bluuebunny/crossref_metadata_2025 huggingface dataset:
Annexin A8 displays unique phospholipid and F‐actin binding properties
Authors: Goebeler Verena , Ruhe Daniela , Gerke Volker , Rescher Ursula
Published: April 2006

Annexin A8 is a poorly characterized member of the annexin family of Ca2+‐regulated membrane binding proteins. Initially only identified at the cDNA level it had been tentatively linked to acute promyelocytic leukaemia (APL) due to its high and regulated expression in APL‐derived cells. Here we identify unique properties of the annexin A8 protein. We show that it binds Ca2+‐dependently and with high specificity to phosphatidylinositol (4,5)‐bisphosphate (PtdIns(4,5)P2) and is also capable of interacting with F‐actin. In line with these characteristics annexin A8 is recruited to F‐actin‐associated PtdIns(4,5)P2‐rich membrane domains formed in HeLa cells upon infection with non‐invading enteropathogenic Escherichia coli. These properties suggest a role of annexin A8 in the organization of certain actin‐associated membrane domains.
Identification of calconectin, a calcium‐binding protein specifically expressed by the mantle of Pinctada margaritifera
Authors: Duplat D. , Puisségur M. , Bédouet L. , Rousseau M. , Boulzaguet H. , Milet C. , Sellos D. , Van Wormhoudt A. , Lopez E.
Published: April 2006

Nacre or mother‐of‐pearl in the shell of Pinctada margaritifera is composed of 95–99% calcium carbonate and 1–5% organic matrix. In this study, we developed an original technique to characterize the genes differentially expressed in nacre‐forming cells (NFC) by combining suppression subtractive hybridization (SSH), to establish a cDNA subtractive library, with rapid amplification of cDNA ends (RACE)‐PCR. Seventy‐two specific cDNA sequences have been obtained so far. These include a protein containing two EF‐hand Ca2+‐binding domains which was completely sequenced after amplification by RACE‐PCR. Its specific expression as well as the specificity of the SSH method was confirmed by semi‐quantitative RT‐PCR on NFC and mantle cells.
Exposure to modeled microgravity induces metabolic idleness in malignant human MCF‐7 and normal murine VSMC cells
Authors: Coinu Rita , Chiaviello Angela , Galleri Grazia , Franconi Flavia , Crescenzi Elvira , Palumbo Giuseppe
Published: April 2006

We investigated the effect of modeled microgravity (MMG) on normal vascular smooth muscle cells (VSMC) and neoplastic human breast cancer cells (MCF‐7). In both cell types, MMG induced partial arrest in G2M and increased p14‐3‐3, HSP70, HSP60 and p21 expression. Cells synchronized by 24 h starvation reentered the normal cycle within 24 h if released in complete medium and exposed to normal gravity, but not if exposed to MMG. Similarly, MMG prevented VSMC and MCF‐7 cells from overcoming growth arrest and re‐synthesizing DNA. This study shows that cells adjust their metabolic rate in response to MMG.
Effect of anti‐tumor ether lipids on ordered domains in model membranes
Authors: Heczková Bohdana , Slotte J. Peter
Published: April 2006

1‐O‐octadecyl‐2‐O‐methyl‐sn‐glycero‐3‐phosphocholine (OMPC, edelfosine) and 1‐hexadecylphosphocholine (HePC, miltefosine) represent two groups of synthetic ether lipid analogues with anti‐tumor activity. Because of their hydrophobic nature, they may become incorporated into plasma membranes of cells, and it has been argued that they may act via association with lipid rafts. With the quenching of steady‐state fluorescence of probes preferentially partitioning into sterol‐rich ordered domains (cholestatrienol and trans‐parinaric acid), we showed that OMPC and HePC by themselves did not form sterol‐rich domains in fluid model membranes, in contrast to the two chain ether lipid 1,2‐O‐dihexadecyl‐sn‐glycero‐3‐phosphocholine. Nevertheless, all three ether lipids significantly stabilized palmitoyl–sphingomyelin/cholesterol‐rich domains against temperature induced melting. In conclusion, this study shows that anti‐tumor ether lipids are likely to affect the properties of cholesterol–sphingomyelin domains (i.e., lipid rafts) when incorporated into cell membranes.
The spindle assembly checkpoint: Preventing chromosome mis‐segregation during mitosis and meiosis
Authors: Malmanche Nicolas , Maia André , Sunkel Claudio E.
Published: April 2006

Aneuploidy is a common feature of many cancers, suggesting that genomic stability is essential to prevent tumorigenesis. Also, during meiosis, chromosome non‐disjunction produces gamete imbalance and when fertilized result in developmental arrest or severe birth defects. The spindle assembly checkpoint prevents chromosome mis‐segregation during both mitosis and meiosis. In mitosis, this control system monitors kinetochore‐microtubule attachment while in meiosis its role is still unclear. Interestingly, recent data suggest that defects in the spindle assembly checkpoint are unlikely to cause cancer development but might facilitate tumour progression. However, in meiosis a weakened checkpoint could contribute to age‐related aneuploidy found in humans.
The derivation of clinical‐grade human embryonic stem cell lines
Authors: Skottman Heli , Dilber M. Sirac , Hovatta Outi
Published: April 2006

