bluuebunny/crossref_metadata_2025 huggingface dataset:
Caveolae Mediate Growth Factor-induced Disassembly of Adherens Junctions to Support Tumor Cell Dissociation
Authors: Orlichenko Lidiya , Weller Shaun G. , Cao Hong , Krueger Eugene W. , Awoniyi Muyiwa , Beznoussenko Galina , Buccione Roberto , McNiven Mark A.
Published: July 2009

Remodeling of cell–cell contacts through the internalization of adherens junction proteins is an important event during both normal development and the process of tumor cell metastasis. Here we show that the integrity of tumor cell–cell contacts is disrupted after epidermal growth factor (EGF) stimulation through caveolae-mediated endocytosis of the adherens junction protein E-cadherin. Caveolin-1 and E-cadherin closely associated at cell borders and in internalized structures upon stimulation with EGF. Furthermore, preventing caveolae assembly through reduction of caveolin-1 protein or expression of a caveolin-1 tyrosine phospho-mutant resulted in the accumulation of E-cadherin at cell borders and the formation of tightly adherent cells. Most striking was the fact that exogenous expression of caveolin-1 in tumor cells that contain tight, well-defined, borders resulted in a dramatic dispersal of these cells. Together, these findings provide new insights into how cells might disassemble cell–cell contacts to help mediate the remodeling of adherens junctions, and tumor cell metastasis and invasion.
Transportin Regulates Major Mitotic Assembly Events: From Spindle to Nuclear Pore Assembly
Authors: Lau Corine K. , Delmar Valerie A. , Chan Rene C. , Phung Quang , Bernis Cyril , Fichtman Boris , Rasala Beth A. , Forbes Douglass J.
Published: July 2009

Mitosis in higher eukaryotes is marked by the sequential assembly of two massive structures: the mitotic spindle and the nucleus. Nuclear assembly itself requires the precise formation of both nuclear membranes and nuclear pore complexes. Previously, importin alpha/beta and RanGTP were shown to act as dueling regulators to ensure that these assembly processes occur only in the vicinity of the mitotic chromosomes. We now find that the distantly related karyopherin, transportin, negatively regulates nuclear envelope fusion and nuclear pore assembly in Xenopus egg extracts. We show that transportin—and importin beta—initiate their regulation as early as the first known step of nuclear pore assembly: recruitment of the critical pore-targeting nucleoporin ELYS/MEL-28 to chromatin. Indeed, each karyopherin can interact directly with ELYS. We further define the nucleoporin subunit targets for transportin and importin beta and find them to be largely the same: ELYS, the Nup107/160 complex, Nup53, and the FG nucleoporins. Equally importantly, we find that transportin negatively regulates mitotic spindle assembly. These negative regulatory events are counteracted by RanGTP. We conclude that the interplay of the two negative regulators, transportin and importin beta, along with the positive regulator RanGTP, allows precise choreography of multiple cell cycle assembly events.
Heterogeneous Nuclear Ribonucleoprotein A2 Is a Common Transcriptional Coactivator in the Nuclear Transcription Response to Mitochondrial Respiratory Stress
Authors: Guha Manti , Pan Hua , Fang Ji-Kang , Avadhani Narayan G.
Published: July 2009

Mitochondrial dysfunction and altered transmembrane potential initiate a mitochondrial respiratory stress response, also known as mitochondrial retrograde response, in a wide spectrum of cells. The mitochondrial stress response activates calcineurin, which regulates transcription factors, including a new nuclear factor-κB (NF-κB) pathway, different from the canonical and noncanonical pathways. In this study using a combination of small interfering RNA-mediated mRNA knock down, transcriptional analysis, and chromatin immunoprecipitation, we report a common mechanism for the regulation of previously established stress response genes Cathepsin L, RyR1, and Glut4. Stress-regulated transcription involves the cooperative interplay between NF-κB (cRel: p50), C/EBPδ, cAMP response element-binding protein, and nuclear factor of activated T cells. We show that the functional synergy of these factors requires the stress-activated heterogeneous nuclear ribonucleoprotein (hnRNP) A2 as a coactivator. HnRNP A2 associates with the enhanceosome, mostly through protein–protein interactions with DNA-bound factors. Silencing of hnRNP A2 as well as other DNA binding signature factors prevents stress-induced transcriptional activation and reverses the invasiveness of mitochondrial DNA-depleted C2C12 cells. Induction of mitochondrial stress signaling by electron transfer chain inhibitors also involved hnRNPA2 activation. We describe a common mechanism of mitochondrial respiratory stress-induced activation of nuclear target genes that involves hnRNP A2 as a transcription coactivator.
Dissection of CENP-C–directed Centromere and Kinetochore Assembly
Authors: Milks Kirstin J. , Moree Ben , Straight Aaron F.
Published: July 2009

