bluuebunny/crossref_metadata_2025 huggingface dataset:
Roots of the Second Green Revolution
Authors: Lynch Jonathan P.
Published: August 2007

The Green Revolution boosted crop yields in developing nations by introducing dwarf genotypes of wheat and rice capable of responding to fertilisation without lodging. We now need a second Green Revolution, to improve the yield of crops grown in infertile soils by farmers with little access to fertiliser, who represent the majority of third-world farmers. Just as the Green Revolution was based on crops responsive to high soil fertility, the second Green Revolution will be based on crops tolerant of low soil fertility. Substantial genetic variation in the productivity of crops in infertile soil has been known for over a century. In recent years we have developed a better understanding of the traits responsible for this variation. Root architecture is critically important by determining soil exploration and therefore nutrient acquisition. Architectural traits under genetic control include basal-root gravitropism, adventitious-root formation and lateral branching. Architectural traits that enhance topsoil foraging are important for acquisition of phosphorus from infertile soils. Genetic variation in the length and density of root hairs is important for the acquisition of immobile nutrients such as phosphorus and potassium. Genetic variation in root cortical aerenchyma formation and secondary development (‘root etiolation’) are important in reducing the metabolic costs of root growth and soil exploration. Genetic variation in rhizosphere modification through the efflux of protons, organic acids and enzymes is important for the mobilisation of nutrients such as phosphorus and transition metals, and the avoidance of aluminum toxicity. Manipulation of ion transporters may be useful for improving the acquisition of nitrate and for enhancing salt tolerance. With the noteworthy exceptions of rhizosphere modification and ion transporters, most of these traits are under complex genetic control. Genetic variation in these traits is associated with substantial yield gains in low-fertility soils, as illustrated by the case of phosphorus efficiency in bean and soybean. In breeding crops for low-fertility soils, selection for specific root traits through direct phenotypic evaluation or molecular markers is likely to be more productive than conventional field screening. Crop genotypes with greater yield in infertile soils will substantially improve the productivity and sustainability of low-input agroecosystems, and in high-input agroecosystems will reduce the environmental impacts of intensive fertilisation. Although the development of crops with reduced fertiliser requirements has been successful in the few cases it has been attempted, the global scientific effort devoted to this enterprise is small, especially considering the magnitude of the humanitarian, environmental and economic benefits being forgone. Population growth, ongoing soil degradation and increasing costs of chemical fertiliser will make the second Green Revolution a priority for plant biology in the 21st century.
Effects of nitrogen fertiliser and wheat straw application on CH4 and N2O emissions from a paddy rice field
Authors: Ma J. , Li X. L. , Xu H. , Han Y. , Cai Z. C. , Yagi K.
Published: August 2007

A 3-year field experiment was conducted to study the effects of nitrogen fertiliser and straw application on CH4 and N2O emissions from a paddy rice field in China from 2003 to 2005. Three rates of nitrogen fertiliser (0, 200, and 270 kg N/ha) and 2 levels of wheat straw (0 and 3.75 × 103 kg/ha) were adopted in this experiment. The effect of nitrogen fertiliser application on CH4 emission seemed to be affected by application rate. Nitrogen fertiliser decreased CH4 emission relative to the control when applied at a rate of 200 kg N/ha, but the effect lessened if the application rate was further increased to a rate of 270 kg N/ha. The depressive effect of nitrogen fertiliser application on CH4 emissions from rice fields became more pronounced when wheat straw was also incorporated with fertiliser, compared with nitrogen fertiliser application alone. Straw incorporation significantly enhanced CH4 emission by 3–11 times (P < 0.05). Nitrogen fertiliser application increased N2O emission by 5–6 times when applied at a rate of 200 kg N/ha and by 10–14 times when applied at a rate of 270 kg N/ha. On average, straw incorporation tended to decrease N2O emission by about 30% significant (P > 0.05). More than 50% of seasonal total amount of N2O was emitted within 11 days after fertiliser application at panicle initiation. The global warming potential caused by both CH4 and N2O emissions was affected by nitrogen fertiliser application rate and significantly stimulated by wheat straw incorporation. The global warming potential was lowest when nitrogen fertiliser was applied at a rate of 200 kg N/ha.
An inhibitor of viral RNA replication is encoded by a plant resistance gene
Authors: Ishibashi Kazuhiro , Masuda Kiyoshi , Naito Satoshi , Meshi Tetsuo , Ishikawa Masayuki
Published: August 2007

The tomato
Tm-1
gene confers resistance to tomato mosaic virus (ToMV). Here, we report that the extracts of
Tm-1
tomato cells (GCR237) have properties that inhibit the
in vitro
RNA replication of WT ToMV more strongly than that of the
Tm-1
-resistance-breaking mutant of ToMV, LT1. We purified this inhibitory activity and identified a polypeptide of ≈80 kDa (p80
GCR237
) using LC–tandem MS. The amino acid sequence of p80
GCR237
had no similarity to any characterized proteins. The

p80
GCR237

gene cosegregated with
Tm-1
; transgenic expression of p80
GCR237
conferred resistance to ToMV within tomato plants; and the knockdown of

p80
GCR237

sensitized
Tm-1
tomato plants to ToMV, indicating that
Tm-1
encodes p80
GCR237
itself. We further show that
in vitro
-synthesized Tm-1 (p80
GCR237
) protein binds to the replication proteins of WT ToMV and inhibits their function at a step before, but not after, the viral replication complex is formed on the membrane surfaces. Such binding was not observed for the replication proteins of LT1. These results suggest that Tm-1 (p80
GCR237
) inhibits the replication of WT ToMV RNA through binding to the replication proteins.
Dissociation of the insulin receptor and caveolin-1 complex by ganglioside GM3 in the state of insulin resistance
Authors: Kabayama Kazuya , Sato Takashige , Saito Kumiko , Loberto Nicoletta , Prinetti Alessandro , Sonnino Sandro , Kinjo Masataka , Igarashi Yasuyuki , Inokuchi Jin-ichi
Published: August 2007

