bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between the summer mean monsoon and the intraseasonal oscillation in the Indian monsoon region
Authors: Qi Yanjun , Zhang Renhe , Li Tim , Wen Min
Published: September 2008

The relationship between interannual variations of the seasonal mean monsoon and intraseasonal oscillation (ISO) during boreal summer over the Indian monsoon region is investigated. The result shows a negative correlation between all‐India summer monsoon rainfall and the ISO intensity. It is argued that the negative correlation is primarily attributed to the impact of the mean state of Indian summer monsoon on ISO. A strong Indian monsoon leads to the weakening of convection over the equatorial eastern Indian Ocean. The latter may further suppress the eastward and northward propagating ISO variances over the Indian Ocean and lead to a weakened intraseasonal activity over the Indian monsoon region. The ISO may feed back to the Indian summer mean monsoon through nonlinear eddy momentum transport. In addition, the ISO intensity over India increases (decreases) during the ENSO developing (decaying) summers.
Scanning tomography of SO2 distribution in a volcanic gas plume
Authors: Wright T. E. , Burton M. , Pyle D. M. , Caltabiano T.
Published: September 2008

Two‐dimensional cross sections of the sulphur dioxide (SO2) distribution in the volcanic gas plume of Mt. Etna were reconstructed using tomographic techniques. The data for these projections were generated by a network of five automated scanning spectrometers, positioned on the flanks of the volcano. These measure slant‐column amounts of SO2 at 105 different angles, every four minutes. Stable wind conditions allow the plume to be monitored on 82% of days. A time‐series of plume cross sections was computed, revealing the potential of this method to track variations in plume position and structure on timescales of minutes to hours, a result of potential importance for air traffic and civil defence in case of eruption, when copious amounts of fine ash can be transported.
A comparison of in situ bottom pressure array measurements with GRACE estimates in the Kuroshio Extension
Authors: Park Jae‐Hun , Watts D. Randolph , Donohue Kathleen A. , Jayne Steven R.
Published: September 2008

Ocean bottom pressure estimates from Gravity Recovery and Climate Experiment (GRACE) have been validated by comparisons with an array of in situ bottom pressure measurements. The 600 km by 600 km array comprised 46 bottom pressure sensors that were part of the Kuroshio Extension System Study (KESS). Validations in other ocean regions have been limited by available data to pointwise bottom pressure measurements. Spatially‐averaged monthly‐mean bottom pressure over the KESS array is highly correlated with GRACE bottom pressure estimated at the center of the array. The correlations are nearly equally high for three standard choices of spatial smoothing radius applied to GRACE estimates, 300, 500, and 750 km. In contrast, pointwise comparisons between GRACE and individual bottom pressures are high or low in sub‐regions of KESS, depending partially upon the local variance of deep mesoscale eddies whose energetic length scales are shorter than 300 km. KESS is a suitable validation experiment for the GRACE estimates at monthly scales with 300 to 750 km spatial radius of smoothing.
Direct observation of the break‐up of a nocturnal inversion layer using elemental mercury as a tracer
Authors: Snyder David C. , Dallmann Timothy R. , Schauer James J. , Holloway Tracey , Kleeman Michael J. , Geller Michael D. , Sioutas Constantinos
Published: September 2008

Concentrations of atmospheric mercury observed during July and August of 2005 in Riverside, CA and during August of 2006 at sites throughout the Los Angeles Basin indicate that a diurnal pattern of elemental mercury frequently exists within the basin during summer months. During these diurnal cycles, elemental mercury is observed to abruptly spike well above global background levels during the morning hours. These peak events were observed to be coincident across several monitoring sites throughout the Basin suggesting that mercury spikes were not a result of source plumes unique to each site but rather the impact of a basin‐wide phenomenon. Atmospheric temperature profiles measured by a Radio Acoustic Sounding System (RASS) located in Moreno Valley, CA indicate that peak events coincided with the shift in surface temperature profile from stable to neutral indicating the presence of fumigation episodes, the occurrence of which is supported by a generic model of basin dispersion. The presence of mercury in the stable layer aloft is a function of point sources within the basin, and in particular a single, elevated point source located in the Port of Long Beach. The unique dynamics of atmospheric mercury observed throughout the Los Angeles Basin combined with the location of this major point source upwind of the Basin provide a novel method of directly observing atmospheric mixing associated with the break‐up of the nocturnal inversion layer.
Three‐dimensional vortices in single pores and their effects on transport
Authors: Cardenas M. Bayani
Published: September 2008

Three‐dimensional Navier‐Stokes flow and transport simulations are conducted for a single pore throat between cubic‐packed grains 1–2 mm in diameter to advance our basic understanding of porous media processes. The grains are considered either spherical or ellipsoidal, and flow between the grains at different Reynolds Number is oriented along or across their long axis. Discharge through the pore varied linearly with imposed pressure gradients. Vortices are present near the pore throats, with narrower and deeper pore throats displaying a series of vortices. The vortices drive tailing of solutes resulting in power‐law residence time distributions. Different tailing behavior is observed since the vortices are sensitive to grain shape and flow orientation. Tailing becomes more pronounced at higher Reynolds Number although the shape of the vortices remains unchanged.
Breaking wave contribution to low grazing angle radar backscatter from the ocean surface
Authors: Hwang Paul A. , Sletten Mark A. , Toporkov Jakov V.
Published: September 2008

