@article{12199, abstract = {The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.}, author = {Feng, Xiaoqi and Dickinson, Hugh G.}, issn = {1477-9129}, journal = {Development}, keywords = {Developmental Biology, Molecular Biology, Anther Tapetum, Arabidopsis, Cell Fate Establishment, EMS1, Reproductive Cell Lineage}, number = {14}, pages = {2409--2416}, publisher = {The Company of Biologists}, title = {{Tapetal cell fate, lineage and proliferation in the Arabidopsis anther}}, doi = {10.1242/dev.049320}, volume = {137}, year = {2010}, } @article{12200, abstract = {Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution.}, author = {Feng, Xiaoqi and Dickinson, Hugh G.}, issn = {0300-5127}, journal = {Biochemical Society Transactions}, keywords = {Biochemistry, Anther Development, Arabidopsis, Cell Fate, Microsporangium, Polarity, Receptor Kinase}, number = {2}, pages = {571--576}, publisher = {Portland Press Ltd.}, title = {{Cell–cell interactions during patterning of the Arabidopsis anther}}, doi = {10.1042/bst0380571}, volume = {38}, year = {2010}, } @article{12653, abstract = {Daily streamflow from stations close to five Swiss glaciers is analyzed for trends with the Mann-Kendall test. We consider a common period of record (1974–2004) and longer periods based on data availability. The trend statistical significance is tested on annual and seasonal bases. We also examine changes in precipitation, temperature, and snow cover characteristics. Highly glacierized basins show statistically significant positive trends in annual streamflow caused by increasing streamflow in spring and summer. Trends are more numerous and stronger at lower and mid than at the upper quantiles. The basin characterized by lower glacier coverage, conversely, does not exhibit consistently statistically significant trends. Changes in precipitation are not sufficient to explain the observed streamflow trends. Air temperature sees an increase in mean, minimum, and maximum values at all sites. Variations in the seasonal snow accumulation and ablation process are evident. Solid precipitation is decreasing at all sites and trends may be due to a shift from snowfall into rainfall. Mean snow depth is also decreasing, and its duration is getting shorter because of a decrease in solid precipitation and enhanced melting. Trend magnitude attenuates with longer time series. Contrasting trends are detected for different subperiods in the last 70 years: statistically significant negative trends are observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast with the results for the common period. These trends are explained by different rates of ice volume changes, and the sign of trends is clearly related to phases of positive or negative glacier mass balance.}, author = {Pellicciotti, Francesca and Bauder, A. and Parola, M.}, issn = {1944-7973}, journal = {Water Resources Research}, keywords = {Water Science and Technology}, number = {10}, publisher = {American Geophysical Union}, title = {{Effect of glaciers on streamflow trends in the Swiss Alps}}, doi = {10.1029/2009wr009039}, volume = {46}, year = {2010}, } @article{1300, abstract = {Motion vision is a major function of all visual systems, yet the underlying neural mechanisms and circuits are still elusive. In the lamina, the first optic neuropile of Drosophila melanogaster, photoreceptor signals split into five parallel pathways, L1-L5. Here we examine how these pathways contribute to visual motion detection by combining genetic block and reconstitution of neural activity in different lamina cell types with whole-cell recordings from downstream motion-sensitive neurons. We find reduced responses to moving gratings if L1 or L2 is blocked; however, reconstitution of photoreceptor input to only L1 or L2 results in wild-type responses. Thus, the first experiment indicates the necessity of both pathways, whereas the second indicates sufficiency of each single pathway. This contradiction can be explained by electrical coupling between L1 and L2, allowing for activation of both pathways even when only one of them receives photoreceptor input. A fundamental difference between the L1 pathway and the L2 pathway is uncovered when blocking L1 or L2 output while presenting moving edges of positive (ON) or negative (OFF) contrast polarity: blocking L1 eliminates the response to moving ON edges, whereas blocking L2 eliminates the response to moving OFF edges. Thus, similar to the segregation of photoreceptor signals in ON and OFF bipolar cell pathways in the vertebrate retina, photoreceptor signals segregate into ON-L1 and OFF-L2 channels in the lamina of Drosophila.