The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae)

RAPDs were generated from plants of six populations of Isotoma petraea F. Muell. The species occurs on rock outcrops in southern and western Australia, with populations exhibiting different breeding systems, including complete autogamy, varying levels of outbreeding and complex hybridity. Non-metric multidimensional scaling (nMDS) analysis of the random amplified polymorphic DNA (RAPD) data set clearly resolved all populations. The Pigeon Rock population, which is home to both complex hybrid and structural homozygote plants, was divided into those two groups by the nMDS analysis. There was little diversity in highly autogamous populations, but levels were higher in the outbred Yackeyackine population. All complex hybrid populations and plants possessed numerous genetic system-specific RAPDs, some of which were shown to be held in fixed heterozygosity. Estimating G _ST using RAPDs has been problematical due to their dominance, and analytical methods usually rely on knowledge of the selfing rate or assume Hardy–Weinberg equilibrium. This assumption does not hold when populations exhibit fixed heterozygosity, and an alternative method, Shannon's Index, was used to partition genetic diversity. The distribution of genetic diversity fit expectations for an inbreeding species, with most of the variation (87.5%) occurring between populations. This compares to an average RAPD-based G _ST of 59.6% for inbreeding species generally and 15.5% for outbreeding species.     

Helix periodicity, topology, and dynamics of membrane-associated alpha-synuclein

The protein alpha-Synuclein (aS) is a synaptic vesicle-associated regulator of synaptic strength and dopamine homeostasis with a pathological role in Parkinson's disease. The normal function of aS depends on a membrane-associated conformation that is adopted upon binding to negatively charged lipid surfaces. Previously we found that the membrane-binding domain of aS is helical and suggested that it may exhibit an unusual structural periodicity. Here we present a study of the periodicity, topology, and dynamics of detergent micelle-bound aS using paramagnetic spin labels embedded in the micelle or attached to the protein. We show that the helical region of aS completes three full turns every 11 residues, demonstrating the proposed 11/3 periodicity. We also find that the membrane-binding domain is partially buried in the micelle surface and bends toward the hydrophobic interior, but does not traverse the micelle. Deeper submersion of certain regions within the micelle, including the unique lysine-free sixth 11-residue repeat, is observed and may be functionally important. There are no long-range tertiary contacts within this domain, indicating a highly extended configuration. The backbone dynamics of the micelle-bound region are relatively uniform with a slight decrease in flexibility observed toward the C-terminal end. These results clarify the topological features of aS bound to membrane-mimicking detergent micelles, with implications for aS function and pathology.     

Late immature mortality is the major influence on reproductive success of African black beetle, Heteronychus arator (Fabricius) (Coleoptera: Scarabaeidae), in a Mediterranean-climate region of Australia

In field and laboratory studies, mortality of African black beetle, Heteronychus arator, in the winter-rainfall, Mediterranean-type climate region of south-western Australia was higher in the late immature stages during summer than in the early immature stages that occur during spring, a contrast to summer-rainfall climatic regions. Greatest mortality occurred around the pupal stage in contrasting soil types, despite drying differences in summer and supplementary watering in some plots. Sampling of natural populations confirmed experimental results that mortality in late immature stages is the major factor limiting H. arator populations under a Mediterranean-type climate. Inter-generation increase in H. arator abundance was uncommon, explaining the consistent abundance typically observed between years in south-western Australia. Random dispersal of newly emerged adults in autumn was inferred to restore uniformity in adult abundance between areas of varying favourability for immature survival.     

Peroxisomal ATP-Binding Cassette Transporter COMATOSE and the Multifunctional Protein ABNORMAL INFLORESCENCE MERISTEM Are Required for the Production of Benzoylated Metabolites in Arabidopsis Seeds

