bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical Investigation of Flow Past a Prolate Spheroid
Authors: Constantinescu George S. , Pasinato Hugo , Wang You-Qin , Forsythe James R. , Squires Kyle D.
Published: December 2002

The flowfield around a 6:1 prolate spheroid at angle of attack is predicted using solutions of the Reynolds-averaged Navier-Stokes (RANS) equations and detached-eddy simulation (DES). The calculations were performed at a Reynolds number of 4.2×106, the flow is tripped at x/L=0.2, and the angle of attack α is varied from 10 to 20 deg. RANS calculations are performed using the Spalart-Allmaras one-equation model. The influence of corrections to the Spalart-Allmaras model accounting for streamline curvature and a nonlinear constitutive relation are also considered. DES predictions are evaluated against experimental measurements, RANS results, as well as calculations performed without an explicit turbulence model. In general, flowfield predictions of the mean properties from the RANS and DES are similar. Predictions of the axial pressure distribution along the symmetry plane agree well with measured values for 10 deg angle of attack. Changes in the separation characteristics in the aft region alter the axial pressure gradient as the angle of attack increases to 20 deg. With downstream evolution, the wall-flow turning angle becomes more positive, an effect also predicted by the models though the peak-to-peak variation is less than that measured. Azimuthal skin friction variations show the same general trend as the measurements, with a weak minima identifying separation. Corrections for streamline curvature improve prediction of the pressure coefficient in the separated region on the leeward side of the spheroid. While initiated further along the spheroid compared to experimental measurements, predictions of primary and secondary separation agree reasonably well with measured values. Calculations without an explicit turbulence model predict pressure and skin-friction distributions in substantial disagreement with measurements.
Detached-Eddy Simulation With Compressibility Corrections Applied to a Supersonic Axisymmetric Base Flow
Authors: Forsythe James R. , Hoffmann Klaus A. , Cummings Russell M. , Squires Kyle D.
Published: December 2002

Detached-eddy simulation is applied to an axisymmetric base flow at supersonic conditions. Detached-eddy simulation is a hybrid approach to modeling turbulence that combines the best features of the Reynolds-averaged Navier-Stokes and large-eddy simulation approaches. In the Reynolds-averaged mode, the model is currently based on either the Spalart-Allmaras turbulence model or Menter’s shear stress transport model; in the large-eddy simulation mode, it is based on the Smagorinski subgrid scale model. The intended application of detached-eddy simulation is the treatment of massively separated, high-Reynolds number flows over complex configurations (entire aircraft, automobiles, etc.). Because of the intented future application of the methods to complex configurations, Cobalt, an unstructured grid Navier-Stokes solver, is used. The current work incorporates compressible shear layer corrections in both the Spalart-Allmaras and shear stress transport-based detached-eddy simulation models. The effect of these corrections on both detached-eddy simulation and Reynolds-averaged Navier-Stokes models is examined, and comparisons are made to the experiments of Herrin and Dutton. Solutions are obtained on several grids—both structured and unstructured—to test the sensitivity of the models and code to grid refinement and grid type. The results show that predictions of base flows using detached-eddy simulation compare very well with available experimental data, including turbulence quantities in the wake of the axisymmetric body.
Computing Blunt Body Flows on Coarse Grids Using Vorticity Confinement
Authors: Fan M. , Wenren Y. , Dietz W. , Xiao M. , Steinhoff J.
Published: December 2002

Over the last few years, a new flow computational methodology, vorticity confinement, has been shown to be very effective in treating concentrated vortical regions. These include thin vortex filaments which can be numerically convected over arbitrary distances on coarse Eulerian grids, while requiring only ∼2 grid cells across their cross section. They also include boundary layers on surfaces “immersed” in nonconforming uniform Cartesian grids, with no requirement for grid refinement or complex logic near the surface. In this paper we use vorticity confinement to treat flow over blunt bodies, including attached and separating boundary layers, and resulting turbulent wakes. In the wake it serves as a new, simple effective large-eddy simulation (LES). The same basic idea is applied to all of these features: At the smallest scales (∼2 cells) the vortical structures are captured and treated, effectively, as solitary waves that are solutions of nonlinear discrete equations on the grid. The method does not attempt to accurately discretize the Euler/Navier-Stokes partial differential equations (pde’s) for these small scales, but, rather, serves as an implicit, nonlinear model of the structures, directly on the grid. The method also allows the boundary layer to be effectively “captured.” In the turbulent wake, where there are many scales, small structures represent an effective small scale energy sink. However, they do not have the unphysical spreading due to numerical diffusion at these scales, which is present in conventional computational methods. The basic modeling idea is similar to that used in shock capturing, where intrinsically discrete equations are satisfied in thin, modeled regions. It is argued that, for realistic high Reynolds number flows, this direct, grid-based modeling approach is much more effective than first formulating model pde’s for the small scale, turbulent vortical regions and then discretizing them. Results are presented for three-dimensional flows over round and square cylinders and a realistic helicopter landing ship. Comparisons with experimental data are given. Finally, a new simpler formulation of vorticity confinement is given together with a related formulation for confinement of passive scalar fields.
Mixed Convection From a Cylinder With Low Conductivity Baffles in Cross-Flow
Authors: Abu-Hijleh Bassam A/K
Published: December 2002

