bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of large ocean waves: the role of local and rapid spectral changes
Authors: Gibson R.S , Swan C
Published: August 2006

This paper concerns the formation of large-focused or near-focused waves in both unidirectional and directional sea-states. When the crests of wave components of varying frequency superimpose at one point in space and time, a large, transient, focused wave can occur. These events are believed to be representative of the largest waves arising in a random sea and, as such, are of importance to the design of marine structures. The details of how such waves form also offer an explanation for the formation of the so-calledfreakorroguewaves in deep water. The physical mechanisms that govern the evolution of focused waves have been investigated by applying both the fully nonlinear wave model of Batemanet al. (Batemanet al. 2001J. Comput. Phys.174, 277–305) and the Zakharov's evolution equation (Zakharov 1968J. Appl. Mech. Tech. Phys.9, 190–194). Aspects of these two wave models are complementary, and their combined use allows the full nonlinearity to be considered and, at the same time, provides insights into the dominant physical processes.

In unidirectional seas, it has been shown that the local evolution of the wave spectrum leads to larger maximum crest elevations. In contrast, in directional seas, the maximum crest elevation is well predicted by a second-order theory based on the underlying spectrum, but the shape of the largest wave is not. The differences between the evolution of large waves in unidirectional and directional sea-states have been investigated by analysing the results of Batemanet al. (2001) using a number of spectral analysis techniques. It has been shown that during the formation of a focused wave event, there are significant and rapid changes to the underlying wave spectrum. These changes alter both the amplitude of the wave components and their dispersive properties. Importantly, in unidirectional sea-states, the bandwidth of the spectrum typically increases; whereas, in directional sea-states it decreases.

The changes to the wave spectra have been investigated using Zakharov's equation (1968). This has shown that the third-orderresonanteffects dominate changes to both the amplitude of the wave components and the dispersive properties of the wave group. While this is the case in both unidirectional and directional sea-states, the consequences are very different. By examining these consequences, directional sea-states in which large wave events that are higher and steeper than second-order theory would predict have been identified. This has implications for the types of sea-states in whichroguewaves are most likely to occur.
Re-entrant corner flows of upper convected Maxwell fluids: the small and high Weissenberg number limits
Authors: Evans J.D
Published: August 2006

We discuss here the steady planar flow of the upper convected Maxwell fluid at re-entrant corners in the singular limits of small and large Weissenberg number. The Weissenberg number is a parameter representing the dimensionless relaxation time and hence the elasticity of the fluid. Its value determines the strength of the fluid memory and thus the influence of elastic effects over viscosity. The small Weissenberg limit is that in which the elastic effects are small and the fluid's memory is weak. It is an extremely singular limit in which the behaviour of a Newtonian fluid is obtained in a main core region away from the corner and walls. Elastic effects are confined to boundary layers at the walls and core regions nearer to the corner. The actual asymptotic structure comprises a complicated four-region structure. The other limit of interest is the large Weissenberg limit (or high Weissenberg number problem) in which the elastic effects now dominate in the main regions of the flow. We explain how the transition in solution from Weissenberg order 1 flows to high Weissenberg flows is achieved, with the singularity in the stress field at the corner remaining the same but its effects now extending over larger length-scales. Implicit in this analysis is the absence of a lip vortex. We also show (for the main core region) that there is a small reduction in the velocity field at the corner and walls where it becomes smoother. This high Weissenberg number limit has a six-region local asymptotic structure and comment is made on its relevance to the case in which a lip vortex is present.
Group decision making in fission–fusion societies: evidence from two-field experiments in Bechstein's bats
Authors: Kerth Gerald , Ebert Cornelia , Schmidtke Christine
Published: August 2006

Group decisions are required when group coordination is beneficial, but individuals can choose between alternatives. Despite the increased interest in animal group decision making, there is a lack of experimental field studies that investigate how animals with conflicting information make group decisions. In particular, no field studies have considered the influence of fission–fusion behaviour (temporary splitting into subgroups) on group decisions. We studied group decision making in two wild Bechstein's bat colonies, which are fission–fusion societies of stable individual composition. Since they frequently switch communal roosts, colony members must regularly make group decisions over where to roost. In the two-field experiments, we provided marked individuals with conflicting information about the suitability of potential roosts. We investigated whether conflicting information led to group decisions that followed a ‘unanimous’ or a ‘majority’ rule, or increased colony fission. Individual behaviour suggests that bats considered both their own information and the behaviour of others when deciding where to roost. Group decisions about communal roosts reflected the information available to a majority of the bats roosting together, but conflicting information led to an increased fission in one colony. Our results suggest that fission–fusion societies allow individuals to avoid majority decisions that are not in their favour.
Control of chaos in nonlinear systems with time-periodic coefficients
Authors: Sinha S.C , Dávid Alexandra
Published: August 2006

