Limb regeneration revisited

The investigation of vertebrate limb regeneration, a favorite topic of early developmental biologists, is enjoying a renaissance thanks to recently developed molecular and genetic tools, as indicated in recent papers in BMC Biology and BMC Developmental Biology. Classical experiments provide a rich context for interpreting modern functional studies

Regeneration review reprise

There have been notable advances in the scientific understanding of regeneration within the past year alone, including two recently published in BMC Biology. Increasingly, progress in the regeneration field is being inspired by comparisons with stem cell biology and enabled by newly developed techniques that allow simultaneous examination of thousands of genes and proteins

Factors Dictating Carbene Formation at (PNP)Ir

The mechanistic subtleties involved with the interaction of an amido/bis(phosphine)-supported (PNP)Ir fragment with a series of linear and cyclic ethers have been investigated using density functional theory. Our analysis has revealed the factors dictating reaction direction toward either an iridium-supported carbene or a vinyl ether adduct. The (PNP)Ir structure will allow carbene formation only from accessible carbons α to the ethereal oxygen, such that d electron back-donation from the metal to the carbene ligand is possible. Should these conditions be unavailable, the main competing pathway to form vinyl ether can occur, but only if the (PNP)Ir framework does not sterically interfere with the reacting ether. In situations where steric hindrance prevents unimpeded access to both pathways, the reaction may progress to the initial C−H activation but no further. Our mechanistic analysis is density functional independent and whenever possible confirmed experimentally by trapping intermediate species experimentally. We have also highlighted an interesting systematic error present in the DFT analysis of reactions where steric environment alters considerably within a reaction

Gating NO Release from Nitric Oxide Synthase

We have investigated the kinetics of NO escape from Geobacillus stearothermophilus nitric oxide synthase (gsNOS). Previous work indicated that NO release was gated at position 223 in mammalian enzymes; our kinetics experiments include mutants at that position along with measurements on the wild type enzyme. Employing stopped-flow UV–vis methods, reactions were triggered by mixing a reduced enzyme/N-hydroxy-l-arginine complex with an aerated buffer solution. NO release kinetics were obtained for wt NOS and three mutants (H134S, I223V, H134S/I223V). We have confirmed that wt gsNOS has the lowest NO release rate of known NOS enzymes, whether bacterial or mammalian. We also have found that steric clashes at positions 223 and 134 hinder NO escape, as judged by enhanced rates in the single mutants. The empirical rate of NO release from the gsNOS double mutant (H134/I223V) is nearly as rapid as that of the fastest mammalian enzymes, demonstrating that both positions 223 and 134 function as gates for escape of the product diatomic molecule

Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound

Coordination Variability after Hip Replacement Surgery: A Case Report

Patients with unilateral hip replacement surgery have an increased risk for additional joint replacement surgeries in the contralateral limb. Reduced coordination variability (Cvar) is associated with orthopedic disorders. Differences in joint Cvar after hip replacement surgery may provide information regarding the progression to a healthier state. The purpose of this study was to examine differences in surgical and contralateral limb knee and hip Cvar before and after surgery. A male participant completed gait analyses prior to total hip arthroplasty, three weeks following surgery (post-op) and ten months after surgery. He walked at a preferred speed while three-dimensional kinematic and kinetic data were recorded. A modified vector coding technique was used to determine the bilateral Cvar throughout stance for thigh-leg and pelvis-thigh flexion/extension and internal/external rotation coordination. Cvar was averaged for the stance phase of gait at each visit. Effect Size (ES) was calculated to determine clinically significant differences in variability both between the surgical and contralateral limbs and for each visit (Tables 1 and 2). In the surgical limb, variability was similar at all visits for pelvis-thigh and thigh-shank flexion/extension and internal/external rotation (ES\u3c0.5). Differences in (Cvar) between the surgical and contralateral limbs diminished with time. While Cvar in the surgical limb did not change, Cvar in the contralateral limb decreased over time. This may indicate a decline in health and an increased risk for orthopedic disorders in the contralateral limb after hip replacement surgery

Pearling: stroke segmentation with crusted pearl strings

We introduce a novel segmentation technique, called Pearling, for the semi-automatic extraction of idealized models of networks of strokes (variable width curves) in images. These networks may for example represent roads in an aerial photograph, vessels in a medical scan, or strokes in a drawing. The operator seeds the process by selecting representative areas of good (stroke interior) and bad colors. Then, the operator may either provide a rough trace through a particular path in the stroke graph or simply pick a starting point (seed) on a stroke and a direction of growth. Pearling computes in realtime the centerlines of the strokes, the bifurcations, and the thickness function along each stroke, hence producing a purified medial axis transform of a desired portion of the stroke graph. No prior segmentation or thresholding is required. Simple gestures may be used to trim or extend the selection or to add branches. The realtime performance and reliability of Pearling results from a novel disk-sampling approach, which traces the strokes by optimizing the positions and radii of a discrete series of disks (pearls) along the stroke. A continuous model is defined through subdivision. By design, the idealized pearl string model is slightly wider than necessary to ensure that it contains the stroke boundary. A narrower core model that fits inside the stroke is computed simultaneously. The difference between the pearl string and its core contains the boundary of the stroke and may be used to capture, compress, visualize, or analyze the raw image data along the stroke boundary

Using Airborne Multispectral Imagery to Evaluate Geomorphic Work Across Floodplains of Gravel-Bed Rivers

Fluvial processes of cut and fill alluviation and channel abandonment or avulsion are essential for maintaining the ecological health of floodplain ecosystems characteristic of gravel-bed rivers. These dynamic processes shape the floodplain landscape, resulting in a shifting mosaic of habitats, both above and below ground. We present a new and innovative methodology to quantitatively assess the geomorphic work potential necessary to maintain a shifting habitat mosaic for gravel-bed river floodplains. This approach can be used to delineate critical habitats for preservation through land acquisition and conservation easements, often critical elements of river restoration plans worldwide. Spatially explicit modeling of water depth, flow velocity, shear stress, and stream power derived from surface hydraulic measurements was combined with airborne multispectral remote sensing for detailed modeling of floodplain water surfaces over tens to hundreds of square kilometers. The model results were then combined within a GIS framework to determine potential nodes of channel avulsion that delineate spatially explicit zones across the floodplain where the potential for geomorphic work is the greatest. Results of this study demonstrate the utility of integrating existing multispectral remote sensing data coupled with time-lagged ground-based measures of flow hydraulics to model fluvial processes at relatively fine spatial resolutions but over broad regional extents

Kinetics of CO recombination to the heme in Geobacillus stearothermophilus nitric oxide synthase

We report the kinetics of CO rebinding to the heme in His134Ser, Ile223Val and His134Ser/Ile223Ser mutants of Geobacillus stearothermophilus nitric oxide synthase (gsNOS). The amplitudes of the two observed kinetics phases, which are insensitive to CO concentration, depend on enzyme concentration. We suggest that two forms of gsNOS are in equilibrium under the conditions employed (6.1–27 μM gsNOS with 20 or 100% CO atmosphere). The kinetics of CO rebinding to the heme do not depend on the identity of the NO-gate residues at positions 134 and 223

Climate, Hydrologic Disturbance, and Succession: Drivers of Floodplain Pattern

Floodplains are among the world\u27s most threatened ecosystems due to the pervasiveness of dams, levee systems, and other modi. cations to rivers. Few unaltered floodplains remain where we may examine their dynamics over decadal time scales. Our study provides a detailed examination of landscape change over a 60-year period ( 1945 - 2004) on the Nyack floodplain of the Middle Fork of the Flathead River, a free-flowing, gravel-bed river in northwest Montana, USA. We used historical aerial photographs and airborne and satellite imagery to delineate habitats ( i.e., mature forest, regenerative forest, water, cobble) within the. oodplain. We related changes in the distribution and size of these habitats to hydrologic disturbance and regional climate. Results show a relationship between changes in. oodplain habitats and annual flood magnitude, as well as between hydrology and the cooling and warming phases of the Pacific Decadal Oscillation (PDO). Large magnitude floods and greater frequency of moderate floods were associated with the cooling phases of the PDO, resulting in a floodplain environment dominated by extensive restructuring and regeneration of floodplain habitats. Conversely, warming phases of the PDO corresponded with decreases in magnitude, duration, and frequency of critical flows, creating a floodplain environment dominated by late successional vegetation and low levels of physical restructuring. Over the 60-year time series, habitat change was widespread throughout the floodplain, though the relative abundances of the habitats did not change greatly. We conclude that the long- and short-term interactions of climate, floods, and plant succession produce a shifting habitat mosaic that is a fundamental attribute of natural. oodplain ecosystems