bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary habits mediate the relationship between socio-economic status and CVD factors among healthy adults: the ATTICA study
Authors: Panagiotakos Demosthenes B , Pitsavos Christos , Chrysohoou Christina , Vlismas Konstantinos , Skoumas Yannis , Palliou Konstantina , Stefanadis Christodoulos
Published: July 2008

Background

The aims of the present work were to investigate whether dietary habits are associated with socio-economic status (SES), and if they modify the relationship between SES and CVD risk factors, in a sample of men and women free from known CVD.

Methods

This population-based study was carried out in the province of Attica, where Athens is a major metropolis. During 2001–2002, information from 1528 men (18–87 years old) and 1514 women (18–89 years old) was collected (75 % participation rate). Among several sociodemographic, clinical and biological factors, adherence to the Mediterranean diet was assessed by a special diet score (Mediterranean Diet Score, MDS) that incorporated the inherent characteristics of this traditional diet. CVD risk factors were examined across the participants’ educational level and annual income that defined their SES.

Results

Low SES groups exhibited higher prevalence of CVD risk factors, such as obesity, hypertension, diabetes mellitus and hypercholesterolaemia (allP< 0·001). Low SES groups also showed less adherence to the Mediterranean diet than high SES groups (MDS: 23·6 (sd8·1)v. 25·6 (sd5·6),P< 0·001). Higher SES index was associated with lower likelihood of having hypercholesterolaemia (OR = 0·91; 95 % CI 0·83, 1·00) and diabetes (OR = 0·83; 95 % CI 0·72, 0·95), after adjusting for various potential confounders. However, the previously mentioned inverse relationship observed between SES and prevalence of CVD risk factors was mainly explained by the dietary habits of the participants.

Conclusions

Low SES groups showed less adherence to the Mediterranean diet compared with high SES groups. This finding may, in part, explain the higher CVD risk factors profile observed among low SES participants.
Infrared measurements of surface renewal and subsurface vortices in nearshore breaking waves
Authors: Watanabe Yasunori , Mori Nobuhito
Published: July 2008

When ocean waves reach a surf zone, jets projecting from the breakers splash sequentially, producing horizontal roller vortices beneath the jets and longitudinal counterrotating vortices behind the rollers; these vortices organize into three‐dimensional structures that evolve into a turbulent bore with wave propagation. This disrupts any uniform temperature distributions on the surface, creating heterogeneous patterns of surface temperatures. In this study, we extracted surface temperature distributions from infrared measurements in small‐ and large‐scale wave flumes, then used those data to study the renewed surfaces created by subsurface vortices beneath spilling and plunging breakers. In our large‐scale experiments, temporal and spatial scales of surface renewal and surface recovery were consistent with earlier work; however, in our small‐scale experiments, the spatial scales showed significant deviations from earlier in situ observations. These inconsistencies may be attributed to scale effects for subsurface vortices, and we show that the Froude number (Fr) can be used to characterize the initial formation of longitudinal counterrotating vortices. Further, for turbulent flows fully developed by wave breaking in a bore region, the frequency of surface renewal correlates exponentially with Reynolds number (Re). The computed vorticity on the breaking wave surface exhibits local patterns which correlate strongly with the gravity induced counterrotating vortices, which in turn renew the rear‐facing surface of the breaking waves. In contrast the turbulent bore which precedes the wave crest rapidly disturbs and renews the surface in front of the crest. These two different mechanisms for surface renewal, during the nearshore breaking process, lead to modulations in the surface temperature distribution and changes in thermal diffusivity during the propagation of the breaking wave.
Hard X rays and low‐energy gamma rays from the Moon: Dependence of the continuum on the regolith composition and the solar activity
Authors: Banerjee D. , Gasnault O.
Published: July 2008

The primary aim of the high‐energy X‐ray spectrometer (HEX) experiment on the Chandrayaan‐1 mission to the Moon is to characterize the movement of volatiles on the lunar surface through the detection of the 46.5 keV line from 210Pb, a decay product of 222Rn. An important consideration for design and operation of HEX is to estimate the continuum background signal expected from the lunar surface, as well as its dependence on solar activity and lunar composition. We have developed a Monte Carlo code utilizing Geant4 for simulating the interaction of cosmic rays in the lunar regolith, and we estimated the variation in the continuum background in the energy region of interest for various lunar compositions. Dependence of the continuum background on solar activity was also evaluated considering ferroan anorthositic (FAN) composition. Our results suggest the viability of inferring lithologic characteristics of planetary surfaces based on a study of low‐energy gamma ray emission.
Seasonal drought stress in the Amazon: Reconciling models and observations
Authors: Baker I. T. , Prihodko L. , Denning A. S. , Goulden M. , Miller S. , da Rocha H. R.
Published: July 2008

