Understanding cellular function and disease with comparative pathway analysis

Pathway analysis is important in interpreting the functional implications of high-throughput experimental results, but robust comparison across platforms and species is problematic. A new approach, Pathprinting, provides a cross-platform, cross-species comparative analysis of pathway expression signatures. This method calculates pathway-level statistics from gene expression across nearly 180,000 microarrays in the Gene Expression Omnibus. Pathprinting can accurately retrieve phenotypically similar samples and identify sets of human and mouse genes that are prognostic in cancer

UPPS-P Model Impulsivity and Marijuana Use Behaviors in Adolescents: A Meta-Analysis

Background Impulsivity is often included as a risk factor in models of adolescent marijuana use behaviors; however, the magnitude of the association between impulsivity and marijuana use behaviors is variable across studies. The present study reviewed existent literature to 1) quantify the relationship between separable impulsivity-related traits and both marijuana use and negative marijuana consequences and 2) quantify the size of the effect of gender on these relationships. Method Thirty-eight studies (41 independent samples) were meta-analyzed using a random effects model to examine the relationship between impulsivity traits and marijuana use behaviors. Results Marijuana use was significantly related to all impulsivity-related traits except lack of perseverance (r’s ranging from 0.13–0.23, p’s < 0.01). Negative marijuana consequences were only significantly related to sensation seeking, lack of planning, and positive urgency (r’s ranging from 0.37–0.39, p’s < 0.01). Effects were small for marijuana use, but medium for negative marijuana consequences. Gender was not a significant moderator of any relationships. Conclusions Impulsivity-related traits had more robust relationships with negative marijuana consequences than marijuana use, suggesting impulsivity-related traits are important in differentiating adolescents most likely to experience negative consequences from marijuana use. Few relationships examined gender and many of the impulsivity-related traits, other than sensation seeking. Data and trends suggest a more multi-dimensional approach to marijuana use and consequences is warranted

The Characterization of Cell Line Crl-2335 as a Basal-Like Breast Carcinoma Model

Basal-like breast cancer has been reported to be the most aggressive and deadly carcinoma sub-type. Patients diagnosed with this subtype have a less than 50% five-year survival. In addition, many studies have reported that this sub-type is more prevalent in specific ethnic groups and is believed to be a key factor that drives certain ethnic disparities in mortality. In order to effectively study this sub-type and determine unique gene expression and biochemical pathways which sustain this cancer’s growth, we sought to identify human breast cancer cell lines that represent a model for the basal-like subtype. Here, we report our findings which indicate the African American cell line CRL-2335 is a true representative of basal-like breast carcinoma

Exploring the functional decapping ability of the dogfish shark Nudt16 homolog

Abstract only availableA nuclear decapping and binding protein, X29/Nudt16, was originally characterized in Xenopus, and has also been characterized in humans. It is suggested that not only the protein's sequence, but also its functions has been preserved through evolution. The purpose of this study is to characterize a homologue of Nudt16 in the dogfish shark, which on an evolutionary scale is quite diverged from frogs and mammals. Here the open reading frame encoding the dogfish shark protein was amplified via PCR and cloned into an expression vector. When placed into bacteria under the proper growth conditions, a Histidine-tagged dogfish shark protein is synthesized. The protein can be purified from bacteria. The purified dogfish shark protein will be tested to determine if it has the same biochemical properties as the mammalian and frog proteins: can the protein decap RNA in vitro and can it bind RNA directly. Does this protein have catalytic activity that is essential for a healthy life?NSF grant to B. Peculus, NSF-REU Program in Biological Sciences & Biochemistr

