bluuebunny/crossref_metadata_2025 huggingface dataset:
Methodological developments for improved bottom detection with the ME70 multibeam echosounder
Authors: Bourguignon Sébastien , Berger Laurent , Scalabrin Carla , Fablet Ronan , Mazauric Valérie
Published: April 2009

Bourguignon, S., Berger, L., Scalabrin, C., Fablet, R., and Mazauric, V. 2009. Methodological developments for improved bottom detection with the ME70 multibeam echosounder. – ICES Journal of Marine Science, 66: 1015–1022. Multibeam echosounders and sonars are increasingly used in fisheries acoustics for abundance estimation. Because of reduced side-lobe levels in the beam-array pattern, the new Simrad ME70 multibeam echosounder installed on board Ifremer’s RV “Thalassa” has been designed to allow improved detection of fish close to the seabed. To achieve this objective, precise and unambiguous detection of the water-bottom interface is required, which raises the issue of bottom detection, especially in the outer beams. The bottom-detection method implemented in the ME70 is based on the amplitude of the reverberated echo. Such an approach is efficient for vertical beams, but less accurate for beams with higher incidence angles, typically 30°–40° for the beam configurations used on RV “Thalassa”, where the incidence angle, the beam opening, and the nature of the seabed contribute to weakening the backscattered signal. Therefore, the aim of this study was twofold. First, we proposed to improve the current bottom-detection method based on the amplitude of the echo. Thanks to the split-beam configuration being available for all beams of the ME70, we also proposed to use the phase information in the backscattered signals of the outer beams, as is more commonly done with multibeam systems dedicated to seabed mapping. Then, we set a Bayesian estimation framework that takes into account the spatial continuity between adjacent echoes, giving more robustness to the bottom estimation itself. Results using data collected at sea for various bottom types are presented here.
Parkinson's Disease
Authors: Taggart Chris , Simon Chantal
Published: April 2009

James Parkinson was born in Hoxton Square, London, in 1755. His most important medical work was ‘An Essay on the Shaking Palsy’ (1817). In this short essay, Parkinson gave the classic, albeit in modern terms limited, clinical description of the illness later termed ‘Parkinson's disease’: ‘Involuntary tremulous motion, with lessened muscular power, in parts not in action and even when supported; with a propensity to bend the trunk forwards, and to pass from a walking to a running pace: the senses and intellect being uninjured’.
Death Certification and Confirmation of Death
Authors: van Hecke Oliver
Published: April 2009

“In this world nothing can be said to be certain, except death and taxes” (Benjamin Franklin)

Few people in the UK are unfamiliar with the name Harold Shipman. In January 2000, Shipman was convicted of murdering 15 of his patients, but in reality probably over 200. He was said to have issued false medical certificates of death without the suspicious circumstances of their deaths coming to light. He, like many other doctors, knew all along that it was doctors who decide whether or not to report a death to the investigating official.
Multiple Sclerosis
Authors: Simon Chantal
Published: April 2009

Multiple sclerosis is a chronic disabling neurological disease due to an autoimmune process of unknown cause. It is characterized by the formation of patches of demyelination (plaques) throughout the brain and spinal cord. There is no peripheral nerve involvement.
The Annual Epilepsy Review
Authors: Alarcon Gonzalo , Simon Chantal
Published: April 2009

Epilepsy is a group of disorders in which fits or seizures occur as a result of spontaneous abnormal electrical discharge in any part of the brain. This may be primary and often due to a genetic tendency (idiopathic epilepsy) or secondary to a structural abnormality of the cerebral cortex, for example as a result of tumour or trauma (symptomatic epilepsy). Seizures take many forms but usually show the same pattern on each occasion for a given individual. An average GP practice will have approximately 20 patients with epilepsy. The Quality and Outcomes Framework requires that a register of patients with epilepsy is kept and patients with epilepsy are reviewed annually. This article aims to provide an overview of epilepsy and its ongoing management and guidance on the areas that should be covered in the annual review.
Recognition of and Response to Dementia Syndrome in Primary Care: Part 2
Authors: Iliffe Steve , Jain Priya , Wilcock Jane
Published: April 2009

This second of two articles on the recognition of and response to dementia syndrome in general practice focuses on the long-term support of patients and their families. It includes guidance on the use of cholinesterase inhibitors, the role of psychosocial interventions and the need to organize systematic follow-up. Sources of support for meeting carers' needs are discussed, including ways of managing behavioural and psychological symptoms that appear in the middle phase of the disease trajectory. Discussion of the issues underlying relocation to a care home, and the practicalities of end-of-life care, lead into ways of assessing the quality of care provided in general practice.
Support for People with Dementia
Authors: Hunt Neil
Published: April 2009

Dementia is a progressive and eventually terminal condition, but with early intervention and the right support, people with dementia can continue to enjoy a good quality of life for many years. Living with dementia can be challenging both for those affected and their families as it can affect all aspects of daily life. It is vital that people with dementia and their carers are signposted to the support services that can help them take control of their condition and help them remain active and independent.
Recognition of and Response to Dementia Syndrome in Primary Care: Part 1
Authors: Iliffe Steve , Jain Priya , Wilcock Jane
Published: April 2009