Membrane microdomains (lipid rafts) are now recognized as critical for proper compartmentalization of insulin signaling. We previously demonstrated that, in adipocytes in a state of TNFα-induced insulin resistance, the inhibition of insulin metabolic signaling and the elimination of insulin receptors (IR) from the caveolae microdomains were associated with an accumulation of the ganglioside GM3. To gain insight into molecular mechanisms behind interactions of IR, caveolin-1 (Cav1), and GM3 in adipocytes, we have performed immunoprecipitations, cross-linking studies of IR and GM3, and live cell studies using total internal reflection fluorescence microscopy and fluorescence recovery after photobleaching techniques. We found that (
i
) IR form complexes with Cav1 and GM3 independently; (
ii
) in GM3-enriched membranes the mobility of IR is increased by dissociation of the IR–Cav1 interaction; and (
iii
) the lysine residue localized just above the transmembrane domain of the IR β-subunit is essential for the interaction of IR with GM3. Because insulin metabolic signal transduction in adipocytes is known to be critically dependent on caveolae, we propose a pathological feature of insulin resistance in adipocytes caused by dissociation of the IR–Cav1 complex by the interactions of IR with GM3 in microdomains.
Role of purine-rich exonic splicing enhancers in nuclear retention of pre-mRNAs
Authors: Taniguchi Ichiro , Masuyama Kaoru , Ohno Mutsuhito
Published: August 2007

Intron-containing pre-mRNAs are normally retained in the nucleus until they are spliced to produce mature mRNAs that are exported to the cytoplasm. Although the detailed mechanism is not well understood, the formation of splicing-related complexes on pre-mRNAs is thought to be responsible for the nuclear retention. Therefore, pre-mRNAs containing suboptimal splice sites should tend to leak out to the cytoplasm. Such pre-mRNAs often contain purine-rich exonic splicing enhancers (ESEs) that stimulate splicing of the adjacent intron. Here, we show that ESEs
per se
possess an activity to retain RNAs in the nucleus through a saturable nuclear retention factor. Cross-competition experiments revealed that intron-containing pre-mRNAs (without ESEs) used the same saturable nuclear retention factor as ESEs. Interestingly, although intronless mRNAs containing ESEs were also poorly exported, spliced mRNAs produced from ESE-containing pre-mRNAs were efficiently exported to the cytoplasm. Thus, the splicing reaction can reset the nuclear retention state caused by ESEs, allowing nuclear export of mature mRNAs. Our results reveal a novel aspect of ESE activity that should contribute to gene expression and RNA quality control.
Unified model of tectonics and heat transport in a frigid Enceladus
Authors: Gioia Gustavo , Chakraborty Pinaki , Marshak Stephen , Kieffer Susan W.
Published: August 2007

Recent data from the Cassini spacecraft have revealed that Enceladus, the 500-km-diameter moon of Saturn, has a southern hemisphere with a distinct arrangement of tectonic features, intense heat flux, and geyser-like plumes. How did the tectonic features form? How is the heat transported from depth? To address these questions, we formulate a simple model that couples the mechanics and thermodynamics of Enceladus and gives a unified explanation of the salient tectonic features, the plumes, and the transport of heat from a source at a depth of tens of kilometers to the surface. Our findings imply that tiny, icy moons can develop complex surficial geomorphologies, high heat fluxes, and geyser-like activity even if they do not have hot, liquid, and/or convecting interiors.
Selective involvement of the mid-dorsolateral prefrontal cortex in the coding of the serial order of visual stimuli in working memory
Authors: Amiez Céline , Petrides Michael
Published: August 2007

There is evidence that the primate prefrontal cortex is involved in the monitoring of the order in which stimuli occur. The prefrontal cortical areas, however, involved in the capacity of the human brain to encode and hold “in mind” the precise order of occurrence of a limited number of visual stimuli after a single exposure are not known. Changes in regional cerebral activity were measured with functional magnetic resonance imaging while subjects were coding the precise order of a short sequence of abstract visual stimuli. The results demonstrate the involvement of areas 46 and 9/46, within the mid-dorsolateral subdivision of the prefrontal cortex, in the coding of the precise order of a short sequence of visual stimuli in working memory, consistent with earlier results from monkey lesion studies. The availability of such detailed serial-order information in working memory allows high-level cognitive planning and mental manipulation, functions that depend on prefrontal cortex.
Flexible energy storage devices based on nanocomposite paper
Authors: Pushparaj Victor L. , Shaijumon Manikoth M. , Kumar Ashavani , Murugesan Saravanababu , Ci Lijie , Vajtai Robert , Linhardt Robert J. , Nalamasu Omkaram , Ajayan Pulickel M.
Published: August 2007

