bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root
Authors: Zhang Yun Zeng , Chen Wen Feng , Li Mao , Sui Xin Hua , Liu Hong-Can , Zhang Xiao Xia , Chen Wen Xin
Published: March 2011

A Gram-positive, aerobic, motile rod, designated strain CCBAU 05776T, was isolated from the inner tissues of a healthy soybean (Glycine max L.) root collected from an agricultural field in the countryside of Shijiazhuang city, Hebei Province, China. Phylogenetic analysis of the 16S rRNA gene indicated that this strain was most closely related to Bacillus muralis LMG 20238T and Bacillus simplex NBRC 15720T with similarity of 96.5 % and 96.3 %, respectively, lower than the suggested threshold (97.0 %) for separating bacterial species. In phenotypic characterization, the novel strain differed from the two most related species in that it did not hydrolyse casein or starch but could grow on MacConkey agar. It grew between 15 and 45 °C and tolerated up to 7 % NaCl (w/v). Strain CCBAU 05776T grew in media with pH 5.5 to 10 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were iso-C15 : 0 (40.81 %) and C16 : 1ω7c alcohol (10.61 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C was 40.8 mol% (T
m). DNA–DNA relatedness of the novel isolate with B. muralis and B. simplex was 42.4 % and 32.7 %, respectively. Based upon the consensus of phylogenetic and phenotypic analyses, strain CCBAU 05776T represents a novel species within the genus Bacillus, for which the name Bacillus endoradicis sp. nov. is proposed. The type strain is CCBAU 05776T ( = LMG 25492T  = HAMBI 3097T).
Intrasporangium chromatireducens sp. nov., a chromate-reducing actinobacterium isolated from manganese mining soil, and emended description of the genus Intrasporangium
Authors: Liu Hongliang , Wang Hui , Wang Gejiao
Published: March 2011

A Gram-positive, aerobic actinobacterium with high chromate [Cr(VI)]-reducing ability, designated strain Q5-1T, was isolated from manganese mining soil in Hunan Province, central-south China. The organism formed branching hyphae and contained ll-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile was characterized by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified phospholipid. The major fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-8(H4). The genomic DNA G+C content was 71.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q5-1T was closely related to Intrasporangium calvum DSM 43043T ( = NRRL B-3866T) and Humihabitans oryzae KV-657T ( = NRRL B-24470T) with similarities of 96.6 and 96.4 %, respectively. Comparison of phenotypic, biochemical and chemotaxonomic characters of strain Q5-1T and phylogenetically related strains revealed that the isolate represents a novel species of the genus Intrasporangium, for which the name Intrasporangium chromatireducens sp. nov. is proposed. The type strain is Q5-1T ( = KCTC 19811T = CCTCC AA 2010019T = CGMCC 1.10750T = NRRL B-59521T). An emended description of the genus Intrasporangium is also proposed.
Knoellia flava sp. nov., isolated from pig manure
Authors: Yu Xiang , Du Yan , Wang Gejiao
Published: March 2011

A Gram-positive, aerobic, non-spore-forming actinobacterial strain, designated strain TL1T, was isolated from pig manure in Wuhan, China. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The predominant menaquinone was MK-8(H4). The major fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0 and C17 : 1ω8c. The genomic DNA G+C content was 70.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TL1T was most closely related to the type strains of Knoellia sinensis (98.5 %), Knoellia subterranea (98.2 %) and Knoellia aerolata (96.9 %). DNA–DNA relatedness values of strain TL1T with the type strains of K. sinensis and K. subterranea were 27.3 and 34.0 %, respectively. Comparison of phenotypic, chemotaxonomic and phylogenetic characteristics among strain TL1T and related organisms revealed that the isolate represents a novel species of the genus Knoellia, for which the name Knoellia flava sp. nov. is proposed; the type strain is TL1T ( = CGMCC 1.10749T = KCTC 19810T).
Arthrobacter cryoconiti sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite
Authors: Margesin Rosa , Schumann Peter , Zhang De-Chao , Redzic Mersiha , Zhou Yu-Guang , Liu Hong-Can , Schinner Franz
Published: March 2011

A Gram-stain-positive, aerobic, non-motile, psychrophilic bacterium, designated strain Cr6-08T, was isolated from alpine glacier cryoconite. Growth of strain Cr6-08T occurred at 1–25 °C. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain Cr6-08T is most closely related to members of the genus Arthrobacter. Strain Cr6-08T possessed chemotaxonomic properties consistent with those of the genus Arthrobacter, such as peptidoglycan type A3α (l-Lys–l-Ala4), MK-9(H2) as major menaquinone and anteiso- and iso-branched compounds (anteiso-C15 : 0 and iso-C15 : 0) as major cellular fatty acids. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown glycolipid and three unknown polar lipids. The genomic DNA G+C content of strain Cr6-08T was 57.3 mol%. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain Cr6-08T is considered to represent a novel species of the genus Arthrobacter, for which the name Arthrobacter cryoconiti sp. nov. is proposed. The type strain is Cr6-08T ( = DSM 23324T  = LMG 26052T  = CGMCC 1.10698T).
Polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster B1 of the genus Polynucleobacter
Authors: Hahn Martin W. , Minasyan Arevik , Lang Elke , Koll Ulrike , Spröer Catrin
Published: March 2011

