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Search Results: 1 - 10 of 489374 matches for " Daniel A. Peterson "
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SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
Murray P Cox, Daniel A Peterson, Patrick J Biggs
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-485
Abstract: We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads.The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.Second-generation technologies are rapidly coming to dominate modern DNA and RNA sequencing efforts [1]. Among the available systems, Illumina sequencing (known informally as Solexa) is playing an increasingly prominent role. However, the error profiles of high-throughput short read sequencing technologies differ markedly from traditional Sanger sequencing [2]; they tend to exhibit a steep, exponential increase in error rates along the read length, and are susceptible to a wider range of chemistry and machine failures (such as air bubbles in system fluidics). Although the quality of second-generation sequencing data affects downstream applications, monitoring and diagnosis of data quality has not kept pace with the rapid rate of improvement seen in other aspects of the technology.Owners of Illumina machines have access to on-board diagnostic tools, which give detailed information about data quality for each lane, tile and nucleotide position. However, these tools are not available to most users, the majority of whom now outsource data collection to dedicated sequencing centers. In our experience, these centers do not usually release data quality information, although we advocate strongly that they should. Lacking this information, users must turn to publicly available software packages to quantify data quality. The R package TileQC [3], which offers similar functionality to Illumina's proprietar
Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (Gossypium hirsutum) Chromosome Substitution Line CS-B25  [PDF]
Chuan-Yu Hsu, Mark A. Arick II, Qing Miao, Sukumar Saha, Johnie N. Jenkins, Mirzakamol S. Ayubov, Ibrokhim Y. Abdurakhmonov, Daniel G. Peterson, Din-Pow Ma
American Journal of Plant Sciences (AJPS) , 2018, DOI: 10.4236/ajps.2018.96098
Abstract: A chromosome substitution line, CS-B25, was developed by the substitution of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbadense, a double haploid Pima 3-79 line. CS-B25 has improved fiber traits compared to its parent TM-1. To explore the molecule mechanisms underlying improved fiber traits, deep sequencing of total RNA was used to compare gene expression in fibers of CS-B25 and TM-1 at 10 days post anthesis (10-DPA). A total of 1872 differentially expressed genes (DEGs) were detected between the two lines, with 1175 up-regulated and 697 down-regulated in CS-B25. Gene Ontology (GO) enrichment analysis of the expression data by Generally Applicable Gene-set Enrichment (GAGE) and ReviGO indicated that the most prevalent Biological Process GO terms associated with DEGs included DNA-templated transcription, response to oxidative stress, and cellulose biosynthesis. Enriched Molecular Function GO terms included structural constituents of cytoskeleton, peroxidase activity, cellulose synthase (UDP-forming) activity, and transcription regulatory region sequence-specific DNA binding factors. GAGE was also used to find enriched KEGG pathways, and the highly represented pathways were Biosynthesis of Amino Acids, Starch and Sucrose Metabolism, Phenylpropanoid Biosynthesis, Protein Processing in Endoplasmic Reticulum, and Plant Hormone Signal Transduction. Many of the identified DEGs are involved in cytoskeleton and cell wall metabolism. The results of gene expression data have provided new insight into the molecular mechanisms of fiber development during the fiber elongation stage and would offer novel candidate genes that may be utilized in cotton fiber quality improvement.
