bluuebunny/crossref_metadata_2025 huggingface dataset:
Ocean thermal advective effect on the annual range of sea surface temperature
Authors: Liu Qinyu , Xie Shang‐Ping , Li Lijuan , Maximenko Nikolai A.
Published: December 2005

Spatial variations in the seasonal cycle of sea surface temperature (SST) are studied over the western North Pacific using a high‐resolution climatology. In addition to monsoon, bathymetry and tidal mixing, western boundary currents and their extensions/branches are found to have a significant effect on the annual range of SST, with reduced values on the paths of warm currents and increased ones on the paths of cold currents. This is due to the asymmetric effect of ocean currents on SST in time: small in summer but large in winter when both the deepened mixed layer and increased SST gradients enhance the relative importance of ocean thermal advection to balance the heat flux to the atmosphere. Along with recent studies of decadal variability, our results reaffirm the role of ocean dynamics in climate.
Retrieval and characterization of ozone vertical profiles from a thermal infrared nadir sounder
Authors: Coheur Pierre‐François , Barret Brice , Turquety Solène , Hurtmans Daniel , Hadji‐Lazaro Juliette , Clerbaux Cathy
Published: December 2005

This paper presents the first retrievals and validations of ozone vertical distributions from a set of high‐resolution nadir thermal infrared measurements. These were obtained by the Interferometric Monitor for Greenhouse gases (IMG) instrument, which has operated on board the Japanese ADEOS platform between 1996 and 1997. The Optimal Estimation Method is used for the retrievals, along with a priori profile and covariance matrix built from model climatologies. We compare the retrieved IMG profiles with high‐vertical‐resolution ozone sonde measurements. Therefore we selected a set of IMG spectra collocated to within 3° of longitude and latitude with a representative distribution of ground‐based stations. We demonstrate that thanks to the two to four independent pieces of vertical information contained in the spectroscopic measurements with a maximum sensitivity in the upper troposphere–middle stratosphere, the thermal infrared nadir sounders are able to capture most of the ozone spatial and temporal variations. In particular, the latitudinal variations of the stratospheric ozone maximum are well represented in the retrievals, as are the high ozone concentrations observed in the upper troposphere–lower stratosphere at northern midlatitudes during springtime. Ozone depletion events in the Arctic vortex are also well reproduced. The measurements provide an accurate view of the tropospheric ozone content, except when the latter is very low. A detailed error budget reveals that the major part of the error in the IMG retrieved ozone profile is due to the smoothing of the true profile by the averaging kernel matrix, with additional contributions associated with the measurement noise and the inaccurate knowledge of the temperature profile and of the Instrument Line Shape (ILS).
Ozone column retrieval from solar UV measurements at ground level: Effects of clouds and results from six European sites
Authors: Brogniez Colette , Houët Mickaël , Siani Anna Maria , Weihs Philipp , Allaart Marc , Lenoble Jacqueline , Cabot Thierry , de la Casinière Alain , Kyrö Esko
Published: December 2005

A differential absorption method, developed by the Laboratoire d'Optique Atmosphérique (LOA), is applied to retrieve the total ozone column from UV global irradiance spectra under clear and cloudy sky conditions. Contrarily to clear sky, cloudy sky generates a high uncertainty in the retrieved ozone column. This study shows that under cloudy conditions the daily ozone mean is a rather good estimation of the true value. The standard deviation allows us to estimate the relative uncertainty of this mean value, i.e., about 7%. Results for all conditions from 3 years at Villeneuve d'Ascq are presented, as well as a comparison with TOMS (Total Ozone Mapping Spectrometer) data. The results are very similar to those obtained for clear days: In 75% of cases both values agree to within 5%; however, some cases present larger relative differences. Over the 3 years considered, there is a bias less than 3% (LOA > TOMS). This method is applied to five other European sites involved in the EDUCE (European Database for UV Climatology and Evaluation) project. Three of them are Brewer stations. The results of the comparison between the LOA‐retrieved ozone and TOMS data show that a relative difference smaller than 5% is obtained in 63–80% of the cases, depending on site and year. Biases smaller than 3% are observed (LOA > TOMS). The comparison between the LOA‐retrieved ozone and total ozone data from direct sun and zenith sky observations of the Brewer instruments shows better agreement. For more than about 80% of cases, except at one site, the relative difference is smaller than 5%, and the biases are smaller than 1%. The LOA method allows us to obtain a complementary data set and hence to provide time series of reliable measurements of total ozone column under all sky conditions.
Global variability of mesospheric temperature: Planetary‐scale perturbations at equatorial and tropical latitudes
Authors: Shepherd Marianna G. , Shepherd Gordon G. , Evans Wayne F. J. , Sridharan S.
Published: December 2005

