Showing papers by "University of Utah published in 2000"

Structure of the 30S ribosomal subunit.

Abstract: Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein–RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.

Recognition of the polyubiquitin proteolytic signal.

Abstract: Polyubiquitin chains linked through Lys48 are the principal signal for targeting substrates to the 26S proteasome. Through studies of structurally defined, polyubiquitylated model substrates, we show that tetraubiquitin is the minimum signal for efficient proteasomal targeting. The mechanism of targeting involves a simple increase in substrate affinity that is brought about by autonomous binding of the polyubiquitin chain. Assigning the proteasomal signaling function to a specific polymeric unit explains how a single ubiquitin can act as a functionally distinct signal, for example in endocytosis. The properties of the substrates studied here implicate substrate unfolding as a kinetically dominant step in the proteolysis of properly folded proteins, and suggest that extraproteasomal chaperones are required for efficient degradation of certain proteasome substrates.

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

Abstract: The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.

Spectrum of Mutations in Long-QT Syndrome Genes KVLQT1, HERG, SCN5A, KCNE1, and KCNE2

Abstract: Background—Long-QT Syndrome (LQTS) is a cardiovascular disorder characterized by prolongation of the QT interval on ECG and presence of syncope, seizures, and sudden death. Five genes have been imp...

The status of the tropical rainfall measuring mission (TRMM) after two years in orbit

Abstract: The Tropical Rainfall Measuring Mission (TRMM) satellite was launched on 27 November 1997, and data from all the instruments first became available approximately 30 days after the launch. Since then, much progress has been made in the calibration of the sensors, the improvement of the rainfall algorithms, and applications of these results to areas such as data assimilation and model initialization. The TRMM Microwave Imager (TMI) calibration has been corrected and verified to account for a small source of radiation leaking into the TMI receiver. The precipitation radar calibration has been adjusted upward slightly (by 0.6 dB Z) to match better the ground reference targets; the visible and infrared sensor calibration remains largely unchanged. Two versions of the TRMM rainfall algorithms are discussed. The at-launch (version 4) algorithms showed differences of 40% when averaged over the global Tropics over 30-day periods. The improvements to the rainfall algorithms that were undertaken after launch are presented, and intercomparisons of these products (version 5) show agreement improving to 24% for global tropical monthly averages. The ground-based radar rainfall product generation is discussed. Quality-control issues have delayed the routine production of these products until the summer of 2000, but comparisons of TRMM products with early versions of the ground validation products as well as with rain gauge network data suggest that uncertainties among the TRMM algorithms are of approximately the same magnitude as differences between TRMM products and ground-based rainfall estimates. The TRMM field experiment program is discussed to describe active areas of measurements and plans to use these data for further algorithm improvements. In addition to the many papers in this special issue, results coming from the analysis of TRMM products to study the diurnal cycle, the climatological description of the vertical profile of precipitation, storm types, and the distribution of shallow convection, as well as advances in data assimilation of moisture and model forecast improvements using TRMM data, are discussed in a companion TRMM special issue in the Journal of Climate (1 December 2000, Vol. 13, No. 23).

Cutting Edge: Repurification of Lipopolysaccharide Eliminates Signaling Through Both Human and Murine Toll-Like Receptor 2

Abstract: Toll-like receptor (TLR) 2 has recently been associated with cellular responses to numerous microbial products, including LPS and bacterial lipoproteins. However, many preparations of LPS contain low concentrations of highly bioactive contaminants described previously as “endotoxin protein,” suggesting that these contaminants could be responsible for the TLR2-mediated signaling observed upon LPS stimulation. To test this hypothesis, commercial preparations of LPS were subjected to a modified phenol re-extraction protocol to eliminate endotoxin protein. While it did not influence the ability to stimulate cells from wild-type mice, repurification eliminated the ability of LPS to activate cells from C3H/HeJ ( Lps d ) mice. Additionally, only cell lines transfected with human TLR4, but not human or murine TLR2, acquired responsiveness to both re-extracted LPS and to a protein-free, synthetic preparation of lipid A. These results suggest that neither human nor murine TLR2 plays a role in LPS signaling in the absence of contaminating endotoxin protein.

