Hiding in plain sight: how HIV evades innate immune responses

Two groups have identified SAMHD1, a protein encoded by an Aicardi-Goutières Syndrome susceptibility gene, as the factor that restricts infection of macrophages and dendritic cells with HIV-1. Here we discuss implications of this discovery for induction of antiviral protective immunity.     

Parameterising a public good: how experiments on predation can be used to predict cheat frequencies

Chemical defence is superficially easy to understand as a means for individuals to protect themselves from enemies. The evolution of chemical defence is however potentially complex because such defences may cause the generation of a public good, protecting members of the population as a whole as well as individuals that deploy toxins defensively. If a public good of protection exists, it may be exploited and degraded by “cheats” that do not invest in defence. This can in turn lead to complex frequency (and density) dependent effects in toxin evolution. To investigate this we used ecologically relevant predators (Great tits, Parus major) and examined how individual and public benefits vary depending on the frequency of non-defended “cheating” prey and their spatial distribution. We found that the public benefit, of reduced attack probability, increased with increasing frequency of defended individuals. In contrast the individual benefit of chemical defence, measured as increased chance of rejection during an attack before injury, did not vary with the frequency of defended forms. Hence the selective dynamics of these two levels of benefits responded differently to the frequency of defended forms. Surprisingly, given the strong associations of chemical defences and grouping in animals, large aggregations did not help individuals in the group regardless of their defence status. The explanation for the result, may be that in our experiment birds did not have information about other potential aggregations (i.e. set up was sequential) and thus their giving up density was lower compared to the situations where set ups were simultaneous. We use behavioural data of our predators to construct a simple model of toxin evolution which can make quantitative predictions about the frequencies to which defence cheats evolve. We use this model to discuss how toxin evolution can be investigated in the wild and in laboratory settings.     

Stem cell competition: how speeding mutants beat the rest

How mutations lead to tumor formation is a central question in cancer research. Although cellular changes that follow the occurrence of common mutations are well characterized, much less is known about their effects on the population level. Now, two recent studies reveal in what way oncogenic aberrations alter stem cell dynamics to provide cells with an evolutionary advantage over their neighbors (Amoyel et al, 2014 ; Baker et al, 2014 ).     

From competition to facilitation: how tree species respond to neighbourhood diversity

Studies on tree communities have demonstrated that species diversity can enhance forest productivity, but the driving mechanisms at the local neighbourhood level remain poorly understood. Here, we use data from a large‐scale biodiversity experiment with 24 subtropical tree species to show that neighbourhood tree species richness generally promotes individual tree productivity. We found that the underlying mechanisms depend on a focal tree's functional traits: For species with a conservative resource‐use strategy diversity effects were brought about by facilitation, and for species with acquisitive traits by competitive reduction. Moreover, positive diversity effects were strongest under low competition intensity (quantified as the total basal area of neighbours) for acquisitive species, and under high competition intensity for conservative species. Our findings demonstrate that net biodiversity effects in tree communities can vary over small spatial scales, emphasising the need to consider variation in local neighbourhood interactions to better understand effects at the community level.     

Palmated antlers of moose may serve as a parabolic reflector of sounds

It has been postulated that the excellent sense of hearing in moose is mostly due to: (1) the large surface of the external ear, (2) better stereophony due to the large distance between ears, (3) independently movable, extremely adjustable pinna, and (4) the amplification of sounds reflected by the palms of the antlers. The last factor, possible reflection of sounds into pinna by the palm of the antlers, was tested in this study on a large antler trophy of Alaskan moose. The reception of a standard tone, broadcast from the frontally placed speaker, was recorded by a sound level meter located in an artificial moose ear. Three locations of the ear, as positioned relative to the speaker, e.g., frontward, sideward, and backward, were tested. The weakest reception was recorded in the backward position of the ear. If the sound pressure measured in the frontward position was set as 100%, the sound pressure in the backward position was 79%. The strongest reception was recorded when the artificial ear was positioned toward the center of the antler palm. In this position, the sound pressure was 119% relative to the frontward position. These findings strongly indicate that the palm of moose antlers may serve as an effective, parabolic reflector which increases the acoustic pressure of the incoming sound.     

TB or Not TB: how Mycobacterium tuberculosis may evade drug treatment

In this issue of Cell, a study by Valerie Mizrahi and her colleagues suggests that a putative error-prone DNA polymerase encoded by the dnaE2 gene of Mycobacterium tuberculosis may bypass certain types of DNA base damage, generating mutations. This may be an important mechanism for generating drug-resistant strains of M. tuberculosis.     

