Neural control exploits changing mechanical advantage and context dependence to generate different feeding responses in <Emphasis Type="Italic">Aplysia</Emphasis>

How does neural control reflect changes in mechanical advantage and muscle function? In the Aplysia feeding system a protractor muscle's mechanical advantage decreases as it moves the structure that grasps food (the radula/odontophore) in an anterior direction. In contrast, as the radula/odontophore is moved forward, the jaw musculature's mechanical advantage shifts so that it may act to assist forward movement of the radula/odontophore instead of pushing it posteriorly. To test whether the jaw musculature's context-dependent function can compensate for the falling mechanical advantage of the protractor muscle, we created a kinetic model of Aplysia's feeding apparatus. During biting, the model predicts that the reduction of the force in the protractor muscle I2 will prevent it from overcoming passive forces that resist the large anterior radula/odontophore displacements observed during biting. To produce protractions of the magnitude observed during biting behaviors, the nervous system could increase I2's contractile strength by neuromodulating I2, or it could recruit the I1/I3 jaw muscle complex. Driving the kinetic model with in vivo EMG and ENG predicts that, during biting, early activation of the context-dependent jaw muscle I1/I3 may assist in moving the radula/odontophore anteriorly during the final phase of protraction. In contrast, during swallowing, later activation of I1/I3 causes it to act purely as a retractor. Shifting the timing of onset of I1/I3 activation allows the nervous system to use a mechanical equilibrium point that allows I1/I3 to act as a protractor rather than an equilibrium point that allows I1/I3 to act as a retractor. This use of equilibrium points may be similar to that proposed for vertebrate control of movement.     

Molecular mechanisms underlying a unique intermediate phase of memory in aplysia

Short- and long-term synaptic facilitation induced by serotonin at Aplysia sensory-motor (SN-MN) synapses has been widely used as a cellular model of short- and long-term memory for sensitization. In recent years, a distinct intermediate phase of synaptic facilitation (ITF) has been described at SN-MN synapses. Here, we identify a novel intermediate phase of behavioral memory (ITM) for sensitization in Aplysia and demonstrate that it shares the temporal and mechanistic features of ITF in the intact CNS: (1) it declines completely prior to the onset of LTM, (2) its induction requires protein but not RNA synthesis, and (3) its expression requires the persistent activation of protein kinase A. Thus, in Aplysia, the same temporal and molecular characteristics that distinguish ITF from other phases of synaptic plasticity distinguish ITM from other phases of behavioral memory.     

Sedimentary microbial community dynamics in a regulated stream: East Fork of the Little Miami River,Ohio

A field study was conducted in the Lower East Fork of the Little Miami River, a regulated stream in Clermont county, Ohio, to determine how changes in streamflow, water temperature and photo-period affect sediment microbial community structure. Surface sediment cores were collected from sampling stations spanning 60 river kilometers three to four times per year between October 1996 and October 1999. During the final year of the field study, water temperature, water depth, conductivity, total suspended solids, dissolved organic carbon, instantaneous streamflow velocity, sediment grain size and sediment organic matter were determined. Total microbial biomass was measured using the phospholipid phosphate technique (PLP) and ranged between 2 and 134 nmol PLP * g(-1) dry weight sediment with a mean of 25 nmol PLP * g(-1). Microbial community structure was determined using the phospholipid fatty acid analysis and indicated seasonal shifts in sedimentary microbial community composition. January to June sedimentary microbial biomass was predominately prokaryotic (60% +/- 2), whereas microeukaryotes dominated samples collected during the late summer (55% +/- 2.4) and fall (60% +/- 2). These changes were correlated with stream discharge and water temperature. Microbial community structure varied spatially about a reservoir with prokaryotic biomass dominant at upstream stations and eukaryotic biomass dominant at downstream stations. These findings reveal that sedimentary microbial communities in streams are dynamic responding to the seasonal variation of environmental factors.     

Multigene DNA prime-boost vaccines for SHIV89.6P

We assessed four prime-boost vaccine regimens with a Gene Gun component for SHIV89.6P in Macaca nemestrina. A dosing experiment using beta-galactosidase plasmid showed that 30 or 45 shots per dose elicited higher titer antibody than smaller doses. For SHIV89.6P, we administered a six-plasmid vaccine capable of producing non-infectious virions in vivo in combination with either vaccinia recombinants or inactivated virus. DNA prime/vaccinia boost, or the reverse, elicited strong immune responses. The SHIV89.6P challenge virus was grown in M. nemestrina peripheral blood mononuclear cells and titered in vivo intrarectally. As has been observed for SHIV89.6P in M. mulatta, the infected M. nemestrina experienced rapid and severe loss of circulating CD4+ T cells. Vaccinated macaques were challenged three weeks after the last boost. DNA prime/vaccina boost or vaccina prime/DNA boost protected 11/12 animals from acute CD4+ T cell depletion and disease, while other regimens were not effective.     

