Chapter I: Selenium in soils and plants from native and irrigated lands at the Kendrick Reclamation Project Area, Wyoming

In response to earlier findings or elevated levels of selenium in the Kendrick area, two detailed geochemical surveys were conducted in 1988 to stud y the distribution of selenium in soils (0-1 m depth), and new growth of associated big sagebrush (Artemisia tridentata Nutt.) and alfalfa (Medicago sativa L.). A survey of the native rangeland focused on specific geologic units as sources of selenium; whereas, a gridded survey of the irrigated lands assessed the extent of its mobilization, transport, and concentration. Only three of the approximately 200 soil samples contained total selenium slightly greater than the 3.3 ppm maximum baseline established for soils from the northern Great Plains. In contrast, selenium concentrations in about one-fifth of the big sagebrush samples exceeded the 1.1 ppm maximum baseline established for this species from the West. Selenium tended to be elevated, but not uniformly so, in both soils and sagebrush collected from areas underlain by the Cody Shale of Cretaceous age. Alfalfa from about 15% of the irrigated fields contained selenium in excess of about 4 ppm, levels reported to be potentially hazardous to livestock if fed over prolonged periods. Most of these samples were concentrated in an area of 11 contiguous sections where selenium-enriched surface and drain waters also occurred. The agricultural soils just to the north of this seleniferous area had slightly higher levels of selenium compared to those elsewhere in the irrigated lands. At present, the cause for this displaced anomaly is unclear. Followup sampling in 1989 of two fields where selenium levels in alfalfa collected in 1988 were 25 and 15 ppm yielded samples that contained only 0.2 and 0.7 ppm, respectively. This dramatic and puzzling temporal disparity may be explained by marked differences in weather patterns and irrigation practices for the 2 years. Such a disparity underscores the need to monitor a potentially seleniferous area over an extended period

Advancing biological understanding and therapeutics discovery with small-molecule probes

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the NIH launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines but also highlight the need to innovate the science of therapeutic discovery

Integrative molecular characterization of malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune-checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options. SIGNIFICANCE: Through a comprehensive integrated genomic study of 74 MPMs, we provide a deeper understanding of histology-independent determinants of aggressive behavior, define a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity, and discovered strong expresssion of the immune-checkpoint gene VISTA in epithelioid MPM

Performance of Myzus persicae (Hemiptera : Aphididae) clones on different host-plants and their host preference

The performance of eighteen clones of Myzus persicae (Sulzer) on pepper and tobacco plants at 20degreesC and L16:D8 and the choice of young adult apterae between tobacco and pepper leaf-discs were examined. The clones were collected from weeds and peach in two tobacco-growing regions: Katerini, northern Greece and Karditsa, central Greece (only from weeds) and from Lehonia, central eastern Greece where tobacco is not cultivated. All clones did well on both hosts. However, the analysis of data revealed a significant effect of 'region / host plant origin' on aphid performance. The mean values of adult weight, intrinsic rate of increase and fecundity of the clones collected in Lehonia and reared on tobacco were significantly lower than the observed values for clones from Katerini and Karditsa. Aphids from Lehonia had significantly higher mean values for developmental time on tobacco than clones from the other regions whereas the opposite was observed when aphids were reared on pepper. Aphids collected in Lehonia performed better on pepper than those originating from the tobacco-growing regions. A choice test revealed differences among the clones originating from different regions. Fifty three percent and 43% of aphids from weeds and peach from Lehonia, respectively, chose pepper. By comparison 41.5% and 40.0% of aphids from peach and weeds from Katerini, respectively and 49.5% of aphids from Karditsa preferred tobacco. The results are discussed in relation to host specialization in M. persicae

Selenium in soils and plants from native and irrigated lands at the Kendrick Reclamation Project Area, Wyoming

Please contact the NWISRL if you have a copy of this publication

Chapter I: Selenium in soils and plants from native and irrigated lands at the Kendrick Reclamation Project Area, Wyoming