Strain AM-8B5T, isolated from Lake Sevan in Armenia, was characterized phenotypically, chemotaxonomically and phylogenetically. This chemo-organoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on NSY medium at NaCl concentrations of 0.0–0.2 % (w/v) and at 4–30 °C. Whole-cell fatty acids were dominated by summed feature 3 (including C16 : 1ω7c and iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. C12 : 0 2-OH and C16 : 1 2-OH were the only hydroxylated fatty acids detected. Phylogenetic analysis as well as phenotypic and chemotaxonomic similarities indicated that the novel isolate was affiliated with the genus Polynucleobacter. 16S rRNA gene similarity values with the four previously described Polynucleobacter species ranged from 96.2 to 98.7 %. DNA–DNA hybridization experiments showed that the isolate did not belong to any of the previously described Polynucleobacter species. The isolate could be distinguished from all previously established Polynucleobacter species based on chemotaxonomic and phenotypic traits. The bacterium possessed a free-living lifestyle and represents a group of bacteria inhabiting the water column of many freshwater lakes. Based on the revealed phylogeny, and chemotaxonomic and phenotypic differences to previously described Polynucleobacter species, it is proposed that the isolate represents a novel species, Polynucleobacter difficilis sp. nov.; the type strain is AM-8B5T ( = DSM 22349T = CIP 110078T).
Massilia oculi sp. nov., isolated from a human clinical specimen
Authors: Kämpfer Peter , Lodders Nicole , Martin Karin , Falsen Enevold
Published: March 2011

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain CCUG 43427AT) was isolated from a patient suffering from endophthalmitis and its taxonomic position was studied. 16S rRNA gene sequence analysis indicated that this strain was a member of the genus Massilia. Strain CCUG 43427AT
was most closely related to the type strains of Massilia timonae (97.4 % 16S rRNA gene sequence similarity) and Massilia aurea (97.2 %); levels of similarity to the type strains of all other recognized Massilia species were below 97.0 %. Chemotaxonomic data [Q-8 as major ubiquinone; phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C12 : 0 and C10 : 0 3-OH as major fatty acids] supported the affiliation of the isolate to the genus Massilia. Levels of DNA–DNA relatedness of strain CCUG 43427AT with M. timonae CCUG 45783T and M. aurea AP13T were 60.6 % (reciprocal, 55.8 %) and 58.1 % (reciprocal, 34.0 %), respectively. Strain CCUG 43427AT could be differentiated from its closest phylogenetic neighbours based on a range of phenotypic characteristics. Strain CCUG 43427AT is therefore considered to represent a novel species of the genus Massilia, for which the name Massilia oculi sp. nov. is proposed. The type strain is CCUG 43427AT ( = CCM 7900T).
Virgibacillus campisalis sp. nov., from a marine solar saltern
Authors: Lee Soo-Young , Kang Chul-Hyung , Oh Tae-Kwang , Yoon Jung-Hoon
Published: March 2011

A Gram-staining-variable, motile, endospore-forming and rod-shaped bacterial strain, IDS-20T, was isolated from a marine solar saltern in Korea and subjected to a polyphasic taxonomic investigation. Strain IDS-20T grew optimally at 37 °C, at pH 7.5–8.0 and in the presence of 4–5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IDS-20T belongs to the genus Virgibacillus. Strain IDS-20T exhibited 93.4–96.6 % 16S rRNA gene sequence similarity to the type strains of species of the genus Virgibacillus. Strain IDS-20T had MK-7 as the predominant menaquinone and a cell-wall peptidoglycan based on meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0 and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. The DNA G+C content was 39.5 mol%. The phylogenetic distinctiveness and differential phenotypic characteristics of strain IDS-20T demonstrated that this strain can be distinguished from recognized species of the genus Virgibacillus. On the basis of the data presented, strain IDS-20T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus campisalis sp. nov. is proposed. The type strain is IDS-20T ( = KCTC 13727T  = CCUG 59308T).
Detection of common single nucleotide polymorphisms synthesizing quantitative trait association of rarer causal variants
Authors: Takeuchi Fumihiko , Kobayashi Shotai , Ogihara Toshio , Fujioka Akihiro , Kato Norihiro
Published: March 2011

