A comparison of foraging strategies in a patchy environment.

In this paper we compare foraging strategies that might be used by predators seeking prey in a patchy environment. The strategies differ in the extent to which predators aggregate in response to prey density. The approach to the comparison is suggested by the idea of evolutionarily stable strategies. A strategy is said to be evolutionarily stable if it cannot be invaded by another strategy. Thus we examine scenarios where a small number of individuals using one strategy are introduced into a situation where a large number of individuals using the other strategy are already present. However, our foraging models do not explicitly incorporate predator population dynamics, so we use net energy uptake as a surrogate for reproductive fitness. In cases where all of the patches visited by predators sustain prey populations, we find that for any pair of strategies one of them will have a higher net energy uptake than the other whether it is the resident or the introduced strain. However, which one is higher will typically depend on the total predator population, which is determined by the resident strain. If the predators leave prey densities high, the more aggregative strain will have the advantage. If the predators reduce prey densities to low levels the less aggregative strain will have the advantage. In cases where one strain of predators aggregates in response to prey density and the other does not, then there might be patches which do not contain prey but do contain (non-aggregating) predators. In those cases, there is the possibility that whichever strategy is used by the introduced strain will yield a higher energy uptake than that used by the resident strain. This suggests that if some patches are empty of prey then aggregative and non-aggregative strategies may be able to coexist.     

Dynamic re-distribution of protein kinase D (PKD) as revealed by a GFP-PKD fusion protein: dissociation from PKD activation.

Protein kinase D (PKD)/protein kinase Cmicro (PKCmicro, a serine/threonine protein kinase with distinct structural and enzymological properties, is rapidly activated in intact cells via PKC. The amino-terminal region of PKD contains a cysteine-rich domain (CRD) that directly binds phorbol esters with a high affinity. Here, we show that treatment of transfected RBL 2H3 cells with phorbol 12,13-dibutyrate (PDB) induces a striking CRD-dependent translocation of PKD from the cytosol to the plasma membrane, as shown by real time visualization of a functional green fluorescent protein (GFP)-PKD fusion protein. A single amino acid substitution in the second cysteine-rich motif of PKD (P287G) prevented PDB-induced membrane translocation but did not affect PKD activation. Our results indicate that PKD translocation and activation are distinct processes that operate in parallel to regulate the activity and localization of this enzyme in intact cells.     

The dynamics of protein kinase B regulation during B cell antigen receptor engagement.

This study has used biochemistry and real time confocal imaging of green fluorescent protein (GFP)-tagged molecules in live cells to explore the dynamics of protein kinase B (PKB) regulation during B lymphocyte activation. The data show that triggering of the B cell antigen receptor (BCR) induces a transient membrane localization of PKB but a sustained activation of the enzyme; active PKB is found in the cytosol and nuclei of activated B cells. Hence, PKB has three potential sites of action in B lymphocytes; transiently after BCR triggering PKB can phosphorylate plasma membrane localized targets, whereas during the sustained B cell response to antigen, PKB acts in the nucleus and the cytosol. Membrane translocation of PKB and subsequent PKB activation are dependent on BCR activation of phosphatidylinositol 3-kinase (PI3K). Moreover, PI3K signals are both necessary and sufficient for sustained activation of PKB in B lymphocytes. However, under conditions of continuous PI3K activation or BCR triggering there is only transient recruitment of PKB to the plasma membrane, indicating that there must be a molecular mechanism to dissociate PKB from sites of PI3K activity in B cells. The inhibitory Fc receptor, the FcgammaRIIB, mediates vital homeostatic control of B cell function by recruiting an inositol 5 phosphatase SHIP into the BCR complex. Herein we show that coligation of the BCR with the inhibitory FcgammaRIIB prevents membrane targeting of PKB. The FcgammaRIIB can thus antagonize BCR signals for PKB localization and prevent BCR stimulation of PKB activity which demonstrates the mechanism for the inhibitory action of the FcgammaRIIB on the BCR/PKB response.     

Bioinspiration as a method of problem‐based STEM education: A case study with a class structured around the COVID‐19 crisis

Bioinspiration is a promising lens for biology instruction as it allows the instructor to focus on current issues, such as the COVID‐19 pandemic. From social distancing to oxygen stress, organisms have been tackling pandemic‐related problems for millions of years. What can we learn from such diverse adaptations in our own applications? This review uses a seminar course on the COVID‐19 crisis to illustrate bioinspiration as an approach to teaching biology content. At the start of the class, students mind‐mapped the entire problem; this range of subproblems was used to structure the biology content throughout the entire class. Students came to individual classes with a brainstormed list of biological systems that could serve as inspiration for a particular problem (e.g., absorptive leaves in response to the problem of toilet paper shortages). After exploration of relevant biology content, discussion returned to the focal problem. Students dug deeper into the literature in a group project on mask design and biological systems relevant to filtration and transparency. This class structure was an engaging way for students to learn principles from ecology, evolution, behavior, and physiology. Challenges with this course design revolved around the interdisciplinary and creative nature of the structure; for instance, the knowledge of the participants was often stretched by engineering details. While the present class was focused on the COVID‐19 crisis, a course structured through a bioinspired approach can be applied to other focal problems, or subject areas, giving instructors a powerful method to deliver interdisciplinary content in an integrated and inquiry‐driven way.     

Synthetic studies on formamidopyrimidines related to clofarabine

Degradation of clofarabine (3) in 0.9% saline solution at 100 degrees C afforded three degradation products which were determined to be formamidopyrimidines 4-6. Compounds 4 and 5 were assigned as C(1') anomers on the basis of one-dimensional and two-dimensional NMR experiments, whereas 6 was found to be the formamidopyrimidine lacking the sugar moiety. An improved procedure for the synthesis of formamidopyrimidines was developed, wherein benzoylated clofarabine (11) was treated with allyl chloroformate, followed by deprotection of the alloc group with catalytic Pd(PPh(3))(4) and dimedone. A synthesis of compound 6 from 4 is also described.     

Bioenergy from Coastal bermudagrass receiving subsurface drip irrigation with advance-treated swine wastewater

Coastal bermudagrass (Cynodon dactylon L.) may be a potentially important source of bio-based energy in the southern US due to its vast acreage. It is often produced as part of a waste management plan with varying nutrient composition and energy characteristics on fields irrigated with livestock wastewater. The objective of this study was to determine the effect of subsurface drip irrigation with treated swine wastewater on both the quantity and quality of bermudagrass bioenergy. The treated wastewater was recycled from an advanced treatment system and used for irrigation of bermudagrass in two crop seasons. The experiment had nine water and drip line spacing treatments arrayed in a randomized complete block-design with four replicates. The bermudagrass was analyzed for calorific and mineral contents. Bermudagrass energy yields for 2004 and 2005 ranged from 127.4 to 251.4 MJ ha⁻¹. Compared to irrigation with commercial nitrogen fertilizer, the least biomass energy density was associated with bermudagrass receiving treated swine wastewater. Yet, in 2004 the wastewater irrigated bermudagrass had greater hay yields leading to greater energy yield per ha. This decrease in energy density of wastewater irrigated bermudagrass was associated with increased concentrations of K, Ca, and Na. After thermal conversion, these compounds are known to remain in the ash portion thereby decreasing the energy density. Nonetheless, the loss of energy density using treated effluent via SDI may be offset by the positive influence of these three elements for their catalytic properties in downstream thermal conversion processes such as promoting a lesser char yield and greater combustible gas formation.     

A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.)

An F_4:5 population of 285 families with each tracing back to a different F₂ plant, derived from a cotton bacterial blight resistant line ‘DeltaOpal’ and a susceptible line ‘DP388’, was artificially inoculated with bacterial blight race 18 (Xanthomonas axonopodis pv. malvacearum) to assay their resistance or susceptibility to the disease. The segregation in the F_4:5 population indicates that the resistance was conditioned by a single dominant gene designated B _12. Simple sequence repeat (SSR) markers identified as putatively linked to the resistance gene by bulked segregant analysis were confirmed on the entire F_4:5 population. Three SSR markers, CIR246, BNL3545 and BNL3644 on chromosome 14, were found closely linked to B ₁₂ . The association between CIR246 and B ₁₂ was validated among 354 plants of 16 diverse varieties. Based on Monsanto SSR/single nucleotide polymorphism (SNP) consensus map, SNP markers closely linked to CIR246 were used to screen ‘DeltaOpal’ and ‘DP388’ for polymorphism. The polymorphic SNP markers were run on the F_4:5 population and the four SNP markers spanning 3.4 cM were found to flank the resistance gene on chromosome 14. The linkage between B ₁₂ and the 4-SNP marker haplotype was validated using 18 elite cotton lines. This 4-SNP marker haplotype can be used for marker assisted selection for bacterial blight resistance breeding programs or for screening germplasm collections for this locus rapidly.     

A Cluster Randomized Trial of Routine HIV-1 Viral Load Monitoring in Zambia: Study Design,Implementation, and Baseline Cohort Characteristics

Background

The benefit of routine HIV-1 viral load (VL) monitoring of patients on antiretroviral therapy (ART) in resource-constrained settings is uncertain because of the high costs associated with the test and the limited treatment options. We designed a cluster randomized controlled trial to compare the use of routine VL testing at ART-initiation and at 3, 6, 12, and 18 months, versus our local standard of care (which uses immunological and clinical criteria to diagnose treatment failure, with discretionary VL testing when the two do not agree).

Methodology

Dedicated study personnel were integrated into public-sector ART clinics. We collected participant information in a dedicated research database. Twelve ART clinics in Lusaka, Zambia constituted the units of randomization. Study clinics were stratified into pairs according to matching criteria (historical mortality rate, size, and duration of operation) to limit the effect of clustering, and independently randomized to the intervention and control arms. The study was powered to detect a 36% reduction in mortality at 18 months.

Principal Findings

From December 2006 to May 2008, we completed enrollment of 1973 participants. Measured baseline characteristics did not differ significantly between the study arms. Enrollment was staggered by clinic pair and truncated at two matched sites.

Conclusions

A large clinical trial of routing VL monitoring was successfully implemented in a dynamic and rapidly growing national ART program. Close collaboration with local health authorities and adequate reserve staff were critical to success. Randomized controlled trials such as this will likely prove valuable in determining long-term outcomes in resource-constrained settings.

Trial Registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00929604","term_id":"NCT00929604"}}NCT00929604