The study examines the source of a cold temperature perturbation observed in the Wind Imaging Interferometer (WINDII) daytime daily zonal mean temperatures at 87 km height during March/April 1993, also seen to some extent in 1995 and 1997 over the latitude range 25°S to 25°N. The perturbation appears centered at 10°S as a departure of 10K to 35K below the semiannual climatological mean, which peaks at equinox. After accounting for tidal contributions to the observations, by adopting tidal parameters determined from the Microwave Limb Sounder (MLS) temperature observations the cold temperature signature still remained in the residual data. The perturbation is a global phenomenon immediately following March equinox and lasts over a period of 2 weeks. The period is marked by the presence of mesospheric temperature inversions over the altitude range of 70–90 km. Harmonic analysis reveals the presence of planetary waves of wave number 1 with periods of 3 days, 4–5 days and 7 days. A cross section of the temperature monthly zonal mean data and month of the year over the period from January 1992 to December 1995 revealed a distinct MSAO, modulated by a QBO with strong cold anomalies in March/April 1993, 1995 and 1997 in excellent agreement with the MSAO easterly phase of correlative MF radar wind observations at Tirunelveli (8.7°N, 77.8°E). It is shown that the observed temperature anomalies can be produced by the residual circulation associated with the wave driving of the MSAO itself.
Effects of bulk ice microphysics on the simulated monsoonal precipitation over east Asia
Authors: Lim Jeong‐Ock Jade , Hong Song‐You
Published: December 2005

This study examines the effects of bulk ice microphysical processes on the simulation of monsoonal precipitation in summer over east Asia, centered over Korea. The mixed phase microphysics scheme of the WRF‐Single‐Moment‐MicroPhysics class 5 (WSM5) is implemented into the fifth‐generation Pennsylvania State University/National Center for Atmospheric Research Mesoscale Model (MM5). The performance of the WSM5 scheme is compared to that of Reisner's mixed phase scheme, that is, the MM5‐Single‐moment‐Microphysics class 5 (MSM5). Together with looking at the impact of ice microphysics, the importance of the sedimentation of falling ice crystals on simulated rainfall events is investigated. The same sensitivity experiments are extended to a 2‐month‐long simulation of the east Asian summer monsoon. It was found that the new microphysics in the WSM5 scheme produces a more realistic vertical distribution of condensates. For a locally developed heavy rainfall event over Korea, the impact of revised ice microphysics is significant. The WSM5 scheme simulates more (less) precipitation in the south (north), compared with that of the MSM5 scheme, by stabilizing the air columns in the rainfall area, leading to a better agreement with the observed precipitation. By contrast, ice sedimentation becomes more important for those cases of heavy rainfall, associated with a mobile surface cyclone system, accomplished by suppressing large‐scale bias through a realistic ice cloud/radiation feedback. The sedimentation of cloud ice is found to be crucial to the successful simulation of monsoonal precipitation and large‐scale features within the east Asian summer monsoon.
Stratosphere‐troposphere evolution during polar vortex intensification
Authors: Limpasuvan Varavut , Hartmann Dennis L. , Thompson David W. J. , Jeev Kumar , Yung Yuk L.
Published: December 2005

