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Search Results: 1 - 10 of 225428 matches for " Alison R. Erickson "
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Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments
Brandi L. Cantarel, Alison R. Erickson, Nathan C. VerBerkmoes, Brian K. Erickson, Patricia A. Carey, Chongle Pan, Manesh Shah, Emmanuel F. Mongodin, Janet K. Jansson, Claire M. Fraser-Liggett, Robert L. Hettich
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027173
Abstract: Accurate protein identification in large-scale proteomics experiments relies upon a detailed, accurate protein catalogue, which is derived from predictions of open reading frames based on genome sequence data. Integration of mass spectrometry-based proteomics data with computational proteome predictions from environmental metagenomic sequences has been challenging because of the variable overlap between proteomic datasets and corresponding short-read nucleotide sequence data. In this study, we have benchmarked several strategies for increasing microbial peptide spectral matching in metaproteomic datasets using protein predictions generated from matched metagenomic sequences from the same human fecal samples. Additionally, we investigated the impact of mass spectrometry-based filters (high mass accuracy, delta correlation), and de novo peptide sequencing on the number and robustness of peptide-spectrum assignments in these complex datasets. In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy.
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
Nathan P. McNulty,Meng Wu,Alison R. Erickson,Chongle Pan,Brian K. Erickson,Eric C. Martens,Nicholas A. Pudlo,Brian D. Muegge,Bernard Henrissat,Robert L. Hettich,Jeffrey I. Gordon
PLOS Biology , 2013, DOI: 10.1371/journal.pbio.1001637
Abstract: The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.
Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease
Alison R. Erickson, Brandi L. Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel F. Mongodin, Chongle Pan, Manesh Shah, Jonas Halfvarson, Curt Tysk, Bernard Henrissat, Jeroen Raes, Nathan C. Verberkmoes, Claire M. Fraser, Robert L. Hettich, Janet K. Jansson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049138
Abstract: Crohn's disease (CD) is an inflammatory bowel disease of complex etiology, although dysbiosis of the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD. Here we combined shotgun metagenomic and metaproteomic approaches to identify potential functional signatures of CD in stool samples from six twin pairs that were either healthy, or that had CD in the ileum (ICD) or colon (CCD). Integration of these omics approaches revealed several genes, proteins, and pathways that primarily differentiated ICD from healthy subjects, including depletion of many proteins in ICD. In addition, the ICD phenotype was associated with alterations in bacterial carbohydrate metabolism, bacterial-host interactions, as well as human host-secreted enzymes. This eco-systems biology approach underscores the link between the gut microbiota and functional alterations in the pathophysiology of Crohn's disease and aids in identification of novel diagnostic targets and disease specific biomarkers.
A Fast Na+/Ca2+-Based Action Potential in a Marine Diatom
Alison R. Taylor
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004966
Abstract: Background Electrical impulses in animals play essential roles in co-ordinating an array of physiological functions including movement, secretion, environmental sensing and development. Underpinning many of these electrical signals is a fast Na+-based action potential that has been fully characterised only in cells associated with the neuromuscular systems of multicellular animals. Such rapid action potentials are thought to have evolved with the first metazoans, with cnidarians being the earliest representatives. The present study demonstrates that a unicellular protist, the marine diatom Odontella sinensis, can also generate a fast Na+/Ca2+ based action potential that has remarkably similar biophysical and pharmacological properties to invertebrates and vertebrate cardiac and skeletal muscle cells. Methodology/Principal Findings The kinetic, ionic and pharmacological properties of the rapid diatom action potential were examined using single electrode current and voltage clamp techniques. Overall, the characteristics of the fast diatom currents most closely resemble those of vertebrate and invertebrate muscle Na+/Ca2+ currents. Conclusions/Significance This is the first demonstration of voltage-activated Na+ channels and the capacity to generate fast Na+-based action potentials in a unicellular photosynthetic organism. The biophysical and pharmacological characteristics together with the presence of a voltage activated Na+/Ca2+ channel homologue in the recently sequenced genome of the diatom Thalassiosira pseudonana, provides direct evidence supporting the hypothesis that this rapid signalling mechanism arose in ancestral unicellular eukaryotes and has been retained in at least two phylogenetically distant lineages of eukaryotes; opisthokonts and the stramenopiles. The functional role of the fast animal-like action potential in diatoms remains to be elucidated but is likely involved in rapid environmental sensing of these widespread and successful marine protists.