Eukaryotic cells ensure accurate chromosome segregation in mitosis by assembling a microtubule-binding site on each chromosome called the kinetochore that attaches to the mitotic spindle. The kinetochore is assembled specifically during mitosis on a specialized region of each chromosome called the centromere, which is constitutively bound by >15 centromere-specific proteins. These proteins, including centromere proteins A and C (CENP-A and -C), are essential for kinetochore assembly and proper chromosome segregation. How the centromere is assembled and how the centromere promotes mitotic kinetochore formation are poorly understood. We have used Xenopus egg extracts as an in vitro system to study the role of CENP-C in centromere and kinetochore assembly. We show that, unlike the histone variant CENP-A, CENP-C is not maintained at centromeres through spermatogenesis but is assembled at the sperm centromere from the egg cytoplasm. Immunodepletion of CENP-C from metaphase egg extract prevents kinetochore formation on sperm chromatin, and depleted extracts can be complemented with in vitro–translated CENP-C. Using this complementation assay, we have identified CENP-C mutants that localized to centromeres but failed to support kinetochore assembly. We find that the amino terminus of CENP-C promotes kinetochore assembly by ensuring proper targeting of the Mis12/MIND complex and CENP-K.
S‐Petasin, the Main Sesquiterpene ofPetasites formosanus,Inhibits Phosphodiesterase Activity and Suppresses Ovalbumin‐Induced Airway Hyperresponsiveness
Authors: Shih Chung-Hung , Huang Tzu-Jung , Chen Chien-Ming , Lin Yun-Lian , Ko Wun-Chang
Published: July 2009

S‐Petasin is the main sesquiterpene ofPetasites formosanus, a traditional folk medicine used to treat hypertension, tumors and asthma in Taiwan. The aim of the present study was to investigate its inhibitory effects on phosphodiesterase (PDE) 1–5, and on ovalbumin (OVA)‐induced airway hyperresponsiveness (AHR) in a murine model of allergic asthma.S‐Petasin concentration‐dependently inhibited PDE3 and PDE4 activities with 50% inhibitory concentrations (IC50) of 25.5, and 17.5 μM, respectively. According to the Lineweaver‐Burk analysis,S‐petasin competitively inhibited PDE3 and PDE4 activities with respective dissociation constants for inhibitor binding (Ki) of 25.3 and 18.1 μM, respectively. Both IC50andKivalues for PDE3 were significantly greater than those for PDE4.S‐Petasin (10–30 μmol/kg, administered subcutaneously (s.c.)) dose‐dependently and significantly attenuated the enhanced pause (Penh) value induced by methacholine (MCh) in sensitized and challenged mice. It also significantly suppressed the increases in total inflammatory cells, lymphocytes, neutrophils, eosinophils and levels of cytokines, including interleukin (IL)‐2, IL‐4 and IL‐5, tumor necrosis factor (TNF)‐αand interferon (IFN)‐γin bronchoalveolar lavage fluid (BALF) of these mice. In addition,S‐petasin (10–30 μmol/kg, s.c.) dose‐dependently and significantly attenuated total and OVA‐specific immunoglobulin E (IgE) levels in the serum and BALF, and enhanced the IgG2alevel in serum of these mice. The PDE4Hvalue ofS‐petasin was >300 μM; therefore, its PDE4H/PDE4Lvalue was calculated to be >17. In conclusion, the present results forS‐petasin at least partially explain whyPetasites formosanusis used as a folk medicine to treat asthma in Taiwan.
Coevolution of non-fertile sperm and female receptivity in a butterfly
Authors: Wedell Nina , Wiklund Christer , Bergström Jonas
Published: July 2009

Sexual conflict can promote rapid evolution of male and female reproductive traits. Males of many polyandrous butterflies transfer nutrients at mating that enhances female fecundity, but generates sexual conflict over female remating due to sperm competition. Butterflies produce both normal fertilizing sperm and large numbers of non-fertile sperm. In the green-veined white butterfly,
Pieris napi
, non-fertile sperm fill the females' sperm storage organ, switching off receptivity and thereby reducing female remating. There is genetic variation in the number of non-fertile sperm stored, which directly relates to the female's refractory period. There is also genetic variation in males' sperm production. Here, we show that females' refractory period and males' sperm production are genetically correlated using quantitative genetic and selection experiments. Thus selection on male manipulation may increase the frequency of susceptible females to such manipulations as a correlated response and
vice versa
.
Coupled relaxations at the protein–water interface in the picosecond time scale
Authors: Paciaroni A. , Cornicchi E. , Marconi M. , Orecchini A. , Petrillo C. , Haertlein M. , Moulin M. , Sacchetti F.
Published: July 2009

The spectral behaviour of a protein and its hydration water has been investigated through neutron scattering. The availability of both hydrogenated and perdeuterated samples of maltose-binding protein (MBP) allowed us to directly measure with great accuracy the signal from the protein and the hydration water alone. Both the spectra of the MBP and its hydration water show two distinct relaxations, a behaviour that is reminiscent of glassy systems. The two components have been described using a phenomenological model that includes two Cole–Davidson functions. In MBP and its hydration water, the two relaxations take place with similar average characteristic times of approximately 10 and 0.2 ps. The common time scales of these relaxations suggest that they may be a preferential route to couple the dynamics of the water hydrogen-bond network around the protein surface with that of protein fluctuations.
Effect of nanoparticulate bioactive glass particles on bioactivity and cytocompatibility of poly(3-hydroxybutyrate) composites
Authors: Misra Superb K. , Ansari Tahera , Mohn Dirk , Valappil Sabeel P. , Brunner Tobias J. , Stark Wendelin J. , Roy Ipsita , Knowles Jonathan C. , Sibbons Paul D. , Jones Eugenia Valsami , Boccaccini Aldo R. , Salih Vehid
Published: July 2009

