bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary advantages of secreted peptide signalling molecules in plants
Authors: Wheeler Janet I. , Irving Helen R.
Published: April 2010

Peptide signalling molecules create diverse modular signals in animal systems, but it is only relatively recently that an expanding array of peptide signalling groups has been identified in plants. Representatives occur in moss although most are in angiosperms (both monocot and dicot) including many agronomically important crops. Some groups show high diversity within a species, whereas other peptide signalling groups are small or represented by a single peptide or only found in a single family of plants. Plant peptide signals regulate meristem organogenesis and growth, modulate plant homeostasis and growth, and recognise damage or imminent danger from pathogen attack. The peptide signalling molecules are secreted into the apoplast where they are often further proteolytically processed before acting on receptors in nearby or adjacent cells with all the hallmarks of paracrine molecules. Where the receptors have been identified, they are receptor-like kinases that form oligomers upon peptide binding and relay messages via phosphorylation cascades. The use of nitrogen rich amino acids in the signalling peptides was analysed and nitrogen scores were obtained that are higher than the mean nitrogen score for the overall average of the Arabidopsis proteome. These findings are discussed in terms of nutritional availability and energy use.
Proton-transfer and hydrogen-bond interactions determine fluorescence quantum yield and photochemical efficiency of bacteriophytochrome
Authors: Toh K. C. , Stojković Emina A. , van Stokkum Ivo H. M. , Moffat Keith , Kennis John T. M.
Published: May 2010

Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C15═C16 double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important new development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Here we report that an unusual Bph, RpBphP3 from
Rhodopseudomonas palustris
, denoted P3, is fluorescent. This Bph modulates synthesis of light-harvesting complex in combination with a second Bph exhibiting classical photochemistry, RpBphP2, denoted P2. We identify the factors that determine the fluorescence and isomerization quantum yields through the application of ultrafast spectroscopy to wild-type and mutants of P2 and P3. The excited-state lifetime of the biliverdin chromophore in P3 was significantly longer at 330–500 ps than in P2 and other classical phytochromes and accompanied by a significantly reduced isomerization quantum yield. H/D exchange reduces the rate of decay from the excited state of biliverdin by a factor of 1.4 and increases the isomerization quantum yield. Comparison of the properties of the P2 and P3 variants shows that the quantum yields of fluorescence and isomerization are determined by excited-state deprotonation of biliverdin at the pyrrole rings, in competition with hydrogen-bond rupture between the D-ring and the apoprotein. This work provides a basis for structure-based conversion of Bph into an efficient near-IR fluorescent marker.
Expression of the yeast NADH dehydrogenase Ndi1 in
Drosophila
confers increased lifespan independently of dietary restriction
Authors: Sanz Alberto , Soikkeli Mikko , Portero-Otín Manuel , Wilson Angela , Kemppainen Esko , McIlroy George , Ellilä Simo , Kemppainen Kia K. , Tuomela Tea , Lakanmaa Matti , Kiviranta Essi , Stefanatos Rhoda , Dufour Eric , Hutz Bettina , Naudí Alba , Jové Mariona , Zeb Akbar , Vartiainen Suvi , Matsuno-Yagi Akemi , Yagi Takao , Rustin Pierre , Pamplona Reinald , Jacobs Howard T.
Published: May 2010

Mutations in mitochondrial oxidative phosphorylation complex I are associated with multiple pathologies, and complex I has been proposed as a crucial regulator of animal longevity. In yeast, the single-subunit NADH dehydrogenase Ndi1 serves as a non-proton-translocating alternative enzyme that replaces complex I, bringing about the reoxidation of intramitochondrial NADH. We have created transgenic strains of
Drosophila
that express yeast
NDI1
ubiquitously. Mitochondrial extracts from
NDI1
-expressing flies displayed a rotenone-insensitive NADH dehydrogenase activity, and functionality of the enzyme in vivo was confirmed by the rescue of lethality resulting from RNAi knockdown of complex I.
NDI1
expression increased median, mean, and maximum lifespan independently of dietary restriction, and with no change in sirtuin activity.
NDI1
expression mitigated the aging associated decline in respiratory capacity and the accompanying increase in mitochondrial reactive oxygen species production, and resulted in decreased accumulation of markers of oxidative damage in aged flies. Our results support a central role of mitochondrial oxidative phosphorylation complex I in influencing longevity via oxidative stress, independently of pathways connected to nutrition and growth signaling.
Ecosystem-based fisheries management requires a change to the selective fishing philosophy
Authors: Zhou Shijie , Smith Anthony D. M. , Punt André E. , Richardson Anthony J. , Gibbs Mark , Fulton Elizabeth A. , Pascoe Sean , Bulman Catherine , Bayliss Peter , Sainsbury Keith
Published: May 2010

