Relating protein pharmacology by ligand chemistry

The identification of protein function based on biological information is an area of intense research. Here we consider a complementary technique that quantitatively groups and relates proteins based on the chemical similarity of their ligands. We began with 65,000 ligands annotated into sets for hundreds of drug targets. The similarity score between each set was calculated using ligand topology. A statistical model was developed to rank the significance of the resulting similarity scores, which are expressed as a minimum spanning tree to map the sets together. Although these maps are connected solely by chemical similarity, biologically sensible clusters nevertheless emerged. Links among unexpected targets also emerged, among them that methadone, emetine and loperamide (Imodium) may antagonize muscarinic M3, alpha2 adrenergic and neurokinin NK2 receptors, respectively. These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves.     

ICAM-1 Targeted Nanogels Loaded with Dexamethasone Alleviate Pulmonary Inflammation

Lysozyme dextran nanogels (NG) have great potential in vitro as a drug delivery platform, combining simple chemistry with rapid uptake and cargo release in target cells with “stealth” properties and low toxicity. In this work, we study for the first time the potential of targeted NG as a drug delivery platform in vivo to alleviate acute pulmonary inflammation in animal model of LPS-induced lung injury. NG are targeted to the endothelium via conjugation with an antibody (Ab) directed to Intercellular Adhesion Molecule-1(ICAM-NG), whereas IgG conjugated NG (IgG-NG) are used for control formulations. The amount of Ab conjugated to the NG and distribution in the body after intravenous (IV) injection have been quantitatively analyzed using a tracer isotope-labeled [¹²⁵I]IgG. As a proof of concept, Ab-NG are loaded with dexamethasone, an anti-inflammatory therapeutic, and the drug uptake and release kinetics are measured by HPLC. In vivo studies in mice showed that: i) ICAM-NG accumulates in mouse lungs (∼120% ID/g vs ∼15% ID/g of IgG-NG); and, ii) DEX encapsulated in ICAM-NG, but not in IgG-NG practically blocks LPS-induced overexpression of pro-inflammatory cell adhesion molecules including ICAM-1 in the pulmonary inflammation.     

Effects of habitat quality and size on extinction in experimental populations

Stochastic population theory makes clear predictions about the effects of reproductive potential and carrying capacity on characteristic time-scales of extinction. At the same time, the effects of habitat size and quality on reproduction and regulation have been hotly debated. To trace the causal relationships among these factors, we looked at the effects of habitat size and quality on extinction time in experimental populations of Daphnia magna. Replicate model systems representative of a broad-spectrum consumer foraging on a continuously supplied resource were established under crossed treatments of habitat size (two levels) and habitat quality (three levels) and monitored until eventual extinction of all populations. Using statistically derived estimates of key parameters, we related experimental treatments to persistence time through their effect on carrying capacity and the population growth rate. We found that carrying capacity and the intrinsic rate of increase were each influenced similarly by habitat size and quality, and that carrying capacity and the intrinsic rate of increase were in turn both correlated with time to population extinction. We expected habitat quality to have a greater influence on extinction. However, owing to an unexpected effect of habitat size on reproductive potential, habitat size and quality were similarly important for population persistence. These results support the idea that improving the population growth rate or carrying capacity will reduce extinction risk and demonstrate that both are possible by improving habitat quality or increasing habitat size.     

Metabolic costs of capital energy storage in a small‐bodied ectotherm

Reproduction is energetically financed using strategies that fall along a continuum from animals that rely on stored energy acquired prior to reproduction (i.e., capital breeders) to those that rely on energy acquired during reproduction (i.e., income breeders). Energy storage incurs a metabolic cost. However, previous studies suggest that this cost may be minimal for small‐bodied ectotherms. Here I test this assumption. I use a laboratory feeding experiment with the European green crab Carcinus maenas to establish individuals with different amounts of energy storage. I then demonstrate that differences in energy storage account for 26% of the variation in basal metabolic costs. The magnitudes of these costs for any individual crab vary through time depending on the amount of energy it has stored, as well as on temperature‐dependent metabolism. I use previously established relationships between temperature‐ and mass‐dependent metabolic rates, combined with a feasible annual pattern of energy storage in the Gulf of Maine and annual sea surface temperature patterns in this region, to estimate potential annual metabolic costs expected for mature female green crabs. Results indicate that energy storage should incur an ~8% increase in metabolic costs for female crabs, relative to a hypothetical crab that did not store any energy. Translated into feeding, for a medium‐sized mature female (45 mm carapace width), this requires the consumption of an additional ~156 mussels annually to support the metabolic cost of energy storage. These results indicate, contrary to previous assumptions, that the cost of energy storage for small‐bodied ectotherms may represent a considerable portion of their basic operating energy budget. An inability to meet these additional costs of energy storage may help explain the recent decline of green crabs in the Gulf of Maine where reduced prey availability and increased consumer competition have combined to hamper green crab foraging success in recent years.     

