bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical distribution of phytoplankton communities in open ocean: An assessment based on surface chlorophyll
Authors: Uitz Julia , Claustre Hervé , Morel André , Hooker Stanford B.
Published: August 2006

The present study examines the potential of using the near‐surface chlorophyllaconcentration ([Chla]surf), as it can be derived from ocean color observation, to infer the column‐integrated phytoplankton biomass, its vertical distribution, and ultimately the community composition. Within this context, a large High‐Performance Liquid Chromatography (HPLC) pigment database was analyzed. It includes 2419 vertical pigment profiles, sampled in case 1 waters with various trophic states (0.03–6 mg Chlam−3). The relationships between [Chla]surfand the chlorophyllavertical distribution, as previously derived by Morel and Berthon (1989), are fully confirmed. This agreement makes it possible to go further and to examine if similar relationships between [Chla]surfand the phytoplankton assemblage composition along the vertical can be derived. Thanks to the detailed pigment composition, and use of specific pigment biomarkers, the contribution to the local chlorophyllaconcentration of three phytoplankton groups can be assessed. With some cautions, these groups coincide with three size classes, i.e., microplankton, nanoplankton and picoplankton. Corroborating previous regional findings (e.g., large species dominate in eutrophic environments, whereas tiny phytoplankton prevail in oligotrophic zones), the present results lead to an empirical parameterization applicable to most oceanic waters. The predictive skill of this parameterization is satisfactorily tested on a separate data set. With such a tool, the vertical chlorophyllaprofiles of each group can be inferred solely from the knowledge of [Chla]surf. By combining this tool with satellite ocean color data, it becomes possible to quantify on a global scale the phytoplankton biomass associated with each of the three algal assemblages.
A nonparametric stochastic downscaling framework for daily rainfall at multiple locations
Authors: Mehrotra R. , Sharma Ashish
Published: August 2006

Use of General Circulation Models (GCMs) for climate change impact assessment is often limited by their incapability at representing local features and dynamics at spatial scales finer than the in‐built GCM grid scale. This has led to the development of downscaling techniques for transfer of coarse GCM simulated weather output to finer spatial resolutions. This paper presents a nonparametric stochastic spatial downscaling framework for multisite daily rainfall occurrence and amount. At site rainfall occurrences are downscaled using a nonparametric nonhomogeneous hidden Markov model (NNHMM) that represents spatial dependence across the rainfall occurrence field using a dynamic weather state indicative of the centroid and average wetness fraction of the rainfall occurrence field. The rainfall amounts on the wet days are downscaled using a nonparametric kernel density approach that accommodates variations in the rainfall downscaling model at individual locations. Spatial dependence in the rainfall amounts is simulated by driving each of the single‐site amounts model with spatially correlated random numbers. The proposed framework is applied for downscaling of rainfall at a network of 30 rain gauge stations around Sydney in Australia, and its performance is evaluated. The analyses of the results show that the logic of providing separate treatments for rainfall occurrence and amounts at individual locations imparts considerable accuracy in the representation of characteristics of interest in hydrologic studies. These characteristics include representation of rainfall spell patterns, spatial distribution of the rainfall occurrence and amount fields, representation of low and high rainfall extremes at individual stations and across the field, as well as common indicators of water balance and variability that are of importance in a catchment scale water balance simulation.
An examination of advection in the northeast Pacific Ocean, 2001–2005
Authors: Jackson Jennifer M. , Myers Paul G. , Ianson Debby
Published: August 2006

Horizontal advection has been assumed negligible within the Alaskan Gyre (AG). With the recently available Argo data this assumption can be tested. To estimate advection, the observed heat content (estimated from Argo data) was compared to the expected (based on surface heat fluxes) and the difference between these was defined as advection. Four stations were investigated. Our proxy suggests periods of greater advection than previously estimated. Most periods of strong advection were associated with oceanographic events such as the migration of the North Pacific Current and the passage of eddies. However, there were also periods of significant advection that were not expected, for example a region‐wide event was observed in the winter of 2004–05. These results show that although advection is minimal in the AG, there are periods in which use of 1‐D models for studies of short (monthly) scale processes is questionable.
Modeling the oxygen‐isotopic composition of the North American Ice Sheet and its effect on the isotopic composition of the ocean during the last glacial cycle
Authors: Sima Adriana , Paul André , Schulz Michael , Oerlemans Johannes
Published: August 2006

We used a 2.5‐dimensional thermomechanical ice‐sheet model including the oxygen‐isotope ratio 18O/16O as a passive tracer to simulate the isotopic composition (δ18O) of the North American Ice Sheet (NAIS) during the last glacial cycle. This model allowed us to estimate the NAIS contribution to the change of seawater δ18O (δw) between the Last Glacial Maximum (LGM) and the Holocene and to evaluate the effect of nonequilibrium isotopic composition of the NAIS on the relationship between ice‐volume variations and the ocean isotopic enrichment. The enrichment due to the NAIS at the LGM was 0.63‰, corresponding to ∼60% of the LGM sea‐level lowstand and to a mean δ18O of the NAIS of approximately −31‰. The modeled NAIS volume variations and the induced δw changes over the past 120,000 years indicated no significant time lag. The inaccuracy associated with linearly inferring ice‐volume variations from δw changes was generally less than 10%.
Comparison of the Newtonian and relativistic predicted trajectories for a low-speed periodically delta-kicked system
Authors: Lan Boon Leong
Published: August 2006

The dynamics of a periodically delta-kicked Hamiltonian system moving at low speed (i.e., at speed much less than the speed of light) is studied numerically. In particular, the trajectory of the system predicted by Newtonian mechanics is compared with the trajectory predicted by special relativistic mechanics for the same parameters and initial conditions. We find that the Newtonian trajectory, although close to the relativistic trajectory for some time, eventually disagrees completely with the relativistic trajectory, regardless of the nature (chaotic, nonchaotic) of each trajectory. However, the agreement breaks down very fast if either the Newtonian or relativistic trajectory is chaotic, but very much slower if both the Newtonian and relativistic trajectories are nonchaotic. In the former chaotic case, the difference between the Newtonian and relativistic values for both position and momentum grows, on average, exponentially. In the latter nonchaotic case, the difference grows much slower, for example, linearly on average.
Fractional statistical mechanics
Authors: Tarasov Vasily E.
Published: August 2006

The Liouville and first Bogoliubov hierarchy equations with derivatives of noninteger order are derived. The fractional Liouville equation is obtained from the conservation of probability to find a system in a fractional volume element. This equation is used to obtain Bogoliubov hierarchy and fractional kinetic equations with fractional derivatives. Statistical mechanics of fractional generalization of the Hamiltonian systems is discussed. Liouville and Bogoliubov equations with fractional coordinate and momenta derivatives are considered as a basis to derive fractional kinetic equations. The Fokker-Planck-Zaslavsky equation that has fractional phase-space derivatives is obtained from the fractional Bogoliubov equation. The linear fractional kinetic equation for distribution of the charged particles is considered.
Bi-induced acceptor states in ZnO by molecular-beam epitaxy
Authors: Xiu F. X. , Mandalapu L. J. , Yang Z. , Liu J. L. , Liu G. F. , Yarmoff J. A.
Published: August 2006

Bi-doped ZnO films were grown on Si (111) substrates by molecular-beam epitaxy. X-ray photoelectron spectroscopy and diffraction measurements reveal that Bi was incorporated into ZnO films without any phase separation. Room-temperature Hall effect measurements show a significant reduction of electron concentration and an increase of resistivity for Bi-doped ZnO films. In addition, a 3.222eV photoluminescence emission was observed particularly in the Bi-doped ZnO films and was identified as a donor-acceptor pair transition by temperature-dependent and excitation power-dependent photoluminescence measurements. These results indicate the possibility of generating acceptor states by Bi doping.
Optical properties of neodymium-containing polymethylmethacrylate films for the organic light emitting diode color filter
Authors: Cho Y. , Choi Y. K. , Sohn S. H.
Published: August 2006

In order to improve the primary color purity of the organic light emitting diode (OLED), neodymium(Nd)-containing polymethylmethacrylate (PMMA) films have been fabricated by a solvent casting method, and their optical properties have been investigated as functions of Nd content in films. The study has revealed that absorption in Nd-containing PMMA films is due to intratransition within the 4f shell of the Nd3+ ion, and that it becomes larger with an increase in the Nd concentration in films. In OLED devices with color filters, luminance from unnecessary emissive light is sufficiently reduced, resulting in a wider color gamut and higher color purity.
Fabrication of carbon nanowire networks by Si ion beam irradiation
Authors: Ni Zhichun , Li Qintao , Zhu Dezhang , Gong Jinlong
Published: August 2006

Multiwalled carbon nanotubes were irradiated by 40keV Si ion beams with different doses, and the irradiation-induced structural transformation was characterized by scanning electron microscopy, transmission electron microscopy, and Raman spectroscopy. The formation of amorphous carbon nanowire and carbon nanowire networks is clearly confirmed. The processes of structural evolution and corresponding mechanism are studied. The results exhibit that the formation of carbon nanowire networks proceeds through three periods: local amorphization of nanotubes, formation of simple junctions, and the formation of networks. Ion irradiation could be a useful tool to interconnect the nanodevices in large-scale fabrication of nanodevices.
Self-assembled composite nano-/micronecklaces with SiO2 beads in boron strings
Authors: Ni Hai , Li Xiaodong
Published: August 2006

Nano-/micronecklaces with SiO2 beads in boron strings were synthesized by simply sublimating the desired powders in a sealed quartz tube at high temperature. The boron strings have a rectangular cross section with width varying from 80to1000nm while the SiO2 beads bear either spindle or spherical shape with a size ranging from 100nmto5μm. The spacing between the SiO2 beads is uniform in each boron string. Both the boron strings and the SiO2 beads are amorphous and free of defects. The supersaturated vapors of silicon and oxygen induced the SiO2 bead formation.
The Affymetrix Medicago GeneChip® array is applicable for transcript analysis of alfalfa (Medicago sativa)
Authors: Tesfaye Mesfin , Silverstein Kevin A. T. , Bucciarelli Bruna , Samac Deborah A. , Vance Carroll P.
Published: August 2006

The recently released Affymetrix GeneChip® Medicago Genome Array contains approximately 52 700 probe sets representing genes in both the model legume Medicago truncatula Gaertn. and the closely related crop species Medicago sativa L. (alfalfa). We evaluated the utility of the Medicago GeneChip® for monitoring genome-wide expression of M. truncatula and alfalfa seedlings grown to the first trifoliate leaf stage. We found that approximately 40–54% of the Medicago probes were detected in leaf or root samples of alfalfa or M. truncatula. Approximately 45–59% of the detected Medicago probes were called ‘present’ in all replicate GeneChips of Medicago species, indicating a considerable overlap in the number and type of Medicago probes detected between root and leaf organs. Nevertheless, gene expression differences between roots and leaf organs accounted for approximately 17% of the total variation, regardless of the Medicago species from which the samples were harvested. The result shows that the Medicago GeneChip® is applicable for transcript analysis for both alfalfa and M. truncatula.
Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula
Authors: Hohnjec Natalija , Henckel Kolja , Bekel Thomas , Gouzy Jerome , Dondrup Michael , Goesmann Alexander , Küster Helge
Published: August 2006

The arbuscular mycorrhizal (AM) association between terrestrial plants and soil fungi of the phylum Glomeromycota is the most widespread beneficial plant–microbe interaction on earth. In the course of the symbiosis, fungal hyphae colonise plant roots and supply limiting nutrients, in particular phosphorus, in exchange for carbon compounds. Owing to the obligate biotrophy of mycorrhizal fungi and the lack of genetic systems to study them, targeted molecular studies on AM symbioses proved to be difficult. With the emergence of plant genomics and the selection of suitable models, an application of untargeted expression profiling experiments became possible. In the model legume Medicago truncatula, high-throughput expressed sequence tag (EST)-sequencing in conjunction with in silico and experimental transcriptome profiling provided transcriptional snapshots that together defined the global genetic program activated during AM. Owing to an asynchronous development of the symbiosis, several hundred genes found to be activated during the symbiosis cannot be easily correlated with symbiotic structures, but the expression of selected genes has been extended to the cellular level to correlate gene expression with specific stages of AM development. These approaches identified marker genes for the AM symbiosis and provided the first insights into the molecular basis of gene expression regulation during AM.
A crispa null mutant facilitates identification of a crispa-like pseudogene in pea
Authors: Sainsbury Frank , Tattersall Alexander D. , Ambrose Michael J. , Turner Lynda , Ellis T. H. Noel , Hofer Julie M. I.
Published: August 2006

The genomes of several legume species contain two Phantastica-like genes. Previous studies on leaf development have found that Phantastica confers leaf blade adaxial identity in plant species with simple leaves and leaflet adaxial identity in pea (Pisum sativum L.), a legume with compound leaves. Previous characterisation of the phantastica mutant of pea, crispa, showed it had radialised leaflets, but stipules were not radialised. This suggested either that mutation of a second redundant gene was required for radialisation of stipules, or, that a null mutation was required. Previously characterised crispa mutants may not have exhibited radialised stipules because they were weak alleles. In this work we show that pea has a second Phantastica-like gene, which lies on a different chromosome to Crispa. The second gene was found to be a pseudogene in several genotypes of pea, therefore it would not have a role in conferring stipule adaxial identity. A new deletion mutant, crispa-4 was identified. The mutant has radialised stipules and leaflets, showing that Crispa confers adaxial identity on both these organs in pea. The nucleotide sequence data reported here are in the EMBL and GenBank Nucleotide Databases under the accession numbers DQ486060 (JI 2822), DQ486061 (JI 15), DQ486062 (JI 281) and DQ486063 (JI 399).
Breakdown of the reciprocal stabilization of QBRICK/Frem1, Fras1, and Frem2 at the basement membrane provokes Fraser syndrome-like defects
Authors: Kiyozumi Daiji , Sugimoto Nagisa , Sekiguchi Kiyotoshi
Published: August 2006

An emerging family of extracellular matrix proteins characterized by 12 consecutive CSPG repeats and the presence of Calx-β motif(s) includes Fras1, QBRICK/Frem1, and Frem2. Mutations in the genes encoding these proteins have been associated with mouse models of Fraser syndrome, which is characterized by subepidermal blistering, cryptophthalmos, syndactyly, and renal dysmorphogenesis. Here, we report that all of these proteins are localized to the basement membrane, and that their basement membrane localization is simultaneously impaired in Fraser syndrome model mice. In
Frem2
mutant mice, not only Frem2 but Fras1 and QBRICK/Frem1 were depleted from the basement membrane zone. This coordinated reduction in basement membrane deposition was also observed in another Fraser syndrome model mouse, in which GRIP1, a Fras1- and Frem2-interacting adaptor protein, is primarily affected. Targeted disruption of
Qbrick/Frem1
also resulted in diminished expression of Fras1 and Frem2 at the epidermal basement membrane, confirming the reciprocal stabilization of QBRICK/Frem1, Fras1, and Frem2 in this location. When expressed and secreted by transfected cells, these proteins formed a ternary complex, raising the possibility that their reciprocal stabilization at the basement membrane is due to complex formation. Given the close association of Fraser syndrome phenotypes with defective epidermal–dermal interactions, the coordinated assembly of three Fraser syndrome-associated proteins at the basement membrane appears to be instrumental in epidermal–dermal interactions during morphogenetic processes.
Notch/Delta signaling constrains reengineering of pro-T cells by PU.1
Authors: Franco Christopher B. , Scripture-Adams Deirdre D. , Proekt Irina , Taghon Tom , Weiss Angela H. , Yui Mary A. , Adams Stephanie L. , Diamond Rochelle A. , Rothenberg Ellen V.
Published: August 2006