The pluripotent nature of human embryonic stem cells (hESC) has attracted great interest in using them as a source of cells or tissue in cell therapy. However, in order to be used in regenerative medicine, the pluripotent hESC lines should be established and propagated according to good manufacturing practice quality requirements. The cultures should be animal substance free in order to exclude the risk of infections and immunogenity. They should also be genetically and epigenetically normal. The detailed molecular mechanisms of their pluripotency are still not defined. Using human feeder cells, a medium containing only human proteins, the mechanical isolation of the inner cell mass and mechanical passaging of hESC, is a safe option until a functional defined medium containing physiological concentrations of regulatory factors is available.
Viruses as pathogens of marine organisms—from bacteria to whales
Authors: Munn Colin B.
Published: April 2006

Viruses are the most abundant members of marine ecosystems and play an enormous role in ocean processes through their interactions with all types of marine organisms. This short review provides examples of the dramatic increase in our knowledge of the diversity of marine viruses as pathogens of bacteria, protists, molluscs, crustaceans, cnidaria, reptiles, fish and mammals. Several examples are provided showing evidence of evolution of new strains, changes in virulence, and transfer of viruses between ecosystems. The natural and anthropogenic causes of these shifts are discussed. Despite considerable advances in recent years, knowledge of the importance of viruses in many important groups of marine organisms is lacking or incomplete. Suggestions for future investigations necessary to understand the dynamics of biogeochemical processes and the impacts of disease in our oceans are proposed.
Genomic and phylogenetic analysis of a single-stranded RNA virus infecting Rhizosolenia setigera (Stramenopiles: Bacillariophyceae)
Authors: Shirai Y. , Takao Y. , Mizumoto H. , Tomaru Y. , Honda D. , Nagasaki K.
Published: April 2006

We report the first complete genome sequence of the marine diatom-infecting, positive-sense single-stranded RNA (ssRNA) virus, Rhizosolenia setigera RNA virus (RsRNAV). The genome is 8877 nucleotides (nt), polyadenylated, lacking a cap structure, and has two large open reading frames (ORFs): ORF-1 (4818 nt), a polyprotein gene coding for replicases, e.g. RNA helicase, RNA-dependent RNA polymerase (RdRp); and ORF-2 (2883 nt), a polyprotein gene coding for structural proteins. The ORFs are separated by a 323 nt intergenic region (IGR), flanked by a 624 nt 5′-untranslated region (UTR) and a 229 nt 3′-UTR. The deduced amino acid sequences for ORF-1 and ORF-2 respectively show considerable similarities to the non-structural and structural proteins of a marine raphidophyte-infecting virus HaRNAV (Heterosigma akashiwo RNA virus). Phylogenetic analyses of concatenated amino acid sequences of RNA helicase and RdRp domains supported the monophyly of RsRNAV, HaRNAV and a marine protist-infecting virus SssRNAV (Schizochytrium single-stranded RNA virus) with moderate bootstrap values of 79–83%, but not at the family level, whilst their monophyly was only weakly supported (50–55%) in the phylogenetic tree based on RdRp whole domain. As a result, comparison of the genome organization and sequence suggests RsRNAV is not a member of any currently defined virus family. In the RdRp tree, the positive-sense ssRNA viruses infecting Stramenopiles (RsRNAV, HaRNAV and SssRNAV) and Alveolata (HcRNAV (Heterocapsa circularisquama RNA virus)) were categorized into phylogenetically distant clades, which suggests a host/virus coevolution. Our study supports the hypothesis that a diverse array of ssRNA viruses exists in marine environments.
Virus isolation studies suggest short-term variations in abundance in natural cyanophage populations of the Indian Ocean
Authors: Clokie Martha R.J. , Millard Andrew D. , Mehta Jaytry Y. , Mann Nicholas H.
Published: April 2006

Cyanophage abundance has been shown to fluctuate over long timescales and with depth, but little is known about how it varies over short timescales. Previous short-term studies have relied on counting total virus numbers and therefore the phages which infect cyanobacteria cannot be distinguished from the total count.

In this study, an isolation-based approach was used to determine cyanophage abundance from water samples collected over a depth profile for a 24 h period from the Indian Ocean. Samples were used to infect Synechococcus sp. WH7803 and the number of plaque forming units (pfu) at each time point and depth were counted. At 10 m phage numbers were similar for most time-points, but there was a distinct peak in abundance at 0100 hours. Phage numbers were lower at 25 m and 50 m and did not show such strong temporal variation. No phages were found below this depth. Therefore, we conclude that only the abundance of phages in surface waters showed a clear temporal pattern over a short timescale. Fifty phages from a range of depths and time points were isolated and purified. The molecular diversity of these phages was estimated using a section of the phage-encoded psbD gene and the results from a phylogenetic analysis do not suggest that phages from the deeper waters form a distinct subgroup.
A temporal and spatial investigation of cyanophage abundance in the Gulf of Aqaba, Red Sea
Authors: Millard Andrew D. , Mann Nicholas H.
Published: April 2006