This work investigated the effect of adding nanoparticulate (29 nm) bioactive glass particles on the bioactivity, degradation and
in vitro
cytocompatibility of poly(3-hydroxybutyrate) (P(3HB)) composites/nano-sized bioactive glass (n-BG). Two different concentrations (10 and 20 wt %) of nanoscale bioactive glass particles of 45S5 Bioglass composition were used to prepare composite films. Several techniques (Raman spectroscopy, scanning electron microscopy, atomic force microscopy, energy dispersive X-ray) were used to monitor their surface and bioreactivity over a 45-day period of immersion in simulated body fluid (SBF). All results suggested the P(3HB)/n-BG composites to be highly bioactive, confirmed by the formation of hydroxyapatite on material surfaces upon immersion in SBF. The weight loss and water uptake were found to increase on increasing bioactive glass content. Cytocompatibility study (cell proliferation, cell attachment, alkaline phosphatase activity and osteocalcin production) using human MG-63 osteoblast-like cells in osteogenic and non-osteogenic medium showed that the composite substrates are suitable for cell attachment, proliferation and differentiation.
Rotationally invariant quadratures for the sphere
Authors: Ahrens Cory , Beylkin Gregory
Published: July 2009

We construct near-optimal quadratures for the sphere that are invariant under the icosahedral rotation group. These quadratures integrate all (N+1)2linearly independent functions in a rotationally invariant subspace of maximal order and degreeN. The nodes of these quadratures are nearly uniformly distributed, and the number of nodes is only marginally more than the optimal (N+1)2/3 nodes. Using these quadratures, we discretize the reproducing kernel on a rotationally invariant subspace to construct an analogue of Lagrange interpolation on the sphere. This representation uses function values at the quadrature nodes. In addition, the representation yields an expansion that uses a single function centred and mostly concentrated at nodes of the quadrature, thus providing a much better localization than spherical harmonic expansions. We show that this representation may be localized even further. We also describe two algorithms of complexityfor using these grids and representations. Finally, we note that our approach is also applicable to other discrete rotation groups.
Focusing of unidirectional wave groups on deep water: an approximate nonlinear Schrödinger equation-based model
Authors: Adcock T. A. A. , Taylor P. H.
Published: July 2009

This paper sets out an approximate analytical model describing the nonlinear evolution of a Gaussian wave group in deep water. The model is derived using the conserved quantities of the cubic nonlinear Schrödinger equation (NLSE). The key parameter for describing the evolution is the amplitude-to-wavenumber bandwidth ratio, a quantity analogous to the Benjamin–Feir index for random sea-states. For smaller values of this parameter, the group is wholly dispersive, whereas for more nonlinear cases, solitons are formed. Our model predicts the characteristics and the evolution of the groups in both regimes. These predictions are found to be in good agreement with numerical simulations using the NLSE and are in qualitative agreement with numerical results from a fully nonlinear potential flow solver and experimental results.
Dynamic arm swinging in human walking
Authors: Collins Steven H. , Adamczyk Peter G. , Kuo Arthur D.
Published: July 2009

Humans tend to swing their arms when they walk, a curious behaviour since the arms play no obvious role in bipedal gait. It might be costly to use muscles to swing the arms, and it is unclear whether potential benefits elsewhere in the body would justify such costs. To examine these costs and benefits, we developed a passive dynamic walking model with free-swinging arms. Even with no torques driving the arms or legs, the model produced walking gaits with arm swinging similar to humans. Passive gaits with arm phasing opposite to normal were also found, but these induced a much greater reaction moment from the ground, which could require muscular effort in humans. We therefore hypothesized that the reduction of this moment may explain the physiological benefit of arm swinging. Experimental measurements of humans (n= 10) showed that normal arm swinging required minimal shoulder torque, while volitionally holding the arms still required 12 per cent more metabolic energy. Among measures of gait mechanics, vertical ground reaction moment was most affected by arm swinging and increased by 63 per cent without it. Walking with opposite-to-normal arm phasing required minimal shoulder effort but magnified the ground reaction moment, causing metabolic rate to increase by 26 per cent. Passive dynamics appear to make arm swinging easy, while indirect benefits from reduced vertical moments make it worthwhile overall.
Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction
Authors: McGinnity Philip , Jennings Eleanor , deEyto Elvira , Allott Norman , Samuelsson Patrick , Rogan Gerard , Whelan Ken , Cross Tom
Published: July 2009

The assessment report of the 4th International Panel on Climate Change confirms that global warming is strongly affecting biological systems and that 20–30% of species risk extinction from projected future increases in temperature. It is essential that any measures taken to conserve individual species and their constituent populations against climate-mediated declines are appropriate. The release of captive bred animals to augment wild populations is a widespread management strategy for many species but has proven controversial. Using a regression model based on a 37-year study of wild and sea ranched Atlantic salmon (
Salmo salar
) spawning together in the wild, we show that the escape of captive bred animals into the wild can substantially depress recruitment and more specifically disrupt the capacity of natural populations to adapt to higher winter water temperatures associated with climate variability. We speculate the mechanisms underlying this seasonal response and suggest that an explanation based on bio-energetic processes with physiological responses synchronized by photoperiod is plausible. Furthermore, we predict, by running the model forward using projected future climate scenarios, that these cultured fish substantially increase the risk of extinction for the studied population within 20 generations. In contrast, we show that positive outcomes to climate change are possible if captive bred animals are prevented from breeding in the wild. Rather than imposing an additional genetic load on wild populations by releasing maladapted captive bred animals, we propose that conservation efforts should focus on optimizing conditions for adaptation to occur by reducing exploitation and protecting critical habitats. Our findings are likely to hold true for most poikilothermic species where captive breeding programmes are used in population management.
Environmental change drove macroevolution in cupuladriid bryozoans
Authors: O'Dea Aaron , Jackson Jeremy
Published: July 2009