PU.1 is essential for early stages of mouse T cell development but antagonizes it if expressed constitutively. Two separable mechanisms are involved: attenuation and diversion. Dysregulated PU.1 expression inhibits pro-T cell survival, proliferation, and passage through β-selection by blocking essential T cell transcription factors, signaling molecules, andRaggene expression, which expression of a rearranged T cell antigen receptor transgene cannot rescue. However, Bcl2 transgenic cells are protected from this attenuation and may even undergo β-selection, as shown by PU.1 transduction of defined subsets of Bcl2 transgenic fetal thymocytes with differentiation in OP9-DL1 and OP9 control cultures. The outcome of PU.1 expression in these cells depends on Notch/Delta signaling. PU.1 can efficiently divert thymocytes toward a myeloid-like state with multigene regulatory changes, but Notch/Delta signaling vetoes diversion. Gene expression analysis distinguishes sets of critical T lineage regulatory genes with different combinatorial responses to PU.1 and Notch/Delta signals, suggesting particular importance for inhibition of E proteins, Myb, and/or Gfi1 (growth factor independence 1) in diversion. However, Notch signaling only protects against diversion of cells that have undergone T lineage specification after Thy-1 and CD25 up-regulation. The results imply that in T cell precursors, Notch/Delta signaling normally acts to modulate and channel PU.1 transcriptional activities during the stages from T lineage specification until commitment.
Rabs and their effectors: Achieving specificity in membrane traffic
Authors: Grosshans Bianka L. , Ortiz Darinel , Novick Peter
Published: August 2006

Rab proteins constitute the largest branch of the Ras GTPase superfamily. Rabs use the guanine nucleotide-dependent switch mechanism common to the superfamily to regulate each of the four major steps in membrane traffic: vesicle budding, vesicle delivery, vesicle tethering, and fusion of the vesicle membrane with that of the target compartment. These different tasks are carried out by a diverse collection of effector molecules that bind to specific Rabs in their GTP-bound state. Recent advances have not only greatly extended the number of known Rab effectors, but have also begun to define the mechanisms underlying their distinct functions. By binding to the guanine nucleotide exchange proteins that activate the Rabs certain effectors act to establish positive feedback loops that help to define and maintain tightly localized domains of activated Rab proteins, which then serve to recruit other effector molecules. Additionally, Rab cascades and Rab conversions appear to confer directionality to membrane traffic and couple each stage of traffic with the next along the pathway.
AMPA receptors regulate experience-dependent dendritic arbor growth
in
vivo
Authors: Haas Kurt , Li Jianli , Cline Hollis T.
Published: August 2006

The size and shape of neuronal dendritic arbors affect the number and type of synaptic inputs, as well as the complexity and function of brain circuits. In the intact brain, dendritic arbor growth and the development of excitatory glutamatergic synapse are concurrent. Consequently, it has been difficult to resolve whether synaptic inputs drive dendritic arbor development. Here, we test the role of AMPA receptor (AMPAR)-mediated glutamatergic transmission in dendrite growth by expressing peptides corresponding to the intracellular C-terminal domains of AMPAR subunits GluR1 (GluR1Ct) and GluR2 (GluR2Ct) in optic tectal neurons of the
Xenopus
retinotectal system. These peptides significantly reduce AMPAR synaptic transmission in transfected neurons while leaving visual system circuitry intact. Daily
in vivo
imaging over 5 days revealed that GluR1Ct or GluR2Ct expression dramatically impaired dendrite growth, resulting in less complex arbors than controls. Time-lapse images collected at 2-h intervals over 6 h show that both GluR1Ct and GluR2Ct decrease branch lifetimes. Ultrastructural analysis indicates that synapses formed onto neurons expressing the GluRCt are less mature than synapses onto control neurons. These data suggest that the failure to form complex arbors is due to reduced stabilization of new synapses and dendritic branches. Although visual stimulation increases dendritic arbor growth rates in control tectal neurons, a weak postsynaptic response to visual experience in GluRCt-expressing cells leads to retraction of branches. These results indicate that AMPAR-mediated transmission underlies experience-dependent dendritic arbor growth by stabilizing branches, and support a competition-based model for dendrite growth.
Drosophila
Rtf1 functions in histone methylation, gene expression, and
Notch
signaling
Authors: Tenney Kristen , Gerber Mark , Ilvarsonn Anne , Schneider Jessica , Gause Maria , Dorsett Dale , Eissenberg Joel C. , Shilatifard Ali
Published: August 2006

