Structure and function of ribosomal RNA

A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+ tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are essential for P-site tRNA binding were identified by a modification interference strategy. Ribosomal subunits were partially inactivated by chemical modification at a low level. Active, partially modified subunits were separated from inactive ones by binding 3'-biotinderivatized tRNA to the 30S subunits and captured with streptavidin beads. Essential bases are those that are unmodified in the active population but modified in the total population. The four essential bases, G926, 2mG966, G1338, and G1401 are a subset of those that are protected from modification by P-site tRNA. They are all located in the cleft of our 30S subunit model. The rRNA neighborhood of the acceptor end of tRNA was probed by hydroxyl radical probing from Fe2+ tethered to the 5' end of tRNA via an EDTA linker. Cleavage was detected in domains IV, V, and VI of 23S rRNA, but not in 5S or 16S rRNA. The sites were all found to be near bases that were protected from modification by the CCA end of tRNA in earlier experiments, except for a set of E-site cleavages in domain IV and a set of A-site cleavages in the alpha-sarcin loop of domain VI. In vitro genetics was used to demonstrate a base-pairing interaction between tRNA and 23S rRNA. Mutations were introduced at positions C74 and C75 of tRNA and positions 2252 and 2253 of 23S rRNA. Interaction of the CCA end of tRNA with mutant ribosomes was tested using chemical probing in conjunction with allele-specific primer extension. The interaction occurred only when there was a Watson-Crick pairing relationship between positions 74 of tRNA and 2252 of 23S rRNA. Using a novel chimeric in vitro reconstitution method, it was shown that the peptidyl transferase reaction depends on this same Watson-Crick base pair.

Acute toxicity of the oil dispersant corexit 9554 to marine organisms

The acute toxicity of a surfactant-based oil dispersant, Corexit 9554, to the early life stages of four marine species was identified using a closed, flow-through exposure system. Standardized, spiked exposures were used in order to impart a measure of reality to the data. The species were taxonomically diverse: a mollusc, the red abalone (Haliotis rufescens); a fish, the topsmelt (Atherinops affinis); a crustacean, the kelp forest mysid (Holmesimysis costata); and a macroalga, the giant kelp (Macrocystis pyrifera). Results indicated the Haliotis test to be most sensitive, followed by the Macrocystis test, and the Atherinops test, with the Holmesimysis test being least sensitive. Median-effect concentration estimates for the four species ranged from 8.0 to 184.3 initial ppm, a > 20-fold difference. Differences in sensitivity of the four tests were likely the result of both internal (morphological, physiological, etc.) and external (life stage, endpoint, etc.) factors.

Lack of general correlation between interstitial fluid pressure and oxygen partial pressure in solid tumors

Several studies have shown a decrease in blood perfusion and oxygen partial pressure (pO2), and an increase in interstitial fluid pressure (IFP) with increasing tumor size. However, it is not evident if the elevated IFP is a key parameter responsible for the poor perfusion and oxygenation of solid tumors. To this end, IFP and pO2 were measured in nine human tumor xenografts in immunodeficient mice at a fixed tumor size (approximately 250 mm3). IFP and pO2 were also measured as a function of tumor volume in one human colon adenocarcinoma (LS174T) and in one human glioblastoma (HGL-9). In LS174T tumors IFP did not vary with size (P < .07); however, median pO2 decreased from approximately 35 mm Hg in 100-mm3 tumors to approximately 15 mm Hg in tumors of approximately 500 mm3 (P < 0.001). In HGL-9 tumors an inverse correlation between IFP and pO2 was found; IFP increased (P < 0.001) and pO2 decreased (P < 0.001) with increasing tumor size. At a fixed tumor size of 250 mm3 no correlation was found between mean IFP and median pO2 (P < 0.5) or between the mean IFP and the hypoxic fraction (pO2 < 2.5 mm Hg) (P < 0.7) in the nine tumors studied. The absence of a general relationship between IFP and pO2 could result in part from differences in vascular resistance between tumors. For example, a high geometric resistance to blood flow on the arterial side will lead to a low IFP and blood flow, whereas an elevation of the venous resistance will reduce blood flow and increase IFP.(ABSTRACT TRUNCATED AT 250 WORDS)