The theme of this article is the recognition of and response to dementia in general practice. Its aim is to clarify the tasks of diagnosing dementia, to advise on the use of cognitive function tests, to suggest ways of establishing the subtype of dementia where possible and to assist general practitioners in talking about dementia with their patients and their families.
Modeling Certainty with Clustered Data: A Comparison of Methods
Authors: Arceneaux Kevin , Nickerson David W.
Published: April 2009

Political scientists often analyze data in which the observational units are clustered into politically or socially meaningful groups with an interest in estimating the effects that group-level factors have on individual-level behavior. Even in the presence of low levels of intracluster correlation, it is well known among statisticians that ignoring the clustered nature of such data overstates the precision estimates for group-level effects. Although a number of methods that account for clustering are available, their precision estimates are poorly understood, making it difficult for researchers to choose among approaches. In this paper, we explicate and compare commonly used methods (clustered robust standard errors (SEs), random effects, hierarchical linear model, and aggregated ordinary least squares) of estimating the SEs for group-level effects. We demonstrate analytically and with the help of empirical examples that under ideal conditions there is no meaningful difference in the SEs generated by these methods. We conclude with advice on the ways in which analysts can increase the efficiency of clustered designs.
A Sweet Potion to Put Embryonic Stem Cells to Sleep
Authors: Deb Kaushik D.
Published: April 2009

Human embryonic stem cells (hESCs) are rapidly revolutionizing the areas of drug screening and therapy. In view of their applications and high operational costs at global multicentric setups, the ability to store and transport hESCs and derivatives under ambient temperatures, and their cryopreservation without compromising the stemness, function, and viability, is becoming imperative. Here we discuss the need for a natural cryoprotectant and biopreservative with a potential to improve cryopreservation, ambient temperature storage, and shipping of hESCs and derivatives. Trehalose, a naturally occurring disaccharide with therapeutic properties, protects the integrity of cells against desiccation, dehydration, and extreme heat or cold, and has been successfully tested for some somatic stem cell types. However, the biggest setback is the inability of mammalian cells to internalize trehalose. Here we review the methods being developed at different laboratories to facilitate its intercellular transport and advocate the need for similar advances in hESCs.
Analysis of Benzene-Induced Effects onRhodococcussp. 33 Reveals that Constitutive Processes Play a Major Role in Conferring Tolerance
Authors: Gutiérrez Tony , Learmonth Robert , Couperwhite Iain
Published: April 2009

Most studies investigating mechanisms that confer microorganisms with tolerance to solvents have often focused on adaptive responses following exposure, while less attention has been given to inherent, or constitutive, processes that prevail at the onset of exposure to a toxic solvent. In this study, we investigated several properties of the highly solvent-tolerant bacteriumRhodococcussp. 33 that confer it with a tolerance to high concentrations of benzene. When challenged with liquid benzene, the growth of both nonadapted and adapted cells was decreased by 0.25¨C0.30% (v/v) liquid benzene, and higher concentrations (≤0.35% v/v) produced a complete cessation in the growth of only nonadapted cells. When exposed to presolubilized benzene, nonadapted cells tolerated ≥1000 mg/l, whereas adapted cells tolerated >1400 mg/l. Measuring the cell membrane fluidity of the cells during these exposure experiments showed that at the onset of exposure, the membranes of adapted cells were less affected by benzene compared to nonadapted cells, although these effects were insignificant in the long term. Several benzene-sensitive mutants were generated from thisRhodococcus, two of which were unable to degrade benzene, yet they still tolerated 500¨C800 mg/l. This confirmed our earlier work suggesting that the benzene-degradation pathway of this organism plays a minor role in tolerance. Under the phase and transmission electron microscope, the mutants were found to have lost the ability to produce extracellular polymers, and many cells appeared pleomorphic, containing intracellular membrane invaginations and mesosome-like structures. As will be discussed, these results identify important functions of the cell membrane, the cell wall, and extracellular polymer in their native state (i.e., before exposure) in conferring this organism with tolerance to benzene.
The origins of apicomplexan sequence innovation
Authors: Wasmuth James , Daub Jennifer , Peregrín-Alvarez José Manuel , Finney Constance A.M. , Parkinson John
Published: April 2009

The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.
PINOID Kinase Regulates Root Gravitropism through Modulation of PIN2-Dependent Basipetal Auxin Transport in Arabidopsis
Authors: Sukumar Poornima , Edwards Karin S. , Rahman Abidur , DeLong Alison , Muday Gloria K.
Published: April 2009