The aim of this study was to determine the abundance of cyanophages over an annual cycle in the Red Sea from the period April 1999 to December 1999 at a range of depths. Cyanophage numbers from 71 water samples were determined by the use of plaque assays using four different Synechococcus strains. The results indicate that cyanophage are found throughout the water column from surface waters to depths of 150 m, with a discrete maximum in the number of cyanophages in the summer months of July, August and September at a depth of 30 m. Eighty-seven cyanophages were isolated and characterized in terms of host range, genome size and possession of a myoviral portal vertex gene. Cyanophages were found to infect multiple strains of Synechococcus from different phylogenetic clades. The genome sizes of cyanophages were also found to be bigger than previously estimated.
Temperate and lytic cyanophages from the Gulf of Mexico
Authors: McDaniel Lauren D. , delaRosa Michéle , Paul John H.
Published: April 2006

The unicellular cyanobacterial species Synechococcus and Prochlorococcus are known to be vital components of marine ecosystems, especially in the vast oligotrophic areas. Lytic cyanophages infecting unicellular phytoplankton are prevalent and have been demonstrated to act as important constraints on community composition contributing to the seasonal succession in genotypes. Lysogeny in Synechococcus has been documented experimentally in natural environments by prophage induction. At this time it is completely unknown how prevalent lysogeny is among Synechococcus populations. This study was performed to document important features such as size, morphology and the incidence of the T4-like capsid portal protein gene (g20) in a group of lytic Synechococcus cyanophages (35 isolates) isolated from the Gulf of Mexico. A group of Synechococcus isolates (24 strains) were isolated concurrently to investigate the virulence and cross-infectivity of the lytic cyanophages and to determine the frequency of lysogeny by detection of inducible prophage. The host range of the cyanophages toward these Synechococcus strains ranged from 1 of 25 (host of isolation only) to 17 of 25 (68%). Of the 35 cyanophage isolates the large majority were myoviruses (94%) and only two (6%) were of the podovirus type. The expected polymerase chain reaction product for g20 was detected in 20 of the phages (63%). The presence of a detectable g20 was associated with low-infectivity cyanophages at the 90% confidence interval. The Synechococcus strains varied in their resistance to lytic infection from 11% to resistance to all of the phage isolates utilized in testing. The prevalence of inducible prophage-like particles was determined in the Synechococcus strains using mitomycin C and enumerating viruses by epifluorescence microscopy. A statistically significant increase in viruses was detected in 11 of the strains (46%) in response to mitomycin C. There was no observed relationship between the occurrence of prophage induction in the Synechococcus isolates and their resistance to lytic infection. One putative lysogen was induced by continuous high light and contained a prophage-like particle with a single-stranded DNA (ssDNA) genome. Such a prophage-like particle is unlike any prophage described to date, implying that the process of lysogeny is unique in certain marine Synechococcus strains.
Diversity of cyanophages infecting the heterocystous filamentous cyanobacterium Nodularia isolated from the brackish Baltic Sea
Authors: Jenkins C.A. , Hayes P.K.
Published: April 2006

A collection of 17 cyanophage isolates able to infect the heterocystous, filamentous cyanobacterium Nodularia spumigena has been established from the Baltic Sea. These cyanophages have been characterized based on their morphology, cross infectivity and genetic structure. Short fragments (450 bp) of the gene encoding the major capsid protein (g23) were amplified and sequenced from several isolates, and the encoded protein was found to be 99% identical across all the N. spumigena-specific cyanophages tested. These results suggest that the Nodularia-specific cyanophages are very closely related. However, these cyanophages were found to be diverse in terms of their morphology and host range. Cyanophages belonging to two families within the order Caudovirales, Myoviridae and Siphoviridae, were included in the collection of isolates. The cyanophage particles are large in comparison with cyanophages previously isolated from the marine environment, with the largest capsid measuring 127×122×888 nm. Host ranges of the cyanophage isolates varied, some being able to infect up to five genotypically distinct strains of Nodularia spumigena, while others were very specific, infecting only one strain. We conclude that Nodularia-specific cyanophages form a diverse community in surface waters during summer and autumn months and that they may play a role both in the transfer of genetic information between Nodularia lineages and in promoting changes in the genetic structure of the host population.
Dynamic modelling of viral impact on cyanobacterial populations in shallow lakes: implications of burst size
Authors: Gons Herman J. , Hoogveld Hans L. , Simis Stefan G.H. , Tijdens Marjolijn
Published: April 2006

Laboratory experiments with whole water-columns from shallow, eutrophic lakes repeatedly showed collapse of the predominant filamentous cyanobacteria. The collapse could be due to viral activity, from the evidence of electron microscopy of infected cyanobacterial cells and observed dynamics of virus-like particles. Burst-size effects on single-host single-virus dynamics was modelled for nutrient-replete growth of the cyanobacteria and fixed viral decay rate in the water column. The model combined previously published equations for nutrient-replete cyanobacterial growth and virus–host relationship. According to the model results, burst sizes greater than 200 to 400 virions per cell would result in host extinction, whereas lower numbers would allow coexistence, and even stable population densities of host and virus. High-nutrient status of the host cells might accommodate a large burst size. The ecological implication could be that burst-size increase accompanying a transition from phosphorus to light-limited cyanobacterial growth might destabilize the virus–host interaction and result in the population collapse observed in the experiments.
Microscale patchiness of virioplankton
Authors: Seymour J.R. , Seuront L. , Doubell M. , Waters R.L. , Mitchell J.G.
Published: April 2006