Globally, many fish species are overexploited, and many stocks have collapsed. This crisis, along with increasing concerns over flow-on effects on ecosystems, has caused a reevaluation of traditional fisheries management practices, and a new ecosystem-based fisheries management (EBFM) paradigm has emerged. As part of this approach, selective fishing is widely encouraged in the belief that nonselective fishing has many adverse impacts. In particular, incidental bycatch is seen as wasteful and a negative feature of fishing, and methods to reduce bycatch are implemented in many fisheries. However, recent advances in fishery science and ecology suggest that a selective approach may also result in undesirable impacts both to fisheries and marine ecosystems. Selective fishing applies one or more of the “6-S” selections: species, stock, size, sex, season, and space. However, selective fishing alters biodiversity, which in turn changes ecosystem functioning and may affect fisheries production, hindering rather than helping achieve the goals of EBFM. We argue here that a “balanced exploitation” approach might alleviate many of the ecological effects of fishing by avoiding intensive removal of particular components of the ecosystem, while still supporting sustainable fisheries. This concept may require reducing exploitation rates on certain target species or groups to protect vulnerable components of the ecosystem. Benefits to society could be maintained or even increased because a greater proportion of the entire suite of harvested species is used.
Protein dynamics investigated by inherent structure analysis
Authors: Rao Francesco , Karplus Martin
Published: May 2010

Molecular dynamics (MD) simulations provide essential information about the thermodynamics and dynamics of proteins. To construct the free-energy surface from equilibrium trajectories, it is necessary to group the individual snapshots in a meaningful way. The inherent structures (IS) are shown to provide an appropriate discretization of the trajectory and to avoid problems that can arise in clustering algorithms that have been employed previously. The IS-based approach is illustrated with a 30-ns room temperature “native” state MD simulation of a 10-residue peptide in a β-hairpin conformation. The transitions between the IS are used to construct a configuration space network from which a one-dimensional free-energy profile is obtained with the mincut method. The results demonstrate that the IS approach is useful and that even for this simple system, there exists a nontrivial organization of the native state into several valleys separated by barriers as high as 3 kcal/mol. Further, by introducing a coarse-grained network, it is demonstrated that there are multiple pathways connecting the valleys. This scenario is hidden when the snapshots of the trajectory are used directly with rmsd clustering to compute the free-energy profile. Application of the IS approach to the native state of the PDZ2 signaling domain indicates its utility for the study of biologically relevant systems.
Facilitating Recycling: Reverse—Distribution Channel Design for Participation and Support
Authors: Thøgersen John
Published: April 2010

While social change research designed to promote recycling has increased rapidly in recent years, empirical documentation of the importance and effectiveness of distribution channel management for enhancing public support and participation is lacking. In this paper, it is argued mat the design of reverse distribution channels for recyclables influences support and participation through at least three distinct mechanisms:

• it influences attitudes and behavior by affecting the perceived costs of recycling; • it influences behavior by affecting the opportunities for acting on recycling intentions, and; • it has the potential for improving attitudes (through dissonance reduction, attribution, and adjusting faulty cost expectations) through inducing trial.

The importance of channel design characteristics through these three mechanisms is illustrated by the results from a continuing research program aimed at boosting the recycling of household waste in Denmark.
Small Charities, Market Orientation, and the Decision to Engage an Advertising Agency
Authors: Bennett Roger
Published: April 2010

A mail survey of 747 small to medium sized charities in the United Kingdom (UK) revealed that 123 of 344 respondents employed a conventional advertising agency (as opposed to a public relations consultant, direct marketing agency or other type of marketing services firm) and that 134 claimed that they completed all aspects of the marketing function in-house. The remainder used a variety of forms of outside help with their advertising and marketing campaigns. Respondents were contacted again by letter and (if necessary) telephone and requested to complete an adaptation of Kohli et al.'s (1993) MARKOR instrument (a set of questions designed to establish the extent of market orientation within organizations). Outcomes were factor analyzed, and significant dimensions of market orientation utilized as independent variables (with others) in a logistic regression that had the state variable 1 = Employs an advertising agency; 0 = Does not employ an agency, as the variable to be explained. Results indicated that key elements of market orientation critically determined small to medium sized charities' (SMC's) decisions to engage advertising agencies. Overall, it seemed that the importance of effective marketing was widely recognized by SMCs.
Marketing Enlightened Self-Interest: A Model of Individual and Community-Oriented Motivations
Authors: Tyson Ben , Coulter Robin
Published: April 2010

What motivates people to act in the community's interest when self-interest is an insufficient motivation?