Reversible protein phosphorylation is a key regulatory mechanism governing polar auxin transport. We characterized the auxin transport and gravitropic phenotypes of the pinoid-9 (pid-9) mutant of Arabidopsis (Arabidopsis thaliana) and tested the hypothesis that phosphorylation mediated by PID kinase and dephosphorylation regulated by the ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1 (RCN1) protein might antagonistically regulate root auxin transport and gravity response. Basipetal indole-3-acetic acid transport and gravitropism are reduced in pid-9 seedlings, while acropetal transport and lateral root development are unchanged. Treatment of wild-type seedlings with the protein kinase inhibitor staurosporine phenocopies the reduced auxin transport and gravity response of pid-9, while pid-9 is resistant to inhibition by staurosporine. Staurosporine and the phosphatase inhibitor, cantharidin, delay the asymmetric expression of DR5∷revGFP (green fluorescent protein) at the root tip after gravistimulation. Gravity response defects of rcn1 and pid-9 are partially rescued by treatment with staurosporine and cantharidin, respectively. The pid-9 rcn1 double mutant has a more rapid gravitropic response than rcn1. These data are consistent with a reciprocal regulation of gravitropism by RCN1 and PID. Furthermore, the effect of staurosporine is lost in pinformed2 (pin2). Our data suggest that reduced PID kinase function inhibits gravitropism and basipetal indole-3-acetic acid transport. However, in contrast to PID overexpression studies, we observed wild-type asymmetric membrane distribution of the PIN2 protein in both pid-9 and wild-type root tips, although PIN2 accumulates in endomembrane structures in pid-9 roots. Similarly, staurosporine-treated plants expressing a PIN2∷GFP fusion exhibit endomembrane accumulation of PIN2∷GFP, but no changes in membrane asymmetries were detected. Our data suggest that PID plays a limited role in root development; loss of PID activity alters auxin transport and gravitropism without causing an obvious change in cellular polarity.
Arabidopsis CHLI2 Can Substitute for CHLI1
Authors: Huang Yi-Shiuan , Li Hsou-min
Published: April 2009

The I subunit of magnesium-chelatase (CHLI) is encoded by two genes in Arabidopsis (Arabidopsis thaliana), CHLI1 and CHLI2. Conflicting results have been reported concerning the functions of the two proteins. We show here that the chli1/chli1 chli2/chli2 double knockout mutant was albino. Comparison with the pale-green phenotype of a chli1/chli1 single knockout mutant indicates that CHLI2 could support some chlorophyll biosynthesis in the complete absence of CHLI1. Real-time quantitative reverse transcription-polymerase chain reaction showed that CHLI2 was expressed at a much lower level than CHLI1. The chli1/chli1 chli2/chli2 double mutant could be fully rescued by expressing a transgene of CHLI2 driven by the CHLI1 promoter. These results suggest that differences between CHLI1 and CHLI2 lie mostly in their expression levels. Furthermore, both the chli1/chli1 and chli2/chli2 single knockout mutants had lower survival rates during de-etiolation than the wild type, suggesting that both genes are required for optimal growth during de-etiolation. In addition, we show that a semidominant chli1 mutant allele and the chli1/chli1 chli2/chli2 double mutant accumulated Lhcb1 transcripts when treated with the herbicide norflurazon, indicating that knocking out the CHLI activity causes the genome-uncoupled phenotype.
Phytochrome B Enhances Photosynthesis at the Expense of Water-Use Efficiency in Arabidopsis
Authors: Boccalandro Hernán E. , Rugnone Matías L. , Moreno Javier E. , Ploschuk Edmundo L. , Serna Laura , Yanovsky Marcelo J. , Casal Jorge J.
Published: April 2009

In open places, plants are exposed to higher fluence rates of photosynthetically active radiation and to higher red to far-red ratios than under the shade of neighbor plants. High fluence rates are known to increase stomata density. Here we show that high, compared to low, red to far-red ratios also increase stomata density in Arabidopsis (Arabidopsis thaliana). High red to far-red ratios increase the proportion of phytochrome B (phyB) in its active form and the phyB mutant exhibited a constitutively low stomata density. phyB increased the stomata index (the ratio between stomata and epidermal cells number) and the level of anphistomy (by increasing stomata density more intensively in the adaxial than in the abaxial face). phyB promoted the expression of FAMA and TOO MANY MOUTHS genes involved in the regulation of stomata development in young leaves. Increased stomata density resulted in increased transpiration per unit leaf area. However, phyB promoted photosynthesis rates only at high fluence rates of photosynthetically active radiation. In accordance to these observations, phyB reduced long-term water-use efficiency estimated by the analysis of isotopic discrimination against 13CO2. We propose a model where active phyB promotes stomata differentiation in open places, allowing plants to take advantage of the higher irradiances at the expense of a reduction of water-use efficiency, which is compensated by a reduced leaf area.
Arabidopsis Chloroplastic Glutathione Peroxidases Play a Role in Cross Talk between Photooxidative Stress and Immune Responses
Authors: Chang Christine C.C. , Ślesak Ireneusz , Jordá Lucía , Sotnikov Alexey , Melzer Michael , Miszalski Zbigniew , Mullineaux Philip M. , Parker Jane E. , Karpińska Barbara , Karpiński Stanisław
Published: April 2009