Genome-wide association (GWA) studies have identified hundreds of common (minor allele frequency ≥5%) single nucleotide polymorphisms (SNPs) associated with phenotype traits or diseases, yet causal variants accounting for the association signals have rarely been determined. A question then raised is whether a GWA signal represents an “indirect association” as a proxy of a strongly correlated causal variant with similar frequency, or a “synthetic association” of one or more rarer causal variants in linkage disequilibrium (D′ ≈ 1, but r2 not large); answering the question generally requires extensive resequencing and association analysis. Instead, we propose to test statistically whether a quantitative trait (QT) association of an SNP represents a synthetic association or not by inspecting the QT distribution at each genotype, not requiring the causal variant(s) to be known. We devised two test statistics and assessed the power by mathematical analysis and simulation. Testing the heterogeneity of variance was powerful when low-frequency causal alleles are linked mostly to one SNP allele, while testing the skewness outperformed when the causal alleles are linked evenly to either of the SNP alleles. By testing a statistic combining these two in 5000 individuals, we could detect synthetic association of a GWA signal when causal alleles sum up to 3% in frequency. Such signal only partially explains the heritability contributed by the whole locus. The proposed test is useful for designing fine mapping after studying association of common SNPs exhaustively; we can prioritize which GWA signal and which individuals to be resequenced, and identify the causal variants efficiently.
Second-order conditioning in Drosophila
Authors: Tabone Christopher J. , de Belle J. Steven
Published: March 2011

Associative conditioning in Drosophila melanogaster has been well documented for several decades. However, most studies report only simple associations of conditioned stimuli (CS, e.g., odor) with unconditioned stimuli (US, e.g., electric shock) to measure learning or establish memory. Here we describe a straightforward second-order conditioning (SOC) protocol that further demonstrates the flexibility of fly behavior. In SOC, a previously conditioned stimulus (CS1) is used as reinforcement for a second conditioned stimulus (CS2) in associative learning. This higher-order context presents an opportunity for reassessing the roles of known learning and memory genes and neuronal networks in a new behavioral paradigm.
Serotonin- and training-induced dynamic regulation of CREB2 in Aplysia
Authors: Liu Rong-Yu , Shah Shreyansh , Cleary Leonard J. , Byrne John H.
Published: March 2011

Long-term memory and plasticity, including long-term synaptic facilitation (LTF) of the Aplysia sensorimotor synapse, depend on the activation of transcription factors that regulate genes necessary for synaptic plasticity. In the present study we found that treatment with 5-HT and behavioral training produce biphasic changes in the expression of CREB2, a transcriptional repressor. An immediate increase in CREB2 protein was followed by a subsequent decrease. The effects of these treatments persist for at least 24 h and are observed in isolated sensory neurons. This study suggests that the dynamics of CREB2 expression could contribute to the consolidation of memory.
Distribution ofSUN, OVATE, LC, andFASin the Tomato Germplasm and the Relationship to Fruit Shape Diversity
Authors: Rodríguez Gustavo R. , Muños Stéphane , Anderson Claire , Sim Sung-Chur , Michel Andrew , Causse Mathilde , Gardener Brian B. McSpadden , Francis David , van der Knaap Esther
Published: March 2011

Phenotypic diversity within cultivated tomato (Solanum lycopersicum) is particularly evident for fruit shape and size. Four genes that control tomato fruit shape have been cloned. SUN and OVATE control elongated shape whereas FASCIATED (FAS) and LOCULE NUMBER (LC) control fruit locule number and flat shape. We investigated the distribution of the fruit shape alleles in the tomato germplasm and evaluated their contribution to morphology in a diverse collection of 368 predominantly tomato and tomato var. cerasiforme accessions. Fruits were visually classified into eight shape categories that were supported by objective measurements obtained from image analysis using the Tomato Analyzer software. The allele distribution of SUN, OVATE, LC, and FAS in all accessions was strongly associated with fruit shape classification. We also genotyped 116 representative accessions with additional 25 markers distributed evenly across the genome. Through a model-based clustering we demonstrated that shape categories, germplasm classes, and the shape genes were nonrandomly distributed among five genetic clusters (P < 0.001), implying that selection for fruit shape genes was critical to subpopulation differentiation within cultivated tomato. Our data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage. Furthermore, LC, OVATE, and FAS mutations may have arisen prior to domestication or early during the selection of cultivated tomato whereas the SUN mutation appeared to be a postdomestication event arising in Europe.
The Membrane Mucin Msb2 Regulates Invasive Growth and Plant Infection in Fusarium oxysporum
Authors: Pérez-Nadales Elena , Di Pietro Antonio
Published: March 2011

Fungal pathogenicity in plants requires a conserved mitogen-activated protein kinase (MAPK) cascade homologous to the yeast filamentous growth pathway. How this signaling cascade is activated during infection remains poorly understood. In the soil-borne vascular wilt fungus Fusarium  oxysporum, the orthologous MAPK Fmk1 (Fusarium MAPK1) is essential for root penetration and pathogenicity in tomato (Solanum lycopersicum) plants. Here, we show that Msb2, a highly glycosylated transmembrane protein, is required for surface-induced phosphorylation of Fmk1 and contributes to a subset of Fmk1-regulated functions related to invasive growth and virulence. Mutants lacking Msb2 share characteristic phenotypes with the Δfmk1 mutant, including defects in cellophane invasion, penetration of the root surface, and induction of vascular wilt symptoms in tomato plants. In contrast with Δfmk1, Δmsb2 mutants were hypersensitive to cell wall targeting compounds, a phenotype that was exacerbated in a Δmsb2 Δfmk1 double mutant. These results suggest that the membrane mucin Msb2 promotes invasive growth and plant infection upstream of Fmk1 while contributing to cell integrity through a distinct pathway.
Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling inArabidopsis thaliana
Authors: Lozano-Durán Rosa , Rosas-Díaz Tabata , Gusmaroli Giuliana , Luna Ana P. , Taconnat Ludivine , Deng Xing Wang , Bejarano Eduardo R.
Published: March 2011

