Transcriptionally inactive oocyte-type 5S RNA genes of Xenopus laevis are complexed with TFIIIA in vitro

An extract from whole oocytes of Xenopus laevis was shown to transcribe somatic-type 5S RNA genes approximately 100-fold more efficiently than oocyte-type 5S RNA genes. This preference was at least 10-fold greater than the preference seen upon microinjection of 5S RNA genes into oocyte nuclei or upon in vitro transcription in an oocyte nuclear extract. The approximately 100-fold transcriptional bias in favor of the somatic-type 5S RNA genes observed in vitro in the whole oocyte extract was similar to the transcriptional bias observed in developing Xenopus embryos. We also showed that in the whole oocyte extract, a promoter-binding protein required for 5S RNA gene transcription, TFIIIA, was bound both to the actively transcribed somatic-type 5S RNA gene and to the largely inactive oocyte-type 5S RNA genes. These findings suggest that the mechanism for the differential expression of 5S RNA genes during Xenopus development does not involve differential binding of TFIIIA to 5S RNA genes

CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study

BACKGROUND: Cyclin E1 (CCNE1) is a potential predictive marker and therapeutic target in tubo-ovarian high-grade serous carcinoma (HGSC). Smaller studies have revealed unfavorable associations for CCNE1 amplification and CCNE1 overexpression with survival, but to date no large-scale, histotype-specific validation has been performed. The hypothesis was that high-level amplification of CCNE1 and CCNE1 overexpression, as well as a combination of the two, are linked to shorter overall survival in HGSC. METHODS: Within the Ovarian Tumor Tissue Analysis consortium, amplification status and protein level in 3029 HGSC cases and mRNA expression in 2419 samples were investigated. RESULTS: High-level amplification (>8 copies by chromogenic in situ hybridization) was found in 8.6% of HGSC and overexpression (>60% with at least 5% demonstrating strong intensity by immunohistochemistry) was found in 22.4%. CCNE1 high-level amplification and overexpression both were linked to shorter overall survival in multivariate survival analysis adjusted for age and stage, with hazard stratification by study (hazard ratio [HR], 1.26; 95% CI, 1.08-1.47, p = .034, and HR, 1.18; 95% CI, 1.05-1.32, p = .015, respectively). This was also true for cases with combined high-level amplification/overexpression (HR, 1.26; 95% CI, 1.09-1.47, p = .033). CCNE1 mRNA expression was not associated with overall survival (HR, 1.00 per 1-SD increase; 95% CI, 0.94-1.06; p = .58). CCNE1 high-level amplification is mutually exclusive with the presence of germline BRCA1/2 pathogenic variants and shows an inverse association to RB1 loss. CONCLUSION: This study provides large-scale validation that CCNE1 high-level amplification is associated with shorter survival, supporting its utility as a prognostic biomarker in HGSC

qPCR Estimates of trfA and 16S rRNA concentrations

The data provided are the estimates that resulted from raw qPCR fluorescence data (available upon request). The data are those used in the analyses described in the associated manuscript. See the ReadMe file for column descriptions

An Analysis of Price Determination and Markups in the Air-Conditioning and Heating Equipment Industry

In this report we calculate the change in final consumer prices due to minimum efficiency standards, focusing on a standard economic model of the air-conditioning and heating equipment (ACHE) wholesale industry. The model examines the relationship between the marginal cost to distribute and sell equipment and the final consumer price in this industry. The model predicts that the impact of a standard on the final consumer price is conditioned by its impact on marginal distribution costs. For example, if a standard raises the marginal cost to distribute and sell equipment a small amount, the model predicts that the standard will raise the final consumer price a small amount as well. Statistical analysis suggest that standards do not increase the amount of labor needed to distribute equipment the same employees needed to sell lower efficiency equipment can sell high efficiency equipment. Labor is a large component of the total marginal cost to distribute and sell air-conditioning and heating equipment. We infer from this that standards have a relatively small impact on ACHE marginal distribution and sale costs. Thus, our model predicts that a standard will have a relatively small impact on final ACHE consumer prices. Our statistical analysis of U.S. Census Bureau wholesale revenue tends to confirm this model prediction. Generalizing, we find that the ratio of manufacturer price to final consumer price prior to a standard tends to exceed the ratio of the change in manufacturer price to the change in final consumer price resulting from a standard. The appendix expands our analysis through a typical distribution chain for commercial and residential air-conditioning and heating equipment

An Analysis of Price Determination and Markups in the Air-Conditioning and Heating Equipment Industry

In this report we calculate the change in final consumer prices due to minimum efficiency standards, focusing on a standard economic model of the air-conditioning and heating equipment (ACHE) wholesale industry. The model examines the relationship between the marginal cost to distribute and sell equipment and the final consumer price in this industry. The model predicts that the impact of a standard on the final consumer price is conditioned by its impact on marginal distribution costs. For example, if a standard raises the marginal cost to distribute and sell equipment a small amount, the model predicts that the standard will raise the final consumer price a small amount as well. Statistical analysis suggest that standards do not increase the amount of labor needed to distribute equipment the same employees needed to sell lower efficiency equipment can sell high efficiency equipment. Labor is a large component of the total marginal cost to distribute and sell air-conditioning and heating equipment. We infer from this that standards have a relatively small impact on ACHE marginal distribution and sale costs. Thus, our model predicts that a standard will have a relatively small impact on final ACHE consumer prices. Our statistical analysis of U.S. Census Bureau wholesale revenue tends to confirm this model prediction. Generalizing, we find that the ratio of manufacturer price to final consumer price prior to a standard tends to exceed the ratio of the change in manufacturer price to the change in final consumer price resulting from a standard. The appendix expands our analysis through a typical distribution chain for commercial and residential air-conditioning and heating equipment

Data from: Persistence of antibiotic resistance plasmids in bacterial biofilms

The emergence and spread of antibiotic resistance is a crisis in health care today. Antibiotic resistance is often horizontally transferred to susceptible bacteria by means of multi-drug resistance plasmids that may or may not persist in the absence of antibiotics. Because bacterial pathogens often grow as biofilms, there is a need to better understand the evolution of plasmid persistence in these environments. Here we compared the evolution of plasmid persistence in the pathogen Acinetobacter baumannii when grown under antibiotic selection in biofilms versus well-mixed liquid cultures. After four weeks, clones in which the plasmid was more stably maintained in the absence of antibiotic selection were present in both populations. On average plasmid persistence increased more in liquid batch cultures, but variation in the degree of persistence was greater among biofilm-derived clones. The results of this study show for the first time that the persistence of MDR plasmids improves in biofilm

Economic Impacts of Climate Change on Agricultural Water Use in California

Economic Impacts of Climate Change on Agricultural Water Use in California describes part of a broad spectrum of studies of the California water system that are being conducted to assess the impacts of climate change on urban and agricultural water agencies.    Study topics include methods for measuring the economic value of water supply reliability to water users in California, and methods for projecting changes in supply reliability caused by climate change.   This report describes preliminary work on the first topic. To measure water supply reliability, researchers collected data on several variables, including water deliveries for project districts spanning 20 years, water rights information, water source information and electricity use data related to groundwater pumping.  To measure the economic value of reliability, they collected land value, water price, water transfers for many years, and cropping by districts. The project found that the average magnitude of change in farmland value due to a potential decrease in water availability appears to be larger than that caused by an increase in temperature. This finding suggests that the impact on the availability and reliability of water supply may be the crucial pathway by which climate change affects California agriculture

Program Area Team Lead

Work Authorization MR-00