The role of site accessibility in microRNA target recognition

MicroRNAs are key regulators of gene expression, but the precise mechanisms underlying their interaction with their mRNA targets are still poorly understood. Here, we systematically investigate the role of target-site accessibility, as determined by base-pairing interactions within the mRNA, in microRNA target recognition. We experimentally show that mutations diminishing target accessibility substantially reduce microRNA-mediated translational repression, with effects comparable to those of mutations that disrupt sequence complementarity. We devise a parameter-free model for microRNA-target interaction that computes the difference between the free energy gained from the formation of the microRNA-target duplex and the energetic cost of unpairing the target to make it accessible to the microRNA. This model explains the variability in our experiments, predicts validated targets more accurately than existing algorithms, and shows that genomes accommodate site accessibility by preferentially positioning targets in highly accessible regions. Our study thus demonstrates that target accessibility is a critical factor in microRNA function.     

Deciphering the BAR code of membrane modulators

The BAR domain is the eponymous domain of the “BAR-domain protein superfamily”, a large and diverse set of mostly multi-domain proteins that play eminent roles at the membrane cytoskeleton interface. BAR domain homodimers are the functional units that peripherally associate with lipid membranes and are involved in membrane sculpting activities. Differences in their intrinsic curvatures and lipid-binding properties account for a large variety in membrane modulating properties. Membrane activities of BAR domains are further modified and regulated by intramolecular or inter-subunit domains, by intermolecular protein interactions, and by posttranslational modifications. Rather than providing detailed cell biological information on single members of this superfamily, this review focuses on biochemical, biophysical, and structural aspects and on recent findings that paradigmatically promote our understanding of processes driven and modulated by BAR domains.     

Effect of evaporite deposition on Early Cretaceous carbon and sulphur cycling

The global carbon and sulphur cycles are central to our understanding of the Earth's history, because changes in the partitioning between the reduced and oxidized reservoirs of these elements are the primary control on atmospheric oxygen concentrations. In modern marine sediments, the burial rates of reduced carbon and sulphur are positively coupled, but high-resolution isotope records indicate that these rates were inversely related during the Early Cretaceous period. This inverse relationship is difficult to reconcile with our understanding of the processes that control organic matter remineralization and pyrite burial. Here we show that the inverse correlation can be explained by the deposition of evaporites during the opening of the South Atlantic Ocean basin. Evaporite deposition can alter the chemical composition of sea water, which can in turn affect the ability of sulphate-reducing bacteria to remineralize organic matter and mediate pyrite burial. We use a reaction-transport model to quantify these effects, and the resulting changes in the burial rates of carbon and sulphur, during the Early Cretaceous period. Our results indicate that deposition of the South Atlantic evaporites removed enough sulphate from the ocean temporarily to reduce biologically mediated pyrite burial and organic matter remineralization by up to fifty per cent, thus explaining the inverse relationship between the burial rates of reduced carbon and sulphur during this interval. Furthermore, our findings suggest that the effect of changing seawater sulphate concentrations on the marine subsurface biosphere may be the key to understanding other large-scale perturbations of the global carbon and sulphur cycles.     

Note on occurrence of Mymaromella pala Huber and Gibson (Hymenoptera: Mymarommatidae) in Montana: a new state record

The parasitic wasp Mymaromella pala Huber and Gibson (Hymenoptera: Mymarommatidae) was collected at 4 sites within a canyon reach of the Kootenai River in Lincoln County, Montana. This minute species has only recently been described, but it appears to have a large distribution throughout the United States and to be associated with upland and riparian forests. La avispa parasitaria Mymaromella pala Huber y Gibson (Hymenoptera: Mymarommatidae) se recolectó en cuatro sitios a lo largo de un cañón del Río Kootenai en Lincoln Co., MT. Hace poco que se describió esta especie diminuta, pero parece tener una distribución extensa en los EE.UU. y estar asociada con bosques altos y ribereños.     

Mass march of termites into the deadly trap.

