bluuebunny/crossref_metadata_2025 huggingface dataset:
Food habits of the wildcat (Felis silvestris) in a peculiar habitat: the Mediterranean high mountain
Authors: Moleón M. , Gil‐Sánchez J. M.
Published: September 2010

The feeding spectrum of the wildcat Felis silvestris Schreber, 1777 was studied in two sites with different ecological characteristics, both situated in the same Mediterranean environment in the high mountain of the Sierra Nevada National Park, south‐east Spain, where the rabbit Oryctolagus cuniculus is absent. Scat analysis (n=101 faeces; n=402 prey items) showed that the diet is based on rodents, fundamentally wood mouse Apodemus sylvaticus, Mediterranean pine vole Microtus duodecimcostatus and south‐western water vole Arvicola sapidus. Results showed strong differences between the two sites (χ2=74.04, d.f.=5, P<0.001), that is a predominance of voles in the mesic Chico river, whereas mice are predominant in the xeric Tejos ravine. Red‐legged partridge Alectoris rufa and carrion also played an important role, especially in biomass terms. The overall diet differed essentially from that of the Mediterranean region, which surrounds the study area, since in these areas rabbits constitute the primary prey. However, the diet of the mountain wildcats is similar to that in the Eurosiberian floral region, despite its distance from the Sierra Nevada. In conclusion, the Iberian wildcat seems to behave as a facultative specialist, since it prefers rabbits whenever they are available, but rodents constitute most of its diet if rabbits are scarce or absent.
Are non‐reproductive male highveld mole‐rats, Cryptomys hottentotus pretoriae physiologically suppressed while in the confines of the natal colony?
Authors: van Rensburg L. Janse , Bennett N. C. , van der Merwe M. , Schoeman A. S. , Brinders J.
Published: September 2010

The highveld mole‐rat, Cryptomys hottentous pretoriae is a social, subterranean, co‐operative breeder with a high reproductive skew. The relationship between reproductive status and reproductive physiology in male highveld mole‐rats was investigated. Testicular morphometrics, histological parameters, plasma testosterone concentrations and sperm motility parameters were studied in 31 males (14 reproductive and 17 non‐reproductive males). Reproductive males were significantly larger than non‐reproductive males, with testicular mass and volume corrected for body mass considerably larger for the reproductive males. Circulating plasma testosterone concentrations of reproductive males were not significantly higher than non‐reproductive males (reproductive males 10.3±1.8 nmol l−1vs non‐reproductive males 7.3±1.74 nmol l−1). Sperm motility parameters were measured, but no significant differences were found between reproductive and non‐reproductive males. All 14 reproductive males had motile sperm, whereas 13 of the 17 (76%) of non‐reproductive males possessed motile sperm. A typical ejaculate of a reproductive male contains 48.3% motile sperm characterized by a high percentage of flagellar defects, whereas the non‐reproductive male has an ejaculate containing 45.6% motile sperm with a high percentage of head defects. It is apparent that non‐reproductive males are not physiologically suppressed from reproducing. Moreover, the non‐reproductive males are excluded from incestuous matings as a result of being the offspring of the reproductive female.
Sexual differentiation and juvenile intersexuality in the European sea bass (Dicentrarchus labrax)
Authors: Saillant Eric , Chatain Béatrice , Menu Bruno , Fauvel Christian , Vidal Marie Odile , Fostier Alexis
Published: September 2010

Sexual differentiation was studied at the histological level using a mixture of 30 families of sea bass Dicentrarchus labrax. Most of the fish (93%) differentiated into males as usually observed in farmed populations. All testes were differentiated when the males reached 12 cm and no more undifferentiated fish were found from 419 days post‐fertilization (p.f.). In 28% of the males, among the biggest, sexual differentiation had already begun at 168 days p.f. (8.3–9.5 cm) and these fish started spermatogenesis in their first year of life. The other males differentiated later and remained immature at the end of their first year of life. Ovaries could be identified at the histological level from the age of 168 days p.f. (7.9–9.0 cm) and the females became significantly longer than the males from the age of 191 days p.f., i.e. during the process of ovarian differentiation. In the studied group, 62% of the males developed intratesticular oocytes. Such intersexuality had no consequence on growth rate. Intratesticular oocytes were also recorded in testes of wild males originating from Atlantic (Britain and Gulf of Gascogne) and West Mediterranean showing that juvenile intersexuality is not restricted to farmed populations but is a widespread phenomenon in sea bass.
Parallelism and convergence in anuran fangs
Authors: Fabrezi Marissa , Emerson Sharon B.
Published: September 2010