Space–time home-range estimates and resource selection for the Critically Endangered Philippine Eagle on Mindanao

Quantifying home-range size and habitat resource selection are important elements in wildlife ecology and are useful for informing conservation action. Many home-range estimators and resource selection functions are currently in use. However, both methods are fraught with analytical issues inherent within autocorrelated movement data from irregular sampling and interpretation of resource selection model parameters to inform conservation management. Here, we apply satellite remote sensing technologies to provide updated estimates of home-range size and first estimates of fine-scale resource selection for six adult Philippine Eagles Pithecophaga jefferyi using a space–time autocorrelated kernel density estimate (AKDE) home-range estimator and non-parametric resource selection functions. All six adult Eagles showed distinct site fidelity, with continuous range residency between 2 and 18 km, 1 month after tagging. The space–time AKDE home-range estimators had a median 95% home-range size = 68 km² (95% confidence interval (95% CI) 62–74 km², range: 39–161 km²), with the median 50% core range size = 13 km² (95% CI 11–14 km², range 9–33 km²). From the resource selection functions, all adult Philippine Eagles used habitat high in photosynthetic leaf and canopy structure but avoided areas of old-growth biomass and denser areas of vegetation. This is possibly due to foraging forays into secondary forest and fragmented agricultural areas away from nesting sites. For the first time, we determine two important fine-scale spatial processes for this Critically Endangered raptor that can help in directing conservation management. Rather than employing traditional home-range estimators and resource selection functions, we recommend that analysts consider space–time approaches and non-parametric resource selection functions to animal movement data to explore fully space–time and resource selection.     

MHC variation reflects the bottleneck histories of New Zealand passerines

Most empirical evidence suggests that balancing selection does not counter the effects of genetic drift in shaping postbottleneck major histocompatibility complex (MHC) genetic diversity when population declines are severe or prolonged. However, few studies have been able to include data from historical specimens, or to compare populations/species with different bottleneck histories. In this study, we examined MHC class II B and microsatellite diversity in four New Zealand passerine (songbird) species that experienced moderate to very severe declines. We compared diversity from historical samples (collected c. 1884–1938) to present‐day populations. Using a Bayesian framework, we found that the change in genetic diversity from historical to contemporary samples was affected by three main factors: (i) whether the data were based on MHC or microsatellite markers, (ii) species (as a surrogate for bottleneck severity) and (iii) whether the comparison between historical and contemporary samples was made using historical samples originating from the mainland, or using historical samples originating from islands. The greatest losses in genetic diversity occurred for the most severely bottlenecked species, particularly between historical mainland and contemporary samples. Additionally, where loss of diversity occurred, the change was greater for MHC genes compared to microsatellite loci.     

EPR spectra and molecular dynamics agree that the nucleotide pocket of myosin V is closed and that it opens on binding actin

We have used EPR spectroscopy and computational modeling of nucleotide-analog spin probes to investigate conformational changes at the nucleotide site of myosin V. We find that, in the absence of actin, the mobility of a spin-labeled diphosphate analog [spin-labeled ADP (SLADP)] bound at the active site is strongly hindered, suggesting a closed nucleotide pocket. The mobility of the analog increases when the MV·SLADP complex (MV = myosin V) binds to actin, implying an opening of the active site in the A·MV·SLADP complex (A = actin). The probe mobilities are similar to those seen with myosin II, despite the fact that myosin V has dramatically altered kinetics. Molecular dynamics (MD) simulation was used to understand the EPR spectra in terms of the X-ray database. The X-ray structure of MV·ADP·BeFx shows a closed nucleotide site and has been proposed to be the detached state. The MV·ADP structure shows an open nucleotide site and has been proposed to be the A·MV·ADP state at the end of the working powerstroke. MD simulation of SLADP docked in the closed conformation gave a probe mobility comparable to that seen in the EPR spectrum of the MV·SLADP complex. The simulation of the open conformation gave a probe mobility that was 35-40° greater than that observed experimentally for the A·MV·SLADP state. Thus, EPR, X-ray diffraction, and computational analysis support the closed conformation as a myosin V state that is detached from actin. The MD results indicate that the MV·ADP crystal structure, which may correspond to the strained actin-bound post-powerstroke conformation resulting from head-head interaction in the dimeric processive motor, is superopened.     

Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda)

Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age-related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH-methylation showed little association with age, both CpG and CHG-methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.