The Amazon Basin is crucial to global circulatory and carbon patterns due to the large areal extent and large flux magnitude. Biogeophysical models have had difficulty reproducing the annual cycle of net ecosystem exchange (NEE) of carbon in some regions of the Amazon, generally simulating uptake during the wet season and efflux during seasonal drought. In reality, the opposite occurs. Observational and modeling studies have identified several mechanisms that explain the observed annual cycle, including: (1) deep soil columns that can store large water amount, (2) the ability of deep roots to access moisture at depth when near‐surface soil dries during annual drought, (3) movement of water in the soil via hydraulic redistribution, allowing for more efficient uptake of water during the wet season, and moistening of near‐surface soil during the annual drought, and (4) photosynthetic response to elevated light levels as cloudiness decreases during the dry season. We incorporate these mechanisms into the third version of the Simple Biosphere model (SiB3) both singly and collectively, and confront the results with observations. For the forest to maintain function through seasonal drought, there must be sufficient water storage in the soil to sustain transpiration through the dry season in addition to the ability of the roots to access the stored water. We find that individually, none of these mechanisms by themselves produces a simulation of the annual cycle of NEE that matches the observed. When these mechanisms are combined into the model, NEE follows the general trend of the observations, showing efflux during the wet season and uptake during seasonal drought.
Analysis of methane production pathways in a riparian wetland of a temperate forest catchment, using δ13C of pore water CH4 and CO2
Authors: Itoh Masayuki , Ohte Nobuhito , Koba Keisuke , Sugimoto Atsuko , Tani Makoto
Published: July 2008

To clarify how hydrological processes affect biogenic methane (CH4) production and emission from soil surfaces, we analyzed the δ13C of CH4 and CO2 and chemical constituents dissolved in groundwater at a wetland in the headwater catchment of a temperate forest in Japan. We estimated the contribution of acetate fermentation using the δ13C isotope mass balance of dissolved CH4 and CO2. CH4 production pathways (e.g., acetate fermentation and carbonate reduction) changed temporally and spatially with hydrologically controlled redox conditions. The proportion of methanogenesis attributable to acetate fermentation usually decreased with temperature, suggesting that carbonate reduction dominated under conditions of high CO2 concentration. In particular, the groundwater table and summer temperatures were key controlling factors in the interannual and intra‐annual changes in CH4 production pathways, controlling oxygen supply and consumption and, therefore, redox conditions in the soil. Under high temperature and high water table conditions during summer, the soil was strongly reduced and the proportion of carbonate reduction increased. Acetate fermentation also increased episodically, resulting in sporadic increases in δ13C‐CH4. The calculated acetate contribution obviously decreased in periods of low water table and high temperature when the soil surface was relatively oxic, implying deactivation of acetoclastic methanogenesis under oxic conditions. Thus, hydrological processes control the supply of these electron donors and acceptors and therefore play an important role in determining the relative proportions of CH4‐producing pathways. Our results also indicate that an increase in acetate contribution under highly reducing conditions stimulates CH4 production and emission from the soil surface.
Holocene millennial‐scale productivity variations in the Sicily Channel (Mediterranean Sea)
Authors: Incarbona Alessandro , Di Stefano Enrico , Patti Bernardo , Pelosi Nicola , Bonomo Sergio , Mazzola Salvatore , Sprovieri Rodolfo , Tranchida Giorgio , Zgozi Salem , Bonanno Angelo
Published: July 2008

The calcareous nannofossil assemblages of Ocean Drilling Program Hole 963D from the central Mediterranean Sea have been investigated to document oceanographic changes in surface waters. The studied site is located in an area sensitive to large‐scale atmospheric and climatic systems and to high‐ and low‐latitude climate connection. It is characterized by a high sedimentation rate (the achieved mean sampling resolution is <70 years) that allowed the Sicily Channel environmental changes to be examined in great detail over the last 12 ka BP. We focused on the species Florisphaera profunda that lives in the lower photic zone. Its distribution pattern shows repeated abundance fluctuations of about 10–15%. Such variations could be related to different primary production levels, given that the study of the distribution of this species on the Sicily Channel seafloor demonstrates the significant correlation to productivity changes as provided by satellite imagery. Productivity variations were quantitatively estimated and were interpreted on the basis of the relocation of the nutricline within the photic zone, led by the dynamics of the summer thermocline. Productivity changes were compared with oceanographic, atmospheric, and cosmogenic nuclide proxies. The good match with Holocene master records, as with ice‐rafted detritus in the subpolar North Atlantic, and the near‐1500‐year periodicity suggest that the Sicily Channel environment responded to worldwide climate anomalies. Enhanced Northern Hemisphere atmospheric circulation, which has been reported as one of the most important forcing mechanisms for Holocene coolings in previous Mediterranean studies, had a remarkable impact on the water column dynamics of the Sicily Channel.
Impact of hydraulic suction history on crack growth mechanics in soil
Authors: Yoshida S. , Hallett P. D.
Published: July 2008

The mechanics of crack formation and the influence of soil stress history were described using the crack tip opening angle (CTOA) measured with fractography. Two soils were studied: a model soil consisting of 40% Ca‐bentonite and 60% fine silica sand and a remolded paddy soil with similar clay content and mineralogy. Fracture testing used deep‐notch bend specimens formed by molding soils at the liquid limit into rectangular bars, equilibrating to soil water suction ranging from 5 kPa to 50 kPa (with some 50 kPa specimens wetted to 5 kPa), and inserting a crack 0.4× specimen thickness. Bend tests at a constant displacement rate of 1 mm min−1 provided data on applied force and load point displacement. The growth and geometry of the cracks were quantified from a series of images to determine the CTOA. Modulus of rupture, evaluated from the peak force, increased as water suction increased. However, rewetting did not alter the peak stress from the 50 kPa value, indicating that shrinkage‐induced consolidation was more important than the soil water suction at the onset of testing. CTOA measured during stable crack growth decreased with drying. CTOA decreased even further when specimens equilibrated initially to 50 kPa were rewetted to 5 kPa. These results suggested that CTOA was primarily governed by the stiffness, although rewetting probably altered the capillary stresses in advance of the crack tip. Our future work will combine CTOA with a model that couples hydrological and mechanical processes to take into account the dependency of CTOA on the soil water regime so that crack propagation in soil can be predicted.
Modeling of Io‐Jupiter decameter arcs, emission beaming and energy source
Authors: Hess S. , Cecconi B. , Zarka P.
Published: July 2008

