bluuebunny/crossref_metadata_2025 huggingface dataset:
Post‐Doctoral Researchers’ Conceptions of Research: A Metaphor Analysis
Authors: Pitcher Rod , Åkerlind Gerlese S.
Published: January 2011

This paper uses the analysis of metaphors to study the conceptions of research held by a sample of post‐doctoral researchers at five Australian universities. It is based on an analysis of the metaphors the researchers use in describing their research. The study produced four concepts that we have labelled “research is explorative”, “research is spatial”, “research is constructive” and “research is organic”. This study is unusual in its focus on post‐doctoral researchers and the use of metaphors to identify their conceptions of research. The primary aim of the study was to produce a view of post‐doctoral researchers conceptions of research. A secondary aim was to demonstrate the usefulness and effectiveness of metaphor analysis as a method of studying those conceptions of research. The study achieves both of those aims.
Beyond research skills training: an opportunity to support the wider “ecosystem” of the part‐time research student
Authors: Edwards Carol
Published: January 2011

This paper presents the findings from a UK study of one hundred part‐time research students. The participants were students attending one of a series of training days provided specifically for part‐time research students. Free text responses were collected on: what it’s like being a part‐time research student; what they would like from training events; and what they thought of this series of training days. The students were particularly appreciative of the opportunity to meet fellow part‐time research students, albeit in different disciplines and at different stages of their PhD. Rather than solely listing specific research skills they would like covered, most of their ideas for future training sessions concerned more nebulous personal and emotional aspects of the experience of studying for a PhD on a part‐time basis. Four dimensions of training need were identified: research techniques; research skills; engagement with the part‐time PhD process; and engagement with their part‐time peers. It is suggested that research training involving part‐time research students, could usefully build in time to focus explicitly on some aspect(s) of the more personal and emotional elements of the parttime doctoral experience, as well as on technical aspects of research work.
Application of grey theory approach to evaluation of organizational vision
Authors: Rahimnia Fariborz , Moghadasian Mahdi , Mashreghi Ebrahim
Published: January 2011

Purpose

The purpose of the paper is to propose a quantitative approach for assessing the qualitative nature of organizational vision.

Design/methodology/approach

The paper uses grey systems method to rank and evaluate the vision of five top‐ranked universities.

Findings

It is shown in the literature that qualitative consideration of organizational vision can be quantified using a mathematical method. This method can be used as a decision‐making tool where the judgments of the decision maker are not exact.

Originality/value

This study expresses the qualitative nature of organizational vision into a quantified shape. It does it through a mathematical method called “grey systems theory”. Moreover, it seems that the application of grey systems theory to the business context has rarely been examined.
Reliability of operations of grey numbers using kernels
Authors: Yang Yingjie , Liu Si‐feng
Published: January 2011

Purpose

The purpose of this paper is to advance new rules about operations of grey numbers based on kernels and greyness and analyze the reliability of these new operations.

Design/methodology/approach

A grey number is usually represented as a closed interval or a discrete set of numbers. Based on the definition of traditional grey number, novel rules that grey numbers can be represented as their kernels and associated degrees of greyness are proposed. In new rules, the operation between kernels of grey numbers has significance in the application of grey numbers. The reliability of operations of grey numbers using their kernels and the degrees of greyness derived from kernel operations and their corresponding interval operations are studied.

Findings

The results show that the novel rules about operation of grey numbers satisfy to the concept of grey system properly. It is useful to calculate the grey degree of grey numbers and the process of calculating is easier than traditional operation rules.

Practical implications

The method exposed in the paper can be used to calculate each two grey numbers. The grey degree and the calculating results of two grey numbers can be given out easily. The method can also be used to calculate grey numbers more than two.

Originality/value

The paper succeeds in constructing novel operation rules of grey numbers. The reliability of novel operation rules is studied and it is new development of grey systems theory, undoubtedly.
p‐Moment exponential robust stability of grey neutral stochastic delay systems
Authors: Su Chunhua
Published: January 2011

Purpose

The purpose of this paper is to obtain the criteria of p‐moment exponential robust stability for a class of grey neutral stochastic delay systems.

