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Search Results: 1 - 10 of 163527 matches for " Corey W. Liu "
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High-Resolution, In Vivo Magnetic Resonance Imaging of Drosophila at 18.8 Tesla
Brian Null, Corey W. Liu, Maj Hedehus, Steven Conolly, Ronald W. Davis
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002817
Abstract: High resolution MRI of live Drosophila was performed at 18.8 Tesla, with a field of view less than 5 mm, and administration of manganese or gadolinium-based contrast agents. This study demonstrates the feasibility of MR methods for imaging the fruit fly Drosophila with an NMR spectrometer, at a resolution relevant for undertaking future studies of the Drosophila brain and other organs. The fruit fly has long been a principal model organism for elucidating biology and disease, but without capabilities like those of MRI. This feasibility marks progress toward the development of new in vivo research approaches in Drosophila without the requirement for light transparency or destructive assays.
Rationally Designed Turn Promoting Mutation in the Amyloid-β Peptide Sequence Stabilizes Oligomers in Solution
Jayakumar Rajadas,Corey W. Liu,Paul Novick,Nicholas W. Kelley,Mohammed Inayathullah,Melburne C. LeMieux,Vijay S. Pande
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0021776
Abstract: Enhanced production of a 42-residue beta amyloid peptide (Aβ42) in affected parts of the brain has been suggested to be the main causative factor for the development of Alzheimer's Disease (AD). The severity of the disease depends not only on the amount of the peptide but also its conformational transition leading to the formation of oligomeric amyloid-derived diffusible ligands (ADDLs) in the brain of AD patients. Despite being significant to the understanding of AD mechanism, no atomic-resolution structures are available for these species due to the evanescent nature of ADDLs that hinders most structural biophysical investigations. Based on our molecular modeling and computational studies, we have designed Met35Nle and G37p mutations in the Aβ42 peptide (Aβ42Nle35p37) that appear to organize Aβ42 into stable oligomers. 2D NMR on the Aβ42Nle35p37 peptide revealed the occurrence of two β-turns in the V24-N27 and V36-V39 stretches that could be the possible cause for the oligomer stability. We did not observe corresponding NOEs for the V24-N27 turn in the Aβ21–43Nle35p37 fragment suggesting the need for the longer length amyloid peptide to form the stable oligomer promoting conformation. Because of the presence of two turns in the mutant peptide which were absent in solid state NMR structures for the fibrils, we propose, fibril formation might be hindered. The biophysical information obtained in this work could aid in the development of structural models for toxic oligomer formation that could facilitate the development of therapeutic approaches to AD.
Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
Daniel A. Kraut,Paul A. Sigala,Brandon Pybus,Corey W. Liu,Dagmar Ringe,Gregory A. Petsko,Daniel Herschlag
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0040099
Abstract: A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p Ka models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p Ka unit, suggesting a bond shortening of ?0.02 ?/p Ka unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = ?0.2 kcal/mol/p Ka unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = ?2.0 kcal/mol/p Ka unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ?300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
Methods for peptide identification by spectral comparison
Jian Liu, Alexander W Bell, John JM Bergeron, Corey M Yanofsky, Brian Carrillo, Christian EH Beaudrie, Robert E Kearney
Proteome Science , 2007, DOI: 10.1186/1477-5956-5-3