The electrodynamic interaction between Io and Jupiter causes electron acceleration in/near the Io flux tube (IFT), which in turn produces intense radio emissions in the hecto‐decameter range, displaying arc shapes in the time‐frequency plane. The shapes depend on the hemisphere of origin of the emission and on the Io‐Jupiter‐observer geometry. Assuming radio wave generation by the cyclotron‐maser instability, we simulate t‐f arc shapes as a function of emission beaming, lead angle between the radio emitting field line and the instantaneous Io field line, and electron energy. A good fit of arcs t‐f location and shape is obtained for loss‐cone driven (oblique) emission beamed in a hollow cone of half‐angle ≥80° around the source magnetic field, closing at high frequencies, and of cone thickness ≤1°. The lead angle is found between a few degrees and ∼40° in both hemispheres. Resonant electron energies are about a few keV. Implications on the absence of a plasma cavity at IFT footprints and on Jupiter's internal magnetic field model are discussed.
THEMIS observations of the dayside traveling compression region and flows surrounding flux transfer events
Authors: Liu J. , Angelopoulos V. , Sibeck D. , Phan T. , Pu Z. Y. , McFadden J. , Glassmeier K. H. , Auster H. U.
Published: July 2008

We present multipoint observations of Flux Transfer Events (FTEs) by the THEMIS spacecraft in a string‐of‐pearls configuration, at the near‐equatorial magnetopause. Common characteristics from a number of cases, examined at various local times, are exemplified here by a case study of FTE trains observed in the pre‐noon sector, on Aug. 18, 2007. We show that the magneto‐pause‐normal flow velocity is consistently towards and away from the magnetopause on the inbound and outbound transit of the FTE, on all spacecraft sufficiently away from the magnetopause. The velocity just outside the FTE at the time of closest proximity to the FTE core is opposite to the FTE direction of motion even when the FTE moves in the same direction as the adjacent sheath. The total pressure inside and just outside the FTE is consistently larger than expected from pressure balance at a nominal (unperturbed) magnetopause and therefore the result of local compression by the passing FTE. The multi‐spacecraft observation enables the reconstruction of the Dayside Traveling Compression Region (DTCR), whose result is consistent with previous theoretical results. Semi‐periodic compressional velocity oscillations were observed and are likely driven by nearby occurrences of FTE trains, implying recurrent reconnection with a similar periodicity.
Aerosol radiative forcing during dust events over New Delhi, India
Authors: Pandithurai G. , Dipu S. , Dani K. K. , Tiwari S. , Bisht D. S. , Devara P. C. S. , Pinker R. T.
Published: July 2008

We present results from sun/sky radiometer measurements of aerosol optical characteristics carried out in New Delhi during March–June, 2006, as part of the Indian Space Research Organization's Integrated Campaign for Aerosol Radiation Budget. For the first time at this site, derived are parameters such as aerosol optical depth (AOD), single scattering albedo (SSA), asymmetry parameter, Ångstrom exponent, and real and imaginary refractive indices in five spectral channels. During the campaign, a consistent increase in aerosol loading from March to June with monthly average AOD values at 0.5μm of 0.55, 0.75, 1.22 and 1.18, respectively, was observed. Ångstrom exponent gradually decreases from 1.28 (March) to 0.47 (June), indicating an increased abundance of coarse particles due to dust storms that transport desert dust from the Thar desert and adjoining regions. SSA at 0.5 μm is found to be in the range of 0.84 to 0.74 from March to June, indicating an increasing contribution from the mixture of anthropogenic and desert dust absorbing aerosols. Optical properties derived during the campaign are used in a radiative‐transfer model to estimate aerosol radiative forcing at the surface and at the top‐of‐the atmosphere. A consistent increase in surface cooling is evident, ranging from −39 W m−2 (March) to −99 W m−2 (June) and an increase in heating of the atmosphere from 27 W m−2 (March) to 123 W m−2 (June). Heating rates in the lower atmosphere (up to 5 km) are 0.6, 1.3, 2.1, and 2.5K/d from March, April, May, and June 2006, respectively. Higher aerosol induced heating in the premonsoon period has been shown to have an impact on the regional monsoon climate.
The O‐linked N‐acetylglucosamine modification in cellular signalling and the immune system
Authors: Golks Alexander , Guerini Danilo
Published: July 2008

The intracellular modification of proteins by the addition of a single O‐linked N‐acetylglucosamine (O‐GlcNAc) molecule is a ubiquitous post‐translational modification in eukaryotic cells. It is catalysed by O‐linked N‐acetylglucosaminyltransferase, which attaches O‐GlcNAc to serine/threonine residues, and it is counter‐regulated by β‐N‐acetylglucosaminidase, which is the antagonistic glycosidase that removes the O‐GlcNAc group. O‐GlcNAc modification competes with phosphorylation by protein kinases at similar sites, thereby affecting important signalling nodes. Accumulating evidence supports a central role for O‐GlcNAc modifications and the corresponding enzymes in the regulation of immune cells, particularly in the activation processes of T and B lymphocytes. Here, we discuss recent advances in the field of O‐GlcNAc modifications, focusing on the cells of the immune system.
Compartmentalized DCC signalling is distinct from DCC localized to lipid rafts
Authors: Petrie Ryan J. , Zhao Beibei , Bedford Fiona , Lamarche‐Vane Nathalie
Published: July 2008

Background information. Netrin‐1 is a bi‐functional cue that attracts or repels different classes of neurons during development. The netrin‐1 receptor DCC (deleted in colorectal cancer) acts as a tyrosine kinase‐associated receptor to mediate the attractive response towards netrin‐1. The lipid raft‐localized Src family kinase Fyn is required for DCC‐mediated axon guidance. DCC functions are also dependent on lipid rafts, membrane microdomains corresponding to a low‐density, detergent‐resistant membrane fraction. However, it remains unclear how the association of DCC with lipid rafts controls netrin‐1 signalling.