The microscale spatial distributions of viruses were investigated in three contrasting environments including oligotrophic open ocean, eutrophic coastal and estuarine habitats. The abundances of two discrete populations of both viruses and heterotrophic bacteria were measured at spatial resolutions of between 1 and 5 cm using purpose-designed microscale sampling equipment and flow cytometric sample analysis. Within open water samples, virus distributions were characterized by non-normal distributions and by ‘hotspots’ in abundance where concentrations varied by up to 17-fold. In contrast to patterns generally observed at larger spatiotemporal scales, there was no correlation between bacterial and viral abundance or correspondence between bacteria and virus hotspots within these samples. Consequently, strong hotspots and gradients in the virus:bacteria ratio (VBR) were also apparent within samples. Within vertical profiles taken from above the sediment–water interface within a temperate mangrove estuary, distributions of planktonic viruses were characterized by gradients in abundance, with highest concentrations observed within the 1–2 cm immediately above the sediment surface, and virus distributions were correlated to bacterial abundance (P<0.01). The patterns observed in these contrasting habitats indicate that microscale patchiness of virus abundance may be a common feature of the marine environment. This form of heterogeneity may have important implications for virus–host dynamics and subsequently influence microbial trophodynamics and nutrient cycling in the ocean.
Plasmids and prophages in Baltic Sea bacterioplankton isolates
Authors: Leitet Cecilia , Riemann Lasse , Hagström Åke
Published: April 2006

Plasmids and phages influence bacterial phenotype and may serve as vectors for transferring genes between bacteria. In the present study, we examined 130 marine bacterioplankton isolates for the presence of plasmids and prophages. Samples were obtained in spring, summer and autumn in the Baltic Sea proper. Plasmids and inducible prophages were found in 19% and 28% of the isolates, respectively. During spring, plasmids and prophages were 41–55% and 30% more common compared to the summer and autumn measurements and prevalence varied up to five-fold between bacterial phylogenetic groups, with the highest plasmid prevalence found in Bacteriodetes (41%), and lysogeny being common in α-, β-, and γ-Proteobacteria (32–50%). Plasmid genome sizes ranged from 1.5–15 kb with most in the 2.1–4.0 kb size-range. No plasmids showed identity to the broad-host-range incompatibility groups N and P. Phage genomes ranged in size from 8–87 kb, with 57% being 35–45 kb in size. Strain typing of phages with similar genome sizes by means of DP-RAPD (degenerated primer randomly amplified polymorphic DNA) showed that all were different (except two that were not resolved). In PFGE (pulsed-field gel electrophoresis) 34% of the lysates produced multiple bands. Transmission electron microscopy suggested that these originated from several phage morphotypes indicating that polylysogeny is common. The widespread distribution of small cryptic plasmids as well as of lysogeny and polylysogeny in Baltic Sea bacterioplankton may have important implications for bacterial phenotype and for lateral gene transfer; hence, the ecological significance of these vectors in marine environments requires further study.
Viral impacts upon marine bacterioplankton assemblage structure
Authors: Hewson Ian , Fuhrman Jed A.
Published: April 2006

This study examined the relationship between viral infection and the richness, diversity and composition of bacterial assemblages in the water column. Viruses were enriched by ultrafiltration, added to water column incubation experiments at 15 locations in the North Atlantic, North Pacific, Gulf of Mexico and Southern California. In a separate experiment, viruses were removed from bacterioplankton by diafiltration at the San Pedro Ocean Time Series Station. Bacterial assemblage composition was observed using a high throughput and sensitive molecular fingerprinting analysis, automated rRNA intergenic spacer analysis (ARISA). Diazotrophs were used as a model functional group to represent rare organisms hypothesized to benefit from viral activity, and their richness and diversity was determined by terminal restriction fragment length polymorphism of a nitrogenase gene fragment (nifH). The enrichment and removal experiments demonstrated mixed impacts of viral pressure upon bacterial communities, and we observed significant effects of viruses on several microbial parameters in all but two experiments. However, there was no consistent response of viral enrichment on total bacterial and diazotroph assemblages at stations with similar environmental conditions, suggesting that untested variables, small spatial scale factors, or stochastic processes influence the outcome of viral activities. Across all experiments, the relative abundance of the more common operational taxonomic units (OTUs) in fingerprints were not significantly impacted compared to the abundance of rare OTUs. These data indicate that viruses may have significant influence upon community structure of bacterioplankton; however, effects were not consistent between sampling locations nor water masses.
Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico)
Authors: Hewson Ian , Winget Danielle M. , Williamson Kurt E. , Fuhrman Jed A. , Wommack K. Eric
Published: April 2006

Viruses are hypothesized to cause enhanced diversity in bacterial communities by regulating the outcome of intertaxon competition. However, concomitant documentation of viral and bacterial assemblage composition in oligotrophic waters are rare, particularly in situ over time, and there is almost no information on the temporal variability in virioplankton assemblage composition in oligotrophic water masses. Assemblage composition of viruses (via pulsed-field gel electrophoresis, PFGE) and bacteria (via automated rRNA intergenic spacer analysis, ARISA) was compared during surface lagrangian drifter deployments in the oligotrophic Gulf of Mexico during summer 2001, 2002, and 2003. In vertical profile, viruses and bacteria both had maximum abundances in surface waters, which decreased with depth; however, the richness of their assemblages was not significantly different between depths, suggesting independence of biomass and diversity. Viral assemblages changed rapidly (0.17–0.32 Jaccard index d−1), which was similar to the rate of change in bacterial assemblages reported in surface waters. Patterns of viral and bacterial assemblage composition were significantly related (P<0.001, r=0.58 between node ranks), and both assemblages clustered primarily by year and then by depth. These cultivation-independent observations demonstrate relationships between viral and bacterial assemblages, which are dynamic in patches of open ocean water. Even at the relatively low phylogenetic resolution of the ARISA and PFGE methods, the results support the idea that viruses may influence the species composition of host assemblages.
Viral lysis of bacteria: an important source of dissolved amino acids and cell wall compounds
Authors: Middelboe Mathias , Jørgensen Niels O.G.
Published: April 2006

Viral infection of bacteria causes release of dissolved organic matter (DOM), which is available for bacterial uptake. In aquatic environments, this virus-mediated transformation of living cells into dissolved and colloidal organic matter may be a quantitatively important process in the pelagic recycling of carbon and nutrients, but little is known about the amount, composition, or bioavailability of viral lysates. By using a model system of a marine bacterium (Cellulophaga sp.) and a virus specific to this bacterium, the present study provides a first quantification of the input of dissolved free and combined amino acids (DFAA and DCAA) and bacterial cell wall compounds following viral lysis. The DCAA constituted 51–86% of the total virus-mediated organic carbon release of 1087–1825 μg C l−1 (estimated biomass of the lysed bacteria), whereas DFAA and glucosamine each accounted for 2–3% of total lysate-C. The viral particles themselves constituted 4–6% of the released organic carbon, and altogether, the applied analyses thus identified 53–92% of the released lysates. Approximately 12% of the identified compounds were derived from bacterial cell wall peptidoglycan, including various D-isomers of DFAA and DCAA, glucosamine and diaminopimelic acid (DAPA). Although a portion of this cell wall material may have entered the pool of refractory material, a significant fraction of some peptidoglycan-derived components, e.g. 83% of the released D-DFAA, were removed from the dissolved phase during the last part of the incubations, suggesting that part of the cell wall material were utilized by the developing virus-resistant Cellulophaga population. Therefore, we suggest that virus-mediated DOM is a source of a variety of organic compounds, which contribute significantly to the pool of rapidly recycling material in the ocean.
Viral burst size of heterotrophic prokaryotes in aquatic systems
Authors: Parada Verónica , Herndl Gerhard J. , Weinbauer Markus G.
Published: April 2006

Viral burst size (BS), i.e. the number of viruses released during cell lysis, is a critical parameter for assessing the ecological and biogeochemical role of viruses in aquatic systems. Burst size is typically estimated by enumerating the viral particles in bacteria using transmission electron microscopy. Here, we review the average BS reported for different aquatic systems, present several hypotheses on the control of the BS and evaluate whether there are relationships between BS and bacterial activity parameters across systems. Based on reports from a variety of different aquatic environments, we calculated a mean BS of 24 and 34 for marine and freshwater environments, respectively. Generally, the BS increased with the trophic status of the environment and with the percentage of infected cells in marine populations. When diel dynamics were investigated or averages from large-scale environments were used, BS was positively related to bacterial production but no trend was detectable across systems. The across systems' finding that BS was significantly related to the frequency of infected cells (FIC) could be due to co-infection or superinfection. At any given site, BS seems to be influenced by a number of factors such as the size of the host cell and the viruses, the metabolic activity of the host and phage and host diversity. Thus, based on the available data collected over the past two decades on a variety of aquatic systems, some relations between BS and bacterial variables were detectable.
Hunting of Microchiroptera in south-western Madagascar
Authors: Goodman Steven M.
Published: April 2006

In February 2005 clear evidence was found of extensive hunting by local people of microchiropteran bats in south-western Madagascar. Hipposideros commersoni (Family Hipposideridae) accumulates heavy fat deposits during this period, weighing on average about 50 g, and is the targeted species. The capture of other smaller species of microchiropterans appears to be incidental. The exploitation of bats for bushmeat in this region takes place during a period of food shortage, and because the level of collection surpasses the breeding potential of these animals it may over time result in extirpation of local populations.
Two remnant populations of the roofed turtle Kachuga trivittata in the upper Ayeyarwady River system, Myanmar
Authors: Kuchling Gerald , Ko Win Ko , Min Sein Aung , Lwin Tint , Myo Khin Myo , Khaing (1) Thin Thin , Khaing (2) Thin Thin , Mar Win Win , Win Ni Ni
Published: April 2006

The endemic roofed turtle Kachuga trivittata has been extirpated over most of its former range in the Ayeyarwady River system of Myanmar. Only two small remnant populations are known to survive. In a small stretch of the upper Chindwin River K. trivittata persists because local Shan villages traditionally ban the killing of large adult K. trivittata. The population has nevertheless declined dramatically during the last few years because of the erosion of the ban by migrant fishermen from central Myanmar who do not observe the local regulation, and because of the overexploitation of eggs. The traditional regulation of the Shan villages offers a basis, through its reinforcement and education of migrants, for a species recovery programme. Further actions will include the protection of nests and eggs, and eventually the banning of camps and seasonal settlements on sandbanks used by K. trivittata for nesting. K. trivittata also still persists in the Dokhtawady River in a small area subjected to low exploitation pressure in the recent past because of the dangers of a frontline between the government army and an army of insurgents. The opening of this area following a truce brought this population close to extinction and a hydroelectric dam under construction will alter the ecology of this stretch of river. We propose to assess the potential use of the future impoundment lake for the recovery of this K. trivittata population.
The song and the page: experiments with form and layout in manuscripts of medieval Latin song
Authors: DEEMING HELEN
Published: April 2006

