Bioinformatic and Proteomic Investigation of Chloroplast Transit Peptide Motifs and Genesis

The eukaryotic mitochondrion was formed by the endosymbiotic association of an - proteobacterium and a primordial phagocytic eukaryote. A second, and later, endosymbiosis between the eukaryote and a cyanobacterium gave rise to the chloroplast of plants. Following each of these events most of the organellar DNA was exported to the nucleus. A system evolved wherein proteins produced on cytosolic ribosomes are targeted to organelle protein translocators by N-terminal targeting sequences. Protein sorting between the chloroplast and the mitochondrion in the plant cell by the general import pathways shows remarkable fidelity despite a lack of sequence conservation among transit peptides and pre-sequences and despite very little sequence difference between these two targeting peptides. There is evidence for a hydrophobic recognition motif in mitochondrial presequences, and a similar motif has been proposed for the chloroplast transit peptide. We have developed novel motif-finding methods and applied them to our own chloroplast proteome data and to literature mitochondrial data. We fail to find a hydrophobic motif that discriminates the chloroplast and the mitochondrion. Another little understood phenomenon of organelle protein trafficking is how the targeting sequence is acquired after transfer of organelle DNA to the nucleus. It has been hypothesized that the transit peptide is acquired by exon shuffling. We find no correlation of transit peptide lengths with exon boundaries. Furthermore, using highly expressed cyanobacterial proteins conserved in plants, we find that the transit peptide appears as likely to be attached within the primordial sequence as without, indicating a more stochastic process for the origin of the transit peptide

Perkin Reaction: Rapid and Efficient Process Optimization Through a Microwave/Design of Experiments Couple

Microwave chemistry and a Design of Experiments (DOE) protocol were employed together in order to rapidly and efficiently optimize a modified Perkin reaction. Microwave heating significantly reduced the reaction time, and the DOE provided a statistically significant understanding of underlying process relationships in a minimum number of experimental runs. In all, the reaction time was reduced from1hour to 2 minutes, factors important to yield were identified, an interesting cross-term interaction was discovered, and it was demonstrated that the more economical sodium acetate trihydrate catalyst was a viable alternative to the more costly anhydrous sodium acetate

Metabolic Routing of Dietary Nutrients in Birds: Effects of Diet Quality and Macronutrient Composition Revealed Using Stable Isotopes

During fall migration many songbirds switch from consuming primarily insects to consuming mostly fruit. Fruits with more carbohydrates and less protein may be sufficient to rebuild expended fat stores, but such fruits may be inadequate to replace catabolized protein. We manipulated the concentrations and isotopic signatures of macronutrients in diets fed to birds to study the effects of diet quality on metabolic routing of dietary nutrients. We estimated that approximately 45% and 75%, respectively, of the carbon in proteinaceous tissue of birds switched to high‐ or low‐protein diets came from nonprotein dietary sources. In contrast, we estimated that approximately 100% and 20%–80%, respectively, of the nitrogen in proteinaceous tissues of birds switched to high‐ or low‐protein diets was attributable to dietary protein. Thus, the routing and assimilation of dietary carbon and nitrogen differed depending on diet composition. As a result, δ15N of tissues collected from wild animals that consume high‐quality diets may reliably indicate the dietary protein source, whereas δ13C of these same tissues is likely the product of metabolic routing of carbon from several macronutrients. These results have implications for how isotopic discrimination is best estimated and how we can study macronutrient routing in wild animals

Costs of Locomotion in Polar Bears: When do the Costs Outweigh the Benefits of Chasing Down Terrestrial Prey?

