Genomic characterization and comparison of seven Myoviridae bacteriophage infecting Bacillus thuringiensis.

Bacillus thuringiensis Kurstaki, a bacterium that is a source of biopesticides and a safe simulant for pathogenic Bacillus species, was used to isolate seven unique bacteriophages. The phage genomes were sequenced and ranged in size from 158,100 to 163,019 bp encoding 290-299 genes, and the GC content of ~38% was similar to that of the host bacterium. All phages had terminal repeats 2-3 kb long. Three of the phages encoded tRNAs and three contained a self-splicing intron in the DNA polymerase gene. They were categorized as a single cluster (>60% nucleotide conservation) containing three subclusters (>80% nucleotide conservation), supported by genomic synteny and phylogenetic analysis. Considering the published genomes of phages that infect the genus Bacillus and noting the ability of many of the Bacillus cereus group phages to infect multiple species, a clustering system based on gene content is proposed.

Phage on the stage.

The resurgence of interest in bacteriophages for use in combating antibiotic resistant bacteria is coincident with an urgent call for more effective science education practices, including hands-on learning opportunities. To address this issue, a number of solutions have been proposed, including a large educational experiment, begun in 2007 by the Howard Hughes Medical Institute and currently involving over 85 colleges and universities, which has students discovering unique phages, obtaining images, and purifying phage DNA. A subset of these phage genomes is sequenced and analyzed using bioinformatics tools. Papers describing individual phage discoveries and comparative genomic studies are being published regularly. The vast majority of students in the program are in their first year of college, a critical time in capturing their interest and retaining them as science majors. This viral discovery model is being adopted and modified by a wide variety of educational institutions using a number of different bacterial hosts. In the opinion of the authors, this program and others like it represent a model accessible to virtually any undergraduate setting. And because of these programs, bacteriophage enthusiasts (academics, health professionals, biotechnology companies) can look forward to more well prepared students entering their ranks and should anticipate many more potentially useful phages discovered and characterized.

A broadly implementable research course in phage discovery and genomics for first-year undergraduate students.

UNLABELLED: Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. IMPORTANCE: Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

Profiles of tamoxifen-related side effects by race and smoking status in women with breast cancer.

BACKGROUND: Tamoxifen (TAM) is a selective estrogen receptor modulator (SERM) that is widely used as adjuvant therapy in breast cancer patients; however, it is also associated with undesirable side effects. The goal of this study was to investigate TAM-related side effects, and determine profiles of side effects by race and by smoking status. METHODS: A secondary data analysis was conducted using cross-sectional study data from 138 African American and Caucasian women with breast cancer taking TAM 20mg daily for at least 30 days prior to enrollment. Participants completed questionnaires that obtained information about demographic characteristics, reproductive history, health and lifestyle characteristics, TAM use and its related side effects. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals. RESULTS: Compared to never smokers, a significantly greater percentage of current smokers reported ever experiencing TAM-related nausea (28.0% versus 5.0%, P=0.007), depression (40.0% versus 7.1%, P=0.001) and migraines (19.2% versus 1.7%, P=0.02). These differences remained statistically significant after controlling for race, age, obesity, tumor stage, and duration of TAM treatment. No significant differences by race were noted in women reporting TAM side effects. CONCLUSION: The findings from this study suggest that current smokers with breast cancer should be informed of the increased probability of reporting TAM-related side effects such as nausea, depression and migraines, and counseled about smoking cessation which may reduce the incidence of these side effects.

The association between menopausal symptoms and quality of life in midlife women.

This cross-sectional study examined 1,096 midlife women, associating menopausal symptoms, including hot flashes, vaginal dryness, sore joints, incontinence, irritability, mood changes, and headache, with quality of life (QOL), as measured using Cantril's Ladder of Life. The results showed that low QOL may be significantly associated with feeling tense and mood changes, but not the other selected symptoms.

Association between race and hot flashes in midlife women.

