Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts.

An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction. The enriched SELEX pool was subjected to deep sequencing, and 8865 sequences were mapped to the E. coli genome. These short sequences represent genomic Hfq-aptamers and are part of potential regulatory elements within RNA molecules. The motif 5'-AAYAAYAA-3' was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq. The motif was confirmed to bind Hfq by DMS footprinting. The Hfq aptamers are 4-fold more frequent on the antisense strand of protein coding genes than on the sense strand. They were enriched opposite to translation start sites or opposite to intervening sequences between ORFs in operons. These results expand the repertoire of Hfq targets and also suggest that Hfq might regulate the expression of a large number of genes via interaction with cis-antisense RNAs.

Gene expression patterns in the lungs of patients with primary pulmonary hypertension: a gene microarray analysis.

Primary pulmonary hypertension (PPH) is a disease of unknown etiology characterized by lumen-obliterating endothelial cell proliferation and vascular smooth muscle hypertrophy of the small precapillary pulmonary arteries. Because the vascular lesions are homogeneously distributed throughout the entire lung, we propose that a tissue fragment of the lung is representative of the whole lung. RNA extracted from the fragments is likely to provide meaningful information regarding the changes in gene expression pattern in PPH when compared with structurally normal lung tissue. We hypothesize that the lung tissue gene expression pattern of patients with PPH has a characteristic profile when compared with the gene expression pattern of structurally normal lungs and that this characteristic gene expression profile provides new insights into the pathobiology of PPH. Using oligonucleotide microarray technology, we characterized the expression pattern in the lung tissue obtained from 6 patients with primary pulmonary hypertension (PPH)-including 2 patients with the familial form of PPH (FPPH)-and from 6 patients with histologically normal lungs. For the data analysis, gene clusters were generated and the gene expression pattern differences between PPH and normal lung tissue and between PPH and FPPH lung tissue were compared. All PPH lung tissue samples showed a decreased expression of genes encoding several kinases and phosphatases, whereas several oncogenes and genes coding for ion channel proteins were upregulated in their expression. Importantly, we could distinguish by pattern comparison between sporadic PPH and FPPH, because alterations in the expression of transforming growth factor-beta receptor III, bone morphogenic protein 2, mitogen-activated protein kinase kinase 5, RACK 1, apolipoprotein C-III, and the gene encoding the laminin receptor 1 were only found in the samples from patients with sporadic PPH, but not in FPPH samples. We conclude that the microarray gene expression technique is a new and useful molecular tool that provides novel information pertinent to a better characterization and understanding of the pathobiology of the distinct clinical phenotypes of pulmonary hypertension.

Calculation of dose coefficients for radionuclides produced in a spallation neutron source utilizing NUBASE and the evaluated nuclear structure data file databases.

Based on a mercury spallation neutron source target, the UNLV Transmutation Research Program has identified 72 radionuclides with a half-life greater than or equal to a minute as lacking an appropriate reference for a published dose coefficient according to existing radiation safety dose coefficient databases. A method was developed to compare the nuclear data presented in the ENSDF and NUBASE databases for these 72 radionuclides. Due to conflicting or lacking nuclear data in one or more of the databases, internal and external dose coefficient values have been calculated for only 14 radionuclides, which are not currently presented in Federal Guidance Reports Nos. 11, 12, and 13 or Publications 68 and 72 of the International Commission on Radiological Protection. Internal dose coefficient values are reported for inhalation and ingestion of 1 microm and 5 microm AMAD particulates along with the f1 values and absorption types for the adult worker. Internal dose coefficient values are also reported for inhalation and ingestion of 1 microm AMAD particulates as well as the f1 values and absorption types for members of the public. Additionally, external dose coefficient values for air submersion, exposure to contaminated ground surface, and exposure to soil contaminated to an infinite depth are also presented.

Quality assurance methods and procedures used to verify consistency in calculating dose coefficients.

The development of a spallation neutron source with a mercury target will lead to the production of rare radionuclides. The dose coefficients for many of these radionuclides have not yet been published. A collaboration of universities and national labs has taken on the task of calculating dose coefficients for the rare radionuclides using the software package DCAL. The working group developed a procedure for calculating dose coefficients and a quality assurance (QA) program to verify the calculations completed. The first portion of this QA program was to verify that each participating group could independently reproduce the dose coefficients for a known set of radionuclides. The second effort was to divide the group of rare radionuclides among the independent participants in a manner that assured that each radionuclide would be redundantly and independently calculated, and the results subsequently be submitted for publication in a separate manuscript. The final aspect of this program was to resolve any discrepancies arising among the participants as a group. The output of the various software programs for six QA radionuclides, 144Nd, 201Au, 50V, 61Co, 41Ar, and 38S were compared among all members of the working group. Initially, a few differences in outputs were identified. This exercise identified weaknesses in the procedure, which has since been revised. After the revisions, dose coefficients were calculated and compared to published dose coefficients with good agreement. The present efforts involve generating dose coefficients for the rare radionuclides anticipated to be produced from the spallation neutron source should a mercury target be employed.

Effect of vitamin A on lung tumorigenesis in irradiated and unirradiated strain A mice.