The anuran lower jaw is composed of three pairs of bones: dentaries, angulosplenials and mentomeckelians. Although the lower jaw is toothless, except in Gastrotheca guentheri, enlarged fangs or odontoids have evolved at least four times independently in some myobatrachids, hylids, ranids and leptodactylids through both parallel and convergent evolutionary events. Fangs seem to represent the single best design solution to enable an anuran to inflict a bite‐like wound, but the biological role of biting varies among species. Fangs are projections of the dentaries in ranids, but in the hylid frog Hemiphractus and in ceratophryine leptodactylids, they form a sinosteotic unit with the dentaries and mentomeckelians. Comparisons of morphology, behaviour and diet among frog taxa with enlarged fangs reveal that the fangs may be the result of either sexual or natural selection. Those fangs that evolved in response to sexual selection seem to be relatively larger than those that resulted of natural selection.
Adult mortality rates in young colonies of a swarm‐founding social wasp (Polybia occidentalis)
Authors: Bouwma Andrew M. , Bouwma Peter E. , Nordheim Erik V. , Jeanne Robert L.
Published: September 2010

The swarm founders are unusual among the social wasps in having socialized the dispersal stage of the life cycle. Colonies are initiated by groups of workers accompanied by smaller numbers of queens. Thus, swarm founders avoid the colony size bottleneck faced by the independent founders, whose colonies start with one or a few queens. Among the advantages of swarm founding is a reduction of the risk of colony failure due to attrition of the founding adults. Stochasticity in adult mortality is less likely to lead to outright extinction of a large founding group before new workers are produced (pre‐emergence period). However, it is not known how important pre‐emergence mortality is as a selective force on founding and dispersal behaviour in swarm founders, since colony‐wide mortality rates have never been reported for a large‐colony social wasp. Sixty‐eight swarms of Polybia occidentalis were censused just before colony initiation and again 24 days later. Mortality over this period averaged 0.41±0.12 of the founding swarm population. Including mortality on the day of emigration and extrapolating to day 30, when the first adult offspring eclose, the original absconding swarm would be reduced by 0.52 of its initial size. Rates of loss during the first week, while the colonies engaged in nest construction, did not differ from rates over the full 24 days. Thus, colony founding in P. occidentalis is both costly and highly variable in terms of mortality of the founding adults.
Use of climatic data to assess the effect of insect harassment on the autumn weight of reindeer (Rangifer tarandus) calves
Authors: Weladji Robert B. , Holand Øystein , Almøy Trygve
Published: September 2010

Considerable behavioural evidence supports harassment by insects as the most important causal link between warm summer temperatures and low body condition of reindeerRangifer tarandus, and that insect activity is influenced by weather condition. However, much less is known about the effect of insect harassment on individual performance, measured as reduced weight gain during summer, and the related consequences on both the reindeer pastoral economy and reindeer as a biological resource. Using climatic data, this paper develops a simple index for the analysis of insect harassment that takes into consideration weather variables known to significantly affect insect activity and/or the level of insect harassment. The insect harassment index, which is based on mid‐day ambient temperature ≥13 °C, wind speed <6 m/s and cloud cover <40%, is further used to test the hypothesis that insect harassment has a negative effect on reindeer performance during summer in three Norwegian populations. Results show that harassment by insects negatively affects the autumn weight of reindeer calves, most probably through reduced grazing time and increased energy expenditure, but also indirectly by negatively influencing milk production of the dam. Moreover, female calves were more vulnerable to insect harassment than males. Insect harassment may have consequences on future reproductive performance, calving time, calf birth weight and hence neonatal mortality, and thus affect reindeer productivity. The presented index is easy to estimate and may be used to quantify and compare harassment levels on various reindeer summer grazing areas for management purposes. Our results also suggest that the expected temperature increase in the course of global warming may increase the insect‐related stress on reindeer.
Free cyclitol unloading from seed coats on stem–leaf–pod explants of low-raffinose, low-stachyose, low-phytin soybean
Authors: Kosina Suzanne M. , Schnebly Steven R. , Obendorf Ralph L.
Published: September 2010

Raffinose, stachyose and phytin are undesirable compounds for soybean food and animal feed products. In seeds, raffinose and stachyose are believed to contribute to desiccation and cold stress tolerance. Thus, removal of these compounds from soybean by genetic mutation has resulted in a more commercially desirable composition, but potentially less physiologically viable seeds. In an effort to develop a method to improve viability and seed storability in soybean, stem–leaf–pod explants of three low raffinose, low stachyose lines, two of which were also low in phytin, and a check line were fed solutions containing d-chiro-inositol, myo-inositol or d-pinitol, free cyclitols which unload through the seed coat to the developing embryo where they accumulate as fagopyritols, galactinol and galactopinitols, respectively, during seed maturation. Increased galactopinitol and fagopyritol accumulation may substitute for the roles of raffinose and stachyose in low raffinose, stachyose and phytin seeds. Explants of all lines unloaded d-chiro-inositol, myo-inositol and d-pinitol. Fed d-chiro-inositol accumulated in leaf tissues demonstrating uptake into explants. Fed d-chiro-inositol and myo-inositol accumulated in pod wall and seed coat tissues of one or more lines. The results indicate that d-chiro-inositol was unloaded from the seed coat to the embryo in increased amounts after feeding. The potential use of increased maternal d-chiro-inositol for synthesis of fagopyritols in embryos to improve seed performance in low-stachyose and low-phytin soybean seeds is supported. The seed coat cup unloading of fed free cyclitols may provide a model system to test effective unloading of upregulated maternally synthesized cyclitols.
Transparency of complex regulation: how should WTO trade policy reviews deal with sanitary and phytosanitary policies?
Authors: ZAHRNT VALENTIN
Published: September 2010