The problem of laminar mixed convection from an isothermal cylinder with low conductivity baffles in cross flow was solved numerically. The average Nusselt number was calculated at different combinations of number of baffles, baffle height, Reynolds number, and buoyancy parameter. The reduction in the Nusselt number is as much as 75 percent. When using a small number of baffles at low values of buoyancy parameter, an odd number of baffles reduced the Nusselt number more than an even number of baffles, especially at high values of Reynolds number. This is not the case at high values of buoyancy parameter. There is an optimal baffle height, Reynolds number dependent, for maximum heat transfer reduction beyond which an increase in baffle height does not result in further decrease in heat transfer.
Computation of Sub-Micron Thermal Transport Using an Unstructured Finite Volume Method
Authors: Murthy J. Y. , Mathur S. R.
Published: December 2002

An unstructured finite volume scheme is applied to the solution of sub-micron heat conduction problems. The phonon Boltzmann transport equation (BTE) in the relaxation time approximation is considered. The similarity between the radiative transfer equation (RTE) and the BTE is exploited in developing a finite volume scheme for the BTE. The spatial domain is divided into arbitrary unstructured polyhedra, the angular domain into control angles, and the frequency domain into frequency bands, and conservation equations for phonon energy are written. The unsteady wave propagation term, not usually present in thermal radiation problems, is differentiated using a fully implicit scheme. A sequential multigrid scheme is applied to solve the nominally linear set. Isotropic scattering due to a variety of mechanisms such as impurity and Umklapp scattering is considered. The numerical scheme is applied to a variety of sub-micron conduction problems, both unsteady and steady. Favorable comparison is found with the published literature and with exact solutions.
Prediction of Critical Heat Flux for Convective Boiling of Saturated Water Jet Impinging on the Stagnation Zone
Authors: Liu Zhen-Hua , Zhu Qun-Zhi
Published: December 2002

A theoretical analysis and an experimental investigation were carried out for predicting the critical heat flux (CHF) of convective boiling for a round saturated water jet impinging on the jet stagnation zone. The model of the maximum liquid subfilm thickness based on the Helmholtz instability is used to derive a semi-theoretical equation and the correlation factor was determined from the experimental data. Finally, a semi-theoretical correlation was proposed for predicting CHF of convective boiling for saturated water jet impinging on the jet stagnation zone.
Measurement of the Heat Transfer Coefficient for Mercury Flowing in a Narrow Channel
Authors: Crye J. M. , Ruggles A. E. , Pointer W. D. , Felde D. K. , Jallouk P. A. , McFee M. T. , Wendel M. W. , Yoder, G. L.
Published: December 2002

The heat transfer coefficient is inferred from measurements for mercury flowing in a channel of cross-section 2 mm×40 mm with flow velocities from 1 m/s to 4 m/s and heat fluxes from 192 kW/m2 to 1.14 MW/m2. Mercury bulk temperatures vary from 67°C to 143°C. Inferred heat transfer coefficients agree with open literature tube data when compared on a Nusselt versus. Peclet number plot, with Nusselt numbers examined from 8 to 17 and Peclet numbers examined from 790 to 3070.
Composition and Formation of Intercellular Junctions in Epithelial Cells
Authors: Knust Elisabeth , Bossinger Olaf
Published: December 2002

The polarized nature of epithelial cells is manifested by the nonrandom partitioning of organelles within the cells, the concentration of intercellular junctions at one pole, and the asymmetric distribution of proteins and lipids within the plasma membrane. These features allow epithelia to fulfill their specific tasks, such as targeted uptake and secretion of molecules and the segregation of different tissue compartments. The accessibility of
Drosophila melanogaster
and
Caenorhabditis elegans
to genetic and cell biological analyses, combined with the study of mammalian cells in culture, provides an ideal basis for understanding the mechanisms that control the establishment and maintenance of epithelial cell polarity and tissue integrity. Here, we focus on some of the best-studied junctions and membrane-associated protein complexes and their relation to cell polarity. Comparisons between fly, worm, and vertebrate epithelia reveal marked similarities with respect to the molecules used, and pronounced differences in the organization of the junctions themselves.
Anterior-Posterior Polarity in
C. elegans
and
Drosophila
--PARallels and Differences
Authors: Pellettieri Jason , Seydoux Geraldine
Published: December 2002

The eggs of
Caenorhabditis elegans
and
Drosophila
bear little similarity to each other, yet both depend on the
par
genes for control of anterior-posterior polarity. Here we explore possible common roles for the
par
genes (
par
s) in converting transient asymmetries into stably polarized axes. Although clear mechanistic parallels remain to be established,
par
-dependent regulation of microtubule dynamics and protein stability emerge as common themes.
Generating and Exploiting Polarity in Bacteria
Authors: Shapiro Lucy , McAdams Harley H. , Losick Richard
Published: December 2002

Bacteria are often highly polarized, exhibiting specialized structures at or near the ends of the cell. Among such structures are actin-organizing centers, which mediate the movement of certain pathogenic bacteria within the cytoplasm of an animal host cell; organized arrays of membrane receptors, which govern chemosensory behavior in swimming bacteria; and asymmetrically positioned septa, which generate specialized progeny in differentiating bacteria. This polarization is orchestrated by complex and dynamic changes in the subcellular localization of signal transduction and cytoskeleton proteins as well as of specific regions of the chromosome. Recent work has provided information on how dynamic subcellular localization occurs and how it is exploited by the bacterial cell.