Results. DCC targeted to lipid rafts represented a minor proportion of total DCC inside the cell, but predominated on the cell surface of both IMR‐32 human neuroblastoma cells and embryonic cortical neurons. Netrin‐1 accumulated in lipid rafts, but had no effect on the targeting of DCC to that compartment, with DCC remaining on the cell surface in lipid rafts through 60 min post‐treatment. However, DCC was able to interact with Fyn, both in the lipid rafts and soluble compartments isolated from embryonic E19 rat brains, whereas early downstream signalling components such as Nck‐1, and total and active focal adhesion kinase were mainly localized to the non‐lipid raft compartment.

Conclusions. Together, these results suggest that DCC can be found in raft and non‐raft portions of the plasma membrane, with early signalling events propagated by non‐raft associated DCC.
Structure–function relationships in Escherichia coli adenylate cyclase
Authors: Linder Jürgen U.
Published: July 2008

Class I adenylate cyclases are found in γ- and δ-proteobacteria. They play central roles in processes such as catabolite repression in Escherichia coli or development of full virulence in pathogens such as Yersinia enterocolitica and Vibrio vulnificus. The catalytic domain (residues 2–446) of the adenylate cyclase of E. coli was overexpressed and purified. It displayed a Vmax of 665 nmol of cAMP·mg−1·min−1 and a Km of 270 μM. Titration of the metal cofactor Mg2+ against the substrate ATP showed a requirement for free metal ions in addition to the MgATP complex, suggesting a two-metal-ion mechanism as is known for class II and class III adenylate cyclases. Twelve residues which are essential for catalysis were identified by mutagenesis of a total of 20 polar residues conserved in all class I adenylate cyclases. Five essential residues (Ser103, Ser113, Asp114, Asp116 and Trp118) were part of a region which is found in all members of the large DNA polymerase β-like nucleotidyltransferase superfamily. Alignment of the E. coli adenylate cyclase with the crystal structure of a distant member of the superfamily, archaeal tRNA CCA-adding enzyme, suggested that Asp114 and Asp116 are the metal-cofactor-ion-binding residues. The S103A mutant had a 17-fold higher Km than wild-type, demonstrating its important role in substrate binding. In comparison with the tRNA CCA-adding enzyme, Ser103 of the E. coli adenylate cyclase apparently binds the γ-phosphate group of ATP. Consistent with this function, the S103A mutation caused a marked reduction of discrimination between ATP- and ADP- or AMP-derived inhibitors.
Copper pretreatment augments ultraviolet B toxicity in the cyanobacterium Anabaena doliolum: a proteomic analysis of cell death
Authors: Bhargava Poonam , Kumar Arvind , Mishra Yogesh , Rai Lal Chand
Published: July 2008

This study provides first-hand proteomic characterisation of Cu-pretreatment-induced augmentation of ultraviolet B toxicity in the cyanobacterium Anabaena doliolum Bharadwaja. Of the three treatments (i.e. Cu, UV-B and Cu + UV-B) tested, the UV-B treatment of Cu-pretreated Anabaena produced a greater inhibition of oxygen evolution, 14C fixation, ATP and NADPH contents than UV-B alone. Proteomic analysis using two-dimensional gel electrophoresis (2DE), MALDI-TOF MS/MS and reverse transcription polymerase chain reaction (RT–PCR) of Cu, UV-B, and Cu + UV-B treated Anabaena exhibited significant and reproducible alterations in 12 proteins. Of these, manganese superoxide dismutase (Mn-SOD), iron superoxide dismutase (Fe-SOD) and peroxiredoxin (PER) are antioxidative enzymes; ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase (PRK), flavodoxin (Flv), plastocyanin (PLC), phosphoglycerate kinase (PGK), phycocyanin (PC) and phycoerythrocyanin α-chain (PC α-chain) are linked with photosynthesis and respiration; and DnaK and nucleoside diphosphate kinase (NDPK) are associated with cellular processes and light signalling, respectively. However, when subjected to a high dose of UV-B, Cu-pretreated Anabaena depicted a severe down-regulation of DnaK, NDPK and Flv, probably because of inevitable oxidative stress. Thus, the augmentation of UV-B toxicity by Cu can be attributed to the down-regulation of DnaK, NDPK and Flv.
Overexpression of the VvLTP1 gene interferes with somatic embryo development in grapevine
Authors: François Julie , Lallemand Magali , Fleurat-Lessard Pierette , Laquitaine Laurent , Delrot Serge , Coutos-Thévenot Pierre , Gomès Eric
Published: July 2008

