ABSTRACT
The Mexican axolotl (Ambystoma mexicanum) presents an excellent model to investigate mechanisms of brain development that are conserved among vertebrates. In particular, metamorphic changes of the brain can be induced in free-living aquatic juveniles and adults by simply adding thyroid hormone (T4) to rearing water. Whole brains were sampled from juvenile A. mexicanum that were exposed to 0, 8, and 18 days of 50 nM T4, and these were used to isolate RNA and make normalized cDNA libraries for 454 DNA sequencing. A total of 1,875,732 high quality cDNA reads were assembled with existing ESTs to obtain 5884 new contigs for human RefSeq protein models, and to develop a custom Affymetrix gene expression array (Amby_002) with approximately 20,000 probe sets. The Amby_002 array was used to identify 303 transcripts that differed statistically (p<0.05, fold change >1.5) as a function of days of T4 treatment. Further statistical analyses showed that Amby_002 performed concordantly in comparison to an existing, small format expression array. This study introduces a new A. mexicanum microarray resource for the community and the first lists of T4-responsive genes from the brain of a salamander amphibian.
Subject(s)
Ambystoma mexicanum/genetics , Brain/drug effects , Gene Expression Regulation , Oligonucleotide Array Sequence Analysis/methods , Thyroxine/pharmacology , Ambystoma mexicanum/metabolism , Animals , Brain/metabolism , Expressed Sequence Tags , Gene Expression Profiling , Gene Library , Metamorphosis, Biological , Sequence Analysis, DNA/methods , Time FactorsABSTRACT
Cellular and molecular changes of the periodontium associated with a higher prevalence of oral diseases (e.g., chronic periodontitis) in aged populations have received little attention. Since impaired apoptosis during aging appears to be related to chronic inflammatory disorders, we hypothesized that the expression of genes associated with apoptotic processes are altered in aged healthy and periodontitis-affected gingival tissue. Ontology analysis of 88 genes related to apoptotic pathways was performed in gingival biopsies of healthy and periodontitis sites from young, adult, and aged non-human primates (Macaca mulatta), using the GeneChip® Rhesus Macaque Genome Array. Lower expression of anti-apoptotic and higher expression of pro-apoptotic genes were associated with healthy gingival tissue from young compared with aged animals. Few differences in gene expression were observed in healthy gingival tissue between adult and aged animals. Comparison between healthy and periodontitis gingival tissues showed that the up- or down-regulated apoptotic genes in diseased gingival tissue are different in adults compared with aged animals. These results suggest that apoptotic events normally occurring in gingival tissues could be reduced in aging,and unique aspects of apoptotic pathways are potentially involved in the pathophysiology of periodontal disease in adult vs. aged gingival tissues.
Subject(s)
Aging/genetics , Apoptosis/genetics , Gingiva/cytology , Gingiva/pathology , Periodontitis/genetics , Animals , Female , Gene Expression Profiling , Macaca mulatta , Male , Oligonucleotide Array Sequence AnalysisABSTRACT
Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tree estimate that is closest on average to the samples. This "median" tree is known as the Bayes estimator (BE). The BE literally maximizes posterior expected accuracy, measured in terms of closeness (distance) to the true tree. We discuss a unified framework of BE trees, focusing especially on tree distances that are expressible as squared euclidean distances. Notable examples include Robinson-Foulds (RF) distance, quartet distance, and squared path difference. Using both simulated and real data, we show that BEs can be estimated in practice by hill-climbing. In our simulation, we find that BEs tend to be closer to the true tree, compared with ML and neighbor joining. In particular, the BE under squared path difference tends to perform well in terms of both path difference and RF distances.
Subject(s)
Models, Genetic , Phylogeny , Animals , Bayes Theorem , Computer Simulation , Software , Urodela/classification , Urodela/geneticsABSTRACT
The present study aimed to investigate the effects of different-sized nasogastric tubes on swallowing speed and function in 10 young normal volunteers. Using X-ray visualization, liquid barium swallows were recorded on video (videofluoroscopy) under three experimental conditions: no nasogastric tube, fine-bore nasogastric tube, and wide-bore nasogastric tube. Nasogastric tubes slowed swallowing but did not alter swallowing function, namely bolus transit and clearance, and airway protection. The presence of a wide-bore nasogastric tube caused significant duration changes in several swallowing measures, namely duration of stage transition, duration of pharyngeal response, duration of pharyngeal transit, and duration of upper esophageal sphincter opening. Similar trends were seen for the fine-bore tube. The implications for nonoral feeding of patients with swallowing disorders are discussed.
Subject(s)
Deglutition Disorders/etiology , Intubation, Gastrointestinal/adverse effects , Adult , Cineradiography/methods , Deglutition Disorders/diagnostic imaging , Female , Humans , Male , Random Allocation , Time FactorsABSTRACT
A seating system for physically handicapped children has been devised in which a series of standard components (neck supports, rolled seats, pommels) can be incorporated to make a seating system appropriate for the individual child.
