Clonal hematopoiesis: Mechanisms driving dominance of stem cell clones

The discovery of clonal hematopoiesis (CH) in older individuals has changed the way hematologists and stem cell biologists view aging. Somatic mutations accumulate in stem cells over time. While most mutations have no impact, some result in subtle functional differences that ultimately manifest in distinct stem cell behaviors. With a large pool of stem cells and many decades to compete, some of these differences confer advantages under specific contexts. Approximately 20 genes are recurrently found as mutated in CH, indicating they confer some advantage. The impact of these mutations has begun to be analyzed at a molecular level by modeling in cell lines and in mice. Mutations in epigenetic regulators such as DNMT3A and TET2 confer an advantage by enhancing self-renewal of stem and progenitor cells and inhibiting their differentiation. Mutations in other genes involved in the DNA damage response may simply enhance cell survival. Here, we review proposed mechanisms that lead to CH, specifically in the context of stem cell biology, based on our current understanding of the function of some of the CH-associated genes

Promiscuous Expression of H2B-GFP Transgene in Hematopoietic Stem Cells

The study of adult stem cells relies on the ability to isolate them using complex combinations of markers for flow cytometry. A recent study has used a tetracycline-regulatable H2B-GFP transgenic mouse model analogous to BrdU pulse-chase methods to fluorescently label quiescent skin stem cells in vivo. In this study, we sought to use these mice to fluorescently label hematopoietic stem cells to study niche interactions.We crossed the H2B-GFP mice to mice carrying a tetracycline-regulated transactivator protein. When these mice were administered doxycycline, we observed a gradual decrease in total bone marrow GFP(+) cells over 12 weeks but the hematopoietic stem cell population remained largely GFP(+) (>85%). In histological bone sections, the long-term GFP label-retaining cells tended to concentrate at the endosteal surface and competitive transplantation assays showed that the majority of hematopoietic stem cell activity was contained in the GFP(+) cell fraction. However, in response to stimulation with 5-fluorouracil, the hematopoietic stem cells of the crossed mice still retained a high level of GFP expression when it was anticipated the label should be lost when the cells divide. Upon further review, it was determined that the founder H2B-GFP mice showed spurious expression of the transgene at high levels in the hematopoietic stem cell population, thus the observed response of hematopoietic stem cells in the double transgenic mice to doxycycline was due to aberrant expression of the transgene and not the correct tetracycline-regulatable system.We observed promiscuous expression of the H2B-GFP transgene in the hematopoietic stem cell compartment of the bone marrow. This leaky expression prohibits the use of this model to study hematopoietic stem cells in vivo and careful characterization for each organ must be done if this transgenic system is to be used to isolate other prospective tissue stem cells

Effects of seawater exchange on water chemistry among coastal lakes with intermittent connections to the sea

Intermittently closed and open lakes and lagoons (ICOLLs) are a dynamic class of coastal waterbodies with the unique feature of intermittently connecting to the sea. Understanding the functioning and potential threats of these globally rare systems is important to their preservation and protection. Coastal dune lakes of northwest Florida are one example of an understudied group of ICOLLs which connect with the Gulf of Mexico for brief periods of time. Using a 17-year, monthly water chemistry dataset, we analyzed long-term patterns in water chemistry among 16 coastal dune lakes. Using salinity as a proxy for frequency of seawater inflows, principal component analysis and linear mixed-effects models indicated significant relationships between salinity and nitrogen, phosphorous, and pH. Salinity was positively associated with pH and phosphorus, and negatively associated with nitrogen, although relationships within individual lakes varied. Nonparametric trend analysis indicated lake-specific significant shifts in water chemistry in several systems, although a majority of systems did not exhibit notable long-term trends. Results indicate the significance of water exchange with the Gulf of Mexico on water chemistry of coastal dune lakes and have implications for management of ICOLLs globall

How Do We Enhance Leadership, Collaboration and Communication Skills in Postgraduate Programs?

This reflection discusses how we can enhance higher level research skills through using the arts, humanities and philosophy. It describes strategies that can be adopted at different stages so that throughout the education process we can support and consistently develop questioning and curiosity. Additionally, it describes the importance of the subjective journey of being, becoming and thriving and how this is necessary alongside subject knowledge to build on research self-analytical skills. Further, it explores the philosophy of Bacon and the role of understanding nature both inside and outside for self-improvement and towards education for the enhancement of humanity and global social justice

Double-stranded RNA elements associated with the MVX disease of Agaricus bisporus

Double-stranded RNA (dsRNA) has been isolated from Agaricus bisporus fruit bodies exhibiting a wide range of disease symptoms. The symptoms which occurred singularly or in combination included; bare cropping areas on commercial beds (primordia disruption), crop delay, premature veil opening, off- or brown-coloured mushrooms, sporophore malformations and loss of crop yield. All symptoms were associated with loss of yield and/or product quality. Collectively, these symptoms are described as mushroom virus X (MVX) disease. The dsRNA titre was much lower than that previously encountered with the La France viral disease of mushrooms and a modified cellulose CF11 protocol was used for their detection. A broad survey of cultivated mushrooms from the British industry identified dsRNA elements ranging between 640 bp and 20.2 kbp; the majority have not previously been described in A. bisporus. 26 dsRNA elements were identified with a maximum of 17, apparently non-encapsidated dsRNA elements, in any one sample. Three dsRNAs (16.2, 9.4 and 2.4 kbp) were routinely found in mushrooms asymptomatic for MVX. Previously, La France disease was effectively contained and controlled by minimising the on-farm production and spread of basidiospores. Our on-farm observations suggest that MVX could be spread by infected spores and/or mycelial fragments

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

TGFβR-SMAD3 signaling induces resistance to PARP inhibitors in the bone marrow microenvironment

Synthetic lethality triggered by PARP inhibitor (PARPi) yields promising therapeutic results. Unfortunately, tumor cells acquire PARPi resistance, which is usually associated with the restoration of homologous recombination, loss of PARP1 expression, and/or loss of DNA double-strand break (DSB) end resection regulation. Here, we identify a constitutive mechanism of resistance to PARPi. We report that the bone marrow microenvironment (BMM) facilitates DSB repair activity in leukemia cells to protect them against PARPi-mediated synthetic lethality. This effect depends on the hypoxia-induced overexpression of transforming growth factor beta receptor (TGFβR) kinase on malignant cells, which is activated by bone marrow stromal cells-derived transforming growth factor beta 1 (TGF-β1). Genetic and/or pharmacological targeting of the TGF-β1-TGFβR kinase axis results in the restoration of the sensitivity of malignant cells to PARPi in BMM and prolongs the survival of leukemia-bearing mice. Our finding may lead to the therapeutic application of the TGFβR inhibitor in patients receiving PARPis

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