Conditional silencing of topoisomerase I gene of Mycobacterium tuberculosis validates its essentiality for cell survival

Topoisomerases are an important class of enzymes for regulating the DNA transaction processes. Mycobacterium tuberculosis (Mtb) is one of the most formidable pathogens also posing serious challenges for therapeutic interventions. The organism contains only one type IA topoisomerase (Rv3646c), offering an opportunity to test its potential as a candidate drug target. To validate the essentiality of M.tuberculosis topoisomerase I (TopoI(Mt)) for bacterial growth and survival, we have generated a conditionally regulated strain of topoI in Mtb. The conditional knockdown mutant exhibited delayed growth on agar plate. In liquid culture, the growth was drastically impaired when TopoI expression was suppressed. Additionally, novobiocin and isoniazid showed enhanced inhibitory potential against the conditional mutant. Analysis of the nucleoid revealed its altered architecture upon TopoI depletion. These studies establish the essentiality of TopoI for the M.tuberculosis growth and open up new avenues for targeting the enzyme.

Limited memory and the essentiality of money

This paper investigates the relationship between memory and the essentiality of money. We consider a random matching economy with a large finite population in which commitment is not possible and memory is limited in the sense that only a fraction m E(0; 1) of the population has publicly observable histories. We show that no matter how limited memory is, there exists a social norm that achieves the first best regardless of the population size. In other words, money can fail to be essential irrespective of the amount of memory in the economy. This suggests that the emphasis on limited memory as a fundamental friction for money to be essential deserves a deeper examination.

A coordination approach to the essentiality of money

The essentiality of money is commonly justi ed on e¢ ciency grounds. In this paper, we propose an alternative view on the essentiality of money. We consider an economy with llimited monitoring where agents have to coordinate on the use of two alternative technologies of exchange, money and credit. We show that although credit strictly dominates money from an e¢ ciency perspective, money is essential for coordination reasons. If agents are patient, the region of parameters where they coordinate in the use of money strictly contains the region of parameters where they coordinate in the use of credit

In silico network topology-based prediction of gene essentiality

The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which could predict gene essentiality with high accuracy would be of great value. We present here a novel computational approach, called NTPGE (Network Topology-based Prediction of Gene Essentiality), that relies on the network topology features of a gene to estimate its essentiality. The first step of NTPGE is to construct the integrated molecular network for a given organism comprising protein physical, metabolic and transcriptional regulation interactions. The second step consists in training a decision-tree-based machine-learning algorithm on known essential and non-essential genes of the organism of interest, considering as learning attributes the network topology information for each of these genes. Finally, the decision-tree classifier generated is applied to the set of genes of this organism to estimate essentiality for each gene. We applied the NTPGE approach for discovering the essential genes in Escherichia coli and then assessed its performance. (C) 2007 Elsevier B.V. All rights reserved.

Essentiality: More with less

Manifesto, idea, light, space.

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Background: Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results: We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion: The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.

A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

Background: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis. Results: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration. Conclusions: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.

Plasmodium berghei glycine cleavage system T-protein is non-essential for parasite survival in vertebrate and invertebrate hosts

T-protein, an aminomethyltransferase, represents one of the four components of glycine cleavage system (GCS) and catalyzes the transfer of methylene group from H-protein intermediate to tetrahydrofolate (THF) forming N-5, N-10-methylene THF (CH2-THF) with the release of ammonia. The malaria parasite genome encodes T-, H- and L-proteins, but not P-protein which is a glycine decarboxylase generating the aminomethylene group. A putative GCS has been considered to be functional in the parasite mitochondrion despite the absence of a detectable P-protein homologue. In the present study, the mitochondrial localization of T-protein in the malaria parasite was confirmed by immunofluorescence and its essentiality in the entire parasite life cycle was studied by targeting the T-protein locus in Plasmodium berghei (Pb). PbT knock out parasites did not show any growth defect in asexual, sexual and liver stages indicating that the T-protein is dispensable for parasite survival in vertebrate and invertebrate hosts. The absence of P-protein homologue and the non-essentiality of T protein suggest the possible redundancy of GCS activity in the malaria parasite. Nevertheless, the H- and L-proteins of GCS could be essential for malaria parasite because of their involvement in alpha-lcetoacid dehydrogenase reactions. (C) 2014 Elsevier B.V. All rights reserved.

