The role of molecular chaperonins in warm ischemia and reperfusion injury in the steatotic liver: A proteomic study

ABSTRACT: BACKGROUND: The molecular basis of the increased susceptibility of steatotic livers to warm ischemia/reperfusion (I/R) injury during transplantation remains undefined. Animal model for warm I/R injury was induced in obese Zucker rats. Lean Zucker rats provided controls. Two dimensional differential gel electrophoresis was performed with liver protein extracts. Protein features with significant abundance ratios (p < 0.01) between the two cohorts were selected and analyzed with HPLC/MS. Proteins were identified by Uniprot database. Interactive protein networks were generated using Ingenuity Pathway Analysis and GRANITE software. RESULTS: The relative abundance of 105 proteins was observed in warm I/R injury. Functional grouping revealed four categories of importance: molecular chaperones/endoplasmic reticulum (ER) stress, oxidative stress, metabolism, and cell structure. Hypoxia up-regulated 1, calcium binding protein 1, calreticulin, heat shock protein (HSP) 60, HSP-90, and protein disulfide isomerase 3 were chaperonins significantly (p < 0.01) down-regulated and only one chaperonin, HSP-1was significantly upregulated in steatotic liver following I/R. CONCLUSION: Down-regulation of the chaperones identified in this analysis may contribute to the increased ER stress and, consequently, apoptosis and necrosis. This study provides an initial platform for future investigation of the role of chaperones and therapeutic targets for increasing the viability of steatotic liver allografts.     

Molecular beacon probes of photodamage in thymine and uracil oligonucleotides

Molecular beacons (MB) are becoming more common as sequence-selective detectors of nucleic acids. Although they can easily detect single-base mismatches, they have never been used to directly detect DNA or RNA damage. To measure the degree of ultraviolet (UV) light damage in oligonucleotides, we report a novel MB approach for general detection of photoproducts in UV-irradiated rU17 and dT17 oligonucleotides. With monochromatic UV light irradiation at ca 280 nm under anoxic conditions, the oligonucleotide absorption decays with a single-exponential time constant of 123+/-1 min for rU17 and with double-exponential time constants of 78+/-0.5 min (99%) and 180+/-5 min (0.05%) for dT17 oligonucleotides. Under the same conditions, the MB fluorescence decays more quickly, with single-exponential time constants of 19+/-2 and 26+/-3 min for rU17 and dT17, respectively. Similar kinetics were observed with broadband UV light irradiation of oligonucleotides. The differences in the UV damage kinetics of dT17 and rU17 and their detection by absorption and fluorescence techniques will be discussed in the context of differential instabilities introduced in the nucleic acid-MB duplex by the different photoproducts formed.     

Parallel ocean general circulation modeling

We have developed a global ocean model on the massively parallel CM-2 Connection Machine based on the Bryan-Cox-Semtner ocean general circulation model. This paper discusses the Connection Machine implementation of the model and its performance, as well as major changes that were made in the algorithms and numerical methods. In order to increase the parallel efficiency, we reformulated the barotropic equations to solve for the surface-pressure field rather than the volume-transport streamfunction. In addition to being more efficient, this method has several other advantages over the streamfunction formulation: (1) any number of islands can be included in the computational grid at no extra cost; (2) the model can handle steep gradients in the bottom topography; and (3) the free-surface height is a prognostic variable, which simplifies assimilation of altimetric data into the model. We have also developed a new parallelizable preconditioning method for the solution of the elliptic equation for the surface-pressure field. In order to use a standard conjugate gradient algorithm, an approximate-factorization technique is used to split off the Coriolis terms and obtain a symmetric operator. We then apply a symmetric local approximate-inverse operator as a preconditioning matrix, which is very effective in accelerating convergence to a solution.     

