Telomeres: not all breaks are equal

ATM, Rad50 and Mre11 have been shown to prevent telomere fusion in Drosophila, thereby extending the protective role of DNA damage checkpoint proteins to non-canonical telomeres formed without telomerase. How do these proteins help chromosomal termini escape fusion through 'repair' while promoting repair of induced DNA breaks?     

Actin nucleation: Nucleation-promoting factors are not all equal

Arp2/3 complex plays a key role in regulated actin polymerization. A recent study has revealed marked differences in the ability of two nucleation-promoting factors - N-WASP and Scar/WAVE1 - to activate the Arp2/3 complex. Further insights have come from determination of the Arp2/3 crystal structure.     

Type I chaperonins: not all are created equal

Type I chaperonins play an essential role in the folding of newly translated and stress-denatured proteins in eubacteria, mitochondria and chloroplasts. Since their discovery, the bacterial chaperonins have provided an excellent model system for investigating the mechanism by which chaperonins mediate protein folding. Due to the high conservation of the primary sequence among Type I chaperonins, it is generally accepted that organellar chaperonins function similar to the bacterial ones. However, recent studies indicate that the chloroplast and mitochondrial chaperonins possess unique structural and functional properties that distinguish them from their bacterial homologs. This review focuses on the unique properties of organellar chaperonins.     

Molecular genetics of MTHFR: polymorphisms are not all benign

Methylenetetrahydrofolate reductase (MTHFR) is a key regulatory enzyme in folate and homocysteine metabolism. Research performed during the past decade has clarified our understanding of MTHFR deficiencies that cause homocystinuria or mild hyperhomocysteinemia. Our cloning of the MTHFR coding sequence was initially followed by the identification of the first deleterious mutations in MTHFR, in patients with homocystinuria and marked hyperhomocysteinemia. Shortly thereafter, we identified the 677C-->T variant and showed that it encoded a thermolabile enzyme with reduced activity. Currently, a total of 41 rare but deleterious mutations in MTHFR, as well as about 60 polymorphisms have been reported. The 677C-->T (Ala222Val) variant has been particularly noteworthy since it has become recognized as the most common genetic cause of hyperhomocysteinemia. The disruption of homocysteine metabolism by this polymorphism influences risk for several complex disorders, including cardiovascular disease, neural tube defects and some cancers. We describe here the complex structure of the MTHFR gene, summarize the current state of knowledge on rare and common mutations in MTHFR and discuss some relevant findings in a mouse model for MTHFR deficiency.     

Diversity of color vision: not all Australian marsupials are trichromatic

Color vision in marsupials has recently emerged as a particularly interesting case among mammals. It appears that there are both dichromats and trichromats among closely related species. In contrast to primates, marsupials seem to have evolved a different type of trichromacy that is not linked to the X-chromosome. Based on microspectrophotometry and retinal whole-mount immunohistochemistry, four trichromatic marsupial species have been described: quokka, quenda, honey possum, and fat-tailed dunnart. It has, however, been impossible to identify the photopigment of the third cone type, and genetically, all evidence so far suggests that all marsupials are dichromatic. The tammar wallaby is the only Australian marsupial to date for which there is no evidence of a third cone type. To clarify whether the wallaby is indeed a dichromat or trichromatic like other Australian marsupials, we analyzed the number of cone types in the "dichromatic" wallaby and the "trichromatic" dunnart. Employing identical immunohistochemical protocols, we confirmed that the wallaby has only two cone types, whereas 20-25% of cones remained unlabeled by S- and LM-opsin antibodies in the dunnart retina. In addition, we found no evidence to support the hypothesis that the rod photopigment (rod opsin) is expressed in cones which would have explained the absence of a third cone opsin gene. Our study is the first comprehensive and quantitative account of color vision in Australian marsupials where we now know that an unexpected diversity of different color vision systems appears to have evolved.     

