Alvira : comparative genomics of viral strains

The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution

Applying a User-centred Approach to Interactive Visualization Design

Analysing users in their context of work and finding out how and why they use different information resources is essential to provide interactive visualisation systems that match their goals and needs. Designers should actively involve the intended users throughout the whole process. This chapter presents a user-centered approach for the design of interactive visualisation systems. We describe three phases of the iterative visualisation design process: the early envisioning phase, the global specification hase, and the detailed specification phase. The whole design cycle is repeated until some criterion of success is reached. We discuss different techniques for the analysis of users, their tasks and domain. Subsequently, the design of prototypes and evaluation methods in visualisation practice are presented. Finally, we discuss the practical challenges in design and evaluation of collaborative visualisation environments. Our own case studies and those of others are used throughout the whole chapter to illustrate various approaches

A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem

<div><p>A nearly complete genome sequence of <em>Candidatus</em> ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that <em>Ca.</em> ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO₂ fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of <em>Ca.</em> ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of <em>Ca.</em> ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H₂-dependent acetogens and methanogenes living in hydrothermal environments.</p> </div

The impact of point mutations in the human androgen receptor : classification of mutations on the basis of transcriptional activity

Peer reviewedPublisher PD

Physico-chemical characterization of the essential oil of Origanum majorana (L.) cultivated in a semi-arid bioclimatic stage (South-east Algeria)

The essential oils (EO) are complex volatile natural compounds,  characterized by a strong odor, produced by the plants as secondary metabolites. The composition of these last is strongly influenced by intrinsic factors twinned with the extrinsic factors such as technology, the cultivation techniques, the édapho-climatic conditions of the culture  medium, like those of the storage of vegetable drug, the techniques of treatment, etc… The extraction of essential oils (EO) of marjoram (O. majorana), by the method of hydro-distillation made it possible to obtain an average essential oil yield of about 0.61% of which the density is low. The chemical characterization by gas chromatography highlighted the wealth of this oil in Bornéol (15.50%) and Cineol (11.33%).Keywords: essential oil (EO); O. majorana L.; cineol; bornéol; Gas chromatography; secondary metabolite

Enterovirus specific anti-peptide antibodies

Enterovirus 71 (EV-71) is the main causative agent of hand, foot, and mouth disease (HFMD) which is generally regarded as a mild childhood disease. In recent years, EV71 has emerged as a significant pathogen capable of causing high mortalities and severe neurological complications in large outbreaks in Asia. A formalin-inactivated EV71 whole virus vaccine has completed phase III trial in China but is currently unavailable clinically. The high cost of manufacturing and supply problems may limit practical implementations in developing countries. Synthetic peptides representing the native primary structure of the viral immunogen which is able to elicit neutralizing antibodies can be made readily and is cost effective. However, it is necessary to conjugate short synthetic peptides to carrier proteins to enhance their immunogenicity. This review describes the production of cross-neutralizing anti-peptide antibodies in response to immunization with synthetic peptides selected from in silico analysis, generation of B-cell epitopes of EV71 conjugated to a promiscuous T-cell epitope from Poliovirus, and evaluation of the neutralizing activities of the anti-peptide antibodies. Besides neutralizing EV71 in vitro, the neutralizing antibodies were cross-reactive against several Enteroviruses including CVA16, CVB4, CVB6, and ECHO13

Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States

In the United States, serogroup Y, ST-23 clonal complex Neisseria meningitidis was responsible for an increase in meningococcal disease incidence during the 1990s. This increase was accompanied by antigenic shift of three outer membrane proteins, with a decrease in the population that predominated in the early 1990s as a different population emerged later in that decade. To understand factors that may have been responsible for the emergence of serogroup Y disease, we used whole genome pyrosequencing to investigate genetic differences between isolates from early and late N. meningitidis populations, obtained from meningococcal disease cases in Maryland in the 1990s. The genomes of isolates from the early and late populations were highly similar, with 1231 of 1776 shared genes exhibiting 100% amino acid identity and an average πN = 0.0033 and average πS = 0.0216. However, differences were found in predicted proteins that affect pilin structure and antigen profile and in predicted proteins involved in iron acquisition and uptake. The observed changes are consistent with acquisition of new alleles through horizontal gene transfer. Changes in antigen profile due to the genetic differences found in this study likely allowed the late population to emerge due to escape from population immunity. These findings may predict which antigenic factors are important in the cyclic epidemiology of meningococcal disease

DRUG POLYMORPHISM IDENTIFICATION USING FOURIER TRANSFORM-RAMAN SPECTROSCOPY: A COMPARATIVE STUDY OF LAMIVUDINE AND FINASTERIDE DRUGS

Objectives: Maintaining the quality of the pharmaceutical drug product during its shelf life is highly desirable. The crystalline form of the drug having the great thermodynamic stability is essential for the manufacturers in pharmaceutical industry in view of their profit and also for the safety of the customer. Many pharmaceutical drugs have the tendency to exhibit polymorphism which is unwanted for pharmaceutical companies, where they have experienced market shortages due to these unpredicted polymorphic and/or pseudomorphic changes. The property of a drug exhibiting more than one crystal form is considerably regarded as polymorphism and each of the crystalline form has its own physicochemical properties, namely, solubility, heat capacity, melting point, and sublimation point. To relieve this ultimate effect on the drug quality and stability, a prior detection of polymorphism in the final dosage form is highly recommended. Hence, many analytical techniques have been proposed for the detection of polymorphism in pharmaceutical drug products. Methods: Fourier transform (FT)-Raman spectrometer is used for the investigation of drug polymorphism and the instrument is advanced with charge coupled device detectors, ease of sample preparation and handling, mitigation of sub-sampling problems using different geometric laser irradiance patterns and having different optical components of Raman spectrometers. Results: In this work, we carefully studied the Raman spectral patterns for Lamivudine as well as Finasteride drug substances for the detection of polymorphism. Further, we have highlighted the advantages of FT-Raman spectroscopy over other polymorphism detection techniques. For example, Raman spectra showed invariably sharp, well resolved bands compare to IR spectra due to the minor contribution of overtone vibrations in Raman spectra, resulting in much less broadening and a better resolution of bands. Besides, Raman spectroscopy does not suffer from the sampling problems that are common in X-ray powder diffraction, where preferred orientation and specimen displacements are serious restrictions for the application of quantitative method. Conclusion: Here, in this paper, we are presented and compared the experimental results regarding the detection of polymorphism in Lamivudine and Finasteride drugs using FT-Raman spectroscopy, to illustrate the advantages of the technique in the detection of polymorphism over other techniques

C1: Uses of Administrative Data for Supporting Education Policy

Moderator: Katie Barghaus Presenters: Sonya R. Porter: Demonstrating the Use of Linked Data to Advance Education Research Chenna Reddy Cotla: Heterogeneous causal effects of perception of school safety on absenteeism and performance: A causal decision tree approach using administrative and survey data from a large school district Sally Wallace: Returns to Late Aged College Degrees Douglas Lauen: Early College High Schools at Scale: Using Administrative Data to Assess the Impacts of an Educational Intervention on Voting and Crime Wesley Greenblatt: Long-Term Effects from Early Exposure to Research: Evidence from the NIH \u27Yellow Berets\u2

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses