Droplet digital PCR for oncogenic KMT2A fusion detection

Acute myeloid leukemia (AML) is an aggressive blood cancer diagnosed in approximately 120,000 individuals worldwide each year. During treatment for AML, detecting residual disease is essential for prognostication and treatment decision-making. Currently, methods for detecting residual AML are limited to identifying approximately 1:100 to 1:1000 leukemic cells (morphology and DNA sequencing) or are difficult to implement (flow cytometry). AML arising after chemotherapy or radiation exposure is termed therapy-related AML (t-AML) and is exceptionally aggressive and treatment resistant. t-AML is often driven by oncogenic fusions that result from prior treatments that introduce double-strand DNA breaks. The most common t-AML-associated translocations affect KMT2A. There are at least 80 known KMT2A fusion partners, but approximately 80% of fusions involve only five partners-AF9, AF6, AF4, ELL, and ENL. We present a novel droplet digital PCR assay targeting the most common KMT2A-rearrangements to enable detection of rare AML cells harboring these fusions. This assay was benchmarked in cell lines and patient samples harboring oncogenic KMT2A fusions and demonstrated a limit of detection of approximately 1:1,000,000 cells. Future application of this assay could improve disease detection and treatment decision-making for patients with t-AML with KMT2A fusions and premalignant oncogenic fusion detection in at-risk individuals after chemotherapy exposure

Influence of salinity on SAV distribution in a series of intermittently connected coastal lakes

Intermittently closed and open lakes and lagoons (ICOLLs) are coastal lakes that intermittently exchange water with the sea and experience saline intrusions. Understanding effects of seawater exchange on local biota is important to preserve ecosystem functioning and ecological integrity. Coastal dune lakes of northwest Florida are an understudied group of ICOLLs in close geographic proximity and with entrance regimes operating along a frequency continuum. We exploited this natural continuum and corresponding water chemistry gradient to determine effects of water chemistry on resident submersed aquatic vegetation (SAV) distributions in these ecosystems. SAV distribution decreased with increases in salinity, but was unaffected by variation in nitrogen, phosphorous, and turbidity. Salinity perturbations corresponding with water exchange with the Gulf of Mexico were associated with reductions in SAV in coastal dune lakes. Potential impacts associated with changes in global climate may increase the frequency of seawater exchange across all coastal dune lakes and potentially reduce the distribution of oligohaline macrophytes among these ecosystems

Spatiotemporal Modeling of Nursery Habitat Using Bayesian Inference: Environmental Drivers of Juvenile Blue Crab Abundance

Nursery grounds provide conditions favorable for growth and survival of juvenile fish and crustaceans through abundant food resources and refugia, and enhance secondary production of populations. While small-scale studies remain important tools to assess nursery value of structured habitats and environmental factors, targeted applications that unify survey data over large spatial and temporal scales are vital to generalize inference of nursery function, identify highly productive regions, and inform management strategies. Using 21 years of spatio-temporally indexed survey data (i.e., water chemistry, turbidity, blue crab, and predator abundance) and GIS information on potential nursery habitats (i.e., seagrass, salt marsh, and unvegetated shallow bottom), we constructed five Bayesian hierarchical models with varying spatial and temporal dependence structures to infer variation in nursery habitat value for young juveniles (20–40 mm carapace width) of the blue crab Callinectes sapidus within three tributaries (James, York and Rappahannock Rivers) in lower Chesapeake Bay. Out-of-sample predictions of juvenile blue crab counts from a model considering fully nonseparable spatiotemporal dependence outperformed predictions from simpler models. Salt marsh surface area and turbidity were the strongest determinants of crab abundance (positive association in both cases). Highest crab abundances occurred near the turbidity maximum where relative salt marsh area was greatest. Relative seagrass area, which has been emphasized as the most valuable nursery in studies conducted at small spatial scales, was not associated with high crab abundance within the three tributaries. Hence, salt marshes should be considered a key nursery habitat for the blue crab, even where extensive seagrass beds occur. The patterns between juvenile blue crab abundance and environmental variables also indicated that identification of nurseries should be based on investigations at broad spatial and temporal scales incorporating multiple potential nursery habitats, and based on statistical analyses that address spatial and temporal statistical dependence

Phase Farming with Trees: A report for the RIRDC/LWRRDC/FWPRDC Joint Venture Agroforestry Program

A scoping study was undertaken to determine the economic and biophysical feasibility of a proposal to research a system of phase farming with trees (PFT) in medium to low (300-600 mm) rainfall areas of southern Australia. This system is designed to use trees grown in very short term rotations (3-5 years) to rapidly de-water farming catchments, at risk of salinity, by depleting unsaturated stored soil water and reducing recharge while producing utilizable products. If feasible, the system will utilize a resource that is currently contributing to environmental problems while building more sustainable agricultural systems. Potential benefits include decreased salinization, improved farm cash flows, improved soil structure and acting as a disease and weed break..

