bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial patterns of plant diversity below‐ground as revealed by DNA barcoding
Authors: KESANAKURTI PRASAD R. , FAZEKAS ARON J. , BURGESS KEVIN S. , PERCY DIANA M. , NEWMASTER STEVEN G. , GRAHAM SEAN W. , BARRETT SPENCER C. H. , HAJIBABAEI MEHRDAD , HUSBAND BRIAN C. 
Published: January 2011

AbstractOur understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above‐ground community structure. We collected 3800 root fragments from four randomly positioned, 1‐m‐deep soil profiles (two vertical transects per plot), located in an old‐field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below‐ground was correlated with their frequency above‐ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above‐ground quadrats. Multivariate analyses indicated that diversity was highly structured below‐ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above‐ground. Furthermore, analyses of species co‐occurrence indicates strong species segregation overall but random co‐occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below‐ground, and also demonstrate the utility of barcoding for the identification of plant roots.
Mycorrhizal specificity in the fully mycoheterotrophic Hexalectris Raf. (Orchidaceae: Epidendroideae)
Authors: KENNEDY AARON H. , TAYLOR D. Lee , WATSON LINDA E. 
Published: January 2011

AbstractMycoheterotrophic species have abandoned an autotrophic lifestyle and obtain carbon exclusively from mycorrhizal fungi. Although these species have evolved independently in many plant families, such events have occurred most often in the Orchidaceae, resulting in the highest concentration of these species in the tracheophytes. Studies of mycoheterotrophic species’ mycobionts have generally revealed extreme levels of mycorrhizal specialization, suggesting that this system is ideal for studying the evolution of mycorrhizal associations. However, these studies have often investigated single or few, often unrelated, species without consideration of their phylogenetic relationships. Herein, we present the first investigation of the mycorrhizal associates of all species of a well‐characterized orchid genus comprised exclusively of mycoheterotrophic species. With the employment of molecular phylogenetic methods, we identify the fungal associates of each of nine Hexalectris species from 134 individuals and 42 populations. We report that Hexalectris warnockii associates exclusively with members of the Thelephoraceae, H. brevicaulis and H. grandiflora associate with members of the Russulaceae and Sebacinaceae subgroup A, while each member of the H. spicata species complex associates primarily with unique sets of Sebacinaceae subgroup A clades. These results are consistent with other studies of mycorrhizal specificity within mycoheterotrophic plants in that they suggest strong selection within divergent lineages for unique associations with narrow clades of mycorrhizal fungi. Our results also suggest that mycorrhizal associations are a rapidly evolving characteristic in the H. spicata complex.
Light inputs shape the Arabidopsis circadian system
Authors: Wenden Bénédicte , Kozma‐Bognár László , Edwards Kieron D. , Hall Anthony J.W. , Locke James C.W. , Millar Andrew J. 
Published: January 2011

SummaryThe circadian clock is a fundamental feature of eukaryotic gene regulation that is emerging as an exemplar genetic sub‐network for systems biology. The circadian system in Arabidopsis plants is complex, in part due to its phototransduction pathways, which are themselves under circadian control. We therefore analysed two simpler experimental systems. Etiolated seedlings entrained by temperature cycles showed circadian rhythms in the expression of genes that are important for the clock mechanism, but only a restricted set of downstream target genes were rhythmic in microarray assays. Clock control of phototransduction pathways remained robust across a range of light inputs, despite the arrhythmic transcription of light‐signalling genes. Circadian interactions with light signalling were then analysed using a single active photoreceptor. Phytochrome A (phyA) is expected to be the only active photoreceptor that can mediate far‐red (FR) light input to the circadian clock. Surprisingly, rhythmic gene expression was profoundly altered under constant FR light, in a phyA‐dependent manner, resulting in high expression of evening genes and low expression of morning genes. Dark intervals were required to allow high‐amplitude rhythms across the transcriptome. Clock genes involved in this response were identified by mutant analysis, showing that the EARLY FLOWERING 4 gene is a likely target and mediator of the FR effects. Both experimental systems illustrate how profoundly the light input pathways affect the plant circadian clock, and provide strong experimental manipulations to understand critical steps in the plant clock mechanism.
Nicotiana benthamiana resistance to non‐adapted Melon necrotic spot virus results from an incompatible interaction between virus RNA and translation initiation factor 4E
Authors: Nieto Cristina , Rodríguez‐Moreno Luis , Rodríguez‐Hernández Ana M. , Aranda Miguel A. , Truniger Verónica 
Published: January 2011

