bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating marine boundary layer clouds over the eastern Pacific in a regional climate model with double‐moment cloud microphysics
Authors: Lauer Axel , Wang Yuqing , Phillips Vaughan T. J. , McNaughton Cameron S. , Bennartz Ralf , Clarke Antony D.
Published: November 2009

A double‐moment cloud microphysics scheme with a prognostic treatment of aerosols inside clouds has been implemented into the International Pacific Research Center Regional Atmospheric Model (iRAM) to simulate marine boundary layer clouds over the eastern Pacific and to study aerosol‐cloud interactions, including the aerosol indirect effect. This paper describes the new model system and presents a comparison of model results with observations. The results show that iRAM with the double‐moment cloud microphysics scheme is able to reproduce the major features, including the geographical patterns and vertical distribution of the basic cloud parameters such as cloud droplet number, liquid water content, or droplet effective radii over the eastern Pacific reasonably well. However, the model tends to underestimate cloud droplet number concentrations near the coastal regions strongly influenced by advection of continental aerosols and precursor gases. In addition, the average location of the stratocumulus deck off South America is shifted to the northwest compared with the satellite observations. We apply the new model system to assess the indirect aerosol effect over the eastern Pacific by comparing a simulation with preindustrial aerosol to an otherwise identical simulation with present‐day aerosol. Resulting changes in the cloud droplet number concentration are particularly pronounced in Gulf of Mexico and along the Pacific coastlines with local changes up to 70 cm−3 (50% of the present‐day value). The modeled domain‐averaged 3‐month (August–October) mean change in top‐of‐atmosphere net cloud forcing over the ocean owing to changes in the aerosol burden by anthropogenic activities is −1.6 W m−2.
The effect of salt crust on the thermal conductivity of one sample of fluvial particulate materials under Martian atmospheric pressures
Authors: Presley Marsha A. , Craddock Robert A. , Zolotova Natalya
Published: November 2009

A line‐heat source apparatus was used to measure thermal conductivities of a lightly cemented fluvial sediment (salinity = 1.1 g · kg−1), and the same sample with the cement bonds almost completely disrupted, under low pressure, carbon dioxide atmospheres. The thermal conductivities of the cemented sample were approximately 3× higher, over the range of atmospheric pressures tested, than the thermal conductivities of the same sample after the cement bonds were broken. A thermal conductivity‐derived particle size was determined for each sample by comparing these thermal conductivity measurements to previous data that demonstrated the dependence of thermal conductivity on particle size. Actual particle‐size distributions were determined via physical separation through brass sieves. When uncemented, 87% of the particles were less than 125 μm in diameter, with 60% of the sample being less than 63 μm in diameter. As much as 35% of the cemented sample was composed of conglomerate particles with diameters greater than 500 μm. The thermal conductivities of the cemented sample were most similar to those of 500‐μm glass beads, whereas the thermal conductivities of the uncemented sample were most similar to those of 75‐μm glass beads. This study demonstrates that even a small amount of salt cement can significantly increase the thermal conductivity of particulate materials, as predicted by thermal modeling estimates by previous investigators.
Three‐dimensional study of Mars upper thermosphere/ionosphere and hot oxygen corona: 2. Solar cycle, seasonal variations, and evolution over history
Authors: Valeille Arnaud , Combi Michael R. , Bougher Stephen W. , Tenishev Valeriy , Nagy Andrew F.
Published: November 2009

The global dynamics of the flow of energetic particles through the Martian upper atmosphere is studied for different cases reflecting variations in solar cycle, seasons, and epochs over history. In this study, the combination of the new 3‐D Direct Simulation Monte Carlo kinetic model and the modern 3‐D Mars Thermosphere General Circulation Model is employed to describe self‐consistently the Martian upper atmosphere (i.e., the thermosphere/ionosphere and the exosphere). The variations in the Martian upper atmosphere over long‐term (seasons and solar cycle) and evolutionary (Martian history) time scales are presented and discussed using the equinox solar low case extensively described in the work of Valeille et al. (2009c) as reference throughout. These characteristic conditions lead to significant variations in the thermosphere/ionosphere temperatures, dynamical heating, winds, and ion/neutral density distributions, which, in turn, affect the exosphere general structure, the hot corona shape, and the escape rate and have important implications for the study of the ion loss, atmospheric sputtering, and interaction with the solar wind in general. Calculations for present conditions are performed for three characteristic seasons (aphelion, equinox, and perihelion), while solar activity is either fixed to low or high conditions. Calculations for past conditions are related to a solar EUV flux enhancement of 1, 3, and 6 times the present values. Spatial‐, seasonal‐, solar cycle–, and evolutionary‐driven variations, although exhibiting very different time scales, are all shown to exert an influence of the same order. Models of Mars upper atmosphere should address them accordingly.
Social science in a water observing system
Authors: Braden John B. , Brown Daniel G. , Dozier Jeff , Gober Patricia , Hughes Sara M. , Maidment David R. , Schneider Sandra L. , Schultz P. Wesley , Shortle James S. , Swallow Stephen K. , Werner Carol M.
Published: November 2009