La justicia y el homo económico. Reflexiones en torno al pensamiento de John Rawls
Vásconez R., Alison
Iconos : Revista de Ciencias Sociales , 2003,
Coliform Bacteria: The Effect of Sediments on Decay Rates and on Required Detention Times in Stormwater BMPs  [PDF]
Alison R. Kinnaman, Cristiane Q. Surbeck, Danielle C. Usner
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.328094
Abstract: Fecal indicator bacteria, such as total coliforms and E. coli, are a challenge to control in urban and rural stormwater runoff. To assess the challenges of improving bacterial water quality standards in surface waters, microcosm experiments were conducted to assess how decay rates of total coliforms and E. coli are affected by sediments and associated organic matter. Samples were collected at a lake embayment to create laboratory microcosms consisting of different combinations of unsterilized and sterilized water and sediment. Calculated first-order decay rate constants ranged from 0.021 to 0.047 h-1 for total coliforms and 0.017 and 0.037 h-1 for E. coli, depending on how each microcosm was prepared. It is evident that sediment in contact with the water column decreases bacteria decay rate, showing that care should be taken when designing stormwater treatment measures. In addition, high organic carbon content in the sediment temporarily increased bacteria concentrations in the water column. The results demonstrate that stormwater treatment measures, such as extended detention basins and constructed wetlands, must hold water for several days to allow for reduction of bacterial concentrations to acceptable levels. In addition, to troubleshoot detention basins and constructed wetlands for causes of high effluent bacterial concentrations, analyses of sediment, organic carbon, and water column depth should be conducted.
Young people at ultra high risk for psychosis: research from the PACE clinic
Yung, Alison R.;Nelson, Barnaby;
Revista Brasileira de Psiquiatria , 2011, DOI: 10.1590/S1516-44462011000600003
Abstract: over the last fifteen years, attempts have been made to prospectively identify individuals in the prodromal phase of schizophrenia and other psychotic disorders. the ultra high risk approach, based on a combination of known trait and state risk factors, has been the main strategy used. the validation of the ultra high risk criteria allowed for predictive research in this population in an attempt to identify clinical, neurocognitive and neurobiological risk factors for psychosis onset. it also led to a series of intervention studies in this population, which have included the use of low dose antipsychotic medication, cognitive therapy, and omega-3 fatty acids. although there is moderate evidence for the effectiveness of specific intervention strategies in this population, the most effective type and duration of intervention is yet to be determined. a current controversy in the field is whether to include an adaption of the ultra high risk criteria (the attenuated psychosis syndrome) in the next version of the diagnostic and statistical manual of mental disorders (fifth edition).