Presence of eosinophilic precursors in the human thymus: evidence for intra-thymic differentiation of cells in eosinophilic lineage

The distribution of myeloid cells in the human thymus was investigated by light and electron microscopy, immunohistochemistry, and/or flow cytometry. A series of 74 thymic samples, from newborn to 37 year old patients, were studied. By light microscopy, aggregates of mononuclear cells were frequently present in intralobular septa and outer medulla. Among those cells, eosinophilic precursors (promyelocyte, myelocytes and metamyelocytes) were readily identified. These immature granular cells were present in all pre-involutional thymi, and were particularly frequent in the thymi of patients who were younger than 5 years of age. The cells made up 30-50% of the total eosinophilic population and were frequently observed as a group of cells at various stages of differentiation, suggesting that they differentiate from pre-existing precursors in the thymus. These eosinophilic precursors were mostly located in the intralobular septa and fibroreticular network at the corticomedullary junction, while mature eosinophils were scattered throughout the thymus. Flow cytometric analyses, using stem cell-enriched preparations, showed that cells expressing CD33 or CD34 constituted on average 2.55% and 3.33% (0.09% and 0.12% of the total cells), respectively. CD33+/CD34+ coexpressors were also identified, and they constituted 0.36% of the analyzed cells (0.01% of the total cells). No statistical difference in the proportions of CD33+ and/or 34+ cells was noted between any age groups. It is concluded that eosinophilic precursors present in the thymus differentiate into cells in the eosinophilic lineage in particular areas such as the intralobular septa and fibroreticular network of the outer medulla in preinvolutional human thymi.

A chemiluminescent immunoassay for the identification of functional single-chain antibodies

Random mutagenesis of a template single-chain Fv (scFv) antibody generates a mutant library with members of varying ligand affinities; however, only a small population of these mutants exhibit strong (Kd approximately 1 nM) or improved affinities. We have therefore designed a chemiluminescent sandwich assay which can identify strong ligand-binding mutants expressed by Escherichia coli. A model system involving scFv 43C9 and selected mutants with varying hapten affinities was used to demonstrate the application of this methodology. Both the plaque and colony lifts of these scFvs were screened for hapten-binding activities with the chemiluminescent assay, and only strong binders were detected.

Chemical platinization and its effect on excitation transfer dynamics and P700 photooxidation kinetics in isolated photosystem I

Isolated photosystem I (PSI) reaction center/core antenna complexes (PSI-40) were platinized by reduction of [PtCl6]2- at 20 degrees C and neutral pH. PSI particles were visualized directly on a gold surface by scanning tunneling microscopy (STM) before and after platinization. STM results showed that PSI particles were monomeric and roughly ellipsoidal with major and minor axes of 6 and 5 nm, respectively. Platinization deposited approximately 1000 platinum atoms on each PSI particle and made the average size significantly larger (9 x 7 nm). In addition to direct STM visualization, the presence of metallic platinum on the PSI complexes was detected by its effect of actinic shading and electrostatic shielding on P700 photooxidation and P700+ reduction. The reaction centers (P700) in both platinized and nonplatinized PSI-40 were photooxidized by light and reduced by ascorbate repeatedly, although at somewhat slower rates in platinized PSI because of the presence of platinum. The effect of platinization on excitation transfer and trapping dynamics was examined by measuring picosecond fluorescence decay kinetics in PSI-40. The fluorescence decay kinetics in both platinized and control samples can be described as a sum of three exponential components. The dominant (amplitude 0.98) and photochemically limited excitation lifetime remained the same (16 ps) before and after platinization. The excitation transfer and trapping in platinized PSI-40 was essentially as efficient as that in the control (without platinization) PSI. The platinization also did not affect the intermediate-lifetime (400-600 ps) and long-lifetime (> 2500 ps) components, which likely are related to intrinsic electron transport and to functionally uncoupled chlorophylls, respectively. The amplitudes of these two components were exceptionally small in both of the samples. These results provide direct evidence that although platinization dramatically alters the photocatalytic properties of PSI, it does not alter the intrinsic excitation dynamics and initial electron transfer reactions in PSI.

