Gene activation using FLP recombinase in C. elegans

Journal ArticleThe FLP enzyme catalyzes recombination between specific target sequences in DNA. Here we use FLP to temporally and spatially control gene expression in the nematode C. elegans. Transcription is blocked by the presence of an "off cassette" between the promoter and the coding region of the desired product. The "off cassette" is composed of a transcriptional terminator flanked by FLP recognition targets (FRT). This sequence can be excised by FLP recombinase to bring together the promoter and the coding region. We have introduced two fluorescent reporters into the system: a red reporter for promoter activity prior to FLP expression and a green reporter for expression of the gene of interest after FLP expression. The constructs are designed using the multisite Gateway system, so that promoters and coding regions can be quickly mixed and matched

\u27Texas Maroon’ Bluebonnet

The Texas state flower, the bluebonnet, encompasses all six of the Lupinus species native to Texas. The most widespread and popular bluebonnet, Lupinus texensis Hook., is a winter annual that produces violet-blue [violet-blue group 96A, Royal Horticultural Society (RHS), 1982] racemes in early to midspring and is predominately self-pollinating. The Texas Dept. of Transportation uses this species widely for floral displays along roadsides throughout much of the state (Andrews, 1986). Rare white and even rarer pink variants exist in native populations, and a breeding project was initiated in 1985 to develop bluebonnets with novel flower colors for use as bedding plants. ‘Abbott Pink’ was the first seed-propagated cultivar to be developed from this program (Parsons and Davis, 1993). The second cultivar, ‘Barbara Bush’ with novel lavender shade flowers, was developed more recently (Parsons et al., 1994). As with the cultivars previously developed, we used recurrent phenotypic selection to develop ‘Texas Maroon’. This cultivar is intended for use as a bedding plant for maroon flower color

System Dynamics Modeling for Cancer Prevention and Control: A systematic review

Cancer prevention and control requires consideration of complex interactions between multilevel factors. System dynamics modeling, which consists of diagramming and simulation approaches for understanding and managing such complexity, is being increasingly applied to cancer prevention and control, but the breadth, characteristics, and quality of these studies is not known. We searched PubMed, Scopus, APA PsycInfo, and eight peer-reviewed journals to identify cancer-related studies that used system dynamics modeling. A dual review process was used to determine eligibility. Included studies were assessed using quality criteria adapted from prior literature and mapped onto the cancer control continuum. Characteristics of studies and models were abstracted and qualitatively synthesized. 32 studies met our inclusion criteria. A mix of simulation and diagramming approaches were used to address diverse topics, including chemotherapy treatments (16%), interventions to reduce tobacco or e-cigarettes use (16%), and cancer risk from environmental contamination (13%). Models spanned all focus areas of the cancer control continuum, with treatment (44%), prevention (34%), and detection (31%) being the most common. The quality assessment of studies was low, particularly for simulation approaches. Diagramming-only studies more often used participatory approaches. Involvement of participants, description of model development processes, and proper calibration and validation of models showed the greatest room for improvement. System dynamics modeling can illustrate complex interactions and help identify potential interventions across the cancer control continuum. Prior efforts have been hampered by a lack of rigor and transparency regarding model development and testing. Supportive infrastructure for increasing awareness, accessibility, and further development of best practices of system dynamics for multidisciplinary cancer research is needed

Gender Differences in Diabetes Attitudes and Adherence

This study focused on three questions: Is there a difference in men's and women's diabetes attitudes? Do health professionals give different recommendations to men and women? Is there a difference between men and women in care adherence? A total of 1201 patients with diabetes were surveyed; 65% of these patients were women. Differences in diabetes attitudes (three of seven attiticdes) were most evident between men and women with insulin-dependent diabetes mellitus (IDDM). No differences were found in the attitudes of men and women with non-insulin-dependent diabetes mellitus (NIDDM) using insulin, and only one attitude was different for patients with NIDDM not using insulin. Few differences were observed in the recommendations given by health professionals to men and women. Gender differences in adherence to the components of self-care also were minimal. These findings may indicate that there are many similarities in the reactions of men and women who have been diagnosed with diabetes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69143/2/10.1177_014572179502100605.pd