The Rtf1 subunit of the Paf1 complex is required for proper monoubiquitination of histone H2B and methylation of histone H3 on lysines 4 (H3K4) and 79 in yeast
Saccharomyces cerevisiae
. Using RNAi, we examined the role of Rtf1 in histone methylation and gene expression in
Drosophila melanogaster
. We show that
Drosophila
Rtf1 (dRtf1) is required for proper gene expression and development. Furthermore, we show that RNAi-mediated reduction of dRtf1 results in a reduction in histone H3K4 trimethylation levels on bulk histones and chromosomes
in vivo
, indicating that the histone modification pathway via Rtf1 is conserved among yeast,
Drosophila
, and human. Recently, it was demonstrated that histone H3K4 methylation mediated via the E3 ligase Bre1 is critical for transcription of
Notch
target genes in
Drosophila
. Here we demonstrate that the dRtf1 component of the Paf1 complex functions in
Notch
signaling.
Monitoring the T cell response to genital tract infection
Authors: Roan Nadia R. , Gierahn Todd M. , Higgins Darren E. , Starnbach Michael N.
Published: August 2006

To date, it has not been possible to study antigen-specific T cell responses during primary infection of the genital tract. The low frequency of pathogen-specific T cells in a naïve mouse makes it difficult to monitor the initial events after antigen encounter. We developed a system to examine the response of pathogen-specific T cells in the genital mucosa after intrauterine infection. We identified the protective CD4+T cell antigen Cta1 fromChlamydia trachomatisand generated T cell receptor (TCR) transgenic (tg) mice with specificity for this protein. By transferring TCR tg T cells into naïve animals, we determined thatChlamydia-specific T cells were activated and proliferated in the lymph nodes draining the genital tract after primary intrauterine infection. Activated T cells migrated into the genital mucosa and secreted IFN-γ. The development ofChlamydia-specific TCR tg mice provides an approach for dissecting how pathogen-specific T cells function in the genital tract.
Theoretical model of temperature regulation in the brain during changes in functional activity
Authors: Sukstanskii Alexander L. , Yablonskiy Dmitriy A.
Published: August 2006

The balance between metabolic heat production, heat removal by blood flow, and heat conductance defines local temperature distribution in a living tissue. Disproportional local increases in blood flow as compared with oxygen consumption during functional brain activity disturb this balance, leading to temperature changes. In this article we have developed a theoretical framework that allows analysis of temperature changes during arbitrary functional brain activity. We established theoretical boundaries on temperature changes and explained how these boundaries depend on physiology (blood flow and metabolism) and external (heat exchange with the environment) experimental conditions. We show that, in regions located deep in the brain, task performance should be accompanied by temperature decreases in regions where blood flow increases (activated regions) and by temperature increases in regions where blood flow decreases (deactivated regions). The sign of temperature effect may be reversed for superficial cortex regions, where the baseline brain temperature is lower than the temperature of incoming arterial blood due to the heat exchange with the environment. Importantly, due to heat conductance, the temperature effect is not localized to the activated region but extends to a surrounding tissue at rest over the distances regulated by the temperature-shielding effect of blood flow. This temperature-shielding effect quantifies the means by which cerebral blood flow prevents “temperature perturbations” from propagating away from the perturbed regions. For small activated regions, this effect also substantially suppresses the magnitude of the temperature response, making it especially important for small animal brains.
Phosphoinositide 3-kinase regulatory subunit p85α suppresses insulin action via positive regulation of PTEN
Authors: Taniguchi Cullen M. , Tran Thien T. , Kondo Tatsuya , Luo Ji , Ueki Kohjiro , Cantley Lewis C. , Kahn C. Ronald
Published: August 2006

The phosphoinositide 3-kinase (PI3K) pathway is central to the metabolic actions of insulin on liver. Here, we show that mice with a liver-specific deletion of the p85α regulatory subunit of PI3K (L-Pik3r1KO) exhibit a paradoxical improvement of hepatic and peripheral insulin sensitivity. Although PI3K enzymatic activity is diminished in L-Pik3r1KO livers because of a reduced level of regulatory and catalytic subunits of PI3K, insulin-stimulated Akt activity is actually increased. This increased Akt activity correlates with increased phosphatidylinositol (3,4,5)-trisphosphate levels which are due, at least in part, to diminished activity of the (3,4,5)-trisphosphate phosphatase PTEN. Thus, the regulatory subunit p85α is a critical modulator of insulin sensitivity
in vivo
not only because of its effects on PI3K activation, but also as a regulator of PTEN activity.
A viral resistance gene from common bean functions across plant families and is up-regulated in a non-virus-specific manner
Authors: Seo Young-Su , Rojas Maria R. , Lee Jung-Youn , Lee Sang-Won , Jeon Jong-Seong , Ronald Pamela , Lucas William J. , Gilbertson Robert L.
Published: August 2006

