Rare earth elements in sands collected from Southern California sea beaches

Rare earth elements (REEs) are considered the limiting resources for advancing clean technologies and electronics. Because global REEs reserve is limited, non-conventional and secondary sources are being investigated for recovery. Here, we investigated wet and dry sand from seven Southern California beaches for sixteen REEs. These include five light REEs, two medium REEs, and nine heavy REEs, separated by their atomic weight. The mass of the magnetically separated compounds ranged from 15.19 to 129.91 g per kg of dry sand in the studied sea beaches in Southern California. The total REEs concentration ranged from 1168.1 to 6816.7 μg per kg of wet sand (dry sand basis) and 1474.7-7483.8 μg per kg of dry sand. Cerium (Ce) and Yttrium (Y) were the most prevalent REEs in these beaches ranging from 387.4 to 2241.1 μg kg-1 and 104.5-2302.3 μg kg-1 of sand respectively. This study found light REEs concentration accounted for 70-80% of total rare earth elements in the studied beaches. The concentrations of the analyzed REEs were significantly different (p < 0.05) from each other in the studied beaches. Additionally, Pearson correlation showed that the REEs were strongly correlated (r ≥ 0.83) with each other in the reported sea beaches, indicating a similar origin of the REEs. The dominant heavy metals in the studied samples were Vanadium (V), Chromium (Cr), Cobalt (Co), Nickel (Ni), Copper (Cu), Zinc (Zn), and Strontium (Sr). Dominant minerals identified in sands were quartz, anorthite, ilmenite, and xenotime. All the beaches are lowly enriched with REEs, and any of the REEs caused no ecological risk or pollution. Similarly, no pollution/ecological risk was observed for the analyzed heavy metals. This study identified beach sand as a potential REEs source and demonstrated an easy separation of REEs containing magnetic compounds from sand.

Quantitative multiplex PCR analysis for large rearrangements in the MLH1 and MSH2 genes for hereditary non- polyposis colorectal cancer

4109

Background: Hereditary non-polyposis colon cancer (HNPCC) is caused by germline mutations in the mismatch repair genes MLH1, MSH2, MSH6 and PMS2. HNPCC patients have ∼80% increased risk of colon cancer, and elevated risk for cancers of the endometrium, ovary, stomach, small intestine and upper urinary tract. Molecular genetic testing in HNPCC families showed that ∼90% of cases are due to MLH1 and MSH2, 7–10% to MSH6, and <5% to PMS2. The majority are point mutations detectable by sequencing; however, about 5% and 20% of mutations in MLH1 and MSH2, respectively, are large rearrangements that require other detection techniques such as Southern blot or multiplex ligation-dependent probe amplification (MLPA). Our laboratory had previously developed and implemented a quantitative multiplex PCR (QMPCR) endpoint assay for clinical testing for large rearrangements in the BRCA1 and BRCA2 genes. We have developed a similar assay for the MLH1 and MSH2 genes in HNPCC which we refer to as CART (Colorectal cancer Rearrangement Test). Methods: CART consists of 9 multiplexes of 8–12 amplicons each, with at least 2 amplicons targeting each coding exon, promoter, and 3’UTR of both genes. Copy numbers are normalized against MLH1, MSH2, and two unlinked control genes. Internally developed software provides automated analysis and statistical confidence levels for the presence or absence of large rearrangements. Results: Initial validation of CART has been performed on 14 MLH1 or MSH2 rearrangement-positive and 30 negative DNA samples. Results were 100% concordant with previous Southern blot data, as well as supplemental MLPA studies. CART has greatly improved turnaround time, accuracy, and consistency compared to Southerns and MLPA. Conclusions: QMPCR is a superior diagnostic tool for detecting large rearrangements in disease genes. Validation of CART for MLH1 and MSH2 rearrangements is underway on a larger set of previously genotyped samples in a blinded manner. In conjunction with sequencing of the MLH1 and MSH2 genes, the CART assay is expected to improve molecular diagnostic testing on individuals at risk for HNPCC.

No significant financial relationships to disclose.

Molecular genetic testing for large genomic deletion and duplication mutations in the BRCA1 and BRCA2 genes for hereditary breast and ovarian cancer

10513

Background: Mutations in the BRCA1 and BRCA2 genes are comprised of a majority of mutations that are detectable by sequence analysis, and a minority of large genomic deletion and duplication mutations that are detected by methods different than sequencing. Our laboratory developed and implemented a clinical assay for large rearrangements that we refer to as BART (BRCA1/2 Rearrangement Test). We validated the performance of BART using a completely anonymous large number of breast/ovarian cancer patient samples. We also demonstrated superior performance of BART versus other dosage-sensitive methods including Multiplex Ligation-dependent Probe Amplification (MLPA). Methods: BART utilizes quantitative endpoint polymerase chain reaction (PCR) in a multiplexed fluorescent format. Eleven multiplex PCR reactions were designed to contain two amplicons targeting the promoter region, all coding exons, and flanking regions of BRCA1 and BRCA2. An automated likelihood-based analysis application normalizes target amplicon copy number between BRCA1, BRCA2 and three control genes. Deletions and duplications are identified with a statistical confidence level. Results: Based on clinical and family history criteria, 1,035 patients were identified as severe-risk during the initial months of clinical BART analysis at Myriad Genetic Laboratories. All patients were initially tested for Comprehensive BRACAnalysis which includes BRCA1 and BRCA2 full gene sequencing plus large rearrangement panel testing for 5 recurrent BRCA1 mutations. Among severe-risk patients, 302 (29.2%) were positive for a BRCA1 or BRCA2 mutation by sequencing, 9 (0.9%) were positive by large rearrangement panel testing and an additional 27(2.6%) tested positive by BART for large genomic rearrangements. The total detection rate for deleterious mutations in severe-risk individuals was therefore 32.7%. Conclusions: Our initial clinical data indicate that BART testing is appropriate for high-risk patients identified on the basis of personal and family history criteria.

No significant financial relationships to disclose.

Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein

At the end of the 35S rRNA gene within ribosomal DNA (rDNA) repeats in Saccharomyces cerevisiae lies an enhancer that has been shown to greatly stimulate rDNA transcription in ectopic reporter systems. We found, however, that the enhancer is not necessary for normal levels of rRNA synthesis from chromosomal rDNA or for cell growth. Yeast strains which have the entire enhancer from rDNA deleted did not show any defects in growth or rRNA synthesis. We found that the stimulatory activity of the enhancer for ectopic reporters is not observed in cells with disrupted nucleolar structures, suggesting that reporter genes are in general poorly accessible to RNA polymerase I (Pol I) machinery in the nucleolus and that the enhancer improves accessibility. We also found that a fob1 mutation abolishes transcription from the enhancer-dependent rDNA promoter integrated at the HIS4 locus without any effect on transcription from chromosomal rDNA. FOB1 is required for recombination hot spot (HOT1) activity, which also requires the enhancer region, and for recombination within rDNA repeats. We suggest that Fob1 protein stimulates interactions between rDNA repeats through the enhancer region, thus helping ectopic rDNA promoters to recruit the Pol I machinery normally present in the nucleolus.