In response to earlier findings or elevated levels of selenium in the Kendrick area, two detailed geochemical surveys were conducted in 1988 to stud y the distribution of selenium in soils (0-1 m depth), and new growth of associated big sagebrush (Artemisia tridentata Nutt.) and alfalfa (Medicago sativa L.). A survey of the native rangeland focused on specific geologic units as sources of selenium; whereas, a gridded survey of the irrigated lands assessed the extent of its mobilization, transport, and concentration. Only three of the approximately 200 soil samples contained total selenium slightly greater than the 3.3 ppm maximum baseline established for soils from the northern Great Plains. In contrast, selenium concentrations in about one-fifth of the big sagebrush samples exceeded the 1.1 ppm maximum baseline established for this species from the West. Selenium tended to be elevated, but not uniformly so, in both soils and sagebrush collected from areas underlain by the Cody Shale of Cretaceous age. Alfalfa from about 15% of the irrigated fields contained selenium in excess of about 4 ppm, levels reported to be potentially hazardous to livestock if fed over prolonged periods. Most of these samples were concentrated in an area of 11 contiguous sections where selenium-enriched surface and drain waters also occurred. The agricultural soils just to the north of this seleniferous area had slightly higher levels of selenium compared to those elsewhere in the irrigated lands. At present, the cause for this displaced anomaly is unclear. Followup sampling in 1989 of two fields where selenium levels in alfalfa collected in 1988 were 25 and 15 ppm yielded samples that contained only 0.2 and 0.7 ppm, respectively. This dramatic and puzzling temporal disparity may be explained by marked differences in weather patterns and irrigation practices for the 2 years. Such a disparity underscores the need to monitor a potentially seleniferous area over an extended period

Selenium in soils and plants from native and irrigated lands at the Kendrick Reclamation Project Area, Wyoming

Please contact the NWISRL if you have a copy of this publication

Selenium in soils and plants from native and irrigated lands at the Kendrick Reclamation Project Area, Wyoming

Please contact the NWISRL if you have a copy of this publication

Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms

Contains fulltext : 153904.pdf (publisher's version ) (Open Access)Breast cancers with BRCA1 germline mutation have a characteristic DNA copy number (CN) pattern. We developed a test that assigns CN profiles to be 'BRCA1-like' or 'non-BRCA1-like', which refers to resembling a BRCA1-mutated tumor or resembling a tumor without a BRCA1 mutation, respectively. Approximately one third of the BRCA1-like breast cancers have a BRCA1 mutation, one third has hypermethylation of the BRCA1 promoter and one third has an unknown reason for being BRCA1-like. This classification is indicative of patients' response to high dose alkylating and platinum containing chemotherapy regimens, which targets the inability of BRCA1 deficient cells to repair DNA double strand breaks. We investigated whether this classification can be reliably obtained with next generation sequencing and copy number platforms other than the bacterial artificial chromosome (BAC) array Comparative Genomic Hybridization (aCGH) on which it was originally developed. We investigated samples from 230 breast cancer patients for which a CN profile had been generated on two to five platforms, comprising low coverage CN sequencing, CN extraction from targeted sequencing panels (CopywriteR), Affymetrix SNP6.0, 135K/720K oligonucleotide aCGH, Affymetrix Oncoscan FFPE (MIP) technology, 3K BAC and 32K BAC aCGH. Pairwise comparison of genomic position-mapped profiles from the original aCGH platform and other platforms revealed concordance. For most cases, biological differences between samples exceeded the differences between platforms within one sample. We observed the same classification across different platforms in over 80% of the patients and kappa values of at least 0.36. Differential classification could be attributed to CN profiles that were not strongly associated to one class. In conclusion, we have shown that the genomic regions that define our BRCA1-like classifier are robustly measured by different CN profiling technologies, providing the possibility to retro- and prospectively investigate BRCA1-like classification across a wide range of CN platforms