In this study, some techniques for the control of chaotic nonlinear systems with periodic coefficients are presented. First, chaos is eliminated from a given range of the system parameters by driving the system to a desired periodic orbit or to a fixed point using a full-state feedback. One has to deal with the same mathematical problem in the event when an autonomous system exhibiting chaos is desired to be driven to a periodic orbit. This is achieved by employing either a linear or a nonlinear control technique. In the linear method, a linear full-state feedback controller is designed by symbolic computation. The nonlinear technique is based on the idea of feedback linearization. A set of coordinate transformation is introduced, which leads to an equivalent linear system that can be controlled by known methods. Our second idea is to delay the onset of chaos beyond a given parameter range by a purely nonlinear control strategy that employs local bifurcation analysis of time-periodic systems. In this method, nonlinear properties of post-bifurcation dynamics, such as stability or rate of growth of a limit set, are modified by a nonlinear state feedback control. The control strategies are illustrated through examples. All methods are general in the sense that they can be applied to systems with no restrictions on the size of the periodic terms.
Anti-control of chaos of single time-scale brushless DC motor
Authors: Ge Zheng-Ming , Chang Ching-Ming , Chen Yen-Sheng
Published: August 2006

Anti-control of chaos of single time-scale brushless DC motors is studied in this paper. In order to analyse a variety of periodic and chaotic phenomena, we employ several numerical techniques such as phase portraits, bifurcation diagrams and Lyapunov exponents. Anti-control of chaos can be achieved by adding an external constant term or an external periodic term.
Coexisting chaotic and periodic dynamics in clock escapements
Authors: Moon Francis C , Stiefel Preston D
Published: August 2006

This paper addresses the nature of noise in machines. As a concrete example, we examine the dynamics of clock escapements from experimental, historical and analytical points of view. Experiments on two escapement mechanisms from the Reuleaux kinematic collection at Cornell University are used to illustrate chaotic-like noise in clocks. These vibrations coexist with the periodic dynamics of the balance wheel or pendulum. A mathematical model is presented that shows how self-generated chaos in clocks can break the dry friction in the gear train. This model is shown to exhibit a strange attractor in the structural vibration of the clock. The internal feedback between the oscillator and the escapement structure is similar to anti-control of chaos models.
Axon pruning: an essential step underlying the developmental plasticity of neuronal connections
Authors: Low Lawrence K , Cheng Hwai-Jong
Published: August 2006

Regressive events play a key role in modifying neural connectivity in early development. An important regressive event is the pruning of neuronal processes. Pruning is a strategy often used to selectively remove exuberant neuronal branches and connections in the immature nervous system to ensure the proper formation of functional circuitry. In the following review, we discuss our present understanding of the cellular and molecular mechanisms that regulate the pruning of axons during neuronal development as well as in neurological diseases. The evidence suggests that there are several similarities between the mechanisms that are involved in developmental axon pruning and axon elimination in disease. In summary, these findings provide researchers with a unique perspective on how developmental plasticity is achieved and how to develop strategies to treat complex neurological diseases.
Recapitulate development to promote axonal regeneration: good or bad approach?
Authors: Filbin Marie T
Published: August 2006

In the past decade there has been an explosion in our understanding, at the molecular level, of why axons in the adult, mammalian central nervous system (CNS) do not spontaneously regenerate while their younger counterparts do. Now a number of inhibitors of axonal regeneration have been described, some of the receptors they interact with to transduce the inhibitory signal are known, as are some of the steps in the signal transduction pathway that is responsible for inhibition. In addition, developmental changes in the environment and in the neurons themselves are also now better understood. This knowledge in turn reveals novel, putative sites for drug development and therapeutic intervention after injury to the brain and spinal cord. The challenge now is to determine which of these putative treatments are the most effective and if they would be better applied in combination rather than alone. In this review I will summarize what we have learnt about these molecules and how they signal. Importantly, I will also describe approches that have been shown to block inhibitors and encourage regeneration
in vivo
. I will also speculate on what the differences are between the neonatal and adult CNS that allow the former to regenerate and the latter not to.
Nucleosome displacement in transcription: Figure 1.
Authors: Workman Jerry L.
Published: August 2006

Recent reports reinforce the notion that nucleosomes are highly dynamic in response to the process of transcription. Nucleosomes are displaced at promoters during gene activation in a process that involves histone modification, ATP-dependent nucleosome remodeling complexes, histone chaperones and perhaps histone variants. During transcription elongation nucleosomes are acetylated and transferred behind RNA polymerase II where they are required to suppress spurious transcription initiation within the body of the gene. It is becoming increasingly clear that the eukaryotic transcriptional machinery is adapted to exploit the presence of nucleosomes in very sophisticated ways.
Cytokines regulate postnatal hematopoietic stem cell expansion: opposing roles of thrombopoietin and LNK
Authors: Buza-Vidas Natalija , Antonchuk Jennifer , Qian Hong , Månsson Robert , Luc Sidinh , Zandi Sasan , Anderson Kristina , Takaki Satoshi , Nygren Jens M. , Jensen Christina T. , Jacobsen Sten Eirik W.
Published: August 2006

The role of cytokines as regulators of hematopoietic stem cell (HSC) expansion remains elusive. Herein, we identify thrombopoietin (THPO) and the cytokine signaling inhibitor LNK, as opposing physiological regulators of HSC expansion. Lnk−/− HSCs continue to expand postnatally, up to 24-fold above normal by 6 mo of age. Within the stem cell compartment, this expansion is highly selective for self-renewing long-term HSCs (LT-HSCs), which show enhanced THPO responsiveness. Lnk−/− HSC expansion is dependent on THPO, and 12-wk-old Lnk−/−Thpo−/− mice have 65-fold fewer LT-HSCs than Lnk−/− mice. Expansions of multiple myeloid, but not lymphoid, progenitors in Lnk−/− mice also proved THPO-dependent.
Two crystal structures of Trichoderma reesei hydrophobin HFBI—The structure of a protein amphiphile with and without detergent interaction
Authors: Hakanpää Johanna , Szilvay Géza R. , Kaljunen Heidi , Maksimainen Mirko , Linder Markus , Rouvinen Juha
Published: August 2006