There is strong recent interest in ultrathin, flexible, safe energy storage devices to meet the various design and power needs of modern gadgets. To build such fully flexible and robust electrochemical devices, multiple components with specific electrochemical and interfacial properties need to be integrated into single units. Here we show that these basic components, the electrode, separator, and electrolyte, can all be integrated into single contiguous nanocomposite units that can serve as building blocks for a variety of thin mechanically flexible energy storage devices. Nanoporous cellulose paper embedded with aligned carbon nanotube electrode and electrolyte constitutes the basic unit. The units are used to build various flexible supercapacitor, battery, hybrid, and dual-storage battery-in-supercapacitor devices. The thin freestanding nanocomposite paper devices offer complete mechanical flexibility during operation. The supercapacitors operate with electrolytes including aqueous solvents, room temperature ionic liquids, and bioelectrolytes and over record temperature ranges. These easy-to-assemble integrated nanocomposite energy-storage systems could provide unprecedented design ingenuity for a variety of devices operating over a wide range of temperature and environmental conditions.
Quasi-steady-state ac plasma current operation in HT-7 tokamak
Authors: Li Jiangang , Luo Jiarong , Wang Shaojie , Fu Peng , Shen Biao , Liu Fukun , Wan Baonian , Shan Jiafang , Xu Guosheng , Huang Juan , Yu Jun , Hu Jiansheng , Yuan Qiping , Hu Yeming
Published: August 2007

A quasi-steady-state alternating current operation assisted by lower hybrid wave (LHW) was achieved on a HT-7 superconducting tokamak with plasma current ofIp= 125 kA, line-averaged density of 1.5 × 1019 m−3, electron temperature ofTe= 500 eV and 30–50 s plasma duration. Plasma current was sustained and smoothly transferred from one direction to the other without loss of ionization. Plasma position control, LHW assistance, strong gas puffing and good wall condition are the key issues to have a smooth transition of plasma current. Our modelling results show that current reversal equilibrium configuration with two oppositely flowing currents in the high-field-side and the low-field-side during current reversal exists. This is in agreement with experimental measurements.
Confinement improvement in high-ion temperature plasmas heated with high-energy negative-ion-based neutral beam injection in the Large Helical Device
Authors: Takeiri Y. , Morita S. , Ikeda K. , Ida K. , Kubo S. , Yokoyama M. , Tsumori K. , Oka Y. , Osakabe M. , Nagaoka K. , Shimozuma T. , Yoshinuma M. , Narihara K. , Funaba H. , Goto M. , Inagaki S. , Tanaka K. , Kaneko O. , Komori A. , Motojima O.
Published: August 2007

An increase in the ion temperature due to transport improvement has been observed in plasmas heated with high-energy negative-ion-based neutral beam injection (NBI), in which the electrons are dominantly heated, in the Large Helical Device. When centrally focused electron-cyclotron-resonance heating is superposed on the NBI plasma, the ion temperature is observed to rise, accompanied by the formation of the electron internal transport barrier (electron-ITB). In the electron-ITB plasmas, an increase in a positive radial electric field is observed, and the transport analysis indicates that the ion transport in the half-radius region is improved with a reduction of the anomalous transport. Thus, this ion temperature rise is ascribed to the ion transport improvement by the transition to the neoclassical electron root. In high-Zplasmas, the ion temperature is increased with an increase in the ion heating power and reaches 13.5 keV. The central ion temperature increases with an increase in a gradient of the electron temperature in an outer plasma region of ρ = 0.8, suggesting the ion transport improvement in the outer plasma region induced by the neoclassical electron root. These results indicate the effectiveness of the electron-root scenario for obtaining high-ion temperature plasmas in helical systems.
Transport and confinement studies in the RFX-mod reversed-field pinch experiment
Authors: Innocente P. , Alfier A. , Carraro L. , Lorenzini R. , Pasqualotto R. , Terranova D.
Published: August 2007

In the modified RFX experiment (RFX-mod) external magnetic field coils and a close fitting thin conductive shell control radial magnetic fields. In the so-called virtual shell (VS) operation, radial field zeroing at the thin shell radius is stationary provided by the feedback-controlled coils. First experiments on RFX-mod proved the capability of the active scheme to steadily reduce the radial magnetic field. Furthermore it has been found that such edge magnetic field control extends its beneficial effects to the whole plasma. With respect to the old RFX, where magnetohydrodynamic modes amplitude was controlled by the use of a passive thick conductive shell, a stationary 2- to 3-fold reduction of theBrfield amplitude in the core is obtained. The reduction of field fluctuations positively reflects on confinement. In fact, a strong reduction of the loop voltage is observed and correspondingly a 3-fold increase in pulse length is achieved by using the same poloidal flux swing. Temperature and particle measurements confirm the improved confinement properties of the VS operation. With a lower ohmic input power, higher electron temperature and lower particle influx are measured. Particle and heat transport have been studied by means of a 1D code. Local power balance was used to compute the heat conductivity profile: for the VS discharges a lower conductivity over a significant region of the plasma is found. The improved properties of RFX-mod VS operation provide a better confinement scaling in terms of plasma current. The results show that compared with the thick shell configuration, a significant confinement improvement can be obtained under stationary conditions by actively controlling the plasma magnetic boundary.
Nuclear Localization of the ERK MAP Kinase Mediated byDrosophilaαPS2βPS Integrin and Importin-7
Authors: James Brian P. , Bunch Thomas A. , Krishnamoorthy Srinivasan , Perkins Lizabeth A. , Brower Danny L.
Published: August 2007