Viruses must create a suitable cell environment and elude defense mechanisms, which likely involves interactions with host proteins and subsequent interference with or usurpation of cellular machinery. Here, we describe a novel strategy used by plant DNA viruses (Geminiviruses) to redirect ubiquitination by interfering with the activity of the CSN (COP9 signalosome) complex. We show that geminiviral C2 protein interacts with CSN5, and its expression in transgenic plants compromises CSN activity on CUL1. Several responses regulated by the CUL1-based SCF ubiquitin E3 ligases (including responses to jasmonates, auxins, gibberellins, ethylene, and abscisic acid) are altered in these plants. Impairment of SCF function is confirmed by stabilization of yellow fluorescent protein–GAI, a substrate of the SCFSLY1. Transcriptomic analysis of these transgenic plants highlights the response to jasmonates as the main SCF-dependent process affected by C2. Exogenous jasmonate treatment of Arabidopsis thaliana plants disrupts geminivirus infection, suggesting that the suppression of the jasmonate response might be crucial for infection. Our findings suggest that C2 affects the activity of SCFs, most likely through interference with the CSN. As SCFs are key regulators of many cellular processes, the capability of viruses to selectively interfere with or hijack the activity of these complexes might define a novel and powerful strategy in viral infections.
TheFT-LikeZCN8Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize
Authors: Meng Xin , Muszynski Michael G. , Danilevskaya Olga N.
Published: March 2011

The mobile floral-promoting signal, florigen, is thought to consist of, in part, the FT protein named after the Arabidopsis thaliana gene FLOWERING LOCUS T. FT is transcribed and translated in leaves and its protein moves via the phloem to the shoot apical meristem where it promotes the transition from vegetative to reproductive development. In our search for a maize FT-like floral activator(s), seven Zea mays CENTRORADIALIS (ZCN) genes encoding FT homologous proteins were studied. ZCN8 stood out as the only ZCN having the requisite characteristics for possessing florigenic activity. In photoperiod sensitive tropical lines, ZCN8 transcripts were strongly upregulated in a diurnal manner under floral-inductive short days. In day-neutral temperate lines, ZCN8 mRNA level was independent of daylength and displayed only a weak cycling pattern. ZCN8 is normally expressed in leaf phloem, but ectopic expression of ZCN8 in vegetative stage shoot apices induced early flowering in transgenic plants. Silencing of ZCN8 by artificial microRNA resulted in late flowering. ZCN8 was placed downstream of indeterminate1 and upstream of delayed flowering1, two other floral activator genes. We propose a flowering model linking photoperiod sensitivity of tropical maize to diurnal regulation of ZCN8.
The Predicted Arabidopsis Interactome Resource and Network Topology-Based Systems Biology Analyses
Authors: Lin Mingzhi , Zhou Xi , Shen Xueling , Mao Chuanzao , Chen Xin
Published: March 2011

Predicted interactions are a valuable complement to experimentally reported interactions in molecular mechanism studies, particularly for higher organisms, for which reported experimental interactions represent only a small fraction of their total interactomes. With careful engineering consideration of the lessons from previous efforts, the Predicted Arabidopsis Interactome Resource (PAIR; ) presents 149,900 potential molecular interactions, which are expected to cover ~24% of the entire interactome with ~40% precision. This study demonstrates that, although PAIR still has limited coverage, it is rich enough to capture many significant functional linkages within and between higher-order biological systems, such as pathways and biological processes. These inferred interactions can nicely power several network topology-based systems biology analyses, such as gene set linkage analysis, protein function prediction, and identification of regulatory genes demonstrating insignificant expression changes. The drastically expanded molecular network in PAIR has considerably improved the capability of these analyses to integrate existing knowledge and suggest novel insights into the function and coordination of genes and gene networks.
The CHD3 Chromatin Remodeler PICKLE and Polycomb Group Proteins Antagonistically Regulate Meristem Activity in the Arabidopsis Root
Authors: Aichinger Ernst , Villar Corina B.R. , Di Mambro Riccardo , Sabatini Sabrina , Köhler Claudia
Published: March 2011