Hydrophobins are small fungal proteins that are highly surface active and possess a unique ability to form amphiphilic membranes through spontaneous self‐assembly. The first crystal structure of a hydrophobin, Trichoderma reesei HFBII, revealed the structural basis for the function of this amphiphilic protein—a patch consisting of hydrophobic side chains on the protein surface. Here, the crystal structures of a native and a variant T. reesei hydrophobin HFBI are presented, revealing the same overall structure and functional hydrophobic patch as in the HFBII structure. However, some structural flexibility was found in the native HFBI structure: The asymmetric unit contained four molecules, and, in two of these, an area of seven residues was displaced as compared to the two other HFBI molecules and the previously determined HFBII structure. This structural change is most probably induced by multimer formation. Both the native and the N‐Cys‐variant of HFBI were crystallized in the presence of detergents, but an association between the protein and a detergent was only detected in the variant structure. There, the molecules were arranged into an extraordinary detergent‐associated octamer and the solvent content of the crystals was 75%. This study highlights the conservation of the fold of class II hydrophobins in spite of the low sequence identity and supports our previous suggestion that concealment of the hydrophobic surface areas of the protein is the driving force in the formation of multimers and monolayers in the self‐assembly process.
Leptin, insulin, insulin‐like growth factors and their binding proteins in cord serum: insight into fetal growth and discordancy
Authors: Davidson S. , Hod M. , Merlob P. , Shtaif B.
Published: August 2006

Objective  Singleton infants with intrauterine growth restriction have an adaptive hormonal profile characterized by decreased levels of IGF‐1, IGF‐2, IGFBP‐3 and insulin and elevated levels of IGFBP‐1 and IGFBP‐2. This study examined the association between cord serum levels of six growth factors and anthropometric features at birth in twins in order to determine the intrauterine growth factor interactions and to characterize the specific hormonal profile of small discordant twins.

Design  Prevalent case‐control study.

Patients  Twenty pairs of discordant twins (5 monozygotic, 15 dizygotic) and 20 pairs of concordant twins (6 monozygotic, 14 dizygotic) matched for gestational age.

Measurements  Cord blood levels of IGF‐1, IGF‐2, IGFBP‐1, IGFBP‐3, insulin, leptin and anthropometric measurements at birth. Intra‐ and inter‐pair differences and correlation coefficients were calculated, and the data were fitted to multivariate regression models.

Results  In both discordant and concordant groups, the smaller twins had a significantly lower level of IGF‐1 (P < 0·03) and significantly higher level of IGFBP‐1 (P < 0·02) than their larger cotwins. IGFBP‐1 was inversely correlated with IGF‐1 (P < 0·05). Insulin levels were significantly higher in the smaller discordant than the smaller concordant twins (P < 0·001) and in the larger discordant than the larger concordant twins (P < 0·004). Among the monozygotic twins, the leptin level was significantly higher in the larger discordant than the larger concordant twins (P < 0·025). Percentage birth weight discordancy was statistically correlated with twin‐pair differences in IGF‐1 and IGFBP‐1.

Conclusions  Of the six factors studied, IGF‐1 appears to be the main indicator of intrauterine growth. Twin discordancy may involve compensatory rather than adaptive mechanisms or a multihormone relative resistance syndrome.
Identification of adiponectin and its receptors in human osteoblast‐like cells and association of T45G polymorphism in exon 2 of adiponectin gene with lumbar spine bone mineral density in Korean women
Authors: Lee Won Young , Rhee Eun Jung , Oh Ki Won , Kim Se Yeon , Jung Chan Hee , Yun Eun Joo , Baek Ki Hyun , Kang Moo Il , Kim Sun Woo
Published: August 2006

Objective  The role of adiponectin in bone metabolism has been recently reported in in vitro and in vivo studies. There has been no report on the association of adiponectin gene polymorphism and bone mineral density (BMD). Therefore, we investigated whether two single nucleotide polymorphisms (SNPs), T45G and G276T, in the adiponectin gene were related to BMD in Koreans. We also report on the identification of adiponectin and its receptors 1 and 2 in human osteoblast‐like cell lines.

Patients and measurements  MG‐63 cells were cultured and osteogenic and adipogenic differentiations from human mesenchymal stem cells (hMSCs) were performed. RNA was then extracted from the cultured cells and reverse transcriptase‐polymerase chain reaction (RT‐PCR) was performed using primers for adiponectin and for the adiponectin receptor genes. In 249 female and 80 male subjects, measurements were made of their lumbar spine and femoral neck BMDs, and biochemical markers of bone turnover. The genotyping of the T45G polymorphism in exon 2 and the G276T polymorphisms in intron 2 in the adiponectin gene was performed using an allelic discrimination assay with a TaqMan probe. Analyses were performed separately in each cohort.