The control of gene expression by the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (ERK) requires its translocation into the nucleus. In Drosophila S2 cells nuclear accumulation of diphospho-ERK (dpERK) is greatly reduced by interfering double-stranded RNA against Drosophila importin-7 (DIM-7) or by the expression of integrin mutants, either during active cell spreading or after stimulation by insulin. In both cases, total ERK phosphorylation (on Westerns) is not significantly affected, and ERK accumulates in a perinuclear ring. Tyrosine phosphorylation of DIM-7 is reduced in cells expressing integrin mutants, indicating a mechanistic link between these components. DIM-7 and integrins localize to the same actin-containing peripheral regions in spreading cells, but DIM-7 is not concentrated in paxillin-positive focal contacts or stable focal adhesions. The Corkscrew (SHP-2) tyrosine phosphatase binds DIM-7, and Corkscrew is required for the cortical localization of DIM-7. These data suggest a model in which ERK phosphorylation must be spatially coupled to integrin-mediated DIM-7 activation to make a complex that can be imported efficiently. Moreover, dpERK nuclear import can be restored in DIM-7–deficient cells by Xenopus Importin-7, demonstrating that ERK import is an evolutionarily conserved function of this protein.
Multiple Myosins Are Required to Coordinate Actin Assembly with Coat Compression during Compensatory Endocytosis
Authors: Yu Hoi-Ying E. , Bement William M.
Published: August 2007

Actin is involved in endocytosis in organisms ranging from yeast to mammals. In activated Xenopus eggs, exocytosing cortical granules (CGs) are surrounded by actin “coats,” which compress the exocytosing compartments, resulting in compensatory endocytosis. Here, we examined the roles of two myosins in actin coat compression. Myosin-2 is recruited to exocytosing CGs late in coat compression. Inhibition of myosin-2 slows coat compression without affecting actin assembly. This differs from phenotype induced by inhibition of actin assembly, where exocytosing CGs are trapped at the plasma membrane (PM) completely. Thus, coat compression is likely driven in part by actin assembly itself, but it requires myosin-2 for efficient completion. In contrast to myosin-2, the long-tailed myosin-1e is recruited to exocytosing CGs immediately after egg activation. Perturbation of myosin-1e results in partial actin coat assembly and induces CG collapse into the PM. Intriguingly, simultaneous inhibition of actin assembly and myosin-1e prevents CG collapse. Together, the results show that myosin-1e and myosin-2 are part of an intricate machinery that coordinates coat compression at exocytosing CGs.
Isoprenylcysteine Carboxy Methylation Is Essential for Development inDictyostelium discoideum
Authors: Chen Ying , McQuade Kyle J. , Guan Xiao-Juan , Thomason Peter A. , Wert Michael S. , Stock Jeffry B. , Cox Edward C.
Published: August 2007

Members of the Ras superfamily of small GTPases and the heterotrimeric G protein γ subunit are methylated on their carboxy-terminal cysteine residues by isoprenylcysteine methyltransferase. In Dictyostelium discoideum, small GTPase methylation occurs seconds after stimulation of starving cells by cAMP and returns quickly to basal levels, suggesting an important role in cAMP-dependent signaling. Deleting the isoprenylcysteine methyltransferase-encoding gene causes dramatic defects. Starving mutant cells do not propagate cAMP waves in a sustained manner, and they do not aggregate. Motility is rescued when cells are pulsed with exogenous cAMP, or coplated with wild-type cells, but the rescued cells exhibit altered polarity. cAMP-pulsed methyltransferase-deficient cells that have aggregated fail to differentiate, but mutant cells plated in a wild-type background are able to do so. Localization of and signaling by RasG is altered in the mutant. Localization of the heterotrimeric Gγ protein subunit was normal, but signaling was altered in mutant cells. These data indicate that isoprenylcysteine methylation is required for intercellular signaling and development in Dictyostelium.
Regulation of Cell Cycle and Stress Responses to Hydrostatic Pressure in Fission Yeast
Authors: George Vinoj T. , Brooks Gavin , Humphrey Timothy C.
Published: August 2007

We have investigated the cellular responses to hydrostatic pressure by using the fission yeast Schizosaccharomyces pombe as a model system. Exposure to sublethal levels of hydrostatic pressure resulted in G2 cell cycle delay. This delay resulted from Cdc2 tyrosine-15 (Y-15) phosphorylation, and it was abrogated by simultaneous disruption of the Cdc2 kinase regulators Cdc25 and Wee1. However, cell cycle delay was independent of the DNA damage, cytokinesis, and cell size checkpoints, suggesting a novel mechanism of Cdc2-Y15 phosphorylation in response to hydrostatic pressure. Spc1/Sty1 mitogen-activated protein (MAP) kinase, a conserved member of the eukaryotic stress-activated p38, mitogen-activated protein (MAP) kinase family, was rapidly activated after pressure stress, and it was required for cell cycle recovery under these conditions, in part through promoting polo kinase (Plo1) phosphorylation on serine 402. Moreover, the Spc1 MAP kinase pathway played a key role in maintaining cell viability under hydrostatic pressure stress through the bZip transcription factor, Atf1. Further analysis revealed that prestressing cells with heat increased barotolerance, suggesting adaptational cross-talk between these stress responses. These findings provide new insight into eukaryotic homeostasis after exposure to pressure stress.
Canonical Heterotrimeric G Proteins Regulating Mating and Virulence ofCryptococcus neoformans
Authors: Li Lie , Shen Gui , Zhang Zheng-Guang , Wang Yan-Li , Thompson Jill K. , Wang Ping
Published: August 2007