The main task of a bacterial cell is to survive and duplicate itself. The bacterium must replicate its genetic material and divide at the correct site in the cell and at the correct time in the cell cycle with high precision. Each kind of bacterium also executes its own strategy to find nutrients in its habitat and to cope with conditions of stress from its environment. This involves moving toward food, adapting to environmental extremes, and, in many cases, entering and exploiting a eukaryotic host. These activities often involve processes that take place at or near the poles of the cell. Here we explore some of the schemes bacteria use to orchestrate dynamic changes at their poles and how these polar events execute cellular functions.

In spite of their small size, bacteria have a remarkably complex internal organization and external architecture. Bacterial cells are inherently asymmetric, some more obviously so than others. The most easily recognized asymmetries involve surface structures, e.g., flagella, pili, and stalks that are preferentially assembled at one pole by many bacteria. “New” poles generated at the cell division plane differ from old poles from the previous round of cell division. Even in
Escherichia coli
, which is generally thought to be symmetrical, old poles are more static than new poles with respect to cell wall assembly (
1
), and they differ in the deposition of phospholipid domains (
2
). There are many instances of differential polar functions; among these is the preferential use of old poles when attaching to host cells as in the interaction of
Bradyrhizobium
with plant root hairs (
3
) or the polar pili-mediated attachment of the
Pseudomonas aeruginosa
pathogen to tracheal epithelia (
4
). An unusual polar organelle that mediates directed motility on solid surfaces is found in the nonpathogenic bacterium
Myxococcus xanthus
. The gliding motility of this bacterium is propelled by a nozzle-like structure that squirts a polysaccharide-containing slime from the pole of the cell (
5
). Interestingly,
M. xanthus
, which has nozzles at both poles, can reverse direction by closing one nozzle and opening the other in response to end-to-end interactions between cells.
Molecular Mechanisms of Axon Guidance
Authors: Dickson Barry J.
Published: December 2002

Axons are guided along specific pathways by attractive and repulsive cues in the extracellular environment. Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules, including netrins, Slits, semaphorins, and ephrins. Guidance cues steer axons by regulating cytoskeletal dynamics in the growth cone through signaling pathways that are still only poorly understood. Elaborate regulatory mechanisms ensure that a given cue elicits the right response from the right axons at the right time but is otherwise ignored. With such regulatory mechanisms in place, a relatively small number of guidance factors can be used to generate intricate patterns of neuronal wiring.
Mitogen-Activated Protein Kinase Pathways Mediated by ERK, JNK, and p38 Protein Kinases
Authors: Johnson Gary L. , Lapadat Razvan
Published: December 2002

Multicellular organisms have three well-characterized subfamilies of mitogen-activated protein kinases (MAPKs) that control a vast array of physiological processes. These enzymes are regulated by a characteristic phosphorelay system in which a series of three protein kinases phosphorylate and activate one another. The extracellular signal–regulated kinases (ERKs) function in the control of cell division, and inhibitors of these enzymes are being explored as anticancer agents. The c-Jun amino-terminal kinases (JNKs) are critical regulators of transcription, and JNK inhibitors may be effective in control of rheumatoid arthritis. The p38 MAPKs are activated by inflammatory cytokines and environmental stresses and may contribute to diseases like asthma and autoimmunity.
Inhibition of Excess Nodal Signaling During Mouse Gastrulation by the Transcriptional Corepressor DRAP1
Authors: Iratni Rabah , Yan Yu-Ting , Chen Canhe , Ding Jixiang , Zhang Yi , Price Sandy M. , Reinberg Danny , Shen Michael M.
Published: December 2002

The formation and patterning of mesoderm during mammalian gastrulation require the activity of Nodal, a secreted mesoderm-inducing factor of the transforming growth factor–β (TGF-β) family. Here we show that the transcriptional corepressor DRAP1 has a very specific role in regulation of
Nodal
activity during mouse embryogenesis. We find that loss of
Drap1
leads to severe gastrulation defects that are consistent with increased expression of
Nodal
and can be partially suppressed by
Nodal
heterozygosity. Biochemical studies indicate that DRAP1 interacts with and inhibits DNA binding by the winged-helix transcription factor FoxH1 (FAST), a critical component of a positive feedback loop for Nodal activity. We propose that DRAP1 limits the spread of a morphogenetic signal by down-modulating the response to the Nodal autoregulatory loop.
Environmental Effects of Large Impacts on Mars
Authors: Segura Teresa L. , Toon Owen B. , Colaprete Anthony , Zahnle Kevin
Published: December 2002