The anomaly of radar sea spikes, defined here as the non‐Bragg scattering events with backscattering cross‐section of horizontal polarization exceeding that of the vertical polarization, has been associated with steep wave features possibly going through wave‐breaking process, with or without whitecap manifestation. This property is exploited for using a dual polarized radar as a remote sensing breaking wave detector. Field data collected in the ocean covering wind speeds from 7 to 15 m/s, grazing angles from 1.4 to 5.5°, and with different levels of background swell influence are analyzed to quantify the radar cross‐section and Doppler velocity from sea surfaces with and without wave breaking. Key results of the breaking effects are increasing significantly the Doppler velocity of both polarizations (about 50% faster), enhancing the horizontally polarized backscattering cross‐section drastically (with 10–15 dB increase), and producing relatively small change in the vertically polarized cross‐section (about 1–2 dB increase). The presence of swell (in the same direction of wind waves) reduces both the radar backscatter and the impact of breaking waves on radar return. By inference, the swell presence decreases the ocean surface roughness and breaking activity. These results are consistent with earlier in‐situ surface wave measurements and our expectation of swell modification of breaking process due to interaction of short waves and the orbital velocity of long swell.
Satellite observations of high nighttime ozone at the equatorial mesopause
Authors: Smith Anne K. , Marsh Daniel R. , Russell James M. , Mlynczak Martin G. , Martin‐Torres F. Javier , Kyrölä Erkki
Published: September 2008

Measurements by the Sounding of the Atmosphere using Broadband Emission Radiometry instrument enable the characterization of the seasonal variation of ozone and temperature in the upper mesosphere. These are the first global measurements that resolve both the structure of the secondary ozone maximum at night and the temperature over all seasons of the year. The average nighttime mixing ratios at the altitude of the maximum vary with latitude and season. Analysis shows that the highest mixing ratios are clustered near the equator during equinoxes. The high ozone mixing ratios are observed in exactly the place and time at which the diurnal tide is largest. The diurnal tidal phase is such that coldest temperatures at 95 km occur near midnight. The high ozone is coincident with regions that have both low temperature and low amounts of atomic hydrogen. We focus particularly on ozone mixing ratios in the range of 18–50 ppmv; these occur intermittently in the equinoctial tropics on days when the night temperature is particularly cold. The occurrence of ozone maxima over 20 ppmv was unexpected but is shown in this paper to be consistent with theory and is a result of large‐amplitude diurnal tides. The same seasonal and latitudinal characteristics are seen in ozone density measured by Global Ozone Monitoring by Occultation of Stars.
Temperature responses of individual soil organic matter components
Authors: Feng Xiaojuan , Simpson Myrna J.
Published: September 2008

Temperature responses of soil organic matter (SOM) remain unclear partly due to its chemical and compositional heterogeneity. In this study, the decomposition of SOM from two grassland soils was investigated in a 1‐year laboratory incubation at six different temperatures. SOM was separated into solvent extractable compounds, suberin‐ and cutin‐derived compounds, and lignin‐derived monomers by solvent extraction, base hydrolysis, and CuO oxidation, respectively. These SOM components have distinct chemical structures and stabilities and their decomposition patterns over the course of the experiment were fitted with a two‐pool exponential decay model. The stability of SOM components was also assessed using geochemical parameters and kinetic parameters derived from model fitting. Compared with the solvent extractable compounds, a low percentage of lignin monomers partitioned into the labile SOM pool. Suberin‐ and cutin‐derived compounds were poorly fitted by the decay model, and their recalcitrance was shown by the geochemical degradation parameter (ω − C16/∑C16), which was observed to stabilize during the incubation. The temperature sensitivity of decomposition, expressed as Q10, was derived from the relationship between temperature and SOM decay rates. SOM components exhibited varying temperature responses and the decomposition of lignin monomers exhibited higher Q10 values than the decomposition of solvent extractable compounds. Our study shows that Q10 values derived from soil respiration measurements may not be reliable indicators of temperature responses of individual SOM components.
Distinct functional capacities of mouse thymic and splenic dendritic cell populations
Authors: Proietto Anna I , Lahoud Mireille H , Wu Li
Published: September 2008