Sanitary and phytosanitary (SPS) measures that protect human, animal, and plant health can impede trade and provoke high-profile disputes. This paper argues that the WTO's Trade Policy Review Mechanism (TPRM) could play an important role in defusing the trade-disrupting potential of SPS regulation. The most promising avenue is to review in greater detail the policy-making procedures that lead to SPS measures. How transparent and independent are countries' risk assessments of health hazards? Which provisions have countries taken to account for trade effects when selecting SPS measures? Do countries give foreign interests adequate possibility to voice their concerns over proposed SPS regulation? If reviews motivate countries to improve their policy-making processes, this will contribute to making SPS regulation less trade-restrictiveandmore effective in protecting health. To reach this objective, special trade policy reviews dedicated exclusively to SPS regulation might be introduced as a complement to the current reviews of countries' overall trade policies. Such a move could serve as a model for establishing further issue-specific reviews that address technical barriers to trade, trade in services, and other complex regulatory challenges.
Assessing inter- and intra-cultivar variation in Greek Prunus avium by SSR markers
Authors: Ganopoulos Ioannis V. , Avramidou Evagellia , Fasoula Dionisia A. , Diamantidis Grigorios , Aravanopoulos Filippos A.
Published: September 2010

Prunus avium cultivars widely used in northern Greece were investigated in terms of inter- and intra-cultivar genetic variation and DNA fingerprinting. Based on 11 simple sequence repeats loci, the average number of alleles per locus (Na = 2.82), probability of identity (PID = 0.327), polymorphic information content (0.451) and expected heterozygosity (He = 0.494) were within the range reported in similar studies. The most informative markers were BPPCT039 and EMPa018. The cultivars were clearly separated in both an unweighted pair group method with arithmetic mean dendrogram and a multivariate space ordination. Any two cultivars differed on the average at 6.30 loci. The null hypothesis of zero intra-cultivar variability was tested and could not be rejected. Two cultivars (Tragana Edessis and Tragana Sarakinon) were genetically similar, but not identical. This study, the first of its kind for sweet cherry in Greece, presents a useful molecular tool for resolving issues of intra-cultivar variability and synonimity and provides a warranty of genetic identity in the handling and management of local traditional germplasm.
A new analysis method for determining polar ionosphere and upper atmosphere characteristics from ESR data: Illustration with IPY period
Authors: Blelly P.‐L. , Alcaydé D. , van Eyken A. P.
Published: September 2010

The one‐year incoherent scatter (IS) data set recorded at the EISCAT Svalbard Radar (ESR) during the International Polar Year (IPY) is an opportunity for studies on long‐term variations in the ionosphere and neutral atmosphere. Such studies place severe requirements on the analysis of any IS observations which result in two major difficulties. First, concerning the ionosphere, the challenge is to make accurate measurements of the temperature profiles in the F1‐region, where the ion composition is changing, highly variable, and unknown. Changes in ion mass and temperature affect the received spectra in almost identical ways, and ambiguities in one present insurmountable difficulties in the determination of the other. The second difficulty, concerning the neutrals, is that it is necessary to separate the contributions from the neutral atmosphere and from frictional heating. In the F1‐region, differential drift induces differential heating of the atomic and molecular ions which can be used to distinguish between frictional and neutral atmosphere coupling. In this paper, we present in detail a method to solve these two difficulties: 13‐moment, parallel, two‐ion (atomic and molecular) energy equations are used to fit the full IS profile along the magnetic field. The molecular‐atomic ion composition transition is assumed to follow an analytical hyperbolic tangent function, and the full altitude profile of the measured ion temperature is then used to fit the desired parameters. The results are validated against simulated data from a numerical model, and then against real measurements. A 36‐hour data set was compared with the numerical model TRANSCAR, making some unknowns available from the numerical model (ion composition, frictional heating, neutral temperature), providing a convincing demonstration of the validity of the method. In particular, this “full profile” method is sufficiently robust for routine use, even for periods with relatively high convection electric fields. Finally, the application of the method to the IPY ESR data set is presented and some initial trends are identified.
An update on blue snow holes
Authors: Barker H. W. , Korolev A. V.
Published: September 2010