Design/methodology/approach

By constructing a Lyapunov‐Krasovskii functional and employing the decomposition technique of continuous matrix‐covered sets of grey matrix and using three key inequalities, the paper investigates the p‐moment exponential robust stability for a class of grey neutral stochastic delay systems. A numeric example is given to demonstrate the effectiveness of the criteria presented in the paper.

Findings

The results not only can be used to judge the p‐moment exponential robust stability of the systems researched in the paper, but also can be applied in the stability analysis of grey non‐neutral stochastic systems.

Practical implications

The method exposed in the paper can be used in the analysis and designation of practical stochastic control systems.

Originality/value

The paper succeeds in obtaining the criteria of p‐moment exponential robust stability for grey neutral stochastic delay systems by constructing a Lyapunov‐Krasovskii functional and employing the decomposition technique of continuous matrix‐covered sets of grey matrix and using three key inequalities.
Research on generalized non‐equidistance GM(1,1) model based on matrix analysis
Authors: Xiao Xinping , Peng Kunkun
Published: January 2011

Purpose

The purpose of this paper is to establish a new model for non‐equidistance sequence and research affine properties of the new model.

Design/methodology/approach

Generalized non‐equidistance GM(1,1) model is put forward based on generalized accumulated generating operation (AGO) theory, and particle swarm optimization is used to solve the parameters of the new model, then affine properties of the new model are researched based on matrix analysis.

Findings

The results are convincing: the simulation and prediction precisions of generalized non‐equidistance GM(1,1) model are raised greatly, and it is proved that the affine transformation sequence has the same simulative accuracy with the raw sequence for generalized non‐equidistance GM(1,1) model.

Practical implications

The method exposed in the paper can be used to model and predict for non‐equidistance sequence in the practical problem.

Originality/value

The paper succeeds in establishing a new non‐equidistance grey model and obtaining the affine properties of generalized non‐equidistance GM(1,1) model.
Research on location‐routing problem of reverse logistics with grey recycling demands based on PSO
Authors: Liu Hong , Zhang Qishan , Wang Wenping
Published: January 2011

Purpose

The purpose of this paper is to realize a location‐routing network optimization in reverse logistics (RL) using grey systems theory for uncertain information.

Design/methodology/approach

There is much uncertain information in network optimization and location‐routing problem (LRP) of RL, including fuzzy information, stochastic information and grey information, etc. Fuzzy information and stochastic information have been studied in logistics, however grey information of RL has not been covered. In the LRP of RL, grey recycling demands are taken into account. Then, a mathematics model with grey recycling demands has been constructed, and it can be transformed into grey chance‐constrained programming (GCCP) model, grey simulation and a proposed hybrid particle swarm optimization (PSO) are combined to resolve it. An example is also computed in the last part of the paper.

Findings

The results are convincing: not only that grey system theory can be used to deal with grey uncertain information about location‐routing problem of RL, but GCCP, grey simulation and PSO can be combined to resolve the grey model.

Practical implications

The method exposed in the paper can be used to deal with location‐routing problem with grey recycling information in RL, and network optimization result with grey uncertain factor could be helpful for logistics efficiency and practicability.

Originality/value

The paper succeeds in realising both a constructed model about location‐routing of RL with grey recycling demands and a solution algorithm about grey mathematics model by using one of the newest developed theories: grey systems theory.
The cell cycle regulator Cdh1 controls the pool sizes of hematopoietic stem cells and mature lineage progenitors by protecting from genotoxic stress
Authors: Ishizawa Jo , Kuninaka Shinji , Sugihara Eiji , Naoe Hideaki , Kobayashi Yusuke , Chiyoda Tatsuyuki , Ueki Arisa , Araki Kimi , Yamamura Ken‐ichi , Matsuzaki Yumi , Nakajima Hideaki , Ikeda Yasuo , Okamoto Shinichiro , Saya Hideyuki
Published: January 2011