Stratosphere‐troposphere evolution associated with polar vortex intensification (VI) events is examined during the Northern Hemisphere winter. The incipient stage of a VI event is marked by anomalously low wave activity and descending westerly anomalies over the depth of the polar stratosphere. Reduced poleward planetary wave heat flux occurs as the circumpolar wind becomes strongest and pressure anomalies penetrate toward the surface. Descending pressure patterns project strongly onto the positive state of the Northern Hemisphere Annular Mode (NAM). Concurrently, anomalous poleward momentum flux develops in the upper troposphere, and the related tropospheric mean meridional circulation maintains the attendant wind and temperature anomalies against surface drag. The gross behavior of the composite VI event is similar in shape but opposite in sign to that associated with sudden stratospheric warming events (SSWs). However, the descent of the wind and temperature anomalies over the VI life cycle is generally weaker and slower than its SSW counterpart preceding the maximum vortex anomaly. Similarly, after the maximum wind event, the weakening of the winds is faster than the strengthening of the winds after a SSW. This is because stratospheric wind reduction anomalies are produced by wave driving, which can be rapid, and increases in wind speed are associated with the radiative cooling of the polar cap, which happens more gradually. While the contributions of the anomalous momentum fluxes by the quasi‐stationary and synoptic eddies are similar to SSWs, the much stronger anomalous momentum flux observed during VI can be attributed to the larger role of eddies with timescales between 15 and 40 days and of wave number 2 scale. Notable differences between VI and SSW appear in the tropical region. In particular, anomalous vortex intensification seems to occur preferentially during La Niña conditions.
Relaxation of the Martian dichotomy boundary: Faulting in the Ismenius Region and constraints on the early evolution of Mars
Authors: Guest Alice , Smrekar Suzanne E.
Published: December 2005

The Martian dichotomy is a global feature separating the cratered southern highlands and smooth northern lowlands. Parts of the boundary are defined by steep slopes with elevation differences of 2–6 km. Here we use constraints from the well‐preserved section of the dichotomy in the Ismenius Region. We study the relaxation of the boundary using both finite element and semianalytical techniques to better constrain the thermomechanical conditions in early Mars. We argue that the steep slopes are the product of faulting resulting from relaxation of the edge of the boundary by lower crustal flow. This relaxation requires that the lower crust must be at least 10 km thick and have a viscosity of ∼1021 Pa s during the first 100–300 Myr of relaxation. We show that a wet crustal rheology and a thermal gradient of ∼15–20 K/km at 4 Ga allows for both the partial relaxation of the Martian dichotomy and preservation of long wavelength topography as observed on Mars. This result is generally consistent with a stagnant‐lid model of cooling of Martian interior. The thermal gradient at 4 Ga is also consistent with the estimated elastic thickness on early Mars. Our modeling constrains the original slope of the boundary to approximately 2°. We cannot constrain the crustal thickness more tightly than the current estimates of 50–100 km. On the basis of our semianalytical modeling, the relaxation of the boundary can contribute to the general north‐south slope observed on Mars.
Equatorial Pacific productivity and dust flux during the mid‐Pleistocene climate transition
Authors: Winckler Gisela , Anderson Robert F. , Schlosser Peter
Published: December 2005

We present a helium isotope record for core TT013‐114PC from the central equatorial Pacific (140°W, 4°N, 4432 m water depth) spanning a period of 1 million years. We focus on the time interval from 560 to 800 kyr, largely coinciding with the mid‐Pleistocene climate transition (MPT) when the dominant period of the Earth's climate variability shifted from 41 kyr to 100 kyr. The terrigenous 4He concentrations from our study correlate very well with published titanium concentrations in this core strongly supporting the use of terrigenous 4He as a monitor of continental dust. Normalizing titanium and terrigenous 4He concentrations to 3He suggests that the dust supply during the MPT was approximately 30% lower compared to the subsequent period (560–100 kyr). The 3He‐normalized barium, aluminum and phosphorus concentrations, trace elements with a predominantly biogenic source in these sediments, are relatively constant. This is in contrast to previous studies that reported an apparent rise of titanium‐normalized productivity proxies. Rather than a significant increase in productivity during the MPT, we conclude that the dust flux to the central equatorial Pacific was reduced and that the export productivity was approximately constant during this period of climate reorganization.
The Influence of Exploration Mode, Orientation, and Configuration on the Haptic Müller-Lyer Illusion
Authors: Heller Morton A , McCarthy Melissa , Schultz Jennifer , Greene Jayme , Shanley Melissa , Clark Ashley , Skoczylas Samantha , Prociuk Jamie
Published: December 2005