Perturbation of pheromone signaling modulates not only mating but also virulence in Cryptococcus neoformans, an opportunistic human pathogen known to encode three Gα, one Gβ, and two Gγ subunit proteins. We have found that Gαs Gpa2 and Gpa3 exhibit shared and distinct roles in regulating pheromone responses and mating. Gpa2 interacted with the pheromone receptor homolog Ste3α, Gβ subunit Gpb1, and RGS protein Crg1. Crg1 also exhibited in vitro GAP activity toward Gpa2. These findings suggest that Gpa2 regulates mating through a conserved signaling mechanism. Moreover, we found that Gγs Gpg1 and Gpg2 both regulate pheromone responses and mating. gpg1 mutants were attenuated in mating, and gpg2 mutants were sterile. Finally, although gpa2, gpa3, gpg1, gpg2, and gpg1 gpg2 mutants were fully virulent, gpa2 gpa3 mutants were attenuated for virulence in a murine model. Our study reveals a conserved but distinct signaling mechanism by two Gα, one Gβ, and two Gγ proteins for pheromone responses, mating, and virulence in Cryptococcus neoformans, and it also reiterates that the link between mating and virulence is not due to mating per se but rather to certain mating-pathway components that encode additional functions promoting virulence.
Transcriptional Modulation of Genes Encoding Structural Characteristics of Differentiating Enterocytes During Development of a Polarized Epithelium In Vitro
Authors: Halbleib Jennifer M. , Sääf Annika M. , Brown Patrick O. , Nelson W. James
Published: August 2007

Although there is considerable evidence implicating posttranslational mechanisms in the development of epithelial cell polarity, little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized the temporal program of gene expression during cell–cell adhesion–initiated polarization of human Caco-2 cells in tissue culture, which develop structural and functional polarity similar to that of enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts between neighboring cells. Expression of genes involved in cell proliferation was down-regulated concomitant with induction of genes necessary for functional specialization of polarized epithelial cells. Transcriptional up-regulation of these latter genes correlated with formation of important structural and functional features in enterocyte differentiation and establishment of structural and functional cell polarity; components of the apical microvilli were induced as the brush border formed during polarization; as barrier function was established, expression of tight junction transmembrane proteins peaked; transcripts encoding components of the apical, but not the basal-lateral trafficking machinery were increased during polarization. Coordinated expression of genes encoding components of functional cell structures were often observed indicating temporal control of expression and assembly of multiprotein complexes.
Parallels between Global Transcriptional Programs of Polarizing Caco-2 Intestinal Epithelial Cells In Vitro and Gene Expression Programs in Normal Colon and Colon Cancer
Authors: Sääf Annika M. , Halbleib Jennifer M. , Chen Xin , Yuen Siu Tsan , Leung Suet Yi , Nelson W. James , Brown Patrick O.
Published: August 2007

Posttranslational mechanisms are implicated in the development of epithelial cell polarity, but little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized temporal patterns of gene expression during cell–cell adhesion-initiated polarization of cultured human Caco-2 cells, which develop structural and functional polarity resembling enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts. Comparison to gene expression patterns in normal human colon and colon tumors revealed that the pattern in proliferating, nonpolarized Caco-2 cells paralleled patterns seen in human colon cancer in vivo, including expression of genes involved in cell proliferation. The pattern switched in polarized Caco-2 cells to one more closely resembling that in normal colon tissue, indicating that regulation of transcription underlying Caco-2 cell polarization is similar to that during enterocyte differentiation in vivo. Surprisingly, the temporal program of gene expression in polarizing Caco-2 cells involved changes in signaling pathways (e.g., Wnt, Hh, BMP, FGF) in patterns similar to those during migration and differentiation of intestinal epithelial cells in vivo, despite the absence of morphogen gradients and interactions with stromal cells characteristic of enterocyte differentiation in situ. The full data set is available at http://microarray-pubs.stanford.edu/CACO2 .
Neurabin-I Is Phosphorylated by Cdk5: Implications for Neuronal Morphogenesis and Cortical Migration
Authors: Causeret Frédéric , Jacobs Tom , Terao Mami , Heath Owen , Hoshino Mikio , Nikolić Margareta
Published: August 2007