Testing the Children: Do Non-Genetic Health-Care Providers Differ in Their Decision to Advise Genetic Presymptomatic Testing on Minors? A Cross-Sectional Study in Five Countries in the European Union

BACKGROUND: Within Europe many guidelines exist regarding the genetic testing of minors. Predictive and presymptomatic genetic testing of minors is recommended for disorders for which medical intervention/preventive measures exist, and for which early detection improves future medical health. AIM: This study, which is part of the larger 5th EU-framework "genetic education" (GenEd) study, aimed to evaluate the self-reported responses of nongenetic health-care providers in five different EU countries (Germany, France, Sweden, the United Kingdom, and the Netherlands) when confronted with a parent requesting presymptomatic testing on a minor child for a treatable disease. METHODS: A cross-sectional study design using postal, structured scenario-based questionnaires that were sent to 8129 general practitioners (GPs) and pediatricians, between July 2004 and October 2004, addressing self-reported management of a genetic case for which early medical intervention during childhood is beneficial, involving a minor. RESULTS: Most practitioners agreed on testing the oldest child, aged 12 years (81.5% for GPs and 87.2% for pediatricians), and not testing the youngest child, aged 6 months (72.6% for GPs and 61.3% for pediatricians). After multivariate adjustment there were statistical differences between countries in recommending a genetic test for the child at the age of 8 years. Pediatricians in France (50%) and Germany (58%) would recommend a test, whereas in the United Kingdom (22%), Sweden (30%), and the Netherlands (32%) they would not. CONCLUSION: Even though presymptomatic genetic testing in minors is recommended for disorders for which medical intervention exists, EU physicians are uncertain at what age starting to do so in young children

Variation in Seagrass-Associated Macroinvertebrate Communities Along the Gulf Coast of Peninsular Florida: An Exploration of Patterns and Ecological Consequences

Seagrasses form vast meadows of structurally complex habitat that support faunal communities with greater numbers of species and individuals than nearby unstructured habitats. The Gulf coast of peninsular Florida represents a natural laboratory ideally suited to the study of processes that shape seagrass-associated invertebrate and fish communities within meadows of a single species of seagrass, Thalassia testudinum. This suitability arises from a pronounced structural and chemical gradient that exists over ecologically relevant spatial and temporal scales, as revealed by extensive monitoring of water quality and seagrass. We hypothesized that seagrass-associated invertebrate communities would vary across five estuarine systems spread along a spatial gradient in phosphorus concentration, an important driver of seagrass and phytoplankton growth in this region. The quantitative results based on data acquired at 25 stations (75 samples, 52,086 specimens, and 161 taxa) indicated that each of the five estuarine systems were distinct with regard to species composition and differences among systems were driven by abundant or relatively common species. In addition, we found evidence to indicate food webs in seagrass meadows along this gradient may differ, especially in the relative dominance of algal grazers and predatory invertebrates. These changes in species composition and trophic roles could be driven by phosphorus directly, through increases in rates of primary production with higher concentrations of phosphorus, or indirectly, through nutrient-mediated changes in the physical structure of the seagrass canopy. Our results suggest that differences in the habitat created by T. testudinum under differing phosphorus supplies lead to ecologically significant shifts in macroinvertebrate communities

Divergent effects of DNMT3A and TET2 mutations on hematopoietic progenitor cell fitness

The DNA methylation regulators DNMT3A and TET2 are recurrently mutated in hematological disorders. Despite possessing antagonistic biochemical activities, loss-of-function murine models show overlapping phenotypes in terms of increased hematopoietic stem cell (HSC) fitness. Here, we directly compared the effects of these mutations on hematopoietic progenitor function and disease initiation. In contrast to Dnmt3a-null HSCs, which possess limitless self-renewal in vivo, Tet2-null HSCs unexpectedly exhaust at the same rate as control HSCs in serial transplantation assays despite an initial increase in self-renewal. Moreover, loss of Tet2 more acutely sensitizes hematopoietic cells to the addition of a common co-operating mutation (Flt

Functional analyses of <i>Agaricus bisporus </i>Serine Proteinase 1 (SPR1) reveals a role in utilisation of humic rich substrates and adaptation to the leaf-litter ecological niche

Agaricus bisporus is a secondary decomposer fungus and an excellent model for the adaptation, persistence and growth of fungi in humic‐rich environments such as soils of temperate woodland and pastures. The A. bisporus serine proteinase SPR1 is induced by humic acids and is highly expressed during growth on compost. Three Spr1 gene silencing cassettes were constructed around sense, antisense and non‐translatable‐stop strategies (pGRsensehph, pGRantihph and pGRstophph). Transformation of A. bisporus with these cassettes generated cultures showing a reduction in extracellular proteinase activity as demonstrated by the reduction, or abolition, of a clearing zone on plate‐based bioassays. These lines were then assessed by detailed enzyme assay, RT‐qPCR and fruiting. Serine proteinase activity in liquid cultures was reduced in 83% of transformants. RT‐qPCR showed reduced Spr1 mRNA levels in all transformants analysed, and these correlated with reduced enzyme activity. When fruiting was induced, highly‐silenced transformant AS5 failed to colonize the compost, whilst for those that did colonize the compost, 60% gave a reduction in mushroom yield. Transcriptional, biochemical and developmental observations, demonstrate that SPR1 has an important role in nutrient acquisition in compost and that SPR1 is a key enzyme in the adaptation of Agaricus to the humic‐rich ecological niche formed during biomass degradation