The martian valley networks formed near the end of the period of heavy bombardment of the inner solar system, about 3.5 billion years ago. The largest impacts produced global blankets of very hot ejecta, ranging in thickness from meters to hundreds of meters. Our simulations indicated that the ejecta warmed the surface, keeping it above the freezing point of water for periods ranging from decades to millennia, depending on impactor size, and caused shallow subsurface or polar ice to evaporate or melt. Large impacts also injected steam into the atmosphere from the craters or from water innate to the impactors. From all sources, a typical 100-, 200-, or 250-kilometers asteroid injected about 2, 9, or 16 meters, respectively, of precipitable water into the atmosphere, which eventually rained out at a rate of about 2 meters per year. The rains from a large impact formed rivers and contributed to recharging aquifers.
Signaling of Rat Frizzled-2 Through Phosphodiesterase and Cyclic GMP
Authors: Ahumada Adriana , Slusarski Diane C. , Liu Xunxian , Moon Randall T. , Malbon Craig C. , Wang Hsien-yu
Published: December 2002

The Frizzled
-
2 receptor (Rfz2) from rat binds Wnt proteins and can signal by activating calcium release from intracellular stores. We show that wild-type Rfz2 and a chimeric receptor consisting of the extracellular and transmembrane portions of the β
2
-adrenergic receptor with cytoplasmic domains of Rfz2 also signaled through modulation of cyclic guanosine 3′,5′-monophosphate (cGMP). Activation of either receptor led to a decline in the intracellular concentration of cGMP, a process that was inhibited in cells treated with pertussis toxin, reduced by suppression of the expression of the heterotrimeric GTP–binding protein (G protein) transducin, and suppressed through inhibition of cGMP-specific phosphodiesterase (PDE) activity. Moreover, PDE inhibitors blocked Rfz2-induced calcium transients in zebrafish embryos. Thus, Frizzled
-
2 appears to couple to PDEs and calcium transients through G proteins.
Regulation of Spermatogenesis by Testis-Specific, Cytoplasmic Poly(A) Polymerase TPAP
Authors: Kashiwabara Shin-ichi , Noguchi Junko , Zhuang Tiangang , Ohmura Ko , Honda Arata , Sugiura Shin , Miyamoto Kiyoko , Takahashi Satoru , Inoue Kimiko , Ogura Atsuo , Baba Tadashi
Published: December 2002

Spermatogenesis is a highly specialized process of cellular differentiation to produce spermatozoa. This differentiation process accompanies morphological changes that are controlled by a number of genes expressed in a stage-specific manner during spermatogenesis. Here we show that in mice, the absence of a testis-specific, cytoplasmic polyadenylate [poly(A)] polymerase, TPAP, results in the arrest of spermiogenesis. TPAP-deficient mice display impaired expression of haploid-specific genes that are required for the morphogenesis of germ cells. The TPAP deficiency also causes incomplete elongation of poly(A) tails of particular transcription factor messenger RNAs. Although the overall cellular level of the transcription factor TAF10 is unaffected, TAF10 is insufficiently transported into the nucleus of germ cells. We propose that TPAP governs germ cell morphogenesis by modulating specific transcription factors at posttranscriptional and posttranslational levels.
A General Model for Designing Networks of Marine Reserves
Authors: Sala Enric , Aburto-Oropeza Octavio , Paredes Gustavo , Parra Ivan , Barrera Juan C. , Dayton Paul K.
Published: December 2002

There is debate concerning the most effective conservation of marine biodiversity, especially regarding the appropriate location, size, and connectivity of marine reserves. We describe a means of establishing marine reserve networks by using optimization algorithms and multiple levels of information on biodiversity, ecological processes (spawning, recruitment, and larval connectivity), and socioeconomic factors in the Gulf of California. A network covering 40% of rocky reef habitat can fulfill many conservation goals while reducing social conflict. This quantitative approach provides a powerful tool for decision-makers tasked with siting marine reserves.
Grassland Responses to Global Environmental Changes Suppressed by Elevated CO
2
Authors: Shaw M. Rebecca , Zavaleta Erika S. , Chiariello Nona R. , Cleland Elsa E. , Mooney Harold A. , Field Christopher B.
Published: December 2002

Simulated global changes, including warming, increased precipitation, and nitrogen deposition, alone and in concert, increased net primary production (NPP) in the third year of ecosystem-scale manipulations in a California annual grassland. Elevated carbon dioxide also increased NPP, but only as a single-factor treatment. Across all multifactor manipulations, elevated carbon dioxide suppressed root allocation, decreasing the positive effects of increased temperature, precipitation, and nitrogen deposition on NPP. The NPP responses to interacting global changes differed greatly from simple combinations of single-factor responses. These findings indicate the importance of a multifactor experimental approach to understanding ecosystem responses to global change.
The Protein Kinase Complement of the Human Genome
Authors: Manning G. , Whyte D. B. , Martinez R. , Hunter T. , Sudarsanam S.
Published: December 2002

We have catalogued the protein kinase complement of the human genome (the “kinome”) using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.
Resetting the Circadian Clock by Social Experience in
Drosophila melanogaster
Authors: Levine Joel D. , Funes Pablo , Dowse Harold B. , Hall Jeffrey C.
Published: December 2002