Most macroevolutionary events are correlated with changes in the environment, but more rigorous evidence of cause and effect has been elusive. We compiled a 10 Myr record of origination and extinction, changes in mode of reproduction, morphologies and abundances of cupuladriid bryozoan species, spanning the time when primary productivity collapsed in the southwestern Caribbean as the Isthmus of Panama closed. The dominant mode of reproduction shifted dramatically from clonal to aclonal, due in part to a pulse of origination followed by extinction that was strongly selective in favour of aclonal species. Modern-day studies predict reduced clonality in increasingly oligotrophic conditions, thereby providing a mechanistic explanation supporting the hypothesis that the collapse in primary productivity was the cause of turnover. However, whereas originations were synchronous with changing environments, extinctions lagged 1–2 Myr. Extinct species failed to become more robust and reduce their rate of cloning when the new environmental conditions arose, and subsequently saw progressive reductions in abundance towards their delayed demise. Environmental change is therefore established as the root cause of macroevolutionary turnover despite the lag between origination and extinction.
A new specimen ofBiseridens qilianicusindicates its phylogenetic position as the most basal anomodont
Authors: Liu Jun , Rubidge Bruce , Li Jinling
Published: July 2009

A new well-preserved basal therapsid skull from the Xidagou Formation, Middle Permian of China, is identified asBiseridens qilianicus. The following synapomorphies distinguishBiseridensas an anomodont and not an eotitanosuchian as previously described: short snout; dorsally elevated zygomatic arch and septomaxilla lacking elongated posterodorsal process between nasal and maxilla. The presence of a differentiated tooth row; denticles on vomer, palatine and pterygoid; contact between tabular and opisthotic; lateral process of transverse flange of pterygoid free of posterior ramus and absence of mandibular foramen exclude it from other anomodonts. Our cladistic analysis indicatesBiseridensto be the most basal anomodont, highlights separate Laurasian and Gondwanan basal anomodont clades and suggests that dicynodonts had their origins in the Gondwanan clade. The co-occurrence of the most basal anomodont (Biseridens) together with the most basal therapsid (Raranimus), basal anteosaurid dinocephalians, bolosaurids and dissorophids suggests that the earliest therapsid faunas are from China.
Complexation and Toxicity of Copper in Higher Plants. I. Characterization of Copper Accumulation, Speciation, and Toxicity inCrassula helmsiias a New Copper Accumulator
Authors: Küpper Hendrik , Götz Birgit , Mijovilovich Ana , Küpper Frithjof C. , Meyer-Klaucke Wolfram
Published: July 2009

The amphibious water plant Crassula helmsii is an invasive copper (Cu)-tolerant neophyte in Europe. It now turned out to accumulate Cu up to more than 9,000 ppm in its shoots at 10 μ  m (=0.6 ppm) Cu2+ in the nutrient solution, indicating that it is a Cu hyperaccumulator. We investigated uptake, binding environment, and toxicity of Cu in this plant under emerged and submerged conditions. Extended x-ray absorption fine structure measurements on frozen-hydrated samples revealed that Cu was bound almost exclusively by oxygen ligands, likely organic acids, and not any sulfur ligands. Despite significant differences in photosynthesis biochemistry and biophysics between emerged and submerged plants, no differences in Cu ligands were found. While measurements of tissue pH confirmed the diurnal acid cycle typical for Crassulacean acid metabolism, Δ13C measurements showed values typical for regular C3 photosynthesis. Cu-induced inhibition of photosynthesis mainly affected the photosystem II (PSII) reaction center, but with some unusual features. Most obviously, the degree of light saturation of electron transport increased during Cu stress, while maximal dark-adapted PSII quantum yield did not change and light-adapted quantum yield of PSII photochemistry decreased particularly in the first 50 s after onset of actinic irradiance. This combination of changes, which were strongest in submerged cultures, shows a decreasing number of functional reaction centers relative to the antenna in a system with high antenna connectivity. Nonphotochemical quenching, in contrast, was modified by Cu mainly in emerged cultures. Pigment concentrations in stressed plants strongly decreased, but no changes in their ratios occurred, indicating that cells either survived intact or died and bleached quickly.
Thiamin Confers Enhanced Tolerance to Oxidative Stress in Arabidopsis
Authors: Tunc-Ozdemir Meral , Miller Gad , Song Luhua , Kim James , Sodek Ahmet , Koussevitzky Shai , Misra Amarendra Narayan , Mittler Ron , Shintani David
Published: July 2009

Thiamin and thiamin pyrophosphate (TPP) are well known for their important roles in human nutrition and enzyme catalysis. In this work, we present new evidence for an additional role of these compounds in the protection of cells against oxidative damage. Arabidopsis (Arabidopsis thaliana) plants subjected to abiotic stress conditions, such as high light, cold, osmotic, salinity, and oxidative treatments, accumulated thiamin and TPP. Moreover, the accumulation of these compounds in plants subjected to oxidative stress was accompanied by enhanced expression of transcripts encoding thiamin biosynthetic enzymes. When supplemented with exogenous thiamin, wild-type plants displayed enhanced tolerance to oxidative stress induced by paraquat. Thiamin application was also found to protect the reactive oxygen species-sensitive ascorbate peroxidase1 mutant from oxidative stress. Thiamin-induced tolerance to oxidative stress was accompanied by decreased production of reactive oxygen species in plants, as evidenced from decreased protein carbonylation and hydrogen peroxide accumulation. Because thiamin could protect the salicylic acid induction-deficient1 mutant against oxidative stress, thiamin-induced oxidative protection is likely independent of salicylic acid signaling or accumulation. Taken together, our studies suggest that thiamin and TPP function as important stress-response molecules that alleviate oxidative stress during different abiotic stress conditions.
Mutations in UDP-Glucose:Sterol Glucosyltransferase in Arabidopsis Cause Transparent Testa Phenotype and Suberization Defect in Seeds
Authors: DeBolt Seth , Scheible Wolf-Rüdiger , Schrick Kathrin , Auer Manfred , Beisson Fred , Bischoff Volker , Bouvier-Navé Pierrette , Carroll Andrew , Hematy Kian , Li Yonghua , Milne Jennifer , Nair Meera , Schaller Hubert , Zemla Marcin , Somerville Chris
Published: July 2009