Summary Nicotiana benthamiana has been described as non‐host for Melon necrotic spot virus (MNSV). We investigated the basis of this resistance using the unique opportunity provided by strain MNSV‐264, a recombinant virus that is able to overcome the resistance. Analysis of chimeric MNSV mutants showed that virulence in N. benthamiana is conferred by a 49 nucleotide section of the MNSV‐264 3′‐UTR, which acts in this host as a cap‐independent translational enhancer (3′‐CITE). Although the 3′‐CITE of non‐adapted MNSV‐Mα5 is active in susceptible melon, it does not promote efficient translation in N. benthamiana, thus preventing expression of proteins required for virus replication. However, MNSV‐Mα5 gains the ability to multiply in N. benthamiana cells if eIF4E from a susceptible melon variety (Cm‐eIF4E‐S) is supplied in trans. These data show that N. benthamiana resistance to MNSV‐Mα5 results from incompatibility between the MNSV‐Mα5 3′‐CITE and N. benthamiana eIF4E in initiating efficient translation of the viral genome. Therefore, non‐host resistance conferred by the inability of a host susceptibility factor to support viral multiplication may be a possible mechanism for this type of resistance to viruses.
The Arabidopsis Myb genes MYR1 and MYR2 are redundant negative regulators of flowering time under decreased light intensity
Authors: Zhao Chengsong , Hanada Atsushi , Yamaguchi Shinjiro , Kamiya Yuji , Beers Eric P. 
Published: January 2011

SummaryChanges in the duration, quality and intensity of light affect flowering time. Compared with the effects of light duration and quality, less is known about the effects of light intensity on flowering. Here we describe two paralogous single Myb domain genes, MYB‐RELATED PROTEIN 1 (MYR1) and MYB‐RELATED PROTEIN 2 (MYR2), and their roles as repressors of responses to decreased light intensity in Arabidopsis. Homozygous myr1 myr2 double mutants flowered early under low light intensities. Additionally, myr1 myr2 mutants exhibited increases in petiole length, leaf angle and apical dominance. Genetic analyses involving mutants in the long‐day, gibberellin (GA) and phyB flowering pathways indicated that all aspects of the myr1 myr2 phenotype required GA biosynthesis. The early‐flowering phenotype of myr1 myr2 also required FLOWERING LOCUS T, and myr1 myr2 mutants showed an epistatic interaction with the phyB‐9 mutant. Over‐expression of MYR1 or MYR2 produced GA‐deficiency symptoms that were rescued by application of gibberellic acid (GA3). Loss of MYR1 and MYR2 function was associated with a twofold increase in GA20ox2 expression and a 30% increase in GA4 levels, while over‐expression of MYR2 led to a threefold decrease in GA20ox2 expression and a 50% decrease in GA4 levels. Considered together, these results suggest that the ability of MYR1 and MYR2 to repress flowering and organ elongation is at least partly due to their negative effect on levels of bioactive GA.
Functional characterization of the CKRC1/TAA1 gene and dissection of hormonal actions in the Arabidopsis root
Authors: Zhou Zhao‐Yang , Zhang Chun‐Guang , Wu Lei , Zhang Cai‐Guo , Chai Juan , Wang Ming , Jha Ajay , Jia Peng‐Fei , Cui Su‐Juan , Yang Ming , Chen Rujin , Guo Guang‐Qin 
Published: January 2011