Circadian clocks are influenced by social interactions in a variety of species, but little is known about the sensory mechanisms underlying these effects. We investigated whether social cues could reset circadian rhythms in
Drosophila melanogaster
by addressing two questions: Is there a social influence on circadian timing? If so, then how is that influence communicated? The experiments show that in a social context
Drosophila
transmit and receive cues that influence circadian time and that these cues are likely olfactory.
Regulation of Oceanic Silicon and Carbon Preservation by Temperature Control on Bacteria
Authors: Bidle Kay D. , Manganelli Maura , Azam Farooq
Published: December 2002

We demonstrated in laboratory experiments that temperature control of marine bacteria action on diatoms strongly influences the coupling of biogenic silica and organic carbon preservation. Low temperature intensified the selective regeneration of organic matter by marine bacteria as the silicon:carbon preservation ratio gradually increased from ∼1 at 33°C to ∼6 at –1.8°C. Temperature control of bacteria-mediated selective preservation of silicon versus carbon should help to interpret and model the variable coupling of silicon and carbon sinking fluxes and the spatial patterns of opal accumulation in oceanic systems with different temperature regimes.
Functional Neuroimaging of Speech Perception in Infants
Authors: Dehaene-Lambertz Ghislaine , Dehaene Stanislas , Hertz-Pannier Lucie
Published: December 2002

Human infants begin to acquire their native language in the first months of life. To determine which brain regions support language processing at this young age, we measured with functional magnetic resonance imaging the brain activity evoked by normal and reversed speech in awake and sleeping 3-month-old infants. Left-lateralized brain regions similar to those of adults, including the superior temporal and angular gyri, were already active in infants. Additional activation in right prefrontal cortex was seen only in awake infants processing normal speech. Thus, precursors of adult cortical language areas are already active in infants, well before the onset of speech production.
A Role for the Protease Falcipain 1 in Host Cell Invasion by the Human Malaria Parasite
Authors: Greenbaum Doron C. , Baruch Amos , Grainger Munira , Bozdech Zbynek , Medzihradszky Katlin F. , Engel Juan , DeRisi Joseph , Holder Anthony A. , Bogyo Matthew
Published: December 2002

Cysteine proteases of
Plasmodium falciparum
are required for survival of the malaria parasite, yet their specific cellular functions remain unclear. We used a chemical proteomic screen with a small-molecule probe to characterize the predominant cysteine proteases throughout the parasite life cycle. Only one protease, falcipain 1, was active during the invasive merozoite stage. Falcipain 1–specific inhibitors, identified by screening of chemical libraries, blocked parasite invasion of host erythrocytes, yet had no effect on normal parasite processes such as hemoglobin degradation. These results demonstrate a specific role for falcipain 1 in host cell invasion and establish a potential new target for antimalarial therapeutics.
Recent Earth Oblateness Variations: Unraveling Climate and Postglacial Rebound Effects
Authors: Dickey Jean O. , Marcus Steven L. , de Viron Olivier , Fukumori Ichiro
Published: December 2002

Earth's dynamic oblateness (
J
2
) has been decreasing due to postglacial rebound (PGR). However,
J
2
began to increase in 1997, indicating a pronounced global-scale mass redistribution within Earth's system. We have determined that the observed increases in
J
2
are caused primarily by a recent surge in subpolar glacial melting and by mass shifts in the Southern, Pacific, and Indian oceans. When these effects are removed, the residual trend in
J
2
(–2.9 x 10
−11
year
−1
) becomes consistent with previous estimates of PGR from satellite and eclipse data. The climatic significance of these rapid shifts in glacial and oceanic mass, however, remains to be investigated.
Ectoderm to Mesoderm Lineage Switching During Axolotl Tail Regeneration
Authors: Echeverri Karen , Tanaka Elly M.
Published: December 2002

Foreign environments may induce adult stem cells to switch lineages and populate multiple tissue types, but whether this mechanism is used for tissue repair remains uncertain. Urodele amphibians can regenerate fully functional, multitissue structures including the limb and tail. To determine whether lineage switching is an integral feature of this regeneration, we followed individual spinal cord cells live during tail regeneration in the axolotl. Spinal cord cells frequently migrate into surrounding tissue to form regenerating muscle and cartilage. Thus, in axolotls, cells switch lineage during a real example of regeneration.
Ancient Roots Forced into Modern Pots
Authors: McClellan James E.
Published: December 2002

Lost Discoveries
. The Ancient Roots of Modern Science --from the Babylonians to the Maya. Dick Teresi. Simon and Schuster, New York, 2002. 463 pp. $27, C$41. ISBN 0-684-83718-8.

