ALBERT

Description: Agronomy, Vol. 8, Pages 61: Developmental Morphology and Biomass Yield of Upland and Lowland Switchgrass Ecotypes Grown in Iowa Agronomy doi: 10.3390/agronomy8050061 Authors: Muhammad Aurangzaib Kenneth J. Moore Andrew W. Lenssen Sotirios V. Archontoulis Emily A. Heaton Shuizhang Fei Sustainable development of the bioenergy industry will depend upon the amount and quality of bioenergy feedstock produced. Switchgrass (Panicum virgatum L.) is a model lignocellulosic bioenergy crop but critical information is lacking for improved management, growth, and development simulation model calibration. A field study was conducted near Ames, IA during 2012–2013 with the objective to evaluate upland (“Cave-in-Rock”, ‘Trailblazer’ and ‘Blackwell’) and lowland (“Kanlow” and “Alamo”) switchgrass ecotypes for harvest timing on morphology (i.e., phenology, leaf area index (LAI), and biomass yield). The experiment used a randomized complete block design, with three upland and two lowland varieties harvested at six dates annually. In both years, delaying harvest to later maturity increased biomass yield; lowland cultivars produced greater biomass yield (6.15 tons ha−1) than upland ecotypes (5.10 tons ha−1). Lowland ecotypes had delayed reproductive development compared with upland ecotypes. At the end of both growing seasons, upland ecotypes had greater mean stage count (MSC) than lowland ecotypes. “Cave-in-Rock” had greatest MSC and LAI, but did not produce the greatest biomass. Relationships were nonlinear between MSC and biomass yield, with significant cultivar–year interaction. The relationship between biomass yield and MSC will be useful for improving switchgrass, including cultivar selection, fertilizer application, and optimum harvest time.

Description: A physical-biogeochemical model is used to produce a retrospective analysis at 3-km resolution of alongshore phytoplankton variability in the California Current during 1988–2010. The simulation benefits from downscaling a regional circulation reanalysis, which provides improved physical ocean state estimates in the high-resolution domain. The emerging pattern is one of local upwelling intensification in response to increased alongshore wind stress in the lee of capes, modulated by alongshore meanders in the geostrophic circulation. While stronger upwelling occurs near most major topographic features, substantial increases in phytoplankton biomass only ensue where local circulation patterns are conducive to on-shelf retention of upwelled nutrients. Locations of peak nutrient delivery and chlorophyll accumulation also exhibit interannual variability and trends noticeably larger than the surrounding shelf regions, thereby suggesting that long-term planktonic ecosystem response in the California Current exhibits a significant local scale (O(100 km)) alongshore component. ©2018. American Geophysical Union. All Rights Reserved.

Description: A procedure to objectively adjust the error covariance matrices of a variational data assimilation system is presented. It is based on popular diagnostics that utilize differences between observations and prior and posterior model solutions at the observation locations. In the application to a data assimilation system that combines a three-dimensional, physical–biogeochemical ocean model with large datasets of physical and chlorophyll a observations, the tuning procedure leads to a decrease in the posterior model-observation misfit and small improvements in short-term forecasting skill. It also increases the consistency of the data assimilation system with respect to diagnostics, based on linear estimation theory, and reduces signs of overfitting. The tuning procedure is easy to implement and only relies on information that is either prescribed to the data assimilation system or can be obtained from a series of short data assimilation experiments. The implementation includes a lognormal representation for biogeochemical variables and associated modifications to the diagnostics. Furthermore, the effect of the length of the observation window (number and distribution of observations) used to compute the diagnostics and the effect of neglecting model dynamics in the tuning procedure are examined.

Description: During the 2014–15 academic year, the National Oceanic and Atmospheric Administration (NOAA) National Weather Service Storm Prediction Center (SPC) and the University of Oklahoma (OU) School of Meteorology jointly created the first SPC-led course at OU focused on connecting traditional theory taught in the academic curriculum with operational meteorology. This class, “Applications of Meteorological Theory to Severe-Thunderstorm Forecasting,” began in 2015. From 2015 through 2017, this spring–semester course has engaged 56 students in theoretical skills and related hands-on weather analysis and forecasting applications, taught by over a dozen meteorologists from the SPC, the NOAA National Severe Storms Laboratory, and the NOAA National Weather Service Forecast Offices. Following introductory material, which addresses many theoretical principles relevant to operational meteorology, numerous presentations and hands-on activities focused on instructors’ areas of expertise are provided to students. Topics include the following: storm-induced perturbation pressure gradients and their enhancement to supercells, tornadogenesis, tropical cyclone tornadoes, severe wind forecasting, surface and upper-air analyses and their interpretation, and forecast decision-making. This collaborative approach has strengthened bonds between meteorologists in operations, research, and academia, while introducing OU meteorology students to the vast array of severe thunderstorm forecast challenges, state-of-the-art operational and research tools, communication of high-impact weather information, and teamwork skills. The methods of collaborative instruction and experiential education have been found to strengthen both operational–academic relationships and students’ appreciation of the intricacies of severe thunderstorm forecasting, as detailed in this article.