Grapevine (Vitis vinifera L.) embryos have an early developmental pattern which differs from the one observed in model angiosperms such as Arabidopsis, in that the plane of divisions show variations from one individual to another. Furthermore, the protoderm (the first tissue to differentiate) does not form in one step but rather, gradually with time during globule formation. In Arabidopsis, expression pattern of a particular lipid transfer protein (LTP) isoform, AtLTP1, appears to be related to protoderm establishment, and is considered as a molecular marker of its differentiation. To investigate whether a similar role for LTPs in the development of grapevine embryos, we investigated the expression pattern of VvLTP1, a Vitis homologue of AtLTP1, in somatic embryo development. Expression of the GUS reporter gene under the control of the VvLTP1 promoter demonstrated that this LTP isoform is a marker of protoderm formation, and confirmed that this tissue forms sequentially over time. Ectopic expression of VvLTP1 under the control of the 35S promoter led to grossly misshapen embryos, which failed to acquire bilateral symmetry and displayed an abnormal epidermal layer. These results indicate that a correct spatial or temporal expression, or both, of this gene is essential for grapevine embryo development.
Identification and characterisation of a novel inorganic carbon acquisition gene, CIA7, from an insertional mutant of Chlamydomonas reinhardtii
Authors: Ynalvez Ruby A. , Moroney James V.
Published: July 2008

Chlamydomonas reinhardtii is a unicellular eukaryotic alga which possesses a CO2-concentrating mechanism (CCM) that enables it to grow at low CO2 concentrations. Previously, insertional mutants were generated to enable isolation of inorganic carbon transporters and other proteins that might be essential for a functional CCM. These mutants have an antibiotic resistance gene that encodes a protein that binds to Zeocin inhibiting Zeocin’s DNA strand cleavage activity. The DNA flanking the BleR insert of one of the high CO2 requiring strains, named cia7, was cloned with inverse-PCR and sequenced. Sequence analysis showed homology to conserved bacterial proteins of unknown function, but there were no ESTs in this region of the genome. However, the presence of a gene was established by PCR and RLM-RACE. CIA7 was found to have four exons and the BleR insert was in the fourth exon. CIA7 encodes a protein of 104 amino acids with a calculated molecular mass of 11.3 kDa. Based on the ChloroP prediction program, the protein is predicted to have a chloroplast targeting signal. Complementation analyses results showed possible partially rescued mutants, and RNAi showed several transformants with a sick on low CO2 phenotype with reduced expression of CIA7. These results suggest that CIA7 is a gene that facilitates growth in C. reinhardtii under low CO2 conditions. One possible role of CIA7 would be in the delivery or storage of a metal ion. It may play a potential role as either a domain of a metal transporter or as a metallochaperone.
Expression of sucrose synthase in the developing endosperm is essential for early seed development in cotton
Authors: Ruan Yong-Ling , Llewellyn Danny J. , Liu Qing , Xu Shou-Min , Wu Li-Min , Wang Lu , Furbank Robert T.
Published: July 2008

Successful seed development requires coordinated interaction of the endosperm and embryo. In most dicotyledonous seeds, the endosperm is crushed and absorbed by the expanding embryo in the later stages of seed development. Little is known about the metabolic interaction between the two filial tissues early in seed development. We examined the potential role of sucrose synthase (Sus) in the endosperm development of cotton. Sus was immunologically localised in the cellularising endosperm, but not in the heart-stage embryo at 10 days after anthesis. The activities of Sus and acid invertase were significantly higher in the endosperm than in the young embryos, which corresponded to a steep concentration difference in hexoses between the endosperm and the embryo. This observation indicates a role for the endosperm in generating hexoses for the development of the two filial tissues. Interestingly, Sus expression and starch deposition were spatially separated in the seeds. Silencing the expression of Sus in the endosperm using an RNAi approach led to the arrest of early seed development. Histochemical analyses revealed a significant reduction in cellulose and callose in the deformed endosperm cells of the Sus-suppressed seed. The data indicate a critical role of Sus in early seed development through regulation of endosperm formation.
Development of fruit cuticle in cherry tomato (Solanum lycopersicum)
Authors: Domínguez Eva , López-Casado Gloria , Cuartero Jesús , Heredia Antonio
Published: July 2008

The cuticle of a plant plays an important role in many physiological events of fruit development and ripening. Despite this, little is known about cuticle formation and development. We include a detailed morphological study at the microscopic level of cuticle during fruit growth and ripening using tomato as a fruit model. In addition, a study of the differences in cuticle thickness and composition during development is included. The four genotypes studied in this work showed a similar timing of the main morphological events: initiation of epidermal differentiation, changes in the distribution of the lipid, pectin and cellulose material within the cuticle, appearance of pegs, beginning of cuticle invaginations, maximum thickness and loss of polysaccharidic material. Fruit growth, measured by fruit diameter, showed a positive correlation with the increase of cuticle thickness and the amount of cuticle and their cutin and polysaccharide components per fruit unit during development. By contrast, cuticle waxes showed a different behaviour. Two important characteristics of cuticle growth were observed during tomato fruit development. First, the amount of cuticle per surface area reached its maximum in the first 15 days after anthesis and remained more or less constant until ripening. Second, there was a significant loss of polysaccharidic material from the beginning of ripening (breaker stage) to full red ripe.
Comparative mapping of a QTL controlling black point formation in barley
Authors: March Timothy J. , Able Jason A. , Willsmore Kerrie , Schultz Carolyn J. , Able Amanda J.
Published: July 2008

