Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Breast Tumor Laterality in the United States Depends Upon The Country of Birth, But Not Race.

More breast cancers are diagnosed in the left breast than the right. The ratio (l/r) is called the laterality ratio. We analyzed 1.2 million cases of breast cancer diagnosed in the US between 1973 and 2010 and recorded by the Surveillance, Epidemiology, and End Results (SEER) program. We found that the laterality ratio depends upon the country of birth, but not race of the patient. We identified five countries of birth that had p-values larger than 0.995, while we expected to see less than 1. Those born in Japan (l/r=1.14, p=0.997), the Ryukyu Islands (l/r= 2.6, p=0.998), Laos (l/r=1.62, p=0.9999) and Algeria (l/r=2.1 p=0.9959) had significantly larger laterality ratios compared to the overall SEER population (l/r=1.04). Those born in Poland (l/r=0.92, p=0.997) had a laterality ratio significantly less than expected. We compared the laterality ratio calculated for tumors occurring in each quadrant of the breast for two immigrant populations: those born in Japan and those born in Poland. We found the only significant difference was in the laterality ratio of the upper outer quadrant. Thus, the birthplace effect appears to only occur in the upper outer quadrant of the breast. Finally, we found a small, but statistically significant, increase in the breast cancer laterality ratio with age, and decrease with birth year and year of diagnosis

Breast tumor laterality in the United States depends upon the country of birth, but not race.

More breast cancers are diagnosed in the left breast than the right. The ratio (l/r) is called the laterality ratio. We analyzed 1.2 million cases of breast cancer diagnosed in the US between 1973 and 2010 and recorded by the Surveillance, Epidemiology, and End Results (SEER) program. We found that the laterality ratio depends upon the country of birth, but not race of the patient. We identified five countries of birth that had p-values larger than 0.995, while we expected to see less than 1. Those born in Japan (l/r = 1.14, p = 0.997), the Ryukyu Islands (l/r = 2.6, p = 0.998), Laos (l/r = 1.62, p = 0.9999) and Algeria (l/r = 2.1 p = 0.9959) had significantly larger laterality ratios compared to the overall SEER population (l/r = 1.04). Those born in Poland (l/r = 0.92, p = 0.997) had a laterality ratio significantly less than expected. We compared the laterality ratio calculated for tumors occurring in each quadrant of the breast for two immigrant populations: those born in Japan and those born in Poland. We found the only significant difference was in the laterality ratio of the upper outer quadrant. Thus, the birthplace effect appears to only occur in the upper outer quadrant of the breast. Finally, we found a small, but statistically significant, increase in the breast cancer laterality ratio with age, and decrease with birth year and year of diagnosis

Breast tumor laterality in the United States depends upon the country of birth, but not race.

More breast cancers are diagnosed in the left breast than the right. The ratio (l/r) is called the laterality ratio. We analyzed 1.2 million cases of breast cancer diagnosed in the US between 1973 and 2010 and recorded by the Surveillance, Epidemiology, and End Results (SEER) program. We found that the laterality ratio depends upon the country of birth, but not race of the patient. We identified five countries of birth that had p-values larger than 0.995, while we expected to see less than 1. Those born in Japan (l/r = 1.14, p = 0.997), the Ryukyu Islands (l/r = 2.6, p = 0.998), Laos (l/r = 1.62, p = 0.9999) and Algeria (l/r = 2.1 p = 0.9959) had significantly larger laterality ratios compared to the overall SEER population (l/r = 1.04). Those born in Poland (l/r = 0.92, p = 0.997) had a laterality ratio significantly less than expected. We compared the laterality ratio calculated for tumors occurring in each quadrant of the breast for two immigrant populations: those born in Japan and those born in Poland. We found the only significant difference was in the laterality ratio of the upper outer quadrant. Thus, the birthplace effect appears to only occur in the upper outer quadrant of the breast. Finally, we found a small, but statistically significant, increase in the breast cancer laterality ratio with age, and decrease with birth year and year of diagnosis

The lines indicate the 95% confidence interval ranges for the laterality, as measured in tumors occurring in different regions of the breast.

<p>The lines indicate the 95% confidence interval ranges for the laterality, as measured in tumors occurring in different regions of the breast.</p

Laterality ratio by country of birth.

<p>Laterality ratio by country of birth.</p

The circles indicate the measured ratio of the number of breast cancers diagnosed in the left breast as compared to the right breast.

<p>The error bars indicate 95% confidence intervals. The solid line is the best fit to a linear model. The best fit slope was −0.0012 (95% confidence interval 0.0104, 0.0042) ratio units per year. The probability that this slope would occur by chance, given that the actual slope is 0, is 0.000008, about one chance in 100,000.</p

The lines indicate the 95% confidence interval ranges for the laterality, as measured in tumors occurring in different regions of the breast.

<p>We compared how these were distributed for people born in Poland, Japan, and the overall population. We found the only significant difference between Poland and Japan occurs in the upper outer quadrant of the breast.</p