The chromatin modifying Polycomb group (PcG) and trithorax group (trxG) proteins are central regulators of cell identity that maintain a tightly controlled balance between cell proliferation and cell differentiation. The opposing activities of PcG and trxG proteins ensure the correct expression of specific transcriptional programs at defined developmental stages. Here, we report that the chromatin remodeling factor PICKLE (PKL) and the PcG protein CURLY LEAF (CLF) antagonistically determine root meristem activity. Whereas loss of PKL function caused a decrease in meristematic activity, loss of CLF function increased meristematic activity. Alterations of meristematic activity in pkl and clf mutants were not connected with changes in auxin concentration but correlated with decreased or increased expression of root stem cell and meristem marker genes, respectively. Root stem cell and meristem marker genes are modified by the PcG-mediated trimethylation of histone H3 on lysine 27 (H3K27me3). Decreased expression levels of root stem cell and meristem marker genes in pkl correlated with increased levels of H3K27me3, indicating that root meristem activity is largely controlled by the antagonistic activity of PcG proteins and PKL.
PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species
Authors: Mutwil Marek , Klie Sebastian , Tohge Takayuki , Giorgi Federico M. , Wilkins Olivia , Campbell Malcolm M. , Fernie Alisdair R. , Usadel Björn , Nikoloski Zoran , Persson Staffan
Published: March 2011

The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species.
The Anaphase-Promoting Complex Is a Dual Integrator That Regulates Both MicroRNA-Mediated Transcriptional Regulation ofCyclin B1and Degradation of Cyclin B1 duringArabidopsisMale Gametophyte Development
Authors: Zheng Binglian , Chen Xuemei , McCormick Sheila
Published: March 2011

The anaphase-promoting complex/cyclosome (APC/C), an essential ubiquitin protein ligase, regulates mitotic progression and exit by enhancing degradation of cell cycle regulatory proteins, such as CYCB1;1, whose transcripts are upregulated by DUO POLLEN1 (DUO1). DUO1 is required for cell division in male gametophytes and is a target of microRNA 159 (miR159) in Arabidopsis thaliana. Whether APC/C is required for DUO1-dependent CYCB1;1 regulation is unknown. Mutants in both APC8 and APC13 had pleiotrophic phenotypes resembling those of mutants affecting microRNA biogenesis. We show that these apc/c mutants had reduced miR159 levels and increased DUO1 and CYCB1;1 transcript levels and that APC/C is required to recruit RNA polymerase II to MIR159 promoters. Thus, in addition to its role in degrading CYCB1;1, APC/C stimulates production of miR159, which downregulates DUO1 expression, leading to reduced CYCB1;1 transcription. Both MIR159 and APC8–yellow fluorescent protein accumulated in unicellular microspores and bicellular pollen but decreased in tricellular pollen, suggesting that spatial and temporal regulation of miR159 by APC/C ensures mitotic progression. Consistent with this, the percentage of mature pollen with no or single sperm-like cells increased in apc/c mutants and plants overexpressing APC8 partially mimicked the duo1 phenotype. Thus, APC/C is an integrator that regulates both microRNA-mediated transcriptional regulation of CYCB1;1 and degradation of CYCB1;1.
An instrument to assess health‐related advertising on college campuses
Authors: Szymona Katie , Quick Virginia , Byrd‐Bredbenner Carol
Published: March 2011

Purpose

Advertising can affect health‐related behaviors of young adults. However, little is known about this environmental influence on college campuses. The purpose of this paper is to create an inventory for assessing health‐related advertisements and use it to assess advertising on/near the campus of a major Northeastern university.

Design/methodology/approach

The inventory was developed from existing instruments, input from experts, and data collected from student focus groups. The instrument was pilot tested, refined, and used by three trained data collectors (inter‐rater reliability =87.5 percent) to assess the advertising in academic buildings (n=10), residence halls (n=3), libraries (n=2), recreation centers (n=3), student centers (n=2), dining halls (n=3), bookstores (n=2), bus stops (n=4), campus student listserves, and retail stores adjacent to campus.

Findings

Of the 130 advertisements, most common types were related to diet/nutrition (41.5 percent) and exercise/fitness (14.6 percent). An evaluation of advertising message polarity revealed 61.5 percent promoted positive health behaviors. Negative messages were mostly related to branded diet/nutrition ads (26 percent). Health‐related advertising on/near this university's campus mostly promoted good health practices in accordance to the university policies. However, improvements in developing university policies with regard to branded diet/nutrition ads on campus are warranted.

Research limitations/implications

The study described in this paper was conducted at one time point at a single university. Future studies should examine seasonal variations and the usefulness of this instrument on other college campuses.

Originality/value

This valid data collection tool will be of benefit to other college campuses and policy makers who wish to identify how to improve campus‐related advertising policies to ensure they promote positive health behaviors.
Reformulated oatmeal and chocolate chip cookies: staling effects
Authors: Kane Alison M. , Swanson Ruthann B. , Lyon Brenda G. , Savage Elizabeth M.
Published: March 2011

Purpose

Staling, the progressive non‐microbial deterioration of quality, is influenced by baked product fat, sugar and moisture levels. Although 50 percent sugar replacement with an acesulfame‐K‐dextrose blend, and/or 50 percent fat replacement with dried plum puree, produces acceptable oatmeal and chocolate chip cookies within one day of baking, flavor and texture changes with continued storage are unknown. The purpose of this paper is to profile three oatmeal and chocolate chip cookie formulations.