Writing for a popular audience, Teresi offers an account of the contributions of non-Western societies to modern science.
Cavitation-Induced Reactions in High-Pressure Carbon Dioxide
Authors: Kuijpers M. W. A. , van Eck D. , Kemmere M. F. , Keurentjes J. T. F.
Published: December 2002

The feasibility of ultrasound-induced in situ radical formation in liquid carbon dioxide was demonstrated. The required threshold pressure for cavitation could be exceeded at a relatively low acoustic intensity, as the high vapor pressure of CO
2
counteracts the hydrostatic pressure. With the use of a dynamic bubble model, the formation of hot spots upon bubble collapse was predicted. Cavitation-induced radical formation was used for the polymerization of methyl methacrylate in CO
2
, yielding high-molecular-weight polymers. These results show that sonochemical reactions can be performed in dense-phase fluids, which allows the environmentally benign CO
2
to replace conventional organic solvents in many reaction systems.
Olmec Origins of Mesoamerican Writing
Authors: Pohl Mary E. D. , Pope Kevin O. , von Nagy Christopher
Published: December 2002

A cylinder seal and carved greenstone plaque bearing glyphs dating to ∼650 B.C. have been uncovered near the Olmec center of La Venta in Tabasco, Mexico. These artifacts, which predate others containing writing, reveal that the key aspects of the Mesoamerican scripts were present in Olmec writing: the combination of pictographic and glyphic elements to represent speech; the use of the sacred 260-day calendar; and the connection between writing, the calendar, and kingship. They imply that Mesoamerican writing originated in the La Venta polity.
Closed-Shell Molecules That Ionize More Readily Than Cesium
Authors: Cotton F. Albert , Gruhn Nadine E. , Gu Jiande , Huang Penglin , Lichtenberger Dennis L. , Murillo Carlos A. , Van Dorn Laura O. , Wilkinson Chad C.
Published: December 2002

We report a class of molecules with extremely low ionization enthalpies, one member of which has been determined to have a gas-phase ionization energy (onset, 3.51 electron volts) lower than that of the cesium atom (which has the lowest gas-phase ionization energy of the elements) or of any other known closed-shell molecule or neutral transient species reported. The molecules are dimetal complexes with the general formula M
2
(hpp)
4
(where M is Cr, Mo, or W, and hpp is the anion of 1,3,4,6,7,8-hexahydro-2
H
-pyrimido[1,2-
a
]pyrimidine), structurally characterized in the solid state, spectroscopically characterized in the gas phase, and modeled with theoretical computations. The low-energy ionization of each molecule corresponds to the removal of an electron from the delta bonding orbital of the quadruple metal-metal bond, and a strong interaction of this orbital with a filled orbital on the hpp ligands largely accounts for the low ionization energies.
Shaping the Vertebrate Body Plan by Polarized Embryonic Cell Movements
Authors: Keller Ray
Published: December 2002

Polarized cell movements shape the major features of the vertebrate body plan during development. The head-to-tail body axis of vertebrates is elongated in embryonic stages by “convergent extension” tissue movements. During these movements cells intercalate between one another transverse to the elongating body axis to form a narrower, longer array. Recent discoveries show that these polarized cell movements are controlled by homologs of genes that control the polarity of epithelial cells in the developing wing and eye of the fruit fly,
Drosophila
.
Wallace in a Colored Spotlight
Authors: Söderqvist Thomas
Published: December 2002

In Darwin's Shadow
. The Life and Science of Alfred Russel Wallace. A Biographical Study on the Psychology of History. Michael Shermer. Oxford University Press, New York, 2002. 442 pp. $35, £25. ISBN 0-19-514830-4.

This account of the life of the coauthor of the theory of natural selection and believer in spiritualism is centered around the question of why some thinkers can break out of the conventional mold while others do not.
Calcium Binding Is Required for Calmodulin Function in
Aspergillus nidulans
Authors: Joseph James D. , Means Anthony R.
Published: December 2002

To explore the structural basis for the essential role of calmodulin (CaM) in
Aspergillus nidulans,
we have compared the biochemical and in vivo properties of
A. nidulans
CaM (AnCaM) with those of heterologous CaMs. Neither
Saccharomyces cerevisiae
CaM (ScCaM) nor a Ca
2+
binding mutant of
A. nidulans
CaM (1234) interacts appreciably with
A. nidulans
CaM binding proteins by an overlay assay or activates two essential CaMKs, CMKA and CMKB. In contrast, although vertebrate CaM (VCaM) binds a spectrum of proteins similar to that for AnCaM, it is unable to fully activate CMKA and CMKB, displaying a higher
K
CaM
and reduced
V
max
for both enzymes. In correlation with the biochemical analysis, neither ScCaM nor 1234 can support
A. nidulans
growth in the absence of the endogenous protein, whereas VCaM only partially complements the absence of wild-type CaM. Analysis of VCaM and AnCaM chimeras demonstrates that amino acid variations in both N- and C-terminal domains contribute to the inability of VCaM to activate CMKB, but differences in the N terminus are largely responsible for the reduced activity towards CMKA. In vivo, the chimeric molecules support growth equivalently, but only to levels intermediate between those of VCaM and AnCaM, suggesting that the reduced ability to activate the CaMKs is not solely responsible for the inability of VCaM to complement the absence of the wild-type protein. Thus, not only is Ca
2+
binding required for CaM function in
A. nidulans,
but the essential in vivo functions of
A. nidulans
CaM are uniquely sensitive to the subtle amino acid variations present in vertebrate CaM.
A Long Terminal Repeat Retrotransposon of Fission Yeast Has Strong Preferences for Specific Sites of Insertion
Authors: Singleton Teresa L. , Levin Henry L.
Published: December 2002