Various key cell cycle components, especially G0/G1 regulators, have effects not only on cell proliferation but also on cell differentiation. Cdh1, one of the co‐activators that maintain anaphase‐promoting complex/cyclosome activity, plays a crucial role in the mitotic phase, but has recently been identified as a G0/G1 regulator, suggesting that the role of Cdh1 in cell differentiation. Here, we generated Cdh1 conditional gene‐trap mice to examine Cdh1 functions in adult tissues by overcoming the embryonic lethality of Cdh1 homozygous gene‐trap mice. We focused on the hematopoietic system and found that Cdh1‐deficient mice exhibited a general decrease in mature lineage progenitor cells and a significant increase in short‐term hematopoietic stem cells. This phenomenon became conspicuous by irradiation shortly after Cdh1 downregulation, suggesting that Cdh1 regulates the pool sizes of the hematopoietic stem cells and mature lineage progenitor cells by protecting cells from genotoxic stress. We also found that the irradiation‐induced G2/M checkpoint was defective in Cdh1‐deficient BM cells, causing the loss of stem/progenitor cells. This is the first report revealing Cdh1 function in adult hematopoiesis and showing a role of Cdh1 in a G2/M checkpoint regulation in vivo. (Cancer Sci 2011; 102: 967–974)
Intraspecific specialization of the generalist parasitoid Cotesia sesamiae revealed by polyDNAvirus polymorphism and associated with different Wolbachia infection
Authors: BRANCA ANTOINE , LE RU BRUNO PIERRE , VAVRE FABRICE , SILVAIN JEAN‐FRANÇOIS , DUPAS STÉPHANE
Published: January 2011

As a result of an intense host–parasite evolutionary arms race, parasitic wasps frequently display high levels of specialization on very few host species. For instance, in braconid wasps very few generalist species have been described. However, within this family, Cotesia sesamiae is a generalist species that is widespread in sub‐Saharan Africa and develops on several lepidopteran hosts. In this study, we tested the hypothesis that C. sesamiae may be a cryptic specialist when examined at the intraspecific level. We sequenced exon 2 of CrV1, a gene of the symbiotic polyDNAvirus that is integrated into the wasp genome and is associated with host immune suppression. We found that CrV1 genotype was more closely associated with the host in which the parasitoid developed than any abiotic environmental factor tested. We also tested a correlation between CrV1 genotype and an infection with Wolbachia bacteria, which are known for their ability to induce reproductive isolation. The Wolbachia bacteria infection polymorphism was also found as a major factor explaining the genetic structure of CrV1, and, in addition, the best model explaining CrV1 genetic structure involved an interaction between Wolbachia infection and host species. We suggest that Wolbachia could act as an agent capable of maintaining advantageous alleles for host specialization in different populations of C. sesamiae. This mechanism could be applicable to other insect models because of the high prevalence of Wolbachia in insects.
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

Our 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

Mycoheterotrophic 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

The 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

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

Changes 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

Cytokinin (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

To 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)

The 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.

Leptin 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.

Recent 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

Vitamin 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

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

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

Five 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.
Shifting the Fermentative/Oxidative Balance in
Saccharomyces cerevisiae
by Transcriptional Deregulation of Snf1 via Overexpression of the Upstream Activating Kinase Sak1p
Authors: Raab Andreas M. , Hlavacek Verena , Bolotina Natalia , Lang Christine
Published: January 2011