Design/methodology/approach

Three oatmeal and chocolate chip cookie formulations (control, reduced‐in‐fat (50 percent) and reduced‐in‐fat and sugar (50 percent)) were profiled 1, 3, 5 and 7 days post‐bake by a trained sensory panel (n=8) using the Spectrum®‐approach on 0‐15 point linescales; three replicates were obtained. Water activity was determined on six replicates. Data were analyzed with PROC Mixed and PDIFF (p<0.05).

Findings

Water activity increased with modification; increases (aW<0.60) do not support microbial growth. Day 1 flavor and texture reformulation effects mirror those previously reported. Storage effects across all formulations (p<0.05) on oatmeal and chocolate chip cookie sensory attributes are within one linescale unit. Different significant (p<0.05) formulation×storage interactions suggest staling patterns differ with cookie type. Water activity increased during storage for chocolate chip cookies only; practical significance is questionable. Panelists' comments suggesting oxidative effects for both controls by day 5 are consistent with water activity.

Originality/value

Consumption of products with improved nutritional profiles can assist consumers in bringing their diets in‐line with dietary recommendations. Maximizing benefits requires continued selection of modified rather than non‐modified products. Technical issues (sensory characteristics, nutritional profile and storage convenience) do not appear to limit consumer selection of these reformulated cookies.
Effect of dehulling/soaking on the chemical, functional and anti‐nutritional contents of three varieties of beans
Authors: Adunni Abiodun Olufunmilola , Olaposi Adeleke Rauf
Published: March 2011

Purpose

The purpose of this paper is to evaluate the effect of dehulling/soaking on the chemical, functional and anti‐nutritional contents of three varieties of beans. This research work involved comparative study of the underutilized bean species with the commonly consumed beans in Nigeria.

Design/methodology/approach

Three species of legumes were used for this study. The cowpea seeds were divided into two parts. One part was milled and packaged for raw flour while the other part was dehulled and soaked for 30 min, dried in the oven, milled and packed. For the pigeon pea and African yam beans, the raw beans were milled and packaged while part of the seeds was steamed for 5 min and the coats were removed. The dehulled beans were soaked for 30 min, dried in the oven, milled and packaged. Chemical, functional and anti‐nutritional content were determined on the samples.

Findings

Fat content ranged from 0.95 to 1.98 per cent. Ash and crude fibre ranged from 1.98 to 6.13 and 2.41 to 7.90 per cent, respectively. Raw cowpea had the highest calcium content (3.86 per cent) while pigeon pea had higher value in magnesium content (2.01 per cent). Raw African yam beans had the highest iron content (23.44 per cent). Bulk density, swelling index and water‐absorption capacity ranged from 0.53 to 0.92 g/cm3, 2.3 to 5.9 and 0.9 to 2.8 ml H2O/g, respectively. African yam bean had higher values in oxalate, phytate and tannin contents while cowpea had higher saponin content. Raw flour of pigeon pea had higher value in trypsin inhibitor.

Originality/value

This work enables us to make use of the underutilized beans. These beans were higher in nutrients than the cowpea used. Processing of these beans will make them useful for human nutrition without imposing any health problem to the consumer. They could also be converted to flour and used in formulating food such as weaning food.
Phenolic constituents and antioxidant properties of some varieties of Indian rice
Authors: Biswas Sinchan , Sircar Debabrata , Mitra Adinpunya , De Bratati
Published: March 2011

Purpose

The purpose of this paper is to determine the antioxidant properties and phenol content of methanolic extracts of six white varieties and six purple/brown varieties of Indian rice and to find some relationship between the antioxidant properties, phenolic content in the varieties analyzed.

Design/methodology/approach

Methanolic extracts of different rice varieties were analyzed for their superoxide radical scavenging activity, 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) radical scavenging activity, total antioxidant capacity, reducing power and ferrous ion chelating properties. The extracts were analyzed for determination of total phenol content, anthocyanin content, oryzanol content. Phenolic acids were determined by HPLC.

Findings

All the rice varieties (white and purple/brown) showed activity in a dose‐dependent manner. Free phenolic acids, e.g. protocatechuic acid, caffeic acid, vanillic acid, p‐coumaric acid (PCA), ferulic acid and sinapic acid and the phenolic aldehyde vanillin could be detected in all the rice samples analyzed. No relationship could be established between activity and metabolite content. Principal component analysis and classification shows that superoxide radical scavenging activity, total phenolic acid, protocatechuic acid and ferulic acid are the components to differentiate the varieties from each other.