We set forth an argument for the integration of social science research with natural science and engineering research in major research infrastructure investments addressing water science. A program of integrated observation of water resources offers great opportunities to address several environmental “grand challenges” identified by the National Research Council, including climate variability, institutions and resource use, and land use dynamics, and their importance for hydrologic forecasting. We argue that such a program has the potential to advance both water science and the contributing disciplines. However, to realize this potential, it is essential to recognize that social science requires critical infrastructure funding on the scale of advanced research facilities in the natural sciences and engineering.
The adenomatous polyposis coli‐associated exchange factors Asef and Asef2 are required for adenoma formation in ApcMin/+mice
Authors: Kawasaki Yoshihiro , Tsuji Shinnosuke , Muroya Ken , Furukawa Shiori , Shibata Yoko , Okuno Masumi , Ohwada Susumu , Akiyama Tetsu
Published: November 2009

Sporadic and familial colorectal tumours usually harbour biallelic adenomatous polyposis coli (APC)‐associated mutations that result in constitutive activation of Wnt signalling. Furthermore, APC activates Asef and Asef2, which are guanine‐nucleotide exchange factors specific for Rac1 and Cdc42. Here, we show that Asef and Asef2 expression is aberrantly enhanced in intestinal adenomas and tumours. We also show that deficiency of either Asef or Asef2 significantly reduces the number and size of adenomas in ApcMin/+ mice, which are heterozygous for an APC mutation and spontaneously develop adenomas in the intestine. We observed that the APC–Asef/Asef2 complex induces c‐Jun amino‐terminal kinase‐mediated transactivation of matrix metalloproteinase 9, and is required for the invasive activity of colorectal tumour cells. Furthermore, we show that Asef and Asef2 are required for tumour angiogenesis. These results suggest that Asef and Asef2 have a crucial role in intestinal adenoma formation and tumour progression, and might be promising molecular targets for the treatement of colorectal tumours.
The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells
Authors: Lozupone Francesco , Perdicchio Maurizio , Brambilla Daria , Borghi Martina , Meschini Stefania , Barca Stefano , Marino Maria Lucia , Logozzi Mariantonia , Federici Cristina , Iessi Elisabetta , de Milito Angelo , Fais Stefano
Published: November 2009

Tumour cannibalism is a characteristic of malignancy and metastatic behaviour. This atypical phagocytic activity is a crucial survival option for tumours in conditions of low nutrient supply, and has some similarities to the phagocytic activity of unicellular microorganisms. In fact, Dictyostelium discoideum has been used widely as a model to study phagocytosis. Recently, phg1A has been described as a protein that is primarily involved in the phagocytic process of this microorganism. The closest human homologue to phg1A is transmembrane 9 superfamily protein member 4 (TM9SF4). Here, we report that TM9SF4 is highly expressed in human malignant melanoma cells deriving from metastatic lesions, whereas it is undetectable in healthy human tissues and cells. TM9SF4 is predominantly expressed in acidic vesicles of melanoma cells, in which it co‐localizes with the early endosome antigens Rab5 and early endosome antigen 1. TM9SF4 silencing induced marked inhibition of cannibal activity, which is consistent with a derangement of intracellular pH gradients, with alkalinization of acidic vesicles and acidification of the cell cytosol. We propose TM9SF4 as a new marker of malignancy, representing a potential new target for anti‐tumour strategies with a specific role in tumour cannibalism and in the establishment of a metastatic phenotype.
Features of bacterial growth and polysaccharide production of Streptococcus pneumoniae serotype 14
Authors: Massaldi Hugo , Bessio M. Inés , Suárez Norma , Texeira Esther , Rossi Silvina , Ferreira Fernando
Published: November 2009

The effect of several cultivation conditions on the kinetics of bacterial growth and polysaccharide production of Streptococcus pneumoniae serotype 14 was studied. The presence in the supernatant of serotype‐specific CPS (capsular polysaccharide) during growth was followed by size‐exclusion HPLC and, in parallel, confirmed by using a specific latex reagent. The agitation level did not affect the production behaviour, whereas pH maintenance above 6 strongly enhanced both growth and CPS production throughout the cultivation period in flasks. Production of high‐molecular‐mass polysaccharide was found to be maximal between 5 and 6 h of cultivation, at the end of the exponential phase. By laser light scattering, 90% of this purified CPS product showed a Mw (molecular mass) range from 350 to 1500 kDa, with an average Mw of 921 kDa. Extending the culture to 24 h gave rise to a clear shift of the Mw distribution of the polysaccharide to values lower than 100 kDa. These findings may have strong implications for the large‐scale manufacture of the polysaccharide and the associated conjugate vaccine.
Doppel and PrPC co-immunoprecipitate in detergent-resistant membrane domains of epithelial FRT cells
Authors: Caputo Anna , Sarnataro Daniela , Campana Vincenza , Costanzo Maddalena , Negro Alessandro , Sorgato M. Catia , Zurzolo Chiara
Published: November 2009