Practical aspects of fluorescent staining for proteomic applications

SYPRO Orange and SYPRO Ruby staining methods, modified for use with large-format two dimensional (2-D) gels, are compared to the manufacturer's recommended protocols to determine sensitivity and reproducibility of the new methods. This study examines the critical aspects of fixation, washing, and staining to develop an optimized fluorescent staining method. It was determined that careful control of sodium dodecyl sulfate (SDS) levels and pH in the gel was critical for successful staining with SYPRO Orange. Overnight fixation in 40% ethanol/2% acetic acid/0.0005% SDS preserved protein content, eliminated ampholyte-generated staining artifacts, and had no detrimental effects on staining. Three one-hour washes in 2% acetic acid/0.0005% SDS, followed by staining with SYPRO Orange diluted 1:5,000 with washing solution for 3 or more hours, produced high sensitivity, low background images using a STORM 860 laser scanner. Gels viewed two years after staining showed no significant changes with respect to the initial protein patterns, and allowed successful mass spectrometric postgel characterization of protein spots. Protocol changes applied to SYPRO Ruby staining improved the contrast of STORM 860-generated images, but had little impact on staining sensitivity. A comparison of the cost benefits of staining with SYPRO Orange vs. SYPRO Ruby is also discussed.     

Anion radicals of di-trans-[12]annulene and heptalene in a one-pot synthesis from a common fire retardant

[reaction: see text] Low temperature (-100 degrees C) dehydrohalogenation of 1,2,5,6,9,10-hexabromocyclododecane (a common fire retardant) with potassium tert-butoxide in THF followed by one-electron reduction yields the anion radical of the di-trans form of [12]annulene. This system yields a well-resolved EPR signal that reveals that most of the spin density resides on one side (the planar side) of the anion radical. Five of the carbons in this [12]annulene system are twisted from the plane of the remaining seven carbons, and the rate of rearrangement between the degenerate conformations is on the EPR time scale (k = 10(6)-10(7) s(-1)). Warming of the solution results in the formation of a sigma-bond between the two internal carbons, loss of molecular hydrogen, and consequent generation of the anion radical of heptalene. Tractable quantities of neutral heptalene can be obtained via the reoxidation of this anion radical with iodine.     

QSAR and CoMFA Study of Cocaine Analogs: Crystal and Molecular Structure of (–)-Cocaine Hydrochloride and N-Methyl-3β-(p-Fluorophenyl)Tropane-2β-Carboxylic Acid Methyl Ester

A QSAR and CoMFA study including 78 cocaine analogs has been completed. These analogs have varied functional groups on the 2 and 3 positions of the tropane ring and include various stereoisomers. The CoMFA program was used to calculate the steric and electrostatic interaction energies as a probe atom or probe charge interacts with the molecules. Shaded contour maps show regions of the cocaine analogs where an increase in bulky substituents is desirable for increased pharmacological activity. The maps also show that small electronegative substituents on the phenyl ring are favored for enhanced activity. The X-ray crystal structures of (–)-cocaine hydrochloride (1) and N-methyl-3-(p-fluorophenyl)tropane-2-carboxylic acid methyl ester (2) are reported. These molecules are mostly rigid except for some rotational flexibility in the orientation of the phenyl and benzoyl functional groups. Crystallographic data: (1) C₁₇H₂₁NO₄·HCl, orthorhombic space group P2₁2₁2₁, a = 7.622(1)Å, b = 10.285(1)Å, c = 21.428(3)Å, Z = 4, final R = 0.035 for 960 observed reflections (I>3(I)). (2) C₁₆H₂₀FNO₂, monoclinic space group C2, a = 22.572(7)Å, b = 5.810(1)Å, c = 15.752(4)Å, = 133.65(2)°, Z = 4, final R = 0.059 for 1511 observed reflections (I>3(I)).     

Rheologically interesting polysaccharides from yeasts

We have examined the relationships between primary, secondary, and tertiary structures of polysaccharides exhibiting the rheological property of friction (drag) reduction in turbulent flows. We found an example of an exopolysaccharide from the yeastCryptococcus laurentii that possessed high molecular weight but exhibited lower than expected drag reducing activity. Earlier correlations by Hoyt (8,10) showing that β1 → 3, β→4, and αl → 3 linkages in polysaccharides favored drag reduction were expanded to include correlations to secondary structure. The effect of sidechains in a series of gellan gums was shown to be related to sidechain length and position. Disruption of secondary structure in drag reducing polysaccharides reduced drag reducing activity for some but not all exopolysaccharides. The polymer fromC. laurentii was shown to be more stable than xanthan gum and other exopolysaccharides under the most vigorous of denaturing conditions. We also showed a direct relationship between extensional viscosity measurements and the drag reducing coefficient for four exopolysaccharides.