Results  We found that the mRNAs for adiponectin and for adiponectin receptor 1 (AdipoR1) and 2 (AdipoR2) were expressed in the MG‐63 cells. Sequencing of the PCR products revealed that they were identical to human adiponectin, AdipoR1 and AdipoR2, respectively. mRNAs for adiponectin, AdipoR1 and AdipoR2 were also expressed in the osteoblastic and adipogenic cell lines differentiated from hMSCs. For the polymorphism study, the frequencies of T45G and G276T in the adiponectin gene were in compliance with Hardy–Weinberg equilibrium and the two polymorphisms were in complete linkage disequilibrium (D′ = −1·0, P < 0·001). In the female cohort, subjects with G alleles at the T45G locus had significantly lower lumbar spine BMD than those subjects with the TT genotype. Although BMD levels showed no association with the G276T locus, the GT genotype group showed significantly higher urine deoxypyridinoline levels than other genotype groups. In the male cohort, no association was observed between adiponectin genotypes and BMD levels.

Conclusions  We observed the expression of adiponectin, AdipoR1 and AdipoR2 in the MG‐63 cell line and the osteoblastic cell line differentiated from hMSCs. T45G polymorphism in exon 2 of the adiponectin gene is associated with lumbar spine BMD and G276T polymorphism in intron 2 of the adiponectin gene is associated with the urine deoxypyridinoline level in Korean women. Additional studies are needed to elucidate the precise contribution of adiponectin to bone mineral metabolism.
Hydraulic conductivity profiles of two clay soils
Authors: YOUNGS E. G. , GOSS M. J.
Published: August 2006

The profiles of hydraulic conductivity for an Evesham Series and a Denchworth Series soil were measured for saturated conditions in the field when the water‐table was near to the soil surface, making use of existing piezometers installed horizontally from inspection pits. The hydraulic conductivity profiles of both soils were found to be practically the same, decreasing from about 100 mm d−1 at a depth of 0.5m to about 0.01 mm d−1 at 1.5m. At any depth the variation in the measured hydraulic conductivity obtained from different piezometer installations in both soils was as great as that between the two soils. Hydraulic conductivity values of the Evesham soil obtained using piezometers agreed with other published results obtained with the auger‐hole method on the same site. Also the hydraulic conductivity profile to 1 m depth obtained for this soil was the same as that found for a monolith, 0.8 m in diameter, taken from an Evesham soil some 100 km away. The results give encouragement to the possibility of inferring hydraulic conductivity values from soil morphological descriptions.
Stimulation of leaf litter decomposition and associated fungi and invertebrates by moderate eutrophication: implications for stream assessment
Authors: GULIS V. , FERREIRA V. , GRAÇA M. A. S.
Published: August 2006

1. We investigated the effect of moderate eutrophication on leaf litter decomposition and associated invertebrates in five reference and five eutrophied streams in central Portugal. Fungal parameters and litter N and P dynamics were followed in one pair of streams. Benthic invertebrate parameters that are considered useful in bioassessment were estimated in all streams. Finally, we evaluated the utility of decomposition as a tool to assess stream ecosystem functional integrity.

2. Decomposition of alder and oak leaves in coarse mesh bags was on average 2.3–2.7× faster in eutrophied than in reference streams. This was attributed to stimulation of fungal activity (fungal biomass accrual and sporulation of aquatic hyphomycetes) by dissolved nutrients. These effects were more pronounced for oak litter (lower quality substrate) than alder. N content of leaf litter did not differ between stream types, while P accrual was higher in the eutrophied than in the reference stream. Total invertebrate abundances and richness associated with oak litter, but not with alder, were higher in eutrophied streams.

3. We found only positive correlations between stream nutrients (DIN and SRP) and leaf litter decomposition rates in both fine and coarse mesh bags, associated sporulation rates of aquatic hyphomycetes and, in some cases, total invertebrate abundances and richness.

4. Some metrics based on benthic invertebrate community data (e.g. % shredders, % shredder taxa) were significantly lower in eutrophied than in reference streams, whereas the IBMWP index that is specifically designed for the Iberian peninsula classified all 10 streams in the highest possible class as having ‘very good’ ecological conditions.

5. Leaf litter decomposition was sufficiently sensitive to respond to low levels of eutrophication and could be a useful functional measure to complement assessment programmes based on structural parameters.
Architectural and physiological mechanisms of reduced size inequality in CO2‐enriched stands of common ragweed (Ambrosia artemisiifolia)
Authors: STINSON KRISTINA A. , TRAN JIMMY H. , PETZOLD JENNIFER L. , BAZZAZ F. A.
Published: August 2006

Testing whether and how subordinate individuals differ from dominants in the utilization of enriched CO2 atmospheres is important for understanding future stand and community structure. We hypothesized that subordinate and dominant Ambrosia artemisiifolia L. (Asteraceae) (common ragweed) plants growing in dense stands would not equally acquire or utilize carbon gains from CO2‐enrichment, and that the resulting disproportionate growth gains to subordinates would reduce size inequalities in competing stands. We grew experimental stands of A. artemisiifolia in either ambient (360 μL L−1) or twice ambient (720 μL L−1) levels of atmospheric CO2. We compared the relative growth, photosynthetic capacity, and architecture of subordinate and dominant plants in each treatment, and assessed size inequalities using the stand‐level coefficient of variation (CV). In elevated CO2, plants grew larger, but subordinate plants shifted more mass to upper stem allocation than dominants. Dominant plants demonstrated reduced leaf‐level photosynthetic gains in elevated CO2 compared with subordinate plants. Reduced CVs in plant size reflected smaller proportional growth gains by dominants over subordinates in elevated vs. ambient stands. We conclude that differences in the architectural and physiological responses of subordinate and dominant ragweed plants reduce competition and allow subordinate plants to catch up to dominants in elevated CO2 conditions.
A novel association between clustered NF‐κB and C/EBP binding sites is required for immune regulation of mosquito Defensin genes
Authors: Meredith J. M. , Munks R. J. L. , Grail W. , Hurd H. , Eggleston P. , Lehane M. J.
Published: August 2006