We studied the impact of manner of exploration, orientation, spatial position, and configuration on the haptic Müller-Lyer illusion. Blindfolded sighted subjects felt raised-line Müller-Lyer and control stimuli. The stimuli were felt by tracing with the index finger, free exploration, grasping with the index finger and thumb, or by measuring with the use of any two or more fingers. For haptic judgments of extent a sliding tangible ruler was used. The illusion was present in all exploration conditions, with overestimation of the wings-out compared to wings-in stimuli. Tracing with the index finger reduced the magnitude of the illusion. However, tracing and grasping induced an overall underestimation of size. The illusion was greatly attenuated when stimuli were felt with the index fingers of both hands. Illusory misperception was not altered by the position in space of the Müller-Lyer stimuli. No effects of changes in the thickness of the line shaft were found, but there were effects of the length of the wing endings for the smaller, 5.1 cm stimuli. The theoretical and practical implications of the results are discussed.
Perception Time Measured with the Slope-Transition Paradigm (STP): Category, Set Size, and Task Manipulations
Authors: Matin Ethel , Nofer David C , Christodoulou Androula , Koski Hope
Published: December 2005

A perception time measure was obtained with the ‘slope-transition paradigm’ (STP), which is described in detail. In two experiments with the paradigm, participants viewed two sequential data frames, each presented for a wide range of durations. They made a binary response based on combined information from the two frames. The results showed piecewise linear response-time versus frame-duration functions with a slope-0 branch at short durations, followed by a slope-1 branch. The duration where the two branches met (the slope transition) was interpreted as the end of the perception of frame 1. For longer durations, the participant had completed the perception of frame 1 and was forced to waste time waiting for data from frame 2. In experiment 1, an odd-digit enumeration task was used, and set size and distractor category (even digits versus consonants) were varied. In experiment 2, a same/different task with digits was used and the type of judgment (literal versus parity) was varied. Perception time increased with set size. Distractor category and judgment type affected post-perceptual processes. The perception time measure of the STP is considered in relation to the attentional blink, repetition blindness, and object files.
Capture of agricultural surplus water determines the productivity and scale of new low-rainfall woody crop industries
Authors: Cooper D. , Olsen G. , Bartle J.
Published: December 2005

This paper presents a conceptual model for estimating the maximum scale of biomass processing industry that may be supported by woody crops grown in the medium and low rainfall agricultural regions of southern Australia. The model integrates paddock scale economics, water capture by woody crops, conversion of water to woody biomass, and estimation of suitable area. It enables estimates to be made of the maximum scale of implementation of commercial woody crops in various climatic regions, and the maximum amount of woody biomass that could be produced commercially within an economic transport distance of a processing facility. To demonstrate the utility of the model, potential biomass supply is estimated for 2 Western Australian wheatbelt towns, Merredin and Narrogin. These estimates are compared with the feedstock requirements of a range of different processing industries.
This paper demonstrates that the rate of converting water to biomass and water capture biomass price are key determinants of the potential scale of biomass crops and processing industries in the southern Australian wheat and wool belts and hence the potential contribution of woody crops to dryland salinity management.
Genetic variation in five populations of strawberry clover (Trifolium fragiferum cv. Palestine) in Western Australia
Authors: McDonald K. S. , Cocks P. S. , Ewing M. A.
Published: December 2005

Genetic variation within and among populations of an outcrossing stoloniferous perennial legume, strawberry clover (Trifolium fragiferum L.), was studied using seed collected from 5 different locations in Western Australia. The sites ranged from Badgingarra to the north of the wheatbelt to Karridale in the southwest of the state. Seed was collected randomly at each site and was grown out at the University of Western Australia Field Station at Shenton Park, Perth. Thirteen morphological plant traits were measured and analysed. Results show that within-population variation was extremely high. In contrast, among-population variation was generally low with most characters showing only 8–15% of the total variation. Despite this, all but 1 of the measured plant traits differed among populations. Principal components analysis highlighted the large amount of variation within the populations with the first 3 principal components accounting for only 59% of the total variation. We suggest that the populations have begun to differentiate into ecotypes more suited to those habitats into which they have been sown but that within-population variation remains high due to the outcrossing nature of strawberry clover.
Multi-disciplinary approaches suggest profitable and sustainable farming systems for valley floors at risk of salinity
Authors: Barrett-Lennard E. G. , George R. J. , Hamilton G. , Norman H. C. , Masters D. G.
Published: December 2005