Dendritic cells (DC) are antigen‐presenting cells that activate naive T cells. Murine DC are a heterogeneous population and can be subdivided into distinct subsets with different immune regulatory functions, namely the conventional DC (cDC), which include the CD8+Sirpα− and CD8−Sirpα+ DC, and the plasmacytoid DC (pDC). In this study, the phenotype and function of DC subsets in both the thymus and spleen were compared. Significant differences between the thymic and splenic DC were observed in the expression of genes encoding chemokine receptors (CCRs), toll‐like receptors (TLRs) and chemokines. Thymic DC expressed high levels of genes encoding a unique set of chemokines (CCL17 and CCL22) known to be important for T‐cell development. Moreover, the capacity of the DC from the two organs to produce IL‐6, IFN‐α and IL‐12p70 in response to the TLR 9 agonist CpG differed markedly, indicating intrinsic functional differences between subsets with similar surface phenotype. These results indicate that the microenvironment is an important factor that contributes to the functional specification of DC subsets in different lymphoid tissues.
Erratum: Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon
Authors: Moisander Pia H , Beinart Roxanne A , Voss Maren , Zehr Jonathan P
Published: September 2008

Correction to: The ISME Journal (2008) 2, 954–967; doi:10.1038/ismej.2008.51 The authors of the above noted an error in the footnote to Table 1. The footnote should read: The three different cyanobacterial symbionts in diatoms are Het-1, Richelia (in Rhizosolenia), Het-2, Richelia (in Hemiaulus) andHet-3, Calothrix (in Chaetoceros).
Just-in-time assembly of cell-cycle protein complexes
Authors: Jensen Lars , de Lichtenberg Ulrik , Jensen Thomas , Brunak Søren , Bork Peer
Published: September 2008

Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs significantly between organisms and is often mirrored by changes in cell-cycle-dependent phosphorylation of the protein products. This indicates that many different solutions have evolved for just-in-time assembly of the same molecular machines.
AAC Language Assessment: Considerations for Adults With Aphasia
Authors: Lasker Joanne P.
Published: September 2008

The process of recommending AAC systems and strategies for adults with aphasia requires clinicians to analyze both the language skills of the client and the specific language demands posed by different AAC systems. This paper describes some of the challenges people with aphasia face when attempting to use AAC approaches and presents a brief overview of language assessment techniques for people with aphasia. We review the AAC-Aphasia Classification System (Garrett & Lasker, 2005)—a tool for describing communication behaviors of people with aphasia. We present a brief analysis of the language features inherent in some AAC systems in terms of language storage and retrieval. We also discuss the importance of matching clients' current and potential language skills with an appropriate AAC tool.
Linguistic Interactions: A Therapeutic Consideration for Adults With Aphasia
Authors: Fox Lynn E.
Published: September 2008

Linguistic interaction models suggest that interrelationships arise between structural language components and between structural and pragmatic components when language is used in social contexts. The linguist, David Crystal (1986, 1987), has proposed that these relationships are central, not peripheral, to achieving desired clinical outcomes. For individuals with severe communication challenges, erratic or unpredictable relationships between structural and pragmatic components can result in atypical patterns of interaction between them and members of their social communities, which may create a perception of disablement. This paper presents a case study of a woman with fluent, Wernicke's aphasia that illustrates how attention to patterns of linguistic interaction may enhance AAC intervention for adults with aphasia.
Augmentative and Alternative Communication Treatment for Persons With Primary Progressive Aphasia
Authors: Fried-Oken Melanie
Published: September 2008

Persons with primary progressive aphasia (PPA) are appearing more frequently in our AAC clinics. The syndrome is identified by the insidious onset and gradual loss of word finding, object naming, or word-comprehension skills with otherwise intact cognitive skills over a 2-year period in adults. Management of persons with this language-based neurodegenerative disease challenges our understanding of language competence and performance in adults. Clients present us with questions about when and how to provide intervention techniques and how to change the treatment as they slowly lose language skills. An AAC framework for intervention during the neurodegenerative language process seen in Nonfluent Progressive Aphasia is proposed. Tools and strategies are presented that have been reported in clinical cases for individual clients.
Spatial-Filtering-Based Contributions to a Critique of Geographically Weighted Regression (GWR)
Authors: Griffith Daniel A
Published: September 2008

Interaction terms are constructed with georeferenced attribute variables and spatial filter eigenvectors, and then used to compute geographically varying regression coefficients. These coefficients, which are analogous to geographically weighted regression (GWR) coefficients, display preferable properties, and this specification is used to critique selected features of GWR. Comparisons are illustrated with the Georgia data appearing in the standard GWR tutorial.
Leisure Home Ownership, Access to Nature, and Health: A Longitudinal Study of Urban Residents in Sweden
Authors: Hartig Terry , Fransson Urban
Published: September 2008

How can societies ensure urban residents' access to health-promoting green spaces while also pursuing the benefits of densification? Evidence of a relationship between leisure home ownership and health can inform efforts to resolve this dilemma. Using longitudinal register data, we assessed the prospective association between ownership of a leisure home and early retirement for health reasons among 42 588 adults residing in high-density Swedish urban municipalities. The research design included controls for ‘drift’ of unhealthy people into particular residential circum-stances, and other potential alternative explanations for the association of focal interest. After adjustment for age, socioeconomic position, and type of primary housing, logistic regression analysis revealed that men with a leisure home had lower odds of early retirement for health reasons than men who did not own a leisure home. Among women, leisure home ownership interacted with socioeconomic position; in contrast to nonowners, women who owned a leisure home had higher odds of early retirement for health reasons if they also had higher levels of education and employment income. The associations we have uncovered provide additional insight on the relationship between access to natural environments and health, and they warrant consideration in efforts to resolve the densification dilemma.
Enclosed Residential Neighborhoods in Israel: From Landscapes of Heritage and Frontier Enclaves to New Gated Communities
Authors: Rosen Gillad , Razin Eran
Published: September 2008