Dpl (doppel) is a paralogue of the PrPC (cellular prion protein), whose misfolded conformer (the scrapie prion protein, PrPSc) is responsible for the onset of TSEs (transmissible spongiform encephalopathies) or prion diseases. It has been shown that the ectopic expression of Dpl in the brains of some lines of PrP-knockout mice provokes cerebellar ataxia, which can be rescued by the reintroduction of the PrP gene, suggesting a functional interaction between the two proteins. It is, however, still unclear where, and under which conditions, this event may occur. In the present study we addressed this issue by analysing the intracellular localization and the interaction between Dpl and PrPC in FRT (Fischer rat thyroid) cells stably expressing the two proteins separately or together. We show that both proteins localize prevalently on the basolateral surface of FRT cells, in both singly and doubly transfected clones. Interestingly we found that they associate with DRMs (detergent-resistant membranes) or lipid rafts, from where they can be co-immunoprecipitated in a cholesterol-dependent fashion. Although the interaction between Dpl and PrPC has been suggested before, our results provide the first clear evidence that this interaction occurs in rafts and is dependent on the integrity of these membrane microdomains. Furthermore, both Dpl and PrPC could be immunoprecipitated with flotillin-2, a raft protein involved in endocytosis and cell signalling events, suggesting that they share the same lipid environment.
Kinetic and chemical characterization of aldehyde oxidation by fungal aryl-alcohol oxidase
Authors: Ferreira Patricia , Hernández-Ortega Aitor , Herguedas Beatriz , Rencoret Jorge , Gutiérrez Ana , Martínez María Jesús , Jiménez-Barbero Jesús , Medina Milagros , Martínez Ángel T.
Published: November 2009

Fungal AAO (aryl-alcohol oxidase) provides H2O2 for lignin biodegradation. AAO is active on benzyl alcohols that are oxidized to aldehydes. However, during oxidation of some alcohols, AAO forms more than a stoichiometric number of H2O2 molecules with respect to the amount of aldehyde detected due to a double reaction that involves aryl-aldehyde oxidase activity. The latter reaction was investigated using different benzylic aldehydes, whose oxidation to acids was demonstrated by GC-MS. The steady- and presteady state kinetic constants, together with the chromatographic results, revealed that the presence of substrate electron-withdrawing or electron-donating substituents had a strong influence on activity; the highest activity was with p-nitrobenzaldehyde and halogenated aldehydes and the lowest with methoxylated aldehydes. Moreover, activity was correlated to the aldehyde hydration rates estimated by 1H-NMR. These findings, together with the absence in the AAO active site of a residue able to drive oxidation via an aldehyde thiohemiacetal, suggested that oxidation mainly proceeds via the gem-diol species. The reaction mechanism (with a solvent isotope effect, 2H2Okred, of approx. 1.5) would be analogous to that described for alcohols, the reductive half-reaction involving concerted hydride transfer from the α-carbon and proton abstraction from one of the gem-diol hydroxy groups by a base. The existence of two steps of opposite polar requirements (hydration and hydride transfer) explains some aspects of aldehyde oxidation by AAO. Site-directed mutagenesis identified two histidine residues strongly involved in gem-diol oxidation and, unexpectedly, suggested that an active-site tyrosine residue could facilitate the oxidation of some aldehydes that show no detectable hydration. Double alcohol and aldehyde oxidase activities of AAO would contribute to H2O2 supply by the enzyme.
Potentially mineralisable nitrogen: relationship to crop production and spatial mapping using infrared reflectance spectroscopy
Authors: Murphy D. V. , Osman M. , Russell C. A. , Darmawanto S. , Hoyle F. C.
Published: November 2009

Accurate and rapid prediction of the spatial structure of soil nitrogen (N) supply would have both economic and environmental benefits with respect to improved inorganic N fertiliser management. Yet traditional biochemical indices of soil N supply have not been widely incorporated into fertiliser decision support systems or environmental risk monitoring programs. Here we illustrate that in a low-input, semi-arid environment, potentially mineralisable N (PMN, as determined by anaerobic incubation) explained 21% of wheat grain yield (P = 0.003), whereas there was no significant relationship between wheat grain yield and inorganic N fertiliser application. We also assessed the spatial pattern of PMN using a structured grid soil sampling strategy over a 10-ha area (180 separate samples, 0–0.1 m). PMN in each soil sample was determined by standard biochemical analysis and also predicted using a fourier transform infrared spectrometer (FTIR). Findings illustrate that FTIR was able to significantly predict (P < 0.001) PMN values in soil and has the advantage of enabling high sample throughput and rapid (within minutes) soil analysis. Given the relatively low cost of FTIR machines and ease of use, such an approach has practical application in situations where analysis cost or access to equipped laboratories has hindered the measurement and monitoring of soil N supply within paddocks and across regions.
Field level digital soil mapping of cation exchange capacity using electromagnetic induction and a hierarchical spatial regression model
Authors: Triantafilis John , Lesch Scott Mitchell , La Lau Kevin , Buchanan Sam Mostyn
Published: November 2009