Australia’s traditional approach to salinity abatement has been to focus primarily on the control of recharge in land not at risk of salinity by incorporating deep-rooted perennial plants (e.g. lucerne, oil mallees and farm trees) into farming systems throughout the landscape. However, in the broad valley floors and sedimentary plains of Australia’s cropping regions (the areas most at risk of salinity), recharge is mainly a 1-dimensional process. Thus, offsite recharge management may have little or no impact on salinity outcomes for the areas at risk. The future of the broad valley floors will be most influenced by the management decisions of landholders in the valley floors.
To be sustainable and profitable, farming systems on valley floors need to (i) target perennial plants to the valley floors and improve soil management to dry the root-zone, decrease recharge and minimise capillary rise, (ii) increase the discharge of groundwater from valley floors using deep drains and stands of perennial plants, (iii) improve surface water management to ameliorate waterlogging, inundation and flooding, and (iv) incorporate better plants and better agronomic methods in the growth of profitable salt tolerant crops and fodder plants.
This paper will illustrate the convergence of new research and development that offers real prospects of low risk, high return farming systems for Australia’s threatened valley floors. We argue that there needs to be a major refocus by farmers, researchers and their funders in the development of profitable sustainable farming systems for valley floors.
Farm, food and resource issues: politics and dryland salinity
Authors: Pannell D. J.
Published: December 2005

Political forces make it difficult to develop effective and efficient policies for dryland salinity. The politics of the day have had major influences on salinity and salinity-related policy, beginning with the clearing of land for agricultural development. Tensions affecting salinity policy include urban political power v. rural salinity; short-term politics v. long-term salinity; crisis-driven politics v. slow and inexorable salinity; simplistic and uniform political solutions v. complex and diverse salinity problems; the need for winners in politics v. the reality of losers from effective salinity policy; east v. west; and national v. state governments. These tensions will interact with our improving scientific knowledge of salinity and ongoing social and economic changes in rural areas to shape future salinity policies. Prospects for changes in salinity policy and outcomes over the next 10 years are suggested, including the following possibilities: more carefully targeted and site-specific investments in salinity prevention; the beginnings of success of current research and development efforts to develop profitable new plant-based systems for salinity management; ongoing debate about the appropriate role for catchment management bodies for in salinity management; greater attention to the problem of salinity impacts on biodiversity and infrastructure; reduced attention to market-based instruments for salinity; and ongoing changes in the economics of agriculture, timber and energy influencing salinity outcomes and, potentially, salinity policy.
Potential of current perennial plant-based farming systems to deliver salinity management outcomes and improve prospects for native biodiversity: a review
Authors: Lefroy E. C. , Flugge F. , Avery A. , Hume I.
Published: December 2005

Existing perennial plant-based farming systems are examined within 4 climatic zones in southern Australia (western winter rainfall, south-eastern low to medium rainfall, south-eastern high rainfall and northern summer rainfall) to assess their potential to improve the management of dryland salinity. If profit is to be the primary driver of adoption, it appears that the available options (lucerne and other perennial pastures, farm forestry, saltland pastures and forage shrubs) will fall short of existing hydrological targets with the exception of the higher rainfall zones. In the 3 eastern zones, the need to preserve fresh water flows to permanent river systems places limitations on the use of perennial plants, while the higher proportion of regional groundwater flow systems increases response times and heightens the need for regional coordination of effort. In the western zone, the prevalence of local and intermediate ground water flow systems increases effectiveness of individual action. Research into new perennial land use systems has been characterised by an emphasis on water use over profit resulting from poor dialogue between paddock, farm and catchment scales. Exploring the water use implications of land use systems that are potentially viable at farm scale is a more promising approach than focusing on the opportunity cost of catchment scale intervention. Perennial plant-based farming systems present both threats and opportunities to native biodiversity. The major threat is the introduction of new environmental weeds. The opportunities are potential improvements in vegetative cover, food sources and habitat for the native biota, but only where nature conservation goals can influence the structural complexity, composition and location of new land use systems.
Improving salt tolerance of wheat and barley: future prospects
Authors: Colmer T. D. , Munns R. , Flowers T. J.
Published: December 2005