Genes involved in a viral resistance response in common bean (
Phaseolus vulgaris
cv. Othello) were identified by inoculating a geminivirus reporter (
Bean dwarf mosaic virus
expressing the green fluorescent protein), extracting RNA from tissue undergoing the defense response, and amplifying sequences with degenerate R gene primers. One such gene (a TIR-NBS-LRR gene,
RT4-4
) was selected for functional analysis in which transgenic
Nicotiana benthamiana
were generated and screened for resistance to a range of viruses. This analysis revealed that
RT4-4
did not confer resistance to the reporter geminivirus; however, it did activate a resistance-related response (systemic necrosis) to seven strains of
Cucumber mosaic virus
(CMV) from pepper or tomato, but not to a CMV strain from common bean. Of these eight CMV strains, only the strain from common bean systemically infected common bean cv. Othello. Additional evidence that
RT4-4
is a CMV R gene came from the detection of resistance response markers in CMV-challenged leaves of RT4-4 transgenic plants, and the identification of the CMV 2a gene product as the elicitor of the necrosis response. These findings indicate that RT4-4 functions across two plant families and is up-regulated in a non-virus-specific manner. This experimental approach holds promise for providing insights into the mechanisms by which plants activate resistance responses against pathogens.
Cellular scaling rules for rodent brains
Authors: Herculano-Houzel Suzana , Mota Bruno , Lent Roberto
Published: August 2006

How do cell number and size determine brain size? Here, we show that, in the order
Rodentia
, increased size of the cerebral cortex, cerebellum, and remaining areas across six species is achieved through greater numbers of neurons of larger size, and much greater numbers of nonneuronal cells of roughly invariant size, such that the ratio between total neuronal and nonneuronal mass remains constant across species. Although relative cerebellar size remains stable among rodents, the number of cerebellar neurons increases with brain size more rapidly than in the cortex, such that the cerebellar fraction of total brain neurons increases with brain size. In contrast, although the relative cortical size increases with total brain size, the cortical fraction of total brain neurons remains constant. We propose that the faster increase in average neuronal size in the cerebral cortex than in the cerebellum as these structures gain neurons and the rapidly increasing glial numbers that generate glial mass to match total neuronal mass at a fixed glia/neuron total mass ratio are fundamental cellular constraints that lead to the relative expansion of cerebral cortical volume across species.
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Authors: Sogin Mitchell L. , Morrison Hilary G. , Huber Julie A. , Welch David Mark , Huse Susan M. , Neal Phillip R. , Arrieta Jesus M. , Herndl Gerhard J.
Published: August 2006

The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This “rare biosphere” is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.
ITK and IL-15 support two distinct subsets of CD8+T cells
Authors: Dubois Sigrid , Waldmann Thomas A. , Müller Jürgen R.
Published: August 2006

CD8+T cells are commonly divided into naïve CD44loCD122loand “memory phenotype” CD44hiCD122hicells. Here we show data suggesting that these two cell populations represent independent CD8+T cell subsets. Whereas IL-15−/−mice lack CD44hiCD122hiCD8+T cells, mice deficient in the kinase ITK lack CD44loCD122locells among CD8+T cells. The same defects were observed during thymus development. CD44hiCD122hicells were found among double-positive thymocytes and increased in frequency during CD8 development in wild-type mice. At the mature stage, IL-15−/−mice harbored virtually no CD44hiCD122hiCD8+thymocytes. In contrast, ITK−/−mice lacked CD44loCD122loCD8+cells at this stage. We generated mice with genetic deletions in both IL-15 and ITK and observed a severe reduction of all CD8+T cells. The two CD44loCD122loand CD44hiCD122hiCD8+T cell subsets differed in the periphery in that natural killer (NK) receptor expression was found only on CD44hiCD122hiCD8+T cells. This expression was paralleled by their ability to respond to both T cell receptor and NK receptor engagements. In contrast, CD44loCD122loCD8+T cells mounted stronger responses to T cell receptor stimulation but failed to recognize NK receptor ligands. Thus, whereas ITK-dependent CD44loCD122loCD8+T cells appear to represent conventional CD8+T cells, IL-15-dependent CD44hiCD122hiCD8+T cells may have functions in both adaptive and innate immunity.
Nonneutralizing antibodies binding to the surface glycoprotein of lymphocytic choriomeningitis virus reduce early virus spread
Authors: Hangartner Lars , Zellweger Raphaël M. , Giobbi Mattia , Weber Jacqueline , Eschli Bruno , McCoy Kathy D. , Harris Nicola , Recher Mike , Zinkernagel Rolf M. , Hengartner Hans
Published: August 2006

The biological relevance of nonneutralizing antibodies elicited early after infection with noncytopathic persistence-prone viruses is unclear. We demonstrate that cytotoxic T lymphocyte–deficient TgH(KL25) mice, which are transgenic for the heavy chain of the lymphocytic choriomeningitis virus (LCMV)–neutralizing monoclonal antibody KL25, mount a focused neutralizing antibody response following LCMV infection, and that this results in the emergence of neutralization escape virus variants. Further investigation revealed that some of the escape variants that arose early after infection could still bind to the selecting antibody. In contrast, no antibody binding could be detected for late isolates, indicating that binding, but nonneutralizing, antibodies exerted a selective pressure on the virus. Infection of naive TgH(KL25) mice with distinct escape viruses differing in their antibody-binding properties revealed that nonneutralizing antibodies accelerated clearance of antibody-binding virus variants in a partly complement-dependent manner. Virus variants that did not bind antibodies were not affected. We therefore conclude that nonneutralizing antibodies binding to the same antigenic site as neutralizing antibodies are biologically relevant by limiting early viral spread.
The MAPK Hog1p Modulates Fps1p-dependent Arsenite Uptake and Tolerance in Yeast
Authors: Thorsen Michael , Di Yujun , Tängemo Carolina , Morillas Montserrat , Ahmadpour Doryaneh , Van der Does Charlotte , Wagner Annemarie , Johansson Erik , Boman Johan , Posas Francesc , Wysocki Robert , Tamás Markus J.
Published: August 2006