In response, this paper proposes a model for predicting behavioral intentions that incorporates an individual's perceived threats to one's self and to one's community, perceived individual and community benefits/consequences of engaging in behaviors that will facilitate desired outcomes, and self-efficacy.

We test the model in three contexts related to environmental conservation and find substantial support for our model. Findings have implications for social marketing of environmental behaviors and may prove relevant when considering behavior supportive of other community-oriented issues such as public health, education, and transportation.
An Introduction to Some Philosophies Relevant to the Ethical Management of Public Health and Social Issues
Authors: Rothschild Michael L.
Published: April 2010

Most societies attempt to manage at least some of the behaviors of at least some of their citizens. To accomplish this, they have at hand the tool sets of education, marketing and law. This presentation. presents a theoretic base for the consideration of ethical behavior management. To that end, it considers a number of well-reasoned moral and political philosophy literatures, and what they might contribute to social marketing.

Utilitarianism calls for the greatest good for the greatest number and suggests that the ends justify the means. Liberalism calls for a focus on individual rights and personal freedoms. Contextualism raises issues about these other philosophies by asking questions about: their meaning in a specific time and place; here, ethicality is judged in the framework of the customs of the culture.
Benefits, Barriers and Enablers of University—Community Research Collaboration: Input from Health and Social Service Agencies
Authors: Sullivan Myrtis , Balch George , Cramer Lina , Willis Marilyn , Chavez Noel
Published: April 2010

Increasingly, it has become clear to social marketers and others that partnerships among organizations are needed to accomplish behavior change and achieve social objectives. While many still take an organization- centered approach, there has been a marked increase in the number of community-based collaborative research endeavors connecting academics and community agencies in mutual investigation of salient problems.

Currently, much of the literature on these efforts is reported by academicians and reflects their perspectives or perceptions of agency viewpoints. More input is needed from the agency perspective to ensure a more balanced understanding of the significant role community partners play in the development and implementation of research that leads to improved health status of communities and other social objectives.

To this end, focus groups were conducted to give community-based agencies the opportunity to share their insights and give their perspective regarding the benefits and barriers to effective collaboration. Representatives of agencies from the Chicago area with experience in collaborative research participated, and results were reviewed and corroborated by additional community agencies.

The most common benefits sought by agencies were evaluation and needs assessment. Participants cite the failure of researchers and agencies to take the time to understand and try to meet each other's needs as the main barrier to effective collaborative efforts.
Model-based analyses: Promises, pitfalls, and example applications to the study of cognitive control
Authors: Mars Rogier B. , Shea Nicholas J. , Kolling Nils , Rushworth Matthew F. S.
Published: May 2010

We discuss a recent approach to investigating cognitive control, which has the potential to deal with some of the challenges inherent in this endeavour. In a model-based approach, the researcher defines a formal, computational model that performs the task at hand and whose performance matches that of a research participant. The internal variables in such a model might then be taken as proxies for latent variables computed in the brain. We discuss the potential advantages of such an approach for the study of the neural underpinnings of cognitive control and its pitfalls, and we make explicit the assumptions underlying the interpretation of data obtained using this approach.
Perceptual Cues in Nonverbal Vocal Expressions of Emotion
Authors: Sauter Disa A. , Eisner Frank , Calder Andrew J. , Scott Sophie K.
Published: May 2010

Work on facial expressions of emotions (Calder, Burton, Miller, Young, & Akamatsu, [2001]) and emotionally inflected speech (Banse & Scherer, [1996]) has successfully delineated some of the physical properties that underlie emotion recognition. To identify the acoustic cues used in the perception of nonverbal emotional expressions like laugher and screams, an investigation was conducted into vocal expressions of emotion, using nonverbal vocal analogues of the “basic” emotions (anger, fear, disgust, sadness, and surprise; Ekman & Friesen, [1971]; Scott et al., [1997]), and of positive affective states (Ekman, [1992], [2003]; Sauter & Scott, [2007]). First, the emotional stimuli were categorized and rated to establish that listeners could identify and rate the sounds reliably and to provide confusion matrices. A principal components analysis of the rating data yielded two underlying dimensions, correlating with the perceived valence and arousal of the sounds. Second, acoustic properties of the amplitude, pitch, and spectral profile of the stimuli were measured. A discriminant analysis procedure established that these acoustic measures provided sufficient discrimination between expressions of emotional categories to permit accurate statistical classification. Multiple linear regressions with participants’ subjective ratings of the acoustic stimuli showed that all classes of emotional ratings could be predicted by some combination of acoustic measures and that most emotion ratings were predicted by different constellations of acoustic features. The results demonstrate that, similarly to affective signals in facial expressions and emotionally inflected speech, the perceived emotional character of affective vocalizations can be predicted on the basis of their physical features.
Animal Identification and Tracing in the United States
Authors: Pendell Dustin L. , Brester Gary W. , Schroeder Ted C. , Dhuyvetter Kevin C. , Tonsor Glynn T.
Published: May 2010