Spatial distribution and cellular composition of adult brain proliferative zones in the teleost, Gymnotus omarorum
Valentina Olivera-Pasilio,Daniel A. Peterson,María E. Castelló
Frontiers in Neuroanatomy , 2014, DOI: 10.3389/fnana.2014.00088
Abstract: Proliferation of stem/progenitor cells during development provides for the generation of mature cell types in the CNS. While adult brain proliferation is highly restricted in the mammals, it is widespread in teleosts. The extent of adult neural proliferation in the weakly electric fish, Gymnotus omarorum has not yet been described. To address this, we used double thymidine analog pulse-chase labeling of proliferating cells to identify brain proliferation zones, characterize their cellular composition, and analyze the fate of newborn cells in adult G. omarorum. Short thymidine analog chase periods revealed the ubiquitous distribution of adult brain proliferation, similar to other teleosts, particularly Apteronotus leptorhynchus. Proliferating cells were abundant at the ventricular-subventricular lining of the ventricular-cisternal system, adjacent to the telencephalic subpallium, the diencephalic preoptic region and hypothalamus, and the mesencephalic tectum opticum and torus semicircularis. Extraventricular proliferation zones, located distant from the ventricular-cisternal system surface, were found in all divisions of the rombencephalic cerebellum. We also report a new adult proliferation zone at the caudal-lateral border of the electrosensory lateral line lobe. All proliferation zones showed a heterogeneous cellular composition. The use of short (24 h) and long (30 day) chase periods revealed abundant fast cycling cells (potentially intermediate amplifiers), sparse slow cycling (potentially stem) cells, cells that appear to have entered a quiescent state, and cells that might correspond to migrating newborn neural cells. Their abundance and migration distance differed among proliferation zones: greater numbers and longer range and/or pace of migrating cells were associated with subpallial and cerebellar proliferation zones.
Effect of Sociality and Season on Gray Wolf (Canis lupus) Foraging Behavior: Implications for Estimating Summer Kill Rate
Matthew C. Metz,John A. Vucetich,Douglas W. Smith,Daniel R. Stahler,Rolf O. Peterson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017332
Abstract: Understanding how kill rates vary among seasons is required to understand predation by vertebrate species living in temperate climates. Unfortunately, kill rates are only rarely estimated during summer.
Concentraciones de apolipoproteína C-III y E en individuos con lesión aterosclerótica coronaria
Aguilar,Daniel; Martínez Amuchástegui,María Victoria; Ba?ares,Virginia; Peterson,Graciela; Tavella,Marcelo;
Acta bioqu?-mica cl?-nica latinoamericana , 2010,
Abstract: apo c-iii and e serum concentrations were evaluated in patients with coronary atherosclerotic disease (cad) diagnosed by angiography. out of 226 individuals under angiographic study, apo c-iii and e were measured by immunoturbidimetric method developed in the laboratory in 148 patients with cad. an apo c-iii serum concentration was 9.8±4.5 mg/dl in cad and 9.1±4.1 mg/dl in non-cad (p:0.25). triglyceride concentrations were 168±83 mg/dl in cad people. apo e concentration was 6.0±3,3 mg/dl, higher concentrations being in women (7.0±3.3 mg/dl) than in men (5.7±3.3 mg/dl), p:0.05. no differences were obtained according to the number of injured vessels. serum concentrations of apo c-iii and e in individuals with cad were above the desirable one proposed of 8.5 mg/dl and 5 mg/dl, respectively. apo c-iii and apo e immunoturbidimetric methods are quick and direct and, especially apo c-iii, is a potentially complementary test, as a marker of triglyceride-rich particles, in the profile of laboratory cardiovascular risk.