The effect of vitamin A (retinyl acetate) on lung tumor development in strain A mice exposed to radiation was assessed. Four groups of 75 mice were utilized. Two groups were fed a low vitamin A diet (less than 100 IU/100 g diet) and the other 2 were fed a high vitamin A diet (800 IU/100 g diet). After 2 weeks one group maintained on the high vitamin A diet and one group maintained on the low vitamin A diet were given an acute dose of 500 rad of gamma radiation to the thoracic region. Circulating levels of plasma vitamin A in all 4 groups of mice were monitored. A difference in circulating vitamin A in the mice maintained on high and low vitamin A diet became evident by 20 weeks and continued for the duration of the experiment. Mice were killed 18, 26 and 40 weeks post-irradiation, their lungs were removed and the number of surface adenomas were counted. There was a significant increase in the number of mice bearing lung tumors and the mean number of lung tumors per mouse in the irradiated group maintained on the high vitamin A diet at 40 weeks post-irradiation as compared to the irradiated group maintained on a low vitamin A diet. Under the conditions of this experiment the development of pulmonary adenomas in irradiated strain A mice appears to relate directly to circulating levels of vitamin A.

Environmentally acquired lead in the laughing gull, Larus atricilla.

Lead concentrations were measured in eggs, prefledgings and adult laughing gulls collected near Galveston, Texas. No lead was found in eggs. Prefledgling and adult birds had lead ranging from zero to 16 mug/g wet tissue. Liver had the greatest lead concentrations followed by brain, heart and skeletal muscle. There were no significant differences in lead concentrations between fledglings and adults or between males and females.

Background atmospheric 222Rn concentrations outdoors and indoors: a review.

The sources of outdoor and indoor atmospheric radon are examined. The variation of outdoor atmospheric radon with time of day, time of year, altitude and geographic location is quantitatively assessed. Average values of outdoor atmospheric radon concentrations are examined and it is estimated that the mean value for normal areas of the contiguous United States lies in the range of 100-400 pCi/m3 and is probably about 250 pCi/m3. Values for Alaska and Hawaii are an order of magnitude lower. Indoor atmospheric radon concentrations are found to vary with time of day, geographic location and story above ground.

Implementation of the MARSSIM philosophy to evaluate the remedial status of a radioactive waste disposal site at the Idaho National Engineering and Environmental Laboratory. Multi-Agency Radiation Survey and Site Investigation Manual.

Implementation of the MARSSIM remedial-verification protocol at a radioactive waste disposal site is described in some detail to provide a record of the utility of this process. The selected site was the Stationary Low-Power Reactor No. 1 burial ground at the Idaho National Engineering and Environmental Laboratory. Evaluation was restricted to 137Cs in the uppermost 10 cm of potentially contaminated soils. According to the MARSSIM, this site warranted a "Class 1" designation based on previous remedial activities within the burial ground, its status as a radioactive disposal facility, and the anticipated presence of discrete radioactive particles. Nine survey units within the confines of the burial ground were selected, based primarily on the presence of physical boundaries and disparate histories. Surface scans with 100% coverage were performed using a hand-held plastic scintillator and rate meter with audible output. In situ gamma-ray spectrometry was not used for the individual stationary measurements due to the limited area and proximity of engineered barriers. Instead, individual soil samples were obtained using a standard hand-held coring device. The number of soil samples taken from the background reference area and each survey unit were determined with the MARSSIM protocol, which resulted in a total of 160 (including quality-control samples). Two of the nine regions exhibited elevated radiation levels and the null hypothesis could not be rejected in one survey unit, thereby indicating the need for additional remediation. The MARSSIM process proved to be flexible, scientifically rigorous, and cost effective in this field application. Several modifications to the procedure are discussed and offered as recommendations for enhancement of the MARSSIM.

An evaluation of 222Rn concentrations in Idaho groundwater.

Factors potentially correlated with 222Rn concentrations in groundwater were evaluated using a database compiled by the U.S. Geological Survey. These included chemical and radiological factors, and both well depth and discharge rate. The 222Rn concentrations contained within this database were examined as a function of latitude and longitude. It was observed that the U.S. Geological Survey sample locations for 222Rn were not uniformly distributed throughout the state. Hence, additional samples were collected in southeastern Idaho, a region where few 222Rn in water analyses had been performed. 222Rn concentrations in groundwater, in Idaho, were found using ANOVA (alpha = 0.05) to be independent of the chemical, radiological, and well parameters thus far examined. This lack of correlation with other water quality and well parameters is consistent with findings in other geographical locations. It was observed that an inverse relationship between radon concentration and water hardness may exist.

Distribution of 137Cs in soil along Ta-han River Valley in Tau-Yuan County in Taiwan.

Environmental 137Cs contamination was suspected from accidents at spent fuel storage pits of a research reactor site in the Ta-han River valley in Taiwan. In order to further characterize this contamination, soil samples were collected and measured by a gamma-spectroscopy system in 1999. It was found that 137Cs contamination is distributed up to 4 km from the reactor in an area covered mostly by rice and plant fields. 137Cs concentration in the topsoil ranged up to about 1000 Bq kg-1, as compared with soil beyond the contaminated area, which does not exceed 15 Bq kg-1. Spatial distribution of 137Cs was characterized by strong non-uniformity, which complicated our understanding of the distribution pathway of the radionuclides. The highest concentrations of 137Cs, up to more than 1000 Bq kg-1, were found within a few rice fields. The relative location of these rice fields and the water supplies from local streams suggested that the 137Cs was distributed along water pathways in the valley.