A comparative analysis identified key cis‐acting regulatory elements responsible for the temporal control of mosquito Defensin gene expression. The promoters of Anopheles gambiae Defensin 1 and two isoforms of Aedes aegypti Defensin A are up‐regulated by immune challenge. This stimulated activity depends upon a cluster of three NF‐κB binding sites and closely associated C/EBP‐like motifs, which function as a unit for optimal promoter activity. Binding of NF‐κB and C/EBP like transcription factors is confirmed by electrophoretic mobility shift assay, including supershifts with antibodies to C/EBP. κB‐like motifs are abundant within antimicrobial peptide gene promoters and most are very closely associated with putative C/EBP binding sites. This novel association between NF‐κB and C/EBP binding sites may, therefore, be of widespread significance.
Genome‐wide analysis of phenobarbital‐inducible genes inDrosophila melanogaster
Authors: Sun W. , Margam V. M. , Sun L. , Buczkowski G. , Bennett G. W. , Schemerhorn B. , Muir W. M. , Pittendrigh B. R.
Published: August 2006

An oligoarray analysis was conducted to determine the differential expression of genes due to phenobarbital exposure inDrosophila melanogaster(w1118strain) third instar larvae. Seventeen genes were observed to be induced with increased expression by a statistical analysis of microarrays approach with aq ≤ 0.05. Atq ≤ 0.12, four more genes (Cyp12d1, DmGstd4, and two genes with unknown function) were found to be up‐regulated, and 11 genes with unknown function were found to be down‐regulated. Fifteen of these genes,Cyp4d14, Cyp6a2,Cyp6a8,Cyp12d1,Cyp6d5,Cyp6w1, CG2065,DmGstd6, DmGstd7, Amy‐p/Amy‐d,Ugt86Dd, GC5724, Jheh1, Jheh2 and CG11893, were verified using quantitative real time polymerase chain reaction. Some of these genes have been shown to be over‐transcribed in metabolically DDT‐resistantDrosophilastrains.
Differential expression of the detoxification genes in the different life stages of the malaria vector Anopheles gambiae
Authors: Strode C. , Steen K. , Ortelli F. , Ranson H.
Published: August 2006

The diverse habitats and diets encountered during the life cycle of an Anopheles mosquito have necessitated the development of extensive families of detoxification enzymes. Expansion of the three detoxification enzyme families (cytochrome P450s, carboxylesterases and glutathione transfereases), has occurred in mosquitoes compared with Drosophila, however, very little is known regarding the developmental expression of theses genes. Using a custom made microarray we determined the expression profile of the detoxification genes in adults, larvae and pupae of the malaria vector A. gambiae. The expression of approximately one quarter of these genes was developmentally regulated. The expression profile of each of these genes and the information this data provides on putative functions of the mosquito detoxification enzymes is discussed.
Crystal structure of the apo‐PerR‐Zn protein from Bacillus subtilis
Authors: Traoré Daouda A. K. , El Ghazouani Abdelnasser , Ilango Sougandi , Dupuy Jérôme , Jacquamet Lilian , Ferrer Jean‐Luc , Caux‐Thang Christelle , Duarte Victor , Latour Jean‐Marc
Published: August 2006

Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor that binds DNA in the presence of a regulatory metal Mn2+ or Fe2+, mediates the adaptive response to H2O2. This study presents the first crystal structure of apo‐PerR‐Zn which shows that all four cysteine residues of the protein are involved in zinc co‐ordination. The Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer. Sequence alignment of PerR‐like proteins supports that this structural site may constitute a distinctive feature of this class of peroxide stress regulators.
The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR‐family regulator DasR and links N‐acetylglucosamine metabolism to the control of development
Authors: Rigali Sébastien , Nothaft Harald , Noens Elke E. E. , Schlicht Maximilian , Colson Sévrine , Müller Marisa , Joris Bernard , Koerten Henk K. , Hopwood David A. , Titgemeyer Fritz , Van Wezel Giles P.
Published: August 2006

Members of the soil‐dwelling, sporulating prokaryotic genus Streptomyces are indispensable for the recycling of the most abundant polysaccharides on earth (cellulose and chitin), and produce a wide range of antibiotics and industrial enzymes. How do these organisms sense the nutritional state of the environment, and what controls the signal for the switch to antibiotic production and morphological development? Here we show that high extracellular concentrations of N‐acetylglucosamine, the monomer of chitin, prevent Streptomyces coelicolor progressing beyond the vegetative state, and that this effect is absent in a mutant defective of N‐acetylglucosamine transport. We provide evidence that the signal is transmitted through the GntR‐family regulator DasR, which controls the N‐acetylglucosamine regulon, including the pts genes ptsH, ptsI and crr needed for uptake of N‐acetylglucosamine. Deletion of dasR or the pts genes resulted in a bald phenotype. Binding of DasR to its target genes is abolished by glucosamine 6‐phosphate, a central molecule in N‐acetylglucosamine metabolism. Extracellular complementation experiments with many bld mutants showed that the dasR mutant is arrested at an early stage of the developmental programme, and does not fit in the previously described bld signalling cascade. Thus, for the first time we are able to directly link carbon (and nitrogen) metabolism to development, highlighting a novel type of metabolic regulator, which senses the nutritional state of the habitat, maintaining vegetative growth until changing circumstances trigger the switch to sporulation. Our work, and the model it suggests, provide new leads towards understanding how microorganisms time developmental commitment.
Phylogenetic analysis based on ITS sequences and conditions affecting the type of conidial germination of Bipolaris oryzae
Authors: Dela Paz M. A. G. , Goodwin P. H. , Raymundo A. K. , Ardales E. Y. , Cruz C. M. Vera
Published: August 2006