Beliefs About the Direct Comparison of E-Cigarettes and Cigarettes

Background: Recent data suggests that positive beliefs about electronic cigarettes (e-cigs) use can lead to later e-cig use. Considering that many advertisements claim that e-cigs are superior to cigarettes, individuals' likelihood to view e-cigs more favorably than cigarettes can also influence subsequent e-cig use; however, no studies have directly assessed such a comparison. Objectives: The present study created and validated the Comparing E-Cigarettes and Cigarettes questionnaire (CEAC), which asks individuals to directly compare e-cigs and cigarettes on a number of dimensions, in two independent samples. Methods: In sample 1 (451 undergraduates; mean age = 20.35, SD = 5.44, 72.4% female, 73.4% Caucasian) we explored the factor structure of the CEAC and in sample 2 (699 community adults collected via Amazon's Mechanical Turk; mean age = 34.04, SD = 10.9, 47.7% female, 83.3% Caucasian) we replicated the factor structure. Results: Exploratory factor analysis suggested a three-factor structure: General Benefits (α = 0.80), General Effects (α = 0.86), and Health Benefits (α = 0.88), which was replicated via confirmatory factor analysis, χ2 = 4.36; RMSEA = 0.07, 90% CI = 0.06–0.08; TLI = 0.99; CFI = 0.99, and was relatively invariant across product use and gender. Individuals reported viewing e-cigs as safer and more beneficial than cigarettes and these beliefs were higher in e-cig users. Conclusions: Future work should establish how these comparative beliefs are influenced by e-cig use and/or influence subsequent transition to and increases in e-cig use. Although e-cigs are likely less harmful than cigarettes, and thus these comparative beliefs represent that state of nature, e-cigs are not completely without risk

Transitioning from cigarettes to electronic cigarettes increases alcohol consumption

Objective Electronic cigarettes (e-cigs) are a nicotine delivery device that have recently been linked to alcohol use. Many individuals that smoke cigarettes transition to e-cigs as an alternative to cigarette use, despite potential negative health effects of e-cigs. No research to date has examined how former smokers that have transitioned to e-cigs differ from former smokers that do not use e-cigs, particularly in relation to alcohol use. Further, no research has examined how former smokers that use e-cigs regularly or socially may differ in alcohol consumption. Method Using an online community dwelling sample (Former smokers N=198, mean age=34.70, SD=11.45, 56.1% female, 78.3% Caucasian, 37.9% e-cig users), the present study assessed smoking status and alcohol use, with the latter assessed using a Timeline Followback calendar and the Alcohol Use Disorder Identification Test (AUDIT). Results In all former smokers, total drinks (b=4.01, p=0.02) and average drinks per drinking day (b=0.61, p=.01) were both related to e-cig use status, with e-cig users reporting higher alcohol consumption. Among e-cig using former smokers, social users, but not regular users, showed positive relationships with AUDIT scores, b=1.90, p=.02, total drinks, b=9.12, p<.001, average drinks, b=0.98, p=.006, and hazardous drinking status, OR=3.21, p=.01. Conclusions Findings suggest that: (1) former smokers who use e-cigs may have a potential for higher alcohol use; and (2) those who use e-cigs socially may be at heightened risk for hazardous patterns of alcohol consumption. This should be taken into consideration by healthcare providers

Automatic, context-specific generation of Gene Ontology slims

Background: The use of ontologies to control vocabulary and structure annotation has added value to genome-scale data, and contributed to the capture and re-use of knowledge across research domains. Gene Ontology (GO) is widely used to capture detailed expert knowledge in genomic-scale datasets and as a consequence has grown to contain many terms, making it unwieldy for many applications. To increase its ease of manipulation and efficiency of use, subsets called GO slims are often created by collapsing terms upward into more general, high-level terms relevant to a particular context. Creation of a GO slim currently requires manipulation and editing of GO by an expert (or community) familiar with both the ontology and the biological context. Decisions about which terms to include are necessarily subjective, and the creation process itself and subsequent curation are time-consuming and largely manual

Protein-protein interaction as a predictor of subcellular location

Background: Many biological processes are mediated by dynamic interactions between and among proteins. In order to interact, two proteins must co-occur spatially and temporally. As protein-protein interactions (PPIs) and subcellular location (SCL) are discovered via separate empirical approaches, PPI and SCL annotations are independent and might complement each other in helping us to understand the role of individual proteins in cellular networks. We expect reliable PPI annotations to show that proteins interacting in vivo are co-located in the same cellular compartment. Our goal here is to evaluate the potential of using PPI annotation in determining SCL of proteins in human, mouse, fly and yeast, and to identify and quantify the factors that contribute to this complementarity

Foley Catheter Priming Device

A lack of a pressure gradient throughout the catheter prevents urine flow from the bladder and through catheter system in a condition referred to as “air-lock.” The purpose of this project was to design a device that could be utilized by person with a catheter faced with the problem of air-lock to restore urine flow and normal functioning of the catheter system. After a prototype was created, the device was put through a series of tests to insure proper functioning, absence of leakage, and durability. The device created can be added in-line with the catheter system, inconspicuously under the user’s clothing, as a primer that the catheter user can push to create a pressure gradient in the system and initiate urine flow. Overall, the device functions as its intended design and has the potential to solve the problem of air-lock for many catheter users