In higher plants, the most abundant sterol derivatives are steryl glycosides (SGs) and acyl SGs. Arabidopsis (Arabidopsis thaliana) contains two genes, UGT80A2 and UGT80B1, that encode UDP-Glc:sterol glycosyltransferases, enzymes that catalyze the synthesis of SGs. Lines having mutations in UGT80A2, UGT80B1, or both UGT80A2 and UGT8B1 were identified and characterized. The ugt80A2 lines were viable and exhibited relatively minor effects on plant growth. Conversely, ugt80B1 mutants displayed an array of phenotypes that were pronounced in the embryo and seed. Most notable was the finding that ugt80B1 was allelic to transparent testa15 and displayed a transparent testa phenotype and a reduction in seed size. In addition to the role of UGT80B1 in the deposition of flavanoids, a loss of suberization of the seed was apparent in ugt80B1 by the lack of autofluorescence at the hilum region. Moreover, in ugt80B1, scanning and transmission electron microscopy reveals that the outer integument of the seed coat lost the electron-dense cuticle layer at its surface and displayed altered cell morphology. Gas chromatography coupled with mass spectrometry of lipid polyester monomers confirmed a drastic decrease in aliphatic suberin and cutin-like polymers that was associated with an inability to limit tetrazolium salt uptake. The findings suggest a membrane function for SGs and acyl SGs in trafficking of lipid polyester precursors. An ancillary observation was that cellulose biosynthesis was unaffected in the double mutant, inconsistent with a predicted role for SGs in priming cellulose synthesis.
Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice
Authors: Zou Cheng , Lehti-Shiu Melissa D. , Thibaud-Nissen Françoise , Prakash Tanmay , Buell C. Robin , Shiu Shin-Han
Published: July 2009

Pseudogenes (Ψ) are nonfunctional genomic sequences resembling functional genes. Knowledge of Ψs can improve genome annotation and our understanding of genome evolution. However, there has been relatively little systemic study of Ψs in plants. In this study, we characterized the evolution and expression patterns of Ψs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). In contrast to animal Ψs, many plant Ψs experienced much stronger purifying selection. In addition, plant Ψs experiencing stronger selective constraints tend to be derived from relatively ancient duplicates, suggesting that they were functional for a relatively long time but became Ψs recently. Interestingly, the regions 5′ to the first stops in the Ψs have experienced stronger selective constraints compared with 3′ regions, suggesting that the 5′ regions were functional for a longer period of time after the premature stops appeared. We found that few Ψs have expression evidence, and their expression levels tend to be lower compared with annotated genes. Furthermore, Ψs with expressed sequence tags tend to be derived from relatively recent duplication events, indicating that Ψ expression may be due to insufficient time for complete degeneration of regulatory signals. Finally, larger protein domain families have significantly more Ψs in general. However, while families involved in environmental stress responses have a significant excess of Ψs, transcription factors and receptor-like kinases have lower than expected numbers of Ψs, consistent with their elevated retention rate in plant genomes. Our findings illustrate peculiar properties of plant Ψs, providing additional insight into the evolution of duplicate genes and benefiting future genome annotation.
Are South Africa's cities changing? Indications from the mid‐1990s
Authors: Seekings Jeremy
Published: July 2009

Books reviewed in this article:

Scott A. Bollens, Urban peace‐building in divided societies: Belfast and Johannesburg

Alan Morris, Bleakness and light: inner‐city transition in Hillbrow, Johannesburg

Robert Cameron, Democratisation of South African local government: a tale of three cities

Susan Parnell, Edgar Pieterse, Mark Swilling and Dominique Wooldridge (eds.), Democratising local government: the South African experiment

Grant R. Saff, Changing Cape Town: urban dynamics, policy and planning during the political transition in South Africa
The Law: Executive Privilege: Definition and Standards of Application
Authors: ROZELL MARK J.
Published: July 2009

Executive privilege is the right of the president and high‐level executive branch officials to withhold information from those with compulsory power—Congress and the courts (and, therefore, ultimately the public). Because it is nowhere mentioned in the Constitution and also due to the occasional abuses of that power, executive privilege is controversial. Although few today question the constitutionality of executive privilege, there is considerable debate about its proper scope and limits. This article traces the historical development of the meaning and standards of executive privilege. The purpose is to show that disputes over executive privilege are best resolved through the normal ebb and flow of our separation of powers system and not through some statutory definition or precise court clarification of that power.
Epidermolysis bullosa nevus arising in a patient with Dowling–Meara type epidermolysis bullosa simplex with a novel K5 mutation
Authors: SUGIYAMA‐FUKAMATSU Hiroko , SUZUKI Norihiro , NAKANISHI Gen , IWATSUKI Keiji
Published: July 2009