One taxonomic characteristic of Bipolaris species is the bipolar germination of conidia, but conidia of Bipolaris oryzae, the causal pathogen of brown spot in rice, are regularly observed to show intercalary germination, a characteristic of Drechslera species. The effect of selection, culture media and culture age on type of conidial germination was determined for three brown spot isolates from Cavinti, San Pablo and Palawan in the Philippines, obtained from infected leaves showing typical disease symptoms. Based on the analyses of their ITS1, ITS2 and 5·8S rDNA nucleotide sequences, the local isolates were clearly identified as B. oryzae. Selection for colonies of the three isolates derived from single conidia with either bipolar or intercalary germination had no effect on the number of spores showing bipolar germination in subsequent cultures. Germination on seven different culture media was tested; of these, rabbit food agar and water agar increased the percentage of bipolar germination of conidia, although this varied between isolates. Incubation of the cultures of all three isolates for longer periods prior to harvesting conidia increased the percentage of bipolar‐germinating conidia from c. 40 to c. 90% with 5‐day‐old and 30‐day‐old cultures, respectively.
Factors affecting the activity of ethephon in stimulating seed germination of Striga hermonthica (Del.) Benth.
Authors: BABIKER A. G. T. , HAMDOUN A. M.
Published: August 2006

Ethephon (2‐chloroethylphosphonic acid), which generates ethylene, stimulated the germination of pre‐conditioned seeds of Striga hermonthica when it was added to the alkaline Gezira clay soil at concentrations of 2.5 to 30 mg kg−1. As little as 5 min contact with treated soil was enough to stimulate germination. Ethephon in soil did not cause germination of unconditioned seeds for periods of up to 12 days and also had an adverse effect on seed germination when such seeds were given a second ethephon exposure after a storage period which was adequate, in untreated soil, to give the necessary pre‐conditioning. Ethephon activity persisted in air‐dry soil but declined over a 14 day period in moist soil. In the field ethephon at 0.6 to 4.8 kg ha−1 decreased the number of Striga shoots and increased sorghum height and flowering.
Leaf herbivory and nutrients increase nectar alkaloids
Authors: Adler Lynn S. , Wink Michael , Distl Melanie , Lentz Amanda J.
Published: August 2006

Correlations between traits may constrain ecological and evolutionary responses to multispecies interactions. Many plants produce defensive compounds in nectar and leaves that could influence interactions with pollinators and herbivores, but the relationship between nectar and leaf defences is entirely unexplored. Correlations between leaf and nectar traits may be mediated by resources and prior damage. We determined the effect of nutrients and leaf herbivory by Manduca sexta on Nicotiana tabacum nectar and leaf alkaloids, floral traits and moth oviposition. We found a positive phenotypic correlation between nectar and leaf alkaloids. Herbivory induced alkaloids in nectar but not in leaves, while nutrients increased alkaloids in both tissues. Moths laid the most eggs on damaged, fertilized plants, suggesting a preference for high alkaloids. Induced nectar alkaloids via leaf herbivory indicate that species interactions involving leaf and floral tissues are linked and should not be treated as independent phenomena in plant ecology or evolution.
Arthropods within the woody element of hedgerows and their distribution pattern
Authors: Pollard K. A. , Holland J. M.
Published: August 2006

1 The diversity and abundance of arthropods within hedgerows was investigated using insecticide fogging. In total, 13 390 arthropods were collected from 181 m3of hedge (2% of the total volume). The taxonomic diversity of the total sample included 51 families in 13 orders, all within the phylum Arthropoda. Five orders accounted for 90% of all arthropods: Araneae, Coleoptera, Diptera, Hemiptera and Hymenoptera. The predators were the dominant functional group accounting for 40% of the total sample.

2 The linear distribution of hedgerow arthropod assemblages was investigated by sampling arthropods in 13 hedges at seven equidistant points along each hedge. Abundance of most arthropod taxa and the four functional groups (predators, parasitoids, herbivores and scavengers) consistently showed a clumped distribution along hedges, with high numbers at both ends and in the middle section. Hedge ends were defined either as a node, where the hedge intersected with another hedge, or as a gateway prior to an adjacent landscape feature such as a wood. Aggregation of arthropods at the nodes may reflect preferable microclimatic conditions at hedgerow junctions, whereas aggregation at a gap suggests the gap acted as a barrier to movement. The aggregation at the centre remains unexplained but may be a manifestation of the movement of individual arthropods along the hedgerow.