Glutathione peroxidases (GPXs; EC 1.11.1.9) are key enzymes of the antioxidant network in plants and animals. In order to investigate the role of antioxidant systems in plant chloroplasts, we generated Arabidopsis (Arabidopsis thaliana) transgenic lines that are depleted specifically in chloroplastic (cp) forms of GPX1 and GPX7. We show that reduced cpGPX expression, either in transgenic lines with lower total cpGPX expression (GPX1 and GPX7) or in a gpx7 insertion mutant, leads to compromised photooxidative stress tolerance but increased basal resistance to virulent bacteria. Depletion of both GPX1 and GPX7 expression also caused alterations in leaf cell and chloroplast morphology. Leaf tissues were characterized by shorter and more rounded palisade cells, irregular spongy mesophyll cells, and larger intercellular air spaces compared with the wild type. Chloroplasts had larger and more abundant starch grains than in wild-type and gpx7 mutant plants. Constitutively reduced cpGPX expression also led to higher foliar ascorbic acid, glutathione, and salicylic acid levels in plants exposed to higher light intensities. Our results suggest partially overlapping functions of GPX1 and GPX7. The data further point to specific changes in the chloroplast ascorbate-glutathione cycle due to reduced cpGPX expression, initiating reactive oxygen species and salicylic acid pathways that affect leaf development, light acclimation, basal defense, and cell death programs. Thus, cpGPXs regulate cellular photooxidative tolerance and immune responses.
A Nonsense Mutation in a Cinnamyl Alcohol Dehydrogenase Gene Is Responsible for the Sorghum brown midrib6 Phenotype
Authors: Sattler Scott E. , Saathoff Aaron J. , Haas Eric J. , Palmer Nathan A. , Funnell-Harris Deanna L. , Sarath Gautam , Pedersen Jeffrey F.
Published: April 2009

brown midrib6 (bmr6) affects phenylpropanoid metabolism, resulting in reduced lignin concentrations and altered lignin composition in sorghum (Sorghum bicolor). Recently, bmr6 plants were shown to have limited cinnamyl alcohol dehydrogenase activity (CAD; EC 1.1.1.195), the enzyme that catalyzes the conversion of hydroxycinnamoyl aldehydes (monolignals) to monolignols. A candidate gene approach was taken to identify Bmr6. Two CAD genes (Sb02g024190 and Sb04g005950) were identified in the sorghum genome based on similarity to known CAD genes and through DNA sequencing a nonsense mutation was discovered in Sb04g005950 that results in a truncated protein lacking the NADPH-binding and C-terminal catalytic domains. Immunoblotting confirmed that the Bmr6 protein was absent in protein extracts from bmr6 plants. Phylogenetic analysis indicated that Bmr6 is a member of an evolutionarily conserved group of CAD proteins, which function in lignin biosynthesis. In addition, Bmr6 is distinct from the other CAD-like proteins in sorghum, including SbCAD4 (Sb02g024190). Although both Bmr6 and SbCAD4 are expressed in sorghum internodes, an examination of enzymatic activity of recombinant Bmr6 and SbCAD4 showed that Bmr6 had 1 to 2 orders of magnitude greater activity for monolignol substrates. Modeling of Bmr6 and SbCAD4 protein structures showed differences in the amino acid composition of the active site that could explain the difference in enzyme activity. These differences include His-57, which is unique to Bmr6 and other grass CADs. In summary, Bmr6 encodes the major CAD protein involved in lignin synthesis in sorghum, and the bmr6 mutant is a null allele.
Mitochondrial and Nuclear Localization of a Novel Pea Thioredoxin: Identification of Its Mitochondrial Target Proteins
Authors: Martí María C. , Olmos Enrique , Calvete Juan J. , Díaz Isabel , Barranco-Medina Sergio , Whelan James , Lázaro Juan J. , Sevilla Francisca , Jiménez Ana
Published: April 2009

Plants contain several genes encoding thioredoxins (Trxs), small proteins involved in the regulation of the activity of many enzymes through dithiol-disulfide exchange. In addition to chloroplastic and cytoplasmic Trx systems, plant mitochondria contain a reduced nicotinamide adenine dinucleotide phosphate-dependent Trx reductase and a specific Trx o, and to date, there have been no reports of a gene encoding a plant nuclear Trx. We report here the presence in pea (Pisum sativum) mitochondria and nuclei of a Trx isoform (PsTrxo1) that seems to belong to the Trx o group, although it differs from this Trx type by its absence of introns in the genomic sequence. Western-blot analysis with isolated mitochondria and nuclei, immunogold labeling, and green fluorescent protein fusion constructs all indicated that PsTrxo1 is present in both cell compartments. Moreover, the identification by tandem mass spectrometry of the native mitochondrial Trx after gel filtration using the fast-protein liquid chromatography system of highly purified mitochondria and the in vitro uptake assay into isolated mitochondria also corroborated a mitochondrial location for this protein. The recombinant PsTrxo1 protein has been shown to be reduced more effectively by the Saccharomyces  cerevisiae mitochondrial Trx reductase Trr2 than by the wheat (Triticum aestivum) cytoplasmic reduced nicotinamide adenine dinucleotide phosphate-dependent Trx reductase. PsTrxo1 was able to activate alternative oxidase, and it was shown to interact with a number of mitochondrial proteins, including peroxiredoxin and enzymes mainly involved in the photorespiratory process.
Atg26-Mediated Pexophagy Is Required for Host Invasion by the Plant Pathogenic Fungus Colletotrichum orbiculare
Authors: Asakura Makoto , Ninomiya Sachiko , Sugimoto Miki , Oku Masahide , Yamashita Shun-ichi , Okuno Tetsuro , Sakai Yasuyoshi , Takano Yoshitaka
Published: April 2009

