Percutaneous intervention of old degenerated saphenous vein grafts

The treatment of failing bypass grafts is difficult because repeat surgery carries a higher mortality rate than a first operation. Percutaneous intervention is more difficult because mechanical manipulation of these soft, friable atherosclerotic plaques have been associated with a significant rate of distal embolization, myocardial infarction, late restenosis and death. Balloon angioplasty alone has proven to have serious limitations in the treatment of older degenerated saphenous vein grafts (SVG). Although directional atherectomy yielded a higher angiographic success in a randomized trial, the restenosis rate was similar, and the procedural complications higher. The transluminal extraction catheter (TEC) has also shown significant limitations for the treatment of degenerated or thrombotic vein grafts with a significant procedural complication rate. A randomized trial comparing stenting versus balloon angioplasty in focal SVG lesions showed a higher freedom from major adverse cardiovascular events in the stent group, but there was no significant difference in the angiographic restenosis rates. More recently, rheolytic thrombectomy and mechanical thrombolysis have proven useful in treating thrombotic lesions in SVG. In addition, the recent development of distal protection devices appears very promising and will probably contribute to decreased distal embolization during percutaneous revascularization of these conduits.     

Enterococcus faecalis multi-drug resistance transporters: application for antibiotic discovery

Using bioinformatics approaches, 34 potential multidrug resistance (MDR) transporter sequences representing 4 different transporter families were identified in the unannotated Enterococcus faecalis database (TIGR). A functional genomics campaign generating single-gene insertional disruptions revealed several genes whose absence confers significant hypersensitivities to known antimicrobials. We constructed specific strains, disrupted in a variety of previously unpublished, putative MDR transporter genes, as tools to improve the success of whole-cell antimicrobial screening and discovery. Each of the potential transporters was inactivated at the gene level and then phenotypically characterized, both with single disruption mutants and with 2-gene mutants built upon a delta norA deleted strain background.     

Sensitive characterization of microbial ubiquinones from biofilms by electrospray/mass spectrometry

Utilizing high-performance liquid chromatography/electrospray/tandem mass spectrometric analysis of the neutral lipid extract of microbial cells and biofilm communities, respiratory ubiquinone (UQ) (1-methyl-2-isoprenyl-3,4-dimethoxyparabenzoquinone) isoprenologues can be separated isocratically in minutes and assayed with a limit of quantification (LOQ) of 9 p.p.b. (11.1 fmol UQ₉ µL⁻¹). This corresponds to about 1.29 × 10⁷ cells of Pseudomonas putida . Highest sensitivity is achieved using flow-injection analysis with multiple reaction monitoring wherein ammoniated molecular ions of specific isoprenologues pass through quadrupole one, are collisionally dissociated in quadrupole two and identified from the product ion fragment at m/z 197.1 in quadrupole three. This assay has a repeatability of between 6% and 10% over three orders of magnitude ( r ² = 0.996). Quinone profiling based on dominant isoprenologue patterns provides taxonomic insights. Detection of prominent UQ isoprenologues indicates presence of microeukaryotes and α Proteobacteria with UQ₁₀, obligatory aerobic Gram-negative bacteria with UQ_4-14, facultative Gram-negative (and some γ Proteobacteria growing in microniches with oxygen or to a much lesser extent nitrate as a terminal electron acceptor with UQ_8, and other γ Proteobacteria with UQ₉. High sensitivity is essential as the phospholipid fatty acid (PLFA) to UQ molar ratios are 130 or greater. Previous studies have established that recovery of sediment communities with high PLFA/UQ ratios corresponded to areas of aerobic metabolism, an important consideration in bioremediation or nuclide mobilization.     

Capillary electrophoresis as a method to study DNA reassociation

To develop analytical methodology to assess the genetic complexity of a DNA sample, capillary electrophoresis with laser-induced fluorescence detection is used to monitor the annealing process of DNA samples. Coated columns are filled with an entangled polymer solution shown to optimally separate DNA through size-selective capillary electrophoresis. DNA samples are denatured by heating in a boiling water bath for approximately 10 min and then cooled to approximately 25 degrees C below the melting point of the DNA sample to initiate the reassociation process. The DNA is detected by means of the laser-induced fluorescence of intercalated ethidium bromide, which produces a substantially greater signal for double- versus single-stranded DNA. The rate of reassociation is dependent upon the rate at which complimentary strands of DNA encounter each other and the degree of repeating base sequences in the sample (hence, the diversity of the DNA). Experimental parameters also influence the reassociation rate. The effects of salt concentration and incubation temperature are presented. Traditional plots of C(o)t (C(o) = DNA concentration and t = reassociation time) versus % recovery of double-stranded DNA signal are generated for PhiX 174 Hae III digest and 50 bp stepladder DNA, individually and combined, to calculate the reassociation rate constants for these samples. Because reassociation of individual fragments is observed by the CE-LIF method, more information about the samples is available than with less specific and time-consuming traditional methods of investigating DNA reassociation.     