Urinary and sexual function after radical prostatectomy for clinically localized prostate cancer : The Prostate Cancer Outcomes Study

Abstract: ContextPatients with prostate cancer and their physicians need knowledge of treatment options and their potential complications, but limited data on complications are available in unselected population-based cohorts of patients.ObjectiveTo measure changes in urinary and sexual function in men who have undergone radical prostatectomy for clinically localized prostate cancer.DesignThe Prostate Cancer Outcomes Study, a population-based longitudinal cohort study with up to 24 months of follow-up.SettingPopulation-based cancer registries in 6 geographic regions of the United States.ParticipantsA total of 1291 black, white, and Hispanic men aged 39 to 79 years who were diagnosed as having primary prostate cancer between October 1, 1994, and October 31, 1995, and who underwent radical prostatectomy within 6 months of diagnosis for clinically localized disease.Main Outcome MeasuresDistribution of and change in urinary and sexual function measures reported by patients at baseline and 6, 12, and 24 months after diagnosis.ResultsAt 18 or more months following radical prostatectomy, 8.4% of men were incontinent and 59.9% were impotent. Among men who were potent before surgery, the proportion of men reporting impotence at 18 or more months after surgery varied according to whether the procedure was nerve sparing (65.6% of non–nerve-sparing, 58.6% of unilateral, and 56.0% of bilateral nerve–sparing). At 18 or more months after surgery, 41.9% reported that their sexual performance was a moderate-to-large problem. Both sexual and urinary function varied by age (39.0% of men aged <60 years vs 15.3%-21.7% of older men were potent at ≥18 months [P<.001]; 13.8% of men aged 75-79 years vs 0.7%-3.6% of younger men experienced the highest level of incontinence at ≥18 months [P = .03]), and sexual function also varied by race (38.4% of black men reported firm erections at ≥18 months vs 25.9% of Hispanic and 21.3% of white men; P = .001).ConclusionsOur study suggests that radical prostatectomy is associated with significant erectile dysfunction and some decline in urinary function. These results may be particularly helpful to community-based physicians and their patients with prostate cancer who face difficult treatment decisions.

Practice parameter: Screening and diagnosis of autism Report of the Quality Standards Subcommittee of the American Academy of Neurology and the Child Neurology Society

Abstract: Autism is a common disorder of childhood, affecting 1 in 500 children. Yet, it often remains unrecognized and undiagnosed until or after late preschool age because appropriate tools for routine developmental screening and screening specifically for autism have not been available. Early identification of children with autism and intensive, early intervention during the toddler and preschool years improves outcome for most young children with autism. This practice parameter reviews the available empirical evidence and gives specific recommendations for the identification of children with autism. This approach requires a dual process: 1) routine developmental surveillance and screening specifically for autism to be performed on all children to first identify those at risk for any type of atypical development, and to identify those specifically at risk for autism; and 2) to diagnose and evaluate autism, to differentiate autism from other developmental disorders.

Combustion aerosols: factors governing their size and composition and implications to human health.

Abstract: Particulate matter (PM) emissions from stationary combustion sources burning coal, fuel oil, biomass, and waste, and PM from internal combustion (IC) engines burning gasoline and diesel, are a significant source of primary particles smaller than 2.5 μm (PM2.5) in urban areas. Combustion-generated particles are generally smaller than geologically produced dust and have unique chemical composition and morphology. The fundamental processes affecting formation of combustion PM and the emission characteristics of important applications are reviewed. Particles containing transition metals, ultrafine particles, and soot are emphasized because these types of particles have been studied extensively, and their emissions are controlled by the fuel composition and the oxidant-tem-perature-mixing history from the flame to the stack. There is a need for better integration of the combustion, air pollution control, atmospheric chemistry, and inhalation health research communities. Epidemiology has demonstrated t...

Lack of Effect of a Low-Fat, High-Fiber Diet on the Recurrence of Colorectal Adenomas

Abstract: Background We tested the hypothesis that dietary intervention can inhibit the development of recurrent colorectal adenomas, which are precursors of most large-bowel cancers. Methods We randomly assigned 2079 men and women who were 35 years of age or older and who had had one or more histologically confirmed colorectal adenomas removed within six months before randomization to one of two groups: an intervention group given intensive counseling and assigned to follow a diet that was low in fat (20 percent of total calories) and high in fiber (18 g of dietary fiber per 1000 kcal) and fruits and vegetables (3.5 servings per 1000 kcal), and a control group given a standard brochure on healthy eating and assigned to follow their usual diet. Subjects entered the study after undergoing complete colonoscopy and removal of adenomatous polyps; they remained in the study for approximately four years, undergoing colonoscopy one and four years after randomization. Results A total of 1905 of the randomized subjects (91....