At the field level the demand for spatial information of soil properties is rapidly increasing owing to its requirements in precision agriculture and soil management. One of the most important properties is the cation exchange capacity (CEC, cmol(+)/kg) because it is an index of the shrink–swell potential and hence is a measure of soil structural resilience to tillage. However, CEC is time-consuming and expensive to measure. Various ancillary datasets and statistical methods can be used to predict CEC, but there is little scientific literature which implements this approach to map CEC or addresses the issue of the amount of ancillary data required to maximise precision and minimise bias of spatial prediction at the field level. We compare a standard least-squares multiple linear regression (MLR) model which includes 2 proximally sensed (EM38 and EM31), 3 remotely sensed (Red, Green and Blue spectral brightness), and 2 trend surface (Easting and Northing) variables as ancillary data or independent variables, and a stepwise MLR model which only includes the statistically valid EM38 signal data and the Easting trend surface vector. The latter is used as the basis for developing a hierarchical spatial regression model to predict CEC. The reliability of the model is analysed by comparing prediction precision (root mean square error) and bias (mean error) using degraded EM38 transect spacing (i.e. 96, 144, 192, 240, and 288 m) and comparing these with predictions achieved with the 48-m spacing. We conclude that the EM38 data available on the 96- and 144-m spacing are suitable at a reconnaissance level (i.e. broad-scale farming) and 24- or 48-m spacing are suitable at smaller levels where detailed information is necessary for siting the location of water reservoirs. In terms of soil management, CEC predictions determine where suitable subsoil exists for the purpose of soil profile inversion to improve the structural resilience of a topsoil that is susceptible to dispersion and surface crusting.
Organic matter kept Al toxicity low in a subtropical no-tillage soil under long-term (21-year) legume-based crop systems and N fertilisation
Authors: Vieira F. C. B. , Bayer C. , Zanatta J. , Ernani P. R.
Published: November 2009

Nitrogen-fixing crops and N fertilisation increase soil acidification, but few studies have attempted to evaluate the capacity of soil organic matter to alleviate the Al toxicity in acid no-tilled soils. This study was carried out in a 21-year-old experiment aiming to evaluate the effect of crop systems [fallow/maize (Zea mays L.), F/M; oat (Avena strigosa Schreb)/maize, O/M; oat + vetch (Vigna sativa L.)/maize, O+V/M; lablab (Dolichos lablab) + maize, L+M; and pigeon pea (Cajanus cajan L. Millsp.) + maize, P+M] and mineral N fertilisation (0 and 149 kg/ha.year) on chemical attributes and Al speciation in the 0–0.05 and 0.05–0.10 m layers of a no-tilled Paleudult of Southern Brazil. The original soil pH (5.8) decreased in all crop systems, declining 0.37–1.52 units in 21 years without re-liming. This decrease was larger in subsoil layers and, in general, was exacerbated by legume-based crop systems and by N fertilisation. The drop in soil pH increased Al content in solid phase (range 0.07–1.85 cmolc/kg) and in soil solution (range 0.01–0.06 mmol/L), and decreased base saturation on cation exchange capacity (range 12.5–61.2%). However, the Al3+ activity in the soil solution (1.03×10−7–9.3×10−8) was kept below threshold values of toxicity to maize roots, primarily due to the formation of organometallic complexes at low pH, which was estimated as up to 90% of the total Al in solution, but also due to the increased ionic strength in this no-till soil (0.0026–0.0104). Our results highlight that, although legume cover crops and N fertilisation can accelerate soil acidification, Al toxicity is offset by increased organic matter in no-till subtropical soils.
Comparison of bicarbonate-extractable soil phosphorus measured by ICP-AES and colourimetry in soils of south-eastern New South Wales
Authors: Hart M. R. , Cornish P. S.
Published: November 2009

Soil testing for plant-available phosphorus (P) in Australia is most commonly conducted using alkaline sodium bicarbonate extraction (Olsen or Colwell tests), followed by a colourimetric assay to measure the concentration of P in solution. Analysis by inductively coupled plasma (ICP) spectroscopy has become increasingly popular internationally for other soil P tests, especially Mehlich 3, due to its efficiency and ability to measure multiple elements in the one extract. The use of ICP in place of colourimetry has been used in some Australian laboratories for bicarbonate-extractable P. However, the method is known to measure forms of P (organic) that are not measured by the colourimetric assay. This study presents data comparing soil Colwell P measured by the 2 methods for 714 soil samples from pastoral sites in south-east New South Wales. Measurement by ICP consistently yielded significantly higher P concentrations than the colourimetric method (ICP-P = 1.122Col-P + 57.0, r2 = 0.95, P < 0.001). Differences between the 2 techniques were more marked in 0–20 mm than 0–100 mm depth soil samples, and in soils with greater clay contents, suggesting that the difference was related to soil organic matter, and thereby organic P contents. Relative differences were greatest in soils with lower P concentrations, i.e. within the agronomic optimum range of most interest to farmers. ICP analysis cannot be directly correlated with colourimetrically measured P in bicarbonate extracts, and would need to be developed and calibrated as a separate, new soil P test.
The oldest modern therian mammal from Europe and its bearing on stem marsupial paleobiogeography
Authors: Vullo Romain , Gheerbrant Emmanuel , de Muizon Christian , Néraudeau Didier
Published: November 2009

