Biomedical subjects

F Kosari

Publications and source records attributed to F Kosari.

6 recordsLinked to original sources

PubMed2006

DNA counterion current and saturation examined by a MEMS-based solid state nanopore sensor.

Reports of DNA translocation measurements have been increasing rapidly in recent years due to advancements in pore fabrication and these measurements continue to provide insight into the physics of DNA translocations through MEMS based solid state nanopores. Specifically, it has recently been demonstrated that in addition to typically observed current blockages, enhancements in current can also be measured under certain conditions. Here, we further demonstrate the power of these nanopores for examining single DNA molecules by measuring these ionic currents as a function of the applied electric field and show that the direction of the resulting current pulse can provide fundamental insight into the physics of condensed counterions and the dipole saturation in single DNA molecules. Expanding on earlier work by Manning and others, we propose a model of DNA counterion ionic current and saturation of this current based on our experimental results. The work can have broad impact in understanding DNA sensing, DNA delivery into cells, DNA conductivity, and molecular electronics.

Biosensing Techniques↗

PubMed2004

Study design considerations in clinical outcome research of lung cancer using microarray analysis.

BACKGROUND: Prognosis following a diagnosis of primary lung cancer is very poor and varies significantly even after adjusting for known predictors. Inherent and acquired gene alterations could cause failure in lung cancer treatment and patient survival. To search for potential molecular markers with significant and independent predictive value in lung cancer survival, we applied oligo-nucleotide microarray analysis, along with patients' phenotypic profile, in a case-control study. The focus of this report is on the methodology used in the identification of potential genes as prognostic factors. METHODS: Selected from 304 patients at Mayo Clinic, 18 stage I squamous cell lung cancer patients who died within 2 years (high-aggressive) or lived beyond 5 years (low-aggressive) were included in this study. Both a one-to-one matched design (paired) and a two-group design (grouped) were utilized. Matching variables were age, gender, tumor size and grade, smoking status, and treatment. Two-GeneChip-array sets from Affymetrix (HG-U133) were used. We applied multiple analytic approaches including Dchip (Harvard University), SAM (Stanford University), ArrayTools (US National Cancer Institute), and MAS5 (Affymetrix); and integrated multiple results to generate the final candidate genes for further investigation. We evaluated the consistency across the methods and the effects of matched versus grouped design on the results. RESULTS: Using the same pre-processed data under the same criteria for type I error and fold-change in expression intensity, results are 94-100% concordant in the list of significant genes by Dchip and by ArrayTools, and 53% concordant between the paired and the grouped analysis. If using differently pre-processed data, the concordance rate is under 6% even by the same analytic tool. Combining results from all analyses, we found 23 potentially important genes that may distinguish the high- versus low-aggressive squamous cell tumors of the lung. CONCLUSION: Given the generally low consistency of results across analytic algorithms and study design, poor agreement is expected from different investigators reporting candidate genes for the same endpoint. A well-designed study with a carefully planned analytic strategy is critical. We are in the process of validating the 23 preliminary candidate genes found from this study among independent yet comparable cases.

Adult↗

PubMed1999

Cloning and functional expression of the mouse epithelial sodium channel.

The epithelial sodium channel (ENaC) plays a major role in the transepithelial reabsorption of sodium in the renal cortical collecting duct, distal colon, and lung. ENaCs are formed by three structurally related subunits, termed alpha-, beta-, and gammaENaC. We previously isolated and sequenced cDNAs encoding a portion of mouse alpha-, beta-, and gammaENaC (alpha-, beta-, and gammamENaC). These cDNAs were used to screen an oligo-dT-primed mouse kidney cDNA library. Full-length betamENaC and partial-length alpha- and gammamENaC clones were isolated. Full-length alpha- and gammamENaC cDNAs were subsequently obtained by 5'-rapid amplification of cDNA ends (5'-RACE) PCR. Injection of mouse alpha-, beta-, and gammaENaC cRNAs into Xenopus oocytes led to expression of amiloride-sensitive (K(i) = 103 nM), Na(+)-selective currents with a single-channel conductance of 4.7 pS. Northern blots revealed that alpha-, beta-, and gammamENaC were expressed in lung and kidney. Interestingly, alphamENaC was detected in liver, although transcript sizes of 9.8 kb and 3.1 kb differed in size from the 3.2-kb message observed in other tissues. A partial cDNA clone was isolated from mouse liver by 5'-RACE PCR. Its sequence was found to be nearly identical to alphamENaC. To begin to identify regions within alphamENaC that might be important in assembly of the native heteroligomeric channel, a series of functional experiments were performed using a construct of alphamENaC encoding the predicted cytoplasmic NH(2) terminus. Coinjection of wild-type alpha-, beta-, and gammamENaC with the intracellular NH(2) terminus of alphamENaC abolished amiloride-sensitive currents in Xenopus oocytes, suggesting that the NH(2) terminus of alphamENaC is involved in subunit assembly, and when present in a 10-fold excess, plays a dominant negative role in functional ENaC expression.

Amino Acid Sequence↗

PubMed1999

Mechanism of action of amiloride: a molecular prospective.

Amiloride is a prototypic inhibitor of epithelial sodium channels. Rapid progress has been made in our understanding of the structure of the sodium channel and related cation-selective channels. This work, coupled with experiments examining how selected sodium channel mutations affect amiloride binding, provides critical clues towards defining sites within the channel that bind amiloride. Residues within the channel pore and within its extracellular domain participate in amiloride binding. These results suggest that sites that interact with amiloride within the channel's extracellular domain may be in close proximity to residues within the channel's pore.

Amiloride↗

PubMed1998

Subunit stoichiometry of the epithelial sodium channel.

The epithelial Na+ Channel (ENaC) mediates Na+ reabsorption in a variety of epithelial tissues. ENaC is composed of three homologous subunits, termed alpha, beta, and gamma. All three subunits participate in channel formation as the absence of any one subunit results in a significant reduction or complete abrogation of Na+ current expression in Xenopus oocytes. To determine the subunit stoichiometry, a biophysical assay was employed utilizing mutant subunits that display significant differences in sensitivity to channel blockers from the wild type channel. Our results indicate that ENaC is a tetrameric channel with an alpha2 beta gamma stoichiometry, similar to that reported for other cation selective channels, such as Kv, Kir, as well as voltage-gated Na+ and Ca2+ channels that have 4-fold internal symmetry.

Animals↗

PubMed1995

Defining topological similarities among ion transport proteins with anti-amiloride antibodies.

The structural features of amiloride binding sites on amiloride-sensitive transport proteins have received limited characterization. An antibody that recognizes limited regions of amiloride and can mimic, in binding specificity, certain amiloride-sensitive transport proteins was used as a model to elucidate potential amino acid residue relationships that might define putative amiloride contact sites. Analysis of the structure of this antibody has allowed us to identify sequence relationships among several Na+ selective transport proteins. A structure-based relational database was employed to re-examine sequence homologies among these ion transport proteins. A search of the protein sequence databank identified representative amino acid tracts among amiloride sensitive proteins involving planar residues that might be involved in interacting with amiloride. Computer models of sites within transmembrane domains of NHE1 and NHE2 isoforms of the Na+/H+ exchanger reflective of these planar tracts indicate that amiloride probably spans two helices for interaction with the Na+/H+ exchanger. Structural analysis of this monoclonal anti-amiloride antibody appears to mimic some of the salient features of amiloride binding sites on these proteins.

Amiloride↗