Laminin isoforms and lung development: all isoforms are not equal

Laminins are a major component of basement membranes. Each laminin molecule is a heterotrimeric glycoprotein composed of one alpha, one beta, and one gamma chain. Fifteen laminin isoforms exist, assembled from various combinations of 5alpha, 3beta, and 3gamma chains. The embryonic lung has abundant laminin isoforms. Increasing evidence suggests that different laminin isoforms have unique functions in lung development. Studies of embryonic lung explants and organotypic co-cultures show that laminin alpha1 and laminin 111 are important for epithelial branching morphogenesis and that laminin alpha2 and laminin 211 have a role in smooth muscle cell differentiation. In vivo studies of laminin alpha5-deficient mice indicate that this laminin chain, found in laminins 511 and 521, is essential for normal lobar septation in early lung development and normal alveolization and distal epithelial cell differentiation and maturation in late lung development. However, not all of the laminin chains present in the developing lung appear to be necessary for normal lung development since laminin alpha4 null mice do not have obvious lung abnormalities and laminin gamma2 null mice have only minimal changes in lung development. The mechanisms responsible for the lung phenotypes in mice with laminin mutations are unknown, but it is clear that multiple laminin isoforms are crucial for lung development and that different laminin isoforms exhibit specific, non-overlapping functions.     

Microbial experiments on adaptive landscapes

The adaptive landscape is one of the most widely used metaphors in evolutionary biology. It is created by plotting fitness against phenotypes or genotypes in a given environment. The shape of the landscape is crucial in predicting the outcome of evolution: whether evolution will result in populations reaching predictable end points, or whether multiple evolutionary outcomes are more likely. In a more applied sense, the landscape will determine whether organisms will evolve to lose 'costly' resistance to antibiotics, herbicides or pesticides when the use of the control agent is stopped. Laboratory populations of microbes allow evolution to be observed in real time and, as such, provide key insights into the topology of adaptive landscapes.     

Novel object exploration in mice: not all objects are created equal

Object exploration is an increasingly popular experimental paradigm in behavioral sciences. We have begun a series of studies with mice specifically looking at the parameters that influence behaviors in this test. The aim of the present study was to examine the effect of object type on performance in the object exploration test. More specifically, adult male C57BL/6J mice were trained and tested using objects that could be climbed (CLIMB) or with those that could only be touched (TOUCH). The results show that activity is affected by the presentation of objects, with object type interacting with some of these changes. C57 mice explored objects that can be climbed over significantly longer than objects that can only be touched and a more rapid habituation was observed using objects that could only be touched. Robust recognition memory was observed in both groups of mice, however mice in the CLIMB group exhibited a significantly greater discrimination index compared to mice in the TOUCH group. Taken together, these findings demonstrate that the selection of objects is of critical importance and it is recommended that special attention be given to the functional (affordant) properties of the objects to-be-used in future studies.     

Targeting mechanisms in myelinated axons: not all nodes are created equal

A recent Neuron paper by Zhang et al. (2012) reveals how ion channels and adhesion molecules essential for rapid nerve conduction in vertebrates are differentially targeted to nodes of Ranvier. Moreover, distinct mechanisms regulate initial clustering and maintenance of specific nodal components.     

Programmed genome rearrangements: in lampreys, all cells are not equal

How can organisms silence deleterious gene loci? A recent study has shed light on a very brute mechanism in a jawless vertebrate: the irreversible deletion of massive chunks of genomic DNA.     