Concentraciones de apolipoproteína C-III y E en individuos con lesión aterosclerótica coronaria Apolipoprotein C-III and E concentrations in patients with coronary atherosclerotic disease
Daniel Aguilar,María Victoria Martínez Amuchástegui,Virginia Ba?ares,Graciela Peterson
Acta bioqu?-mica cl?-nica latinoamericana , 2010,
Abstract: Se evaluaron las concentraciones séricas de apo E y C-III en pacientes con lesión aterosclerótica coronaria demostrada por angiografía. En 148 pacientes con lesión de un total de 226 individuos sometidos a angiografía, se midieron las apo C-III y E, mediante inmunoturbidimetría desarrollada en el laboratorio y se dosaron los triglicéridos. La media de apo C-III fue de 9,8±4,5 mg/dL en pacientes con lesiones ateroscleróticas y de 9,1±4,1 mg/dL en pacientes no lesionados (p=0,25). La media de los triglicéridos fue de 168±83 mg/dL en lesionados. La apo E tuvo una media de 6,0±3,3 mg/dL, siendo más alta la concentración en mujeres (7,0±3,3 mg/dL) que en hombres (5,7±3,3 mg/dL), p=0,05. No se obtuvieron diferencias según el número de vasos lesionados. Las concentraciones de apo C-III y apo E en lesionados estuvieron por encima del valor deseable propuesto de 8,5 mg/dL y 5 mg/dL, respectivamente. Se concluye que las concentraciones de apo C-III y apo E en los individuos con lesión aterosclerótica coronaria estuvieron por encima del valor propuesto como deseable, aunque no fueron significativamente diferentes de los valores de los pacientes sin lesiones coronarias y que ambas son una determinación rápida y directa, donde, especialmente apo C-III podría complementar el perfil del laboratorio de riesgo cardiovascular, como marcador de partículas ricas en triglicéridos. Apo C-III and E serum concentrations were evaluated in patients with coronary atherosclerotic disease (CAD) diagnosed by angiography. Out of 226 individuals under angiographic study, Apo C-III and E were measured by immunoturbidimetric method developed in the laboratory in 148 patients with CAD. An Apo C-III serum concentration was 9.8±4.5 mg/dL in CAD and 9.1±4.1 mg/dL in non-CAD (p:0.25). Triglyceride concentrations were 168±83 mg/dL in CAD people. Apo E concentration was 6.0±3,3 mg/dL, higher concentrations being in women (7.0±3.3 mg/dL) than in men (5.7±3.3 mg/dL), p:0.05. No differences were obtained according to the number of injured vessels. Serum concentrations of apo C-III and E in individuals with CAD were above the desirable one proposed of 8.5 mg/dL and 5 mg/dL, respectively. Apo C-III and apo E immunoturbidimetric methods are quick and direct and, especially apo C-III, is a potentially complementary test, as a marker of triglyceride-rich particles, in the profile of laboratory cardiovascular risk.
Gait-Related Brain Activity in People with Parkinson Disease with Freezing of Gait
Daniel S. Peterson, Kristen A. Pickett, Ryan Duncan, Joel Perlmutter, Gammon M. Earhart
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0090634
Abstract: Approximately 50% of people with Parkinson disease experience freezing of gait, described as a transient inability to produce effective stepping. Complex gait tasks such as turning typically elicit freezing more commonly than simple gait tasks, such as forward walking. Despite the frequency of this debilitating and dangerous symptom, the brain mechanisms underlying freezing remain unclear. Gait imagery during functional magnetic resonance imaging permits investigation of brain activity associated with locomotion. We used this approach to better understand neural function during gait-like tasks in people with Parkinson disease who experience freezing- “FoG+” and people who do not experience freezing- ”FoG?“. Nine FoG+ and nine FoG? imagined complex gait tasks (turning, backward walking), simple gait tasks (forward walking), and quiet standing during measurements of blood oxygen level dependent (BOLD) signal. Changes in BOLD signal (i.e. beta weights) during imagined walking and imagined standing were analyzed across FoG+ and FoG? groups in locomotor brain regions including supplementary motor area, globus pallidus, putamen, mesencephalic locomotor region, and cerebellar locomotor region. Beta weights in locomotor regions did not differ for complex tasks compared to simple tasks in either group. Across imagined gait tasks, FoG+ demonstrated significantly lower beta weights in the right globus pallidus with respect to FoG?. FoG+ also showed trends toward lower beta weights in other right-hemisphere locomotor regions (supplementary motor area, mesencephalic locomotor region). Finally, during imagined stand, FoG+ exhibited lower beta weights in the cerebellar locomotor region with respect to FoG?. These data support previous results suggesting FoG+ exhibit dysfunction in a number of cortical and subcortical regions, possibly with asymmetric dysfunction towards the right hemisphere.