Contemporary studies of gated communities largely associate this phenomenon with global forces, emphasizing recent urban processes that operate across national borders. However, the Israeli experience demonstrates that multiple forces work simultaneously to produce various forms of enclosed residential communities that follow very different evolutionary routes. Older forms of gated spaces such as traditional and frontier enclaves, characterized by religious–cultural or ethno-national identities, coexist and evolve alongside newer forms of postwelfare-state market-driven enclaves also referred to as neoliberal enclaves. Although gated enclaves share some similar defining features, they differ significantly in reasons for enclosure, developmental mechanisms and gating effects. The diverse landscape of enclaves results from ongoing interactions of macrosocietal processes influenced by global trends, with place-specific institutional and cultural settings.
Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield
Authors: Shaw A. Joe , Podkaminer Kara K. , Desai Sunil G. , Bardsley John S. , Rogers Stephen R. , Thorne Philip G. , Hogsett David A. , Lynd Lee R.
Published: September 2008

We report engineering
Thermoanaerobacterium saccharolyticum
, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations in continuous culture. The growth rate of strain ALK2 was similar to the wild-type strain, with a reduction in cell yield proportional to the decreased ATP availability resulting from acetate kinase inactivation. Glucose and xylose are co-utilized and utilization of mannose and arabinose commences before glucose and xylose are exhausted. Using strain ALK2 in simultaneous hydrolysis and fermentation experiments at 50°C allows a 2.5-fold reduction in cellulase loading compared with using
Saccharomyces cerevisiae
at 37°C. The maximum ethanol titer produced by strain ALK2, 37 g/liter, is the highest reported thus far for a thermophilic anaerobe, although further improvements are desired and likely possible. Our results extend the frontier of metabolic engineering in thermophilic hosts, have the potential to significantly lower the cost of cellulosic ethanol production, and support the feasibility of further cost reductions through engineering a diversity of host organisms.
Rules of engagement for NMDA receptor subunits
Authors: Ulbrich Maximilian H. , Isacoff Ehud Y.
Published: September 2008

Canonical NMDA receptors assemble from two glycine-binding NR1 subunits with two glutamate-binding NR2 subunits to form glutamate-gated excitatory receptors that mediate synaptic transmission and plasticity. The role of glycine-binding NR3 subunits is less clear. Whereas in
Xenopus laevis
oocytes, two NR3 subunits coassemble with two NR1 subunits to form a glycine-gated receptor, such a receptor has yet to be found in mammalian cells. Meanwhile, NR1, NR2, and NR3 appear to coassemble into triheteromeric receptors in neurons, but it is not clear whether this occurs in oocytes. To test the rules that govern subunit assembly in NMDA receptors, we developed a single-molecule fluorescence colocalization method. The method focuses selectively on the plasma membrane and simultaneously determines the subunit composition of hundreds of individual protein complexes within an optical patch on a live cell. We find that NR1, NR2, and NR3 follow an exclusion rule that yields separate populations of NR1/NR2 and NR1/NR3 receptors on the surface of oocytes. In contrast, coexpression of NR1, NR3A, and NR3B yields triheteromeric receptors with a fixed stoichiometry of two NR1 subunits with one NR3A and one NR3B. At least part of this regulation of subunit stoichiometry appears to be caused by internal retention. Thus, depending on the mixture of subunits, functional receptors on the cell surface may follow either an exclusion rule or a stoichiometric combination rule, providing an important constraint on functional diversity. Cell-to-cell differences in the rules may help sculpt distinct physiological properties.
Multiple deleterious effects of experimentally aged sperm in a monogamous bird
Authors: White Joël , Wagner Richard H. , Helfenstein Fabrice , Hatch Scott A. , Mulard Hervé , Naves Liliana C. , Danchin Etienne
Published: September 2008

