual cost growth and 20% total program schedule slip. At a rate of approximately 5% annual cost growth from these factors, it is easy to see that even conservative estimates of the cost benefits to be gained from acquisition reforms and process improvements can quickly be eclipsed by the added cost associated with program instability. Program management practices involving the integration of stakeholders from throughout the value chain into the decision making process were rated the most effective at avoiding program instability. The use of advanced information technologies was rated the most effective at mitigating the negative impact of program instability.

The Perception of Subjective Surfaces

It is proposed that subjective contours are an artifact of the perception of natural three-dimensional surfaces. A recent theory of surface interpolation implies that "subjective surfaces" are constructed in the visual system by interpolation between three-dimensional values arising from interpretation of a variety of surface cues. We show that subjective surfaces can take any form, including singly and doubly curved surfaces, as well as the commonly discussed fronto-parallel planes. In addition, it is necessary in the context of computational vision to make explicit the discontinuities, both in depth and in surface orientation, in the surfaces constructed by interpolation. It is proposed that subjective surfaces and subjective contours are demonstrated. The role played by figure completion and enhanced brightness contrast in the determination of subjective surfaces is discussed. All considerations of surface perception apply equally to subjective surfaces.

Complexity of Human Language Comprehension

The goal of this article is to reveal the computational structure of modern principle-and-parameter (Chomskian) linguistic theories: what computational problems do these informal theories pose, and what is the underlying structure of those computations? To do this, I analyze the computational complexity of human language comprehension: what linguistic representation is assigned to a given sound? This problem is factored into smaller, interrelated (but independently statable) problems. For example, in order to understand a given sound, the listener must assign a phonetic form to the sound; determine the morphemes that compose the words in the sound; and calculate the linguistic antecedent of every pronoun in the utterance. I prove that these and other subproblems are all NP-hard, and that language comprehension is itself PSPACE-hard.

Bases documentales para programas de formación de directores escolares.

1. Situar contextualmente la figura del director. 2. Presentar y recomponer el marco teórico en que se inscribe la dirección escolar y analizar conceptos desde la perspectiva de los principales enfoques de la teoría organizacional: bases, aportaciones y dificultades. 3. Analizar el estado actual de la investigación en torno a la dirección escolar. 4. Revisar las publicaciones en castellano. 5. Revisar las publicaciones en otros idiomas. 6. Analizar aquellos aspectos que la investigación y la literatura consideran prioritarios.. Prospectiva histórica del tema en nuestro país y en los países de nuestro entorno cultural.. Se recompone y analiza el corpus teórico en el que se asienta el tema, tanto en España como en otros países. Se establece una amplia revisión de la literatura específica en torno a la figura del director. A continuación, se seleccionan cinco tópicos que se consideran puntuales dentro de su esfera de actuación: cambio y reforma escolar; dirección o animación pedagógica; desarrollo profesional del profesorado; revisión y supervisión escolar; relaciones con la comunidad circundante.. Bibliografía en castellano e inglés. Documentos de la base de datos ERIC. Publicaciones relacionadas con el tema y resultados de investigaciones sin publicar.. A través de un análisis comparativo, se intenta perfilar la situación práctica y real del director en España y, por comparación, en el mundo.. 1. La figura del director está sufriendo una revisión que ha de tenerse en cuenta para no anquilosar las escuelas. 2. La posición del director es clave en una serie de cuestiones cruciales para la vida educativa y profesional de la escuela. 3. La función directiva necesita tiempo y autonomía. 4. Sus funciones necesitan de una formación y readecuación constantes. 5. Para la literatura, aunque no para la legislación, se trata de una figura clave, enmarcada en contínuos dilemas, que necesita de mucha ayuda, formación y, sobre todo, redefinición de roles. 6. No puede seguir hablándose del director como término medio: cada director tiene su estilo y sus conductas, su contexto escolar y comunitario y se relaciona con unos profesionales determinados. Hay que tender a ayudar a cada uno de ellos, pero disponiendo una formación en la práctica y dotándole de los instrumentos y habilidades que necesite. 7. Es necesaria una investigación y una mayor preocupación en nuestro país por esta figura. Son muy pocos los libros y publicaciones, en general, que se ocupan de su figura y, cuando lo hacen, es un 'collage' de temas variados que enmascaran la pobreza de posicionamientos.. Se ha perseguido asentar las bases, servir de paso previo, para el desarrollo de un programa universitario serio, sistemático y moderno de formación de directores escolares. No puede caerse hoy en día en la dinámica de repetición de esquemas en una tema tan candente e importante. Hay que partir de unas bases actuales y fundamentadas en una teoría actualizada, una investigación al día y una práctica real..