A simple radiative transfer model, new estimates of the imaginary part of ice's refractive index k, and color matching functions are used to simulate colors, as seen by humans, in holes made in snowpacks. This study was inspired by recent photographs, made under overcast skies, that show a dramatic contrast between the lack‐lustre, near‐gray of holes made in a midlatitude snowpack and the vivid blue of snow holes at the South Pole. While this phenomenon has been studied before, new values of k, which are 1–2 orders of magnitude smaller than the old ones in the violet‐blue region, lead to simulated sRGB color profiles that resemble closely the color photographs. Basically, colors are governed by the dependence of snow grain single‐scattering albedo on snow grain size, spectrally varying k, and the number of times photons are scattered by snow grains. It is demonstrated that profiles of upwelling fluxes within a pure snowpack at wavelengths near 0.75 μm can be used to estimate profiles of effective grain size in the uppermost 20–30 cm.
Influence of convection on the water isotopic composition of the tropical tropopause layer and tropical stratosphere
Authors: Sayres D. S. , Pfister L. , Hanisco T. F. , Moyer E. J. , Smith J. B. , St. Clair J. M. , O'Brien A. S. , Witinski M. F. , Legg M. , Anderson J. G.
Published: September 2010

We present the first in situ measurements of HDO across the tropical tropopause, obtained by the integrated cavity output spectroscopy (ICOS) and Hoxotope water isotope instruments during the Costa Rica Aura Validation Experiment (CR‐AVE) and Tropical Composition, Cloud and Climate Coupling (TC4) aircraft campaigns out of Costa Rica in winter and summer, respectively. We use these data to explore the role convection plays in delivering water to the tropical tropopause layer (TTL) and stratosphere. We find that isotopic ratios within the TTL are inconsistent with gradual ascent and dehydration by in‐situ cirrus formation and suggest that convective ice lofting and evaporation play a strong role throughout the TTL. We use a convective influence model and a simple parameterized model of dehydration along back trajectories to demonstrate that the convective injection of isotopically heavy water can account for the predominant isotopic profile in the TTL. Air parcels with significantly enhanced water vapor and isotopic composition can be linked via trajectory analysis to specific convective events in the Western Tropical Pacific, Southern Pacific Ocean, and South America. Using a simple model of dehydration and hydration along trajectories we show that convection during the summertime TC4 campaign moistened the upper part of the TTL by as much as 2.0 ppmv water vapor. The results suggest that deep convection is significant for the moisture budget of the tropical near‐tropopause region and must be included to fully model the dynamics and chemistry of the TTL and lower stratosphere.
Risk assessment of hurricane storm surge for New York City
Authors: Lin N. , Emanuel K. A. , Smith J. A. , Vanmarcke E.
Published: September 2010

Hurricane storm surge presents a major hazard for the United States. We apply a model‐based risk assessment methodology to investigate hurricane storm surge risk for New York City (NYC). We couple a statistical/deterministic hurricane model with the hydrodynamic model SLOSH (sea, lake, and overland surges from hurricanes) to generate a large number of synthetic surge events; the SLOSH model simulations are compared to advanced circulation model simulations. Statistical analysis is carried out on the empirical data. It is observed that the probability distribution of hurricane surge heights at the Battery, NYC, exhibited a heavy tail, which essentially determines the risk of New York City being struck by a catastrophic coastal flood event. The peaks‐over‐threshold method with the generalized Pareto distribution is applied to estimate the upper tail of the surge heights. The resulting return periods of surge heights are consistent with those of other studies for the New York area. This storm surge risk assessment methodology may be applied to other coastal areas and can be extended to consider the effect of future climate change.
Quantifying regolith erosion rates with cosmogenic nuclides 10Be and 26Al in the McMurdo Dry Valleys, Antarctica
Authors: Morgan Daniel , Putkonen Jaakko , Balco Greg , Stone John
Published: September 2010

The McMurdo Dry Valleys, Antarctica (MDV) are among the oldest landscapes on Earth, and some landforms there present an intriguing apparent contradiction such that millions of years old surface deposits maintain their meter‐scale morphology despite the fact that measured erosion rates are 0.1–4 m Ma−1. We analyzed the concentration of cosmic ray‐produced 10Be and 26Al in quartz sands from regolith directly above and below two well‐documented ash deposits in the MDV, the Arena Valley ash (40Ar/39Ar age of 4.33 Ma) and the Hart ash (K‐Ar age of 3.9 Ma). Measured concentrations of 10Be and 26Al are significantly less than expected given the age of the in situ air fall ashes and are best interpreted as reflecting the degradation rate of the overlying sediments. The erosion rate of the material above the Arena Valley ash that best explains the observed isotope profiles is 3.5 ± 0.41 × 10−5 g cm−2 yr−1 (∼0.19 m Ma−1) for the past ∼4 Ma. For the Hart ash, the erosion rate is 4.8 ± 0.21 × 10−4 g cm−2 yr−1 (∼2.6 m Ma−1) for the past ∼1 Ma. The concentration profiles do not show signs of mixing, creep, or deflation caused by sublimation of ground ice. These results indicate that the slow, steady lowering of the surface without vertical mixing may allow landforms to maintain their meter‐scale morphology even though they are actively eroding.
Scaling properties of heavy rainfall at short duration: A regional analysis
Authors: Ceresetti D. , Molinié G. , Creutin J.‐D.
Published: September 2010

