Data bank homology search algorithm with linear computation complexity

A new algorithm for data bank homology search is proposed. The principal advantages of the new algorithm are: (i) linear computation complexity; (ii) low memory requirements; and (iii) high sensitivity to the presence of local region homology. The algorithm first calculates indicative matrices of k-tuple 'realization' in the query sequence and then searches for an appropriate number of matching k-tuples within a narrow range in database sequences. It does not require k-tuple coordinates tabulation and in-memory placement for database sequences. The algorithm is implemented in a program for execution on PC-compatible computers and tested on PIR and GenBank databases with good results. A few modifications designed to improve the selectivity are also discussed. As an application example, the search for homology of the mouse homeotic protein HOX 3.1 is given.

The exon-intron organization of the human X-linked gene (FLN1) encoding actin-binding protein 280

We have determined the exon-intron organization of the human X-linked gene (FLN1) encoding actin-binding protein 280 (filamin), a ubiquitous protein that plays an important role in the mechanochemical activities of cells through its association with actin filaments and membrane components. The gene is composed of 47 exons spanning approximately 26 kb. The first and part of the second exon are untranslated. The actin-binding domain at the N-terminus is encoded by exons 2 to 5. The 96-amino-acid repeats corresponding to the elongated rod backbone of the protein are encoded by the remaining 42 exons: size, location, and boundaries of the exons cannot be easily correlated with the repeated structure, while sequences interrupting the repeats (the two hinge segments preceding repeats 16 and 24 and the 8-amino-acid (aa) segment interrupting the 15th repeat) were encoded by separate exons, suggesting that they may be recent additions to the X-linked protein. The 8-aa segment is encoded by exon 29, which is alternatively spliced.

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites

We developed the computer system SITEVIDEO for analysis and recognition of the functional sites in DNA and RNA molecules. It reveals contextual features essential for site function and thus enable the user to design efficient methods for recognition of the functional sites. We mainly considered only quantitative characteristics reflecting the uneven distribution of oligonucleotides in the sequences of functional sites of interest. The approach suggested makes use of available information about the hierarchical organization of the functional sites, and ensures highly precise prediction of the sites. The present analysis is concerned with the human donor and acceptor splice sites. A method for recognizing these sites in the sequences with an accuracy of approximately 90% was developed.

Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices

We present a new pairwise alignment algorithm that uses iterative statistical analysis of homologous subsequences. Apart from the classical conversion of the DOT-matrix characteristic of the Needleman-Wunsch algorithm (NW), we used only those matrix elements that corresponded to the most non-random subsequence homologies. The most reliable elements of the DOT-matrix are written to the compact competition matrices. The algorithm then searches for alignment on the base of only these matrix elements. Our algorithm has low storage and memory requirements, but provides a reliable alignment for the sequences of weak homology (or, at least for the homology regions). In such cases classical NW algorithms often produce unreliable results on the level of statistical noise due to accumulation of random matchings throughout the aligned sequences.

Methylation and sequence analysis around EagI sites: identification of 28 new CpG islands in XQ24-XQ28

Thirty-two probes for CpG islands of the distal long arm of the human X chromosome have been identified. From a genomic library of DNA of the hamster-human cell hybrid X3000.1 digested with the rare cutter restriction enzyme EagI, 53 different human clones have been isolated and characterized by methylation and sequence analysis. The characteristic pattern of DNA methylation of CpG islands at the 5' end of genes of the X chromosome has been used to distinguish between EagI sites in CpG islands versus isolated EagI sites. The sequence analysis has confirmed and completed the characterization showing that sequences at the 5' end of known genes were among the clones defined CpG islands and that the non-CpG islands clones were mostly repetitive sequences with a non-methylated or variably methylated EagI site. Thus, since clones corresponding to repetitive sequences can be easily identified by sequencing, such libraries are a very good source of CpG islands. The methylation analysis of 28 different new probes allows to state that demethylation of CpG islands of the active X and methylation of those on the inactive X chromosome are the general rule. Moreover, the finding, in all instances, of methylation differences between male and female DNA is in very strong support of the notion that most genes of the distal long arm of the X chromosome are subject to X inactivation.