The correct morphology and migration of neurons, which is essential for the normal development of the nervous system, is enabled by the regulation of their cytoskeletal elements. We reveal that Neurabin-I, a neuronal-specific F-actin–binding protein, has an essential function in the developing forebrain. We show that gain and loss of Neurabin-I expression affect neuronal morphology, neurite outgrowth, and radial migration of differentiating cortical and hippocampal neurons, suggesting that tight regulation of Neurabin-I function is required for normal forebrain development. Importantly, loss of Neurabin-I prevents pyramidal neurons from migrating into the cerebral cortex, indicating its essential role during early stages of corticogenesis. We demonstrate that in neurons Rac1 activation is affected by the expression levels of Neurabin-I. Furthermore, the Cdk5 kinase, a key regulator of neuronal migration and morphology, directly phosphorylates Neurabin-I and controls its association with F-actin. Mutation of the Cdk5 phosphorylation site reduces the phenotypic consequences of Neurabin-I overexpression both in vitro and in vivo, suggesting that Neurabin-I function depends, at least in part, on its phosphorylation status. Together our findings provide new insight into the signaling pathways responsible for controlled changes of the F-actin cytoskeleton that are required for normal development of the forebrain.
Regulation of Ubiquitin-Proteasome System–mediated Degradation by Cytosolic Stress
Authors: Kelly Sean M. , VanSlyke Judy K. , Musil Linda S.
Published: August 2007

ER-associated, ubiquitin-proteasome system (UPS)-mediated degradation of the wild-type (WT) gap junction protein connexin32 (Cx32) is inhibited by mild forms of cytosolic stress at a step before its dislocation into the cytosol. We show that the same conditions (a 30-min, 42°C heat shock or oxidative stress induced by arsenite) also reduce the endoplasmic reticulum (ER)-associated turnover of disease-causing mutants of Cx32 and the cystic fibrosis transmembrane conductance regulator (CFTR), as well as that of WT CFTR and unassembled Ig light chain. Stress-stabilized WT Cx32 and CFTR, but not the mutant/unassembled proteins examined, could traverse the secretory pathway. Heat shock also slowed the otherwise rapid UPS-mediated turnover of the cytosolic proteins myoD and GFPu, but not the degradation of an ubiquitination-independent construct (GFP-ODC) closely related to the latter. Analysis of mutant Cx32 from cells exposed to proteasome inhibitors and/or cytosolic stress indicated that stress reduces degradation at the level of substrate polyubiquitination. These findings reveal a new link between the cytosolic stress-induced heat shock response, ER-associated degradation, and polyubiquitination. Stress-denatured proteins may titer a limiting component of the ubiquitination machinery away from pre-existing UPS substrates, thereby sparing the latter from degradation.
Landscape epidemiology of plant diseases
Authors: Plantegenest Manuel , Le May Christophe , Fabre Frédéric
Published: August 2007

Many agricultural landscapes are characterized by a high degree of heterogeneity and fragmentation. Landscape ecology focuses on the influence of habitat heterogeneity in space and time on ecological processes. Landscape epidemiology aims at applying concepts and approaches originating from landscape ecology to the study of pathogen dynamics at the landscape scale. However, despite the strong influence that the landscape properties may have on the spread of plant diseases, landscape epidemiology has still received little attention from plant pathologists. Some recent methodological and technological progress provides new and powerful tools to describe and analyse the spatial patterns of host–pathogen interactions. Here, we review some important topics in plant pathology that may benefit from a landscape perspective. These include the influence of: landscape composition on the global inoculum pressure; landscape heterogeneity on pathogen dynamics; landscape structure on pathogen dispersal; and landscape properties on the emergence of pathogens and on their evolution.
Accounting for biological variability and sampling scale: a multi-scale approach to building epidemic models
Authors: Soubeyrand S , Thébaud G , Chadœuf J
Published: August 2007

When one considers the fine-scale spread of an epidemic, one usually knows the sources of biological variability and their qualitative effect on the epidemic process. The force of infection on a susceptible unit depends on the locations and the strengths of the infectious units, and on the environmental and intrinsic factors affecting infectivity and/or susceptibility. The infection probability for the susceptible unit can then be modelled as a function of these factors. Thus, one can build a conceptual model at the fine scale. However, the epidemic is generally observed at a larger scale and one has to build a model adapted to this larger scale. But how can the sources of variation identified at the fine scale be integrated into the model at the larger scale? To answer this question, we present, in the context of plant epidemiology, a multi-scale approach which consists of defining a base model built at the fine scale and upscaling it to match the scale of the sampling and the data. This approach will enable comparing experiments involving different observational processes.
An inversion technique to retrieve the source of a tracer with an application to synthetic satellite measurements
Authors: Issartel Jean-Pierre , Sharan Maithili , Modani Manish
Published: August 2007

An increasing number of satellites are being launched to observe the atmospheric concentrations of a variety of trace species. They cover a wide area at once and are expected to provide more extensive information than the rare ground-based concentration measurements. The paper introduces an adjoint technique to retrieve the emissions based on a recent concept of renormalization. This technique is used with a set of synthetic column-averaged measurements for an idealized satellite corresponding to a prescribed ground-level source. The Indian region is considered with two contrast meteorological conditions in the months of January and July, corresponding to winter and monsoon season. Since it is not feasible to handle a large volume of satellite data in the inversion due to the time involved in the computation of the matrices, a preprocessing is suggested to extract the manageable data set as a representative of the whole data.