Sperm aging is known to be detrimental to reproductive performance. However, this apparently general phenomenon has seldom been studied in an evolutionary context. The negative impact of sperm aging on parental fitness should constitute a strong selective pressure for adaptations to avoid its effects. We studied the impact of sperm aging on black-legged kittiwakes (
Rissa tridactyla
), a monogamous seabird. Kittiwakes comprise a model system because (
i
) of evidence that females eject their mates' sperm to prevent fertilization by sperm that would be old and degraded by the time of fertilization and result in reduced reproductive performance and (
ii
) the lack of extra-pair fertilization in this species makes cryptic female choice an unlikely explanation of postcopulatory sperm ejection by females. We experimentally manipulated the age of the sperm fertilizing kittiwake eggs by fitting males with anti-insemination rings for variable periods of time preceding egg-laying. We found evidence that sperm aging negatively affected four sequential stages of reproduction: fertilization potential, rate of embryonic development, embryonic mortality, and chick condition at hatching. These results may be produced by a continuum of a single process of sperm aging that differentially affects various aspects of development, depending on the degree of damage incurred to the spermatozoa. The marked impact of sperm age on female fitness may thus drive postcopulatory sperm ejection by females. These results provide experimental evidence of deleterious effects of sperm aging on a nondomestic vertebrate, underlining its taxonomic generality and its potential to select for a wide array of adaptations.
On the relationship between folding and chemical landscapes in enzyme catalysis
Authors: Roca Maite , Messer Benjamin , Hilvert Donald , Warshel Arieh
Published: September 2008

Elucidating the relationship between the folding landscape of enzymes and their catalytic power has been one of the challenges of modern enzymology. The present work explores this issue by using a simplified folding model to generate the free-energy landscape of an enzyme and then to evaluate the activation barriers for the chemical step in different regions of the landscape. This approach is used to investigate the recent finding that an engineered monomeric chorismate mutase exhibits catalytic efficiency similar to the naturally occurring dimer even though it exhibits the properties of an intrinsically disordered molten globule. It is found that the monomer becomes more confined than its native-like counterpart upon ligand binding but still retains a wider catalytic region. Although the overall rate acceleration is still determined by reduction of the reorganization energy, the detailed contribution of different barriers yields a more complex picture for the chemical process than that of a single path. This work provides insight into the relationship between folding landscapes and catalysis. The computational approach used here may also provide a powerful strategy for modeling single-molecule experiments and designing enzymes.
Gender differences in human cortical synaptic density
Authors: Alonso-Nanclares L. , Gonzalez-Soriano J. , Rodriguez J. R. , DeFelipe J.
Published: September 2008

Certain cognitive functions differ in men and women, although the anatomical and functional substrates underlying these differences remain unknown. Because neocortical activity is directly related with higher brain function, numerous studies have focused on the cerebral cortex when searching for possible structural correlates of cognitive gender differences. However, there are no studies on possible gender differences at the synaptic level. In the present work we have used stereological and correlative light and electron microscopy to show that men have a significantly higher synaptic density than women in all cortical layers of the temporal neocortex. These differences may represent a microanatomical substrate contributing to the functional gender differences in brain activity.
A role for the mitochondrial deacetylase Sirt3 in regulating energy homeostasis
Authors: Ahn Bong-Hyun , Kim Hyun-Seok , Song Shiwei , Lee In Hye , Liu Jie , Vassilopoulos Athanassios , Deng Chu-Xia , Finkel Toren
Published: September 2008

Here, we demonstrate a role for the mitochondrial NAD-dependent deacetylase Sirt3 in the maintenance of basal ATP levels and as a regulator of mitochondrial electron transport. We note that Sirt3
−/−
mouse embryonic fibroblasts have a reduction in basal ATP levels. Reconstitution with wild-type but not a deacetylase-deficient form of Sirt3 restored ATP levels in these cells. Furthermore in wild-type mice, the resting level of ATP correlates with organ-specific Sirt3 protein expression. Remarkably, in mice lacking Sirt3, basal levels of ATP in the heart, kidney, and liver were reduced >50%. We further demonstrate that mitochondrial protein acetylation is markedly elevated in Sirt3
−/−
tissues. In addition, in the absence of Sirt3, multiple components of Complex I of the electron transport chain demonstrate increased acetylation. Sirt3 can also physically interact with at least one of the known subunits of Complex I, the 39-kDa protein NDUFA9. Functional studies demonstrate that mitochondria from Sirt3
−/−
animals display a selective inhibition of Complex I activity. Furthermore, incubation of exogenous Sirt3 with mitochondria can augment Complex I activity. These results implicate protein acetylation as an important regulator of Complex I activity and demonstrate that Sirt3 functions
in vivo
to regulate and maintain basal ATP levels.
Stage-specific predator species help each other to persist while competing for a single prey
Authors: De Roos A. M. , Schellekens T. , Van Kooten T. , Persson L.
Published: September 2008

Prey in natural communities are usually shared by many predator species. How predators coexist while competing for the same prey is one of the fundamental questions in ecology. Here, we show that competing predator species may not only coexist on a single prey but even help each other to persist if they specialize on different life history stages of the prey. By changing the prey size distribution, a predator species may in fact increase the amount of prey available for its competitor. Surprisingly, a predator may not be able to persist at all unless its competitor is also present. The competitor thus significantly increases the range of conditions for which a particular predator can persist. This “emergent facilitation” is a long-term, population-level effect that results from asymmetric increases in the rate of prey maturation and reproduction when predation relaxes competition among prey. Emergent facilitation explains observations of correlated increases of predators on small and large conspecific prey as well as concordance in their distribution patterns. Our results suggest that emergent facilitation may promote the occurrence of complex, stable, community food webs and that persistence of these communities could critically depend on diversity within predator guilds.
Licorice β-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin
Authors: Seki Hikaru , Ohyama Kiyoshi , Sawai Satoru , Mizutani Masaharu , Ohnishi Toshiyuki , Sudo Hiroshi , Akashi Tomoyoshi , Aoki Toshio , Saito Kazuki , Muranaka Toshiya
Published: September 2008