Arsenic is widely distributed in nature and all organisms possess regulatory mechanisms to evade toxicity and acquire tolerance. Yet, little is known about arsenic sensing and signaling mechanisms or about their impact on tolerance and detoxification systems. Here, we describe a novel role of the S. cerevisiae mitogen-activated protein kinase Hog1p in protecting cells during exposure to arsenite and the related metalloid antimonite. Cells impaired in Hog1p function are metalloid hypersensitive, whereas cells with elevated Hog1p activity display improved tolerance. Hog1p is phosphorylated in response to arsenite and this phosphorylation requires Ssk1p and Pbs2p. Arsenite-activated Hog1p remains primarily cytoplasmic and does not mediate a major transcriptional response. Instead, hog1Δ sensitivity is accompanied by elevated cellular arsenic levels and we demonstrate that increased arsenite influx is dependent on the aquaglyceroporin Fps1p. Fps1p is phosphorylated on threonine 231 in vivo and this phosphorylation critically affects Fps1p activity. Moreover, Hog1p is shown to affect Fps1p phosphorylation. Our data are the first to demonstrate Hog1p activation by metalloids and provides a mechanism by which this kinase contributes to tolerance acquisition. Understanding how arsenite/antimonite uptake and toxicity is modulated may prove of value for their use in medical therapy.
Reliable gene signatures for microarray classification: assessment of stability and performance
Authors: Davis Chad A. , Gerick Fabian , Hintermair Volker , Friedel Caroline C. , Fundel Katrin , Küffner Robert , Zimmer Ralf
Published: August 2006

Motivation: Two important questions for the analysis of gene expression measurements from different sample classes are (1) how to classify samples and (2) how to identify meaningful gene signatures (ranked gene lists) exhibiting the differences between classes and sample subsets. Solutions to both questions have immediate biological and biomedical applications. To achieve optimal classification performance, a suitable combination of classifier and gene selection method needs to be specifically selected for a given dataset. The selected gene signatures can be unstable and the resulting classification accuracy unreliable, particularly when considering different subsets of samples. Both unstable gene signatures and overestimated classification accuracy can impair biological conclusions.

Methods: We address these two issues by repeatedly evaluating the classification performance of all models, i.e. pairwise combinations of various gene selection and classification methods, for random subsets of arrays (sampling). A model score is used to select the most appropriate model for the given dataset. Consensus gene signatures are constructed by extracting those genes frequently selected over many samplings. Sampling additionally permits measurement of the stability of the classification performance for each model, which serves as a measure of model reliability.

Results: We analyzed a large gene expression dataset with 78 measurements of four different cartilage sample classes. Classifiers trained on subsets of measurements frequently produce models with highly variable performance. Our approach provides reliable classification performance estimates via sampling. In addition to reliable classification performance, we determined stable consensus signatures (i.e. gene lists) for sample classes. Manual literature screening showed that these genes are highly relevant to our gene expression experiment with osteoarthritic cartilage. We compared our approach to others based on a publicly available dataset on breast cancer.

Availability: R package at

Contact:  ralf.zimmer@bio.ifi.lmu.de
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
Authors: Ruan Quansong , Dutta Debojyoti , Schwalbach Michael S. , Steele Joshua A. , Fuhrman Jed A. , Sun Fengzhu
Published: August 2006

Motivation: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored.

Results: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial.

Availability: The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.

Contact:  fsun@usc.edu
Studies of Advanced Stages of Meditation in the Tibetan Buddhist and Vedic Traditions. I: A Comparison of General Changes
Authors: Hankey Alex
Published: August 2006

This article is the first of two comparing findings of studies of advanced practitioners of Tibetan Buddhist meditation in remote regions of the Himalayas, with established results on long‐term practitioners of the Transcendental Meditation programs. Many parallel levels of improvement were found, in sensory acuity, perceptual style and cognitive function, indicating stabilization of aspects of attentional awareness. Together with observed increases in EEG coherence and aspects of brain function, such changes are consistent with growth towards a state of total brain functioning, i.e. development of full mental potential. They are usually accompanied by improved health parameters. How they may be seen to be consistent with growth of enlightenment will be the subject of a second article.
Immunology and Homeopathy. 4. Clinical Studies—Part 2
Authors: Bellavite Paolo , Ortolani Riccardo , Pontarollo Francesco , Piasere Valeria , Benato Giovanni , Conforti Anita
Published: August 2006