We report the discovery of mammalian tribosphenic teeth from the basal Cenomanian of southwestern France that we refer to a new primitive marsupial-like form identified as a basal taxon of Marsupialiformes, a new clade recognized here to include the crown group Marsupialia and primitive stem lineages more closely related to Marsupialia than to Deltatheroida.
Arcantiodelphys marchandi
gen et sp nov. shares several significant marsupial-like features (
s.l.
) with marsupialiform taxa known from the North American Mid-Cretaceous. Among marsupialiforms, it shows a closer resemblance to
Dakotadens
. This resemblance, which is plesiomorphic within “tribotherians,” makes
Arcantiodelphys
one of the most archaic known Marsupialiformes. Moreover,
Arcantiodelphys
is characterized by an original and precocious crushing specialization. Both the plesiomorphic and autapomorphic characteristics of
Arcantiodelphys
among Marsupialiformes might be explained by an Eastern origin from Asian stem metatherians, with some in situ European evolution. In addition, the presence of a mammal with North American affinities in western Europe during the early Late Cretaceous provides further evidence of a large Euramerican biogeographical province at this age or slightly before. Concerning the paleobiogeographical history of the first stem marsupialiforms during the Albian–Cenomanian interval, 2 possible dispersal routes from an Asian metatherian ancestry can be proposed: Asia to Europe via North America and Asia to North America via Europe. The main significance of the Archingeay-Les Nouillers mammal discovery is that it indicates that the beginning of the stem marsupialiforms history involved not only North America but also Europe, and that this early history in Europe remains virtually unknown.
Exogenous α-synuclein fibrils seed the formation of Lewy body-like intracellular inclusions in cultured cells
Authors: Luk Kelvin C. , Song Cheng , O'Brien Patrick , Stieber Anna , Branch Jonathan R. , Brunden Kurt R. , Trojanowski John Q. , Lee Virginia M.-Y.
Published: November 2009

Cytoplasmic inclusions containing α-synuclein (α-Syn) fibrils, referred to as Lewy bodies (LBs), are the signature neuropathological hallmarks of Parkinson's disease (PD). Although α-Syn fibrils can be generated from recombinant α-Syn protein in vitro, the production of fibrillar α-Syn inclusions similar to authentic LBs in cultured cells has not been achieved. We show here that intracellular α-Syn aggregation can be triggered by the introduction of exogenously produced recombinant α-Syn fibrils into cultured cells engineered to overexpress α-Syn. Unlike unassembled α-Syn, these α-Syn fibrils “seeded” recruitment of endogenous soluble α-Syn protein and their conversion into insoluble, hyperphosphorylated, and ubiquitinated pathological species. Thus, this cell model recapitulates key features of LBs in human PD brains. Also, these findings support the concept that intracellular α-Syn aggregation is normally limited by the number of active nucleation sites present in the cytoplasm and that small quantities of α-Syn fibrils can alter this balance by acting as seeds for aggregation.
The physical state of water in bacterial spores
Authors: Sunde Erik P. , Setlow Peter , Hederstedt Lars , Halle Bertil
Published: November 2009

The bacterial spore, the hardiest known life form, can survive in a metabolically dormant state for many years and can withstand high temperatures, radiation, and toxic chemicals. The molecular basis of spore dormancy and resistance is not understood, but the physical state of water in the different spore compartments is thought to play a key role. To characterize this water in situ, we recorded the water
2
H and
17
O spin relaxation rates in D
2
O-exchanged
Bacillus subtilis
spores over a wide frequency range. The data indicate high water mobility throughout the spore, comparable with binary protein–water systems at similar hydration levels. Even in the dense core, the average water rotational correlation time is only 50 ps. Spore dormancy therefore cannot be explained by glass-like quenching of molecular diffusion but may be linked to dehydration-induced conformational changes in key enzymes. The data demonstrate that most spore proteins are rotationally immobilized, which may contribute to heat resistance by preventing heat-denatured proteins from aggregating irreversibly. We also find that the water permeability of the inner membrane is at least 2 orders of magnitude lower than for model membranes, consistent with the reported high degree of lipid immobilization in this membrane and with its proposed role in spore resistance to chemicals that damage DNA. The quantitative results reported here on water mobility and transport provide important clues about the mechanism of spore dormancy and resistance, with relevance to food preservation, disease prevention, and astrobiology.
Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease
Authors: Shin Yongdae , Davis Joseph H. , Brau Ricardo R. , Martin Andreas , Kenniston Jon A. , Baker Tania A. , Sauer Robert T. , Lang Matthew J.
Published: November 2009

ClpXP is an ATP-fueled molecular machine that unfolds and degrades target proteins. ClpX, an AAA+ enzyme, recognizes specific proteins, and then uses cycles of ATP hydrolysis to denature any native structure and to translocate the unfolded polypeptide into ClpP for degradation. Here, we develop and apply single-molecule fluorescence assays to probe the kinetics of protein denaturation and degradation by ClpXP. These assays employ a single-chain variant of the ClpX hexamer, linked via a single biotin to a streptavidin-coated surface, and fusion substrates with an N-terminal fluorophore and a C-terminal GFP-titin-ssrA module. In the presence of adenosine 5′-[γ-thio]triphosphate (ATPγS), ClpXP degrades the titin-ssrA portion of these substrates but stalls when it encounters GFP. Exchange into ATP then allows synchronous resumption of denaturation and degradation of GFP and any downstream domains. GFP unfolding can be monitored directly, because intrinsic fluorescence is quenched by denaturation. The time required for complete degradation coincides with loss of the substrate fluorophore from the protease complex. Fitting single-molecule data for a set of related substrates provides time constants for ClpX unfolding, translocation, and a terminal step that may involve product release. Comparison of these single-molecule results with kinetics measured in bulk solution indicates similar levels of microscopic and macroscopic ClpXP activity. These results support a stochastic engagement/unfolding mechanism that ultimately results in highly processive degradation and set the stage for more detailed single-molecule studies of machine function.
Modular behavior of tauD provides insight into the origin of specificity in α-ketoglutarate-dependent nonheme iron oxygenases
Authors: McCusker Kevin P. , Klinman Judith P.
Published: November 2009

