The protein folding problem: when will it be solved?

The protein folding problem can be viewed as three different problems: defining the thermodynamic folding code; devising a good computational structure prediction algorithm; and answering Levinthal's question regarding the kinetic mechanism of how proteins can fold so quickly. Once regarded as a grand challenge, protein folding has seen much progress in recent years. Folding codes are now being used to successfully design proteins and non-biological foldable polymers; aided by the Critical Assessment of Techniques for Structure Prediction (CASP) competition, protein structure prediction has now become quite good. Even the once-challenging Levinthal puzzle now seems to have an answer--a protein can avoid searching irrelevant conformations and fold quickly by making local independent decisions first, followed by non-local global decisions later.     

The timing of hibernation in Tasmanian echidnas: why do they do it when they do?

We investigated the patterns of hibernation and arousals in seven free-ranging echidnas Tachyglossus aculeatus setosus (two male, five female) in Tasmania using implanted temperature data loggers. All echidnas showed a ‘classical’ pattern of mammalian hibernation, with bouts of deep torpor interrupted by periodic arousals to euthermia (mean duration 1.04±0.05 (n=146). Torpor bout length increased as body temperature fell during the hibernation season, and became more variable as temperature rose again. Hibernation started in late summer (February 28±5 days, n=6) and males aroused just before the winter solstice (June 15±3 days, n=3), females that subsequently produced young aroused 40 days later (July 25±3, n=4) while females that did not produce young hibernated for a further two months (arousal Sept 27±5, n=7). We suggest that hibernation in Tasmanian echidnas can be divided into two phases, the first phase, marked by declining minimum body temperatures as ambient temperature falls, appears to be obligatory for all animals, while the second phase is ‘optional’ and is utilised to varying amounts by females. We suggest that early arousal and breeding is the favoured option for females in good condition, and that the ability to completely omit breeding in some years, and hibernate through to spring is an adaptation to an uncertain climate.     

Lateral gene transfer: when will adolescence end?

The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.     

Sympatric speciation: when is it possible?

This paper is written to compare the results of theoretical investigations of sympatric speciation with the relevant experimental data. We understand sympatric speciation as a formation of species out of a population whose spatial structure is not important genetically. A necessary prerequisite for speciation is an action of disruptive selection on sufficiently polymorphic traits. The present analysis confirms the view that such a selection is ecologically realistic. The genetical part of speciation begins with a development of reproductive isolation between those individuals that are opposed in some characters. It is shown that selection for reproductive isolation may be quite strong. Extinction of intermediate individuals, which completes speciation, proceeds under a wide range of conditions, including those when the newly formed species differ in quantitative characters, though most of the genes arc likely to remain the same in both species. The whole process seems possible if differences in several (up to 10) loci are sufficient to adapt the forming species to different niches and to establish reproductive isolation. It is shown that populations with bimodal distributions of some genetically determined quantitative characters can have a considerable life-time. Such distributions may be formed either as a transition stage of sympatric speciation or represent a stationary state under conditions close to those necessary to complete speciation. They are very important for experimental investigations. Sympatric speciation always follows the same principal course; it does not contradict the idea of a genome coadaptedness. The occurrence of sympatric speciation is different for different taxa depending rather on how frequently populations are subjected to the appropriate kind of selection than on their ability to obey it.     

Does insect mother know under what conditions it will make their offspring live?

According to the optimal oviposition theory, the larval success of insects depends on the oviposition site selection by females. Females are expected to choose a site with many resources and few competitors or predators to allow the best performance for their progeny, assuming that “mother knows best.” However, this is not systematically observed. The Aphidoletes aphidimyza larvae are generalist aphid predators and females consequently lay their eggs near or inside aphid colonies. The goal of this study was to investigate the impact of intraspecific competition on oviposition behavior of A. aphidimyza females. First, we counted the number of eggs laid by a female on a leaf with 20 aphids, in the presence of 0, 2, 4, or 6 conspecific eggs or in the absence of eggs but in presence of 3 virgin females. The same experiment was also performed under choice condition with 2 oviposition sites. Our results show that the presence of low densities of conspecific eggs, or the presence of conspecific females, have no significant impact on the number of eggs laid by A. aphidimyza females. One of the hypotheses advanced to explain these results is the advantages of conspecifics presence. At low densities, the presence of eggs on an oviposition site can indicate the suitability of the site for the females. The conspecific presence can also insure a dilution effect against predator and increase the presence of potential mating partners for this monogenic species.     

Androgens in rheumatoid arthritis: when are they effectors?