Considering a limited number of observations, it is shown that the emissions are underestimated without and with the renormalization procedure. The degree of underestimation is relatively more with non-renormalized estimates. The non-renormalized estimate is degraded further by a refined resolution of the model, whereas the renormalized estimate is not altered appreciably. The preprocessing based on aggregation of data is found to retrieve the prescribed emissions up to 75% in the month of January and 90% in the month of July. The relatively computationally expensive renormalization may be avoided except in the case of partial visibility of the area of interest, due to cloud cover or a technical constraint. A simple criterion for the optimum design of a monitoring network is suggested.
Seed release by invasive thistles: the impact of plant and environmental factors
Authors: Jongejans Eelke , Pedatella Nicholas M , Shea Katriona , Skarpaas Olav , Auhl Richard
Published: August 2007

Dispersal is a key process in biological studies of spatial dynamics, but the initiation of dispersal has often been neglected, despite strong indications that differential timing of dispersal can significantly affect dispersal distances. To investigate which plant and environmental factors determine the release of plumed seeds by the invasive thistlesCarduus acanthoidesandCarduus nutans, we exposed 192 flower heads of each species to increasing wind speeds in a full-factorial wind tunnel experiment with four air flow turbulence, three flower head wetness and two flower head temperature levels. The number of seed releases was highest under dry and turbulent conditions and from heads that had already lost a considerable number of seeds, but was not affected by flower head size, head angle or temperature. Inspection of the trials on video showed that higher wind speeds were needed to meet the seed release threshold in laminar flows and forC. acanthoidesheads that had been wet for a longer time. Species differences were minimal, although seed release was more sensitive to lower levels of turbulence in the larger-headed and more openC. nutansheads. Knowledge of seed release biases towards weather conditions favourable for long-distance dispersal improves our understanding of the spread of invaders and allows managers to increase the efficiency of their containment strategies by applying them at crucial times.
The effects of sulphide on growth and behaviour of the thiotrophicZoothamnium niveumsymbiosis
Authors: Rinke Christian , Lee Raymond , Katz Sigrid , Bright Monika
Published: August 2007

Zoothamnium niveum(Ciliophora, Oligohymenophora) is a giant, colonial marine ciliate from sulphide-rich, shallow-water habitats, obligatorily associated with the ectosymbiotic, chemoautotrophic, sulphide-oxidizing bacterium ‘CandidatusThiobios zoothamnicoli’. The aims of this study were to characterize the natural habitat and investigate growth, reproduction, survival and maintenance of the symbiosis fromCorsica, France (Mediterranean Sea) using a flow-through respirometer providing stable chemical conditions. We were able to successfully cultivate theZ. niveumsymbiosis during its entire lifespan and document reproduction, whereby the optimum conditions were found to range from 3 to 33 μmol l−1ΣH2S in normoxic seawater. Starting with an inoculum of 13 specimens, we found up to 173 new specimens that were asexually produced after only 11 days. Observed mean lifespan of theZ. niveumcolonies was approximately 11 days and mean colony size reached 51 branches, from which rapid host division rates of up to every 4.1 hours were calculated. Comparing the ectosymbiotic population fromZ. niveumcolonies collected from their natural habitat with those cultivated under optimal conditions, we found significant differences in the bacterial morphology and the frequency of dividing cells on distinct host parts, which is most likely caused by behaviour of the host ciliate. Applying different sulphide concentrations we revealed that the symbiosis was not able to survive without sulphide and was harmed by high sulphide conditions. To our knowledge, this study reports the first successful cultivation of a thiotrophic ectosymbiosis.
Source–sink dynamics shape the evolution of antibiotic resistance and its pleiotropic fitness cost
Authors: Perron Gabriel G , Gonzalez Andrew , Buckling Angus
Published: August 2007

Understanding the conditions that favour the evolution and maintenance of antibiotic resistance is the central goal of epidemiology. A crucial feature explaining the adaptation to harsh, or ‘sink’, environments is the supply of beneficial mutations via migration from a ‘source’ population. Given that antibiotic resistance is frequently associated with antagonistic pleiotropic fitness costs, increased migration rate is predicted not only to increase the rate of resistance evolution but also to increase the probability of fixation of resistance mutations with minimal fitness costs. Here we reportin vitroexperiments using the nosocomial pathogenic bacteriumPseudomonas aeruginosathat support these predictions: increasing rate of migration into environments containing antibiotics increased the rate of resistance evolution and decreased the associated costs of resistance. Consistent with previous theoretical work, we found that resistance evolution arose more rapidly in the presence of a single antibiotic than two. Evolution of resistance was also more rapid when bacteria were subjected to sequential exposure with two antibiotics (cycling therapy) compared with simultaneous exposure (bi-therapy). Furthermore, pleiotropic fitness costs of resistance to two antibiotics were higher than for one antibiotic, and were also higher under bi-therapy than cycling therapy, although the cost of resistance depended on the order of the antibiotics through time. These results may be relevant to the clinical setting where immigration is known to be important between chemotherapeutically treated patients, and demonstrate the importance of ecological and evolutionary dynamics in the control of antibiotic resistance.
Neopolyploidy and pathogen resistance
Authors: Oswald Benjamin P , Nuismer Scott L
Published: August 2007