Taurine α-ketoglutarate dioxygenase (tauD) is one of the best-studied α-ketoglutarate (αKG)-dependent nonheme iron oxygenases. As with all oxygenases, a fine balance must be struck between generating a species sufficiently reactive for the required chemistry and controlling that species to prevent undesirable side reactions [Klinman JP (2007)
Accts Chem Res
40:325–333]. In the case of tauD, the substrate oxidizing species has been shown to be a ferryl-oxo, and the introduction of deuterium at the reactive position of substrate results in an enormous kinetic isotope effect together with a partial uncoupling of oxygen activation from substrate oxidation [Price JC, Barr EW, Glass TE, Krebs C, Bollinger JM (2003)
J Am Chem Soc
125:13008–13009]. We have generated a series of site-specific variants at a position that resides directly behind bound substrate (F159 to L, V, A, and G). Decreasing side-chain bulk diminishes the coupling of oxygen activation to C-H cleavage, which is further reduced by substrate deuteration. Despite this impact, oxygen activation remains completely coupled to the oxidative decarboxylation of αKG. The concentration of bis-Tris buffer impacts the extent of coupling of oxygen activation to C-H cleavage, implicating the buffer in the uncoupling pathway. These data indicate a critical role for residue 159 in substrate positioning and reaction in tauD and show that minor active-site perturbations in these enzymes could allow for changes in substrate reactivity while maintaining substrate triggering and oxygen binding/activation.
Effect of Study Context on Item Recollection
Authors: Skinner Erin I. , Fernandes Myra A.
Published: November 2009

We examined how visual context information provided during encoding, and unrelated to the target word, affected later recollection for words presented alone using a remember–know paradigm. Experiments 1A and 1B showed that participants had better overall memory—specifically, recollection—for words studied with pictures of intact faces than for words studied with pictures of scrambled or inverted faces. Experiment 2 replicated these results and showed that recollection was higher for words studied with pictures of faces than when no image accompanied the study word. In Experiment 3 participants showed equivalent memory for words studied with unique faces as for those studied with a repeatedly presented face. Results suggest that recollection benefits when visual context information high in meaningful content accompanies study words and that this benefit is not related to the uniqueness of the context. We suggest that participants use elaborative processes to integrate item and meaningful contexts into ensemble information, improving subsequent item recollection.
Conceptual similarity effects on working memory in sentence contexts: Testing a theory of anaphora
Authors: Cowles H. Wind , Garnham Alan , Simner Julia
Published: November 2009

The degree of semantic similarity between an anaphoric noun phrase (e.g., the bird) and its antecedent (e.g., a robin) is known to affect the anaphor resolution process, but the mechanisms that underlie this effect are not known. One proposal (Almor, 1999) is that semantic similarity triggers interference effects in working memory and makes two crucial assumptions: First, semantic similarity impairs working memory just as phonological similarity does (e.g., Baddeley, 1992), and, second, this impairment interferes with processes of sentence comprehension. We tested these assumptions in two experiments that compared recall accuracy between phonologically similar, semantically similar, and control words in sentence contexts. Our results do not provide support for Almor's claims: Phonological overlap decreased recall accuracy in sentence contexts, but semantic similarity did not. These results shed doubt on the idea that semantic interference in working memory is an underlying mechanism in anaphor resolution.
Methods for combining peptide intensities to estimate relative protein abundance
Authors: Carrillo Brian , Yanofsky Corey , Laboissiere Sylvie , Nadon Robert , Kearney Robert E.
Published: November 2009

Motivation: Labeling techniques are being used increasingly to estimate relative protein abundances in quantitative proteomic studies. These techniques require the accurate measurement of correspondingly labeled peptide peak intensities to produce high-quality estimates of differential expression ratios. In mass spectrometers with counting detectors, the measurement noise varies with intensity and consequently accuracy increases with the number of ions detected. Consequently, the relative variability of peptide intensity measurements varies with intensity. This effect must be accounted for when combining information from multiple peptides to estimate relative protein abundance.

Results: We examined a variety of algorithms that estimate protein differential expression ratios from multiple peptide intensity measurements. Algorithms that account for the variation of measurement error with intensity were found to provide the most accurate estimates of differential abundance. A simple Sum-of-Intensities algorithm provided the best estimates of true protein ratios of all algorithms tested.

Contact:  robert.kearney@mcgill.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
GATE: software for the analysis and visualization of high-dimensional time series expression data
Authors: MacArthur Ben D. , Lachmann Alexander , Lemischka Ihor R. , Ma'ayan Avi
Published: November 2009

Summary: We present Grid Analysis of Time series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional biomolecular time series. GATE uses a correlation-based clustering algorithm to arrange molecular time series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of the molecular component to which they are assigned, to create animated movies of systems-level molecular regulatory dynamics. In order to infer potential regulatory control mechanisms from patterns of correlation, GATE also allows interactive interroga-tion of movies against a wide variety of prior knowledge datasets. GATE movies can be paused and are interactive, allowing users to reconstruct networks and perform functional enrichment analyses. Movies created with GATE can be saved in Flash format and can be inserted directly into PDF manuscript files as interactive figures.