Structural Basis for Feed-Forward Transcriptional Regulation of Membrane Lipid Homeostasis in Staphylococcus aureus

11 p.

O direito humano de acesso à internet

O tema da dissertação é o direito humano de acesso à internet. O primeiro capítulo busca afirmar a existência desse direito e seu caráter essencial. Para isso, são apresentados fundamentos de quatro espécies. O primeiro é de direito internacional dos direitos humanos e baseia-se na análise de três documentos da Organização das Nações Unidas. O segundo é material e procura demonstrar que a internet tornou-se um instrumento indispensável à realização de diversos deveres e direitos, muitos deles humanos. Dessa forma, o acesso deve ser considerado um direito em si, dotado do mesmo status jurídico dos direitos dele dependentes. O terceiro fundamento é filosófico. Ressalta-se o aspecto comunitário da internet e demonstra-se que há um cidadão virtual que é titular de direitos e deveres na rede. Nesse momento, com base na lição de Hannah Arendt, é afirmado que se há uma dimensão digital da cidadania, deve haver um direito a adquiri-la, o que se dá pelo direito de acesso à internet. O quarto fundamento é positivo e direciona-se especificamente ao reconhecimento de um direito fundamental de acesso à internet na ordem constitucional brasileira, decorrente e não escrito. Após, é feito um estudo de direito comparado, analisando-se como a questão tem sido tratada pela lei e pela jurisprudência de diversos países. Ao final do primeiro capítulo, são apresentadas e refutadas as objeções mais comuns ao reconhecimento do direito humano de acesso à internet, incluindo a questão dos custos do direito. Afirmada a existência do direito, o segundo capítulo analisa seu conteúdo e seus limites jurídicos. Inicialmente, o direito é subdividido em uma dimensão de acesso à infraestrutura física e uma dimensão de acesso ao conteúdo. São apresentadas as principais políticas públicas brasileiras que visam a concretizar ambas as dimensões. Em um segundo momento, são estudadas hipóteses de violação do direito. Uma hipótese de lesão é a ausência do serviço em certas localidades. Outra hipótese é a censura virtual, que é dividida em função do método utilizado, se pelo hardware ou pelo software, e em função do agente que a realiza, se estatal ou privado. É analisada a constitucionalidade de penas de desconexão, perpétuas ou temporárias, e de medidas de interrupção total do serviço, em conjunto com a Lei 12.737/2012. São apresentados requisitos para que as filtragens de conteúdo na rede sejam lícitas. Coteja-se o estudado com o Projeto de Lei 2.126/2011, o chamado marco civil da internet. Por fim, é estudada a exigibilidade do direito com relação às duas dimensões.

Transtorno de pânico um estudo sobre as matrizes sociais de seu surgimento: a sociedade do risco e a construção contemporânea de bioidentidades