The successful dispersal of transposons depends on the critical balance between the fitness of the host and the ability of the transposon to insert into the host genome. One method transposons may use to avoid the disruption of coding sequences is to target integration into safe havens. We explored the interaction between the long terminal repeat retrotransposon Tf1 and the genome of the yeast
Schizosaccharomyces
pombe
. Using techniques that were specifically designed to detect integration of Tf1 throughout the genome and to avoid bias in this detection, we generated 51 insertion events. Although 60.2% of the genome of
S
.
pombe
is coding sequence, all but one of the insertions occurred in intergenic regions. We also found that Tf1 was significantly more likely to insert into intergenic regions that included polymerase II promoters than into regions between convergent gene pairs. Interestingly, 8 of the 51 insertion sites were isolated multiple times from genetically independent cultures. This result suggests that specific sites in intergenic regions are targeted by Tf1. Perhaps the most surprising observation was that per kilobase of nonrepetitive sequence, Tf1 was significantly more likely to insert into chromosome 3 than into one of the other two chromosomes. This preference was found not to be due to differences in the distribution or composition of intergenic sequences within the three chromosomes.
Saccharomyces
cerevisiae
C-Type Cyclin Ume3p/Srb11p Is Required for Efficient Induction and Execution of Meiotic Development
Authors: Cooper Katrina F. , Strich Randy
Published: December 2002

The yeast C-type cyclin Ume3p/Srb11p and its cyclin-dependent kinase partner Ume5p/Srb10p repress the transcription of several genes required for meiotic recombination or meiosis I nuclear division. To relieve this repression, Srb11p is destroyed early in meiosis, prior to the first meiotic division. This report identifies two roles for Srb11p in regulating meiotic development. First,
SRB11
is required for the normal exit from the mitotic cell cycle prior to meiotic induction. Specifically, mutants lacking
SRB11
(
srb11
Δ) uncouple bud growth from chromosome segregation, producing small buds with nuclei. The bud growth defect is most likely due to the failure of
srb11
Δ mutants to reestablish polarized actin fibers at the bud tip following exposure to sporulation medium. Second, Srb11p is required for the efficient execution of meiosis I.
srb11
Δ mutants either exhibited a delay in performing meiosis I and meiosis II or skipped meiosis I entirely. This meiotic defect is not due to the activation of the recombination or spindle assembly checkpoint pathways. However, the expression of several meiotic genes is delayed and reduced in the mutant strains. These results suggest a positive role for Srb10-Srb11p in regulating the transcription program. This model is supported by the finding that overexpression of the meiotic inducer
IME2
partially restored the ability of
srb11
mutants to perform meiosis I. In conclusion, these findings indicate that Srb11p is required for both entry into and execution of the meiotic program, thus describing multiple roles for a C-type cyclin in the regulation of a developmental pathway.
Pumilio Homologue from
Saprolegnia parasitica
Specifically Expressed in Undifferentiated Spore Cysts
Authors: Andersson M. Gunnar , Cerenius Lage
Published: December 2002

The expression of spore-specific marker transcripts at different stages of the asexual life cycle of
Saprolegnia parasitica
was analyzed. One of the markers, designated
puf1
, was found to be expressed transiently upon each of several cycles of zoospore encystment and reemergence. The transcript is induced immediately upon zoospore encystment and is rapidly lost when a cyst is triggered to germinate. In nongerminating cysts,
puf1
is maintained until a time point when the cysts can no longer be triggered to germinate and thus have become determined for zoospore reemergence. The results show that the cyst stage has two phases, of about equal duration, which are physiologically and transcriptionally distinct and that the transcriptional machinery of oomycetes is also active in nongerminating spores.
puf1
encodes a putative mRNA binding protein belonging to a conserved class of proteins including the
Drosophila melanogaster
Pumilio protein,
Caenorhabditis elegans
FBF, and
Saccharomyces cerevisiae
Puf5, all of which are involved in regulation of gene expression by posttranscriptional mechanisms.
Role of Uridylate-Specific Exoribonuclease Activity in
Trypanosoma brucei
RNA Editing
Authors: Igo Robert P. , Weston David S. , Ernst Nancy Lewis , Panigrahi Aswini K. , Salavati Reza , Stuart Kenneth
Published: December 2002

Editing of mitochondrial mRNAs in kinetoplastid protozoa occurs by a series of enzymatic steps that insert and delete uridylates (U's) as specified by guide RNAs (gRNAs). The characteristics of the 3" exonuclease activity that removes the U's following cleavage during deletion editing were determined by using an in vitro precleaved deletion assay that is based on ATPase subunit 6 pre-mRNA and gA6[14] gRNA. The exonuclease in partially purified editing complexes is specific for U's. The specificity occurs in the absence of gRNA, but its activity is enhanced by the presence of gRNA. The 3" pre-mRNA fragment enhances the specificity, but not the efficiency, of U removal. The activity is sensitive to the 5" phosphate of the 3" fragment, which is not required for U removal. The ability of the 3" U's to base pair with purines in the gRNA protects them from removal, suggesting that the U-specific 3" exonuclease (exoUase) is specific for U's which are not base paired. ExoUase is stereospecific and cannot remove (

