Search results for " sequence"

Addition of α-Aminonitriles to α,β-Unsaturated Carbonyl Compounds: A One-Pot Synthesis of Polysubstituted Pyrrolidines.

2003

The vinylogous addition of deprotonated N-alkyl-α-aminonitriles to α,β-unsaturated carbonyl compounds yields cyclic intermediates which can be reduced to form polysubstituted pyrrolidines in a one-pot reaction sequence. Since the cyano substituent is lost in the reduction step, the aminonitriles serve as easily accessible (N-alkylamino)-substituted carbanion equivalents.

Developments in the Synthesis of Glycopeptides Containing Glycosyl l-Asparagine, l-Serine, and l-Threonine

1994

Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses

2021

Guanine quadruplexes (G4) structures in viral genome have a key role in modulating viruses’ biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modelling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.

ElaC Encodes a Novel Binuclear Zinc Phosphodiesterase

2002

ElaC is a widespread gene found in eubacteria, archaebacteria, and mammals with a highly conserved sequence. Two human ElaC variants were recently associated with cancer (Tavtigian, S. V., Simard, J., Teng, D. H., Abtin, V., Baumgard, M., Beck, A., Camp, N. J., Carillo, A. R., Chen, Y., Dayananth, P., Desrochers, M., Dumont, M., Farnham, J. M., Frank, D., Frye, C., Ghaffari, S., Gupte, J. S., Hu, R., Iliev, D., Janecki, T., Kort, E. N., Laity, K. E., Leavitt, A., Leblanc, G., McArthur-Morrison, J., Pederson, A., Penn, B., Peterson, K. T., Reid, J. E., Richards, S., Schroeder, M., Smith, R., Snyder, S. C., Swedlund, B., Swensen, J., Thomas, A., Tranchant, M., Woodland, A. M., Labrie, F., Sko…

The importance of consecutive spells of poverty: a longitudinal poverty index

2009

Traditional measures of poverty persistence, such as ’poverty rate’ (i.e., the number of years spent in poverty upon the total number of observations) or the ’persistent-risk-of-poverty rate’, do not devote enough attention to the sequence of poverty spells. In particular, they are insufficient in underlining the different effects associated with occasional single spells of poverty and the consecutive years of poverty. Here, we propose a new index which measures the severity of poverty, taking into account the way poverty and non-poverty spells follow one another along individual life courses. The index is normalized and increases with the number of consecutive years in poverty along the se…

Serological and molecular characteristics of Vibrio vulnificus biotype 3: evidence for high clonality.

2007

Vibrio vulnificus biotype 3 has been implicated as the causative pathogen of an ongoing disease outbreak that erupted in Israel in 1996. Recent work based on multi-locus sequence typing (MLST) showed that V. vulnificus biotype 3 is genetically homogeneous. The aim of this study was to investigate the existence of subpopulations within this homogeneous biotype by characterizing the surface antigens and analysing the sequence diversity of selected outer-membrane protein (OMP)-encoding genes. Rabbit antisera were prepared against biotype 1, 2 and 3 strains. The results of the slide-agglutination test, dot-blot assay (using fresh and boiled cells), and immunoblotting of lipopolysaccharides (LPS…

S-type lectins occur also in invertebrates: high conservation of the carbohydrate recognition domain in the lectin genes from the marine sponge Geodi…

1993

The marine sponge Geodia cydonium contains several lectins. The main component, called lectin-1, is composed of three to four identical subunits. The subunits of the lectins were cloned from a cDNA library; two clones were obtained. From the deduced aa sequence of one clone, LECT-1, a mol. wt of 15,313 Da is calculated; this value is in good agreement with mass spectrometric analysis of 15,453 +/- 25 Da. The sequence of another clone, LECT-2, was analysed and the aa sequence was deduced (15,433 Da). The two subunits have a framework sequence of 38 conserved aa which are characteristic for the carbohydrate-binding site of vertebrate S-type lectins. Clustering of lectin sequences of various s…

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…

2008

Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…

Analysing Complex Life Sequence Data with Hidden Markov Modelling

2016

When analysing complex sequence data with multiple channels (dimensions) and long observation sequences, describing and visualizing the data can be a challenge. Hidden Markov models (HMMs) and their mixtures (MHMMs) offer a probabilistic model-based framework where the information in such data can be compressed into hidden states (general life stages) and clusters (general patterns in life courses). We studied two different approaches to analysing clustered life sequence data with sequence analysis (SA) and hidden Markov modelling. In the first approach we used SA clusters as fixed and estimated HMMs separately for each group. In the second approach we treated SA clusters as suggestive and …

Hierarchical structures in Complex Systems: from DNA to financial markets

2000

In this paper we discuss the concepts of short-range and long-range correlated stochastic processes and we investigate the presence of such variables in two model complex systems. The selected model systems are DNA sequences of complete genomes and financial time series of equities traded in a stock market. Specifically, by starting from our research results, we discuss the statistical properties of (i) coding and non-coding regions of DNA and (ii) equity returns and volatility in financial markets. The stylized facts about these variables are presented and discussed with a focus on the statistical tools already used and/or still needed to better characterize these model complex systems.