O transtorno de pânico é uma das questões preocupantes em termos de saúde coletiva. Pensamos que tal transtorno se configura como uma nova forma de adoecimento psíquico, categoria que tem penetrado em diferentes espaços sociais, e suas descrições vêm sendo incorporadas ao arcabouço identitário dos sujeitos. Problematizar as matrizes culturais da emergência e difusão deste transtorno, no campo da construção de subjetividade e de identidade, é o objetivo deste estudo. Na pós-modernidade, por um lado, nos centramos nas características do que se denomina sociedade de risco, (BECK, 1998) a qual gera sentimentos de imprevisibilidade, desenraizamento e desfiliação; por outro, juntamente com o desprestígio do ideal da interioridade, observa-se um recurso a se recorrer ao registro do corpo e da biologia como âncora subjetiva. (COSTA, 2005). Com a predominância de um cenário de incerteza e de risco permanente, cria-se uma atmosfera em que a previsibilidade e a confiabilidade são constantemente ameaçadas, Ou seja, o valor da confiança no registro da ontologia refere-se à existência de um ambiente suficientemente confiável e previsível para que os sujeitos experienciem uma constância dos ambientes de ação social e material circundante (WINNICOTT, 1963). Verificaremos, em meio a um cenário de risco ambiente, como o pânico emerge e é difundido com base em matrizes desviantes. O transtorno de pânico, pretensamente radicado no cérebro e determinado pela genética, parece ser uma das entidades às quais as pessoas aderem e ao redor das quais se agregam. Nesse sentido, defendendo que os tipos de patologia, nos quais se inclui o transtorno de pânico, podem servir também como redes de pertencimento, formas de sociabilidade que se organizam em torno de predicados físicos, tanto na esfera da normalidade quanto da patologia, entre as quais o corpo anatomofisiológico se destaca como fenômeno identitário, denominado por alguns autores de bioidentidade (ORTEGA, 2000). Humanizar o conceito transtorno de pânico, portanto, é afirmar que tais sintomas já conheceram outras utilizações. Entendendo o sujeito como um conjunto de crenças podem ser alteradas, revistas, repensadas, redimensionadas (COSTA, 1994). Ao sair da esfera da universalidade e essencialidade, típicas de classificações reducionistas no campo da psiquiatria, para a perspectiva de que existem jogos de linguagem diferentes para se referir ao pânico, percebemos que em vez de o transtorno de pânico existem os pânicos, ou seja, são plurais e diversificadas as diferentes gramáticas para se falar daquilo a que se reduz hoje essa classificação psiquiátrica.

The Essential Role of Endogenous Ghrelin in Growth Hormone Expression during Zebrafish Adenohypophysis Development

Ghrelin, a multifunctional hormone, including potent GH stimulation activity, has been suggested to be important during embryonic development. Expression of ghrelin has been confirmed in the zebrafish pancreas during embryonic stages. Interfering with ghrelin function using two specific antisense morpholino oligonucleotides causes defects during zebrafish embryonic development. In ghrelin morphants the expression of GH was abolished in zebrafish somatotropes, whereas the expression patterns of the other key molecules involved in hypothalamic-pituitary development and distinct pituitary hormones genes remain largely intact at the appropriate time during zebrafish adenohypophysis development. Effective rescue of the ghrelin morphants with exogenous ghrelin mRNA showed that the correct gene had been targeted. Moreover, by analyzing the efficiencies of the ghrelin morphants rescue experiments with various forms of exogenous mutant ghrelin mRNAs, we also demonstrated the essentiality of the form acyl-ghrelin on GH stimulation during zebrafish adenohypophysis development. Our in vivo experiments, for the first time, also provided evidence of the existence of functional obestatin in the C-terminal part of zebrafish proghrelin peptides. Our research here has demonstrated that zebrafish is a unique model for functional studies of endogenous ghrelin, especially during embryonic development. (Endocrinology 150: 2767-2774, 2009)

A time-varying controllable fault-tolerant field associative memory model and its simulation

A time-varying controllable fault-tolerant field associative memory model and the realization algorithms are proposed. On the one hand, this model simulates the time-dependent changeability character of the fault-tolerant field of human brain's associative memory. On the other hand, fault-tolerant fields of the memory samples of the model can be controlled, and we can design proper fault-tolerant fields for memory samples at different time according to the essentiality of memory samples. Moreover, the model has realized the nonlinear association of infinite value pattern from n dimension space to m dimension space. And the fault-tolerant fields of the memory samples are full of the whole real space R-n. The simulation shows that the model has the above characters and the speed of associative memory about the model is faster.

基于Stewart平台六维力传感器的分区静态标定方法

基于Stewart平台的六维力传感器具有结构紧凑、刚度大、量程宽等特点,它在工业机器人、空间站对接等领域具有广泛的应用前景。好的标定方法是正确使用传感器的基础。由于基于Stewart平台的六维力传感器是一个复杂的非线性系统,所以采用常规的线性标定方法必将带来较大的标定误差从而影响其使用性能。标定的实质是,由测量值空间到理论值空间的映射函数的确定过程。由函数逼近理论可知,当只在已知点集上给出函数值时,可用多项式或分段多项式等较简单函数逼近待定函数。基于上述思想,本文将整个测量空间划分为若干连续的子测量空间,再对每个子空间进行线性标定,从而提高了整个测量系统的标定精度。实验分析结果表明了该标定方法有效。