Carnivorous pitcher plants of the genus Nepenthes are not usually very selective about their prey, catching anything that is careless enough to walk on their slippery peristome, but Nepenthes albomarginata is an exception. We show here that this plant uses a fringe of edible white hairs to lure and then trap its prey, which consists exclusively of termites in enormous numbers. This singular feature accounts for the specialization of N. albomarginata for one prey taxon, unique so far among carnivorous plants.     

Cadherin 23 is a component of the tip link in hair-cell stereocilia

Mechanoelectrical transduction, the conversion of mechanical force into electrochemical signals, underlies a range of sensory phenomena, including touch, hearing and balance. Hair cells of the vertebrate inner ear are specialized mechanosensors that transduce mechanical forces arising from sound waves and head movement to provide our senses of hearing and balance; however, the mechanotransduction channel of hair cells and the molecules that regulate channel activity have remained elusive. One molecule that might participate in mechanoelectrical transduction is cadherin 23 (CDH23), as mutations in its gene cause deafness and age-related hearing loss. Furthermore, CDH23 is large enough to be the tip link, the extracellular filament proposed to gate the mechanotransduction channel. Here we show that antibodies against CDH23 label the tip link, and that CDH23 has biochemical properties similar to those of the tip link. Moreover, CDH23 forms a complex with myosin-1c, the only known component of the mechanotransduction apparatus, suggesting that CDH23 and myosin-1c cooperate to regulate the activity of mechanically gated ion channels in hair cells.     

The principle of temperature-dependent gating in cold- and heat-sensitive TRP channels

The mammalian sensory system is capable of discriminating thermal stimuli ranging from noxious cold to noxious heat. Principal temperature sensors belong to the TRP cation channel family, but the mechanisms underlying the marked temperature sensitivity of opening and closing ('gating') of these channels are unknown. Here we show that temperature sensing is tightly linked to voltage-dependent gating in the cold-sensitive channel TRPM8 and the heat-sensitive channel TRPV1. Both channels are activated upon depolarization, and changes in temperature result in graded shifts of their voltage-dependent activation curves. The chemical agonists menthol (TRPM8) and capsaicin (TRPV1) function as gating modifiers, shifting activation curves towards physiological membrane potentials. Kinetic analysis of gating at different temperatures indicates that temperature sensitivity in TRPM8 and TRPV1 arises from a tenfold difference in the activation energies associated with voltage-dependent opening and closing. Our results suggest a simple unifying principle that explains both cold and heat sensitivity in TRP channels.     

Consumer versus resource control of species diversity and ecosystem functioning

A key question in ecology is which factors control species diversity in a community. Two largely separate groups of ecologists have emphasized the importance of productivity or resource supply, and consumers or physical disturbance, respectively. These variables show unimodal relationships with diversity when manipulated in isolation. Recent multivariate models, however, predict that these factors interact, such that the disturbance diversity relationship depends on productivity, and vice versa. We tested these models in marine food webs, using field manipulations of nutrient resources and consumer pressure on rocky shores of contrasting productivity. Here we show that the effects of consumers and nutrients on diversity consistently depend on each other, and that the direction of their effects and peak diversity shift between sites of low and high productivity. Factorial meta-analysis of published experiments confirms these results across widely varying aquatic communities. Furthermore, our experiments demonstrate that these patterns extend to important ecosystem functions such as carbon storage and nitrogen retention. This suggests that human impacts on nutrient supply and food-web structure have strong and interdependent effects on species diversity and ecosystem functioning, and must therefore be managed together.     

A bisexually reproducing all-triploid vertebrate

Green toads are common in the Palaearctic region, where they have differentiated into several taxa. The toads exist with variable amounts of ploidy, similar to other anuran species or reptiles. In vertebrate biology, the very rare occurrence of triploidy is coupled with infertility or unisexuality, or requires the coexistence of individuals of different ploidy in a reproductive community. The reproduction of naturally occurring triploids has been reported to occur only through parthenogenesis, gynogenesis or hybridogenesis. The bisexual reproduction of pure triploids has been considered to be impossible because of the problem of equally distributing three chromosome sets in meiosis. Here we report geographically isolated populations of green toads (Bufo viridis complex) that are all-triploid and reproduce bisexually.