Cloning of human adenosine kinase cDNA: sequence similarity to microbial ribokinases and fructokinases.

Adenosine kinase catalyzes the phosphorylation of adenosine to AMP and hence is a potentially important regulator of extracellular adenosine concentrations. Despite extensive characterization of the kinetic properties of the enzyme, its primary structure has never been elucidated. Full-length cDNA clones encoding catalytically active adenosine kinase were obtained from lymphocyte, placental, and liver cDNA libraries. Corresponding mRNA species of 1.3 and 1.8 kb were noted on Northern blots of all tissues examined and were attributable to alternative polyadenylylation sites at the 3' end of the gene. The encoding protein consists of 345 amino acids with a calculated molecular size of 38.7 kDa and does not contain any sequence similarities to other well-characterized mammalian nucleoside kinases, setting it apart from this family of structurally and functionally related proteins. In contrast, two regions were identified with significant sequence identity to microbial ribokinase and fructokinases and a bacterial inosine/guanosine kinase. Thus, adenosine kinase is a structurally distinct mammalian nucleoside kinase that appears to be akin to sugar kinases of microbial origin.

Sequence similarity analysis of Escherichia coli proteins: functional and evolutionary implications.

A computer analysis of 2328 protein sequences comprising about 60% of the Escherichia coli gene products was performed using methods for database screening with individual sequences and alignment blocks. A high fraction of E. coli proteins--86%--shows significant sequence similarity to other proteins in current databases; about 70% show conservation at least at the level of distantly related bacteria, and about 40% contain ancient conserved regions (ACRs) shared with eukaryotic or Archaeal proteins. For > 90% of the E. coli proteins, either functional information or sequence similarity, or both, are available. Forty-six percent of the E. coli proteins belong to 299 clusters of paralogs (intraspecies homologs) defined on the basis of pairwise similarity. Another 10% could be included in 70 superclusters using motif detection methods. The majority of the clusters contain only two to four members. In contrast, nearly 25% of all E. coli proteins belong to the four largest superclusters--namely, permeases, ATPases and GTPases with the conserved "Walker-type" motif, helix-turn-helix regulatory proteins, and NAD(FAD)-binding proteins. We conclude that bacterial protein sequences generally are highly conserved in evolution, with about 50% of all ACR-containing protein families represented among the E. coli gene products. With the current sequence databases and methods of their screening, computer analysis yields useful information on the functions and evolutionary relationships of the vast majority of genes in a bacterial genome. Sequence similarity with E. coli proteins allows the prediction of functions for a number of important eukaryotic genes, including several whose products are implicated in human diseases.

Transcription in archaea: similarity to that in eucarya.

We present homologies between archaeal and eucaryal DNA-dependent RNA polymerase (RNAP) subunits and transcription factors. The sequences of the Sulfolobus acidocaldarius subunits D, E, and N and alignments with eucaryal homologs are presented here. The similarities between archaeal transcription factors and their eucaryal homologs TFIIB and TBP have been established in other laboratories. The archaeal RNAP subunits H, K, and N, respectively, show high sequence similarity to ABC27, ABC23, and ABC10 beta (found in all three eucaryal RNAPs); subunit D, to AC40 (common to polymerase II and polymerase III) and B44 (polymerase II); and subunit L, to AC19 and B12.5. The similarity of subunit D and its eucaryal homologs to bacterial alpha is limited to the "alpha-motif," which is also present in subunit L and its eucaryal homologs. Genes encoding homologs of the related eucaryal RNAP subunits A12.2/B12.6 and also homologs of eucaryal transcription elongation factors of the TFIIS family have been detected in Sulfolobus acidocaldarius and Thermococcus celer. In archaea, the protein is not an RNAP subunit. Together with the sequence similarities between archaeal box A-containing and eucaryal TATA box-containing promoters, this shows that the archaeal and eucaryal transcription systems are truly homologous and that they differ structurally and functionally from the bacterial transcription machinery. In contrast, however, a number of genes for the archaeal transcription apparatus are organized in clusters resembling the clusters of transcription-associated genes in Bacteria.

Propagation, structural similarity and image quality

Póster presentado en SPIE Photonics Europe, Brussels, 16-19 April 2012.

Retinal image quality assessment through a visual similarity index

Retinal image quality is commonly analyzed through parameters inherited from instrumental optics. These parameters are defined for ‘good optics’ so they are hard to translate into visual quality metrics. Instead of using point or artificial functions, we propose a quality index that takes into account properties of natural images. These images usually show strong local correlations that help to interpret the image. Our aim is to derive an objective index that quantifies the quality of vision by taking into account the local structure of the scene, instead of focusing on a particular aberration. As we show, this index highly correlates with visual acuity and allows inter-comparison of natural images around the retina. The usefulness of the index is proven through the analysis of real eyes before and after undergoing corneal surgery, which usually are hard to analyze with standard metrics.

Identity construction through phonetic crossing among young Capetonian gang members

Uncountable gangs operate in post-Apartheid South Africa, particularly in greater Cape Town, competing over turf and controlling the drug trade. Consequently, gang violence is rife in Western Cape and especially widespread in urban areas. In this paper young Capetonians’ narratives of gang violence are analyzed. In the narratives of attacks on Black or White South Africans by Coloured gang members, the Coloured narrators make use of their victims’ varieties of English, more precisely, of phonetic features. Hence, the aggressors do language crossing towards their targets when narrating their feats. Rampton (1995a:485) considers language crossing a ‘code alternation by people who are not accepted members of the group associated with the second language that they are using (code switching into varieties that are not generally thought to belong to them)’. This switching involves a transgression of social or ethnic boundaries that allows the young gangsters to construct, negotiate, uphold and manage their social identities, as language still functions as an utterly important identity marker in post-Apartheid South Africa.

Similarity Measurement of Biological Signals Using Dynamic Time Warping Algorithm

The problem of similarity measurement of biological signals is considered on this article. The dynamic time warping algorithm is used as a possible solution. A short overview of this algorithm and its modifications are given. Testing procedure for different modifications of DTW, which are based on artificial test signals, are presented.

The Lyon phonetic manual,

This printing includes an introductory notice with the Directors and Officers of the Association listed.

The psychological basis of phonetic law and analogy.

"Reprinted from the Publications of the Modern language association of America, vol. IX, no. 2."

Hindustani self-taught. With English phonetic pronunciation. Containing alphabet and pronunciation - vocabularies - idiomatic phrases & dialogues - travel talk - military, legal, religious, commercial, shooting, fishing terms - Indian titles, castes, servants - money, weights, measures.

Mode of access: Internet.

Marsh's manual of reformed phonetic short-hand: being a complete guide to the best system of phonography and verbatim reporting.

Mode of access: Internet.

American manual of phonography a complete guide to the acquisition of Pitman's phonetic shorthand.

Mode of access: Internet.

Descriptions of cairns, cromlechs, kistvaens, and other Celtic, druidical, or Scythian monuments in the Dekhan. To which are added, Results of examination of a group of ancient cairns on Twizell Moor, in Northumberland, exhibiting similarity in construction and contents with cairns in the Dekhan.

"From the Transactions of the Royal Irish academy, volume XXIV.--Antiquities."

A manual of phonography, or, Writing by sound : a natural method of writing by signs that represent the sounds of language, and adapted to the English language as a complete system of phonetic shorthand /

Mode of access: Internet.