Trade-offs between locomotory costs and foraging gains are key elements in determining constraints on predator–prey interactions. One intriguing example involves polar bears pursuing snow geese on land. As climate change forces polar bears to spend more time ashore, they may need to expend more energy to obtain land-based food. Given that polar bears are inefficient at terrestrial locomotion, any extra energy expended to pursue prey could negatively impact survival. However, polar bears have been regularly observed engaging in long pursuits of geese and other land animals, and the energetic worth of such behaviour has been repeatedly questioned. We use data-driven energetic models to examine how energy expenditures vary across polar bear mass and speed. For the first time, we show that polar bears in the 125–235 kg size range can profitably pursue geese, especially at slower speeds. We caution, however, that heat build-up may be the ultimate limiting factor in terrestrial chases, especially for larger bears, and this limit would be reached more quickly with warmer environmental temperatures

Spatially explicit model of wintering common loons: conservation implications

Common loons Gavia immer are a conservation concern in New England due to a variety of anthropogenic factors, yet little is known about biotic and abiotic environmental factors determining their wintering distribution and abundance in nearshore and offshore waters. The primary objective of this study was to develop a spatially explicit abundance model of wintering common loons in the maritime waters of southern New England (USA) that could inform decisions about offshore development. Aerial line-transect surveys were conducted throughout a 3800 km2 study area off the coast of Rhode Island during the winters of 2010–2011 and 2011–2012. A density surface model (DSM) approach was used to account for imperfect detection and incorporate spatially explicit environmental covariates. Common loon densities were greatest in watersdeep, with high chl a surface concentrations (\u3e2 mg m−3). The DSM predicted 5047 (95% CI = 3993−6379) common loons in the study area during winter, which suggests this region provides key habitat for this species in eastern North America. This study highlights important areas for common loons in the region, suggests key biotic (primary productivity as measured by long-term chl a surface concentrations) and abiotic covariates (water depth) driving the spatial distribution and abundance of common loons in southern New England, and identifies sites that should be considered for protection from offshore development, including offshore wind facilities

Fruit Quality And Consumption By Songbirds During Autumn Migration

Seasonal fruits are an important food resource for small songbirds during autumn migration in southern New England. Therefore, conservation and management of important stopover sites used by migrating birds requires knowledge about nutritional requirements of songbirds and nutritional composition of commonly consumed fruits. We measured nutrient composition and energy density of nine common fruits on Block Island, Rhode Island, and conducted a field experiment to estimate consumption rates of three of these fruits by birds during autumn migration. Most common fruits on Block Island contained primarily carbohydrates (41.3–91.2% dry weight), and little protein (2.6–8.6%) and fat (0.9–3.7%), although three contained more fat: Myrica pennsylvanica (50.3%), Viburnum dentatum (41.3%), and Parthenocissus quinquefolia (23.6%). Bird consumption of high-fat, high-energy V. dentatum fruit and high-carbohydrate, low-energy Phytolacca americana fruit was greater than consumption of Aronia melanocarpa, a high-carbohydrate, low-energy fruit. We estimated that migratory birds on Block Island must eat up to four times their body mass in fruit wet weight each day to satisfy their energy requirements when eating low-energy fruits such as P. americana, and they cannot satisfy their protein requirements when eating only certain high-energy fruits such as V. dentatum. Our results suggest that many migratory birds must eat both fruits and insects to meet their dietary needs. Thus, shrubland habitat at important migratory stopover sites such as Block Island should be managed so that it contains a variety of preferred fruit-bearing shrubs and an adequate abundance of insects

Migration- and exercise-induced changes to flight muscle size in migratory birds and association with \u3cem\u3eIGF1\u3c/em\u3e and \u3cem\u3emyostatin\u3c/em\u3e mRNA expression