3 The great abundance and diversity of arthropods found in the present study emphasizes the status of hedges as one of the most important noncrop habitats on farmland. The arthropods that they contain may act as food for other farmland species, aid pest control and contribute to crop pollination.
Effects of delayed mating on reproductive output of female oriental beetle Anomala orientalis (Coleoptera: Scarabaeidae)
Authors: Wenninger Erik J. , Averill Anne L.
Published: August 2006

1 Although management of the oriental beetle Anomala orientalis (Waterhouse) by mating disruption shows promise across a range of agricultural systems, relatively little is known about aspects of the reproductive biology of this species relevant to its management. We studied the effects of delayed mating on several aspects of the oviposition behaviour and biology of the oriental beetle using females mated in the laboratory at 4–13 days posteclosion.

2 Females exhibited a gradual decline in fecundity with increased age at mating that was largely a function of a decline in duration of the oviposition period, as well as lower female fertility: females mated at 11 days were less likely to lay any fertile eggs. However, egg fertility did not vary with female age at mating.

3 Because mating delay did not affect longevity, females mated at older ages experienced decreased oviposition periods; however, females laid more eggs per day with increased age at mating, which partially offset shorter oviposition periods.

4 A mating delay of ≥ 6 days relative to females mated within the first day of reaching sexual maturity resulted in an approximately 35–50% lower mean fecundity.

5 These results suggest that, for mating disruption to be a successful management tool for the oriental beetle, mating must be prevented rather than delayed. We compare the findings of the present study with the published research on delayed mating in moths and discuss the importance of these results in relation to management of the oriental beetle using female sex pheromones.
Responses of ovipositing moths to host plant deprivation: life history aspects and implications for intercropping
Authors: Åsman Karolina , Ekbom Barbara
Published: August 2006

1. When considering intercropping as a strategy to reduce pest oviposition, knowledge about the insect’s oviposition behaviour is very important. Physiological effects on the insect because of difficulties in finding a suitable oviposition site may also be important.

2. In the present study, the effects that delays in access to host plants have on lifetime fecundity on diamondback moth and leek moth were examined. The ability to postpone egg laying, fecundity and lifetime oviposition are discussed in relation to intercrop/cover crop as a strategy to reduce oviposition on crop plants.

3. When faced with host plant deprivation, the diamondback moth is relatively more dependent upon host plant stimuli for the onset of egg production. By contrast, leek moth is able to postpone egg production for a longer time. There even appeared to be a tendency for leek moth females to extend their lifetime when faced with host plant deprivation.

4. We conclude that leek moths have the ability to postpone production of eggs and lay them later in life when finally encountering host plants after a period of host plant deprivation. Therefore, the use of intercropping as a strategy to reduce oviposition is questionable. For such an insect, use of a trap crop might be a better option because the female will lay her eggs in the trap crop and not get the opportunity to lay them later in life when finally encountering crop plants.
Verbenone‐releasing flakes protect individualPinus contortatrees from attack byDendroctonus ponderosaeandDendroctonus valens(Coleoptera: Curculionidae, Scolytinae)
Authors: Gillette Nancy E. , Stein John D. , Owen Donald R. , Webster Jeffrey N. , Fiddler Gary O. , Mori Sylvia R. , Wood David L.
Published: August 2006

1 In a study site in interior northern California, twenty individual lodgepole pinesPinus contortawere sprayed with a suspension of DISRUPT Micro‐Flake®Verbenone (4,6,6‐trimethylbicyclo(3.1)hept‐3‐en‐2‐one) Bark Beetle Anti‐Aggregant flakes (Hercon Environmental, Emigsville, Pennsylvania) in water, with sticker and thickener, from ground level to a height of 7 m. Twenty trees sprayed with just water, sticker and thickener served as controls. All trees were baited immediately after spraying with mountain pine beetleDendroctonus ponderosaeaggregation pheromone lures, and lures were refreshed after 4 weeks.

2 Trees treated with verbenone had significantly lower attack density byD. ponderosaethan controls at 2, 4, 6 and 8 weeks after application of flakes.

3 None of the treated trees was attacked by red turpentine beetleDendroctonus valens, whereas control trees averaged nearly twoD. valensattacks per tree, 8 weeks after treatment.

4 A dry frass index, used to predict ultimate tree mortality, was significantly higher in control trees than treated trees for all four sampling intervals. This index proved to be a significant predictor of ultimate tree mortality.

5 Ten months after application, treated trees showed significantly lower mortality than control trees.
Oxalate ions and calcium oxalate crystal‐induced up‐regulation of osteopontin and monocyte chemoattractant protein‐1 in renal fibroblasts
Authors: UMEKAWA TOHRU , IGUCHI MASANORI , UEMURA HIROTSUGU , KHAN SAEED R.
Published: August 2006

OBJECTIVE

To examine the responses of renal fibroblasts to high oxalate (Ox) and calcium Ox (CaOx) crystals, as the latter are found in the renal interstitium of patients with primary or enteric hyperoxaluria, and in animals with experimental CaOx nephrolithiasis, and are associated with tubulointerstitial inflammation (TI). TI might begin with the production of chemoattractants by the renal epithelial cells exposed to high Ox and/or CaOx crystals; as Ox levels are also high in the renal interstitium and crystal deposition in nephrolithiasis might start in the interstitium, we hypothesized that renal fibroblasts might also be involved in the development of TI.