Abstract: This paper investigates computational issues related to this spectral comparison approach. Different methods have been empirically evaluated over several large sets of spectra. First, we illustrate that the peak intensities follow a Poisson distribution. This implies that applying a square root transform will optimally stabilize the peak intensity variance. Our results show that the square root did indeed outperform other transforms, resulting in improved accuracy of spectral matching. Second, different measures of spectral similarity were compared, and the results illustrated that the correlation coefficient was most robust. Finally, we examine how to assemble multiple spectra associated with the same peptide to generate a synthetic reference spectrum. Ensemble averaging is shown to provide the best combination of accuracy and efficiency.Our results demonstrate that when combined, these methods can boost the sensitivity and specificity of spectral comparison. Therefore they are capable of enhancing and complementing existing tools for consistent and accurate peptide identification.One key issue in proteomics is to identify proteins and characterize their expressions in cells. Tandem mass spectrometry paired with advanced liquid chromatography has emerged as the standard technique for high throughput protein identification [1,2]. This shotgun technology does not require the initial separation of individual proteins and therefore can be applied to complex mixtures. Typically, a tissue sample is first fractionated, the resulting mixture of proteins is digested into peptides by an enzyme such as trypsin. The peptide mixture is then separated by High Performance Liquid Chromatography (HPLC), ionized and sent to a mass spectrometer to measure the mass/charge ratio of each peptide. Peptides of interest are selected for further fragmentation in a collision cell to produce tandem (MS/MS) mass spectra. A MS/MS spectrum consists of a sequence of peaks, each characterizing the
Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
Daniel A Kraut,Paul A Sigala,Brandon Pybus,Corey W Liu,Dagmar Ringe,Gregory A Petsko,Daniel Herschlag
PLOS Biology , 2006, DOI: 10.1371/journal.pbio.0040099
Abstract: A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p Ka models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p Ka unit, suggesting a bond shortening of ?0.02 ?/p Ka unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = ?0.2 kcal/mol/p Ka unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = ?2.0 kcal/mol/p Ka unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ?300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.
Can the packing efficiency of binary hard spheres explain the glass-forming ability of bulk metallic glasses?
Kai Zhang,W. Wendell Smith,Minglei Wang,Yanhui Liu,Jan Schroers,Mark D. Shattuck,Corey S. O'Hern
Physics , 2014, DOI: 10.1103/PhysRevE.90.032311
Abstract: We perform molecular dynamics simulations to compress binary hard spheres into jammed packings as a function of the compression rate $R$, size ratio $\alpha$, and number fraction $x_S$ of small particles to determine the connection between the glass-forming ability (GFA) and packing efficiency in bulk metallic glasses (BMGs). We define the GFA by measuring the critical compression rate $R_c$, below which jammed hard-sphere packings begin to form "random crystal" structures with defects. We find that for systems with $\alpha \gtrsim 0.8$ that do not de-mix, $R_c$ decreases strongly with $\Delta \phi_J$, as $R_c \sim \exp(-1/\Delta \phi_J^2)$, where $\Delta \phi_J$ is the difference between the average packing fraction of the amorphous packings and random crystal structures at $R_c$. Systems with $\alpha \lesssim 0.8$ partially de-mix, which promotes crystallization, but we still find a strong correlation between $R_c$ and $\Delta \phi_J$. We show that known metal-metal BMGs occur in the regions of the $\alpha$ and $x_S$ parameter space with the lowest values of $R_c$ for binary hard spheres. Our results emphasize that maximizing GFA in binary systems involves two competing effects: minimizing $\alpha$ to increase packing efficiency, while maximizing $\alpha$ to prevent de-mixing.