With the aim to reduce fermentation by-products and to promote respiratory metabolism by shifting the fermentative/oxidative balance, we evaluated the constitutive overexpression of the
SAK1
and
HAP4
genes in
Saccharomyces cerevisiae
. Sak1p is one of three kinases responsible for the phosphorylation, and thereby the activation, of the Snf1p complex, while Hap4p is the activator subunit of the Hap2/3/4/5 transcriptional complex. We compared the physiology of a
SAK1
-overexpressing strain with that of a strain overexpressing the
HAP4
gene in wild-type and
sdh2
deletion (respiratory-deficient) backgrounds. Both
SAK1
and
HAP4
overexpressions led to the upregulation of glucose-repressed genes and to reduced by-product formation rates (ethanol and glycerol).
SAK1
overexpression had a greater impact on growth rates than did
HAP4
overexpression. Elevated transcript levels of
SAK1
, but not
HAP4
, resulted in increased biomass yields in batch cultures grown on glucose (aerobic and excess glucose) as well as on nonfermentable carbon sources.
SAK1
overexpression, but not the combined overexpression of
SAK1
and
HAP4
or the overexpression of
HAP4
alone, restored growth on ethanol in an
sdh2
deletion strain. In glucose-grown shake flask cultures, the
sdh2
deletion strain with
SAK1
and
HAP4
overexpression produced succinic acid at a titer of 8.5 g liter
−1
and a yield of 0.26 mol (mol glucose)
−
1
within 216 h. We here report for the first time that a constitutively high level of expression of
SAK1
alleviates glucose repression and shifts the fermentative/oxidative balance under both glucose-repressed and -derepressed conditions.
Single-Nucleotide-Polymorphism Genotyping ofCoxiella burnetiiduring a Q Fever Outbreak in The Netherlands
Authors: Huijsmans Cornelis J. J. , Schellekens Jeroen J. A. , Wever Peter C. , Toman Rudolf , Savelkoul Paul H. M. , Janse Ingmar , Hermans Mirjam H. A.
Published: January 2011

Coxiella burnetiiis the etiological agent of Q fever. Currently, the Netherlands is facing the largest Q fever epidemic ever, with almost 4,000 notified human cases. Although the presence of a hypervirulent strain is hypothesized, epidemiological evidence, such as the animal reservoir(s) and genotype of theC. burnetiistrain(s) involved, is still lacking. We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. Ten discriminatory SNPs were carefully selected and detected by real-time PCR. SNP genotyping appeared to be highly suitable for discrimination ofC. burnetiistrains and easy to perform with clinical samples. With this new method, we show that the Dutch outbreak is caused by at least 5 differentC. burnetiigenotypes. SNP typing of 14 human samples from the outbreak revealed the presence of 3 dissimilar genotypes. Two genotypes were also present in livestock at 9 farms in the outbreak area. SNP analyses of bulk milk from 5 other farms, commercial cow milk, and cow colostrum revealed 2 additional genotypes that were not detected in humans. SNP genotyping data from clinical samples clearly demonstrate that at least 5 differentC. burnetiigenotypes are involved in the Dutch outbreak.
Prevalence and Genetic Diversity of Aichi Viruses in Wastewater and River Water in Japan
Authors: Kitajima Masaaki , Haramoto Eiji , Phanuwan Chanetta , Katayama Hiroyuki
Published: January 2011

Aichi virus (AiV) genomes were detected in 12 (100%) influent and 11 (92%) effluent wastewater and 36 (60%) river water samples. Among 260 strains identified, 255 were genotype A and 5 were genotype B. This is the first report describing the molecular characterization of AiVs in aquatic environments in Japan.
Cupriavidus taiwanensis
Bacteroids in
Mimosa pudica
Indeterminate Nodules Are Not Terminally Differentiated
Authors: Marchetti Marta , Catrice Olivier , Batut Jacques , Masson-Boivin Catherine
Published: January 2011

The beta-rhizobium
Cupriavidus taiwanensis
forms indeterminate nodules on
Mimosa pudica. C. taiwanensis
bacteroids resemble free-living bacteria in terms of genomic DNA content, cell size, membrane permeability, and viability, in contrast to bacteroids in indeterminate nodules of the galegoid clade. Bacteroid differentiation is thus unrelated to nodule ontogeny.
Ecophysiology of Uncultured Filamentous Anaerobes Belonging to the Phylum KSB3 That Cause Bulking in Methanogenic Granular Sludge
Authors: Yamada Takeshi , Kikuchi Kae , Yamauchi Toshihiro , Shiraishi Koji , Ito Tsukasa , Okabe Satoshi , Hiraishi Akira , Ohashi Akiyoshi , Harada Hideki , Kamagata Yoichi , Nakamura Kazunori , Sekiguchi Yuji
Published: January 2011