Cropping on saline land is restricted by the low tolerance of crops to salinity and waterlogging. Prospects for improving salt tolerance in wheat and barley include the use of: (i) intra-specific variation, (ii) variation for salt tolerance in the progenitors of these cereals, (iii) wide-hybridisation with halophytic ‘wild’ relatives (an option for wheat, but not barley), and (iv) transgenic techniques. In this review, key traits contributing to salt tolerance, and sources of variation for these within the Triticeae, are identified and recommendations for use of these traits in screening for salt tolerance are summarised. The potential of the approaches to deliver substantial improvements in salt tolerance is discussed, and the importance of adverse interactions between waterlogging and salinity are emphasised. The potential to develop new crops from the diverse halophytic flora is also considered.
Interaction between the dihydropyridine receptor Ca
2+
channel β-subunit and ryanodine receptor type 1 strengthens excitation-contraction coupling
Authors: Cheng Weijun , Altafaj Xavier , Ronjat Michel , Coronado Roberto
Published: December 2005

Previous studies have shown that the skeletal dihydropyridine receptor (DHPR) pore subunit Ca
V
1.1 (α1S) physically interacts with ryanodine receptor type 1 (RyR1), and a molecular signal is transmitted from α1S to RyR1 to trigger excitation-contraction (EC) coupling. We show that the β-subunit of the skeletal DHPR also binds RyR1 and participates in this signaling process. A novel binding site for the DHPR β1a-subunit was mapped to the M
3201
to W
3661
region of RyR1.
In vitro
binding experiments showed that the strength of the interaction is controlled by K
3495
KKRR _ _ R
3502
, a cluster of positively charged residues. Phenotypic expression of skeletal-type EC coupling by RyR1 with mutations in the K
3495
KKRR _ _ R
3502
cluster was evaluated in dyspedic myotubes. The results indicated that charge neutralization or deletion severely depressed the magnitude of RyR1-mediated Ca
2+
transients coupled to voltage-dependent activation of the DHPR. Meantime the Ca
2+
content of the sarcoplasmic reticulum was not affected, and the amplitude and activation kinetics of the DHPR Ca
2+
currents were slightly affected. The data show that the DHPR β-subunit, like α1S, interacts directly with RyR1 and is critical for the generation of high-speed Ca
2+
signals coupled to membrane depolarization. These findings indicate that EC coupling in skeletal muscle involves the interplay of at least two subunits of the DHPR, namely α1S and β1a, interacting with possibly different domains of RyR1.
Maintenance of presynaptic function by AMPA receptor-mediated excitatory postsynaptic activity in adult brain
Authors: Kakizawa Sho , Miyazaki Taisuke , Yanagihara Dai , Iino Masamitsu , Watanabe Masahiko , Kano Masanobu
Published: December 2005

Activity-dependent synaptic modification occurs in both developing and mature animals. For reliable information transfer and storage, however, once established, synapses must be maintained stably. We investigated how chronic blockade of neuronal activity or α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors affects excitatory climbing fiber (CF) to Purkinje cell (PC) synapses in adult mouse cerebellum. Both treatments caused reduced glutamate concentration transient at the synaptic cleft, decreased frequency of quantal excitatory postsynaptic current, and diminished CF innervation of PC shaft dendrites but no change in CF's release probability. These results indicate that, in the mature cerebellum, AMPA receptor-mediated excitatory postsynaptic activity maintains CF's functional glutamate-release sites and its innervation of PC shaft dendrites.
The global transcriptional regulatory network for metabolism inEscherichia coliexhibits few dominant functional states
Authors: Barrett Christian L. , Herring Christopher D. , Reed Jennifer L. , Palsson Bernhard O.
Published: December 2005