We examine the impacts of adopting animal identification and tracing systems on the U.S. meat and livestock industry. Using a multimarket equilibrium displacement model, we find that a modest increase in domestic demand for beef would offset the costs of an animal identification system. Similarly, an increase in beef export demand equivalent to Japan's beef export market share prior to the 2003 U.S. discovery of bovine spongiform encephalopathy would offset animal identification system costs.
The Genomedata format for storing large-scale functional genomics data
Authors: Hoffman Michael M. , Buske Orion J. , Noble William Stafford
Published: May 2010

Summary: We present a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. We have also developed utilities to load data into this format. We show that retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files.

Availability and Implementation: Reference implementation in Python and C components available at http://noble.gs.washington.edu/proj/genomedata/ under the GNU General Public License.

Contact:  william-noble@uw.edu
Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake
Authors: Hahn Martin W. , Lang Elke , Tarao Mitsunori , Brandt Ulrike
Published: May 2010

The heterotrophic, aerobic, facultatively anaerobic under denitrifying conditions, catalase- and oxidase-positive, non-motile strain MT-CBb6A5T, which was isolated from an acidic lake located in Wisconsin (USA), was characterized. The strain grew on NSY medium over a temperature range of 15–30 °C and a NaCl range of 0.0–0.3 % (w/v). The predominant fatty acids were C16 : 0, C18 : 1ω7c, 11-methyl C18 : 1ω7c, feature 3 (including C16 : 1ω7c), and feature 2 (including C14 : 0 3-OH). The DNA G+C content of the strain was 40.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene sequence similarity values with the two described species of the genus Polynucleobacter ranged from 95.6 to 96.0 %. The strain differs from the two described species of the genus Polynucleobacter in the ability to assimilate oxalic and glycolic acids, and in the presence of the fatty acids C15 : 1ω8c and C16 : 0 3-OH as well as in quantitative differences in fatty acid composition. It has to be assumed that the strain shares with other free-living bacteria of the genus Polynucleobacter a planktonic lifestyle in the water column of freshwater habitats. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from Polynucleobacter necessarius and Polynucleobacter cosmopolitanus, we propose to establish the novel species Polynucleobacter rarus sp. nov. with the type strain MT-CBb6A5T ( = DSM 21648T  = CIP 109928T).
Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil
Authors: Iguchi Hiroyuki , Yurimoto Hiroya , Sakai Yasuyoshi
Published: May 2010

A novel methanotroph, designated strain HT12T, was isolated from forest soil in Japan. Cells of strain HT12T were Gram-reaction-negative, aerobic, non-motile, coccoid and formed pale-brown colonies. The strain grew only with methane and methanol as sole carbon and energy sources. Cells grew at 5–34 °C (optimum 24–32 °C). The strain possessed both particulate and soluble methane monooxygenases and assimilated formaldehyde using the ribulose monophosphate pathway. The major cellular fatty acids were C16 : 0 (46.9 %) and C14 : 0 (34.2 %), whereas unsaturated C16 fatty acids, typical of type I methanotrophs, were absent. Comparative 16S rRNA gene sequence analysis showed that the most closely related strains were Methylosoma difficile LC 2T (93.1 % sequence similarity) and Methylobacter tundripaludum SV96T (92.6 % similarity). Phylogenetic analysis based on the pmoA gene indicated that strain HT12T formed a distinct lineage within the type I methanotrophs and analysis of the deduced pmoA amino acid sequence of strain HT12T showed that it had a 7 % divergence from that of its most closely related species. The DNA G+C content was 49.3 mol%. Based on this evidence, strain HT12T represents a novel species and genus of the family Methylococcaceae, for which the name Methylovulum miyakonense gen. nov., sp. nov. is proposed. The type strain of the type species is HT12T ( = NBRC 106162T  = DSM 23269T  = ATCC BAA-2070T).
Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaça fermentation process
Authors: Pereira Luciana Filgueira , Costa César Raimundo Lima , Brasileiro Bereneuza Tavares Ramos Valente , de Morais Marcos Antonio
Published: May 2010