Glycyrrhizin, a major bioactive compound derived from the underground parts of
Glycyrrhiza
(licorice) plants, is a triterpene saponin that possesses a wide range of pharmacological properties and is used worldwide as a natural sweetener. Because of its economic value, the biosynthesis of glycyrrhizin has received considerable attention. Glycyrrhizin is most likely derived from the triterpene β-amyrin, an initial product of the cyclization of 2,3-oxidosqualene. The subsequent steps in glycyrrhizin biosynthesis are believed to involve a series of oxidative reactions at the C-11 and C-30 positions, followed by glycosyl transfers to the C-3 hydroxyl group; however, no genes encoding relevant oxidases or glycosyltransferases have been identified. Here we report the successful identification of
CYP88D6
, a cytochrome P450 monooxygenase (P450) gene, as a glycyrrhizin-biosynthetic gene, by transcript profiling-based selection from a collection of licorice expressed sequence tags (ESTs). CYP88D6 was characterized by
in vitro
enzymatic activity assays and shown to catalyze the sequential two-step oxidation of β-amyrin at C-11 to produce 11-oxo-β-amyrin, a possible biosynthetic intermediate between β-amyrin and glycyrrhizin. CYP88D6 coexpressed with β-amyrin synthase in yeast also catalyzed
in vivo
oxidation of β-amyrin to 11-oxo-β-amyrin.
CYP88D6
expression was detected in the roots and stolons by RT-PCR; however, no amplification was observed in the leaves or stems, which is consistent with the accumulation pattern of glycyrrhizin
in planta
. These results suggest a role for CYP88D6 as a β-amyrin 11-oxidase in the glycyrrhizin pathway.
Positional cloning of the
Igl
genes controlling rheumatoid factor production and allergic bronchitis in rats
Authors: Rintisch Carola , Ameri Jacqueline , Olofsson Peter , Luthman Holger , Holmdahl Rikard
Published: September 2008

Rheumatoid factors (RF), autoantibodies that bind the Fc region of IgG, are one of the major diagnostic marker in rheumatoid arthritis (RA) but occur with lower frequency also in other infectious and inflammatory conditions. Through positional cloning of the previously described quantitative trait locus (QTL)
Rf1
in congenic and advanced intercrossed rats, we identified the Ig lambda light chain locus as a locus that regulates the production of RF in rats. The congenic rats produce RF-Igλ and have significant higher levels of RF-IgG and RF-IgM in serum, while the DA rat has an impaired RF production and does not produces RF-Igλ. Thus, we could investigate the role of RF in pristane-induced arthritis (PIA) as well as ovalbumin-induced airway inflammation. We show that there was no difference in the development and severity of PIA between congenic and parental DA rats, suggesting that RF using lambda light chains have no impact on PIA. However, the RF producing congenic rats developed a more severe airway inflammation as indicated in the significantly increased number of eosinophils in bronchoalveolar lavage fluid as well as total IgE in serum. In addition, RF congenic rats had a significantly enhanced immune response toward OVA due to increased OVA-Igk but not OVA-Igl antibodies, suggesting a possible involvement of RF in the regulation of the humoral immune response.
Dicer-dependent endothelial microRNAs are necessary for postnatal angiogenesis
Authors: Suárez Yajaira , Fernández-Hernando Carlos , Yu Jun , Gerber Scott A. , Harrison Kenneth D. , Pober Jordan S. , Iruela-Arispe M. Luisa , Merkenschlager Matthias , Sessa William C.
Published: September 2008

Posttranscriptional gene regulation by microRNAs (miRNAs) is important for many aspects of development, homeostasis, and disease. Here, we show that reduction of endothelial miRNAs by cell-specific inactivation of
Dicer
, the terminal endonuclease responsible for the generation of miRNAs, reduces postnatal angiogenic response to a variety of stimuli, including exogenous VEGF, tumors, limb ischemia, and wound healing. Furthermore, VEGF regulated the expression of several miRNAs, including the up-regulation of components of the c-Myc oncogenic cluster miR-17-92. Transfection of endothelial cells with components of the miR-17-92 cluster, induced by VEGF treatment, rescued the induced expression of thrombospondin-1 and the defect in endothelial cell proliferation and morphogenesis initiated by the loss of Dicer. Thus, endothelial miRNAs regulate postnatal angiogenesis and VEGF induces the expression of miRNAs implicated in the regulation of an integrated angiogenic response.
Hierarchies of networked phases induced by multiple liquid–liquid critical points
Authors: Hsu Chia Wei , Largo Julio , Sciortino Francesco , Starr Francis W.
Published: September 2008

Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network-forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid–gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus, bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in single-component systems, suggested to occur in some atomic and molecular network-forming fluids, including water and silica.
When to stop managing or surveying cryptic threatened species
Authors: Chadès Iadine , McDonald-Madden Eve , McCarthy Michael A. , Wintle Brendan , Linkie Matthew , Possingham Hugh P.
Published: September 2008

Threatened species become increasingly difficult to detect as their populations decline. Managers of such cryptic threatened species face several dilemmas: if they are not sure the species is present, should they continue to manage for that species or invest the limited resources in surveying? We find optimal solutions to this problem using a Partially Observable Markov Decision Process and rules of thumb derived from an analytical approximation. We discover that managing a protected area for a cryptic threatened species can be optimal even if we are not sure the species is present. The more threatened and valuable the species is, relative to the costs of management, the more likely we are to manage this species without determining its continued persistence by using surveys. If a species remains unseen, our belief in the persistence of the species declines to a point where the optimal strategy is to shift resources from saving the species to surveying for it. Finally, when surveys lead to a sufficiently low belief that the species is extant, we surrender resources to other conservation actions. We illustrate our findings with a case study using parameters based on the critically endangered Sumatran tiger (Panthera tigris sumatrae), and we generate rules of thumb on how to allocate conservation effort for any cryptic species. Using Partially Observable Markov Decision Processes in conservation science, we determine the conditions under which it is better to abandon management for that species because our belief that it continues to exist is too low.
Peripheral Aβ subspecies as risk biomarkers of Alzheimer's disease
Authors: Schupf Nicole , Tang Ming X. , Fukuyama Hide , Manly Jennifer , Andrews Howard , Mehta Pankaj , Ravetch Jeffery , Mayeux Richard
Published: September 2008

Plasma Aβ42 and Aβ40 levels are putative biomarkers for Alzheimer's disease (AD), but their significance and predictive value have been inconclusive. In AD transgenic models, plasma and cerebrospinal fluid levels of Aβ42 and Aβ40 increase with age but subsequently decrease when Aβ begins to accumulate in brain and with the onset of cognitive impairment. To determine the predictive value of Aβ levels in elderly populations, we investigated how plasma Aβ42, Aβ40, and a protofibrillar subspecies of Aβ42 changed over time and with the onset of cognitive impairment or AD. In a cohort of 1,125 elderly persons without dementia, 104 (9.2%) of the participants developed AD over 4.6 years of follow-up. Higher plasma Aβ42 levels at the onset of the study were associated with a threefold increased risk of AD. However, conversion to AD was accompanied by a significant decline in plasma Aβ42, a decreased Aβ42/Aβ40 ratio and, with the onset of cognitive impairment, decreased protofibrillar Aβ42 levels. Our results suggest individuals with elevated plasma Aβ42 are at increased risk of AD and that with the onset of disease, the decline in some forms of Aβ may reflect compartmentalization of Aβ peptides in the brain.
Cross-talk between GlcNAcylation and phosphorylation: Site-specific phosphorylation dynamics in response to globally elevated
O
-GlcNAc
Authors: Wang Zihao , Gucek Marjan , Hart Gerald W.
Published: September 2008

Protein GlcNAcylation serves as a nutrient/stress sensor to modulate the functions of many nuclear and cytoplasmic proteins.
O
-GlcNAc cycles on serine or threonine residues like phosphorylation, is nearly as abundant, and functions, at least partially, via its interplay with phosphorylation. Here, we describe changes in site-specific phosphorylation dynamics in response to globally elevated GlcNAcylation. By combining sequential phospho-residue enrichment, iTRAQ labeling, and high throughput mass spectrometric analyses, phosphorylation dynamics on 711 phosphopeptides were quantified. Based upon their insensitivity to phosphatase inhibition, we conclude that ≈48% of these phosphorylation sites were not actively cycling in the conditions of the study. However, increased GlcNAcylation influenced phosphate stoichiometry at most of the sites that did appear to be actively cycling. Elevated GlcNAcylation resulted in lower phosphorylation at 280 sites and caused increased phosphorylation at 148 sites. Thus, the cross-talk or interplay between these two abundant posttranslational modifications is extensive, and may arises both by steric competition for occupancy at the same or proximal sites and by each modification regulating the other's enzymatic machinery. The phosphoproteome dynamics presented by this large set of quantitative data not only delineates the complex interplay between phosphorylation and GlcNAcyation, but also provides insights for more focused investigations of specific roles of
O
-GlcNAc in regulating protein functions and signaling pathways.
STAT92E is a positive regulator ofDrosophilainhibitor of apoptosis 1 (DIAP/1) and protects against radiation-induced apoptosis
Authors: Betz Aurel , Ryoo Hyung Don , Steller Hermann , Darnell James E.
Published: September 2008