Epidemiology, Diagnosis, and Treatment of HIV-Associated Non-Hodgkin Lymphoma in Resource-Limited Settings
Matthew Ulrickson,Oliver W. Press,Corey Casper
Advances in Hematology , 2012, DOI: 10.1155/2012/932658
Abstract: Lymphoma was a common complication of HIV infection in the pre-antiretroviral era, and the incidence of HIV-associated lymphoma has dropped dramatically since the introduction of combination antiretroviral therapy (cART) in resource-rich regions. Conversely, lymphoma is an increasingly common complication of HIV infection in resource-limited settings where the prevalence of HIV infection is high. Relatively little is known, however, about the true incidence and optimal treatment regimens for HIV-associated lymphoma in resource-poor regions. We review the epidemiology, diagnosis, and treatment of HIV-associated non-Hodgkin lymphoma in developing nations and highlight areas for further research that may benefit care in both settings. Examples include risk modification and dose modification of chemotherapy based on HIV risk factors, improving our understanding of the current burden of disease through national cancer registries, and developing cost-effective hematopathological diagnostic strategies to optimize care delivery and maximize use of available chemotherapy. 1. Introduction An association between the acquired immunodeficiency syndrome (AIDS) and lymphoma was first suggested in 1982 after four young men in San Francisco with severe immunodeficiency were diagnosed with a “Burkitt-like lymphoma” [1, 2]. Since that time, HIV has been identified as the causative agent of the underlying immunodeficiency and non-Hodgkin lymphoma (NHL) was designated as an AIDS-defining malignancy [3]. While most of the early descriptions of the emerging immunodeficiency syndrome were reported in patients living in the United States, most of the burden of HIV disease now affects resource-limited nations, with approximately two-thirds of HIV-positive individuals living in sub-Saharan Africa and only 8% within Western nations [4]. The discovery and widespread use of combination antiretroviral therapy (cART) in resource-rich countries has both decreased the incidence of HIV-associated lymphoma and improved its prognosis [5, 6]. While the availability of cART has improved in resource-poor nations due to extraordinary recent efforts, similar changes in the incidence and outcome of HIV-associated lymphomas have not yet been noted. Therefore, increased efforts should be dedicated to improving the diagnosis, supportive care, and treatment of this disorder in these nations. 2. History and Epidemiology The incidence of the three AIDS-defining NHLs, diffuse large B-cell lymphoma (DLBCL), primary CNS lymphoma, and Burkitt lymphoma (BL), increased steadily in the United States between
Pilonidal Disease Mimicking Fistula-in-Ano in a 15-Year-Old Female
Corey W. Iqbal,Alessandra C. Gasior,Charles L. Snyder
Case Reports in Surgery , 2012, DOI: 10.1155/2012/310187
Abstract: Pilonidal disease typically presents with an abscess or intermittent pain and drainage in the sacrococcygeal region during the pubertal years. Further examination typically reveals pits in the midline of the sacrococcyx area due to entrapment of hair with recurrent entrapment, infection, and drainage. The following paper describes an unusual presentation of a pilonidal cyst with fissure and perianal drainage.
Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure
Nicolas M. Berbenetz,Corey Nislow ,Grant W. Brown
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1001092
Abstract: Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers) positions nucleosomes adjacent to the origin to promote replication origin function.
Spot the match – wildlife photo-identification using information theory
Conrad W Speed, Mark G Meekan, Corey JA Bradshaw
Frontiers in Zoology , 2007, DOI: 10.1186/1742-9994-4-2
Abstract: Validation of matched and non-matched images provided a threshold IC weight (approximately 0.2) below which match certainty was not assured. Most images tested were assigned correctly; however, scores for the by-eye comparison were lower than expected, possibly due to the low sample size. The effect of increasing horizontal angle of sharks in images reduced matching likelihood considerably. There was a negative linear relationship between the number of matching spot pairs and matching score, but this relationship disappeared when using the IC algorithm.The software and use of easily applied information-theoretic scores of match parsimony provide a reliable and freely available method for individual identification of wildlife, with wide applications and the potential to improve mark-recapture studies without resorting to invasive marking techniques.Effective approaches for the management and conservation of wildlife populations require a sound knowledge of population demographics [1]. For many species, such information is provided by studies that recognize individual animals so that their fate can be followed through time, thus allowing for the estimation of demographic rates like survival [2]. Individual recognition may be achieved either by applying an artificial mark to an animal or by using an animal's natural markings [3]. The former technique is pervasive in ecological studies addressing questions from the purely theoretical [e.g., [4]] to the highly applied [5], and it has been used on both marine and terrestrial species of vastly different sizes [e.g., [6,7]].Applying artificial marks to wildlife can, however, alter natural behaviour and reduce individual performance [e.g., [8]]. The marking process itself may be disruptive [9] due to the necessity of handling and restraining for mark application [10]. The loss of marks over time [11] and the non-reporting of retrieved marks [12] can also compromise the estimation of demographic parameters. Additionally, ther
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