}, author = {Maximilian Jösch and Schnell, Bettina and Raghu, Shamprasad V and Reiff, Dierk F and Borst, Alexander}, journal = {Nature}, number = {7321}, pages = {300 -- 304}, publisher = {Nature Publishing Group}, title = {{ON and off pathways in Drosophila motion vision}}, doi = {10.1038/nature09545}, volume = {468}, year = {2010}, } @article{1301, abstract = {Motion vision is essential for navigating through the environment. Due to its genetic amenability, the fruit fly Drosophila has been serving for a lengthy period as a model organism for studying optomotor behavior as elicited by large-field horizontal motion. However, the neurons underlying the control of this behavior have not been studied in Drosophila so far. Here we report the first whole cell recordings from three cells of the horizontal system (HSN, HSE, and HSS) in the lobula plate of Drosophila. All three HS cells are tuned to large-field horizontal motion in a direction-selective way; they become excited by front-to-back motion and inhibited by back-to-front motion in the ipsilateral field of view. The response properties of HS cells such as contrast and velocity dependence are in accordance with the correlation-type model of motion detection. Neurobiotin injection suggests extensive coupling among ipsilateral HS cells and additional coupling to tangential cells that have their dendrites in the contralateral hemisphere of the brain. This connectivity scheme accounts for the complex layout of their receptive fields and explains their sensitivity both to ipsilateral and to contralateral motion. Thus the main response properties of Drosophila HS cells are strikingly similar to the responses of their counterparts in the blowfly Calliphora, although we found substantial differences with respect to their dendritic structure and connectivity. This long-awaited functional characterization of HS cells in Drosophila provides the basis for the future dissection of optomotor behavior and the underlying neural circuitry by combining genetics, physiology, and behavior.}, author = {Schnell, Bettina and Jösch, Maximilian A and Förstner, Friedrich and Raghu, Shamprasad and Otsuna, Hideo and Ito, Kei and Borst, Alexander and Reiff, Dierk}, issn = {1522-1598}, journal = {Journal of Neurophysiology}, number = {3}, pages = {1646 -- 1657}, publisher = {American Physiological Society}, title = {{Processing of horizontal optic flow in three visual interneurons of the Drosophila brain}}, doi = {10.1152/jn.00950.2009}, volume = {103}, year = {2010}, } @article{8472, abstract = {Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins.}, author = {Schanda, Paul and Meier, Beat H. and Ernst, Matthias}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {45}, pages = {15957--15967}, publisher = {American Chemical Society}, title = {{Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy}}, doi = {10.1021/ja100726a}, volume = {132}, year = {2010}, } @article{8473, abstract = {β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant.}, author = {Corazza, Alessandra and Rennella, Enrico and Schanda, Paul and Mimmi, Maria Chiara and Cutuil, Thomas and Raimondi, Sara and Giorgetti, Sofia and Fogolari, Federico and Viglino, Paolo and Frydman, Lucio and Gal, Maayan and Bellotti, Vittorio and Brutscher, Bernhard and Esposito, Gennaro}, issn = {0021-9258}, journal = {Journal of Biological Chemistry}, keywords = {Cell Biology, Biochemistry, Molecular Biology}, number = {8}, pages = {5827--5835}, publisher = {American Society for Biochemistry & Molecular Biology}, title = {{Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR}}, doi = {10.1074/jbc.m109.061168}, volume = {285}, year = {2010}, } @inbook{8506, author = {Hunt, Brian R. and Kaloshin, Vadim}, booktitle = {Handbook of Dynamical Systems}, isbn = {9780444531414}, issn = {1874-575X}, pages = {43--87}, publisher = {Elsevier}, title = {{Prevalence}}, doi = {10.1016/s1874-575x(10)00310-3}, volume = {3}, year = {2010}, } @inproceedings{8507, abstract = {We study a Cr nearly integrable Hamiltonian system defined on 𝕋3 × ℝ3. Let and µΣ1 be the restriction of Lebesgue measure on 𝕋3 × ℝ3 to ∑. We prove there is a perturbation , and an orbit (q(t), p(t)): ℝ → 𝕋3 × ℝ3 of the Hamiltonian equation such that .}, author = {Kaloshin, Vadim and ZHANG, KE and ZHENG, YONG}, booktitle = {XVIth International Congress on Mathematical Physics}, isbn = {9789814304627}, location = {Prague, Czech Republic}, pages = {314--322}, publisher = {World Scientific}, title = {{Almost dense orbit on energy surface}}, doi = {10.1142/9789814304634_0017}, year = {2010}, } @article{857, abstract = {The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.