The dark discoloration of the embryo end of barley grain (known as black point) is a physiological disorder and the discovery of a quantitative trait locus (QTL) on 2H confirms this trait is controlled genetically. The mechanisms underlying black point tolerance can now be dissected through identification of candidate genes. Comparisons between the QTL identified on chromosomes 2H of barley and 2B of wheat suggest that they are in similar positions near the centromere. In silico analysis, using rice, identified genes residing on two comparative chromosomes (4 and 7) of the rice genome. Analysis of the 12.6 Mb region revealed 1928 unique annotations classified into 11 functional categories. Expressed sequence tags (ESTs) with high sequence similarity to enzymes proposed to be involved in black point formation were used to develop restriction fragment length polymorphisms (RFLPs). To ensure an even coverage of markers across the QTL, RFLP markers were also developed from other ESTs. Mapping of these markers has reduced the QTL region from 28 to 18 cM. This study has identified candidate genes for the control of black point formation and paves the way for future research to develop black point resistant barley cultivars.
The protist,
Monosiga brevicollis
, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan
Authors: Manning Gerard , Young Susan L. , Miller W. Todd , Zhai Yufeng
Published: July 2008

Tyrosine kinase signaling has long been considered a hallmark of intercellular communication, unique to multicellular animals. Our genomic analysis of the unicellular choanoflagellate
Monosiga brevicollis
discovers a remarkable count of 128 tyrosine kinases, 38 tyrosine phosphatases, and 123 phosphotyrosine (pTyr)-binding SH2 proteins, all higher counts than seen in any metazoan. This elaborate signaling network shows little orthology to metazoan counterparts yet displays many innovations reminiscent of metazoans. These include extracellular domains structurally related to those of metazoan receptor kinases, alternative methods for membrane anchoring and phosphotyrosine interaction in cytoplasmic kinases, and domain combinations that link kinases to small GTPase signaling and transcription. These proteins also display a wealth of combinations of known signaling domains. This uniquely divergent and elaborate signaling network illuminates the early evolution of pTyr signaling, explores innovative ways to traverse the cellular signaling circuitry, and shows extensive convergent evolution, highlighting pervasive constraints on pTyr signaling.
Par3/Par6 polarity complex coordinates apical ectoplasmic specialization and blood–testis barrier restructuring during spermatogenesis
Authors: Wong Elissa W. P. , Mruk Dolores D. , Lee Will M. , Cheng C. Yan
Published: July 2008

The Par3/Par6/aPKC and the CRB3/Pals1/PATJ polarity complexes are involved in regulating apical ectoplasmic specialization (ES) and blood–testis barrier (BTB) restructuring in the testis. Par6 was a component of the apical ES and the BTB. However, its level was considerably diminished at both sites at stage VIII of the cycle. Par6 also formed a stable complex with Pals1 and JAM-C (a component of the apical ES) in normal testes. When rats were treated with adjudin to induce apical ES restructuring without compromising the BTB, Par6 staining virtually disappeared at the apical ES in misaligned spermatids before their depletion. Additionally, the Par6/Pals1 complex became tightly associated with Src kinase, rendering a loss of association of the Par6/Pals1 complex with JAM-C, thereby destabilizing apical ES to facilitate spermatid loss. Primary Sertoli cell cultures with established functional BTB, but without apical ES, were next used to assess the Par6-based complex on BTB dynamics. When either Par6 or Par3 was knocked down by RNAi in Sertoli cell epithelium, a significant loss of the corresponding protein by ≈60% in cells vs. controls was detected, alongside with a decline in aPKC after Par6, but not Par3, knockdown. This Par3 or Par6 knockdown also led to a transient loss of selected BTB proteins at the cell–cell interface, thereby compromising the BTB integrity. These findings illustrate that the Par6/Par3-based polarity complex likely coordinates the events of apical ES and BTB restructuring that take place concurrently at the opposing ends of adjacent Sertoli cells in the seminiferous epithelium during spermatogenesis.
Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in
Drosophila melanogaster
Authors: Kroiss Matthias , Schultz Jörg , Wiesner Julia , Chari Ashwin , Sickmann Albert , Fischer Utz
Published: July 2008

In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2–8. Here we have studied the evolution of this machinery using complete genome assemblies of multiple model organisms. The SMN complex has gained complexity in evolution by a blockwise addition of Gemins onto an ancestral core complex composed of SMN and Gemin2. In contrast to this overall evolutionary trend to more complexity in metazoans, orthologs of most Gemins are missing in dipterans. In accordance with these bioinformatic data a previously undescribed biochemical purification strategy elucidated that the dipteran
Drosophila melanogaster
contains an SMN complex of remarkable simplicity. Surprisingly, this minimal complex not only mediates the assembly reaction in a manner very similar to its vertebrate counterpart, but also prevents misassembly onto nontarget RNAs. Our data suggest that only a minority of Gemins are required for the assembly reaction
per se
, whereas others may serve additional functions in the context of UsnRNP biogenesis. The evolution of the SMN complex is an interesting example of how the simplification of a biochemical process contributes to genome compaction.
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
Authors: Hyeon Changbong , Morrison Greg , Thirumalai D.
Published: July 2008

The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated by using single-molecule force-clamp experiments by attaching semiflexible polymers to the ends of hairpins, have been used to infer their folding landscapes. Using simulations and theory, we study the effect of the dynamics of the attached handles on the handle-free RNA free-energy profileFoeq(zm), wherezmis the molecular extension of the hairpin. Accurate measurements ofFoeq(zm) requires stiff polymers with smallL/lp, whereLis the contour length of the handle, andlpis the persistence length. Paradoxically, reliable estimates of the hopping rates can only be made by using flexible handles. Nevertheless, we show that the equilibrium free-energy profileFoeq(zm) at an external tensionfm, the force (f) at which the folded and unfolded states are equally populated, in conjunction with Kramers' theory, can provide accurate estimates of the force-dependent hopping rates in the absence of handles at arbitrary values off. Our theoretical framework shows thatzmis a good reaction coordinate for nucleic acid hairpins under tension.
The relationship between dNTP pool levels and mutagenesis in an
Escherichia coli
NDP kinase mutant
Authors: Nordman Jared , Wright Andrew
Published: July 2008