The clinical studies on the effectiveness of homeopathy in respiratory allergy (18 randomized trials and 9 observational studies) are described. The literature of common immunologic disorders including also upper respiratory tract infections (URTI) and otorhinolaryngology (reported in part 1), is evaluated and discussed. Most of initial evidence‐based research was addressed to the question of whether homeopathic high dilutions are placebos or possess specific effects, but this question has been often equivocal and is still a matter of debate. The evidence demonstrates that in some conditions homeopathy shows significant promise, e.g. Galphimia glauca (low dilutions/potencies) in allergic oculorhinitis, classical individualized homeopathy in otitis and possibly in asthma and allergic complaints, and a few low‐potency homeopathic complexes in sinusitis and rhinoconjunctivitis. A general weakness of evidence derives from lack of independent confirmation of reported trials and from presence of conflicting results, as in case of homeopathic immunotherapy and of classical homeopathy for URTI. The suitable methods to evaluate homeopathy effectiveness, without altering the setting of cure, are also analyzed.
‘EXAMEN D'IDENTITÉ’: VOYAGEUR PROFESSIONNEL ET IDENTIFICATION DIASPORIQUE CHEZ JEAN-PHILIPPE TOUSSAINT ET ABDELKÉBIR KHATIBI
Authors: Hennuy Jean-Frédéric
Published: August 2006

À travers la question du rapport à l'autre et à soi-même, la lecture des romans de Jean-Philippe Toussaint et Abdelkébir Khatibi nous forcent à une analyse où l'on est appelé à redoubler de vigilance face à des certitudes identitaires considèrèes, bien trop souvent encore, comme inébranlables et indéfectibles. Jean-Philippe Toussaint et Abdelkébir Khatibi nous rendent sensibles au fait qu'en début de ce troisième millénaire notre identité personnelle est toujours
déterritorialisée
. Nos voyages, nos traversées chroniques des frontières ne visent plus à fonder des territoires, mais nous forcent à faire en permanence l'examen de notre identité, à créer des
identités diasporiques
. Identitaires, nos voyages le sont parce qu'ils nous contraignent à former et reformer une carte d'identité composée d'une multiplicité d'appartenances. Identitaires, nos voyages le sont aussi et avant tout parce qu'ils nous mettent face au caractère protéiforme de notre étrangeté.
THÉÂTRE ET RELIGION DANS LA SECONDE MOITIÉ DU XVI
E
SIÈCLE (1550–1610)
Authors: Mazouer Charles
Published: August 2006

Cet article examine la question capitale, pour le théâtre français ancien, des rapports entre le théâtre et la religion, laquelle a favorisé et vu naître au sein de sa liturgie le théâtre occidental au Moyen Âge. Jusqu'en 1550, l'Église aide évidemment la représentation des mystères, théâtre religieux par excellence, et supporte plus ou moins bien le développement d'un théâtre profane. Les choses changent avec la Renaissance et l'apparition de genres nouveaux. Dans la comédie humaniste, la religion est fort présente parmi les autres réalités de la vie du temps portées sur la scène et les pièces sont loin d'être anticléricales; mais la conduite morale des personnages ne correspond guère aux commandements de l'Église, du moins jusqu'au dénouement qui fait triompher le conformisme moral plus que vraiment l'ordre religieux. Quant à la tragédie humaniste, avec ses sujets antiques (mythologiques ou historiques) et ses sujets bibliques, elle n'échappe pas toujours aux contradictions entre une pensée antique (la philosophie antique des tragédies grecques avec leur transcendance méchante), comme amenée par la forme imitée, et une théologie authentiquement chrétienne. Un Jean de La Taille ou un Monchrestien illustrent parfaitement cette difficulté, qui n'est autre que le grand problème culturel et philosophique de la Renaissance: comment faire cohabiter ensemble l'univers tragique des Anciens et les convictions chrétiennes des Modernes?
IMPROVISING VIRTUE: PERFORMATIVE MORALITY IN MOISSY'S
THÉÂTRE D'ÉDUCATION
Authors: Brown Penny
Published: August 2006

In
Les Jeux de la petite Thalie, ou petits drames, dialogués sur des proverbes
(1769), Alexandre-Guillaume Mouslier de Moissy appropriated the
proverbe dramatique
, a popular pastime in eighteenth-century drawing-rooms, for pedagogical use with the young. This was the first volume in an ambitious three-volume work offering short dramatic pieces for all the different stages in life. Far less well known than the later
théâtre d'éducation
of Mme de Genlis and Berquin, Moissy's project of moral instruction through performance in
Les Jeux de la petite Thalie
was typical of the genre in its portrayal of character flaws and transgressive behaviour, but it was also innovative in that it offered the participants opportunities for improvisation, albeit well-controlled, marked by ‘Impromptu’ passages in the text. Moissy's recommendation was that the young ‘actors’ should be chosen for their resemblance to the role, so that they were playing themselves in scenarios that ultimately forced them to recognize and acknowledge their faults. This paper draws on modern theories of improvisation in drama to assess Moissy's implementation of his didactic agenda and the implications of involvement for the young participants in performances that were, in effect, rehearsals for their future in society in which the correct fulfilment of their role and the ability to improvise in word and deed from a basic moral script would be essential skills.