A structural basis for drug-induced long QT syndrome

Abstract: Mutations in the HERG K+ channel gene cause inherited long QT syndrome (LQT), a disorder of cardiac repolarization that predisposes affected individuals to lethal arrhythmias [Curran, M. E., Splawski, I., Timothy, K. W., Vincent, G. M., Green, E. D. & Keating, M. T. (1995) Cell 80, 795–804]. Acquired LQT is far more common and is most often caused by block of cardiac HERG K+ channels by commonly used medications [Roden, D. M., Lazzara, R., Rosen, M., Schwartz, P. J., Towbin, J. & Vincent, G. M. (1996) Circulation 94, 1996–2012]. It is unclear why so many structurally diverse compounds block HERG channels, but this undesirable side effect now is recognized as a major hurdle in the development of new and safe drugs. Here we use alanine-scanning mutagenesis to determine the structural basis for high-affinity drug block of HERG channels by MK-499, a methanesulfonanilide antiarrhythmic drug. The binding site, corroborated with homology modeling, is comprised of amino acids located on the S6 transmembrane domain (G648, Y652, and F656) and pore helix (T623 and V625) of the HERG channel subunit that face the cavity of the channel. Other compounds that are structurally unrelated to MK-499, but cause LQT, also were studied. The antihistamine terfenadine and a gastrointestinal prokinetic drug, cisapride, interact with Y652 and F656, but not with V625. The aromatic residues of the S6 domain that interact with these drugs (Y652 and F656) are unique to eag/erg K+ channels. Other voltage-gated K+ (Kv) channels have Ile and Val (Ile) in the equivalent positions. These findings suggest a possible structural explanation for how so many commonly used medications block HERG but not other Kv channels and should facilitate the rational design of drugs devoid of HERG channel binding activity.

Measurement of the quantum of thermal conductance

Abstract: The physics of mesoscopic electronic systems has been explored for more than 15 years. Mesoscopic phenomena in transport processes occur when the wavelength or the coherence length of the carriers becomes comparable to, or larger than, the sample dimensions. One striking result in this domain is the quantization of electrical conduction, observed in a quasi-one-dimensional constriction formed between reservoirs of two-dimensional electron gas. The conductance of this system is determined by the number of participating quantum states or 'channels' within the constriction; in the ideal case, each spin-degenerate channel contributes a quantized unit of 2e^2/h to the electrical conductance. It has been speculated that similar behaviour should be observable for thermal transport in mesoscopic phonon systems. But experiments attempted in this regime have so far yielded inconclusive results. Here we report the observation of a quantized limiting value for the thermal conductance, G_(th), in suspended insulating nanostructures at very low temperatures. The behaviour we observe is consistent with predictions for phonon transport in a ballistic, one-dimensional channel: at low temperatures, G_(th) approaches a maximum value of g_0 = π^2k^2BT/3h, the universal quantum of thermal conductance.

Strengthening the case for pair programming

Abstract: The software industry has practiced pair programming (two programmers working side by side at one computer on the same problem) with great success for years, but people who haven't tried it often reject the idea as a waste of resources. The authors demonstrate that using pair programming in the software development process yields better products in less time-and happier, more confident programmers.

Effectiveness and Limitations of β-Blocker Therapy in Congenital Long-QT Syndrome

Abstract: Background—β-blockers are routinely prescribed in congenital long-QT syndrome (LQTS), but the effectiveness and limitations of β-blockers in this disorder have not been evaluated. Methods and Results—The study population comprised 869 LQTS patients treated with β-blockers. Effectiveness of β-blockers was analyzed during matched periods before and after starting β-blocker therapy, and by survivorship methods to determine factors associated with cardiac events while on prescribed β-blockers. After initiation of β-blockers, there was a significant (P<0.001) reduction in the rate of cardiac events in probands (0.97±1.42 to 0.31±0.86 events per year) and in affected family members (0.26±0.84 to 0.15±0.69 events per year) during 5-year matched periods. On-therapy survivorship analyses revealed that patients with cardiac symptoms before β-blockers (n=598) had a hazard ratio of 5.8 (95% CI, 3.7 to 9.1) for recurrent cardiac events (syncope, aborted cardiac arrest, or death) during β-blocker therapy compared with ...