SummaryCytokinin (CK) influences many aspects of plant growth and development, and its function often involves intricate interactions with other phytohormones such as auxin and ethylene. However, the molecular mechanisms underlying the role of CK and its interactions with other growth regulators are still poorly understood. Here we describe the isolation and characterization of the Arabidopsis CK‐induced root curling 1 (ckrc1) mutant. CKRC1 encodes a previously identified tryptophan aminotransferase (TAA1) involved in the indole‐3‐pyruvic acid (IPA) pathway of indole‐3‐acetic acid (IAA) biosynthesis. The ckrc1 mutant exhibits a defective root gravitropic response (GR) and an increased resistance to CK in primary root growth. These defects can be rescued by exogenous auxin or IPA. Furthermore, we show that CK up‐regulates CKRC1/TAA1 expression but inhibits polar auxin transport in roots in an AHK3/ARR1/12‐dependent and ethylene‐independent manner. Our results suggest that CK regulates root growth and development not only by down‐regulating polar auxin transport, but also by stimulating local auxin biosynthesis.
A fast brassinolide‐regulated response pathway in the plasma membrane of Arabidopsis thaliana
Authors: Caesar Katharina , Elgass Kirstin , Chen Zhonghua , Huppenberger Peter , Witthöft Janika , Schleifenbaum Frank , Blatt Michael R. , Oecking Claudia , Harter Klaus 
Published: January 2011

SummaryTo understand molecular processes in living plant cells, quantitative spectro‐microscopic technologies are required. By combining fluorescence lifetime spectroscopy with confocal microscopy, we studied the subcellular properties and function of a GFP‐tagged variant of the plasma membrane‐bound brassinosteroid receptor BRI1 (BRI1–GFP) in living cells of Arabidopsis seedlings. Shortly after adding brassinolide, we observed BRI1‐dependent cell‐wall expansion, preceding cell elongation. In parallel, the fluorescence lifetime of BRI1–GFP decreased, indicating an alteration in the receptor’s physico‐chemical environment. The parameter modulating the fluorescence lifetime of BRI1–GFP was found to be BL‐induced hyperpolarization of the plasma membrane. Furthermore, for induction of hyperpolarization and cell‐wall expansion, activation of the plasma membrane P‐ATPase was necessary. This activation required BRI1 kinase activity, and was mediated by BL‐modulated interaction of BRI1 with the P‐ATPase. Our results were used to develop a model suggesting that there is a fast BL‐regulated signal response pathway within the plasma membrane that links BRI1 with P‐ATPase for the regulation of cell‐wall expansion.
Joint British Diabetes Societies guideline for the management of diabetic ketoacidosis
Authors: Savage M. W. , Dhatariya K. K. , Kilvert A. , Rayman G. , Rees J. A. E. , Courtney C. H. , Hilton L. , Dyer P. H. , Hamersley M. S. ,   for the Joint British Diabetes Societies
Published: January 2011

Diabet. Med. 28, 508–515 (2011)AbstractThe Joint British Diabetes Societies guidelines for the management of diabetic ketoacidosis (these do not cover Hyperosmolar Hyperglycaemic Syndrome) are available in full at:
http://www.diabetes.org.uk/About_us/Our_Views/Care_recommendations/The‐Management‐of‐Diabetic‐Ketoacidosis‐in‐Adults;
http://www.diabetes.nhs.uk/publications_and_resources/reports_and_guidance;
http://www.diabetologists‐abcd.org.uk/JBDS_DKA_Management.pdf.
This article summarizes the main changes from previous guidelines and discusses the rationale for the new recommendations.The key points are:Monitoring of the response to treatment
The method of choice for monitoring the response to treatment is bedside measurement of capillary blood ketones using a ketone meter.
If blood ketone measurement is not available, venous pH and bicarbonate should be used in conjunction with bedside blood glucose monitoring to assess treatment response.
Venous blood should be used rather than arterial (unless respiratory problems dictate otherwise) in blood gas analysers.
Intermittent laboratory confirmation of pH, bicarbonate and electrolytes only.
Insulin administration
Insulin should be infused intravenously at a weight‐based fixed rate until the ketosis has resolved.
When the blood glucose falls below 14 mmol/l, 10% glucose should be added to allow the fixed‐rate insulin to be continued.
If already taking, long‐acting insulin analogues such as insulin glargine (Lantus®, Sanofi Aventis, Guildford, Surry, UK) or insulin detemir (Levemir®, Novo Nordisk, Crawley, West Sussex, UK.) should be continued in usual doses.
Delivery of care
The diabetes specialist team should be involved as soon as possible.
Patients should be nursed in areas where staff are experienced in the management of ketoacidosis.
Chronic central leptin infusion modifies the response to acute central insulin injection by reducing the interaction of the insulin receptor with IRS2 and increasing its association with SOCS3
Authors: Burgos‐Ramos Emma , Chowen Julie A. , Arilla‐Ferreiro Eduardo , Canelles Sandra , Argente Jesús , Barrios Vicente 
Published: January 2011