The aim of this paper is to assess the scaling properties of heavy point rainfall with respect to duration. In the region of interest, the probability distribution tails of hourly to daily rainfall display log‐log linearity. The log‐log linearity of tails is a feature of fat‐tailed distributions. The conservation of this property throughout the scales will be investigated in the framework of scale‐invariant analysis. Evidence of the scaling of heavy rainfall is shown for one particularly long rainfall series through the conservation of the survival probability shape at durations in the range 1–24 h. An objective method is implemented to estimate the hyperbolic‐tail parameters of rainfall distributions. This method is automatized and detects the lower bound above which the distributions exhibit power law tails and determines the power law exponent α using a maximum likelihood estimator. The application of unbiased estimation methods and scale‐invariant properties for the estimation of the power law exponent provides a significant reduction of the intergage power law variability. This achievement is essential for a correct use of geostatistical approaches to interpolate the power law parameters at ungaged sites. The method is then applied to the rain gage network in the Cévennes‐Vivarais region, a Mediterranean mountainous region located in southern France. The maps show thicker rainfall distribution tails in the flat area between the seashore and the foothill. It is shown that in a flat region closer to the Mediterranean Sea the rainfall distribution tails are hyperbolic and the power law exponent is quasi‐constant with duration, whereas, over the mountain, the power law behavior is less defined. The physical reasons for such results and the consequences for the statistical modeling of heavy rainfall are then discussed, providing an innovative point of view for the comprehension of the rainfall extremes behavior at different temporal scales.
Assessing the potential of Medium‐Resolution Imaging Spectrometer (MERIS) and Moderate‐Resolution Imaging Spectroradiometer (MODIS) data for monitoring total suspended matter in small and intermediate sized lakes and reservoirs
Authors: Tarrant P. E. , Amacher J. A. , Neuer S.
Published: September 2010

Satellite remote sensing has been used extensively for many years to monitor the open oceans and coastal waters. These methods have been extended more recently to the study of inland waters. In this study we consider the potential application of data from two ocean color sensors, Moderate‐Resolution Imaging Spectroradiometer (MODIS) and Medium‐Resolution Imaging Spectrometer (MERIS), for monitoring the levels of suspended solids in small and intermediate sized lakes and reservoirs. We measured total suspended matter (TSM) in four southwestern United States lakes, Roosevelt Lake, Saguaro Lake, Bartlett Lake, and Lake Pleasant, and compared these field data with images obtained from these medium resolution satellite sensors. Our regression analysis of the complete data set identified a linear relationship between the field TSM values and both MODIS 250 m data (r2 = 0.461) and MERIS 290 m data (r2 = 0.521). This relationship improved substantially when data from the smallest lake in the study (Saguaro Lake) were excluded from the analysis (r2 = 0.819 and r2 = 0.888, respectively). The resultant linear models produced estimates with a root‐mean‐square error (RMSE) ranging from 3.14 mg/L (MODIS) and 2.04 mg/L (MERIS) for all four lakes combined, improving to 1.32 mg/L (MODIS) and 0.47 mg/L (MERIS) for a lake‐specific regression. These results suggest that these satellite sensors have the potential to effectively monitor TSM in lakes and reservoirs, although a minimum practical lake size does appear to exist.
Reformulation of the bed load equation of Meyer‐Peter and Müller in light of the linearity theory for alluvial channel flow
Authors: Huang He Qing
Published: September 2010

Due to a lack of sufficient theoretical relations, equations for bed load transport in alluvial channel flow have been developed using a variety of empirical assumptions. A linear relationship exhibited in the complex interactions among the three essential components of a river (channel geometry, bed load transport and flow resistance) has led this study to develop a more accurate form of the Meyer‐Peter and Müller (1948, hereafter MPM) relationship, one of the world's most widely used bed load transport equations. This study demonstrates that the application of linearity theory can significantly improve its performance. On the basis of the dataset originally used by MPM, it is shown that the applicable form of the Manning‐Strickler flow resistance relationship can be very satisfactorily determined. The MPM equation is consequently found to be expressible more accurately as Φ = 6[ητb* − 0.047]5/3, where Φ, η and τ*b are the normalized, dimensionless bed load transport rate, bed‐form correction, and flow‐strength parameters, respectively.
SBUV observations of polar mesospheric clouds compared with MLS temperature and water vapor measurements
Authors: Shettle Eric P. , Nedoluha Gerald E. , DeLand Matthew T. , Thomas Gary E. , Olivero John J.
Published: September 2010

Earlier studies have shown that Polar Mesospheric Clouds (PMC) occur more frequently in the northern hemisphere (NH) than the SH, consistent with colder NH temperatures. Coincident PMC observations with the Solar Backscatter Ultraviolet instruments on the NOAA‐16 and NOAA‐18 satellite and temperature and water vapor measurements with the Microwave Limb Sounder on the Aura satellite support this result. These coincident measurements also show that, for similar temperatures and water vapor mixing ratios, PMCs occur more frequently and are brighter in the NH than the SH. Possible reasons for these hemispheric differences are discussed.
Modeling convective‐stratiform precipitation processes on a Mei‐Yu front with the Weather Research and Forecasting model: Comparison with observations and sensitivity to cloud microphysics parameterizations
Authors: Luo Yali , Wang Yanjie , Wang Hongyan , Zheng Yongjun , Morrison Hugh
Published: September 2010