The number of peroxisomes in a cell can change rapidly in response to changing environmental and physiological conditions. Pexophagy, a type of selective autophagy, is involved in peroxisome degradation, but its physiological role remains to be clarified. Here, we report that cells of the cucumber anthracnose fungus Colletotrichum orbiculare undergo peroxisome degradation as they infect host plants. We performed a random insertional mutagenesis screen to identify genes involved in cucumber pathogenesis by C. orbiculare. In this screen, we isolated a homolog of Pichia pastoris ATG26, which encodes a sterol glucosyltransferase that enhances pexophagy in this methylotrophic yeast. The C. orbiculare atg26 mutant developed appressoria but exhibited a specific defect in the subsequent host invasion step, implying a relationship between pexophagy and fungal phytopathogenicity. Consistent with this, its peroxisomes are degraded inside vacuoles, accompanied by the formation of autophagosomes during infection-related morphogenesis. The autophagic degradation of peroxisomes was significantly delayed in the appressoria of the atg26 mutant. Functional domain analysis of Atg26 suggested that both the phosphoinositide binding domain and the catalytic domain are required for pexophagy and pathogenicity. In contrast with the atg26 mutant, which is able to form appressoria, the atg8 mutant, which is defective in the entire autophagic pathway, cannot form normal appressoria in the earlier steps of morphogenesis. These results indicate a specific function for Atg26-enhanced pexophagy during host invasion by C. orbiculare.
Seasonal climate manipulations result in species‐specific changes in leaf nutrient levels and isotopic composition in a sub‐arctic bog
Authors: Aerts Rien , Callaghan Terry V. , Dorrepaal Ellen , Van Logtestijn Richard S. P. , Cornelissen Johannes H. C.
Published: April 2009

Climate change in cold biomes not only involves higher summer temperatures, but also warmer springs and more winter precipitation. So far, little is known about species responses to these seasonal components of climate change.

We experimentally manipulated spring and summer temperatures and winter snow accumulation and temperatures independently in a peatland in sub‐arctic Sweden. This yielded six climate scenarios and we studied the responses of the peat moss Sphagnum fuscum, the evergreen dwarf shrubs Empetrum hermaphroditum and Andromeda polifolia, the deciduous dwarf shrubs Betula nana and Vaccinium uliginosum, the grass Calamagrostis lapponica and the forb Rubus chamaemorus.

We found substantial interspecific differences in leaf nutrient and carbon exchange variables that reflect the response of tundra plants to climate change. S. fuscum had the lowest N and P concentrations, with increasing N and P concentrations (and decreasing C/N and C/P ratios) going from evergreen dwarf shrubs, to the grass, deciduous dwarf shrubs and the forb. Leaf N/P ratios varied between 10 and 14 which points to N‐limited plant growth.

The natural abundance of 15N varied very strongly among species and growth forms. These differences corresponded with the presence and type of mycorrhizal association in the plant roots. Leaf carbon isotope discrimination also differed strongly among species and growth forms, but the absolute differences were relatively small (< 5‰). The rank order was: forb and graminoid < moss and evergreen shrubs < deciduous shrubs.

After 4 years, the effects of realistic climate change manipulations on leaf nutrient and carbon exchange variables were idiosyncratic with respect to species and generally small compared to the differences among species and growth forms. At the phenotypic level, spring warming or winter snow addition effects occurred as frequently as summer warming effects.

This implies that the changes in the species composition and structure of plant communities that have been observed in medium‐term warming studies in cold biomes will have much more impact on plant‐mediated nutrient and carbon cycling pathways and rates than climate‐change induced phenotypic responses, irrespective of the seasonal timing of these climate changes.
Differences in growth patterns between co‐occurring forest and savanna trees affect the forest–savanna boundary
Authors: Rossatto Davi Rodrigo , Hoffmann William Arthur , Franco Augusto César
Published: April 2009

Patterns of growth, activity and renewal of stems and branches are primary determinants of ecosystem function and strongly influence net primary productivity, water and energy balance. Here we compare patterns of leaf phenology, stem radial growth and branch growth of co‐occurring savanna and forest trees in the Cerrado region of central Brazil to gain insight into the influence of these parameters in forest–savanna boundary dynamics. We hypothesized that forest species would have higher radial growth rates but later leaf flush than savanna species.

We studied 12 congeneric species pairs, each containing one savanna species and one forest species. All individuals were growing in savanna conditions under full sun. We measured specific leaf area (SLA), light‐saturated photosynthesis and monthly increments in stem circumference, branch length, leaf flush and leaf fall.

Relative to savanna species, forest species had 68% higher diameter growth rates, 38% higher SLA, and displayed a greater crown area for a given basal area. Across species, radial growth was positively correlated with SLA (r2 = 0·31), but not with CO2 assimilation.

Peak leaf production of savanna species was in the late dry season, 1 month earlier than for forest species, which suggests a strategy to avoid nutrient losses during leaf expansion due to herbivory or leaching. However, savanna and forest species did not differ in annual branch growth, number of leaves produced per branch, or in timing of leaf fall.

Radial growth was tightly coupled to monthly rainfall in forest species whereas the growth of savanna species ceased before the end of the wet season. The cessation of above‐ground growth at a time of active photosynthesis may reflect a shift in allocation to roots and reserves.

