PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 8808573

Object-oriented data handler for sequence analysis software development.

A A Ptitsyn·D A Grigorovich
View original source ↗Export metadata ↓

Abstract

We report an object-oriented data handler and supplementary tools for the development of molecular genetics application software for various sequence analyses. Our data handler has a flexible and expandable format that supports the most common data types for molecular genetic software. New data types can be constructed in an object-oriented manner from the basic units. The data handler includes an object library, a format-converting program and a viewer that can visualize simultaneously the data contained in several files to construct a general picture from separate data. This software has been implemented on an IBM PC-compatible personal computer.

Explore related subjects

Atrial Natriuretic FactorBase SequenceDNAData Interpretation, StatisticalDatabases, FactualEvaluation Studies as TopicHumansMicrocomputersMolecular BiologyMolecular Sequence DataProtein PrecursorsSequence Analysis, DNASoftwareJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

A A Ptitsyn, D A Grigorovich. 1995. Object-oriented data handler for sequence analysis software development.. https://doi.org/10.1093/bioinformatics%2F11.6.583

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed1999

A novel cGMP-regulated K+ channel in immortalized human kidney epitheliall cells (IHKE-1).

1. K+ channels from the apical membrane of immortalized human kidney epithelial (IHKE-1) cells were investigated in the cell-attached membrane configuration as well as in excised membranes using the patch clamp technique. 2. In cell-attached membrane patches the open probability (Po) of the K+ channel was 0.42 +/- 0.06 (mean +/- s.e.m. , n = 22) and its conductance was 94 +/- 5 pS with 145 mM K+ in the pipette (n = 25). In excised membrane patches the Po of the channel was 0.55 +/- 0.03 (n = 86) and its conductance was 65 +/- 2 pS (n = 68) with 145 mM K+ on one side of the membrane and 3.6 mM K+ on the other. The I-V curve of the K+ channel was not rectifying. 3. The channel was inhibited by several blockers of K+ channels such as 1 mM Ba2+ (cell-attached membrane: 78 +/- 8 %, n = 9; excised: 80 +/- 4 %, n = 26), 10 mM TEA+ (excised inside-out: 48 +/- 5 %, n = 34; excised outside-out: 100 +/- 0 %, n = 26), 0.1 mM verapamil (excised: 73 +/- 9 %, n = 12), and 10 nM charybdotoxin (excised outside-out: 67 +/- 9 %, n = 9). 4. The K+ channel was activated by depolarization and rising cytosolic Ca2+. Half-maximal activity occurred at a cytosolic Ca2+ concentration of 200 nM. In the cell-attached membrane configuration the K+ channel was inhibited in a concentration-dependent manner by atrial natriuretic peptide (ANP). Powas blocked equally well by 10 nM ANP (52 +/- 7 %, n = 10), brain natriuretic peptide (BNP; 37 +/- 11 %, n = 6) and C-type natriuretic peptide (CNP; 44 +/- 13 %, n = 8). 8-Bromoguanosine 3',5' cyclic monophosphate (8-Br-cGMP, 0.1 mM) also inhibited Poof this K+ channel, by 70 +/- 10 % (n = 5). 5. In excised membrane patches cGMP inhibited Po of this K+ channel in a concentration-dependent manner. The first significant effects were measured at a concentration of 1 microM (22 +/- 7 %, n = 6), and greatest effects were obtained at 0.1 mM (34 +/- 5 %, n = 15). cAMP (0.1 mM, n = 5) as well as GTP (0.1 mM, n = 5) had no significant effects on Po of this K+ channel. ATP (0.1 mM) had a weak inhibitory effect (17 +/- 5 %, n = 14). Addition of Mg-ATP to cGMP did not increase the inhibitory effect (30 +/- 4 %, n = 14). KT5823 (1 microM), a specific inhibitor of cGMP-dependent protein kinases, did not significantly alter the cGMP-induced reduction in Po of the K+ channel in three excised membrane patches. 6. The results present the first electrophysiological characterization of a mammalian K+ channel that is directly regulated by cGMP.

Atrial Natriuretic Factor↗
PubMed1999

Functional expression of components of the natriuretic peptide system in human ocular nonpigmented ciliary epithelial cells.

The expression of the natriuretic peptide system in the human ocular ciliary epithelium (CE) and in cultured nonpigmented (NPE) ciliary epithelial cells was examined. By RT-PCR and DNA sequencing, we demonstrated that the CE and NPE cells express mRNA for (i) ANP; (ii) BNP; (iii) NPR-A, NPR-B, and NPR-C receptors; and (iv) the neutral endopeptidase 24.11. Radioimmunoassay results indicate that BNP is secreted by cultured NPE cells at much higher levels than ANP. NPR-A and NPR-B receptors elicited a cGMP response to ANP, BNP, and CNP, in a rank order of potency (CNP >> ANP >/= BNP), indicative that the NPR-B receptor is predominant in NPE cells. A71915, an inhibitor of NPR-A activity, attenuated (65-75%) cGMP response to ANP and BNP, but not to CNP. C-ANP4-23 elicited an inhibitory effect (30-37%) on basal levels of cAMP in NPE cells and on forskolin NPE-treated cells, indicative that the NPR-C receptor is functional in these cells. PMA induced, in NPE cells, a long-term downregulation (75-85%) of NPR-C receptor mRNA, but not of NPR-A or NPR-B receptor mRNA, suggesting a differential regulation of NPR-C receptor mRNA via activation of PKC. Collectively, our data provide molecular evidence that all the components of the natriuretic peptide system with the exception of CNP are coexpressed in the ocular NPE ciliary epithelial cells, where they may function as local autocrine/paracrine modulators to influence eye pressure.

Atrial Natriuretic Factor↗