► Identifying genetic markers for yield requires rapid quantification of crop traits. ► Proximal sensing offers promise for field-based phenotyping (FBP). ► Efficient data integration and ...modeling-assisted analysis are key for FBP. ► FBP scaled to thousands of field plots is a feasible, attainable goal. ► FBP systems require new, integrative collaborations that cross disciplines.
A major challenge for crop research in the 21st century is how to predict crop performance as a function of genetic architecture. Advances in “next generation” DNA sequencing have greatly improved genotyping efficiency and reduced genotyping costs. Methods for characterizing plant traits (phenotypes), however, have much progressed more slowly over the past 30 years, and constraints in phenotyping capability limit our ability to dissect the genetics of quantitative traits, especially those related to harvestable yield and stress tolerance. As a case in point, mapping populations for major crops may consist of 20 or more families, each represented by as many as 200 lines, necessitating field trials with over 20,000 plots at a single location. Investing in the resources and labor needed to quantify even a few agronomic traits for linkage with genetic markers in such massive populations is currently impractical for most breeding programs. Herein, we define key criteria, experimental approaches, equipment and data analysis tools required for robust, high-throughput field-based phenotyping (FBP). The focus is on simultaneous proximal sensing for spectral reflectance, canopy temperature, and plant architecture where a vehicle carrying replicated sets of sensors records data on multiple plots, with the potential to record data throughout the crop life cycle. The potential to assess traits, such as adaptations to water deficits or acute heat stress, several times during a single diurnal cycle is especially valuable for quantifying stress recovery. Simulation modeling and related tools can help estimate physiological traits such as canopy conductance and rooting capacity. Many of the underlying techniques and requisite instruments are available and in use for precision crop management. Further innovations are required to better integrate the functions of multiple instruments and to ensure efficient, robust analysis of the large volumes of data that are anticipated. A complement to the core proximal sensing is high-throughput phenotyping of specific traits such as nutrient status, seed composition, and other biochemical characteristics, as well as underground root architecture. The ability to “ground truth” results with conventional measurements is also necessary. The development of new sensors and imaging systems undoubtedly will continue to improve our ability to phenotype very large experiments or breeding nurseries, with the core FBP abilities achievable through strong interdisciplinary efforts that assemble and adapt existing technologies in novel ways.
To understand the genetic mechanisms driving variant and IGHV4-34-expressing hairy-cell leukemias, we performed whole-exome sequencing of leukemia samples from ten affected individuals, including six ...with matched normal samples. We identified activating mutations in the MAP2K1 gene (encoding MEK1) in 5 of these 10 samples and in 10 of 21 samples in a validation set (overall frequency of 15/31), suggesting potential new strategies for treating individuals with these diseases.
To assess the influence of drug; dosing regimen; and traditional, nontraditional, and genetic risk factors on the incidence of choroidal neovascularization (CNV) in the fellow eye of patients treated ...for CNV with ranibizumab or bevacizumab.
Cohort study of patients enrolled in a multicenter, randomized clinical trial.
Patients with no CNV in the fellow eye at the time of enrollment in the Comparison of Age-Related Macular Degeneration Treatments Trials (CATT).
Eligibility criteria for the clinical trial required that study eyes have evidence on fluorescein angiography and optical coherence tomography of CNV secondary to age-related macular degeneration (AMD) and visual acuity between 20/25 and 20/320. Treatment for the study eye was assigned randomly to either ranibizumab or bevacizumab and to 3 different regimens for dosing over a 2-year period. The genotypes for 4 single nucleotide polymorphisms (SNPs) associated with risk of AMD were determined. Only patients without CNV in the fellow eye at baseline were considered at risk. The CATT ophthalmologists examined patients every 4 weeks through 2 years and recorded treatment for CNV in the fellow eye.
Development of CNV in the fellow eye.
Among 1185 CATT participants, 727 (61%) had no CNV in the fellow eye at enrollment. At 2 years, CNV had developed in 75 (20.6%) of 365 patients treated with ranibizumab and in 60 (16.6%) of 362 patients treated with bevacizumab (absolute difference, 4.0%; 95% confidence interval CI, -1.7% to 9.6%; P = 0.17). The risk ratio for pro re nata dosing relative to monthly dosing was 1.1 (95% CI, 0.8-1.6). Greater elevation of the retinal pigment epithelium and fluid in the foveal center of the study eye were associated with increased incidence of CNV in the fellow eye. Incidence was not associated with genotype on rs1061170 (CFH), rs10490924 (ARMS2), rs11200638 (HTRA1), and rs2230199 (C3; P>0.35).
Through 2 years, there was no statistically significant difference between ranibizumab and bevacizumab in incidence of CNV in the fellow eye. Genotype on 4 SNPs previously found to be associated with AMD did not affect the risk of CNV in the fellow eye among CATT patients.