Meis1 specifies positional information in the retina and tectum to organize the zebrafish visual system
Timothy Erickson, Curtis R French, Andrew J Waskiewicz
Neural Development , 2010, DOI: 10.1186/1749-8104-5-22
Abstract: meis1 is expressed in both the presumptive retina and tectum. An analysis of retinal patterning reveals that Meis1 is required to correctly specify both dorsal-ventral and nasal-temporal identity in the zebrafish retina. Meis1-knockdown results in a loss of smad1 expression and an upregulation in follistatin expression, thereby causing lower levels of Bmp signalling and a partial ventralization of the retina. Additionally, Meis1-deficient embryos exhibit ectopic Fgf signalling in the developing retina and a corresponding loss of temporal identity. Meis1 also positively regulates ephrin gene expression in the tectum. Consistent with these patterning phenotypes, a knockdown of Meis1 ultimately results in retinotectal mapping defects.In this work we describe a novel role for Meis1 in regulating Bmp signalling and in specifying temporal identity in the retina. By patterning both the retina and tectum, Meis1 plays an important role in establishing the retinotectal map and organizing the visual system.In order to preserve the spatial coordinates of visual input, retinal ganglion cell (RGC) axons are topographically organized in the visual processing centres of the midbrain. Retinotopic mapping has been most extensively studied in the optic tectum of fish, amphibians, and chick, and in the superior colliculus of mice. Within both the retina and the tectum, axially restricted expression of the Eph and Ephrin families of axon guidance molecules provides some of the positional information required for retinotectal map formation. Interactions between Eph receptor tyrosine kinases and their cognate Ephrin ligands result in cytoskeletal rearrangements and changes in cell adhesion, thereby eliciting either repulsive or attractive responses. By interpreting the molecular Eph and Ephrin code, RGC axons form a precisely ordered arrangement within the optic tectum that accurately reflects their axial position within the retina [1,2].Axial patterning of the retina is required to estab
R. C. Erickson,M. L. Scott,梁宝勇
心理科学进展 , 1983,
Abstract: 从最广泛的意义上说,记忆是一种复杂的高级过程,它包括信息的搜集、贮存和提取。记忆功能的缺陷是器质性和功能性精神障碍的一种常见的伴随症状,无论从诊断,还是从康复的观点看都是临床家所关心的。记忆功能的粗略估计是每个精神状态检查的一部份。精神状态检查可对心理功能的一些方面作出经济的筛选,但它可以提出,也可以不提出合适的资料。整个的心理测量
Platelet function testing to predict hyporesponsiveness to clopidogrel in patients with chest pain seen in the emergency department
Sharma RK,Erickson SW,Sharma R,Voelker DJ
Vascular Health and Risk Management , 2013,
Abstract: Rakesh K Sharma,1 Stephen W Erickson,1 Rohit Sharma,2 Donald J Voelker,1 Hanumanth K Reddy,1 Harvinder Dod,2 James D Marsh1 1Division of Cardiovascular Medicine, University of Arkansas for Medical Sciences, Little Rock, 2Medical Center of South Arkansas, El Dorado, AR, USA Background: A dual antiplatelet regimen has been shown to reduce the risk of major adverse cardiovascular events after percutaneous coronary intervention. However, there is little information available on inhibition of platelet aggregation in patients with a prior coronary stent presenting with chest pain. This study evaluated the prevalence of hyporesponsiveness to clopidogrel and factors associated with this in patients presenting to our emergency department with chest pain who had previously undergone coronary stent placement and were prescribed dual antiplatelet therapy. Methods: Responsiveness to clopidogrel was evaluated in a cohort of 533 consecutive stented patients presenting to the emergency department with chest pain. P2Y12 reaction units (PRU) and percent P2Y12 inhibition with clopidogrel were measured in all patients. Of 533 patients, 221 (41.6%) had PRU ≥ 230. A multivariate logistic regression model was used to determine the relationship between hyporesponsiveness to clopidogrel (defined as PRU ≥ 230) and several potential risk factors, ie, gender, age, race, type 1 or type 2 diabetes, hypertension, smoking, chronic renal failure, and obesity. Results: There was a greater risk of hyporesponsiveness in African Americans than in non-African American patients (adjusted odds ratio [OR] = 2.165), in patients with type 2 diabetes than in those without (adjusted OR = 2.109), and in women than in men (adjusted OR = 1.813), as well as a greater risk of hyporesponsiveness with increasing age (adjusted OR = 1.167 per decade). Conclusion: There was a high prevalence of hyporesponsiveness to clopidogrel in patients presenting with chest pain and a prior coronary stent. Non-insulin-dependent diabetes mellitus and African American race were the strongest predictors of hyporesponsiveness to clopidogrel, followed by gender and age. Keywords: clopidogrel, platelet function testing, chest pain, emergency department
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