}, author = {Povolotskaya, Inna and Fyodor Kondrashov}, journal = {Nature}, number = {7300}, pages = {922 -- 926}, publisher = {Nature Publishing Group}, title = {{Sequence space and the ongoing expansion of the protein universe}}, doi = {10.1038/nature09105}, volume = {465}, year = {2010}, } @article{862, abstract = {A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.}, author = {Meer, Margarita V and Kondrashov, Alexey S and Artzy-Randrup, Yael and Fyodor Kondrashov}, journal = {Nature}, number = {7286}, pages = {279 -- 282}, publisher = {Nature Publishing Group}, title = {{Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness}}, doi = {10.1038/nature08691}, volume = {464}, year = {2010}, } @article{872, abstract = {The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.}, author = {Fyodor Kondrashov and Kondrashov, Alexey S}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1544}, pages = {1169 -- 1176}, publisher = {Royal Society, The}, title = {{Measurements of spontaneous rates of mutations in the recent past and the near future}}, doi = {10.1098/rstb.2009.0286}, volume = {365}, year = {2010}, } @article{884, abstract = {Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.}, author = {Kondrashov, Alexey S and Povolotskaya, Inna and Ivankov, Dmitry N and Fyodor Kondrashov}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Rate of sequence divergence under constant selection}}, doi = {10.1186/1745-6150-5-5}, volume = {5}, year = {2010}, } @article{89, abstract = {We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.}, author = {Wright, Ian and Higginbotham, Andrew P and Baker, Shenda and Donnelly, Tom}, journal = {ACS Applied Materials and Interfaces}, number = {8}, pages = {2360 -- 2364}, publisher = {American Chemical Society}, title = {{Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution}}, doi = {10.1021/am100375w}, volume = {2}, year = {2010}, } @article{891, abstract = {Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.}, author = {Innan, Hideki and Fyodor Kondrashov}, journal = {Nature Reviews Genetics}, number = {2}, pages = {97 -- 108}, publisher = {Nature Publishing Group}, title = {{The evolution of gene duplications: Classifying and distinguishing between models}}, doi = {10.1038/nrg2689}, volume = {11}, year = {2010}, } @article{901, abstract = {Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).}, author = {Breen, Michael S and Fyodor Kondrashov}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Mitochondrial pathogenic mutations are population-specific}}, doi = {10.1186/1745-6150-5-68}, volume = {5}, year = {2010}, } @article{9012, abstract = {In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.}, author = {Palacci, Jérémie A and Abécassis, Benjamin and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Colloidal motility and pattern formation under rectified diffusiophoresis}}, doi = {10.1103/physrevlett.104.138302}, volume = {104}, year = {2010}, } @article{9013, abstract = {In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.}, author = {Palacci, Jérémie A and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society }, title = {{Sedimentation and effective temperature of active colloidal suspensions}}, doi = {10.1103/physrevlett.105.088304}, volume = {105}, year = {2010}, } @article{9145, abstract = {We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs. As for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well. As for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies. We carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve.}, author = {Canuto, V.M. and Howard, A.M. and Cheng, Y. and Muller, Caroline J and Leboissetier, A. and Jayne, S.R.}, issn = {1463-5003}, journal = {Ocean Modelling}, keywords = {Computer Science (miscellaneous), Geotechnical Engineering and Engineering Geology, Atmospheric Science, Oceanography}, number = {3-4}, pages = {70--91}, publisher = {Elsevier}, title = {{Ocean turbulence, III: New GISS vertical mixing scheme}}, doi = {10.1016/j.ocemod.2010.04.006}, volume = {34}, year = {2010}, } @article{9146, abstract = {The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude. Clausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1. Surface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.}, author = {O’Gorman, P A and Muller, Caroline J}, issn = {1748-9326}, journal = {Environmental Research Letters}, keywords = {Renewable Energy, Sustainability and the Environment, Public Health, Environmental and Occupational Health, General Environmental Science}, number = {2}, publisher = {IOP Publishing}, title = {{How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?}}, doi = {10.1088/1748-9326/5/2/025207}, volume = {5}, year = {2010}, }