Proprietary or commercial disclosure may be found after the references.
The Extracellular RNA Communication Consortium (ERCC) was launched to accelerate progress in the new field of extracellular RNA (exRNA) biology and to establish whether exRNAs and their carriers, ...including extracellular vesicles (EVs), can mediate intercellular communication and be utilized for clinical applications. Phase 1 of the ERCC focused on exRNA/EV biogenesis and function, discovery of exRNA biomarkers, development of exRNA/EV-based therapeutics, and construction of a robust set of reference exRNA profiles for a variety of biofluids. Here, we present progress by ERCC investigators in these areas, and we discuss collaborative projects directed at development of robust methods for EV/exRNA isolation and analysis and tools for sharing and computational analysis of exRNA profiling data.
The Extracellular RNA Communication Consortium (ERCC) presents progress toward understanding the biology of extracellular RNAs and their use as biomarkers and therapeutics.
Reference standard NIST SRM 1633b and FA 345, a fly ash sample from an eastern U.S. coal power plant, were analyzed to determine and quantify the mineralogical association of rare earth elements ...(REE). These analyses were completed using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and a scanning electron microscope, equipped with an energy-dispersive X-ray spectrometer (SEM-EDS). Internal standardization was avoided by quantifying elemental concentrations by normalizing to 100% oxides. Mineral grains containing elevated REE concentrations were found in diverse chemical environments, but were most commonly found in regions where Al and Si were predominant. Dividing the spot analyses into time segments yielded plots that showed the REE content changing over time as individual mineral grains were being ablated. SEM-EDS images of FA 345 confirmed the trends that were found in the LA-ICP-MS results. Small grains of apatite, monazite, or zircon were frequently observed as free mineral grains or embedded in amorphous aluminosilicate glass and were not associated with ferrous particles. This finding is consistent with previous reports that magnetic enrichment may be an effective way of concentrating non-magnetic REE phases. Furthermore, aggressive mechanical and chemical-based separation schemes will be required to separate and recover REE from aluminosilicate glass.
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•Mineral grains containing elevated REE were located within fly ash samples, usually in regions where Al and Si were predominant.•Dividing the LA-ICP-MS spots into time segments yielded plots showing REE content changing over time as individual mineral grains were ablated.•SEM-EDS images confirmed that small free REE mineral grains were frequently observed or embedded in amorphous glass, but not with ferrous particles.•Findings are consistent with previous reports that magnetic enrichment of fly ash may be an effective way of concentrating non-magnetic REE phases.
Abstract
Motivation
When rare missense variants are clinically interpreted as to their pathogenicity, most are classified as variants of uncertain significance (VUS). Although functional assays can ...provide strong evidence for variant classification, such results are generally unavailable. Multiplexed assays of variant effect can generate experimental ‘variant effect maps’ that score nearly all possible missense variants in selected protein targets for their impact on protein function. However, these efforts have not always prioritized proteins for which variant effect maps would have the greatest impact on clinical variant interpretation.
Results
Here, we mined databases of clinically interpreted variants and applied three strategies, each building on the previous, to prioritize genes for systematic functional testing of missense variation. The strategies ranked genes (i) by the number of unique missense VUS that had been reported to ClinVar; (ii) by movability- and reappearance-weighted impact scores, to give extra weight to reappearing, movable VUS and (iii) by difficulty-adjusted impact scores, to account for the more resource-intensive nature of generating variant effect maps for longer genes. Our results could be used to guide systematic functional testing of missense variation toward greater impact on clinical variant interpretation.
Availability and implementation
Source code available at: https://github.com/rothlab/mave-gene-prioritization
Supplementary information
Supplementary data are available at Bioinformatics online.
