Differential Survival of Chaparral Shrub Species in Response to Severe Drought

In this experiment, we examined how the plants in the Santa Monica Mountains are responding to the driest period in recorded history for California. Our hypothesis was that plant species with the deepest roots would have highest survivorship. We thought this because deep-rooted shrubs will have greater access to soil moisture. This hypothesis was tested by collecting data on plant survival, in a mixed chaparral stand, containing eleven species, growing in the Green Valley Preserve off of Stunt road, in the Santa Monica Mountains. The chaparral stand was 21 years old, having last burned in 1993 (Old Topanga Canyon Fire). In the end, we discovered that our hypothesis was supported. Our data indicated that deep-rooted species had significantly higher survivorship during severe drought than shallow rooted species

Difference in Water Status between Oak Trees (Quercus berberidifolia) with Brown and Green Leaves During Severe Drought

In this experiment, we examined cavitation in Quercus berberidifolia plants. We hypothesized that as the amount of water stress increases, then the pressure to cause embolism will decrease. We thought this because as a plant loses more water, the more air bubbles will form within the plant and therefore the pressure to cause this will decrease. We tested this hypothesis by comparing dry Quercus berberidifolia to more hydrated Quercus berberidifolia in Tapia Park, near Malibu, California. We measured and compared these plants by the use of the Scholander Pressure chamber and a parometer. In the end, we discovered that our hypothesis was correct. Our data showed us that less hydrated plants that had more water stress had a lower atmospheric pressure than the more hydrated plants

Rapid and reversible knockdown of endogenously tagged endosomal proteins via an optimized HaloPROTAC degrader

Inducing post-translational protein knockdown is an important approach to probe biology and validate drug targets. An efficient strategy to achieve this involves expression of a protein of interest fused to an exogenous tag, allowing tag-directed chemical degraders to mediate protein ubiquitylation and proteasomal degradation. Here, we combine improved HaloPROTAC degrader probes with CRISPR/Cas9 genome editing technology to trigger rapid degradation of endogenous target proteins. Our optimized probe, HaloPROTAC-E, a chloroalkane conjugate of high-affinity VHL binder VH298, induced reversible degradation of two endosomally localized proteins, SGK3 and VPS34, with a DC₅₀ of 3–10 nM. HaloPROTAC-E induced rapid (∼50% degradation after 30 min) and complete (<i>D</i>_max of ∼95% at 48 h) depletion of Halo-tagged SGK3, blocking downstream phosphorylation of the SGK3 substrate NDRG1. HaloPROTAC-E more potently induced greater steady state degradation of Halo tagged endogenous VPS34 than the previously reported HaloPROTAC3 compound. Quantitative global proteomics revealed that HaloPROTAC-E is remarkably selective inducing only degradation of the Halo tagged endogenous VPS34 complex (VPS34, VPS15, Beclin1, and ATG14) and no other proteins were significantly degraded. This study exemplifies the combination of HaloPROTACs with CRISPR/Cas9 endogenous protein tagging as a useful method to induce rapid and reversible degradation of endogenous proteins to interrogate their function

Staging, nomograms and other predictive tools in retroperitoneal soft tissue sarcoma.

Patient outcomes following surgical resection of retroperitoneal sarcomas (RPSs) are variable and therefore predicting prognosis is challenging. The risk of recurrence varies according to several patient- tumour- and treatment-related characteristics, including histological subtype and tumour grade. In an era of increased movement towards individualised patient care, the ability to predict prognosis following surgery for RPS is essential. The accurate prediction of an individual patient's outcome is important to allow adequate patient counselling and to ensure the optimal therapeutic strategy is selected. The outcomes of patients who have undergone resection for RPS can be predicted using tools such as nomograms. Nomograms take into account the relative contribution of each variable by giving them different weights and then combining them. This review aims to discuss current staging systems available for RPS and to critically appraise predictive tools that are currently available for use in clinical practice

Methods and measures for investigating microscale motility

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we give an overview of different experimental, analytical, and mathematical methods used to study a suite of microscale motility mechanisms across different scales encompassing molecular-, individual- to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.Comment: 24 pages, 2 figure

Recommendations for best practice for iron speciation by competitive ligand exchange adsorptive cathodic stripping voltammetry with salicylaldoxime

The method of competitive ligand exchange followed by adsorptive cathodic stripping voltammetry (CLE-AdCSV) allows for the determination of dissolved iron (DFe) organic speciation parameters, i.e., ligand concentration (LFe) and conditional stability constant (log KFe′Lcond). Investigation of DFe organic speciation by CLE-AdCSV has been conducted in a wide range of marine systems, but aspects of its application pose challenges that have yet to be explicitly addressed. Here, we present a set of observations and recommendations to work toward establishing best practice for DFe organic speciation measurements using the added ligand salicylaldoxime (SA). We detail conditioning procedures to ensure a stable AdCSV signal and discuss the processes at play during conditioning. We also present step-by-step guidelines to simplify CLE-AdCSV data treatment and interpretation using the softwares ECDSoft and ProMCC and a custom spreadsheet. We validate our application and interpretation methodology with the model siderophore deferoxamine B (DFO-B) in a natural seawater sample. The reproducibility of our application and interpretation methodology was evaluated by running duplicate titrations on 19 samples, many of which had been refrozen prior to the duplicate analysis. Nevertheless, 50% of the duplicate analyses agreed within 10% of their relative standard deviation (RSD), and up to 80% within 25% RSD, for both LFe and log KFe′Lcond. Finally, we compared the sequential addition and equilibration of DFe and SA with overnight equilibration after simultaneous addition of DFe and SA on 24 samples. We found a rather good agreement between both procedures, with 60% of samples within 25% RSD for LFe (and 43% of samples for log KFe′Lcond), and it was not possible to predict differences in LFe or log KFe′Lcond based on the method applied, suggesting specific association/dissociation kinetics for different ligand assemblages. Further investigation of the equilibration kinetics against SA may be helpful as a potential way to distinguish natural ligand assemblages