Effect of Vernalization, Photoperiod, and Light Quality on the Flowering Phenotype of Arabidopsis Plants Containing the FRIGIDA Gene

We have compared the flowering response to vernalization, photoperiod, and far-red (FR) light of the Columbia (Col) and Landsberg erecta (Ler) ecotypes of Arabidopsis into which the flowering-time locus FRIGIDA (FRI) has been introgressed with that of the wild types Col, Ler, and San Feliu-2 (Sf-2). In the early-flowering parental ecotypes, Col and Ler, a large decrease in flowering time in response to vernalization was observed only under short-day conditions. However, Sf-2 and the Ler and Col genotypes containing FRI showed a strong response to vernalization when grown in either long days or short days. Although vernalization reduced the responsiveness to photoperiod, plants vernalized for more than 80 d still showed a slight photoperiod response. The effect of FRI on flowering was eliminated by 30 to 40 d of vernalization; subsequently, the response to vernalization in both long days and short days was the same in Col and Ler with or without FRI. FR-light enrichment accelerated flowering in all ecotypes and introgressed lines. However, the FR-light effect was most conspicuous in the FRI-containing plants. Saturation of the vernalization effect eliminated the effect of FR light on flowering, although vernalization did not eliminate the increase of petiole length in FR light.

Significance of magnetic resonance signal enhancement in evaluation of myocardial infarction in cats

RATIONALE AND OBJECTIVES

To correlate magnetic resonance (MR) signal enhancement with pathophysiologic changes occurring during ischemia and reperfusion in evaluation of myocardial infarction in cats.

METHODS

Seven cats were subjected to 150 minutes of occlusion of the left anterior descending coronary artery followed by 90 minutes of reperfusion. Gadolinium (Gd) diethylenetriaminepentaacetic acid-polylysine (molecular weight [mw] = 40 to 50 kd, DP230) contrast-enhanced MR images were acquired with coinjection of poly-L-lysine-fluorescein isothiocyanate (mW = 40 to 50 kd, DP219) as a fluorescent tracer molecule of the contrast agent. Signal intensities on the MR images and fluorescence activities on the resected cardiac specimens were measured. Pathologic examinations by electron and light microscopes and 2,3,5-triphenyltetrazolium chloride histochemical staining were performed on the specimens.

RESULTS

Magnetic resonance signal intensity was lower in the center (3.49 +/- 0.36) than in the periphery (4.71 +/- 0.89) of the enhanced area. Fluorescence activities were absent in the normal myocardium; they were scant as nonspecific discrete dots in the center and numerous as specific interstitial distribution in the periphery of the ischemic myocardium. Electron and light microscopic examinations showed severely damaged ultrastructures of the center and moderately distorted ultrastructures of the periphery.

CONCLUSIONS

The center of the MR signal-enhanced area is the infarct center with severe ultrastructural damages, which also might be an area of little or absent of blood reflow. Conversely, the peripheral-enhanced area is the infarct periphery with moderate myocardial damages.