We report herein a 4‐year‐old girl with Dowling–Meara type epidermolysis bullosa (EB) who presented with peculiar pigmented nevi. Blister formation had repeatedly occurred on the erythematous plaques in a circinate fashion since birth, and marked hyperkeratosis was observed on the palms and soles associated with nail deformity. Her mother and maternal grandmother also had similar symptoms. In addition to the blistering lesions, the patient had three large, asymmetrical, pigmented plaques with color variegation. Light and electron microscopic findings of the blistering lesions showed a subepidermal blister with intracytoplasmic granules in keratinocytes as well as degeneration of basal cells and aggregation of tonofilaments. The pigmented lesions revealed histopathological features of compound nevus without malignant changes. Gene analysis revealed an E478K (Glu to Lys) mutation in exon 5 of the keratin 5 (K5) gene. These findings, together with clinical features, were consistent with those of Dowling–Meara type EB associated with so‐called EB nevus.
Case of follicular mucinosis: Nestin‐expression in mucin‐producing cells
Authors: SAKUMA Hiroyuki , AMOH Yasuyuki , NIIYAMA Shiro , KANOH Maho , KATSUOKA Kensei
Published: July 2009

A 29‐year‐old Japanese man had an asymptomatic, solitary, indurated, erythematous plaque measuring 30 mm × 30 mm on his jaw that had been present for a month. The skin lesion had follicular hyperkeratosis, and lacked hair. A skin biopsy specimen showed a dense perifollicular infiltration composed of lymphocytes, with an admixture of eosinophils in the full thickness of the dermis. The hair follicles and sebaceous glands had reticular epithelial degeneration by mucoid material of the outer root sheath and sebaceous epithelium. The mucoid material stained with Alcian blue at pH 2.5. The clinical and histological features were consistent with the diagnosis of follicular mucinosis. On immunohistochemistry, the outer root sheath cells with reticular epithelial degeneration were nestin‐positive and keratin 15‐negative. These results suggest that the outer root sheath cells with reticular epithelial degeneration come from the nestin‐positive, multipotent, hair follicle stem cells.
Human papillomavirus 16-specific T cell responses in classic HPV-related vulvar intra-epithelial neoplasia. Determination of strongly immunogenic regions from E6 and E7 proteins
Authors: Bourgault Villada I , Moyal Barracco M , Berville S , Bafounta M L , Longvert C , Prémel V , Villefroy P , Jullian E , Clerici T , Paniel B , Maillère B , Choppin J , Guillet J G
Published: July 2009

Cell-mediated immunity directed against human papillomavirus 16 (HPV-16) antigens was studied in 16 patients affected with classic vulvar intra-epithelial neoplasia (VIN), also known as bowenoid papulosis (BP). Ten patients had blood lymphocyte proliferative T cell responses directed against E6/2 (14–34) and/or E6/4 (45–68) peptides, which were identified in the present study as immunodominant among HPV-16 E6 and E7 large peptides. Ex vivo enzyme-linked immunospot–interferon (IFN)-γ assay was positive in three patients who had proliferative responses. Twelve months later, proliferative T cell responses remained detectable in only six women and the immunodominant antigens remained the E6/2 (14–34) and E6/4 (45–68) peptides. The latter large fragments of peptides contained many epitopes able to bind to at least seven human leucocyte antigen (HLA) class I molecules and were strong binders to seven HLA-DR class II molecules. In order to build a therapeutic anti-HPV-16 vaccine, E6/2 (14–34) and E6/4 (45–68) fragments thus appear to be good candidates to increase HPV-specific effector T lymphocyte responses and clear classic VIN (BP) disease lesions.
Determinants of biodiversity in subtropical shallow lakes (Atlantic coast, Uruguay)
Authors: KRUK CARLA , RODRÍGUEZ‐GALLEGO LORENA , MEERHOFF MARIANA , QUINTANS FEDERICO , LACEROT GISSELL , MAZZEO NÉSTOR , SCASSO FLAVIO , PAGGI JUAN C. , PEETERS EDWIN T. H. M. , MARTEN SCHEFFER
Published: July 2009

1. Shallow lakes and ponds contribute disproportionally to species richness relative to other aquatic ecosystems. In‐lake conditions (e.g. presence of submerged plants) seem to play a key role in determining diversity, as has been demonstrated for temperate lakes. When water quality deteriorates and turbidity increases, conditions in such lakes are affected drastically resulting in a loss of diversity. However, it is not clear whether subtropical lakes show the same pattern and whether the richness of all groups reacts similarly to environmental changes.

2. Our aim was to analyse the main factors explaining patterns of species richness in plankton, fish and submerged macrophyte assemblages in both turbid and clear subtropical shallow lakes. We analysed abiotic and biotic features of 18 subtropical, small‐ to medium‐sized, shallow lakes along the Uruguayan coast. We compared both turbid and clear ecosystem states and evaluated the relative variance explained by the factors measured.

3. Variables describing lake and catchment morphology, as well as the percentage of the water column occupied by submerged macrophytes (%PVI) and water turbidity, had strong effects on taxon richness. Interestingly, individual biotic groups had dissimilar richness patterns. Macrophyte %PVI decreased with increasing lake area, while fish species richness showed the opposite pattern. Phytoplankton species richness increased with macrophyte %PVI, while the zooplankton richness pattern varied depending on the taxonomic group considered.