A principal aim of systems biology is to developin silicomodels of whole cells or cellular processes that explain and predict observable cellular phenotypes. Here, we use a model of a genome-scale reconstruction of the integrated metabolic and transcriptional regulatory networks forEscherichia coli, composed of 1,010 gene products, to assess the properties of all functional states computed in 15,580 different growth environments. The set of all functional states of the integrated network exhibits a discernable structure that can be visualized in 3-dimensional space, showing that the transcriptional regulatory network governing metabolism inE. coliresponds primarily to the available electron acceptor and the presence of glucose as the carbon source. This result is consistent with recently published experimental data. The observation that a complex network composed of 1,010 genes is organized to achieve few dominant modes demonstrates the utility of the systems approach for consolidating large amounts of genome-scale molecular information about a genome and its regulation to elucidate an organism's preferred environments and functional capabilities.
Embryonic stem cell-derived hematopoietic stem cells
Authors: Wang Yuan , Yates Frank , Naveiras Olaia , Ernst Patricia , Daley George Q.
Published: December 2005

Despite two decades of studies documenting thein vitroblood-forming potential of murine embryonic stem cells (ESCs), achieving stable long-term blood engraftment of ESC-derived hematopoietic stem cells in irradiated mice has proven difficult. We have exploited theCdx-Hoxpathway, a genetic program important for blood development, to enhance the differentiation of ESCs along the hematopoietic lineage. Using an embryonic stem cell line engineered with tetracycline-inducibleCdx4, we demonstrate that ectopicCdx4expression promotes hematopoietic mesoderm specification, increases hematopoietic progenitor formation, and, together withHoxB4, enhances multilineage hematopoietic engraftment of lethally irradiated adult mice. Clonal analysis of retroviral integration sites confirms a common stem cell origin of lymphoid and myeloid populations in engrafted primary and secondary mice. These data document the cardinal stem cell features of self-renewal and multilineage differentiation of ESC-derived hematopoietic stem cells.
Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses
Authors: Khayat Reza , Tang Liang , Larson Eric T. , Lawrence C. Martin , Young Mark , Johnson John E.
Published: December 2005

Archaea and their viruses are poorly understood when compared with the Eukarya and Bacteria domains of life. We report here the crystal structure of the major capsid protein (MCP) of the
Sulfolobus
turreted icosahedral virus, an archaeal virus isolated from an acidic hot spring (pH 2–4, 72–92°C) in Yellowstone National Park. The structure is nearly identical to the MCP structures of the eukaryotic
Paramecium bursaria Chlorella
virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenovirus. Structural analysis of the capsid architecture, determined by fitting the subunit into the electron cryomicroscopy reconstruction of the virus, identified a number of key interactions that are akin to those observed in adenovirus and PRD1. The similar capsid proteins and capsid architectures strongly suggest that these viral capsids originated and evolved from a common ancestor. Hence, this work provides a previously undescribed example of a viral relationship spanning the three domains of life (Eukarya, Bacteria, and Archaea). The MCP structure also provides insights into the stabilizing forces required for extracellular hyperthermophilic proteins to tolerate high-temperature hot springs.
Role for hypocretin in mediating stress-induced reinstatement of cocaine-seeking behavior
Authors: Boutrel Benjamin , Kenny Paul J. , Specio Sheila E. , Martin-Fardon Rémi , Markou Athina , Koob George F. , de Lecea Luis
Published: December 2005

Hypocretin-1 and -2 (Hcrt-1 and Hcrt-2), also referred to as orexin-A and -B, are neuropeptides synthesized by a few thousand neurons in the lateral hypothalamus. Hypocretin-containing neurons project throughout the brain, with a prominent input to basal forebrain structures involved in motivation, reward, and stress. However, the role of hypocretins in addiction-related behaviors remains largely unexplored. Here we show that intracerebroventricular infusions of Hcrt-1 lead to a dose-related reinstatement of cocaine seeking without altering cocaine intake in rats. Hcrt-1 also dramatically elevates intracranial self-stimulation thresholds, indicating that, unlike treatments with reinforcing properties such as cocaine, Hcrt-1 negatively regulates the activity of brain reward circuitries. Hypocretin-induced reinstatement of cocaine seeking was prevented by blockade of noradrenergic and corticotropin-releasing factor systems, suggesting that Hcrt-1 reinstated drug seeking through induction of a stress-like state. Consistent with this interpretation, the selective Hcrt-1 receptor antagonist SB-334867 blocked footshock-induced reinstatement of previously extinguished cocaine-seeking behavior. These findings reveal a previously unidentified role for hypocretins in driving drug seeking through activation of stress pathways in the brain.
A therapeutic aptamer inhibits angiogenesis by specifically targeting the heparin binding domain of VEGF
165
Authors: Lee Joon-Hwa , Canny Marella D. , De Erkenez Andrea , Krilleke Dominik , Ng Yin-Shan , Shima David T. , Pardi Arthur , Jucker Fiona
Published: December 2005