Deep convective‐scale simulations of the linear mesoscale convective systems (MCSs) formed on a Mei‐Yu front over the Huai River basin in China on 7–8 July 2007 were conducted using the Advanced Research Weather Research and Forecasting model to investigate impacts of cloud microphysics parameterizations on simulated convective‐stratiform precipitation processes. Eight simulations were performed with identical configurations, except for differences in the cloud microphysics parameterizations. Measurements from rain gauges, ground‐based weather radars, and the Tropical Rainfall Measuring Mission satellite Precipitation Radar were used to quantitatively evaluate the model results. While all of the simulations largely capture the observed large‐scale characteristics of the precipitation event, notable differences among the simulations are found in the morphology and evolution of the MCSs at mesoscale and cloud scale. Significant influences on the coupling between dynamical and microphysical processes at the resolved deep convective scale by the various microphysical parameterizations are evident. On the one hand, the different microphysical schemes produce not only substantial differences in intensity of convective precipitation but also distinguishable vertical distributions of latent heating and condensate loading in the deep convective regions, which in turn results in significant differences in the vertical distributions of vertical air velocity and in the heights and strength of detrainment from deep convective regions. Consequently, detrainment of hydrometeors and positively buoyant air from the deep convective regions to the stratiform regions is significantly different, which impacts the formation and growth of ice‐phase hydrometeors at the upper levels and thus surface rainfall rates in the stratiform regions. On the other hand, prediction of rain size distribution significantly impacts the simulated rain evaporation rates and mass‐weighted rain fall speeds, and hence rain flux. Improper determination of the intercept parameter of rain size distribution can result in unrealistic features in the morphology of the storm and can have substantial impacts on precipitation distribution and evolution.
Lack of DNA helicase Pif1 disrupts zinc and iron homoeostasis in yeast
Authors: Guirola María , Barreto Lina , Pagani Ayelen , Romagosa Miriam , Casamayor Antonio , Atrian Silvia , Ariño Joaquín
Published: September 2010

The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1Δ strain is tolerant to zinc overload. In the present study we demonstrate that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1Δ cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1Δ cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1Δ cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild-type cells. Coincidently, pif1Δ mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1Δ cells contain normal amounts of the Aco1 (yeast aconitase) protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as a nucleoid protein and that this triggers a domino effect on iron homoeostasis resulting in increased zinc tolerance.
Human OGA binds substrates in a conserved peptide recognition groove
Authors: Schimpl Marianne , Schüttelkopf Alexander W. , Borodkin Vladimir S. , van Aalten Daan M. F.
Published: September 2010

Modification of cellular proteins with O-GlcNAc (O-linked N-acetylglucosamine) competes with protein phosphorylation and regulates a plethora of cellular processes. O-GlcNAcylation is orchestrated by two opposing enzymes, O-GlcNAc transferase and OGA (O-GlcNAcase or β-N-acetylglucosaminidase), which recognize their target proteins via as yet unidentified mechanisms. In the present study, we uncovered the first insights into the mechanism of substrate recognition by human OGA. The structure of a novel bacterial OGA orthologue reveals a putative substrate-binding groove, conserved in metazoan OGAs. Guided by this structure, conserved amino acids lining this groove in human OGA were mutated and the activity on three different substrate proteins [TAB1 (transforming growth factor-β-activated protein kinase 1-binding protein 1), FoxO1 (forkhead box O1) and CREB (cAMP-response-element-binding protein)] was tested in an in vitro deglycosylation assay. The results provide the first evidence that human OGA may possess a substrate-recognition mechanism that involves interactions with O-GlcNAcylated proteins beyond the GlcNAc-binding site, with possible implications for differential regulation of cycling of O-GlcNAc on different proteins.
The O-GlcNAc modification: three-dimensional structure, enzymology and the development of selective inhibitors to probe disease
Authors: Davies Gideon J. , Martinez-Fleites Carlos
Published: September 2010

Carbohydrates, their structures and the enzymes responsible for their synthesis and degradation, offer numerous possibilities for the design and application of probes with which to study and treat disease. The intracellular dynamic O-GlcNAc (O-linked β-N-acetylglucosamine) modification is one such glycosylation with considerable medical interest, reflecting its implication in diseases such as Type 2 diabetes and neurodegeneration. In the present paper, we review recent structural and mechanistic studies into the enzymes responsible for this modification, highlighting how mechanism-inspired small-molecule probes may be applied to study potential disease processes. Such studies have questioned a causal link between O-GlcNAc and Type 2 diabetes, but do offer potential for the study, and perhaps the treatment, of tauopathies.
Building and analysing genome-scale metabolic models
Authors: Fell David A. , Poolman Mark G. , Gevorgyan Albert
Published: September 2010