The non-liturgical songs of twelfth- and thirteenth-century England were recorded, for the most part, not in dedicated song books, but on occasional pages in manuscript miscellanies. Away from the context of fully musical books, there were no fixed procedures for the layout of music, and scribes devised new approaches to layout as they worked. This article considers three Latin songs from such sources and explores the evidence for experimentation, both in scribal technique and in musical procedures, that may have contributed to their specific manuscript presentations.
Melodiarium Hymnologicum Bohemiae
Authors: Christiansen Paul
Published: April 2006

Melodiarium Hymnologicum Bohemiae is a digital database of facsimiles of sources of Czech, German and Latin sacred monody and is essentially sui generis; there are no other such digital databases of comparable scope for this repertory. Its address is www.firmadat.cz/melodiarium/, and the English version can be reached by clicking on the Union Jack icon. The idea of Czech musicologist Stanislav Tesař, MHB is an extremely ambitious project, which has involved a team of several Czech musicologists in its realization. It is now yielding the fruits of two three-year grants from the Czech Science Foundation and further support from the Ministry of Education, Youth and Sports of the Czech Republic, which has funded the project from its inception. The amount of work that has been accomplished here is considerable but the sheer volume of material dictates that the catalogue will be for a long time a work in progress – it will not be complete for perhaps a decade. There is still much work to do; therefore this account is really more of a progress report than a conventional review.
Thermometric measurements of the molecular sublayer at the air‐water interface
Authors: Ward B. , Donelan M. A.
Published: April 2006

A series of measurements was conducted in the Air‐Sea Interaction Saltwater Tank (ASIST) to study the response of the air‐water interfacial molecular sublayer under various heat flux and wind speed conditions. In‐situ gradients were measured with a platinum‐plated tungsten wire microthermometer, which resolved the temperature of the thermally conductive sublayer. Air‐sea heat flux was controlled by changing the air‐water temperature difference (ΔTAW) and the wind speed, and measurements were made for three ΔTAW regimes over a range of wind speeds. A function was fitted to the measured temperature profiles as a way of extracting the boundary layer thickness in a consistent fashion, from which the λ coefficient after Saunders (1967) was computed. This dataset returned a mean λ coefficient of 2.4 ± 0.5, which was generally lower than previous studies, and was found to be independent of wind speed in the range of 1 to 9 ms−1.
Arctic Oscillation response to volcanic eruptions in the IPCC AR4 climate models
Authors: Stenchikov Georgiy , Hamilton Kevin , Stouffer Ronald J. , Robock Alan , Ramaswamy V. , Santer Ben , Graf Hans‐F.
Published: April 2006

Stratospheric sulfate aerosol particles from strong volcanic eruptions produce significant transient cooling of the troposphere and warming of the lower stratosphere. The radiative impact of volcanic aerosols also produces a response that generally includes an anomalously positive phase of the Arctic Oscillation (AO) that is most pronounced in the boreal winter. The main atmospheric thermal and dynamical effects of eruptions typical of the past century persist for about two years after each eruption. In this paper we evaluate the volcanic responses in simulations produced by seven of the climate models included in the model intercomparison conducted as part of the preparation of the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4). We consider global effects as well as the regional circulation effects in the extratropical Northern Hemisphere focusing on the AO responses forced by volcanic eruptions. Specifically we analyze results from the IPCC historical runs that simulate the evolution of the circulation over the last part of the 19th century and the entire 20th century using a realistic time series of atmospheric composition (greenhouse gases and aerosols). In particular, composite anomalies over the two boreal winters following each of the nine largest low‐latitude eruptions during the period 1860–1999 are computed for various tropospheric and stratospheric fields. These are compared when possible with observational data. The seven IPCC models we analyzed use similar assumptions about the amount of volcanic aerosols formed in the lower stratosphere following the volcanic eruptions that have occurred since 1860. All models produce tropospheric cooling and stratospheric warming as in observations. However, they display a considerable range of dynamic responses to volcanic aerosols. Nevertheless, some general conclusions can be drawn. The IPCC models tend to simulate a positive phase of the Arctic Oscillation in response to volcanic forcing similar to that typically observed. However, the associated dynamic perturbations and winter surface warming over Northern Europe and Asia in the post‐volcano winters is much weaker in the models than in observations. The AR4 models also underestimate the variability and long‐term trend of the AO. This deficiency affects high‐latitude model predictions and may have a similar origin. This analysis allows us to better evaluate volcanic impacts in up‐to‐date climate models and to better quantify the model Arctic Oscillation sensitivity to external forcing. This potentially could lead to improving model climate predictions in the extratropical latitudes of the Northern Hemisphere.
How corticosteroids control inflammation: Quintiles Prize Lecture 2005
Authors: Barnes Peter J
Published: April 2006