Originality/value

Little work has been done on the antioxidant activity of white rice. The authors report superoxide radical scavenging activity, DPPH radical scavenging activity, total antioxidant activity, reducing power and ferrous ion chelating properties and phenolic contents of six white varieties and six purple/brown varieties of Indian rice. Free phenolic acids like protocatechuic acid, caffeic acid, vanillic acid, PCA, ferulic acid and sinapic acid are reported from all the 12 varieties of rice.
Role of fermented milk in treating the histopathological and histochemical changes induced by the toxic mutagen
Authors: Mehanna Nayra Sh. , Rayes Amna A.H. , El‐Naggar Sabah M.M.
Published: March 2011

Purpose

The purpose of this paper is to examine the potential effects of the intake of fermented milk containing the probiotic bacteria Lactobacilli spp. and Befidobacteria sp. as a supplementation for daily food and the possible prevention of hepatic lesions induced by the oral administration of a carcinogenic mutagen 3 amino‐I methyl‐5H‐pyrido (4, 3‐b) indole.

Design/methodology/approach

In total, 20 mice were divided into four groups. A control group was fed the murine pallet food for 30 days. Another three groups were given orally one dose of the toxic mutagen at the beginning of the experimental period and then fed the normal diet. At the 15th day, mice of the first group were dissected while the mice of the second group were given a second dose then continued feeding normal diet. Animals of the third group were given the second dose of the toxic mutagen and started feeding fermented milk for another 15 days. The quality of life was measured by specific strain count in stool, histopathological, histochemical changes of liver and count of lymphocytes were studied.

Findings

The variable count of Lac. sp. and Bif. sp. in stool of mice indicated that feeding these mice on the fermented milk repaired the slightly damaged areas and prevented the progressive damage effects of the toxic mutagen in these areas, while those which were severely damaged remained unrepaired. Moreover, the presented histochemical study recorded slight depletion in the total carbohydrate and total protein contents only in group C in comparison with controls.

Originality/value

The paper shows that the potential effect of fermented milk ingestion was capable of endorsing protective measures to hepatic tissue architecture and decreasing the toxic effect induced by mutagen administration.
BIM adoption and implementation for architectural practices
Authors: Arayici Y. , Coates P. , Koskela L. , Kagioglou M. , Usher C. , O'Reilly K.
Published: March 2011

Purpose

This paper aims to present a systematic approach for building information modelling (BIM) implementation for architectural SMEs at the organizational level

Design/methodology/approach

The research is undertaken through a knowledge transfer partnership (KTP) project between the University of Salford and John McCall Architects (JMA) a SME based in Liverpool. The overall aim of the KTP is to develop lean design practice through BIM adoption. The BIM implementation approach uses a socio‐technical view, which does not only consider the implementation of technology but also considers the socio‐cultural environment that provides the context for its implementation. The action research oriented qualitative and quantitative research is used for discovery, comparison, and experimentation as it provides “learning by doing”.

Findings

The strategic approach to BIM adoption incorporated people, process and technology equally and led to capacity building through the improvements in process, technological infrastructure and upskilling of JMA staff to attain efficiency gains and competitive advantages.

Originality/value

The paper introduces a systematic approach for BIM adoption based on the action research philosophy and demonstrates a roadmap for BIM adoption at the operational level for SME companies.
The Bribery Act 2010: implications for building surveyors
Authors: Donohoe Steve
Published: March 2011

Purpose

This paper aims to explore the Bribery Act 2010 and its likely implications for building surveyors. The paper also aims to report a small‐scale research project exploring whether building surveyors are prepared for the Act.

Design/methodology/approach

The method used was a survey questionnaire completed by 53 building surveyors.

Findings

The findings revealed that many building surveyors, while having heard of the Act, had no idea when it would come into force nor were they aware of what steps to take to comply with the provisions of the Act. The survey revealed that very few building‐surveying firms had existing policies to cover anti‐competitive behaviour or corrupt practices. The conclusion of this paper is that building surveyors need to review their procedures urgently if they are to comply with the provisions of the Bribery Act 2010.

Research limitations/implications

The small sample size of the study suggests that some caution should be exercised in believing that such ignorance is typical of the entire industry.

Originality/value

The Bribery Act comes into force in April 2011 and the level of knowledge of this new legislation revealed by this study is a cause for concern.
The development of a condition survey protocol matrix
Authors: Ifran Che‐Ani Adi , Samsul Mohd Tazilan Azimin , Afizi Kosman Kamarul
Published: March 2011

Purpose

Building inspection is one of the key components of building maintenance. The primary purpose of performing a building inspection is to evaluate the building's condition. Without inspection, it is difficult to determine a built asset's current condition, so failure to inspect can contribute to the asset's future failure. Traditionally, a longhand survey description has been widely used for property condition reports. Surveys that employ ratings instead of descriptions are gaining wide acceptance in the industry because they cater to the need for a quantitative approach. These kinds of surveys are also in keeping with the new RICS HomeBuyer Report 2009. This paper aims to describe an assessment method.

Design/methodology/approach

The paper proposes a new assessment method, derived from the current rating systems, for assessing the building's condition and rating the seriousness of each defect identified. These two assessment criteria are then multiplied to find the building's score, which is called the condition survey protocol (CSP) 1 matrix. The matrix is assessed by means of a case study.

