Alternative Splicing: Associating Frequency with Isoforms

In the simplest model of protein production, a gene gives rise to a single protein; DNA is transcribed to form pre-mRNA, which is converted to mRNA by splicing or removing introns. The result is a chain of exons that is translated to form a protein. Alternative splicing of exons may result in the formation of multiple proteins from the same gene sequence. However, not all of these proteins may be functional. Thus, we ask whether we can predict and rank (in order of frequency of occurrence and functional importance) the set of possible proteins for a gene. Herein we describe a tool that predicts the relative frequencies of isoforms that can be produced from a given gene

Interactive Anatomy Online

The scientific community and general public can best take advantage of the benefits of 3D digital reconstructions if they are stored in a Web-accessible, easy-to-access database. We describe MorphologyNet/sup /spl copy// a Web-based digital library of realistic, 3D interactive and customizable images of anatomy currently in development at the University of Missouri-Rolla

Determining Domain Similarity and Domain-Protein Similarity using Functional Similarity Measurements of Gene Ontology Terms

Protein domains typically correspond to major functional sites of a protein. Therefore, determining similarity between domains can aid in the comparison of protein functions, and can provide a basis for grouping domains based on function. One strategy for comparing domain similarity and domain-protein similarity is to use similarity measurements of annotation terms from the Gene Ontology (GO). In this paper five methods are analyzed in terms of their usefulness for comparing domains, and comparing domains to proteins based on GO terms

Promoting cognitive support technology use and employment success among postsecondary students with traumatic brain injuries

OBJECTIVE: This article applies positive psychology principles to the purpose and objectives of a five-year, federally-funded initiative to provide cognitive support technology (CST) training and career preparatory services for undergraduate college students with mild and moderate traumatic brain injuries (TBI). METHODS: A total of 48 students with TBI have participated in the project during its first 18 months of operation - 14 of whom are military veterans with disabilities who were in the Iraq and/or Afghanistan theaters. CONCLUSION: Positive psychology interventions such as Best Possible Self, Intensely Positive Experiences, and Asset-based Assessments provide a framework for examining the activities of this multi-site development project

Identifying Character Non-Independence in Phylogenetic Data using Data Mining Techniques

Undiscovered relationships in a data set may confound analyses, particularly those that assume data independence. Such problems occur when characters used for phylogenetic analyses are not independent of one another. A main assumption of phylogenetic inference methods such as maximum likelihood and parsimony is that each character serves as an independent hypothesis of evolution. When this assumption is violated, the resulting phylogeny may not reflect true evolutionary history. Therefore, it is imperative that character non-independence be identified prior to phylogenetic analyses. To identify dependencies between phylogenetic characters, we applied three data mining techniques: 1) Bayesian networks, 2) decision tree induction, and 3) rule induction from coverings. We briefly discuss the main ideas behind each strategy, show how each technique performs on a small sample data set, and apply each method to an existing phylogenetic data set. We discuss the interestingness of the results of each method, and show that, although each method has its own strengths and weaknesses, rule induction from coverings presents the most useful solution for determining dependencies among phylogenetic data at this time

Stable Aqueous Nanoparticle Film Assemblies with Covalent and Charged Polymer Linking Networks

The construction of highly stable and efficiently assembled multilayer films of purely water soluble gold nanoparticles is reported. Citrate-stabilized nanoparticles (CS-NPs) of average core diameter of 10 nm are used as templates for stabilization-based exchange reactions with thioctic acid to form more robust aqueous NPs that can be assembled into multilayer films. The thioctic acid stabilized nanoparticles (TAS-NPs) are networked via covalent and electrostatic linking systems, employing dithiols and the cationic polymer poly(l-lysine), respectively. Multilayer films of up to 150 nm in thickness are successfully grown at biological pH with no observable degradation of the NPs within the film. The characteristic surface plasmon band, an optical feature of certain NP film assemblies that can be used to report the local environment and core spacing within the film, is preserved. Growth dynamics and film stability in solution and in the air are examined, with poly(l-lysine) linked films showing no evidence of aggregation for at least 50 days. We believe these films represent a pivotal step toward exploring the potential of aqueous NP film assemblies as a sensing apparatus

Polyelectrolyte-Linked Film Assemblies of Nanoparticles and Nanoshells: Growth, Stability, and Optical Properties

Multi-layer films of nanoparticles and nanoshells featuring various polymeric linkage molecules have been assembled and their optical properties characterized. The growth dynamics, including molecular weight effects, and stability of the various nanoparticle film constructions, using both single polymer as well as combinations of alternating charge polyelectrolytes as linking mechanisms, are presented. The polymeric linkers studied include poly-L-lysine, poly-L-arginine, poly(allylamine hydrochloride), and polyamidoamine dendrimers. Significantly air stable films were achieved with the use of multi-layered polymeric bridges between the nanoparticles and nanoshells. Optical sensitivity normally observed with these nanomaterials in solution was observed for their corresponding film geometries, with the nanoshell films exhibiting a markedly higher ability to report their local dielectric environment

Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico

Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestockand human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E. coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections. IMPORTANCE Escherichia coli is a clinically important bacterial species implicated in humanand livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.Peer reviewe

Treating Women Who Are Pregnant and Parenting for Opioid Use Disorder and the Concurrent Care of Their Infants and Children: Literature Review to Support National Guidance

The prevalence of opioid use disorder (OUD) during pregnancy is increasing. Practical recommendations will help providers treat pregnant women with OUD and reduce potentially negative health consequences for mother, fetus, and child. This article summarizes the literature review conducted using the RAND/University of California, Los Angeles Appropriateness Method project completed by the US Department of Health and Human Services Substance Abuse and Mental Health Services Administration to obtain current evidence on treatment approaches for pregnant and parenting women with OUD and their infants and children

Increasing Glucose 6-Phosphate Dehydrogenase Activity Restores Redox Balance in Vascular Endothelial Cells Exposed to High Glucose

Previous studies have shown that high glucose increases reactive oxygen species (ROS) in endothelial cells that contributes to vascular dysfunction and atherosclerosis. Accumulation of ROS is due to dysregulated redox balance between ROS-producing systems and antioxidant systems. Previous research from our laboratory has shown that high glucose decreases the principal cellular reductant, NADPH by impairing the activity of glucose 6-phosphate dehydrogenase (G6PD). We and others also have shown that the high glucose-induced decrease in G6PD activity is mediated, at least in part, by cAMP-dependent protein kinase A (PKA). As both the major antioxidant enzymes and NADPH oxidase, a major source of ROS, use NADPH as substrate, we explored whether G6PD activity was a critical mediator of redox balance. We found that overexpression of G6PD by pAD-G6PD infection restored redox balance. Moreover inhibition of PKA decreased ROS accumulation and increased redox enzymes, while not altering the protein expression level of redox enzymes. Interestingly, high glucose stimulated an increase in NADPH oxidase (NOX) and colocalization of G6PD with NOX, which was inhibited by the PKA inhibitor. Lastly, inhibition of PKA ameliorated high glucose mediated increase in cell death and inhibition of cell growth. These studies illustrate that increasing G6PD activity restores redox balance in endothelial cells exposed to high glucose, which is a potentially important therapeutic target to protect ECs from the deleterious effects of high glucose