Corticosteroids are the most effective anti‐inflammatory therapy for many chronic inflammatory diseases, such as asthma but are relatively ineffective in other diseases such as chronic obstructive pulmonary disease (COPD). Chronic inflammation is characterised by the increased expression of multiple inflammatory genes that are regulated by proinflammatory transcription factors, such as nuclear factor‐kappaB and activator protein‐1, that bind to and activate coactivator molecules, which then acetylate core histones to switch on gene transcription. Corticosteroids suppress the multiple inflammatory genes that are activated in chronic inflammatory diseases, such as asthma, mainly by reversing histone acetylation of activated inflammatory genes through binding of liganded glucocorticoid receptors (GR) to coactivators and recruitment of histone deacetylase‐2 (HDAC2) to the activated transcription complex. At higher concentrations of corticosteroids GR homodimers also interact with DNA recognition sites to active transcription of anti‐inflammatory genes and to inhibit transcription of several genes linked to corticosteroid side effects. In patients with COPD and severe asthma and in asthmatic patients who smoke HDAC2 is markedly reduced in activity and expression as a result of oxidative/nitrative stress so that inflammation becomes resistant to the anti‐inflammatory actions of corticosteroids. Theophylline, by activating HDAC, may reverse this corticosteroid resistance. This research may lead to the development of novel anti‐inflammatory approaches to manage severe inflammatory diseases.

British Journal of Pharmacology (2006) 148, 245–254. doi:10.1038/sj.bjp.0706736
Inhibition of TRPM2 cation channels by N‐(p‐amylcinnamoyl)anthranilic acid
Authors: Kraft Robert , Grimm Christian , Frenzel Henning , Harteneck Christian
Published: April 2006

TRPM2 is a Ca2+‐permeable nonselective cation channel activated by intracellular ADP‐ribose (ADPR) and by hydrogen peroxide (H2O2). We investigated the modulation of TRPM2 activity by N‐(p‐amylcinnamoyl)anthranilic acid (ACA). ACA has previously been reported to inhibit phospholipase A2 (PLA2).

Using patch‐clamp and calcium‐imaging techniques, we show that extracellular application of 20 μM ACA completely blocked ADPR‐induced whole‐cell currents and H2O2‐induced Ca2+ signals (IC50=1.7 μM) in HEK293 cells transfected with human TRPM2. Two other PLA2 inhibitors, p‐bromophenacyl bromide (BPB; 100 μM) and arachidonyl trifluoromethyl ketone (20 μM), had no significant effect on ADPR‐stimulated TRPM2 activity.

Inhibition of TRPM2 whole‐cell currents by ACA was voltage independent and accelerated at decreased pH. ACA was ineffective when applied intracellularly. The single‐channel conductance was not changed during ACA treatment, suggesting a reduction of TRPM2 open probability by modulating channel gating.

ACA (20 μM) also blocked currents through human TRPM8 and TRPC6 expressed in HEK293 cells, while BPB (100 μM) was ineffective. TRPC6‐mediated currents (IC50=2.3 μM) and TRPM8‐induced Ca2+ signals (IC50=3.9 μM) were blocked in a concentration‐dependent manner.

ADPR‐induced currents in human U937 cells, endogeneously expressing TRPM2 protein, were fully suppressed by 20 μM ACA.

Our data indicate that ACA modulates the activity of different TRP channels independent of PLA2 inhibition. Owing to its high potency and efficacy ACA can serve, in combination with other blockers, as a useful tool for studying the unknown function of TRPM2 in native cells.

British Journal of Pharmacology (2006) 148, 264–273. doi:10.1038/sj.bjp.0706739
Lattice model of equilibrium polymerization. V. Scattering properties and the width of the critical regime for phase separation
Authors: Rah Kyunil , Freed Karl F. , Dudowicz Jacek , Douglas Jack F.
Published: April 2006

Dynamic clustering associated with self-assembly in many complex fluids can qualitatively alter the shape of phase boundaries and produce large changes in the scale of critical fluctuations that are difficult to comprehend within the existing framework of theories of critical phenomena for nonassociating fluids. In order to elucidate the scattering and critical properties of associating fluids, we consider several models of equilibrium polymerization that describe widely occurring types of associating fluids at equilibrium and that exhibit the well defined cluster geometry of linear polymer chains. Specifically, a Flory-Huggins-type lattice theory is used, in conjunction with the random phase approximation, to compute the correlation length amplitude ξo and the Ginzburg number Gi corresponding, respectively, to the scale of composition fluctuations and to a parameter characterizing the temperature range over which Ising critical behavior is exhibited. Our calculations indicate that upon increasing the interparticle association energy, the polymer chains become increasingly long in the vicinity of the critical point, leading naturally to a more asymmetric phase boundary. This increase in the average degree of polymerization implies, in turn, a larger ξo and a drastically reduced width of the critical region (as measured by Gi). We thus obtain insight into the common appearance of asymmetric phase boundaries in a wide range of “complex” fluids and into the observation of apparent mean field critical behavior even rather close to the critical point.
Mesoscopic nonequilibrium thermodynamics of solid surfaces and interfaces with triple junction singularities under the capillary and electromigration forces in anisotropic three-dimensional space
Authors: Ogurtani Tarik Omer
Published: April 2006