Reconstructing a model of the metabolic network of an organism from its annotated genome sequence would seem, at first sight, to be one of the most straightforward tasks in functional genomics, even if the various data sources required were never designed with this application in mind. The number of genome-scale metabolic models is, however, lagging far behind the number of sequenced genomes and is likely to continue to do so unless the model-building process can be accelerated. Two aspects that could usefully be improved are the ability to find the sources of error in a nascent model rapidly, and the generation of tenable hypotheses concerning solutions that would improve a model. We will illustrate these issues with approaches we have developed in the course of building metabolic models of Streptococcus agalactiae and Arabidopsis thaliana.
Predicting novel pathways in genome-scale metabolic networks
Authors: Schuster Stefan , de Figueiredo Luís F. , Kaleta Christoph
Published: September 2010

Elementary-modes analysis has become a well-established theoretical tool in metabolic pathway analysis. It allows one to decompose complex metabolic networks into the smallest functional entities, which can be interpreted as biochemical pathways. This analysis has, in medium-size metabolic networks, led to the successful theoretical prediction of hitherto unknown pathways. For illustration, we discuss the example of the phosphoenolpyruvate-glyoxylate cycle in Escherichia coli. Elementary-modes analysis meets with the problem of combinatorial explosion in the number of pathways with increasing system size, which has hampered scaling it up to genome-wide models. We present a novel approach to overcoming this obstacle. That approach is based on elementary flux patterns, which are defined as sets of reactions representing the basic routes through a particular subsystem that are compatible with admissible fluxes in a (possibly) much larger metabolic network. The subsystem can be made up by reactions in which we are interested in, for example, reactions producing a certain metabolite. This allows one to predict novel metabolic pathways in genome-scale networks.
Computational optimization and biological evolution
Authors: Goryanin Igor
Published: September 2010

Modelling and optimization principles become a key concept in many biological areas, especially in biochemistry. Definitions of objective function, fitness and co-evolution, although they differ between biology and mathematics, are similar in a general sense. Although successful in fitting models to experimental data, and some biochemical predictions, optimization and evolutionary computations should be developed further to make more accurate real-life predictions, and deal not only with one organism in isolation, but also with communities of symbiotic and competing organisms. One of the future goals will be to explain and predict evolution not only for organisms in shake flasks or fermenters, but for real competitive multispecies environments.
The principle of sufficiency and the evolution of control: using control analysis to understand the design principles of biological systems
Authors: Brown Guy C.
Published: September 2010

Control analysis can be used to try to understand why (quantitatively) systems are the way that they are, from rate constants within proteins to the relative amount of different tissues in organisms. Many biological parameters appear to be optimized to maximize rates under the constraint of minimizing space utilization. For any biological process with multiple steps that compete for control in series, evolution by natural selection will tend to even out the control exerted by each step. This is for two reasons: (i) shared control maximizes the flux for minimum protein concentration, and (ii) the selection pressure on any step is proportional to its control, and selection will, by increasing the rate of a step (relative to other steps), decrease its control over a pathway. The control coefficient of a parameter P over fitness can be defined as (∂N/N)/(∂P/P), where N is the number of individuals in the population, and ∂N is the change in that number as a result of the change in P. This control coefficient is equal to the selection pressure on P. I argue that biological systems optimized by natural selection will conform to a principle of sufficiency, such that the control coefficient of all parameters over fitness is 0. Thus in an optimized system small changes in parameters will have a negligible effect on fitness. This principle naturally leads to (and is supported by) the dominance of wild-type alleles over null mutants.
Signalling over a distance: gradient patterns and phosphorylation waves within single cells
Authors: Muñoz-García Javier , Kholodenko Boris N.
Published: September 2010

Recent discoveries of phosphorylation gradients and microdomains with different protein activities have revolutionized our perception of information transfer within single cells. The different spatial localization of opposing reactions in protein-modification cycles has been shown to bring about heterogeneous stationary patterns and travelling waves of protein activities. We review spatial patterns and modes of signal transfer through phosphorylation/dephosphorylation and GDP/GTP exchange cycles and cascades. We show how switches between low-activity and high-activity states in a bistable activation–deactivation cycle can initiate the propagation of travelling protein-modification waves in the cytoplasm. Typically, an activation wave is initiated at the plasma membrane and propagates through the cytoplasm until it reaches the nucleus. An increase in deactivator activity is followed by the initiation of an inactivation wave that moves in the reverse direction from the nucleus. We show that the ratio of opposing enzyme rates is a key parameter that controls both the spread of activation through cascades and travelling waves.
Spatial and temporal information coding and noise in the NF-κB system
Authors: Marcello Marco , White Michael R.H.
Published: September 2010