The proapoptotic factors Reaper, Hid, Grim, and Sickle regulate apoptosis inDrosophilaby inhibiting the antiapoptotic factor DIAP1 (Drosophilainhibitor of apoptosis 1). Heat, UV light, x-rays, and developmental signals can all increase the proapoptotic factors, but the control of transcription of thediap1gene is unclear. We show that in imaginal discs the singleDrosophilaSTAT protein (STAT92E) when activated can directly increase DIAP1 through binding to STAT DNA-binding sites in thediap1promoter. The STAT92E contribution to DIAP1 production is required for cell survival after x-irradiation but not under unstressed conditions. Because DIAP1 prevents apoptosis after a variety of stresses, STAT92E may have a role in regulating stress responses in general.
The molecular switch that activates the cell wall anchoring step of pilus assembly in gram-positive bacteria
Authors: Mandlik Anjali , Das Asis , Ton-That Hung
Published: September 2008

Cell surface pili in Gram-positive bacteria orchestrate the colonization of host tissues, evasion of immunity, and the development of biofilms. Recent work revealed that pilus assembly is a biphasic process wherein pilus polymerization is catalyzed by a pilus-specific sortase followed by cell wall anchoring of the pilus that is promoted by the housekeeping sortase. Here, we present molecular genetic and biochemical studies of a heterotrimeric pilus in
Corynebacterium diphtheriae
, uncovering the molecular switch that terminates pilus polymerization in favor of cell wall anchoring. The prototype pilus contains a major pilin (SpaA) forming the shaft, a tip pilin (SpaC), and another minor pilin (SpaB). Cells lacking SpaB form pilus fibers, but they are largely secreted in the medium, a phenotype also observed when cells lack the housekeeping sortase. Furthermore, the average pilus length is greatly increased in the absence of SpaB. Remarkably, a SpaB mutant that lacks the cell wall sorting signal but contains a critical lysine residue is incorporated in the pilus. However, the resulting pili fail to anchor to the cell wall. We propose that a specific minor pilin acts as the terminal subunit in pilus assembly. Cell wall anchoring ensues when the pilus polymer assembled on the pilus-specific sortase is transferred to the minor pilin presented by the housekeeping sortase via lysine-mediated transpeptidation.
Minimally invasive neuroradiologic model of preclinical transient middle cerebral artery occlusion in canines
Authors: Rink Cameron , Christoforidis Greg , Abduljalil Amir , Kontzialis Marinos , Bergdall Valerie , Roy Sashwati , Khanna Savita , Slivka Andrew , Knopp Michael , Sen Chandan K.
Published: September 2008

Stroke is currently the third leading cause of death in the United States, with approximately 780,000 Americans affected by a new or recurring stroke each year. Although a variety of therapeutic approaches have shown promise in small-animal models of stroke, the vast majority of clinical trials to test the efficacy of such modalities have failed. To bridge the translational gap between laboratory and clinical research, we developed a preclinical model of acute ischemic stroke in dogs. Using a minimally invasive endovascular approach, a platinum coil was intravascularly guided through the vertebrobasilar system under C-arm fluoroscopy to occlude the M1 segment of the middle cerebral artery (MCA) for 1 h. The approach included femoral artery catheterization to access the MCA and therefore eliminated the occurrence of head trauma associated with other preclinical stroke models relying on transorbital or craniectomy approaches. After 1 h of focal MCA ischemia, the coil was retrieved to cause reperfusion, which was verified by arteriograms. At 24 h, T2-weighted coronal magnetic resonance (MR) images were acquired and processed for three-dimensional reconstruction of the brain and its vasculature. Infarction, limited to the area at risk, was noted. Two independent observers calculated the mean percentage hemispherical lesion volumes as follows: observer 1, 30.9 ± 2.1%; observer 2, 31.2 ± 4.3%. Infarct-affected changes in histology were determined by hematoxylin and eosin as well as by Fluoro-Jade staining. This work reports the successful development of a powerful preclinical model of stroke that lends itself to the study of biologic mechanisms as well as to testing experimental therapeutics.
Physiological significance of a peripheral tissue circadian clock
Authors: Lamia Katja A. , Storch Kai-Florian , Weitz Charles J.
Published: September 2008

Mammals have circadian clocks in peripheral tissues, but there is no direct evidence of their physiological importance. Unlike the suprachiasmatic nucleus clock that is set by light and drives rest–activity and fasting–feeding cycles, peripheral clocks are set by daily feeding, suggesting that at least some contribute metabolic regulation. The liver plays a well known role in glucose homeostasis, and we report here that mice with a liver-specific deletion of
Bmal1
, an essential clock component, exhibited hypoglycemia restricted to the fasting phase of the daily feeding cycle, exaggerated glucose clearance, and loss of rhythmic expression of hepatic glucose regulatory genes. We conclude that the liver clock is important for buffering circulating glucose in a time-of-day-dependent manner. Our findings suggest that the liver clock contributes to homeostasis by driving a daily rhythm of hepatic glucose export that counterbalances the daily cycle of glucose ingestion resulting from the fasting–feeding cycle.