Seasonal adjustments to muscle size in migratory birds may result from preparatory physiological changes or responses to changed workloads. The mechanisms controlling these changes in size are poorly understood. We investigated some potential mediators of flight muscle size (myostatin and insulin-like growth factor, IGF1) in pectoralis muscles of wild wintering or migrating white-throated sparrows (Zonotrichia albicollis), captive white-throated sparrows that were photoperiod manipulated to be in a `wintering\u27 or `migratory\u27 (Zugunruhe) state, and captive European starlings (Sturnus vulgaris) that were either exercised for 2 weeks in a wind tunnel or untrained. Flight muscle size increased in photo-stimulated `migrants\u27 and in exercised starlings. Acute exercise but not long-term training caused increased expression of IGF1, but neither caused a change in expression of myostatin or its metalloprotease activator TLL1. Photo-stimulated `migrant\u27 sparrows demonstrated increased expression of both myostatin and IGF1, but wild sparrows exhibited no significant seasonal changes in expression of either myostatin or IGF1. Additionally, in both study species we describe several splice variants of myostatin that are shared with distantly related bird species. We demonstrate that their expression patterns are not different from those of the typical myostatin, suggesting that they have no functional importance and may be mistakes of the splicing machinery. We conclude that IGF1 is likely to be an important mediator of muscle phenotypic flexibility during acute exercise and during endogenous, seasonal preparation for migration. The role of myostatin is less clear, but its paradoxical increase in photo-stimulated `migrants\u27 may indicate a role in seasonal adjustments of protein turnover

Sheared-flow induced confinement transition in a linear magnetized plasma

A magnetized plasma cylinder (12 cm in diameter) is induced by an annular shape obstacle at the Large Plasma Device [W. Gekelman, H. Pfister, Z. Lucky, J. Bamber, D. Leneman, and J. Maggs, Rev. Sci. Instrum. 62, 2875 (1991)]. Sheared azimuthal flow is driven at the edge of the plasma cylinder through edge biasing. Strong fluctuations of density and potential (δn/n~eδφ/kTe~0.5) are observed at the plasma edge, accompanied by a large density gradient (Ln=∣∣∇lnn∣∣−1~2cm) and shearing rate (γ~300kHz). Edge turbulence and cross-field transport are modified by changing the bias voltage (Vbias) on the obstacle and the axial magnetic field (Bz) strength. In cases with low Vbias and large Bz, improved plasma confinement is observed, along with steeper edge density gradients. The radially sheared flow induced by E×B drift dramatically changes the cross-phase between density and potential fluctuations, which causes the wave-induced particle flux to reverse its direction across the shear layer. In cases with higher bias voltage or smaller Bz, large radial transport and rapid depletion of the central plasma density are observed. Two-dimensional cross-correlation measurement shows that a mode with azimuthal mode number m=1 and large radial correlation length dominates the outward transport in these cases. Linear analysis based on a two-fluid Braginskii model suggests that the fluctuations are driven by both density gradient (drift wave like) and flow shear (Kelvin-Helmholtz like) at the plasma edge

Radiologic imaging in cystic fibrosis: cumulative effective dose and changing trends over 2 decades

Objective: With the increasing life expectancy for patients with cystic fibrosis (CF), and a known predisposition to certain cancers, cumulative radiation exposure from radiologic imaging is of increasing significance. This study explores the estimated cumulative effective radiation dose over a 17-year period from radiologic procedures and changing trends of imaging modalities over this period. Methods: Estimated cumulative effective dose (CED) from all thoracic and extrathoracic imaging modalities and interventional radiology procedures for both adult and pediatric patients with CF, exclusively attending a nationally designated CF center between 1992-2009 for > 1 year, was determined. The study period was divided into three equal tertiles, and estimated CED attributable to all radiologic procedures was estimated for each tertile. Results: Two hundred thirty patients met inclusion criteria (2,240 person-years of follow-up; 5,596 radiologic procedures). CED was > 75 mSv for one patient (0.43%), 36 patients (15.6%) had a CED between 20 and 75 mSv, 56 patients (24.3%) had a CED between 5 and 20 mSv, and in 138 patients (60%) the CED was estimated to be between 0 and 5 mSv over the study period. The mean annual CED per patient increased consecutively from 0.39 mSv/y to 0.47 mSv/y to 1.67 mSv/y over the tertiles one to three of the study period, respectively (P < .001). Thoracic imaging accounted for 46.9% of the total CED and abdominopelvic imaging accounted for 42.9% of the CED, respectively. There was an associated 5.9-fold increase in the use of all CT scanning per patient (P < .001). Conclusions: This study highlights the increasing exposure to ionizing radiation to patients with CF as a result of diagnostic imaging, primarily attributable to CT scanning. Increased awareness of CED and strategies to reduce this exposure are needed