OBJECTIVE: Studies suggest that African American women may have a greater risk of hot flashes compared to Caucasian women, but the reasons for this are unknown. This study tested the hypothesis that African American women have an increased risk of hot flashes due to racial differences in risk factors for hot flashes, including high body mass index (BMI) and lower estrogen levels. METHODS: A population-based study was conducted among women aged 45-54 years. Participants were divided into women who reported ever experiencing hot flashes (n=356) and women who reported never experiencing hot flashes (n=257). Participants provided a blood sample for hormone assays, were weighed and measured, and completed a questionnaire. RESULTS: Among peri-menopausal women, African American women were more likely than Caucasian women to report any hot flashes (RR=2.08), severe hot flashes (RR=2.19), and hot flashes for more than 5 years (RR=1.61). The risk ratios for the associations between race and the hot flash outcomes were attenuated after controlling for other important hot flash risk factors (i.e. obesity and low estrogen levels). CONCLUSIONS: African American women have an increased risk of hot flashes compared to Caucasian women due to racial differences in a number of risk factors for hot flashes, including advanced age, obesity, current smoking, less than 12 drinks in the past year, and lower estrogen levels.

Cigarette smoking, estrogen levels, and hot flashes in midlife women.

OBJECTIVE: The aims of this study were to examine the association of smoking with the occurrence, frequency, and severity of hot flashes and to determine whether the mechanism by which active cigarette smoking increases the risk of hot flashes is by lowering estradiol and estrone levels. METHODS: A case-control study was conducted among women aged 45-54 years to examine risk factors for hot flashes. Cases were women who reported ever experiencing hot flashes (n = 353). Controls were women who reported never experiencing hot flashes (n = 258). Each participant completed a questionnaire and provided a blood sample that was used to measure estradiol and estrone levels. RESULTS: The results showed that both current and ever smokers had higher odds than never smokers of experiencing any and more severe hot flashes. Further, significant positive associations were observed between frequency and duration of smoking and the experiencing of any and more severe hot flashes. Smoking was not associated with estradiol or estrone levels in univariate analyses. In addition, the odds ratios for the associations between the cigarette smoking variables and hot flashes did not change when the hormone variables were added to the model. CONCLUSIONS: These findings indicate that smoking is associated with the occurrence of any and more severe hot flashes, independent of estrogen levels.

Cytochrome gene polymorphisms, serum estrogens, and hot flushes in midlife women.

OBJECTIVE: The purpose of this study was to evaluate whether genetic polymorphisms in selected cytochrome P450 enzymes (CYPc17alpha, CYP1A1, and CYP1B1), estradiol (E2) levels, and estrone levels were associated with hot flushes. METHODS: Women with hot flushes were those aged 45-54 years who reported ever experiencing hot flushes (n = 354). Women without hot flushes were those aged 45-54 years who reported never experiencing hot flushes (n = 258). Each participant completed a questionnaire and provided a blood sample for determination of genotypes, E2 levels, and estrone levels. RESULTS: Carriers of the CYP1B1 (Val432Leu) polymorphism were more likely to report having any hot flushes (risk ratio [RR] 1.16, 95% confidence interval (CI) 0.98-1.37) and at least weekly hot flushes (RR 1.29, 95% CI 0.98-1.70) than women without the polymorphism, although these associations were of borderline statistical significance. In addition, carriers of the CYP1B1 polymorphism were likely to have a statistically significant 30% increased risk of reporting moderate to severe hot flushes (RR 1.30, 95% CI 1.02-1.67) and a statistically significant 27% increased risk of reporting hot flushes lasting a year or more (RR 1.27, 95% CI 1.00-1.61) compared with women without the polymorphism. There were no associations between CYP1A1 or CYPc17alpha polymorphisms and hot flushes. Low E2 and estrone levels were associated with hot flushes, but they did not alter the association between the CYP1B1 polymorphism and hot flushes. CONCLUSION: These data suggest that a CYP1B1 polymorphism may be associated with severe and persistent hot flushes, independent of E2 and estrone levels.

Body mass, estrogen levels, and hot flashes in midlife women.