R
p

)α-thio-U. The specificity of the exoUase activity thus contributes to the precision of RNA editing.
CulB, a Putative Ubiquitin Ligase Subunit, Regulates Prestalk Cell Differentiation and Morphogenesis in
Dictyostelium
spp
Authors: Wang Bin , Kuspa Adam
Published: December 2002

Dictyostelium
amoebae accomplish a starvation-induced developmental process by aggregating into a mound and forming a single fruiting body with terminally differentiated spores and stalk cells.
culB
was identified as the gene disrupted in a developmental mutant with an aberrant prestalk cell differentiation phenotype. The
culB
gene product appears to be a homolog of the cullin family of proteins that are known to be involved in ubiquitin-mediated protein degradation. The
culB
mutants form supernumerary prestalk tips atop each developing mound that result in the formation of multiple small fruiting bodies. The prestalk-specific gene
ecmA
is expressed precociously in
culB
mutants, suggesting that prestalk cell differentiation occurs earlier than normal. In addition, when
culB
mutant cells are mixed with wild-type cells, they display a cell-autonomous propensity to form stalk cells. Thus, CulB appears to ensure that the proper number of prestalk cells differentiate at the appropriate time in development. Activation of cyclic AMP-dependent protein kinase (PKA) by disruption of the regulatory subunit gene (
pkaR
) or by overexpression of the catalytic subunit gene (
pkaC
) enhances the prestalk/stalk cell differentiation phenotype of the
culB
mutant. For example,
culB
−
pkaR
−
cells form stalk cells without obvious multicellular morphogenesis and are more sensitive to the prestalk O (pstO) cell inducer DIF-1. The sensitized condition of PKA activation reveals that CulB may govern prestalk cell differentiation in
Dictyostelium
, in part by controlling the sensitivity of cells to DIF-1, possibly by regulating the levels of one or more proteins that are rate limiting for prestalk differentiation.
A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of
Trypanosoma brucei
Authors: Bringaud Frédéric , Biteau Nicolas , Melville Sara E. , Hez Stéphanie , El-Sayed Najib M. , Leech Vanessa , Berriman Matthew , Hall Neil , Donelson John E. , Baltz Théo
Published: December 2002

We describe a novel gene family that forms clusters in subtelomeric regions of
Trypanosoma brucei
chromosomes and partially accounts for the observed clustering of retrotransposons. The
ingi
and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the
T. brucei
genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or
ingi
retrotransposon inserted at exactly the same relative position. Here these genes are called the
RHS
family, for retrotransposon hot spot. Comparison of the protein sequences encoded by
RHS
genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/
ingi
insertion site. The RHS proteins share between 13 and 96% identity, and six subfamilies,
RHS1
to
RHS6
, can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the
Trypanosoma brucei
diploid genome contains about 280
RHS
(pseudo)-genes. Among the 52 identified
RHS
(pseudo)genes, 48 copies are in three
RHS
clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in
T. brucei
strain TREU927/4 GUTat10.1.
RHS
genes comprise the remaining sequence of the size-polymorphic “repetitive region” described for
T. brucei
chromosome I, and a homologous gene family is present in the
Trypanosoma cruzi
genome.
Neurospora
Clock-Controlled Gene 9 (
ccg-9
) Encodes Trehalose Synthase: Circadian Regulation of Stress Responses and Development
Authors: Shinohara Mari L. , Correa Alejandro , Bell-Pedersen Deborah , Dunlap Jay C. , Loros Jennifer J.
Published: December 2002

The circadian clock of
Neurospora crassa
regulates the rhythmic expression of a number of genes encoding diverse functions which, as an ensemble, are adaptive to life in a rhythmic environment of alternating levels of light and dark, warmth and coolness, and dryness and humidity. Previous differential screens have identified a number of such genes based solely on their cycling expression, including clock-controlled gene 9 (
ccg-9
). Sequence analysis now shows the predicted CCG-9 polypeptide to be homologous to a novel form of trehalose synthase; as such it would catalyze the synthesis of the disaccharide trehalose, which plays an important role in protecting many cells from environmental stresses. Consistent with this, heat, glucose starvation, and osmotic stress induce
ccg-9
transcript accumulation. Surprisingly, however, a parallel role in development is suggested by the finding that inactivation of
ccg-9
results in altered conidiophore morphology and abolishes the normal circadian rhythm of asexual macroconidial development. Examination of a clock component, FRQ, in the
ccg-9
-null strain revealed normal cycling, phosphorylation, and light induction, indicating that loss of the conidiation rhythm is not due to changes in either the circadian oscillator or light input into the clock but pointing instead to a defect in circadian output. These data imply an interplay between a role of trehalose in stress protection and an apparent requirement for trehalose in clock regulation of conidiation under constant environmental conditions. This requirement can be bypassed by a daily light signal which drives a light-entrained rhythm in conidiation in the
ccg-9
-null strain; this bypass suggests that the trehalose requirement is related to clock control of development and not to the developmental process itself. Circadian control of trehalose synthase suggests a link between clock control of stress responses and that of development.