Availability: GATE is available for download and is free for academic use from http://amp.pharm.mssm.edu/maayan-lab/gate.htm

Contact:  avi.maayan@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Rationale and design of a randomized, double‐blind, placebo‐controlled outcome trial of ivabradine in chronic heart failure: the Systolic Heart Failure Treatment with the If Inhibitor Ivabradine Trial (SHIFT)
Authors: Swedberg Karl , Komajda Michel , Böhm Michael , Borer Jeffrey S. , Ford Ian , Tavazzi Luigi
Published: November 2009

Aims

Elevated heart rate is a significant marker for mortality and morbidity in cardiovascular disease including heart failure. Despite background treatment with a beta‐blocker, many patients with heart failure and low ejection fraction maintain a heart rate above 70 b.p.m. Ivabradine reduces heart rate directly through inhibition of the If ionic current.

Methods

SHIFT is a randomized, double‐blind study designed to compare ivabradine with placebo on outcomes in patients with symptomatic chronic heart failure (NYHA class II–IV), left‐ventricular ejection fraction ≤35%, and a prior hospitalization for worsening heart failure within the previous 12 months. Randomized treatment is given on top of guidelines‐based therapy for chronic heart failure, including a beta‐blocker at optimized dose. Resting heart rate at baseline must be ≥70 b.p.m. The primary endpoint is the composite of the time to first event of cardiovascular death or hospitalization for worsening heart failure. Secondary endpoints include all‐cause, cardiovascular and heart failure mortality, and hospitalization. The randomized treatment period lasts approximately 12–48 months. The study will include approximately 6500 patients and will continue until ≥1600 primary endpoints have occurred. The first patient was randomized in October 2006, and the study is expected to end in 2010.

Conclusion

The SHIFT study will assess if a heart rate reduction by direct sinus node inhibition can reduce cardiovascular outcomes in patients with chronic heart failure and left‐ventricular systolic dysfunction.
Comparing methods for building trophic spectra of ecological data
Authors: Libralato Simone , Solidoro Cosimo
Published: November 2009

Libralato, S., and Solidoro, C. 2010. Comparing methods for building trophic spectra of ecological data. – ICES Journal of Marine Science, 67: 426–434. The distribution of biomass, production, and catches over trophic levels (TLs) of the foodweb has been shown theoretically and empirically to provide powerful insights into ecosystem functioning and the effects of fishing. One approach for building trophic spectra of ecological data is based on smoothing original data and assuming zeroes when no values are available for a TL (smoothing-based method). An alternative method is proposed, based on the distribution of ecological data according to density functions (dispersion-based method), and a systematic review of the different alternatives is presented. Six different methods for building trophic spectra, i.e. the smoothing-based and five alternative forms for dispersion-based (using normal, lognormal, and Weibull distributions, also including shifted lognormal and Weibull with zero at TL 2), were applied to ecological properties (i.e. production, biomass, and catches) derived for 24 foodweb models to test their relative performance. The smoothing-based method suffers from the lack of consistency with original data and from unrealistic emergent properties, such as transfer efficiency. The analysis demonstrates the advantages of the dispersion-based method for overcoming these issues and shows, using transfer efficiencies estimated from the models (flow-based estimates) as a reference, that the normal density distribution function performs better.
The construction of next-generation matrices for compartmental epidemic models
Authors: Diekmann O. , Heesterbeek J. A. P. , Roberts M. G.
Published: November 2009

The basic reproduction number ℛ
0
is arguably the most important quantity in infectious disease epidemiology. The next-generation matrix (NGM) is the natural basis for the definition and calculation of ℛ
0
where finitely many different categories of individuals are recognized. We clear up confusion that has been around in the literature concerning the construction of this matrix, specifically for the most frequently used so-called compartmental models. We present a detailed easy recipe for the construction of the NGM from basic ingredients derived directly from the specifications of the model. We show that two related matrices exist which we define to be the
NGM with large domain
and the
NGM with small domain
. The three matrices together reflect the range of possibilities encountered in the literature for the characterization of ℛ
0
. We show how they are connected and how their construction follows from the basic model ingredients, and establish that they have the same non-zero eigenvalues, the largest of which is the basic reproduction number ℛ
0
. Although we present formal recipes based on linear algebra, we encourage the construction of the NGM by way of direct epidemiological reasoning, using the clear interpretation of the elements of the NGM and of the model ingredients. We present a selection of examples as a practical guide to our methods. In the appendix we present an elementary but complete proof that ℛ
0
defined as the dominant eigenvalue of the NGM for compartmental systems and the Malthusian parameter
r
, the real-time exponential growth rate in the early phase of an outbreak, are connected by the properties that ℛ
0
> 1 if and only if
r
> 0, and ℛ
0
= 1 if and only if
r
= 0.
Calm before the spawn: global coral spawning patterns are explained by regional wind fields
Authors: van Woesik R.
Published: November 2009