A filamentous bulking of a methanogenic granular sludge caused by uncultured filamentous bacteria of the candidate phylum KSB3 in an upflow anaerobic sludge blanket (UASB) system has been reported. To characterize the physiological traits of the filaments, a polyphasic approach consisting of rRNA-based activity monitoring of the KSB3 filaments using the RNase H method and substrate uptake profiling using microautoradiography combined with fluorescencein situhybridization (MAR-FISH) was conducted. On the basis of rRNA-based activity, the monitoring of a full-scale UASB reactor operated continuously revealed that KSB3 cells became active and predominant (up to 54% of the total 16S rRNA) in the sludge when the carbohydrate loading to the system increased. Batch experiments with a short incubation of the sludge with maltose, glucose, fructose, and maltotriose at relatively low concentrations (approximately 0.1 mM) in the presence of yeast extract also showed an increase in KSB3 rRNA levels under anaerobic conditions. MAR-FISH confirmed that the KSB3 cells took up radioisotopic carbons from [14C]maltose and [14C]glucose under the same incubation conditions in the batch experiments. These results suggest that one of the important ecophysiological characteristics of KSB3 cells in the sludge is carbohydrate degradation in wastewater and that high carbohydrate loadings may trigger an outbreak of KSB3 bacteria, causing sludge bulking in UASB systems.
Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples
Authors: van den Bogert Bartholomeus , de Vos Willem M. , Zoetendal Erwin G. , Kleerebezem Michiel
Published: January 2011

Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of
Actinobacteria
strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the
Veillonella
group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice.
Mutational Analysis of Residues in the Helical Region of the Class IIa Bacteriocin Pediocin PA-1
Authors: Haugen Helén Sophie , Fimland Gunnar , Nissen-Meyer Jon
Published: January 2011

A 15-mer fragment that is derived from the helical region in the C-terminal half of pediocin PA-1 inhibited the activity of pediocin PA-1. Of 13 other pediocin-like (hybrid) bacteriocins, only the hybrid bacteriocin Sak/Ped was markedly inhibited by the 15-mer fragment. Sak/Ped was the only one of these bacteriocins that had a sequence (in the C-terminal helix-containing half) identical to that of the 15-mer fragment, indicating that the fragment inhibits pediocin-like bacteriocins in a sequence-dependent manner. By replacing (one at a time) all 15 residues in the fragment with Ala or Leu, five residues (K1, A2, T4, N8, and A15) were identified as being especially important for the inhibitory action of the fragment. The results suggest that the corresponding residues (K20, A21, T23, N27, and A34, respectively) in pediocin PA-1 might be involved in interactions between pediocin PA-1 and its receptor. To characterize the environment surrounding these five residues when pediocin PA-1 interacts with target cells, these residues were replaced (one at a time) with a hydrophobic large (Leu) residue, a hydrophilic charged (Asp or Arg) residue, and a small (Ala or Gly) residue. The results revealed that residues A21 and A34 are in a spatially constrained environment, since the replacement with a small (Gly) residue was the only substitution that did not markedly reduce the bacteriocin activity. The positive charge in K20 and the polar amide group in N27 appeared to interact with electronegative groups, since the replacement of these two residues with a positive (Arg) residue was well tolerated, while replacement with a negative (Asp) residue was detrimental to the bacteriocin activity. K20 was in a less constrained environment than N27, since the replacement of K20 with a large hydrophobic (Leu) residue was tolerated fairly well and to a greater extent than N27. T23 seemed to be in an environment that was not restricted with respect to size, polarity, and charge, since replacements with large (Leu) and small (Ala) hydrophobic residues and a hydrophilic negative (Asp) residue were tolerated fairly well (2- to 6-fold reduction in activity). Moreover, the replacement of T23 with a large positive (Arg) residue resulted in wild-type or better-than-wild-type activity.