Increased production of yersiniabactin and an anthranilate analog through media optimization

Yersiniabactin (Ybt) is a mixed nonribosomal peptide‐polyketide natural product that binds a wide range of metals with the potential to impact processes requiring metal retrieval and removal. In this work, we substantially improved upon the heterologous production of Ybt and an associated anthranilate analog through systematic screening and optimization of culture medium components. Specifically, a Plackett‐Burman design‐of‐experiments methodology was used to screen 22 components and to determine those contributing most to siderophore production. L‐cysteine, L‐serine, glucose, and casamino acids significantly contributed to the production of both compounds. Using this approach together with metabolic engineering of the base biosynthetic process, Ybt and the anthranilate analog titers were increased to 867 ± 121 mg/L and 16.6 ± 0.3 mg/L, respectively, an increase of ～38 and ～79‐fold relative to production in M9 medium. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1193–1200, 2017     

Immunotoxicity Biomarkers in Fish: Development,Validation and Application for Field Studies and Risk Assessment

Imunocompetence is usually monitored using a tiered approach that is based upon several parameters including immunopathology, immune function, and host resistance. Through the efforts of numerous investigations, well-characterized immune assays validated in rodents for their sensitivity and reproducibility in assessing xenobiotic-induced immunotoxicity are currently available. Recently, many of these same endpoints have been utilized in non-mammalian species as indicators to predict chemical-induced immunotoxicity. In this laboratory, immune assays that measure immunopathology, antibody-forming cell response to T-dependent antigens, lymphocyte proliferation, macrophage function, antioxidant activity, and host resistance against infectious bacteria have been employed successfully to assess metal-, pesticide-, aromatic hydrocarbon-, and mixture-induced immunotoxicity in laboratory-reared Japanese medaka (Oryzias latipes). These same assays have also proven successful in feral fish populations for predicting risk(s) associated with habitation in contaminated aquatic environments. For example, smallmouth bass (Micropterus dolomieu) collected from a polychlorinated biphenyl-contaminated site had reduced phagocyte function, oxyradical production, and antioxidant levels (compared to reference fish), while circulating leukocyte profiles and lymphocyte proliferation by splenic T-cells were altered in organochlorine-exposed walleye (Stizostedium vitreum vitreum). Results of the aforementioned studies demonstrate that immune assays developed and validated in a laboratory fish model can be successfully applied to feral fish populations to predict the toxicological hazards associated with exposure to immunomodulating aquatic pollutants.     

Recruitment in the harvester ant, Pogonomyrmex occidentalis: effects of experimental removal

We examined the importance of experimental removal of mature colonies on colony recruitment in the western harvester ant Pogonomyrmex occidentalis. To test the common assumption that established colonies suppress the establishment of new colonies we removed all colonies in ten 0.25 ha plots in 1996 and an additional five plots in 1997 and measured new colony recruitment in 1997, 1998, and 1999. Using a blocked, paired plot design we found that removal of colonies increased new colony recruitment in some areas of the site, but not others. Spatial variation in the importance of established colonies to recruitment was consistent across years; blocks in which density dependence was important in one year exhibited density dependent recruitment in following years. We estimated that in the blocks where recruitment was affected by established colonies, they accounted for less than 10% of the mortality of foundress queens. The increase in the number of new recruits (on average two additional new colonies) was considerably less than the number of colonies removed; average colony density in the removal plots was 14 colonies per 0.25 ha plot. The consistent lack of importance of established colonies to recruitment in one block and the relatively small response to colony removal in the other blocks suggests that the number of new colonies in a year may not be equivalent to the number of deaths of established colonies in that year. Space limitation is an important influence on recruitment in P. occidentalis, but the magnitude of the limitation varies spatially.