J. Neurochem. (2011) 117, 175–185.AbstractLeptin and insulin have overlapping intracellular signaling mechanisms and exert anorexigenic actions in the hypothalamus. We aimed to determine how chronic exposure to increased leptin affects the hypothalamic response to a rise in insulin. We analyzed the activation and interactions of components of the phosphatidylinositol 3‐kinase (PI3K)/Akt pathway in the hypothalamus of rats treated icv for 14 days with leptin followed by a central injection of insulin and killed 15 min later. Insulin increased glycemia and chronic leptin reduced this insulin induced rise in glucose. Leptin decreased the association between the insulin receptor beta chain (IRβ) and insulin receptor substrate 2 (IRS2), augmented the association between Janus kinase 2 and IRS2, increased levels of the catalytic subunit of PI3K and pAkt‐Ser473 and decreased forkhead box O number 1 levels. Insulin reduced the association between suppressor of the cytokine signaling 3 and IRβ, increased IRβ–IRS2 association and pAkt‐Thr308 levels, with chronic leptin exposure blunting these effects. In conclusion, chronic exposure to leptin decreases the central response to insulin by increasing suppressor of the cytokine signaling 3 association to IR, which inhibits insulin signaling at the level of interaction of its receptor with IRS2 and activates PI3K by promoting Janus kinase 2–IRS2 association. Thus, these results suggest that this mechanism could be a target for the treatment of insulin resistance.
Mechanism of GABAB receptor‐induced BDNF secretion and promotion of GABAA receptor membrane expression
Authors: Kuczewski Nicola , Fuchs Celine , Ferrand Nadine , Jovanovic Jasmina N. , Gaiarsa Jean‐Luc , Porcher Christophe 
Published: January 2011

J. Neurochem. (2011) 118, 533–545.AbstractRecent studies have shown that GABAB receptors play more than a classical inhibitory role and can function as an important synaptic maturation signal early in life. In a previous study, we reported that GABAB receptor activation triggers secretion of brain‐derived neurotrophic factor (BDNF) and promotes the functional maturation of GABAergic synapses in the developing rat hippocampus. To identify the signalling pathway linking GABAB receptor activation to BDNF secretion in these cells, we have now used the phosphorylated form of the cAMP response element‐binding protein as a biological sensor for endogenous BDNF release. In the present study, we show that GABAB receptor‐induced secretion of BDNF relies on the activation of phospholipase C, followed by the formation of diacylglycerol, activation of protein kinase C, and the opening of L‐type voltage‐dependent Ca2+ channels. We further show that once released by GABAB receptor activation, BDNF increases the membrane expression of β2/3‐containing GABAA receptors in neuronal cultures. These results reveal a novel function of GABAB receptors in regulating the expression of GABAA receptor through BDNF‐tropomyosin‐related kinase B receptor dependent signalling pathway.
Serum Vitamin D Levels in Office Workers in a Subtropical Climate
Authors: Vu Lan H. , Whiteman David C. , van der Pols Jolieke C. , Kimlin Michael G. , Neale Rachel E. 
Published: January 2011