Secondary metabolites derived from benzoic acid (BA) are of central importance in the interactions of plants with pests, pathogens, and symbionts and are potentially important in plant development. Peroxisomal β-oxidation has recently been shown to contribute to BA biosynthesis in plants, but not all of the enzymes involved have been defined. In this report, we demonstrate that the peroxisomal ATP-binding cassette transporter COMATOSE is required for the accumulation of benzoylated secondary metabolites in Arabidopsis (Arabidopsis thaliana) seeds, including benzoylated glucosinolates and substituted hydroxybenzoylcholines. The ABNORMAL INFLORESCENCE MERISTEM protein, one of two multifunctional proteins encoded by Arabidopsis, is essential for the accumulation of these compounds, and MULTIFUNCTIONAL PROTEIN2 contributes to the synthesis of substituted hydroxybenzoylcholines. Of the two major 3-ketoacyl coenzyme A thiolases, KAT2 plays the primary role in BA synthesis. Thus, BA biosynthesis in Arabidopsis employs the same core set of β-oxidation enzymes as in the synthesis of indole-3-acetic acid from indole-3-butyric acid.Many important secondary metabolites in plants are derived from, or incorporate, benzoic acid (BA). These include compounds found in root exudates, inflorescences, stems, and flower volatiles (D’Auria and Gershenzon, 2005). BA is also potentially a precursor for the plant hormone salicylic acid (SA; Wildermuth et al., 2001). In Arabidopsis (Arabidopsis thaliana), benzoylated glucosinolates (BGs) accumulate in seeds, presumably as a deterrent against animal feeding. Thus, BA metabolites are believed to play key roles in the interactions of plants with microbial and animal pests as well as in beneficial relationships such as pollination systems (Boatright et al., 2004). Understanding the pathways and control of BA synthesis in plants, therefore, is very important.Three different pathways for the synthesis of BA have been proposed for plants (Boatright et al., 2004; Wildermuth, 2006). These begin with the first committed step of the phenylpropanoid pathway, the deamination of Phe by Phe ammonia lyase to produce trans-cinnamic acid (CA). CA can then be oxidized by CoA-independent reactions in the cytosol, or it may be activated with CoA and proceed through one cycle of peroxisomal β-oxidation. Alternatively, BA synthesis may proceed via a third, CoA-dependent but β-oxidation-independent, pathway that combines elements of the first two pathways (Wildermuth, 2006). Recent studies in Petunia hybrida have highlighted the importance of the peroxisomal β-oxidation pathway in the production of BA for incorporation into floral volatile benzenoids. Enzymes identified in this pathway to date are a cinnamate:CoA ligase (PhCNL/PhAAE [for acyl-activating enzyme]) that activates CA (Colquhoun et al., 2012; Klempien et al., 2012), a multifunctional protein (PhMFP) that hydrates and oxidizes the trans-cinnamoyl-CoA (Qualley et al., 2012), and a 3-ketoacyl CoA thiolase (PhKAT1) that cleaves the resultant β-keto thioester (Van Moerkercke et al., 2009).Seeds of Arabidopsis accumulate appreciable amounts of BGs (Reichelt et al., 2002; Kliebenstein et al., 2007). Thus, while free BA is not detected in Arabidopsis seeds (Ibdah and Pichersky, 2009), the accumulation of BGs and other BA-containing secondary metabolites in Arabidopsis seeds provides a powerful experimental system with which to determine the pathway and potential control of BA synthesis in plants. For example, a peroxisomal acyl-CoA ligase (BZO1, for benzoyloxy glucosinolate) has been identified in Arabidopsis that is closely related to PhCNL1 and is required for BG production in seeds (Kliebenstein et al., 2007). BZO1 has recently been shown to be an AAE with cinnamate:CoA ligase activity (Lee et al., 2012).To further investigate the requirement for peroxisomal β-oxidation in BA synthesis, and to identify key enzymes involved in Arabidopsis, we analyzed BA-containing secondary metabolites (BGs and substituted hydroxybenzoylated choline esters) of seeds from a suite of β-oxidation mutants covering the key steps of β-oxidation, including substrate import, activation, oxidation, and thiolysis. This work identifies specific isozymes in Arabidopsis that mediate these steps, defines a new role for ABNORMAL INFLORESCENCE MERISTEM (AIM1), and determines a route for the entry of CA into peroxisomes.     

Changes in the immune response and metabolic fingerprint of the mussel, Mytilus edulis (Linnaeus) in response to lowered salinity and physical stress