4. Overall, our results indicate that, as found for temperate lakes, a greater submerged plant cover promotes higher species richness in several groups, and that this may overwhelm the otherwise expected positive effect of lake size on species richness. On the other hand, small‐bodied zooplankton predominated in lakes with high plant abundance. Our findings concur with recent studies, indicating that refuge capacity of aquatic plants might be weaker in (sub)tropical than in temperate shallow lakes.

5. The extremely high plant cover, frequently observed in warm lakes, could potentially lead to different richness patterns in some groups. This conclusion has important consequences for local managers and conservationists.
Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasms
Authors: Kakar Sanjay , Chen Xin , Ho Coral , Burgart Lawrence J , Adeyi Oyedele , Jain Dhanpat , Sahai Viabhav , Ferrell Linda D
Published: July 2009

Aims:  To explore the utility of cytogenetic abnormalities in the distinction of hepatic adenoma (HA) and well‐differentiated hepatocellular carcinoma (HCC).

Methods and results:  Array‐based comparative genomic hybridization (CGH) was used to determine chromosomal abnormalities in 39 hepatocellular neoplasms: 12 HA, 15 atypical hepatocellular neoplasms (AHN) and 12 well‐differentiated HCC. The designation of AHN was used in two situations: (i) adenoma‐like neoplasms (n = 8) in male patients (any age) and women >50 years and <15 years old; (ii) adenoma‐like neoplasms with focal atypical features (n = 7). CGH abnormalities were seen in none of the HAs (0/12), eight (53%) AHNs and 11 (92%) HCCs. The number and nature of abnormalities in AHN was similar to HCC with gains in 1q, 8q and 7q being the most common. Although follow‐up information was limited, recurrence and/or metastasis were observed in three AHNs (two with abnormal, one with normal CGH).

Conclusions:  Adenoma‐like neoplasms with focal atypical morphological features or unusual clinical settings such as male gender or women outside the 15–50 year age group can show chromosomal abnormalities similar to well‐differentiated HCC. Even though these tumours morphologically mimic adenoma, they can recur and metastasize. Determination of chromosomal abnormalities can be useful in the diagnosis of AHN.
Guanylyl cyclase C is a specific marker for differentiating primary and metastatic ovarian mucinous neoplasms
Authors: Ciocca Vincenzo , Bombonati Alessandro , Palazzo Juan P , Schulz Stephanie , Waldman Scott A
Published: July 2009

Aims:  The aim was to assess the value of GCC in distinguishing primary ovarian mucinous neoplasms from metastatic mucinous adenocarcinomas with ovarian involvement. Guanylyl cyclase C (GCC) is a brush border membrane receptor for the endogenous peptides guanylin and uroguanylin, and the homologous diarrhoeagenic bacterial heat‐stable enterotoxins that is selectively expressed by epithelial cells from the duodenum to the rectum, but not by normal epithelia of the stomach or oesophagus, or normal extramucosal cells in humans.

Methods and results:  Fifty ovarian tumours: 27 primary ovarian mucinous neoplasms (seven cystadenomas, 10 borderline tumours and 10 cystadenocarcinomas) and 23 metastatic mucinous adenocarcinomas with ovarian involvement [13 colorectal adenocarcinomas, four gastric adenocarcinomas, six appendiceal mucinous tumours (four adenocarcinomas, one with neuroendocrine features, and two appendiceal mucinous cystadenomas)] were studied. For primary ovarian mucinous neoplasms, 25 of 27 were negative for GCC. Twelve of 13 cases of colorectal adenocarcinoma (except for one neuroendocrine adenocarcinoma) were positive for GCC. Three of four appendiceal mucinous adenocarcinomas were positive for GCC in both the primary and metastatic tumours (except for one neuroendocrine adenocarcinoma). Two of two appendiceal mucinous cystadenomas were positive for GCC. Of four cases of gastric adenocarcinoma with ovarian involvement, only one (primary tumour) exhibited focal GCC staining.

Conclusions:  GCC is a useful marker for differentiating between primary and secondary ovarian mucinous neoplasms.
Neutrophil/eosinophil‐rich type of primary cutaneous anaplastic large cell lymphoma: a clinicopathological, immunophenotypic and molecular study of nine cases
Authors: Kong Yun‐Yi , Dai Bo , Kong Jin‐Cheng , Lu Hong‐Fen , Shi Da‐Ren
Published: July 2009

Aims:  To elucidate the clinicopathological, immunophenotypic and molecular features of neutrophil/eosinophil‐rich primary cutaneous anaplastic large cell lymphoma (CALCL), and to emphasize the cutaneous manifestations, differential diagnosis and prognosis of this peculiar entity.

Methods and results:  We described the clinical presentations, histopathology, immunophenotype, molecular features and follow‐up courses of nine neutrophil/eosinophil‐rich CALCL cases. Various clinical lesions including multiple nodules, plaques and solitary exophytic masses with or without ulceration or crusting were noted in nine patients. Two patients died of disease progression, with one developing multiple lymph node involvement. Histologically, cohesive sheets or small clusters of neoplastic cells were admixed with large numbers of neutrophils and/or eosinophils, representing 10–40% of cells per high‐power field. All nine cases showed T‐cell phenotypes. The frequency of rearranged TCRB, TCRG and TCRD genes in six cases with available paraffin‐embedded tissue was 100%, 83% and 33%, respectively.