These results contribute to recent studies showing that savanna and forest species represent different functional types and that despite the limiting resources in savanna environments, forest trees that invade the savanna tend to present higher growth rates and larger and denser crowns, which enhance shading and could promote changes in equilibrium of forest–savanna boundaries.
Cannabinoid receptor 1 signalling dampens activity and mitochondrial transport in networks of enteric neurones
Authors: Boesmans W. , Ameloot K. , Van Den Abbeel V. , Tack J. , Vanden Berghe P.
Published: April 2009

Abstract  Cannabinoid (CB) receptors are expressed in the enteric nervous system (ENS) and CB1 receptor activity slows down motility and delays gastric emptying. This receptor system has become an important target for GI‐related drug development such as in obesity treatment. The aim of the study was to investigate how CB1 ligands and antagonists affect ongoing activity in enteric neurone networks, modulate synaptic vesicle cycling and influence mitochondrial transport in nerve processes. Primary cultures of guinea‐pig myenteric neurones were loaded with different fluorescent markers: Fluo‐4 to measure network activity, FM1‐43 to image synaptic vesicles and Mitotracker green to label mitochondria. Synaptic vesicle cluster density was assessed by immunohistochemistry and expression of CB1 receptors was confirmed by RT‐PCR. Spontaneous network activity, displayed by both excitatory and inhibitory neurones, was significantly increased by CB1 receptor antagonists (AM‐251 and SR141716), abolished by CB1 activation (methanandamide, mAEA) and reduced by two different inhibitors (arachidonylamide serotonin, AA‐5HT and URB597) of fatty acid amide hydrolase. Antagonists reduced the number of synaptic vesicles that were recycled during an electrical stimulus. CB1 agonists (mAEA and WIN55,212) reduced and antagonists enhanced the fraction of transported mitochondria in enteric nerve fibres. We found immunohistochemical evidence for an enhancement of synaptophysin‐positive release sites with SR141716, while WIN55,212 caused a reduction. The opposite effects of agonists and antagonists suggest that enteric nerve signalling is under the permanent control of CB1 receptor activity. Using inhibitors of the endocannabinoid degrading enzyme, we were able to show there is endogenous production of a CB ligand in the ENS.
Inhibition of cell death results in hyperganglionosis: implications for enteric nervous system development
Authors: Wallace A. S. , Barlow A. J. , Navaratne L. , Delalande J‐m. , Tauszig‐delamasure S. , Corset V. , Thapar N. , Burns A. J.
Published: April 2009

Abstract  The enteric nervous system (ENS) is derived from vagal and sacral neural crest cells (NCC) that delaminate from the neural tube and undergo extensive migration and proliferation in order to colonize the entire length of the gut and differentiate into many millions of neurons and glial cells. Although apoptotic programmed cell death is an essential physiological process during development of the majority of the vertebrate nervous system, apoptosis within early ENS development has not been comprehensively investigated. The aim of this study was to determine the presence and extent of apoptosis within the vagal NCC population that gives rise to most of the ENS in the chick embryo. We demonstrated that apoptotic cells, as shown by terminal deoxynucleotidyl transferase biotin‐dUTP nick end labelling and active caspase‐3 immunoreactivity, are present within an electroporated green fluorescent protein (GFP) and human natural killer‐1 (HNK‐1) immunopositive NCC population migrating from the vagal region of the neural tube to the developing foregut. Inhibition of caspase activity in vagal NCC, by electroporation with a dominant‐negative form of caspase‐9, increased the number of vagal NCC available for ENS formation, as shown by 3‐dimensional reconstruction of serial GFP or HNK‐1 labelled sections, and resulted in hyperganglionosis within the proximal foregut, as shown by NADPH‐diaphorase whole gut staining. These findings suggest that apoptotic cell death may be a normal process within the precursor pool of pre‐enteric NCC that migrates to the gut, and as such it may play a role in the control of ENS formation.
Immunomodulatory effects of dietary protein during Nippostrongylus brasiliensis re‐infection in lactating rats
Authors: JONES L. A. , HOUDIJK J. G. M. , KNOX D. P. , KYRIAZAKIS I.
Published: April 2009

Periparturient relaxation of immunity (PPRI) to secondary infection with nematodes is believed to have a nutritional basis due to differential partitioning of scarce nutrient resources, particularly protein, to reproductive rather than immune functions. At times of protein scarcity, an increase in protein supply has been reported to assuage this phenomenon. The Nippostrongylus brasiliensis reinfected lactating rat model is now being utilized to investigate the immune reactions underlying the modifying role of dietary protein on PPRI. Herein, we demonstrate that lactating rats reinfected with N. brasiliensis under high protein (HP) dietary conditions exhibit decreased worm burdens and reduced colon egg counts compared to their low protein (LP) counterparts. These reductions correlated with increased mastocytosis and greater goblet cell hyperplasia. Additionally, the local antibody profile revealed that HP reinfected lactating rats developed a stronger antigen specific IgG2b response earlier in infection in comparison with their LP counterparts. Our study provides evidence that increased dietary protein content reduces the PPRI to N. brasiliensis re‐infection in the lactating rat through improved mucosal immune responses.
Dysregulation of macrophage signal transduction by Toxoplasma gondii: past progress and recent advances
Authors: LENG J. , BUTCHER B. A. , DENKERS E. Y.
Published: April 2009