Description: Cytogenetically normal acute myeloid leukaemia (CN-AML) accounts for approximately 25%-30% of paediatric AML cases and carries a high risk of relapse. Minimal residual disease (MRD) is an essential factor in predicting relapse in acute leukaemia but is difficult to track for many CN-AML patients, due to the lack of a distinct and stable molecular marker. Consequently, new biomarkers are urgently required for MRD monitoring of the disease. Splicing variants, products of another hallmark of human cancers, aberrant splicing, have been shown informative in predicting responses to cancer treatment. Therefore, we characterized splicing events according to different cytogenetic features by targeted RNA-seq and interrogated the use of splicing variants in MRD monitoring of CN-AML. A total of 29 AML samples, collected from 18 de novo paediatric AML patients (median age 5.66 years, range 0.67 - 16.38 years) were analysed for this study. Among the 29 samples, 52% harboured a chromosome translocation, 21% were cytogenetically normal, and 28% showed a complex karyotype (defined as having 3 or more cytogenetic features). 100ng of total RNA, extracted from peripheral blood or bone marrow were subjected to library preparation using the Archer™ FusionPlex™ Heme and Myeloid panels, then sequenced using Illumina MiSeq® or NextSeq®. Novel splicing events and genetic mutations were identified by the Archer Dx analysis software in conjunction with normalisations against the library size and probe numbers. Splicing variants were validated using splicing junction-specific probe assays. Our results revealed 3249 novel splicing events in 29 AML samples. These events were classified into 4 major types (65% intron retention, 10% exon skipping, 8% exon out of order and 8% intra-exon gap), and 9 minor events that were combinations of the major types (9%). The number of splicing events per sample was not associated with the disease status or the presence of the mutations in the spliceosome encoding gene, SF3B1 or U2AF1. Instead, splicing variants were associated with cytogenetic features. Of note, an intron 13 retention of the KMT2A (MLL) gene was identified in all CN-AML samples, and was consistently expressed approximately 100 times higher in the CN-AML compared to other AML cases or remission samples. To assess whether KMT2A intron 13 retention could be a potential molecular MRD marker to monitor CN-AML, we measured its expression in samples from 5 independent CN-AML patients who had available samples for 3 time-points of disease progression. Our results demonstrated, with 95% detection power, that KMT2A intron 13 retention was differentially expressed at different time points (Figure 1). Moreover, the expression level of this splicing variant correlated with disease progression in every patient examined. In conclusion, these data suggest that intron 13 retention of KMT2A may be a novel molecular marker for MRD monitoring in CN-AML. Disclosures No relevant conflicts of interest to declare.

Description: Rearrangements of the mixed lineage leukemia gene (MLL, re-named KMT2A) result in aggressive leukemia. Current risk stratification of MLL-rearranged (MLL-r) leukemia is directed by the fusion partner gene and, increasingly, by minimal residual disease (MRD) assessment after induction therapy. The clinical significance of quantifying fusion transcript levels in leukemia patients is firmly established in chronic myeloid leukemia and acute promyelocytic leukemia but is less well studied in MLL-r patients. Real-time quantitative PCR (RQ-PCR) is the standardized assay for molecular MRD monitoring in patients with MLL-rearranged leukemia. However, this method is less precise when few leukemic cells are present, thus limiting its application for highly sensitive MRD monitoring. Droplet digital PCR (ddPCR) allows for absolute quantification of fusion transcripts when multiple copies of fusion transcripts are present per cell. Therefore, we aimed to evaluate whether determining MLL fusion transcript levels by ddPCR could improve the sensitivity of MRD monitoring in MLL-r leukemia. A total of 44 diagnostic and follow-up samples obtained from paediatric MLL-r leukemia patients (26 ALL, 18 AML) were subjected to targeted next-generation sequencing to obtain patient-specific fusion sequences. MLL fusion transcripts were quantified by ddPCR in a total of 17 samples obtained from 4 paediatric AML patients with MLL fusions involving MLLT3 (n = 3) and MLLT10 (n = 1). Fusion-specific probe assays were designed from each of the patient specific fusion sequences for MRD assessment by ddPCR. To determine the detection limit of this method in quantifying MLL fusion transcripts, two MLL-r AML cell lines (MV4-11 and THP-1), and one MLL-wt cell line (Kasumi-1) were used. MLL fusion transcript level of detection of ddPCR was determined by serially diluting MLL-r cDNA into MLL-wt cDNA (Kasumi-1). Using 20ng of MLL-r cDNA in 200ng diluent as the highest concentration, a 10-fold dilution series was performed to make concentrations ranging from 10−2 to 10−7. Each ddPCR reaction mixture contained 11ul of cDNA mix as template with 1X Supermix no dUTP (Bio-Rad), 500 nM of both F/R primers and 250 nM of 5'-FAM labelled probe (IDT). Droplets were generated using a QX200 Droplet Generator (Bio-Rad). A general thermal cycler protocol with annealing at 61°C for 1 minute was performed and positive fluorescence droplets were read using QX200 Droplet Reader (Bio-Rad). MRD of patient samples, derived from ddPCR, was then compared to MRD derived from DNA-based RQ-PCR, following the guidelines established by the EuroMRD group. Our ddPCR method showed high reliability and sensitivity, with the detection limit determined to be 10-5 for a cell line with low MLL fusion transcript expression (THP-1), and 10-6 for a cell line with high MLL fusion transcript expression (MV4-11). Comparison of results obtained by RQ- PCR and ddPCR in a total of 17 diagnostic and follow-up samples from 4 AML patients showed excellent/good concordance between methods for 13 samples with moderate MRD levels. The 4 samples with low levels of MRD (10-4 to 10-5) below the quantitative range as defined by EuroMRD for RQ-PCR were all detectable by ddPCR, highlighting that ddPCR could provide robust and highly sensitive MRD assays compared to the standardized RQ-PCR assays. In conclusion, ddPCR is a promising technique that can reproducibly and reliably quantify MLL-r transcripts for MRD monitoring of MLL-r leukemia. Highly sensitive and robust molecular MRD monitoring by ddPCR holds promise for improving response-based therapeutic stratification and prediction of molecular relapse before overt hematological relapse. Disclosures No relevant conflicts of interest to declare.