NF-κB (nuclear factor κB) regulates cellular stress and the immune responses to infection. Its activation results in oscillations in nuclear NF-κB abundance. We treated cells with repeated short pulses of TNFα (tumour necrosis factor α) at various intervals to mimic pulsatile inflammatory signals. At all pulse intervals analysed, we observed synchronous cycles of NF-κB nuclear translocation. Lower frequency stimulations gave repeated full-amplitude translocations, whereas higher frequency pulses gave translocations with reduced amplitude, indicating that the system failed to reset completely. Deterministic and stochastic mathematical models predicted how negative feedback loops might regulate both system resetting and cellular heterogeneity. Altering the stimulation interval gave different patterns of NF-κB-dependent gene expression, supporting a functional role for oscillation frequency. The causes of cell-to-cell variation and the possible functions of these processes in cells and tissues are discussed. The NF-κB system is just one of a number of known biological oscillators that include calcium signalling, transcription cycles, p53, the segmentation clock, the circadian clock, the cell cycle and seasonal rhythms. The way such cycles are integrated could be part of the answer as to how organisms achieve complexity while retaining the robustness of cellular decision-making processes.
Cross-talk in transcription, splicing and chromatin: who makes the first call?
Authors: Alexander Ross , Beggs Jean D.
Published: September 2010

The complex processes of mRNA transcription and splicing were traditionally studied in isolation. In vitro studies showed that splicing could occur independently of transcription and the perceived wisdom was that, to a large extent, it probably did. However, there is now abundant evidence for functional interactions between transcription and splicing, with important consequences for splicing regulation. In the present paper, we summarize the evidence that transcription affects splicing and vice versa, and the more recent indications of epigenetic effects on splicing, through chromatin modifications. We end by discussing the potential for a systems biology approach to obtain better insight into how these processes affect each other.
Adaptation and control circuits in bacterial chemotaxis
Authors: Roberts Mark A.J. , Papachristodoulou Antonis , Armitage Judith P.
Published: September 2010

Bacteria are capable of sensing and responding to changes in their environment. One of the ways they do this is via chemotaxis, regulating swimming behaviour. The chemotaxis pathway senses chemoattractant gradients and uses a feedback loop to change the bacterial swimming pattern; this feedback loop differs in detail between species. In the present article, we summarize the current understanding of the regulatory mechanisms in three species and how these pathways can be viewed and analysed through the ideas of feedback control systems engineering.
Systems biology of the metabolism of Mycobacterium tuberculosis
Authors: Beste Dany J.V. , McFadden Johnjoe
Published: September 2010

Despite decades of research, many aspects of the biology of Mycobacterium tuberculosis remain unclear, and this is reflected in the antiquated tools available to treat and prevent tuberculosis and consequently this disease remains a serious public health problem. Important discoveries linking the metabolism of M. tuberculosis and pathogenesis has renewed interest in this area of research. Previous experimental studies were limited to the analysis of individual genes or enzymes, whereas recent advances in computational systems biology and high-throughput experimental technologies now allows metabolism to be studied on a genome scale. In the present article, we discuss the progress being made in applying system-level approaches to study the metabolism of this important pathogen.
Modelling the effects of inhibitors of guanine nucleotide synthesis: implications for studies of cellular differentiation pathways
Authors: Thomas Geraint M.H.
Published: September 2010

Mizoribine induces the differentiation of promyelocytes by an unknown mechanism that relies on compromised guanine nucleotide synthesis. I have found that mizoribine also perturbs adenosine nucleotide levels in HL-60 promyelocytes, particularly ATP. To reconcile these observations with the known actions of mizoribine I have adapted an existing model of human purine metabolism composed as an S-system familiar from Biochemical Systems Theory. Mizoribine's actions were then simulated and compared with experimental data.
Correction of radiolabel pulse–chase data by a mathematical model: application to mitochondrial turnover studies
Authors: Miwa Satomi , Lawless Conor , von Zglinicki Thomas
Published: September 2010

Metabolic labelling pulse–chase experiments are important means to study molecular turnover rates. However, the inherent problem associated with the method is precursor re-utilization, which can cause a significant overestimation of the actual rates of molecular degradation. In published studies on mitochondrial degradation, this problem has led to widely differing results. Practically, the extra information required to correct these errors is not easy to obtain. Using an example of a mitochondrial protein degradation study with NaH14CO3 as the precursor label, we explain the limitations of the method and our approaches to mathematical correction. A dynamic model, including error, used the full power of the data and resulted in sensitive and specific distributed parameter estimates, helping to reduce numbers of experimental animals. This example has important implications not only for similar pulse–chase experiments, but also in a more general context where comparable types of data are generated.
Structural insights into chondroitin sulfate binding in pregnancy-associated malaria
Authors: Khunrae Pongsak , Higgins Matthew K.
Published: September 2010

Malaria during pregnancy is caused when parasite-infected erythrocytes accumulate within the placenta through interactions between the VAR2CSA protein on the infected erythrocyte surface and placental CSPGs (chondroitin sulfate proteoglycans). This interaction is the major target for therapeutics to treat or prevent pregnancy-associated malaria. Here we review the structural characterization of CSPG-binding DBL (Duffy-binding like) domains from VAR2CSA and summarize the growing evidence that the exquisite ligand specificity of VAR2CSA results from the adoption of higher-order architecture in which these domains fold together to form a ligand-binding pocket.