Ty1 proteolytic cleavage sites are required for transposition: all sites are not created equal

The retroviral protease is a key enzyme in a viral multienzyme complex that initiates an ordered sequence of events leading to virus assembly and propagation. Viral peptides are initially synthesized as polyprotein precursors; these precursors undergo a number of proteolytic cleavages executed by the protease in a specific and presumably ordered manner. To determine the role of individual protease cleavage sites in Ty1, a retrotransposon from Saccharomyces cerevisiae, the cleavage sites were systematically mutagenized. Altering the cleavage sites of the yeast Ty1 retrotransposon produces mutants with distinct retrotransposition phenotypes. Blocking the Gag/PR site also blocks cleavage at the other two cleavage sites, PR/IN and IN/RT. In contrast, mutational block of the PR/IN or IN/RT sites does not prevent cleavage at the other two sites. Retrotransposons with mutations in each of these sites have transposition defects. Mutations in the PR/IN and IN/RT sites, but not in the Gag/PR site, can be complemented in trans by endogenous Ty1 copies. Hence, the digestion of the Gag/PR site and release of the protease N terminus is a prerequisite for processing at the remaining sites; cleavage of PR/IN is not required for the cleavage of IN/RT, and vice versa. Of the three cleavage sites in the Gag-Pol precursor, the Gag/PR site is processed first. Thus, Ty1 Gag-Pol processing proceeds by an ordered pathway.     

The sensory ecology of adaptive landscapes

In complex environments, behavioural plasticity depends on the ability of an animal to integrate numerous sensory stimuli. The multidimensionality of factors interacting to shape plastic behaviour means it is difficult for both organisms and researchers to predict what constitutes an adaptive response to a given set of conditions. Although researchers may be able to map the fitness pay-offs of different behavioural strategies in changing environments, there is no guarantee that the study species will be able to perceive these pay-offs. We thus risk a disconnect between our own predictions about adaptive behaviour and what is behaviourally achievable given the umwelt of the animal being studied. This may lead to erroneous conclusions about maladaptive behaviour in circumstances when the behaviour exhibited is the most adaptive possible given sensory limitations. With advances in the computational resources available to behavioural ecologists, we can now measure vast numbers of interactions among behaviours and environments to create adaptive behavioural surfaces. These surfaces have massive heuristic, predictive and analytical potential in understanding adaptive animal behaviour, but researchers using them are destined to fail if they ignore the sensory ecology of the species they study. Here, we advocate the continued use of these approaches while directly linking them to perceptual space to ensure that the topology of the generated adaptive landscape matches the perceptual reality of the animal it intends to study. Doing so will allow predictive models of animal behaviour to reflect the reality faced by the agents on adaptive surfaces, vastly improving our ability to determine what constitutes an adaptive response for the animal in question.     

Fitness-associated recombination on rugged adaptive landscapes

A negative correlation between fitness and recombination rates seems to exist in various organisms. In this article we suggest that a correlation of that kind may play an important role in the evolution of complex traits. We study the effects of such fitness-associated recombination (FAR) in a simple two-locus deterministic model, as well as in a multi-loci NK rugged adaptive landscape. In both models studied, FAR results in faster adaptation and higher average population fitness, compared with uniform-rate recombination.     

Colour perception in three-spined sticklebacks: sexes are not so different after all

Sexual selection theory implies a tight coupling between the evolution of male sexual display and the sensory capabilities of the female. In sexually dimorphic species it is proposed that this might lead to sex differences in a species’ perceptive abilities. However, supporting evidence for this is rare, and to date there is only one example; three-spined sticklebacks, Gasterosteus aculeatus. Here, the female’s visual system is reported to become more red-sensitive during the summer breeding season; a time when sexually mature males display a red throat and belly to potential mates. In contrast, a shift in sensitivity is not apparent in males. These results, although commonly quoted, are surprising because previous observations suggest that both sexes may benefit from the detection of the male’s red colour patch; in females the intensity of red coloration can influence the choice of mate, and in males the conspicuous red colouration can aid the detection of rival males. To investigate this paradox we repeated the original optomotor experiment using a fully controlled design. In contrast to the earlier result, we found that both males and females exhibit a shift in their sensitivity to red during the reproductive period. These new data therefore do not support the hypothesis that sex differences in perceptual abilities occur in sexually dimorphic species.