Epigenetics: deciphering how environmental factors may modify autoimmune type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease that has increased two- to threefold over the past half century by as yet unknown means. It is generally accepted that T1D is the result of gene–environment interactions, but such rapid increases in incidence are not explained by Mendelian inheritance. There have been numerous advances in our knowledge of the pathogenesis of T1D. Indeed, there has been a large number of genes identified that contribute to risk for this disease and several environmental factors have been proposed. The complexity of such interactions is yet to be understood for any major chronic disease. Epigenetic regulation is one way to explain the rapid increase in incidence and could be a central mechanism by which environmental factors influence development of diabetes. However, there is remarkably little known about the contribution of epigenetics to T1D pathogenesis. Here we speculate on various candidate processes and molecules of the immune and endocrine systems that could modify risk for T1D through epigenetic regulation.     

Control of IS911 target selection: how OrfA may ensure IS dispersion

IS911 transposition involves a closed circular insertion sequence intermediate (IS-circle) and two IS-encoded proteins: the transposase OrfAB and OrfA which regulates IS911 insertion. OrfAB alone promotes insertion preferentially next to DNA sequences resembling IS911 ends while the addition of OrfA strongly stimulates insertion principally into DNA targets devoid of the IS911 end sequences. OrfAB shares its N-terminal region with OrfA. This includes a helix-turn-helix (HTH) motif and the first three of four heptads of a leucine zipper (LZ). OrfAB binds specifically to IS911 ends via its HTH whereas OrfA does not. We show here: that OrfA binds DNA non-specifically and that this requires the HTH; that OrfA LZ is required for its multimerization; and that both motifs are essential for OrfA activity. We propose that these OrfA properties are required to assemble a nucleoprotein complex committed to random IS911 insertion. This control of IS911 insertion activity by OrfA in this way would assure its dispersion.     

Mother guarding: how offspring may influence the extra-pair behaviour of their parents

In this paper we propose a novel form of social control of mate choice. Through mother guarding, offspring can help in protecting the paternity of their father by preventing their mother from engaging in extra-pair matings. We present a model that predicts the circumstances under which mothers should be selected to seek or avoid extra-pair matings, and existing offspring should be selected to prevent or promote such matings. In its simplest form, our model shows that offspring are selected to mother guard as long as the viability of extra-pair young is less than twice that of within-pair young; when the relative viability is greater, offspring are selected to promote extra-pair mating by their mother. If the existing offspring are not necessarily sired by their mother's social mate, then the potential for conflict is further reduced. We also consider whether offspring have an interest in the extra-pair reproduction of their fathers. We show that when the costs of the father's infidelity to the mother's brood are high, existing offspring are selected to prevent extra-pair mating by their father; when such costs are low, offspring are selected to promote extra-pair mating by their father. In principle, our model applies to all species where offspring show delayed dispersal and where breeding pairs raise multiple broods or litters. This situation exists in, but is not limited to, the majority of cooperatively breeding species. The significance of this model with regard to our current understanding of the evolution of extra-pair behaviour in such species is discussed.     

Paradigm lost: how parasite control may alter pattern and process in human helminthiases

Knowledge of pattern and process in helminth population biology is mostly based on the endemic equilibrium state that characterises infections before control. Current large-scale intervention programmes aim at controlling/eliminating helminth infection, transmission and morbidity. As a result, age-infection profiles will be modified; immune responses will be affected; underlying parasite distributions may become more aggregated; density-dependent regulatory processes will relax; and the contribution to transmission and morbidity of different host population groups will shift. There is an urgent need to understand how the paradigm that has guided parasite population biology research is changing under chemotherapy-based control programmes for this research to continue supporting parasite control efforts effectively.     

Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA

We have previously shown that stable base-pairing at a translational initiation site in Escherichia coli can inhibit translation by competing with the binding of ribosomes. When the base-pairing is not too strong, this competition is won by the ribosomes, resulting in efficient translation from a structured ribosome binding site (RBS). We now re-examine these results in the light of RNA folding kinetics and find that the window during which a folded RBS is open is generally much too short to recruit a 30S ribosomal subunit from the cytoplasm. We argue that to achieve efficient expression, a 30S subunit must already be in contact with the mRNA while this is still folded, to shift into place as soon as the structure opens. Single-stranded regions flanking the structure may constitute a standby site, to which the 30S subunit can attach non-specifically. We propose a steady-state kinetic model for the early steps of translational initiation and use this to examine various quantitative aspects of standby binding. The kinetic model provides an explanation of why the earlier equilibrium competition model predicted implausibly high 30S-mRNA affinities. Because all RNA is structured to some degree, standby binding is probably a general feature of translational initiation.