Targeted attenuation of electrical activity in Drosophila using a genetically modified K(+) channel

We describe here a general technique for the graded inhibition of cellular excitability in vivo. Inhibition is accomplished by expressing a genetically modified Shaker K(+) channel (termed the EKO channel) in targeted cells. Unlike native K(+) channels, the EKO channel strongly shunts depolarizing current: activating at potentials near E(K) and not inactivating. Selective targeting of the channel to neurons, muscles, and photoreceptors in Drosophila using the Gal4-UAS system results in physiological and behavioral effects consistent with attenuated excitability in the targeted cells, often with loss of neuronal function at higher transgene dosages. By permitting the incremental reduction of electrical activity, the EKO technique can be used to address a wide range of questions regarding neuronal function.     

Lung hypoplasia and neonatal death in Fgf9-null mice identify this gene as an essential regulator of lung mesenchyme

Mammalian lung develops as an evagination of ventral gut endoderm into the underlying mesenchyme. Iterative epithelial branching, regulated by the surrounding mesenchyme, generates an elaborate network of airways from the initial lung bud. Fibroblast growth factors (FGFs) often mediate epithelial-mesenchymal interactions and mesenchymal Fgf10 is essential for epithelial branching in the developing lung. However, no FGF has been shown to regulate lung mesenchyme. In embryonic lung, Fgf9 is detected in airway epithelium and visceral pleura at E10.5, but is restricted to the pleura by E12.5. We report that mice homozygous for a targeted disruption of Fgf9 exhibit lung hypoplasia and early postnatal death. Fgf9(-/-) lungs exhibit reduced mesenchyme and decreased branching of airways, but show significant distal airspace formation and pneumocyte differentiation. Our results suggest that Fgf9 affects lung size by stimulating mesenchymal proliferation. The reduction in the amount of mesenchyme in Fgf9(-/-) lungs limits expression of mesenchymal Fgf10. We suggest a model whereby FGF9 signaling from the epithelium and reciprocal FGF10 signaling from the mesenchyme coordinately regulate epithelial airway branching and organ size during lung embryogenesis.     

A computational system for simulating and analyzing arrays of biological and artificial chemical sensors

We have designed an approach for modeling olfactory pathways by which one can explore how the properties of individual receptors affect the information coding capacity of an entire system. The effect of receptor tuning breadth on system performance was explored explicitly. We presented model sensory arrays with sets of stimuli randomly and uniformly distributed in an "olfactory space". Arrays of uniformly sized model receptors responding to 25-35% of the stimuli gave the best performance as measured by the ability to capture the most information about the stimulus set. Arrays of variably sized model receptors that were both more broadly and more narrowly tuned than this optimum could, however, perform better than uniform arrays. This method and the results obtained using it suggest a framework for considering the growing body of evidence on the functional properties of individual olfactory receptor and relay neurons from a systems coding perspective.     

Comprehensive detection of genomic duplications and deletions in the DMD gene,by use of multiplex amplifiable probe hybridization

Duplications and deletions are known to cause a number of genetic disorders, yet technical difficulties and financial considerations mean that screening for these mutations, especially duplications, is often not performed. We have adapted multiplex amplifiable probe hybridization (MAPH) for the screening of the DMD gene, mutations in which cause Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy. MAPH involves the quantitative recovery of specifically designed probes following hybridization to immobilized genomic DNA. We have engineered probes for each of the 79 exons of the DMD gene, and we analyzed them by using a 96-capillary sequencer. We screened 24 control individuals, 102 patients, and 23 potential carriers and detected a large number of novel rearrangements, especially small, one- and two-exon duplications. A duplication of exon 2 alone was the most frequently occurring mutation identified. Our analysis indicates that duplications occur in 6% of patients with DMD. The MAPH technique as modified here is simple, quick, and accurate; furthermore, it is based on existing technology (i.e., hybridization, PCR, and electrophoresis) and should not require new equipment. Together, these features should allow easy implementation in routine diagnostic laboratories. Furthermore, the methodology should be applicable to any genetic disease, it should be easily expandable to cover >200 probes, and its characteristics should facilitate high-throughput screening.