Nanocrystalline Ge Flash Memories: Electrical Characterization and Trap Engineering

Conventional floating gate non-volatile memories (NVMs) present critical issues for device scalability beyond the sub-90 nm node, such as gate length and tunnel oxide thickness reduction. Nanocrystalline germanium (nc-Ge) quantum dot flash memories are fully CMOS compatible technology based on discrete isolated charge storage nodules which have the potential of pushing further the scalability of conventional NVMs. Quantum dot memories offer lower operating voltages as compared to conventional floating-gate (FG) Flash memories due to thinner tunnel dielectrics which allow higher tunneling probabilities. The isolated charge nodules suppress charge loss through lateral paths, thereby achieving a superior charge retention time. Despite the considerable amount of efforts devoted to the study of nanocrystal Flash memories, the charge storage mechanism remains obscure. Interfacial defects of the nanocrystals seem to play a role in charge storage in recent studies, although storage in the nanocrystal conduction band by quantum confinement has been reported earlier. In this work, a single transistor memory structure with threshold voltage shift, Vth, exceeding ~1.5 V corresponding to interface charge trapping in nc-Ge, operating at 0.96 MV/cm, is presented. The trapping effect is eliminated when nc-Ge is synthesized in forming gas thus excluding the possibility of quantum confinement and Coulomb blockade effects. Through discharging kinetics, the model of deep level trap charge storage is confirmed. The trap energy level is dependent on the matrix which confines the nc-Ge.

Preliminary Observations on Program Instability

This white paper reports emerging findings at the end of Phase I of the Lean Aircraft Initiative in the Policy focus group area. Specifically, it provides details about research on program instability. Its objective is to discuss high-level findings detailing: 1) the relative contribution of different factors to a program’s overall instability; 2) the cost impact of program instability on acquisition programs; and 3) some strategies recommended by program managers for overcoming and/or mitigating the negative effects of program instability on their programs. Because this report comes as this research is underway, this is not meant to be a definitive document on the subject. Rather, is it anticipated that this research may potentially produce a number of reports on program instability-related topics. The government managers of military acquisition programs rated annual budget or production rate changes, changes in requirements, and technical difficulties as the three top contributors, respectively, to program instability. When asked to partition actual variance in their program’s planned cost and schedule to each of these factors, it was found that the combined effects of unplanned budget and requirement changes accounted for 5.2% annual cost growth and 20% total program schedule slip. At a rate of approximately 5% annual cost growth from these factors, it is easy to see that even conservative estimates of the cost benefits to be gained from acquisition reforms and process improvements can quickly be eclipsed by the added cost associated with program instability. Program management practices involving the integration of stakeholders from throughout the value chain into the decision making process were rated the most effective at avoiding program instability. The use of advanced information technologies was rated the most effective at mitigating the negative impact of program instability.

Studies in stoichiometry with compositional data

Geochemical data that is derived from the whole or partial analysis of various geologic materials represent a composition of mineralogies or solute species. Minerals are composed of structured relationships between cations and anions which, through atomic and molecular forces, keep the elements bound in specific configurations. The chemical compositions of minerals have specific relationships that are governed by these molecular controls. In the case of olivine, there is a well-defined relationship between Mn-Fe-Mg with Si. Balances between the principal elements defining olivine composition and other significant constituents in the composition (Al, Ti) have been defined, resulting in a near-linear relationship between the logarithmic relative proportion of Si versus (MgMnFe) and Mg versus (MnFe), which is typically described but poorly illustrated in the simplex. The present contribution corresponds to ongoing research, which attempts to relate stoichiometry and geochemical data using compositional geometry. We describe here the approach by which stoichiometric relationships based on mineralogical constraints can be accounted for in the space of simplicial coordinates using olivines as an example. Further examples for other mineral types (plagioclases and more complex minerals such as clays) are needed. Issues that remain to be dealt with include the reduction of a bulk chemical composition of a rock comprised of several minerals from which appropriate balances can be used to describe the composition in a realistic mineralogical framework. The overall objective of our research is to answer the question: In the cases where the mineralogy is unknown, are there suitable proxies that can be substituted? Kew words: Aitchison geometry, balances, mineral composition, oxides

Avaluació de les emissions de gasos d’ efecte hivernacle a la ciutat de Girona i propostes de reeducació

En els últims 30 anys, la comunitat internacional ha anat agafant consciència dels efectes que pot tenir l’ increment de les emissions de gasos d’ efecte hivernacle (GEH). És per aquest motiu, entre d’ altres que es fan inventaris d’ emissions de GEH a nivell estatal i a gran escala. Aquest projecte té com a principal objectiu determinar i quantificar les emissions de GEH a escala local del municipi de Girona. Per tal de poder dur a terme aquest treball ha calgut buscar metodologies i softwares, que s’ han hagut d’ adaptar a la singularitat que té Girona, sobretot pel que fa al transport. Finalment es fan propostes que s’ adapten a la problemàtica del municipi

Honoris causa

El 18 de novembre de 2008 la Universitat de Girona va investir Eric J. Hobsbawm i Miquel Roca doctors honoris causa en un acte solemne que va aplegar gairebé tres-centes persones. La rectora, Anna M. Geli, va definir aquesta manifestació acadèmica com el “compromís d’acceptar, de manera crítica i constructiva, la transmissió de saber i de coneixement del llegat dels doctors Hobsbawm i Roca Junyent”. Així mateix, va manifestar que ambdós doctors “són part del segle XX” perquè “l’han viscut i l’han explicat” i han contribuït a fer “un món més habitable i a mostrar-nosen les deficiències”

Doctor honoris causa [novembre 2008]

Parlaments de la cerimònia d’investidura llegits el dia 18 de novembre de 2008 a l’Aula Magna de la Universitat de Girona