OBJECTIVE: This study was undertaken to determine whether body mass index (BMI) is associated with hot flashes and whether the mechanism by which BMI increases the risk of hot flashes is by lowering estrogen levels. STUDY DESIGN: A case-control study was conducted among midlife women to examine risk factors for hot flashes. Cases were women who reported experiencing hot flashes (n = 353). Controls were women who reported never experiencing hot flashes (n = 258). Each participant completed a questionnaire and provided a blood sample for estrogen measurement. RESULTS: Compared with normal weight women, very obese women had significantly higher odds of hot flashes. The odds ratios remained elevated although attenuated when the hormone variables were added to the model. CONCLUSION: These results indicate that very obese women are at increased risk for hot flashes compared with normal weight women. Estrogen levels may partly explain this relationship; however, other mechanisms appear to be involved as well.

Current alcohol use is associated with a reduced risk of hot flashes in midlife women.

AIMS: To examine the relation between current alcohol use, estradiol, estrone, and testosterone levels, and hot flashes in midlife women using a case-control study design. METHODS: Cases were midlife women (45-54 years) who reported ever experiencing hot flashes. Controls were midlife women (45-54 years) who reported never experiencing hot flashes. Each participant completed a questionnaire and provided a blood sample that was used to measure estradiol, estrone, and testosterone levels by enzyme-linked immunosorbent assay. RESULTS: The results indicate that current alcohol use (at least one day per month) was significantly associated with a reduced risk of hot flashes compared to non-use of alcohol, independent of age and smoking habits. The hot flashes experienced by current alcohol users were less severe and less frequent than those experienced by non-users of alcohol. Further, current alcohol users had similar levels of estradiol, estrone, and testosterone compared to non-users of alcohol. CONCLUSIONS: These data suggest that current alcohol use is associated with a reduced risk of any, severe, and frequent hot flashes in midlife women by a mechanism that may not include changes in sex steroid hormone levels.

Polymorphisms in cytochrome P4503A5 (CYP3A5) may be associated with race and tumor characteristics, but not metabolism and side effects of tamoxifen in breast cancer patients.

Tamoxifen (TAM) is widely used for treatment and prevention of breast cancer. TAM is metabolized by cytochrome P450 (CYP450) enzymes, including CYP3A5. Although two genetic polymorphisms in CYP3A5 are known (CYP3A5*3 and CYP3A5*6), the effects of these polymorphisms on TAM metabolism, TAM side effects, and tumor characteristics are unknown. Thus, this work tested the hypothesis that CYP3A5 polymorphisms are associated with differential TAM levels, TAM side effects, and tumor characteristics in breast cancer patients. Postmenopausal women with breast cancer (n=98) were recruited from a single cancer center. Polymorphic status was established using polymerase chain reactions (PCR). The associations between polymorphic status, race, TAM levels, side effects, and tumor characteristics were assessed using t-tests and logistic regression models. The data indicate that 40.7% of the breast cancer patients had the CYP3A5*3 polymorphism, and 9.1% had the CYP3A5*6 polymorphism. In addition, Caucasian women were 26 times more likely to carry the CYP3A5*3 polymorphism than African American (AA) women, whereas AA women were nine times more likely to carry the CYP3A5*6 polymorphism than Caucasian women. No significant differences were seen in TAM or TAM metabolite levels or TAM side effects by polymorphic status. There was a significant difference, however, in mean tumor size in women with the CYP3A5*6 polymorphism (3.6+/-0.98 cm) compared to those without the polymorphism (2.0+/-0.18 cm) (P<0.02). Taken together, these data suggest that racial differences in CYP3A5 polymorphisms exist although the polymorphisms do not appear to be associated with levels of TAM metabolites and side effects.

Medication use, tamoxifen (TAM), and TAM metabolite concentrations in women with breast cancer.