Most corals in tropical localities broadcast their gametes into the water column, yet we have a poor understanding of what forces reproductive schedules. Moreover, recent studies show considerable geographical variation in the duration of the coral spawning season. For example, on the Great Barrier Reef, corals display tight coupling, while corals in Kenya spawn over seven months. This study reconciles the regional variance by testing the hypothesis that regional wind fields are the corals' ultimate reproductive proxy. Regions with short calm periods should be more tightly coupled than regions with calm periods extending for several months. Regional wind fields were assessed at seven localities, between 1997 and 2006, using the 11 GHz channel radiometer tropical microwave imager (TMI) onboard the tropical rainfall measuring mission (TRMM). There was a direct positive relationship between the duration of regional calm periods and the coupling of mass coral spawning. Ultimate long-term evolutionary advantages of releasing gametes during calm periods ensure fertilization and facilitate larval retention and local recruitment. Coupling mass spawning with seasonally calm periods agrees strongly with recent genetic evidence of local dispersal and high local retention.
Evaluation of a PCR melting profile method for intraspecies differentiation of Trichophyton rubrum and Trichophyton interdigitale
Authors: Leibner-Ciszak Justyna , Dobrowolska Anita , Krawczyk Beata , Kaszuba Aleksandra , Stączek Paweł
Published: November 2009

In order to identify the source of infections caused by dermatophytes, as well as the pathogen transmission pathway, there is a need to determine methods that allow detailed genetic differentiation of the strains within the dermatophyte genera. In this work, a PCR melting profile (PCR-MP) technique based on the ligation of adaptors and the difference in melting temperatures of DNA restriction fragments was used for the first time for intraspecies genotyping of dermatophytes. Clinical isolates and reference strains of dermatophytes isolated from skin, scalp, toenails and fingernails were used for this study. PCR-MP and random amplification of polymorphic DNA (RAPD) were used to type 11 isolates ofTrichophyton rubrum, 40 isolates ofTrichophyton interdigitaleand 14 isolates ofMicrosporum canis. The results distinguished five types (containing one subtype) characteristic forT. rubrumand seven types characteristic forT. interdigitaleusing the PCR-MP technique. Analysis conducted using RAPD revealed five types forT. rubrumand four types forT. interdigitaleisolates. No differentiation was observed for theM. canisisolates with either method. These results demonstrate that PCR-MP is a reliable method for the differentiation ofT. rubrumandT. interdigitalestrains and yields a discriminatory power that is at least equal to that of RAPD.
Listeria monocytogenes does not survive ingestion by Acanthamoeba polyphaga
Authors: Akya Alisha , Pointon Andrew , Thomas Connor
Published: November 2009

Listeria monocytogenes is a ubiquitous bacterium capable of infecting humans, particularly pregnant women and immunocompromised individuals. Although the intracellular invasion and pathogenesis of listeriosis in mammalian tissues has been well studied, little is known about the ecology of L. monocytogenes, and in particular the environmental reservoir for this bacterium has not been identified. This study used short-term co-culture at 15, 22 and 37 °C to examine the interaction of L. monocytogenes strains with Acanthamoeba polyphaga ACO12. Survival of L. monocytogenes cells phagocytosed by monolayers of trophozoites was assessed by culture techniques and microscopy. A. polyphaga trophozoites eliminated bacterial cells within a few hours post-phagocytosis, irrespective of the incubation temperature used. Wild-type L. monocytogenes and a phenotypic listeriolysin O mutant were unable to either multiply or survive within trophozoites. By contrast, Salmonella enterica serovar Typhimurium C5 cells used as controls were able to survive and multiply within A. polyphaga trophozoites. The data presented indicate that A. polyphaga ACO12 is unlikely to harbour L. monocytogenes, or act as an environmental reservoir for this bacterium.
Quorum-sensing-regulated virulence factors in Pseudomonas aeruginosa are toxic to Lucilia sericata maggots
Authors: Andersen A. S. , Joergensen B. , Bjarnsholt T. , Johansen H. , Karlsmark T. , Givskov M. , Krogfelt K. A.
Published: November 2009

Maggot debridement therapy (MDT) is widely used for debridement of chronic infected wounds; however, for wounds harbouring specific bacteria limited effect or failure of the treatment has been described. Here we studied the survival of Lucilia sericata maggots encountering Pseudomonas aeruginosa PAO1 in a simple assay with emphasis on the quorum-sensing (QS)-regulated virulence. The maggots were challenged with GFP-tagged P. aeruginosa wild-type (WT) PAO1 and a GFP-tagged P. aeruginosa ΔlasR
rhlR (ΔRR) QS-deficient mutant in different concentrations. Maggots were killed in the presence of WT PAO1 whereas the challenge with the QS mutant showed a survival reduction of ∼25 % compared to negative controls. Furthermore, bacterial intake by the maggots was lower in the presence of WT PAO1 compared to the PAO1 ΔRR mutant. Maggot excretions/secretions (ES) were assayed for the presence of QS inhibitors; only high doses of ES showed inhibition of QS in P. aeruginosa. Thus P. aeruginosa was shown to be toxic to L. sericata maggots. This, coupled to the preferential feeding by the maggots and reduced ingestion of P. aeruginosa, could explain MDT failure in wounds colonized by P. aeruginosa. Wounds heavily colonized with P. aeruginosa should be a counterindication for MDT unless used in combination with a pre-treatment with other topical therapeutics targeting P. aeruginosa.