The role of motile aeromonads in the fish disease, ulcerative disease syndrome (UDS)

Ulcerative Disease Syndrome (UDS) is an epizootic fish disease characterized by the presence of severe, open dermal ulcers on the head, midbody, and dorsal regions of the fish. Aeromonas hydrophila and A. sobria were recovered more often from UDS fish than other bacteria from the genera Vibrio, Alteromonas and Plesiomonas. Representative isolates of A. hydrophila, A. sobria, V. anguillarum, V. vulnificus, Alteromonas putrefaciens, and P. shigelloides taken from UDS and healthy fish were assayed for virulence-associated factors. The aeromonads produced a wide variety of hydrolytic enzymes and expressed cell surface characteristics linked to virulence whereas the other bacterial species rarely produced the same enzymes or cell surface characteristics. The role of aeromonads in UDS is believed to be opportunistic or secondary and these bacteria are thought to play an important role in this degenerative disease.

Objective and subjective dimensions of travel impedance as determinants of commuting stress

The stressful characteristics of commuting constraints are conceptualized in terms of both physical and perceptual conditions of travel impedance. This study develops and operationalizes the concept of subjective impedance, as a complement to our previously developed concept of impedance as a physically defined condition of commuting stress. The stress impacts of high-impedance commuting were examined in a study of 79 employees of two companies in the follow-up testing of a longitudinal study. Subjective impedance was overlapping but not isomorphic with physical impedance, and these two dimensions have differential relationships with health and well-being outcomes. The physical impedance construct received further confirmation in validational analyses and in predicted effects on various illness measures and job satisfaction. The newly constructed subjective impedance index was significantly related to evening home mood, residential satisfaction, and chest pain. Job change was also influenced primarily by commuting satisfaction. The results are discussed within an ecological framework emphasizing interdomain transfer effects and situational moderators of commuting stress.

Assessment and comparison of three scatter correction techniques in single photon emission computed tomography

The detection of scattered radiation is recognized as one of the major sources of error in single photon emission computed tomography (SPECT). In this work three scatter correction techniques have been assessed and compared. Scatter coefficients and parameters characteristic of each technique have been calculated through Monte Carlo simulations and experimentally measured for various source geometries. Their dependence on the source/matter distribution and their spatial non-stationarity have been described. Each of the three scatter correction methods has then been tested on several SPECT phantom studies. The three methods provided comparable results. Following scatter compensation, both image quality and quantitative accuracy improved. In particular a slight improvement in spatial resolution and a statistically significant increase in cold lesion contrast, hot lesion recovery coefficient, and signal/noise ratio have been demonstrated with all methods.

Biomedical applications of cyclotrons and review of commercially available models

The growing use of cyclotrons in biomedicine, both for clinical and research purposes and in particular for the production of short-lived radionuclides which are extremely useful in nuclear medicine diagnosis, has reached a stage in which commercial companies are able to offer several models with different performances, in order to satisfy the demand of different users. Many of these commercially produced accelerators are installed all over the world and some of them have been operating for several years, demonstrating that this category of machine has reached a high degree of reliability. A brief description of the operating principle of the cyclotron is presented, together with an illustration of its possible applications in the medical field. A list of the models presently available on the market is given and the installation problems and the criteria to be followed in the choice of a model are discussed. Finally, likely future developments in the field are briefly discussed.

[Cyclotrons in medicine. A survey of commercial models and their biomedical applications]

At present in Italy there is a great interest in the use of cyclotrons for medical applications: according to a plan of CNR (National Research Council), accelerators of this kind are going to be installed in some hospitals. After the explanation of the cyclotron operation principles, an outline is given of the possible applications with particular care for the clinical ones. An up-to-date review of commercial models so far developed is reported and finally, after a short note concerning installation problems, some suggestions are given about criteria to be followed in the choice of a model, according to the foreseen scientific program.

Quantitative radionuclide angiocardiography using gold-195m

A limitation of first-pass radionuclide angiocardiography is the limited repeatability because of the relatively long half-life of technetium-99m (Tc-99m). The feasibility, reproducibility and validity of multiple sequential quantitative first-pass studies were assessed in humans using the short-lived isotope gold-195m (Au-195m) (half-life of 30.6 seconds, 262 keV), which can be directly obtained from a generator made of its parent isotope, mercury-195m (half-life of 41.6 hours). Thirty-three subjects (13 normal volunteers and 20 cardiac patients) were studied using a large-field gamma camera equipped with a medium-energy collimator. After Au-195m intravenous injections, repeat first-pass studies were performed in the left anterior oblique projection. A left anterior oblique study was then obtained after i.v. injection of Tc-99m. Left ventricular ejection fraction calculations were performed separately by 2 observers. Reproducibility of Au-195m first-pass studies was excellent. The correlation coefficients for left ventricular ejection fraction from the first and the second Au-195m injections were 0.93 and 0.98 for observers 1 and 2, respectively. The correlation coefficients between Au-195m and Tc-99m first-pass studies were 0.95 and 0.98, respectively.