The opportunistic protozoan parasite Toxoplasma gondii is well known as a strong inducer of cell‐mediated immunity, largely as a result of proinflammatory cytokine induction during in vivo infection. Yet, during intracellular infection the parasite suppresses signal transduction pathways leading to these proinflammatory responses. The opposing responses are likely to reflect the parasite’s need to stimulate immunity allowing host survival and parasite persistence, and at the same time avoiding excessive responses that could result in parasite elimination and host immunopathology. This Review summarizes past and present investigations into the effects of Toxoplasma on host cell signal transduction. These studies reveal insight into the profound suppression of proinflammatory cytokine responses that occurs when the parasite infects macrophages and other cells of innate immunity.
Aggressiveness of Phytophthora infestans on detached potato leaflets in four Nordic countries
Authors: Lehtinen A. , Andersson B. , Le V. H. , Nærstad R. , Rastas M. , Ketoja E. , Hannukkala A. O. , Hermansen A. , Nielsen B. J. , Hansen J. G. , Yuen J.
Published: April 2009

Potato fields in Denmark, Finland, Norway and Sweden were sampled for single‐lesion isolates of Phytophthora infestans. The aggressiveness of the isolates was determined on detached leaflets of potato cvs Bintje (susceptible) and Matilda (moderately resistant). The aggressiveness tests were carried out in the respective home countries of the isolates, with the exception of the Danish isolates. Fifteen Danish isolates were studied in each of the other three countries, including five isolates tested in all three laboratories. Results obtained from the Danish isolates revealed substantial differences between the test laboratories for infection efficiency, lesion growth rate and sporulation capacity on detached leaflets. When the laboratory effect was taken into account, the differences in aggressiveness between the countries were generally small or inconsistent between the test cultivars and epidemiologically insignificant. By contrast, variation among isolates within countries was substantial. The magnitude of the variation depended on country and cultivar. Maximal variation for the means of the isolates was between 89 and 185 h for latent period, between 100 and 1297 sporangia mm−2 for sporulation capacity and between nearly zero and 6 mm day−1 for lesion growth rate. Typically less than 1% of sporangia were able to cause infections, except in Norway. These extraordinarily low values may be an artefact of the testing method. High variation in results between the test laboratories emphasizes the need for caution when comparing results obtained by different research groups.
Arabidopsis CER8 encodes LONG‐CHAIN ACYL‐COA SYNTHETASE 1 (LACS1) that has overlapping functions with LACS2 in plant wax and cutin synthesis
Authors: Lü Shiyou , Song Tao , Kosma Dylan K. , Parsons Eugene P. , Rowland Owen , Jenks Matthew A.
Published: April 2009

Plant cuticle is an extracellular lipid‐based matrix of cutin and waxes, which covers aerial organs and protects them from many forms of environmental stress. We report here the characterization of CER8/LACS1, one of nine Arabidopsis long‐chain acyl‐CoA synthetases thought to activate acyl chains. Mutations in LACS1 reduced the amount of wax in all chemical classes on the stem and leaf, except in the very long‐chain fatty acid (VLCFA) class wherein acids longer than 24 carbons (C24) were elevated more than 155%. The C16 cutin monomers on lacs1 were reduced by 37% and 22%, whereas the C18 monomers were increased by 28% and 20% on stem and leaf, respectively. Amounts of wax and cutin on a lacs1‐1 lacs2‐3 double mutant were much lower than on either parent, and lacs1‐1 lacs2‐3 had much higher cuticular permeability than either parent. These additive effects indicate that LACS1 and LACS2 have overlapping functions in both wax and cutin synthesis. We demonstrated that LACS1 has synthetase activity for VLCFAs C20–C30, with highest activity for C30 acids. LACS1 thus appears to function as a very long‐chain acyl‐CoA synthetase in wax metabolism. Since C16 but not C18 cutin monomers are reduced in lacs1, and C16 acids are the next most preferred acid (behind C30) by LACS1 in our assays, LACS1 also appears to be important for the incorporation of C16 monomers into cutin polyester. As such, LACS1 defines a functionally novel acyl‐CoA synthetase that preferentially modifies both VLCFAs for wax synthesis and long‐chain (C16) fatty acids for cutin synthesis.
Systematic analysis of cell‐cycle gene expression during Arabidopsis development
Authors: De Almeida Engler Janice , De Veylder Lieven , De Groodt Ruth , Rombauts Stephane , Boudolf Véronique , De Meyer Bjorn , Hemerly Adriana , Ferreira Paulo , Beeckman Tom , Karimi Mansour , Hilson Pierre , Inzé Dirk , Engler Gilbert
Published: April 2009

The steady‐state distribution of cell‐cycle transcripts in Arabidopsis thaliana seedlings was studied in a broad in situ survey to provide a better understanding of the expression of cell‐cycle genes during plant development. The 61 core cell‐cycle genes analyzed were expressed at variable levels throughout the different plant tissues: 23 genes generally in dividing and young differentiating tissues, 34 genes mostly in both dividing and differentiated tissues and four gene transcripts primarily in differentiated tissues. Only 21 genes had a typical patchy expression pattern, indicating tight cell‐cycle regulation. The increased expression of 27 cell‐cycle genes in the root elongation zone hinted at their involvement in the switch from cell division to differentiation. The induction of 20 cell‐cycle genes in differentiated cortical cells of etiolated hypocotyls pointed to their possible role in the process of endoreduplication. Of seven cyclin‐dependent kinase inhibitor genes, five were upregulated in etiolated hypocotyls, suggesting a role in cell‐cycle arrest. Nineteen genes were preferentially expressed in pericycle cells activated by auxin that give rise to lateral root primordia. Approximately 1800 images have been collected and can be queried via an online database. Our in situ analysis revealed that 70% of the cell‐cycle genes, although expressed at different levels, show a large overlap in their localization. The lack of regulatory motifs in the upstream regions of the analyzed genes suggests the absence of a universal transcriptional control mechanism for all cell‐cycle genes.
Calcium‐dependent protein kinases regulate polarized tip growth in pollen tubes
Authors: Myers Candace , Romanowsky Shawn M. , Barron Yoshimi D. , Garg Shilpi , Azuse Corinn L. , Curran Amy , Davis Ryan M. , Hatton Jasmine , Harmon Alice C. , Harper Jeffrey F.
Published: April 2009