Neither hormone receptor genes nor plasma androgens seem significantly altered in female subjects before they became affected by rheumatoid arthritis (RA) and, therefore, do not seem to play a role as risk factors for its development. However, serum testosterone levels are inversely correlated with RA activity and dehydro-epiandrosterone sulfate (DHEAS) plasma levels are inversely correlated with both disease duration and clinical severity in patients already affected by active RA. In particular, gonadal and adrenal androgens (that is, testosterone and DHEAS) are significantly decreased in inflamed synovial tissue/fluids during active disease as a consequence of the inflammatory reaction, which supports a pro-inflammatory milieu in RA joints. Recently, male gender has been found to be a major predictor of remission in early RA.     

Stand and shuffle: When does it make energetic sense?

Many reasons for the emergence of bipedalism have been proposed, including postural arguments which highlight that a sub-optimal form of bipedalism ("shuffling") might have been used by protohominids to cover short distances between resources that require bipedal standing. Bipedal shuffling may have been employed because it avoids the cost of raising the trunk from the quadrupedal orientation, which we assume is the habitual locomotor stance of protohominids. To date, these postural proposals have not been analytically assessed, a lack we rectify herein. Our model seeks to specify a threshold distance, below which bipedal shuffling uses less energy than quadrupedalism. Parameters for the model include the mechanical cost of transport, the ratio of bipedal to quadrupedal cost, and the cost associated with raising the trunk. We found that, using reasonable model parameters, open distances of approximately 9-16 m support the use of bipedal shuffling. Protohominids may have used shuffling as an energetically effective way to traverse between resource patches.     

Pesticide resistance: can we make it a renewable resource?

Negative cross-resistance (NCR) occurs when a mutant allele confers (i) resistance to one toxic chemical and (ii) hyper-susceptibility to another. Sequential deployment of NCR toxins is useful for insect control in few situations (Pittendrigh et al., 2000). Using Monte Carlo simulations, we investigated the concurrent use of a pair of NCR toxins to control a hypothetical insect pest population. When the toxins killed more heterozygotes than homozygotes, the resistance allele became either extremely common or rare depending on starting allelic frequency. If the NCR toxins did not kill the two homozygous groups equally, then the toxin with lesser toxicity eventually played a greater role in the control of the pest population. Based on our results, we present an approach for the systematic development of an NCR toxin after the commercial release of the first toxin. First, large-scale screens are performed to find chemicals that kill the resistant homozygous insects, but not the susceptible ones. Chemicals that preferentially kill resistant insects are then tested for toxicity to the heterozygotes. Those highly toxic to both homo- and heterozygotes are given the highest priority for development. This screen can be adapted to identify compounds useful in controlling antibiotic-, herbicide- or fungicide-resistant organisms.     

Mechanosensitive channels: what can they do and how do they do it?

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.     

Polyunsaturated fatty acid synthesis: what will they think of next?

Polyunsaturated fatty acids have crucial roles in membrane biology and signaling processes in most living organisms. However, it is only recently that molecular genetic approaches have allowed detailed studies of the enzymes involved in their synthesis. New evidence has revealed a range of pathways in different organisms. These include a complex sequence for synthesis of docosahexaenoic acid (22:6) in mammals and a polyketide synthase pathway in marine microbes.     

If you build it,will they come? Use of restored dunes by beach mice

Restoration of coastal habitat fragmented, degraded, or destroyed by development and climate‐related processes such as sea level rise and storm surge usually involves planting native plants to restore habitat structure, but whether and how restored areas benefit taxa other than plants is rarely reported. Installing restoration plantings is one method used to build habitat such as beach dunes where dunes have been lost, potentially creating habitat for dune‐dependent species. We compared use of natural vegetated dunes, open sand gaps, and restoration plantings (habitat treatment) by Perdido Key beach mice (Peromyscus polionotus trissyllepsis) over 3 years using tracking tubes to assess the value of restoration plantings for beach mice. Tubes were monitored in two seasons (early and mid‐summer), and under new and full moon conditions. Mice used restoration plantings less than natural vegetated dunes but more than open sand gaps, which suggests restoration plantings may facilitate movement of mice across fragmented areas. Both season and moon phase influenced the effect of habitat treatment, interactions which may be attributable to perceived risk associated with movement under a combination of different conditions of ambient light, vegetation cover, and habitat novelty. Our results show restoration plantings provide habitat for movement and foraging, and may ameliorate some consequences of sea level rise and storms for beach mice and potentially other dune‐dependent species into the future.     

Adaptation in isolated populations: when does it happen and when can we tell?

Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affect the ability of outlier scans for selection to identify adaptive alleles using both single‐site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur and yet the adaptive variants are most likely to derive from a single ancestor (a ‘hard’ selective sweep); in this zone, four commonly used statistics detect selection with high power. Real‐world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole‐genome sequencing of differentiated populations.