Despite the well-documented historical importance of polyploidy, the mechanisms responsible for the establishment and evolutionary success of novel polyploid lineages remain unresolved. One possibility, which has not been previously evaluated theoretically, is that novel polyploid lineages are initially more resistant to pathogens than the diploid progenitor species. Here, we explore this possibility by developing and analysing mathematical models of interactions between newly formed polyploid lineages and their pathogens. We find that for the genetic mechanisms of pathogen resistance with the best empirical support, newly formed polyploid populations of hosts are expected to be more resistant than their diploid progenitors. This effect can be quite strong and, in the case of perennial species with recurrent polyploid formation, may last indefinitely, potentially providing a general explanation for the successful establishment of novel polyploid lineages.
The evolution of the social brain: anthropoid primates contrast with other vertebrates
Authors: Shultz Susanne , Dunbar R.I.M
Published: August 2007

The social brain hypothesis argues that large brains have arisen over evolutionary time as a response to the social and ecological conflicts inherent in group living. We test predictions arising from the hypothesis using comparative data from birds and four mammalian orders (Carnivora, Artiodactyla, Chiroptera and Primates) and show that, across all non-primate taxa, relative brain size is principally related to pairbonding, but with enduring stable relationships in primates. We argue that this reflects the cognitive demands of the behavioural coordination and synchrony that is necessary to maintain stable pairbonded relationships. However, primates differ from the other taxa in that they also exhibit a strong effect of group size on brain size. We use data from two behavioural indices of social intensity (enduring bonds between group members and time devoted to social activities) to show that primate relationships differ significantly from those of other taxa. We suggest that, among vertebrates in general, pairbonding represents a qualitative shift from loose aggregations of individuals to complex negotiated relationships, and that these bonded relationships have been generalized to all social partners in only a few taxa (such as anthropoid primates).
Stable isotopes, ecological integration and environmental change: wolves record atmospheric carbon isotope trend better than tree rings
Authors: Bump Joseph K , Fox-Dobbs Kena , Bada Jeffrey L , Koch Paul L , Peterson Rolf O , Vucetich John A
Published: August 2007

Large-scale patterns of isotope ratios are detectable in the tissues of organisms, but the variability in these patterns often obscures detection of environmental trends. We show that plants and animals at lower trophic levels are relatively poor indicators of the temporal trend in atmospheric carbon isotope ratios (δ13C) when compared with animals at higher trophic levels. First, we tested how differences in atmospheric δ13C values were transferred across three trophic levels. Second, we compared contemporary δ13C trends (1961–2004) in atmospheric CO2to δ13C patterns in a tree species (jack pine,Pinus banksiana), large herbivore (moose,Alces alces) and large carnivore (grey wolf,Canis lupus) from North America. Third, we compared palaeontological (approx. 30 000 to 12 00014C years before present) atmospheric CO2trends to δ13C patterns in a tree species (Pinus flexilis,Juniperussp.), a megaherbivore (bison,Bison antiquus) and a large carnivore (dire wolf,Canis dirus) from the La Brea tar pits (southern California, USA) and Great Basin (western USA). Contrary to previous expectations, we found that the environmental isotope pattern is better represented with increasing trophic level. Our results indicate that museum specimens of large carnivores would best reflect large-scale spatial and temporal patterns of carbon isotopes in the palaeontological record because top predators can act as ecological integrators of environmental change.
Deep molluscan phylogeny: synthesis of palaeontological and neontological data
Authors: Sigwart Julia D , Sutton Mark D
Published: August 2007

The position of the earliest-derived living molluscs, the Polyplacophora (chitons) and shell-less vermiform Aplacophora, remains highly contentious despite many morphological, developmental and molecular studies of extant organisms. These two groups are thought to represent either a basal molluscan grade or a clade (Aculifera) sister to the ‘higher’ molluscs (Conchifera). These incompatible hypotheses result in very different predictions about the earliest molluscs. A new cladistic analysis incorporating both Palaeozoic and extant molluscs is presented here. Our results support the monophyly of Aculifera and suggest that extant aplacophorans and polyplacophorans both derive from a disparate group of multivalved molluscs in two major clades. Reanalysis of the critical Ordovician taxon
‘Helminthochiton’ thraivensis
shows that this animal lacks a true foot despite bearing polyplacophoran-like valves. Its position within our phylogenetic reconstruction indicates that many fossil ‘polyplacophorans’ in the order Palaeoloricata are likely to represent footless stem-group aplacophorans.
‘H.’ thraivensis
and similar forms such as
Acaenoplax
may be morphological stepping stones between chitons and the shell-less aplacophorans. Our results imply that crown-group molluscan synapomorphies include serial repetition, the presence of a foot, a mineralized scleritome and a creeping rather than worm-like mode of life.
Ontogenic growth of the haemopoietic stem cell pool in humans
Authors: Dingli David , Pacheco Jorge M
Published: August 2007

Recently, the size of the active stem cell pool has been predicted to scale allometrically with the adult mass of mammalian species with a 3/4 power exponent, similar to what has been found to occur for the resting metabolic rate across species.

Here we investigate the allometric scaling of human haemopoietic stem cells (HSCs) during ontogenic growth and predict a linear scaling with body mass. We also investigate the allometric scaling of resting metabolic rate during growth in humans and find a linear scaling with mass similar to that of the haemopoietic stem cell pool.

Our findings suggest a common underlying organizational principle determining the linear scaling of both the stem cell pool and resting metabolic rate with mass during ontogenic growth within the human species, combined with a 3/4 scaling with adult mass across mammalian species. It is possible that such common principles remain valid for haemopoiesis in other mammalian species.