Nicotinamide phosphoribosyltransferase (NAMPT) has been extensively studied due to its essential role in NAD+ biosynthesis in cancer cells and the prospect of developing novel therapeutics. To ...understand how NAMPT regulates cellular metabolism, we have shown that the treatment with FK866, a specific NAMPT inhibitor, leads to attenuation of glycolysis by blocking the glyceraldehyde 3-phosphate dehydrogenase step (Tan, B., Young, D. A., Lu, Z. H., Wang, T., Meier, T. I., Shepard, R. L., Roth, K., Zhai, Y., Huss, K., Kuo, M. S., Gillig, J., Parthasarathy, S., Burkholder, T. P., Smith, M. C., Geeganage, S., and Zhao, G. (2013) Pharmacological inhibition of nicotinamide phosphoribosyltransferase (NAMPT), an enzyme essential for NAD+ biosynthesis, in human cancer cells: metabolic basis and potential clinical implications. J. Biol. Chem. 288, 3500–3511). Due to technical limitations, we failed to separate isotopomers of phosphorylated sugars. In this study, we developed an enabling LC-MS methodology. Using this, we confirmed the previous findings and also showed that NAMPT inhibition led to accumulation of fructose 1-phosphate and sedoheptulose 1-phosphate but not glucose 6-phosphate, fructose 6-phosphate, and sedoheptulose 7-phosphate as previously thought. To investigate the metabolic basis of the metabolite formation, we carried out biochemical and cellular studies and established the following. First, glucose-labeling studies indicated that fructose 1-phosphate was derived from dihydroxyacetone phosphate and glyceraldehyde, and sedoheptulose 1-phosphate was derived from dihydroxyacetone phosphate and erythrose via an aldolase reaction. Second, biochemical studies showed that aldolase indeed catalyzed these reactions. Third, glyceraldehyde- and erythrose-labeling studies showed increased incorporation of corresponding labels into fructose 1-phosphate and sedoheptulose 1-phosphate in FK866-treated cells. Fourth, NAMPT inhibition led to increased glyceraldehyde and erythrose levels in the cell. Finally, glucose-labeling studies showed accumulated fructose 1,6-bisphosphate in FK866-treated cells mainly derived from dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Taken together, this study shows that NAMPT inhibition leads to attenuation of glycolysis, resulting in further perturbation of carbohydrate metabolism in cancer cells. The potential clinical implications of these findings are also discussed.
NAMPT inhibition leads to attenuation of glycolysis in cancer cells.
NAMPT inhibition also perturbs other carbohydrate metabolism, resulting in elevated fructose 1-phosphate, sedoheptulose 1-phosphate, glyceraldehyde, and erythrose levels.
Condensation of dihydroxyacetone phosphate/glyceraldehyde and dihydroxyacetone phosphate/erythrose by aldolase leads to increased fructose 1-phosphate and sedoheptulose 1-phosphate, respectively.
NAMPT plays a key role in regulating glycolysis-related carbohydrate metabolism in cancer cells.
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The supply and price of rare earth elements (REEs) have become a concern to many countries in the world, which has led to renewed interest in exploration and recovery of REEs from ...secondary or waste sources. Potential high REE waste sources that are of particular interest are coal mining, preparation, combustion, and other fossil energy by-products, including those from natural gas production. In this work, we have examined a set of five solid samples from the treatment of produced and flowback water containing elevated concentrations of barium. In order to confirm the correct concentrations of Eu, we studied these materials using sector field inductively coupled plasma mass spectrometry (SF-ICP-MS), which is capable of resolving species of nearly identical masses, including Eu and BaO. While the use of quadrupole inductively coupled plasma mass spectrometry (Q-ICP-MS) for the REE analysis of most geological sample matrices should pose no problem, the presence of large amounts of Ba, as encountered in water treatment solids from natural gas produced and flowback samples may require SF-ICP-MS for accurate determination of all REEs.
PAX-fusion negative rhabdomyosarcoma (FN RMS) is driven by alterations in the RAS/MAP kinase pathway and is partially responsive to MEK inhibition. Overexpression of IGF1R and its ligands is also ...observed in FN RMS. Preclinical and clinical studies have suggested that IGF1R is itself an important target in FN RMS. Our previous studies revealed preclinical efficacy of the MEK1/2 inhibitor, trametinib, and an IGF1R inhibitor, BMS-754807, but this combination was not pursued clinically due to intolerability in preclinical murine models. Here, we sought to identify a combination of an MEK1/2 inhibitor and IGF1R inhibitor, which would be tolerated in murine models and effective in both cell line and patient-derived xenograft models of RAS-mutant FN RMS.
Using proliferation and apoptosis assays, we studied the factorial effects of trametinib and ganitumab (AMG 479), a mAb with specificity for human and murine IGF1R, in a panel of RAS-mutant FN RMS cell lines. The molecular mechanism of the observed synergy was determined using conventional and capillary immunoassays. The efficacy and tolerability of trametinib/ganitumab was assessed using a panel of RAS-mutated cell-line and patient-derived RMS xenograft models.
Treatment with trametinib and ganitumab resulted in synergistic cellular growth inhibition in all cell lines tested and inhibition of tumor growth in four of six models of RAS-mutant RMS. The combination had little effect on body weight and did not produce thrombocytopenia, neutropenia, or hyperinsulinemia in tumor-bearing SCID beige mice. Mechanistically, ganitumab treatment prevented the phosphorylation of AKT induced by MEK inhibition alone. Therapeutic response to the combination was observed in models without a mutation in the PI3K/PTEN axis.
We demonstrate that combined trametinib and ganitumab is effective in a genomically diverse panel of RAS-mutated FN RMS preclinical models. Our data also show that the trametinib/ganitumab combination likely has a favorable tolerability profile. These data support testing this combination in a phase I/II clinical trial for pediatric patients with relapsed or refractory RAS-mutated FN RMS.
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