New directions for studying selection in nature: studies of performance and communities

Natural and sexual selection are crucial factors in the evolutionary process, yet recent reviews show that researchers have focused narrowly on this topic, with the majority of research centered on the morphological traits of single species. However, in the past several years, several bodies of work have emerged that have examined both selection on performance capacity and selection in a community context, and our goal is to highlight these two growing areas and point toward future directions. Recent studies of selection on performance capacity point toward directional selection favoring high levels of performance, and we detected less evidence for selection favoring intermediate (i.e., stabilizing) or bimodal (i.e., disruptive) kinds of performance levels. Studies of selection in a community context, using the paradigm of indirect genetic effects, show significant community heritability and strong capacity for evolution to occur in a community context via the force of natural selection. For future directions, we argue that researchers should shift toward longer-term studies of selection on both individual species and communities, and we also encourage researchers to publish negative selection results for both performance and community studies to act as balancing influences on published positive selection results.     

Studies on the mechanism of interaction of a bioresponsive endosomolytic polyamidoamine with interfaces. 1. Micelles as model surfaces

Polymers are appealing as pH-responsive elements of multicomponent systems designed to promote cytosolic delivery of macromolecular drugs (including proteins and genes), but so far the delivery efficiency achieved has been relatively modest. Therefore, the aim of this study was to apply several physicochemical techniques that are well established in the colloid field (surface tension measurements, small-angle neutron scattering (SANS), and electron paramagnetic resonance (EPR)) to probe the mechanism of endosomolytic polymer-surface interaction over the pH range 7.4 to 5.5 using the poly(amidoamine) (PAA) ISA23 x HCl and a series of "model" micelle surfaces. These micellar models were chosen to represent increasing complexity from simple, single surfactant sodium dodecylsulfate (SDS) micelles, surfactant mixtures containing bulky malono-bis-N-methylglucamide headgroups, or highly extended ethylene oxide headgroups. Spherical micelles composed of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (lyso-PC) were also used. Changes in the onset of micellization, micelle surface fluidity, and in selected cases, the overall micelle shape and size were all quantified as a function of pH in the presence and absence of ISA23 x HCl. This amphoteric PAA is negatively charged at pH 7.4 and becomes gradually more protonated on exposure to lower pH values representative of the endosomal-lysosomal pathway. As expected, the strength of polymer interaction with anionic micelles increased with a decrease in pH, while for cationic micelles the opposite was observed. Addition of bulky, nonionic surfactant headgroups led to weaker interactions. The observations from surface tension and SANS studies showed a complex pattern of interaction with both an electrostatic and hydrophobic component. Using EPR it was confirmed that ISA23 x HCl perturbed the micelle palisade layer leading to a decrease in fluidity of the interface with a lower degree of headgroup hydration, and a significant change in micelle morphology. Surprisingly, there was no interaction between ISA23 x HCl and globular micelles formed from lyso-PC (a more biologically relevant model), and this suggests that the PAA structure could be better optimized to promote rapid interaction with endosomal membranes at the physiologically relevant pH 6.5.     

Using small-angle neutron scattering to study the solution conformation of N-(2-hydroxypropyl)methacrylamide copolymer-doxorubicin conjugates

Our past research developed two N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-doxorubicin (Dox) conjugates that became the first synthetic polymer-anticancer conjugates to be evaluated clinically. The first, FCE28068, contained Dox bound to the polymeric carrier via a tetrapeptidic linker (glycine-phenylalanine-leucine-glycine (GFLG)) (Mw approximately 30,000 g/mol; approximately 8 wt % drug), and the second, FCE28069, contained additionally galactosamine (Gal) (Mw approximately 30,000 g/mol; approximately 7.5 wt % Dox) again bound by a GFLG linker. Galactosamine was included to promote hepatocyte/hepatoma targeting via the asialoglycoprotein receptor. Both conjugates showed antitumor activity and were clinically less toxic than free Dox (2-5 fold). However, despite their similar chemical characteristics, the conjugates displayed a significantly different maximum-tolerated dose (MTD) in patients. The aim of this study, therefore, was to use small-angle neutron scattering (SANS) to explore the solution behavior of a small library of HPMA polymer conjugates including FCE28068, FCE28069, and their pharmaceutical formulations, plus as reference compounds HPMA copolymer-GFLG conjugates containing aminopropanol (Ap) or galactosamine (Gal) alone (i.e., without Dox). The SANS data obtained showed that HPMA copolymer-GFLG-Ap conjugates (containing 5 and 10 mol % side chains) showed evidence of polymer aggregation, however, no indication of aggregation was observed for FCE28068 and FCE28069 over the concentration range studied (2.5-50 mg/mL). Clear differences in the scattering behavior for the two conjugates were observed at equivalent concentration. Data were best fitted by a model for polydisperse Gaussian coils, and the HPMA copolymer-Dox conjugate with Gal (FCE28069) exhibited a larger radius of gyration (Rg) (by approximately 2.5 nm) compared to FCE28068. In conclusion, we have shown that SANS will be a valuable tool to elucidate conformation-performance relationships for polymer-drug conjugates.     

Safeguarding marine life: conservation of biodiversity and ecosystems

Reviews in Fish Biology and Fisheries - Marine ecosystems and their associated biodiversity sustain life on Earth and hold intrinsic value. Critical marine ecosystem services include maintenance of...     

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.     

Key mutations stabilize antigen‐binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage

Affinity maturation, the process in which somatic hypermutation and positive selection generate antibodies with increasing affinity for an antigen, is pivotal in acquired humoral immunity. We have studied the mechanism of affinity gain in a human B‐cell lineage in which two main maturation pathways, diverging from a common ancestor, lead to three mature antibodies that neutralize a broad range of H1 influenza viruses. Previous work showed that increased affinity in the mature antibodies derives primarily from stabilization of the CDR H3 loop in the antigen‐binding conformation. We have now used molecular dynamics simulations and existing crystal structures to identify potentially key maturation mutations, and we have characterized their effects on the CDR H3 loop and on antigen binding using further simulations and experimental affinity measurements, respectively. In the two maturation pathways, different contacts between light and heavy chains stabilize the CDR H3 loop. As few as two single‐site mutations in each pathway can confer substantial loop stability, but none of them confers experimentally detectable stability on its own. Our results support models of the germinal center reaction in which two or more mutations can occur without concomitant selection and show how divergent pathways have yielded functionally equivalent antibodies. Proteins 2014; 83:771–780. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high‐throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.