Conclusions:  Neutrophil/eosinophil‐rich CALCL should be differentiated from various infectious and non‐infectious diseases, especially from non‐neoplastic cutaneous CD30+ infiltrates rich in neutrophils and eosinophils. Precise correlation of clinical presentation, morphological features, phenotypic and molecular analysis can help to establish the correct diagnosis. Whether this rare variant has a significantly different prognosis from classical CALCL needs further investigation.
The pathology of depopulated bovine ureter xenografts utilized for vascular access in haemodialysis patients
Authors: Kingston Gearoid T , Darby Christopher R , Roberts Ian S D
Published: July 2009

Aims:  Vascular access for long‐term haemodialysis is obtained through the surgical fashioning of arteriovenous fistulae, utilizing the patients’ native blood vessels, or by insertion of synthetic grafts or non‐synthetic gluteraldehyde cross‐linked biological xenografts. These non‐native grafts have high complication rates and a depopulated bovine ureter xenograft has recently been developed as an alternative. The aim was to undertake the first systematic review of the histopathology of bovine ureter xenografts (n = 25) utilized for haemodialysis vascular access in humans.

Methods and results:  Pre‐insertion specimens (n = 7) showed preservation of some cellular architecture and histological antigenicity. Uncomplicated segments of post‐insertion specimens (n = 18) showed myofibroblastic in‐growth but no luminal endothelialization and no vascularization of the wall, other than at sites of needle puncture. Post‐insertion, 50% showed a severe adventitial host inflammatory response with a dominant granulomatous and eosinophil‐rich infiltrate. Inflammation was present in grafts with various complications (stenosis, thrombosis, aneurysm), but there was no clear pathogenic link.

Conclusions:  We conclude that repopulation of bovine ureter xenografts by host cells is limited and that, in specimens removed for complications, an inflammatory reaction to the xenograft is common. This could reflect retention of some antigenicity following pre‐insertion ‘depopulation’ of the grafts.
Urothelial carcinoma following augmentation cystoplasty: an aggressive variant with distinct clinicopathological characteristics and molecular genetic alterations
Authors: Sung Ming‐Tse , Zhang Shaobo , Lopez‐Beltran Antonio , Montironi Rodolfo , Wang Mingsheng , Davidson Darrell D , Koch Michael O , Cain Mark P , Rink Richard C , Cheng Liang
Published: July 2009

Aims:  Patients who have undergone intestinal augmentation cystoplasty are at risk for developing latent vesicle malignancy. The aim was to evaluate the histological and immunohistochemical characteristics and molecular genetic alterations in these neoplasms.

Methods and results:  Four patients developing urothelial neoplasms after augmentation cystoplasty were included in the current study. The mean age of the patients, including two men and two women, was 37 years. The latency from bladder augmentation to developing malignancy ranged from 17 to 21 years (mean 19 years). All patients died of cancer shortly after diagnosis (mean 5 months). In the morphological evaluation, all tumours were high‐grade (grade 3) invasive urothelial carcinoma comprising various architectural patterns with brisk mitoses and tumour necrosis. Three harboured glandular differentiation and the remaining one showed squamous differentiation. All cases revealed abnormal decreasing β‐catenin expression. Two tumours showed nuclear expression of CDX2. On UroVysion fluorescence in situ hybridization (FISH) analysis, all tumours displayed characteristic chromosomal abnormalities. Point mutations of both FGFR3 and p53 genes were identified in one case.

Conclusions:  Urothelial carcinomas developed after augmentation cystoplasty are extremely aggressive and exhibit distinct morphological, immunohistochemical and genetic characteristics. UroVysion FISH analysis may offer a surveillance strategy in patients who undergo augmentation cystoplasty.
New opportunities for an old method: using fluorescent colours to measure seed dispersal
Authors: Lemke Andreas , Von Der Lippe Moritz , Kowarik Ingo
Published: July 2009

1. Seed dispersal is of high applied relevance as it governs colonization processes in rare species and during plant invasions. Seed tracking is a powerful approach to analysing dispersal processes and usually requires seed tagging. Marking diaspores with fluorescent colours is a promising tagging method, but comes with several technical limitations.

2. We analysed the durability of different colours, associated changes in weight gain and lift‐off velocity, visibility under ultraviolet (UV) light and recapture rates for different diaspore types (samaras, plumed diaspores and small, round diaspores).

3. Weight gain ranged from 20% to 61% and loss of colour after 1 month of outdoor exposure ranged from 1% to 31%, with airbrush technique offering the best retention of colour, followed by pigment colour application and common aerosol spray treatment. Seed tagging with aerosol spray paint or by airbrush technique increased the lift‐off velocity of samaras by 6–7%.

4. Good results for recapture experiments with fluorescently marked diaspores can be achieved using UV torches: large diaspores are visible at distances of up to 8 m in open habitats, and small diaspores up to 3·5 m. Recapture rates on asphalt and grass lawn were close to 100% for large diaspores, and ranged from 85% to 90% for other diaspores. An area of c. 0·1 ha could by thoroughly searched within 1 h.

5. Pigment colour application is suitable for large diaspores (>3 cm in length). Aerosol spray application is easy but induces a high weight gain and is practicable only for use over short sampling periods. Airbrush application requires special equipment but combines the advantages of low weight gain and high durability and is even appropriate for plumed diaspores.

6. Synthesis and applications. Our study revealed strengths and weaknesses of different methods of tagging diaspores with fluorescent colours. Quantifying the changes that colouring has on seed traits helps to reduce data bias, especially in modelling. The choice of the appropriate tagging method combined with the use of modern UV torches provides considerable methodological advance in studying seed dispersal over long distances and could improve studies on colonization processes of endangered species and on plant invasions.