Image enhancement via adaptive unsharp masking

Abstract: This paper presents a new method for unsharp masking for contrast enhancement of images. The approach employs an adaptive filter that controls the contribution of the sharpening path in such a way that contrast enhancement occurs in high detail areas and little or no image sharpening occurs in smooth areas.

Carbon isotope ratios in belowground carbon cycle processes

Abstract: Analyses of carbon isotope ratios (δ13C) in soil organic matter (SOM) and soil respired CO2 provide insights into dynamics of the carbon cycle. δ13C analyses do not provide direct measures of soil CO2 efflux rates but are useful as a constraint in carbon cycle models. In many cases, δ13C analyses allow the identification of components of soil CO2 efflux as well as the relative contribution of soil to overall ecosystem CO2 fluxes. δ13C values provide a unique tool for quantifying historical shifts between C3 and C4 ecosystems over decadal to millennial time scales, which are relevant to climate change and land-use change issues. We identify the need to distinguish between δ13C analyses of SOM and those of soil CO2 efflux in carbon cycle studies, because time lags in the turnover rates of different soil carbon components can result in fluxes and stocks that differ in isotopic composition (disequilibrium effect). We suggest that the frequently observed progressive δ13C enrichment of SOM may be related to a g...

Are tropical fungal endophytes hyperdiverse

Abstract: Fungal endophytes are ubiquitous fungi that inhabit healthy plant tissues without causing disease. Endophytes have been found in every plant species examined to date and may be important, but often overlooked, components of fungal biodiversity. In two sites in a lowland, moist tropical forest of central Panama, we quantified endophyte colonization patterns, richness, host preference, and spatial variation in healthy leaves of two co-occurring, understory tree species [Heisteria concinna (Olacaceae) and Ouratea lucens (Ochnaceae)]. From 83 leaves, all of which were colonized by endophytes, we isolated 418 endophyte morphospecies (estimated 347 genetically distinct taxa), most of which were represented by only a single isolate (59%). Among morphospecies encountered in more than one leaf (nonsingletons), we found evidence of host preference and spatial heterogeneity using both morphospecies frequencies and presence/absence records. Based on these data, we postulate that tropical endophytes themselves may be hyperdiverse and suggest that extrapolative estimates that exclude them will markedly underestimate fungal species diversity.

Dnm1p Gtpase-Mediated Mitochondrial Fission Is a Multi-Step Process Requiring the Novel Integral Membrane Component Fis1p

Abstract: Yeast Dnm1p is a soluble, dynamin-related GTPase that assembles on the outer mitochondrial membrane at sites where organelle division occurs. Although these Dnm1p-containing complexes are thought to trigger constriction and fission, little is known about their composition and assembly, and molecules required for their membrane recruitment have not been isolated. Using a genetic approach, we identified two new genes in the fission pathway, FIS1 and FIS2. FIS1 encodes a novel, outer mitochondrial membrane protein with its amino terminus exposed to the cytoplasm. Fis1p is the first integral membrane protein shown to participate in a eukaryotic membrane fission event. In a related study (Tieu, Q., and J. Nunnari. 2000. J. Cell Biol. 151:353–365), it was shown that the FIS2 gene product (called Mdv1p) colocalizes with Dnm1p on mitochondria. Genetic and morphological evidence indicate that Fis1p, but not Mdv1p, function is required for the proper assembly and distribution of Dnm1p-containing fission complexes on mitochondrial tubules. We propose that mitochondrial fission in yeast is a multi-step process, and that membrane-bound Fis1p is required for the proper assembly, membrane distribution, and function of Dnm1p-containing complexes during fission.