Loss of nucleoside diphosphate kinase (Ndk) function in
Escherichia coli
results in an increased frequency of spontaneous mutation and an imbalance in dNTP pool levels. It is presumed that the imbalance in dNTP pool levels is responsible for the mutator phenotype of an
E. coli ndk
mutant. A human homologue of Ndk and potential suppressor of tumor metastasis,
nm23-H2
, can complement the mutagenic phenotype of an
E. coli ndk
mutant. Here, we show that the antimutagenic property of
nm23-H2
in
E. coli
is independent of dNTP pool levels, indicating that dNTP pool imbalance is not responsible for the mutator phenotype associated with the loss of
ndk
function. We have identified multiple genetic interactions between
ndk
and genes involved in the metabolism of dUTP, a potentially mutagenic precursor of thymidine biosynthesis. We show that loss of
ndk
function is synergistic with a
dut-1
mutation and synthetically lethal with the loss of thymidine kinase function. Our results suggest that Ndk prevents the accumulation of dUTP
in vivo
. Based on these results and biochemical studies of Ndk, we propose that the mutagenic phenotype of an
ndk
mutant is caused by excess misincorporation of uracil in place of thymidine combined with a defect in the uracil base excision pathway.
Class 1A PI3K regulates vessel integrity during development and tumorigenesis
Authors: Yuan Tina L. , Choi Hak Soo , Matsui Aya , Benes Cyril , Lifshits Eugene , Luo Ji , Frangioni John V. , Cantley Lewis C.
Published: July 2008

PI3K is important in the regulation of growth, proliferation, and survival of tumor cells. We show that class 1A PI3K is also critical in the tumor microenvironment by regulating the integrity of the tumor vasculature. Using Tie2Cre-mediated deletion of the PI3K regulatory subunits (p85α, p55α, p50α, and p85β), we generated mice with endothelial cell-specific loss of class 1A PI3K. Complete loss of all subunits caused acute embryonic lethality at E11.5 due to hemorrhaging, whereas retention of a single p85α allele yielded viable mice that survived to adulthood. These heterozygous mice exhibited no vascular defects until challenged with a pathological insult, such as tumor cells or high levels of VEGF. Under these pathological conditions, heterozygous mice exhibited localized vascular abnormalities, including vessel leakage and the inability to maintain large vessels, which caused a deceleration of tumorigenesis. Furthermore, we show that a PI3K inhibitor can mimic the effects of class 1A PI3K loss, which suggests that targeting class 1A PI3K may be a promising therapy for blocking tumor angiogenesis.
Nutritional considerations for captive Charadriiformes (shorebirds, gulls and alcids).
Authors: McWilliams D. A.
Published: July 2008

A progressive decline in Charadriiforme populations prioritizes appropriate life-stage nutrition for captive Charadriiformes as conservation efforts continue to develop. These species are opportunistic feeders on fish and aquatic invertebrates. Appropriate life-stage nutrition for captive Charadriiformes requires nutrient provision beyond simple piscivory. This review presents existing data on relevant dietary components (protein, fat, carotenoids, minerals and vitamins) and examines the importance of these components in life-stage nutrition (embryonic development, neonates (chicks), juveniles, adults, breeding, incubation and chick rearing). The issue of determining metabolic rates of captive Charadriiformes populations is briefly presented. Eight recommendations for the amelioration of diet deficiencies are outlined.
Ruptured aneurysm of noncoronary sinus of valsalva: demonstration with magnetic resonance imaging
Authors: Dincer T. C. , Basarici I. , Calisir C. , Mete A. , Ermis C. , Deger N.
Published: July 2008

There are few published reports regarding imaging findings of sinus of Valsalva aneurysms (SVA) with magnetic resonance imaging (MRI). We present an unusual form of ruptured SVA, emphasizing the diagnostic importance of MRI among a range of imaging techniques. This case report describes a case of idiopathic (thought to be congenital in origin), acutely symptomatic ruptured noncoronary SVA diagnosed by MRI and confirmed with conventional angiography and surgery. MRI accurately showed aneurysm size, location, and rupture into the right atrium and provided valuable information about this rare lesion.
The noncommutative Choquet boundary
Authors: Arveson William
Published: July 2008

Let

S
S

be an operator system–a self-adjoint linear subspace of a unital

C
∗

C^*

-algebra

A
A

such that

1

∈
S

\mathbf 1\in S

and

A
=

C
∗

(
S
)

A=C^*(S)

is generated by

S
S

. A boundary representation for

S
S

is an irreducible representation

π
\pi

of

C
∗

(
S
)

C^*(S)

on a Hilbert space with the property that

π

↾
S

\pi \restriction _S

has a unique completely positive extension to

C
∗

(
S
)

C^*(S)

. The set

∂
S

\partial _S

of all (unitary equivalence classes of) boundary representations is the noncommutative counterpart of the Choquet boundary of a function system

S
⊆
C
(
X
)

S\subseteq C(X)

that separates points of

X
X

. It is known that the closure of the Choquet boundary of a function system

S
S

is the Šilov boundary of

X
X

relative to

S
S

. The corresponding noncommutative problem of whether every operator system has “sufficiently many" boundary representations was formulated in 1969, but has remained unsolved despite progress on related issues. In particular, it was unknown if