Mussels, such as Mytilus edulis, are common keystone species on open coasts and in estuaries and are frequently used in environmental monitoring programmes. Mussels experience a wide range of environmental conditions at these locations, including rapid changes in salinity and physical disturbance (both natural and from aquaculture practices).This paper addressed the hypothesis that reduced salinity will lower mussel blood immune function and influence mussel blood metabolic responses, and that this will in turn increase the susceptibility of mussels to other stresses such as physical disturbance. To test these hypotheses, experiments were conducted in controlled laboratory tank conditions and mussel blood was analysed using a combination of metabolic fingerprinting with FT-IR and immunological assay techniques.Reducing seawater salinity to half that of normal caused a significant reduction in several measures of immune function, including the concentration of haemocytes, percentage of eosinophilic haemocytes and phagocytosis. Mechanical shaking of mussels for 10 min caused a reduction in the level of respiratory burst activity. However, there was no evidence of additive or interactive effects of lowered salinity with shaking on the immune response. Analysis of mussel blood metabolic fingerprints revealed differences in response to half salinity (vs. full salinity) but there were no detectable effects of shaking. Increasing frequency and magnitude of flood events at coastal sites due to climate change could lead to longer, and more frequent, periods of reduced salinity. The potential impact on the immune function of this keystone species within or near estuaries could have knock-on effects on the wider ecosystem including altered nutrient cycling, changes in biodiversity and aquaculture production.     

On the determination of optimal thermal enclosures

The paper presents a method for a quantitative study of the influence of the diurnal air temperature cycle, the incidence of solar energy on exposed surfaces and transmission through glass areas, the longwave radiation exchange with the surroundings, and the energy exchange resulting from natural ventilation. The thermal response of a room in a typical concrete office building with glass areas facing south in the northern hemisphere is treated in detail by means of a digital computer program sufficiently general to handle a large variety of problems. For the first time the influence of programmed natural ventilation can be determined in advance. The design of optimal thermal enclosures can be achieved through the technique of exhaustive analysis using methods described in this paper.

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Zusammenfassung Es wird über eine Methode für die quantitative Untersuchung der Einflüsse des tÄglichen Gangs der Lufttemperatur, der Sonnenenergieaufnahme an den bestrahlten OberflÄchen und durch die Glasfenster, des langwelligen Strahlungsaustausches mit der Umgebung und des Energieaustausches durch die natürliche Ventilation berichtet. Das thermische Verhalten eines Raumes in einem typischen Beton-Bürohaus mit südlich orientierten GlasfensterflÄchen auf der nördlichen Halbkugel ist ausführlich durch das digital Rechenmaschinenprogramm untersucht worden, das genügt, um eine ausführliche Anzahl verschiedener Probleme zu behandeln. Zum erstenmal kann der Einfluss der programmierten natürlichen Ventilation vorausbestimmt werden. Der Entwurf eines thermisch optimalen eingeschlossenen Raumes kann durch die hier beschriebenen erschöpfenden Analysen gegeben werden.

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Resume Ce mémoire présente une méthode qui permet d'étudier quantitativement l'influence des facteurs suivants: Le cycle diurne de la température de l'air, l'angle d'incidence de l'énergie solaire sur les parois qui y sont exposées, la transmission de la chaleur à travers des surfaces de verre, les échanges d'énergie avec le milieu ambiant par rayonnement calorifique sur ondes longues et, enfin, les échanges d'énergie par ventilation naturelle. On étudie en détail les conditions thermiques d'une chambre située dans un bâtiment de béton pourvu de parois de verre exposées au sud, le tout étant situé à une latitude boréale. Cette étude est effectuée au moyen d'un programme d'ordinateur digital suffisament général pour s'appliquer à la solution de nombreux problèmes de transmission de chaleur. On montre, pour la première fois, que l'on peut déterminer d'avance l'influence d'une ventilation naturelle programmée. L'établissement de l'optimum thermique des intérieurs peut se faire par une analyse très poussée, c'est à dire à l'aide des méthodes décrites dans cette étude.

     

Effect of hydrodynamic interactions on the diffusion of integral membrane proteins: tracer diffusion in organelle and reconstituted membranes.

A persistent discrepancy exists between theoretical predictions and experimental observations for the diffusion coefficients of integral membrane proteins in lipid bilayers free of immobilized proteins. Current thermodynamic theories overestimate tracer diffusion coefficients at high area fractions. We explore the hypothesis that the combined effect of hydrodynamic and thermodynamic interactions reconciles theory with experiment. We have determined previously the short- and long-time tracer diffusivities, Ds and Dl, respectively, of integral membrane proteins in lipid bilayers as a function of their area fraction, phi. The results are based on two-particle hydrodynamic and thermodynamic interactions and are precise to O(phi). Here we extend the results for Dl to high phi by combining the hydrodynamic results for Ds into theories for Dl based on many-particle thermodynamic interactions. The results compare favorably with the experimental measurements of Dl as a function of protein area fraction for bacteriorhodopsin in reconstituted membranes and for complex III of the mitochondrial inner membrane. The agreement suggests that both hydrodynamic and thermodynamic interactions are important determinants of diffusion coefficients of proteins in lipid bilayers. Additional experiments are required to verify the role of hydrodynamic interactions in protein diffusion in reconstituted systems.     