Isolation and characterization of the chicken trypsinogen gene family

Based on genomic Southern hybridizations and cDNA sequence analyses, the chicken trypsinogen gene family can be divided into two multi-member subfamilies, a six-member trypsinogen I subfamily which encodes the cationic trypsin isoenzymes and a three-member trypsinogen II subfamily which encodes the anionic trypsin isoenzymes. The chicken cDNA and genomic clones containing these two subfamilies were isolated and characterized by DNA sequence analysis. The results indicated that the chicken trypsinogen genes encoded a signal peptide of 15 to 16 amino acid residues, an activation peptide of 9 to 10 residues and a trypsin of 223 amino acid residues. The chicken trypsinogens contain all the common catalytic and structural features for trypsins, including the catalytic triad His, Asp and Ser and the six disulphide bonds. The trypsinogen I and II subfamilies share approximately 70% sequence identity at the nucleotide and amino acid level. The sequence comparison among chicken trypsinogen subfamily members and trypsin sequences from other species suggested that the chicken trypsinogen genes may have evolved in coincidental or concerted fashion.

Molecular electronics of a single photosystem I reaction center: studies with scanning tunneling microscopy and spectroscopy

Thylakoids and photosystem I (PSI) reaction centers were imaged by scanning tunneling microscopy. The thylakoids were isolated from spinach chloroplasts, and PSI reaction centers were extracted from thylakoid membranes. Because thylakoids are relatively thick nonconductors, they were sputter-coated with Pd/Au before imaging. PSI photosynthetic centers and chemically platinized PSI were investigated without sputter-coating. They were mounted on flat gold substrates that had been treated with mercaptoacetic acid to help bind the proteins. With tunneling spectroscopy, the PSI centers displayed a semiconductor-like response with a band gap of 1.8 eV. Lightly platinized (platinized for 1 hr) centers displayed diode-like conduction that resulted in dramatic contrast changes between images taken with opposite bias voltages. The electronic properties of this system were stable under long-term storage.

Changing the inhibitory specificity and function of Cucurbita maxima trypsin inhibitor-V by site-directed mutagenesis

Cucurbita maxima trypsin inhibitor-V (CMTI-V) is also a specific inhibitor of human blood coagulation factor beta-factor XIIa. A recombinant version of CMTI-V has allowed probing of roles of individual amino acid residues including the reactive site residue, lysine (P1), by site-directed mutagenesis. The K44R showed at least a 5-fold increase in inhibitory activity toward human beta-factor XIIa, while there was no change toward bovine trypsin. This result demonstrates that beta-factor-XIIa prefers an arginine residue over lysine residue, while trypsin is non-specific to lysine or arginine in its binding pocket. On the other hand, the specificity of CMTI-V could be changed from trypsin to chymotrypsin inhibition by mutation of the P1 residue to either leucine or methionine (K44L or K44M).

Identification and characterization of a human cDNA homologous to yeast SKI2

A monoclonal antibody, 170A1, which recognizes a nucleolar peptide of molecular weight 90,000, was raised. The protein was conserved among various vertebrates. To characterize the antigen, we screened a human fetal liver expression library using the monoclonal antibody as a probe. Molecular analyses of immunopositive clones suggested the presence of a novel cDNA. It appeared to be a single-copy gene and encoded about 4- and 5-kb mRNAs. The gene appeared to be expressed in every cell tested so far. Its deduced amino acid sequence revealed an overall homology to recently described yeast SKI2. The SKI2 gene of Saccharomyces cerevisiae encoded a nucleolar protein that is involved in the antiviral system. We report here the partial human cDNA sequence and the localization of the corresponding gene on chromosome 6p21.

Adhered platelet morphology in diabetes mellitus

We compared the morphology of platelets obtained from diabetic patients in various stages of retinopathy and nephropathy with those of control patients. The platelets were collected on to polyethylene films, processed and observed under scanning electron microscopy. Different platelet morphologies were observed within the diabetic group, correlating with the severity of complications, whereas platelets appeared normal in the control group. After more extensive follow-up and comparative studies, these preliminary observations could provide another diagnostic tool for detecting and evaluating severe complications associated with diabetes.