Tamoxifen (TAM) is commonly used as an adjuvant treatment for breast cancer. Although patients taking TAM are often taking medications for comorbidities, data regarding the interaction of TAM with other medications are limited. Thus, this study was carried out to determine whether medications co-prescribed with TAM significantly influence the plasma concentrations of TAM and its metabolites (N-desmethyltamoxifen; N-DMT and 4-hydroxytamoxifen; 4-OHT) in 98 women diagnosed with breast cancer. Participants taking diuretics had significantly higher plasma concentrations of TAM and N-DMT than participants not taking a diuretic. Arthritis/pain medication intake was negatively associated with plasma TAM concentrations. Chemotherapeutic agents, allergy drugs, anti-depressants, and diabetes medications did not significantly alter plasma TAM or metabolite concentrations. This suggests that diuretic or an arthritis/pain medication may affect TAM metabolism.

Association of tamoxifen (TAM) and TAM metabolite concentrations with self-reported side effects of TAM in women with breast cancer.

The positive effects of tamoxifen (TAM) on breast cancer recurrence and survival as well as on overall mortality have led to its use as the predominant adjuvant therapy among women with breast cancer. However, the association of TAM intake with undesirable side effects has been reported in numerous studies. This analysis was carried out to assess whether the concentrations of TAM or TAM metabolites, N -desmethyltamoxifen ( N -DMT) and 4-hydroxytamoxifen (4-OHT), were associated with self-reported side effects of TAM. Participants were 99 breast cancer patients who had been taking TAM for at least 30 days. Each participant completed a questionnaire that was used to ascertain whether she experienced certain specific symptoms while taking TAM. In addition, each woman provided a blood sample that was used to measure plasma concentrations of TAM, N -DMT, and 4-OHT by high performance liquid chromatography. Results of the analysis showed that women who experienced at least one TAM-related side effect had significantly higher levels of TAM than women not experiencing any TAM-related side effects. Furthermore, women who reported experiencing visual problems had significantly higher levels of both TAM and N -DMT compared to those women who reported experiencing no visual problems. The levels of 4-OHT were negatively associated with the occurrence of vaginal discharge. The results of this study suggest that the self-reported occurrence of certain symptoms during TAM treatment is related to TAM metabolism. Future studies should assess subgroups of women with specific TAM and TAM metabolite profiles to determine whether alternate, equally effective therapies would decrease their risk of experiencing certain undesirable side effects.

Aging may be associated with concentrations of tamoxifen and its metabolites in breast cancer patients.

BACKGROUND: Although tamoxifen (TAM) is the predominant adjuvant therapy for estrogen receptor positive (ER(+)) breast tumors, 50% of breast cancer patients do not respond positively to this therapy, or they experience adverse side effects. This variability in TAM responsiveness may be due to differences in TAM metabolism that stem from differences in race, age, and body mass index (BMI). Thus, the purpose of this study was to test the hypothesis that race, age, and BMI are associated with the metabolism of TAM to two primary metabolites, N-desmethyltamoxifen (N-DMT) and 4-hydroxytamoxifen (4-OHT). METHODS: The study design was cross-sectional, and data were analyzed using independent sample t tests and multiple linear regression models. Breast cancer patients (n = 99) taking TAM for at least 30 days were recruited from a local hospital clinic. Each participant provided informed consent, completed a questionnaire, and donated a blood sample. The questionnaire was used to ascertain race, age, and BMI. The blood samples were used to measure plasma concentrations of TAM, N-DMT, and 4-OHT. RESULTS: Plasma concentrations of TAM, N-DMT, and 4-OHT differed among individual patients. Age, but not race and BMI, was positively associated with plasma concentrations of TAM and N-DMT, even after adjustment for potential confounders (p = 0.02 for TAM and p = 0.03 for N-DMT). CONCLUSIONS: This study suggests that aging may alter the metabolism of TAM. As increased levels of TAM and TAM metabolites may provide a possible explanation for why older women taking TAM are at increased risk for adverse side effects, future studies should determine whether age-related differences in the concentrations of TAM and TAM metabolites are associated with differences in TAM toxicity or responsiveness.