A theory of irreversible thermodynamics of curved surfaces and interfaces with triple junction singularities is elaborated to give a full consideration of the effects of the specific surface Gibbs free energy anisotropy in addition to the diffusional anisotropy, on the morphological evolution of surfaces and interfaces in crystalline solids. To entangle this intricate problem, the internal entropy production associated with arbitrary virtual displacements of triple junction and ordinary points on the interfacial layers, embedded in a multicomponent, multiphase, anisotropic composite continuum system, is formulated by adapting a mesoscopic description of the orientation dependence of the chemical potentials in terms of the rotational degree of freedom of individual microelements. The rate of local internal entropy production resulted generalized forces and conjugated fluxes not only for the grain boundary triple junction transversal and longitudinal movements, but also for the ordinary points. The natural combination of the mesoscopic approach coupled with the rigorous theory of irreversible thermodynamics developed previously by the global entropy production hypothesis yields a well-posed, nonlinear, moving free-boundary value problem in two-dimensional (2D) space, as a unified theory. The results obtained for 2D space are generalized into the three-dimensional continuum by utilizing the invariant properties of the vector operators in connection with the descriptions of curved surfaces in differential geometry. This mathematical model after normalization and scaling procedures may be easily adapted for computer simulation studies without introducing any additional phenomenological system parameters (the generalized mobilities), other than the enlarged concept of the surface stiffness.
A spinorial formulation of the maximum clique problem of a graph
Authors: Budinich Marco , Budinich Paolo
Published: April 2006

We present a new formulation of the maximum clique problem of a graph in complex space. We start observing that the adjacency matrix A of a graph can always be written in the form A=B2 where B is a complex, symmetric matrix formed by vectors of zero length (null vectors) and the maximum clique problem can be transformed in a geometrical problem for these vectors. This problem, in turn, is translated in spinorial language and we show that each graph uniquely identifies a set of pure spinors, that is vectors of the endomorphism space of Clifford algebras, and the maximum clique problem is formalized in this setting so that, this much studied problem, may take advantage from recent progresses of pure spinor geometry.
Reverse inequalities in μ-deformed Segal-Bargmann analysis
Authors: Angulo Aguila Carlos , Sontz Stephen Bruce
Published: April 2006

We prove reverse hypercontractivity inequalities as well as reverse log-Sobolev inequalities in the context of a space of holomorphic functions, which is called the μ-deformed Segal-Bargmann space and arises in the works of Wigner, Rosenblum, and Marron. To achieve this we define μ-deformations of energy and entropy. Our principle results generalize earlier works of Carlen and Sontz. We also show that the semigroup of this theory is Lp bounded, and we conjecture that it is Lp contractive and, even more strongly, that it is hypercontractive.
A formula for the first eigenvalue of the Dirac operator on compact spin symmetric spaces
Authors: Milhorat Jean-Louis
Published: April 2006

Let G∕K be a simply connected spin compact inner irreducible symmetric space, endowed with the metric induced by the Killing form of G sign-changed. We give a formula for the square of the first eigenvalue of the Dirac operator in terms of a root system of G. As an example of application, we give the list of the first eigenvalues for the spin compact irreducible symmetric spaces endowed with a quaternion-Kähler structure.
Excited state geometry optimizations by analytical energy gradient of long-range corrected time-dependent density functional theory
Authors: Chiba Mahito , Tsuneda Takao , Hirao Kimihiko
Published: April 2006

An analytical excitation energy gradient of long-range corrected time-dependent density functional theory (LC-TDDFT) is presented. This is based on a previous analytical TDDFT gradient formalism, which avoids solving the coupled-perturbed Kohn-Sham equation for each nuclear degree of freedom. In LC-TDDFT, exchange interactions are evaluated by combining the short-range part of a DFT exchange functional with the long-range part of the Hartree-Fock exchange integral. This LC-TDDFT gradient was first examined by calculating the excited state geometries and adiabatic excitation energies of small typical molecules and a small protonated Schiff base. As a result, we found that long-range interactions play a significant role even in valence excited states of small systems. This analytical LC-TDDFT gradient was also applied to the investigations of small twisted intramolecular charge transfer (TICT) systems. By comparing with calculated ab initio multireference perturbation theory and experimental results, we found that LC-TDDFT gave much more accurate absorption and fluorescence energies of these systems than those of conventional TDDFTs using pure and hybrid functionals. For optimized excited state geometries, LC-TDDFT provided fairly different twisting and wagging angles of these small TICT systems in comparison with conventional TDDFT results.
Evidence of the C60∕Cu contact formation after thermal treatment
Authors: Cho S. W. , Seo J. H. , Kim C. Y. , Yoo K.-H. , Jeong K. , Whang C.-N. , Yi Y. , Kang S. J. , Noh M.
Published: April 2006

The origin of the lowered electron injection barrier height of C60∕Cu was investigated by in situ ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy (XPS). The onset of the highest occupied molecular orbital level was shifted by 0.2eV toward high binding energy upon the heat treatment, resulting in the improved injection characteristics of the device. Moreover, an unexpected gap state has been observed at 1.2eV below the Fermi level. The XPS core-level spectra revealed that the chemical reaction between C60 and Cu at the interface induced the gap state after heat treatment. The gap state pinned the Fermi level close to the lowest unoccupied molecular orbital of C60. We obtained the complete energy level diagram of C60∕Cu before and after the heat treatment.