Comparative evaluation of bipolar atrial electrogram amplitude during everyday activities: atrial active fixation versus two types of single pass VDD/R leads

Endocardial P wave amplitude (PWA) is an important determinant of the atrial sensing capabilities of an atrial-based pacing system. Although changes in PWA during physical activities are known to occur in DDD/R pacing, there is little information on the P wave stability in single pass lead VDD/R pacemakers using floating P wave sensing. We investigated the variation of PWA during daily life activities using telemetry recorded atrial electrograms in 21 patients with DDDR pacemakers (Relay or Elite) and 29 patients with single lead VDD/R pacemakers (Unity or Thera). Physical activities resulted in marked individual variability of PWA but, as a group, there was no significant difference between PWA during sitting, standing, lying down, and coughing in both DDDR and VDD/R pacing. In the Elite II pacemaker, walking at 2 miles per hour resulted in significant reduction of PWA (11.6% compared with sitting, P < 0.05). The most consistent reduction in PWA occurred in the relaxation phase of the Valsalva maneuver (VM), with all pacemakers showing a reduction in PWA (mean reduction in PWA compared with sitting in DDDR and VDD/R were 16.6% and 12.8%, respectively). Two patients with DDDR pacemakers (Relay) and three patients with VDD/R pacemakers (1 Unity and 2 Thera) had atrial sensing failure during VM or walking. In conclusion, large variation in PWA occurs during daily life activities. The extent of variation is dependent on the patients, types of atrial lead, and the maneuvers performed. A twice sensing threshold may be insufficient to ensure adequate atrial sensing during these activities.(ABSTRACT TRUNCATED AT 250 WORDS)

Tissue-isolated human tumor xenografts in athymic nude mice

An ex vivo perfused solid tumor preparation provides control over the physiological, biochemical, and pharmacological composition of the arterial input and easy access to the venous output. This is advantageous for studies of transport and metabolism in solid tumors. Here we present a tissue-isolated tumor preparation adapted to the nude mouse, allowing ex vivo perfusion of human tumor xenografts. Previously, such preparations have only been developed in rats, to study primarily rodent tumors. In the present study this new tumor preparation is physiologically characterized in comparison with subcutaneously transplanted tumors in nude mice using the human colon adenocarcinoma LS174T.

Quantitative comparison of rate response and oxygen uptake kinetics between different sensor modes in multisensor rate adaptive pacing

Although multisensor pacing may mitigate the inadequacy of rate adaptation in a single sensor system, the clinical role of multisensor driven rate adaptive pacing remains unclear. The cardiopulmonary performance of six patients (mean age 63.5 +/- 10 years) who had undergone the implant of combined QT and activity VVIR (Topaz) pacemakers was assessed during submaximal and maximal treadmill exercise with the rate response sensor randomly programmed to either single sensor mode, QT and activity (ACT), or dual sensor mode, with equal contribution of QT and ACT (QT = ACT). The rate of response, the proportionality, oxygen kinetics, and maximal exercise performance of the various sensor modes during exercise were measured and compared. The ACT sensor mode "overpaced" and the QT and QT = ACT sensor modes "underpaced" during the first three quartiles of exercise (P < 0.05). The ACT sensor mode also gave the fastest rate of response with the shortest delay (13 +/- 1.5 sec vs 145 +/- 58 sec and 41 +/- 17 sec, P < 0.05), time to 50% rate response (39 +/- 2.7 sec vs 275 +/- 48 sec and 203 +/- 40 sec, P < 0.05), and time to 90% of rate response (107 +/- 21 sec vs 375 +/- 34 sec and 347 +/- 34 sec, P < 0.05) and a smaller oxygen debt (0.87 +/- 0.16 L vs 1.10 +/- 0.2 L and 1.07 +/- 0.18 L, P < 0.05) compared to the QT and QT = ACT sensor modes, respectively. These differences were most significant at low exercise workloads. Thus, different sensor combinations result in different rate response profiles and oxygen delivery, especially during low level exercise.(ABSTRACT TRUNCATED AT 250 WORDS)