MATERIALS AND METHODS

We exposed renal fibroblast cells of line NRK 49F in vitro to Ox ions (500 µmol/L) or CaOx monohydrate crystals (67 µg/cm2). We assessed the production of osteopontin and monocyte chemoattractant protein‐1 (MCP‐1), and expression of their mRNA, in the cells. We also determined the cellular malondialdehyde content as a marker of reactive oxygen species (ROS)‐induced lipid peroxidation, and Trypan blue staining and the release of lactate dehydrogenase as markers of injury.

RESULTS

Similar to renal epithelial cells, renal fibroblasts were stimulated by exposure to Ox and CaOx crystals. They showed signs of injury and ROS‐induced lipid peroxidation. The mRNA expression and production of osteopontin and MCP‐1 increased significantly.

CONCLUSIONS

These results indicate that fibroblasts respond to high Ox and CaOx crystals by up‐regulating specific pathways producing pro‐inflammatory conditions. Migration of monocytes/macrophages to sites of interstitial crystal deposits can lead to localized interstitial inflammation and fibrosis.
Percentage of positive biopsy cores, preoperative prostate‐specific antigen (PSA) level, pT and Gleason score as predictors of PSA recurrence after radical prostatectomy: a multi‐institutional outcome study in Japan
Authors: YOKOMIZO AKIRA , MURAI MASARU , BABA SHIRO , OGAWA OSAMU , TSUKAMOTO TAIJI , NIWAKAWA MASASHI , TOBISU KEN‐ICHI , KINUKAWA NAOKO , NAITO SEIJI
Published: August 2006

OBJECTIVE

To evaluate the clinical outcome of radical prostatectomy (RP) in Japan, by retrospectively analysing the clinicopathological data in patients with clinical T1‐T2 prostate cancer treated by RP, as there can be prostate‐specific antigen (PSA) recurrence after RP in substantially many patients, and its character can differ according to ethnic group and/or country.

PATIENTS AND METHODS

We reviewed 1192 patients who had a RP from 1993 to 2002 with no neoadjuvant/adjuvant therapy and whose PSA level after RP decreased at least once to undetectable levels (<0.2 ng/mL). PSA recurrence was defined as ≥ 0.20 ng/mL. The patient data were collected from the Urological Oncology Study Group, a subgroup of Japan Clinical Oncology Group.

RESULTS

The patients’ median (range) age was 67  (47–83) years and their PSA level before RP was 8.7 (1.0–153) ng/mL. During the median follow‐up of 45.6 months, 302 of the 1192 patients (25.3%) developed PSA recurrence. The median time to recurrence was 369  (61–2128) days after RP. A log‐rank test showed that five significant clinicopathological factors were associated with PSA recurrence after RP: The percentage of prostate needle‐biopsy cores with cancer, the biopsy Gleason score, PSA level before RP, pathological stage, and the Gleason score of the RP specimen (P < 0.001 for all). In multivariate analyses, the percentage of positive biopsy cores, PSA level before RP, pT and the Gleason score of the RP specimen were all independent significant predictors of PSA recurrence after RP in Japanese men.

CONCLUSIONS

The frequency of PSA recurrence after RP was 25.3% in Japan and the percentage of positive biopsy cores, PSA level before RP, pT and the Gleason score of the RP specimen were independent significant factors for PSA recurrence.
Different vascular endothelial growth factor (VEGF), VEGF‐receptor 1 and ‐2 mRNA expression profiles between clear cell and papillary renal cell carcinoma
Authors: LJUNGBERG BÖRJE J. , JACOBSEN JAN , RUDOLFSSON STINA HÄGGSTRÖM , LINDH GUDRUN , GRANKVIST KJELL , RASMUSON TORGNY
Published: August 2006

OBJECTIVES

To examine vascular endothelial growth factor (VEGF), VEGF‐receptor‐(R)1, and R2 mRNA levels in renal cell carcinoma (RCC), a tumour generally refractory to most medical therapy, but for which a potentially useful therapeutic alternative is inhibition of angiogenesis.

PATIENTS AND METHODS

VEGF, VEGF‐R1 and ‐R2 mRNA levels were analysed using the quantitative reverse transcription‐polymerase chain reaction. RNA was extracted from 84 conventional (clear cell) RCCs (cRCC), 20 papillary (pRCC), six chromophobe (chRCC), and 27 corresponding kidney cortex tissues, obtained from 110 patients in whom high‐quality RNA was available from the tumours (53 women and 57 men, mean age 64.7 years, range 25–85).

RESULTS

The VEGF, VEGF‐R1, and ‐R2 mRNA levels were higher in tumour than in kidney cortex tissues. Among the RCC types, cRCC had higher VEGF levels than pRCC. In cRCC, VEGF‐R2 levels were higher in stage I–II than in more advanced stages. In pRCC, VEGF and VEGF‐R2 levels were higher in stage III than in stage I–II tumours. In cRCC, patients with VEGF levels below the median had a significantly shorter survival time than those with higher levels. By contrast, in pRCC, VEGF, VEGF‐R1 and ‐R2 RNA levels above the median were related to adverse survival. Using multivariate analysis in cRCCs, VEGF‐R1 mRNA level was the last factor to be omitted after stepwise elimination analysis.

CONCLUSION

VEGF and its receptors were associated with tumour stage and survival, but were not independent prognostic factors. Different RCC types had different expression patterns of VEGF and receptor mRNA levels. We conclude that different pathways might be involved in regulating angiogenesis in the specific RCC types. Detailed knowledge of angiogenesis in RCC is essential when designing new treatment trials where angiogenesis inhibition is used.