Climate change and the collapse of the Akkadian empire: Evidence from the deep sea

Abstract: The Akkadian empire ruled Mesopotamia from the headwaters of the Tigris-Euphrates Rivers to the Persian Gulf during the late third millennium B.C. Archeological evidence has shown that this highly developed civilization collapsed abruptly near 4170 ± 150 calendar yr B.P., perhaps related to a shift to more arid conditions. Detailed paleoclimate records to test this assertion from Mesopotamia are rare, but changes in regional aridity are preserved in adjacent ocean basins. We document Holocene changes in regional aridity using mineralogic and geochemical analyses of a marine sediment core from the Gulf of Oman, which is directly downwind of Mesopotamian dust source areas and archeological sites. Our results document a very abrupt increase in eolian dust and Mesopotamian aridity, accelerator mass spectrometer radiocarbon dated to 4025 ± 125 calendar yr B.P., which persisted for ~300 yr. Radiogenic (Nd and Sr) isotope analyses confirm that the observed increase in mineral dust was derived from Mesopotamian source areas. Geochemical correlation of volcanic ash shards between the archeological site and marine sediment record establishes a direct temporal link between Mesopotamian aridification and social collapse, implicating a sudden shift to more arid conditions as a key factor contributing to the collapse of the Akkadian empire.

Evaluation of Nine Automated High-Sensitivity C-Reactive Protein Methods: Implications for Clinical and Epidemiological Applications. Part 2

Abstract: Background: C-Reactive protein (CRP) can provide prognostic information about risk of future coronary events in apparently healthy subjects. This application requires higher sensitivity assays than have traditionally been available in the clinical laboratory. Methods: Nine high-sensitivity CRP (hs-CRP) methods from Dade Behring, Daiichi, Denka Seiken, Diagnostic Products Corporation, Iatron, Kamiya, Olympus, Roche, and Wako were evaluated for limit of detection, linearity, precision, prozone effect, and comparability with samples from 388 apparently healthy individuals. Results: All methods had limits of detection that were lower than the manufacturers’ claimed limit of quantification except for the Kamiya, Roche, and Wako methods. All methods were linear at 0.3–10 mg/L. The Diagnostic Products Corporation, Kamiya, Olympus, and Wako methods had imprecision (CVs) >10% at 0.15 mg/L. The Iatron, Olympus, and Wako methods demonstrated prozone effects at hs-CRP concentrations of 12, 206, and 117 mg/L, respectively. hs-CRP concentrations demarcating each quartile in a healthy population were method-dependent. Ninety-two to 95% of subjects were classified into the same quartile of hs-CRP established by the Dade Behring method by the Denka Seiken, Diagnostic Products Corporation, Iatron, and Wako methods. In contrast, 68–77% of subjects were classified into the same quartile by the Daiichi, Kamiya, Olympus, and Roche methods. No subject varied by more than one quartile by any method. Conclusions: Four of the nine examined hs-CRP methods classified apparently healthy subjects into quartiles of hs-CRP similar to the classifications assigned by the comparison method. Additional standardization efforts are required because an individual patient’s results will be interpreted using population-based cutpoints.

Gene targeting by homologous recombination in Drosophila

Abstract: Drosophila offers many advantages as an experimental organism. However, in comparison with yeast and mouse, two other widely used eukaryotic model systems, Drosophila suffers from an inability to perform homologous recombination between introduced DNA and the corresponding chromosomal loci. The ability to specifically modify the genomes of yeast and mouse provides a quick and easy way to generate or rescue mutations in genes for which a DNA clone or sequence is available. A method is described that enables analogous manipulations of the Drosophila genome. This technique may also be applicable to other organisms for which gene-targeting procedures do not yet exist.

Two-Dimensional Electronic Excitations in Self-Assembled Conjugated Polymer Nanocrystals

Abstract: Several spectroscopic methods were applied to study the characteristic properties of the electronic excitations in thin films of regioregular and regiorandom polythiophene polymers. In the regioregular polymers, which form two-dimensional lamellar structures, increased interchain coupling strongly influences the traditional one-dimensional electronic properties of the polymer chains. The photogenerated charge excitations (polarons) show two-dimensional delocalization that results in a relatively small polaronic energy, multiple absorption bands in the gap where the lowest energy band becomes dominant, and associated infrared active vibrations with reverse absorption bands caused by electron-vibration interferences. The relatively weak absorption bands of the delocalized polaron in the visible and near-infrared spectral ranges may help to achieve laser action in nanocrystalline polymer devices using current injection.