In the present work, a novel ascomycete species, Lachancea mirantina sp. nov., isolated from the fermentation process that produces cachaça, a Brazilian spirit, is proposed. Nucleotide sequence analysis of the 26S D1/D2 rDNA locus showed that L. mirantina sp. nov. was genetically related to Lachancea cidri and Lachancea fermentati, although some physiological traits showed remarkable differences. Analysis of the D1/D2 large-subunit rDNA molecular marker showed a clear distinction among all three species, confirming that L. mirantina sp. nov. belongs to a separate taxonomic species in the Lachancea clade. The type strain of Lachancea mirantina sp. nov. is URM 5925T ( = CLIB 1160T  = CBS 11717T).
Agromyces tropicus sp. nov., isolated from soil
Authors: Thawai Chitti , Tanasupawat Somboon , Suwanborirux Khanit , Kudo Takuji
Published: May 2010

Two actinomycete strains, CM9-9T and AK2-48, which produced straight rod-shaped, non-motile cells, were isolated from soils in Chiang Mai and Phuket provinces, respectively, Thailand. The morphological and chemotaxonomic characteristics of the isolates coincided with those of the genus Agromyces. Phylogenetic analysis using 16S rRNA gene sequences also indicated that the isolates were clearly separated from their closest relative, Agromyces aurantiacus YIM 21741T, and should be classified in the genus Agromyces. Furthermore, a combination of DNA–DNA hybridization results and physiological and biochemical properties indicated that the isolates could be distinguished from all recognized members of the genus Agromyces. The isolates therefore represent a novel species, for which the name Agromyces tropicus sp. nov. is proposed. The type strain is CM9-9T (=JCM 15672T =BCC 34764T).
Nonomuraea endophytica sp. nov., an endophytic actinomycete isolated from Artemisia annua L.
Authors: Li Jie , Zhao Guo-Zhen , Huang Hai-Yu , Zhu Wen-Yong , Lee Jae-Chan , Xu Li-Hua , Kim Chang-Jin , Li Wen-Jun
Published: May 2010

A Gram-stain-positive, aerobic, non-motile actinomycete strain, designated YIM 65601T, was studied by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM 65601T should be assigned to the genus Nonomuraea, with highest 16S rRNA gene sequence similarities to Nonomuraea candida HMC10T (98.8 %), N. salmonea DSM 43678T (98.7 %), N. turkmeniaca DSM 43926T (98.5 %), N. roseola DSM 43767T (98.4 %), N. dietziae IFO 14309T (98.2 %) and N. kuesteri GW 14-1925T (98.1 %). 16S rRNA gene sequence similarities to strains of other Nonomuraea species were below 98.0 %. Morphological and chemotaxonomic properties of the isolate were consistent with those of members of the genus Nonomuraea. The results of DNA–DNA hybridization and physiological and biochemical tests and fatty acid profiles allowed genotypic and phenotypic differentiation of strain YIM 65601T from closely related species. Thus, YIM 65601T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea endophytica sp. nov. is proposed, with YIM 65601T ( = CCTCC AA 209037T  = DSM 45385T) as the type strain.
Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa
Authors: Kraatz Mareike , Wallace R. John , Svensson Liselott
Published: May 2010

Strain A2 is an anaerobic, variably Gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of ‘Olsenella (basonym Atopobium) oviles’. Three phenotypically similar bacterial strains (lac15, lac16 and lac31T) were isolated in concert with Veillonella magna lac18T from the mucosal jejunum of a pig. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strains A2, lac15, lac16 and lac31T formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella–Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31T were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA–DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31T represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31T ( = CCUG 58604T  = DSM 22620T  = JCM 16156T) as the type strain and A2 ( = CCUG 58212  = DSM 22619  = JCM 16157) as an additionally available reference strain. Also, based on our data, we propose emended descriptions of the genus Olsenella and the species Olsenella uli and Olsenella profusa.
Longispora fulva sp. nov., isolated from a forest soil, and emended description of the genus Longispora
Authors: Shiratori-Takano Hatsumi , Yamada Koji , Beppu Teruhiko , Ueda Kenji
Published: May 2010

A novel actinomycete, strain KZ0017T, was isolated from a forest soil collected in Ohnuma, Fukushima, Japan. Strain KZ0017T formed spore chains borne on top of short sporophores arising from vegetative hyphae. Spores were non-motile and cylindrical with smooth surfaces. Strain KZ0017T contained meso-diaminopimelic (A2pm) acid, 3-OH A2pm, d-glutamic acid, glycine and l-alanine in the cell-wall peptidoglycan, and xylose, mannose, galactose, rhamnose and ribose in cell-wall hydrolysates. The acyl type of the cell-wall polysaccharides was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and several unknown lipids and glycolipids. The major fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 70.7 mol%. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the single member of the genus Longispora in the family Micromonosporaceae. On the basis of morphological, chemotaxonomic and phylogenetic properties, strain KZ0017T represents a novel species of the genus Longispora, for which the name Longispora fulva sp. nov. is proposed; the type strain is KZ0017T ( = NBRC 105670T = DSM 45356T).
Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria
Authors: Hahn Martin W. , Lang Elke , Brandt Ulrike , Spröer Cathrin
Published: May 2010

The heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3T, isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0–0.3 % (w/v). Whole-cell fatty acids were dominated by C16 : 1ω7c (feature 3), C18 : 1ω7c and straight-chain C16 : 0; furthermore, the components C12 : 0 and C14 : 0 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8 %. DNA–DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3T ( = DSM 21994T  = CIP 110079T).
Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome
Authors: Schwaiger Michaela , Kohler Hubertus , Oakeley Edward J. , Stadler Michael B. , Schübeler Dirk
Published: May 2010

The replication of a chromosomal region during S phase can be highly dynamic between cell types that differ in transcriptome and epigenome. Early replication timing has been positively correlated with several histone modifications that occur at active genes, while repressive histone modifications mark late replicating regions. This raises the question if chromatin modulates the initiating events of replication. To gain insights into this question, we have studied the function of heterochromatin protein 1 (HP1), which is a reader of repressive methylation at histone H3 lysine 9, in genome-wide organization of replication. Cells with reduced levels of HP1 show an advanced replication timing of centromeric repeats in agreement with the model that repressive chromatin mediates the very late replication of large clusters of constitutive heterochromatin. Surprisingly, however, regions with high levels of interspersed repeats on the chromosomal arms, in particular on chromosome 4 and in pericentromeric regions of chromosome 2, behave differently. Here, loss of HP1 results in delayed replication. The fact that these regions are bound by HP1 suggests a direct effect. Thus while HP1 mediates very late replication of centromeric DNA, it is also required for early replication of euchromatic regions with high levels of repeats. This observation of opposing functions of HP1 suggests a model where HP1-mediated repeat inactivation or replication complex loading on the chromosome arms is required for proper activation of origins of replication that fire early. At the same time, HP1-mediated repression at constitutive heterochromatin is required to ensure replication of centromeric repeats at the end of S phase.
Characterization of the Branched-Chain Amino Acid Aminotransferase Enzyme Family in Tomato
Authors: Maloney Gregory S. , Kochevenko Andrej , Tieman Denise M. , Tohge Takayuki , Krieger Uri , Zamir Dani , Taylor Mark G. , Fernie Alisdair R. , Klee Harry J.
Published: May 2010

Branched-chain amino acids (BCAAs) are synthesized in plants from branched-chain keto acids, but their metabolism is not completely understood. The interface of BCAA metabolism lies with branched-chain aminotransferases (BCAT) that catalyze both the last anabolic step and the first catabolic step. In this study, six BCAT genes from the cultivated tomato (Solanum lycopersicum) were identified and characterized. SlBCAT1, -2, -3, and -4 are expressed in multiple plant tissues, while SlBCAT5 and -6 were undetectable. SlBCAT1 and -2 are located in the mitochondria, SlBCAT3 and -4 are located in chloroplasts, while SlBCAT5 and -6 are located in the cytosol and vacuole, respectively. SlBCAT1, -2, -3, and -4 were able to restore growth of Escherichia coli BCAA auxotrophic cells, but SlBCAT1 and -2 were less effective than SlBCAT3 and -4 in growth restoration. All enzymes were active in the forward (BCAA synthesis) and reverse (branched-chain keto acid synthesis) reactions. SlBCAT3 and -4 exhibited a preference for the forward reaction, while SlBCAT1 and -2 were more active in the reverse reaction. While overexpression of SlBCAT1 or -3 in tomato fruit did not significantly alter amino acid levels, an expression quantitative trait locus on chromosome 3, associated with substantially higher expression of Solanum pennellii BCAT4, did significantly increase BCAA levels. Conversely, antisense-mediated reduction of SlBCAT1 resulted in higher levels of BCAAs. Together, these results support a model in which the mitochondrial SlBCAT1 and -2 function in BCAA catabolism while the chloroplastic SlBCAT3 and -4 function in BCAA synthesis.
DAY NEUTRAL FLOWERING Represses CONSTANS to Prevent Arabidopsis Flowering Early in Short Days
Authors: Morris Karl , Thornber Sarah , Codrai Lesley , Richardson Christine , Craig Adam , Sadanandom Ari , Thomas Brian , Jackson Stephen
Published: May 2010