Findings

Instead of a longhand description of a building's defects, the matrix requires concise explanations about the defects identified, thus saving on‐site time during a building inspection. The full score is used to give the building an overall rating: good, fair or dilapidated. The overall findings reflect the reliability of the CSP1 matrix.

Practical implications

The matrix needs to be tested on more and larger buildings to further assess its reliability.

Originality/value

The paper focuses on the CSPI Matrix, a reliable and practical assessment method for building inspections performed under reasonable property conditions.
The flexural strength of earth‐block masonry for sustainable walling
Authors: Williams Colin , Goodhew Steve , Griffiths Richard
Published: March 2011

Purpose

The purpose of the paper is to explore the structural feasibility of substituting traditional thick joint mortars with earth slurry mortars modified with varying amounts of sand. Thin jointing of earth blocks would reduce the cost of sustainable earth construction.

Design/methodology/approach

Compressive strength of earth‐block cubes was determined. Flexural strength was measured using the BRE electronic bond wrench, which enables block couplets to be tested quickly and accurately. Three samples of earth block, one from southwest England and two from East Anglia, together with nine examples of earth slurry mortar jointing were studied, including the effect of reinforcing the joint and or the block using hessian.

Findings

The 28‐day cube characteristic compressive strengths were determined for Appley soil, Norfolk lump and Beeston soil, the last with 0 per cent sand, 25 per cent sand and with 25 per cent sand with hessian. The flexural strengths of Appley and Beeston earth slurries were determined, along with Thermalite thin jointed cement and cement mortar for comparison. The Beeston soil flexural strength increased with increasing sand content. Earth slurry with 40 per cent sand and hessian present in the joint gave the greatest strength. It is important to use blocks and slurry mortars of the same soil. Extruded and compressed earth blocks are best suited to slurry jointing.

Originality/value

This work successfully demonstrates the structural feasibility of carefully reducing the thickness of earth mortars when constructing sustainable earth block walling. Characteristic flexural strengths are suggested where the test results were sufficiently consistent, and of a magnitude likely to be useful in design.
Fibre reinforced polymer and steel rebar comparative performance
Authors: Richardson Alan , Drew Paula
Published: March 2011

Purpose

This paper aims to investigate the necessary requirements that a concrete reinforcement material must satisfy; namely the ability to resist tensile forces and have good bond strength while providing structural qualities of toughness and flexural strength.

Design/methodology/approach

The bond and strength properties were mainly tested in a paired comparison test using 6 mm diameter steel and fibre reinforced polymer (FRP) rebar specimens in beams and cubes. Bond strength was examined using 12 concrete cube specimens of 150 mm, six cubes had steel rebar and six had FRP rebar inserted through the full depth of the cube and they were subject to pull out tests. To determine flexural strength and toughness, a three point loading test was performed to provide load/extension data on 28 500×100×100 mm concrete beams. A total of 14 beams were cast with steel rebar and 14 were cast with FRP rebar.

Findings

The results showed for equal diameter bars the FRP specimens had outperformed steel in each test. Failure modes of FRP specimens showed higher degrees of toughness when compared to steel.

Originality/value

Steel rebar has a long and proven track record of satisfactory use in reinforced concrete. For designers and clients to change from traditionally used materials, there is a need for investigative research to prove the worth of the new material. This paper goes part of the way to fulfil this need.
Champions of practice: context and habitus for unbounded learning in construction projects
Authors: Love Peter , Edwards David , Love Joanne , Irani Zahir
Published: March 2011

Purpose

Knowledge is recognised as a valuable resource for organizational growth and sustained competitive advantage, especially for organizations operating in uncertain and challenging environments such as construction. Within the construction industry, communities of practice (CoP) have not been effectively embraced as a strategic tool for knowledge creation and sharing within and between organizations. Accordingly, this paper aims to review CoP and present a pragmatic approach for their utilisation.

Design/methodology/approach

A review of the literature on CoPs is provided and examples from the authors' experience are provided to demonstrate their usefulness in addressing problems that are being confronted within the construction industry.

Findings

The construction industry is sceptical about adopting “management fads” and gimmick technologies that provide no strategic competitive advantage. Evidence of this can be seen with the industry's reluctance, particularly in Australia, to embrace re‐engineering and concepts associated with lean construction. The industry has been informally using CoP, or aspects thereof, for many years but it has not been formally recognised as a performance improvement tool. Organizations may find it difficult to build, sustain and integrate CoP within their organization, especially when staff are geographically spread over numerous remote locations. It is suggested that the underlying concept of CoP can create and sustain learning and knowing in projects.

Originality/value

The challenge for construction organizations is not necessarily to use intra‐organizational forms of CoP, but to learn how they can use them within the project environment within which they operate. A proposal for using communities of practice, namely “champions of practice” (CoPE), at an inter‐organizational level is proposed in this paper. This hybrid form of CoP is dependent on the sharing of knowledge within and across organizational boundaries. For this to happen effectively within a project environment, the right set of communication tools, incentives, motivation, organizational and managerial mechanisms need to be in place for “best practice” to be formalised and shared in a meaningful and reflective way.