Rapid single nucleotide polymorphism mapping in C. elegans

BACKGROUND: In C. elegans, single nucleotide polymorphisms (SNPs) can function as silent genetic markers, with applications ranging from classical two- and three-factor mapping to measuring recombination across whole chromosomes. RESULTS: Here, we describe a set of 48 primer pairs that flank SNPs evenly spaced across the C. elegans genome and that work under identical PCR conditions. Each SNP in this set alters a DraI site, enabling rapid and parallel scoring. We describe a procedure using these reagents to quickly and reliably map mutations. We show that these techniques correctly map a known gene, dpy-5. We then use these techniques to map mutations in an uncharacterized strain, and show that its behavioral phenotype can be simultaneously mapped to three loci. CONCLUSION: Together, the reagents and methods described represent a significant advance in the accurate, rapid and inexpensive mapping of genes in C. elegans

Mapping Mental Models Through an Improved Method for Identifying Causal Structures in Qualitative Data

Qualitative data are commonly used in the development of system dynamicsmodels, but methods for systematically identifying causal structures in qualita-tive data have not been widely established. This article presents a modifiedprocess for identifying causal structures (e.g., feedback loops) that are commu-nicated implicitly or explicitly and utilizes software to make coding, tracking,and model rendering more efficient. This approach draws from existingmethods, system dynamics best practice, and qualitative data analysis tech-niques. Steps of this method are presented along with a description of causalstructures for an audience new to system dynamics. The method is applied to aset of interviews describing mental models of clinical practice transformationfrom an implementation study of screening and treatment for unhealthy alco-hol use in primary care. This approach has the potential to increase rigour andtransparency in the use of qualitative data for model building and to broadenthe user base for causal-loop diagramming

Tai chi mind-body exercise in patients with COPD: study protocol for a randomized controlled trial

Background: Chronic obstructive pulmonary disease (COPD) is a chronic, progressively debilitating condition that is prevalent in the US and worldwide. Patients suffer from progressive dyspnea and exercise intolerance. Physical exercise is beneficial, but conventional pulmonary rehabilitation programs are underutilized. There remains a need for novel interventions that improve symptoms, quality-of-life, and functional capacity. Tai chi is an increasingly popular mind-body exercise that includes physical exercise, breathing training, mindful awareness, and stress management--components that are essential to the self-management of COPD. There are, however, limited data on the effectiveness of tai chi as a therapeutic intervention in this population. Methods/Design The Primary Aims are to evaluate the efficacy, safety, and feasibility of a 12-week tai chi program for patients with COPD. We utilize a randomized controlled trial design, with participants assigned in a 2:1 ratio to either a group tai chi program (N = 63) or a time/attention-matched education control (N = 31). Our primary outcomes are COPD-specific quality-of-life and exercise capacity. Secondary outcomes include dyspnea, mood, functional status, self-efficacy, and lung function. Cardiopulmonary exercise testing is done in a subset of patients (N = 50). To explore optimal training duration, a subgroup of patients in tai chi are randomly assigned to complete an additional 12 weeks training (total 24 weeks) (Exploratory Aim 1). To explore the impact of a simplified seated intervention including only a subset of tai chi’s training components, a third randomly assigned group (N = 31) receives a 12- week mind-body breathing program (N = 31) (Exploratory Aim 2). Discussion Results of the BEAM study (Breathing, Education, Awareness, Movement) will provide preliminary evidence regarding the value of tai chi for improving quality of life and exercise capacity in patients with COPD, including information regarding optimal duration. They will also inform the feasibility and potential benefit of an alternative mind-body breathing intervention, and provide insight regarding how isolated mind-body exercise components contribute to the overall effects of tai chi. Should the results be positive, tai chi and related mind-body practices may offer a novel exercise option that is potentially accessible to a large proportion of patients with COPD. Trial registration This trial is registered in Clinical Trials.gov, ID number NCT01551953. Date of Registration March 1 2012. Electronic supplementary material The online version of this article (doi:10.1186/1745-6215-15-337) contains supplementary material, which is available to authorized users

Molecular genetics and pathophysiology of 17 beta-hydroxysteroid dehydrogenase 3 deficiency.