Upper Extremity Freezing and Dyscoordination in Parkinson’s Disease: Effects of Amplitude and Cadence Manipulations
April J. Williams,Daniel S. Peterson,Michele Ionno,Kristen A. Pickett,Gammon M. Earhart
Parkinson's Disease , 2013, DOI: 10.1155/2013/595378
Abstract: Purpose. Motor freezing, the inability to produce effective movement, is associated with decreasing amplitude, hastening of movement, and poor coordination. We investigated how manipulations of movement amplitude and cadence affect upper extremity (UE) coordination as measured by the phase coordination index (PCI)—only previously measured in gait—and freezing of the upper extremity (FO-UE) in people with Parkinson's disease (PD) who experience freezing of gait (PD?+?FOG), do not experience FOG (PD-FOG), and healthy controls. Methods. Twenty-seven participants with PD and 18 healthy older adults made alternating bimanual movements between targets under four conditions: Baseline; Fast; Small; SmallFast. Kinematic data were recorded and analyzed for PCI and FO-UE events. PCI and FO-UE were compared across groups and conditions. Correlations between UE PCI, gait PCI, FO-UE, and Freezing of Gait Questionnaire (FOG-Q) were determined. Results. PD?+?FOG had poorer coordination than healthy old during SmallFast. UE coordination correlated with number of FO-UE episodes in two conditions and FOG-Q score in one. No differences existed between PD?/+FOG in coordination or number of FO-UE episodes. Conclusions. Dyscoordination and FO-UE can be elicited by manipulating cadence and amplitude of an alternating bimanual task. It remains unclear whether FO-UE and FOG share common mechanisms. 1. Introduction A motor block, or “freezing” event, is the sudden inability to produce effective movement, which has been documented during speech, upper extremity (UE) movements, and gait, and is often experienced by individuals with Parkinson’s disease (PD) [1–4]. Freezing of gait (FOG) is arguably the most debilitating motor block, as it contributes to increased risk of falls and is associated with reduced quality of life and depression [5]. FOG is difficult to study because it is not easily elicited within the laboratory setting. Individuals with PD who experience FOG (PD+FOG) often demonstrate decreasing steplength in combination with increased cadence prior to a freezing event [4, 6]. Additionally, studies have demonstrated that people with PD+FOG exhibit greater steplength variability, increased cadence, increased step-time asymmetry, and poorer coordination compared to individuals with PD who do not experience FOG (PD-FOG) [7–9]. Plotnik et al. suggest that each of these gait parameters may have a certain level of dependency on each other, and that decline in one or more of these parameters can push an individual past the threshold for functional gait resulting in an episode
The Colitis-Associated Transcriptional Profile of Commensal Bacteroides thetaiotaomicron Enhances Adaptive Immune Responses to a Bacterial Antigen
Jonathan J. Hansen, Yong Huang, Daniel A. Peterson, Laura Goeser, Ting-Jia Fan, Eugene B. Chang, R. Balfour Sartor
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042645
Abstract: Background Inflammatory bowel diseases (IBD) may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta). Healthy, germ-free HLA-B27 transgenic (Tg) rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg) rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. Methods Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA) software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. Results B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function “receptor activity”, most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. Conclusions B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to the identification of novel microbial targets for IBD therapies.
Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines
Philippe Chouvarine, Amanda M. Cooksey, Fiona M. McCarthy, David A. Ray, Brian S. Baldwin, Shane C. Burgess, Daniel G. Peterson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0029850
Abstract: Background Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus × giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations. Results A SNP comparative analysis of rhizome-derived cDNA sequences was successfully utilized to distinguish three Miscanthus × giganteus cultivars from each other and from other Miscanthus species. Moreover, the resulting phylogenetic tree generated from SNP frequency data parallels the known breeding history of the plants examined. Some of the giant miscanthus plants exhibit considerable sequence divergence. Conclusions Here we describe an analysis of Miscanthus in which high-throughput exome sequencing was utilized to differentiate between closely related genotypes despite the current lack of a reference genome sequence. We functionally annotated the exome sequences and provide resources to support Miscanthus systems biology. In addition, we demonstrate the use of the commercial high-performance cloud computing to do computational GO annotation.
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