The photoperiodic response in Arabidopsis thaliana requires the precise regulation of CONSTANS (CO) expression in relation to the light period during the day. In short days (SDs) levels of CO expression are normally low during the light period, and this results in delayed flowering compared with long days (LDs) when CO expression rises to high levels before the end of the light period. We identified a novel flowering time gene called DAY NEUTRAL FLOWERING (DNF) that acts in the same flowering pathway as CO. DNF is a membrane-bound E3 ligase that represses CO expression and plays an important role in maintaining low levels of CO expression in SDs. The effect of DNF on the rhythm of CO expression is essential for the photoperiodic response of Arabidopsis, enabling it to have a different flowering response in LDs and SDs.
Morphogenesis of Simple and Compound Leaves: A Critical Review
Authors: Efroni Idan , Eshed Yuval , Lifschitz Eliezer
Published: May 2010

The leaves of seed plants evolved from a primitive shoot system and are generated as determinate dorsiventral appendages at the flanks of radial indeterminate shoots. The remarkable variation of leaves has remained a constant source of fascination, and their developmental versatility has provided an advantageous platform to study genetic regulation of subtle, and sometimes transient, morphological changes. Here, we describe how eudicot plants recruited conserved shoot meristematic factors to regulate growth of the basic simple leaf blade and how subsets of these factors are subsequently re-employed to promote and maintain further organogenic potential. By comparing tractable genetic programs of species with different leaf types and evaluating the pros and cons of phylogenetic experimental procedures, we suggest that simple and compound leaves, and, by the same token, leaflets and serrations, are regulated by distinct ontogenetic programs. Finally, florigen, in its capacity as a general growth regulator, is presented as a new upper-tier systemic modulator in the patterning of compound leaves.
Integrative Transcript and Metabolite Analysis of Nutritionally Enhanced DE-ETIOLATED1 Downregulated Tomato Fruit
Authors: Enfissi Eugenia M.A. , Barneche Fredy , Ahmed Ikhlak , Lichtlé Christiane , Gerrish Christopher , McQuinn Ryan P. , Giovannoni James J. , Lopez-Juez Enrique , Bowler Chris , Bramley Peter M. , Fraser Paul D.
Published: May 2010

Fruit-specific downregulation of the DE-ETIOLATED1 (DET1) gene product results in tomato fruits (Solanum lycopersicum) containing enhanced nutritional antioxidants, with no detrimental effects on yield. In an attempt to further our understanding of how modulation of this gene leads to improved quality traits, detailed targeted and multilevel omic characterization has been performed. Metabolite profiling revealed quantitative increases in carotenoid, tocopherol, phenylpropanoids, flavonoids, and anthocyanidins. Qualitative differences could also be identified within the phenolics, including unique formation in fruit pericarp tissues. These changes resulted in increased total antioxidant content both in the polar and nonpolar fractions. Increased transcription of key biosynthetic genes is a likely mechanism producing elevated phenolic-based metabolites. By contrast, high levels of isoprenoids do not appear to result from transcriptional regulation but are more likely related to plastid-based parameters, such as increased plastid volume per cell. Parallel metabolomic and transcriptomic analyses reveal the widespread effects of DET1 downregulation on diverse sectors of metabolism and sites of synthesis. Correlation analysis of transcripts and metabolites independently indicated strong coresponses within and between related pathways/processes. Interestingly, despite the fact that secondary metabolites were the most severely affected in ripe tomato fruit, our integrative analyses suggest that the coordinated activation of core metabolic processes in cell types amenable to plastid biogenesis is the main effect of DET1 loss of function.
Operation of an auto‐initiated pulsed plasma thruster
Authors: Kushari Abhijit , Loh Kelvin
Published: May 2010

Purpose

The purpose of this paper is to develop and characterize a pulsed plasma thruster (PPT) that does not need a spark plug to initiate the plasma discharge.

Design/methodology/approach

Two parallel rail thrusters were built and their performances were characterized inside a vacuum chamber to elucidate the effect of vacuum level and thruster geometry on the performance. The thruster electrical performance was quantified by measuring the voltage output from a Rogowski coil connected to the power supply. The thrust produced by the developed thruster was estimated by measuring the force exerted by the plume on a light weight pendulum, whose deflection was measured using a laser displacement sensor.

Findings

The thruster can operate without a spark plug. In general, the performance parameters such as thrust, mass ablation, impulse bit, and specific impulse per discharge, would increase with increasing pressure levels up to an optimum level due to the increase in discharge energy as well as the decrease in the total impedance of the plasma discharge. The discharge frequency is function of the breakdown potential, the total resistance in the equivalent circuit, and the capacitance of the circuit. The total impedance of the circuit decreases with pressure level and hence the discharge energy increases. The thrust efficiency is found to be affected by the thruster geometry as well as the discharge energy.