Crystallographic and Electron Microscopic Analyses of a Bacterial Phytochrome Reveal Local and Global Rearrangements during Photoconversion

Phytochromes are multidomain photoswitches that drive light perception in plants and microorganisms by coupling photoreversible isomerization of their bilin chromophore to various signaling cascades. How changes in bilin conformation affect output by these photoreceptors remains poorly resolved and might include several species-specific routes. Here, we present detailed three-dimensional models of the photosensing module and a picture of an entire dimeric photoreceptor through structural analysis of the Deinococcus radiodurans phytochrome BphP assembled with biliverdin (BV). A 1.16-Å resolution crystal structure of the bilin-binding pocket in the dark-adapted red light-absorbing state illuminated the intricate network of bilin/protein/water interactions and confirmed the protonation and ZZZssa conformation of BV. Structural and spectroscopic comparisons with the photochemically compromised D207A mutant revealed that substitutions of Asp-207 allow inclusion of cyclic porphyrins in addition to BV. A crystal structure of the entire photosensing module showed a head-to-head, twisted dimeric arrangement with bowed helical spines and a hairpin protrusion connecting the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) and phytochrome-specific (PHY) domains. A key conserved hairpin feature is its anti-parallel, two β-strand stem, which we show by mutagenesis to be critical for BphP photochemistry. Comparisons of single particle electron microscopic images of the full-length BphP dimer in the red light-absorbing state and the photoactivated far-red light-absorbing state revealed a large scale reorientation of the PHY domain relative to the GAF domain, which alters the position of the downstream histidine kinase output module. Together, our data support a toggle model whereby bilin photoisomerization alters GAF/PHY domain interactions through conformational modification of the hairpin, which regulates signaling by impacting the relationship between sister output modules.     

Genomic analysis of a novel spontaneous albino C57BL/6N mouse strain

We report an albino C57BL/6N mouse strain carrying a spontaneous mutation in the tyrosinase gene (C57BL/6N‐Tyr^cWTSI). Deep whole genome sequencing of founder mice revealed very little divergence from C57BL/6NJ and C57BL/6N (Taconic). This coisogenic strain will be of great utility for the International Mouse Phenotyping Consortium (IMPC), which uses the EUCOMM/KOMP targeted C57BL/6N ES cell resource, and other investigators wishing to work on a defined C57BL/6N background. genesis 51:523–528. © 2013 The Authors. Genesis Published by Wiley Periodicals, Inc.     

An ecological genetic delineation of local seed‐source provenance for ecological restoration

An increasingly important practical application of the analysis of spatial genetic structure within plant species is to help define the extent of local provenance seed collection zones that minimize negative impacts in ecological restoration programs. Here, we derive seed sourcing guidelines from a novel range‐wide assessment of spatial genetic structure of 24 populations of Banksia menziesii (Proteaceae), a widely distributed Western Australian tree of significance in local ecological restoration programs. An analysis of molecular variance (AMOVA) of 100 amplified fragment length polymorphism (AFLP) markers revealed significant genetic differentiation among populations (Φ_PT = 0.18). Pairwise population genetic dissimilarity was correlated with geographic distance, but not environmental distance derived from 15 climate variables, suggesting overall neutrality of these markers with regard to these climate variables. Nevertheless, Bayesian outlier analysis identified four markers potentially under selection, although these were not correlated with the climate variables. We calculated a global R‐statistic using analysis of similarities (ANOSIM) to test the statistical significance of population differentiation and to infer a threshold seed collection zone distance of ~60 km (all markers) and 100 km (outlier markers) when genetic distance was regressed against geographic distance. Population pairs separated by >60 km were, on average, twice as likely to be significantly genetically differentiated than population pairs separated by <60 km, suggesting that habitat‐matched sites within a 30‐km radius around a restoration site genetically defines a local provenance seed collection zone for B. menziesii. Our approach is a novel probability‐based practical solution for the delineation of a local seed collection zone to minimize negative genetic impacts in ecological restoration.