∂
S

≠
∅

\partial _S\neq \emptyset

for generic

S
S

. In this paper we show that every separable operator system has sufficiently many boundary representations. Our methods use separability in an essential way.
On the superrigidity of malleable actions with spectral gap
Authors: Popa Sorin
Published: July 2008

We prove that if a countable group

Γ
\Gamma

contains infinite commuting subgroups

H
,

H
′

⊂
Γ

H, H’\subset \Gamma

with

H
H

non-amenable and

H
′

H’

“weakly normal” in

Γ
\Gamma

, then any measure preserving

Γ
\Gamma

-action on a probability space which satisfies certain malleability, spectral gap and weak mixing conditions (e.g. a Bernoulli

Γ
\Gamma

-action) is cocycle superrigid. If in addition

H
′

H’

can be taken non-virtually abelian and

Γ
↷
X

\Gamma \curvearrowright X

is an arbitrary free ergodic action while

Λ
↷
Y
=

T

Λ

\Lambda \curvearrowright Y=\mathbb {T}^{\Lambda }

is a Bernoulli action of an arbitrary infinite conjugacy class group, then any isomorphism of the associated II

1

_{1}

factors
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper L Superscript normal infinity Baseline upper X right-normal-factor-semidirect-product normal upper Gamma asymptotically-equals upper L Superscript normal infinity Baseline upper Y right-normal-factor-semidirect-product normal upper Lamda">

L

∞

X
⋊
Γ
≃

L

∞

Y
⋊
Λ

L^{\infty }X \rtimes \Gamma \simeq L^{\infty }Y \rtimes \Lambda

comes from a conjugacy of the actions.
Stable self-similar blow up dynamics for the three dimensional relativistic gravitational Vlasov-Poisson system
Authors: Lemou Mohammed , Méhats Florian , Raphaël Pierre
Published: July 2008

The three dimensional gravitational Vlasov-Poisson system

∂
t

f
+
v
⋅

∇
x

f
−

E
f

⋅

∇
v

f
=
0

\partial _tf+v\cdot \nabla _x f-E_f\cdot \nabla _vf=0

, where

E
f

(
x
)
=

∇
x

ϕ
f

(
x
)

E_f(x)=\nabla _x \phi _f(x)

,

Δ
x

ϕ
f

=

ρ
f

(
x
)

\Delta _x\phi _f=\rho _f(x)

,

ρ
f

(
x
)
=

∫

R

N

f
(
x
,
v
)
d
v

\rho _f(x)=\int _{\mathbb {R}^N} f(x,v)dv

, describes the mechanical state of a stellar system subject to its own gravity. Smooth initial data yield unique global in time solutions from a celebrated result by Pfaffelmoser. There exists a hierarchy of physical models which aim at taking into account further relativistic effects. The simplest one is the three dimensional relativistic gravitational Vlasov-Poisson system
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="partial-differential Subscript t Baseline f plus StartFraction v Over StartRoot 1 plus StartAbsoluteValue v EndAbsoluteValue squared EndRoot EndFraction dot nabla Subscript x Baseline f minus upper E Subscript f Baseline dot nabla Subscript v Baseline f equals 0">

∂
t

f
+

v

1
+

|

v

|

2

⋅

∇
x

f
−

E
f

⋅

∇
v

f
=
0

\partial _tf+\frac {v}{\sqrt {1+|v|^2}}\cdot \nabla _x f-E_f\cdot \nabla _vf=0

which we study here. A striking feature as observed by Glassey and Schaeffer is that this system now admits finite blow up solutions. Nevertheless, the existence argument is purely obstructive and provides no insight into the description of the singularity formation. We exhibit in this paper a family of finite time blow up self-similar solutions and prove that their blow up dynamic is stable with respect to radially symmetric perturbations. Our analysis applies to the four dimensional gravitational Vlasov-Poisson system as well.
Localization for quantum groups at a root of unity
Authors: Backelin Erik , Kremnizer Kobi
Published: July 2008

In the paper Quantum flag varieties, equivariant quantum

D

\mathcal {D}

-modules, and localization of Quantum groups, Backelin and Kremnizer defined categories of equivariant quantum

O

q

\mathcal {O}_q

-modules and

D

q

\mathcal {D}_q

-modules on the quantum flag variety of

G
G

. We proved that the Beilinson-Bernstein localization theorem holds at a generic

q
q

. Here we prove that a derived version of this theorem holds at the root of unity case. Namely, the global section functor gives a derived equivalence between categories of

U
q

U_q

-modules and

D

q

\mathcal {D}_q

-modules on the quantum flag variety.

For this we first prove that

D

q

\mathcal {D}_q

is an Azumaya algebra over a dense subset of the cotangent bundle

T
⋆

X

T^\star X

of the classical (char

0
0

) flag variety

X
X

. This way we get a derived equivalence between representations of

U
q

U_q

and certain

O

T
⋆

X

\mathcal {O}_{T^\star X}

-modules.

In the paper Localization for a semi-simple Lie algebra in prime characteristic, by Bezrukavnikov, Mirkovic, and Rumynin, similar results were obtained for a Lie algebra

g

p

\mathfrak {g}_p

in char

p
p

. Hence, representations of

g

p

\mathfrak {g}_p

and of

U
q

U_q

(when

q
q

is a

p
p

’th root of unity) are related via the cotangent bundles

T
⋆

X

T^\star X

in char

0
0

and in char

p
p

, respectively.