AbstractVitamin D is necessary to maintain healthy bones, and may prevent other chronic diseases. There is limited information regarding the vitamin D status of people living in climates with relatively high ambient ultraviolet radiation. We therefore aimed to determine serum 25(OH)D levels in a group of office‐workers in subtropical Australia. We collected blood from 129 office workers in summer (n = 129) and 175 in winter (91 in both seasons). Serum 25(OH)D was estimated using a commercial chemiluminescent immunoassay and we asked participants to complete questionnaires about sun exposure and diet for the month prior to blood collection. Summer and winter mean serum 25(OH)D was 74 (95% CI 70–77) nmol L−1 and 54 (95% CI 51–57) nmol L−1, respectively. In summer, 14% of participants were classed as “insufficient,” compared with 51% in winter. High 25(OH)D levels in summer were associated with time spent outdoors in nonpeak UV periods, while in winter high levels were associated with intake of vitamin D from food or supplements. The high prevalence of vitamin D insufficiency observed in this population highlights the need for further examination of the relation between sunlight and vitamin D production to enable more accurate sun exposure recommendations.
Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard
Authors: Teske A. , Durbin A. , Ziervogel K. , Cox C. , Arnosti C. 
Published: January 2011

ABSTRACT
Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.
[NiFe] Hydrogenase from
Alteromonas macleodii
with Unusual Stability in the Presence of Oxygen and High Temperature
Authors: Vargas Walter A. , Weyman Philip D. , Tong Yingkai , Smith Hamilton O. , Xu Qing 
Published: January 2011

ABSTRACT

Hydrogenases are enzymes involved in the bioproduction of hydrogen, a clean alternative energy source whose combustion generates water as the only end product. In this article we identified and characterized a [NiFe] hydrogenase from the marine bacterium
Alteromonas macleodii
“deep ecotype” with unusual stability toward oxygen and high temperature. The
A. macleodii
hydrogenase (HynSL) can catalyze both H
2
evolution and H
2
uptake reactions. HynSL was expressed in
A. macleodii
under aerobic conditions and reached the maximum activity when the cells entered the late exponential phase. The higher level of hydrogenase activity was accompanied by a greater abundance of the HynSL protein in the late-log or stationary phase. The addition of nickel to the growth medium significantly enhanced the hydrogenase activity. Ni treatment affected the level of the protein, but not the mRNA, indicating that the effect of Ni was exerted at the posttranscriptional level. Hydrogenase activity was distributed ∼30% in the membrane fraction and ∼70% in the cytoplasmic fraction. Thus, HynSL appears to be loosely membrane-bound. Partially purified
A. macleodii
hydrogenase demonstrated extraordinary stability. It retained 84% of its activity after exposure to 80°C for 2 h. After exposure to air for 45 days at 4°C, it retained nearly 100% of its activity when assayed under anaerobic conditions. Its catalytic activity in the presence of O
2
was evaluated by the hydrogen-deuterium (H-D) exchange assay. In 1% O
2
, 20.4% of its H-D exchange activity was retained. The great stability of HynSL makes it a potential candidate for biotechnological applications.
Naringenin Regulates Expression of Genes Involved in Cell Wall Synthesis inHerbaspirillum seropedicae
Authors: Tadra-Sfeir M. Z. , Souza E. M. , Faoro H. , Müller-Santos M. , Baura V. A. , Tuleski T. R. , Rigo L. U. , Yates M. G. , Wassem R. , Pedrosa F. O. , Monteiro R. A. 
Published: January 2011

ABSTRACTFive thousand mutants ofHerbaspirillum seropedicaeSmR1 carrying random insertions of transposon pTnMod-OGmKmlacZwere screened for differential expression of LacZ in the presence of naringenin. Among the 16 mutants whose expression was regulated by naringenin were genes predicted to be involved in the synthesis of exopolysaccharides, lipopolysaccharides, and auxin. These loci are probably involved in establishing interactions with host plants.