Calcium signals are critical for the regulation of polarized growth in many eukaryotic cells, including pollen tubes and neurons. In plants, the regulatory pathways that code and decode Ca2+ signals are poorly understood. In Arabidopsis thaliana, genetic evidence presented here indicates that pollen tube tip growth involves the redundant activity of two Ca2+‐dependent protein kinases (CPKs), isoforms CPK17 and ‐34. Both isoforms appear to target to the plasma membrane, as shown by imaging of CPK17–yellow fluorescent protein (YFP) and CPK34–YFP in growing pollen tubes. Segregation analyses from two independent sets of T‐DNA insertion mutants indicate that a double disruption of CPK17 and ‐34 results in an approximately 350‐fold reduction in pollen transmission efficiency. The near sterile phenotype of homozygous double mutants could be rescued through pollen expression of a CPK34–YFP fusion. In contrast, a transgene rescue was blocked by mutations engineered to disrupt the Ca2+‐activation mechanism of CPK34 (CPK34–YFP–E465A,E500A), providing in vivo evidence linking Ca2+ activation to a biological function of a CPK. While double mutant pollen tubes displayed normal morphology, relative growth rates for the most rapidly growing tubes were reduced by more than three‐fold compared with wild type. In addition, while most mutant tubes appeared to grow far enough to reach ovules, the vast majority (>90%) still failed to locate and fertilize ovules. Together, these results provide genetic evidence that CPKs are essential to pollen fitness, and support a mechanistic model in which CPK17 and ‐34 transduce Ca2+ signals to increase the rate of pollen tube tip growth and facilitate a response to tropism cues.
Arabidopsis mitogen‐activated protein kinase MPK18 mediates cortical microtubule functions in plant cells
Authors: Walia Ankit , Lee Jin S. , Wasteneys Geoffrey , Ellis Brian
Published: April 2009

Mitogen‐activated protein kinase (MAPK) signalling networks are important regulators of environmental responses and developmental processes in plants. To understand the role of MAPK signalling modules in the regulation of plant microtubule functions, we searched for MAPKs that interact with the dual‐specificity MAPK phosphatase, PROPYZAMIDE HYPERSENSITIVE 1 (PHS1), whose mutation has previously been reported to confer hypersensitivity to microtubule‐disrupting drugs in Arabidopsis. Yeast two‐hybrid assays demonstrated that PHS1 specifically interacts with two MAPKs, MPK12 and MPK18. Bimolecular fluorescence complementation (BiFC) studies confirmed that the PHS1 and MPK18 proteins are physically coupled, and that this interaction occurs in the cytoplasm. At the biochemical level, in vitro dephosphorylation assays indicated that phospho‐MPK18 can be dephosphorylated by recombinant PHS1. Mutant mpk18 seedlings show defects in microtubule‐related functions, and have moderately stabilized microtubules. Absence of MPK18 in the phs1‐1 background partially complements the phs1‐1 root growth phenotypes, providing genetic evidence for involvement of MPK18 signalling in microtubule‐related functions. We propose a model whereby the PHS1–MPK18 signalling module is involved in a phosphorylation/dephosphorylation switch that regulates cortical microtubule functions.
Flow cytometric purification ofColletotrichum higginsianumbiotrophic hyphae from Arabidopsis leaves for stage‐specific transcriptome analysis
Authors: Takahara Hiroyuki , Dolf Andreas , Endl Elmar , O’Connell Richard
Published: April 2009

Generation of stage‐specific cDNA libraries is a powerful approach to identify pathogen genes that are differentially expressed during plant infection. Biotrophic pathogens develop specialized infection structures inside living plant cells, but sampling the transcriptome of these structures is problematic due to the low ratio of fungal to plant RNA, and the lack of efficient methods to isolate them from infected plants. Here we established a method, based on fluorescence‐activated cell sorting (FACS), to purify the intracellular biotrophic hyphae ofColletotrichum higginsianumfrom homogenates of infected Arabidopsis leaves. Specific selection of viable hyphae using a fluorescent vital marker provided intact RNA for cDNA library construction. Pilot‐scale sequencing showed that the library was enriched with plant‐induced and pathogenicity‐related fungal genes, including some encoding small, soluble secreted proteins that represent candidate fungal effectors. The high purity of the hyphae (94%) prevented contamination of the library by sequences derived from host cells or other fungal cell types. RT‐PCR confirmed that genes identified in the FACS‐purified hyphae were also expressedin planta. The method has wide applicability for isolating the infection structures of other plant pathogens, and will facilitate cell‐specific transcriptome analysis via deep sequencing and microarray hybridization, as well as proteomic analyses.