Research limitations/implications

The studies reported in this paper have been carried out at relatively higher pressure levels compared than prevail in space. However, it should be possible to extrapolate these results to the lower vacuum levels at which the performance is independent of the geometry.

Practical implications

The results reported in this paper suggest a design guideline for auto‐initiated PPT.

Originality/value

If the spark plug is eliminated, the size of the thrusters can be reduced and arrays of such thrusters can be manufactured using micro electro mechanical systems techniques, which can provide tremendous control authority over the satellite positioning.
Drucker's theory of the business and organisations: challenging business assumptions
Authors: Daly Pat , Walsh James S.
Published: May 2010

Purpose

This paper considers Drucker's “theory of the business” as a management concept applicable to the challenging of firm performance. The paper seeks to do this by using the theoretical framework developed by Drucker as a tool to apply to organisation planning. In addition the paper aims to demonstrate the often “silent” but influential role assumptions have on organisations. Thus, the paper seeks to invite a reassessment of the role assumptions play in organisations and to present a new and topical perspective on Drucker's original “theory of the business” argument.

Design/methodology/ approach

A close review of Drucker's “theory of the business” article is outlined and a range of recently published (1994‐2008) works on related subject matter is reviewed. It is argued that the “assumptive design framework” at the heart of the theory of the business has potential to act as a powerful planning and strategy tool for enterprises. In addition the review demonstrates the “silent” positive and negative influences business assumptions have on organisation and management practice.

Findings

As a general review the paper provides new knowledge about the practical potential of one of Peter Drucker's seminal published articles in an area largely untouched by business or management research. It illustrates how research employing Drucker's “theory of the business” concept in the context of assumptions in business can have major benefit for organisations, especially growth‐oriented businesses.

Originality/value

This is the first paper to address the empirical potential of Drucker's conceptualisation of the “theory of the business” and exposes a unique Drucker‐inspired business and planning proposition that has significant potential for business management, especially in turbulent times
Is there a transatlantic divide?
Authors: Bardy Roland , Rubens Arthur
Published: May 2010

Purpose

Drucker has often been criticized for his pejorative interpretation of business ethics and the use of the term “casuistry”. This paper aims to show that Drucker was just the opposite of unethical in his viewpoint regarding the behavior of managers and organizations, and that in fact much of his writings pointed to discourse‐ethics‐universalism and away from casuistic particularism. Specifically, the paper seeks to analyze and contrast the ways in which US and European institutions take action (a “transatlantic divide”) when management and society eventually reposition their stance on ethics, as forecast by Drucker.

Design/methodology/approach

This is a comparative study emphasizing the main day‐to‐day perspectives of ethical issues in businesses and how they are handled in the USA and in Europe. This is complemented by references to what Drucker's position would be on those issues and how he would have shown that “good ethics” serves to ensure that entrepreneurial energies end up by serving society and not destroying it.

Findings

The paper provides an insight about how change is successfully brought about in current management practices by adhering to discourse and right behavior as pointed out by Drucker. It suggests that leaders acting responsibly are intrinsically ethical and will transfer their individual positions into their organization.

Research limitations/implications

The research primarily concentrates around the implications of Drucker's writings on the “transatlantic divide” and does not extensively explore how this relates to businesses in Asia and other areas outside the Western world.

Practical implications

The paper displays a number of standards and guidelines that have been adopted by practitioners and thus provides an input for further applications. Businesses that have adopted Drucker's philosophies will find useful directions on how to connect them to other philosophical developments.

Originality/value

This paper fulfils an identified need to reject claims that Drucker is an “efficiency enthusiast” pursuing “global change in a manner that has little to do with minimal standards of human decency, to say nothing of democracy, much less of emancipation”. It proves that the changes and the repositioning required for the current economic situation need a full understanding of Drucker in all respects of his work.
Intellectual capital and knowledge productivity: the Taiwan biotech industry
Authors: Huang Yi‐Chun , Jim Wu Yen‐Chun
Published: May 2010

Purpose

This purpose of this paper is to examine and test the effects of human capital, organization capital, and social capital on knowledge productivity and the interactive effects between intellectual capital and knowledge productivity.

Design/methodology/approach

The study adopts questionnaires to conduct a case investigation of the Taiwan biotechnology industry (TBI) and Taiwanese pharmaceutical manufacturers.

Findings

All dimensions of intellectual capital positively and significantly influence knowledge productivity. The study proves there are interactive effects between the components of intellectual capital and knowledge productivity.

Originality/value

The paper presents a synthesis of two different literature streams – intellectual capital and knowledge productivity – in order to understand their linkage. This paper is the first to conduct a large‐sample survey to examine the relationship between intellectual capital and knowledge productivity.