Autosomal recessive mutations in the 17 beta-hydroxysteroid dehydrogenase 3 gene impair the formation of testosterone in the fetal testis and give rise to genetic males with female external genitalia. Such individuals are usually raised as females, but virilize at the time of expected puberty as the result of increases in serum testosterone. Here we describe mutations in 12 additional subjects/families with this disorder. The 14 mutations characterized to date include 10 missense mutations, 3 splice junction abnormalities, and 1 small deletion that results in a frame shift. Three of these mutations have occurred in more than 1 family. Complementary DNAs incorporating 9 of the 10 missense mutations have been constructed and expressed in reporter cells; 8 of the 9 missense mutations cause almost complete loss of enzymatic activity. In 2 subjects with loss of function, missense mutations testosterone levels in testicular venous blood were very low. Considered together, these findings strongly suggest that the common mechanism for testosterone formation in postpubertal subjects with this disorder is the conversion of circulating androstenedione to testosterone by one or more of the unaffected 17 beta-hydroxysteroid dehydrogenase isoenzymes

Identification of Relationships Between Patients Through Elements in a Data Warehouse Using the Familial, Associational, and Incidental Relationship (FAIR) Initiative: A Pilot Study

BACKGROUND: Over the last several years there has been widespread development of medical data warehouses. Current data warehouses focus on individual cases, but lack the ability to identify family members that could be used for dyadic or familial research. Currently, the patient\u27s family history in the medical record is the only documentation we have to understand the health status and social habits of their family members. Identifying familial linkages in a phenotypic data warehouse can be valuable in cohort identification and in beginning to understand the interactions of diseases among families. OBJECTIVE: The goal of the Familial, Associational, and Incidental Relationships (FAIR) initiative is to identify an index set of patients\u27 relationships through elements in a data warehouse. METHODS: Using a test set of 500 children, we measured the sensitivity and specificity of available linkage algorithm identifiers (eg, insurance identification numbers and phone numbers) and validated this tool/algorithm through a manual chart audit. RESULTS: Of all the children, 52.4% (262/500) were male, and the mean age of the cohort was 8 years old (SD 5). Of the children, 51.6% (258/500) were identified as white in race. The identifiers used for FAIR were available for the majority of patients: insurance number (483/500, 96.6%), phone number (500/500, 100%), and address (497/500, 99.4%). When utilizing the FAIR tool and various combinations of identifiers, sensitivity ranged from 15.5% (62/401) to 83.8% (336/401), and specificity from 72% (71/99) to 100% (99/99). The preferred method was matching patients using insurance or phone number, which had a sensitivity of 72.1% (289/401) and a specificity of 94% (93/99). Using the Informatics for Integrating Biology and the Bedside (i2b2) warehouse infrastructure, we have now developed a Web app that facilitates FAIR for any index population. CONCLUSIONS: FAIR is a valuable research and clinical resource that extends the capabilities of existing data warehouses and lays the groundwork for family-based research. FAIR will expedite studies that would otherwise require registry or manual chart abstraction data sources

Familial, Associational, & Incidental Relationships (FAIR)

Identifying familial linkages in a phenotypic data warehouse can be valuable in cohort identification, and beginning to understand interactions of diseases among families. The goal of the Familial, Associational, & Incidental Relationships (FAIR) system is to identify an index set patients’ relationships through elements in a data warehouse. Using a test set of 500 children, we measured the sensitivity and specificity of available linkage algorithm (e.g.: insurance id and phone numbers) and validated this tool/algorithm through a manual chart audit. Sensitivity varied from 16% to 87%, and specificity from 70% to 100% using various combinations of identifiers. Using the “i2b2” warehouse infrastructure, we have now developed a web app that facilitates FAIR for any index population