Aptamers recognize their targets with extraordinary affinity and specificity. The aptamer-based therapeutic, Macugen, is derived from a modified 2′fluoro pyrimidine RNA inhibitor to vascular endothelial growth factor (VEGF) and is now being used to treat the wet form of age-related macular degeneration. This VEGF
165
aptamer binds specifically to the VEGF
165
isoform, a dimeric protein with a receptor-binding domain and a heparin-binding domain (HBD). To understand the molecular recognition between VEGF and this aptamer, binding experiments were used to show that the HBD contributes the majority of binding energy in the VEGF
165
–aptamer complex. A tissue culture-based competition assay demonstrated that the HBD effectively competes with VEGF
165
for aptamer binding
in vivo
. Comparison of NMR spectra revealed that structural features of the smaller HBD–aptamer complex are present in the full-length VEGF
164
–aptamer complex. These data show that the HBD provides the binding site for the aptamer and is the primary determinant for the affinity and specificity in the VEGF
165
–aptamer complex.
How to make a curved
Drosophila
bristle using straight actin bundles
Authors: Tilney Lewis G. , DeRosier David J.
Published: December 2005

This, our Inaugural Article as Academy Members, is ironically our swan song from the field of the actin cytoskeleton. By reviewing what we have learned and what we think is going on during development, we hope to lure you, the reader, into applying your skills to the bristle cell. The processes of the assembly and disassembly of actin bundles is laid out in time and space in an organism that lends itself to genetic manipulation. The cell provides every process you could want: filament nucleation, growth of microvilli, joining of microvillar bundles into modules, assembly of modules into bundles, time-dependent use of at least two crossbridging proteins, filament turnover, treadmilling, disassembly, and filament translocation.
Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat
Authors: Devos Katrien M. , Ma Jianxin , Pontaroli Ana C. , Pratt Lee H. , Bennetzen Jeffrey L.
Published: December 2005

The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4- to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was <1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from “gene-rich” regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is ≈1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization.
MicroRNA1 influences cardiac differentiation in
Drosophila
and regulates Notch signaling
Authors: Kwon Chulan , Han Zhe , Olson Eric N. , Srivastava Deepak
Published: December 2005

MicroRNAs (miRNAs) are genomically encoded small RNAs that hybridize with messenger RNAs, resulting in degradation or translational inhibition of targeted transcripts. The potential for miRNAs to regulate cell-lineage determination or differentiation from pluripotent progenitor or stem cells is unknown. Here, we show that microRNA1 (
miR-1
) is an ancient muscle-specific gene conserved in sequence and expression in
Drosophila
.
Drosophila miR-1
(
dmiR-1
) is regulated through a serum response factor-like binding site in cardiac progenitor cells. Loss- and gain-of-function studies demonstrated a role for
dmiR-1
in modulating cardiogenesis and in maintenance of muscle-gene expression. We provide
in vivo
evidence that
dmiR-1
targets transcripts encoding the Notch ligand Delta, providing a potential mechanism for the expansion of cardiac and muscle progenitor cells and failure of progenitor cell differentiation in some
dmiR-1
mutants. These findings demonstrate that
dmiR-1
may “fine-tune” critical steps involved in differentiation of cardiac and somatic muscle progenitors and targets a pathway required for progenitor cell specification and asymmetric cell division.
Processes conducive to the release and transport of arsenic into aquifers of Bangladesh
Authors: Polizzotto Matthew L. , Harvey Charles F. , Sutton Steve R. , Fendorf Scott
Published: December 2005

Arsenic is a contaminant in the groundwater of Holocene aquifers in Bangladesh, where ≈57 million people drink water with arsenic levels exceeding the limits set by the World Health Organization. Although arsenic is native to the sediments, the means by which it is released to groundwater remains unresolved. Contrary to the current paradigm, ferric (hydr)oxides appear to dominate the partitioning of arsenic in the near surface but have a limited impact at aquifer depths where wells extract groundwater with high arsenic concentrations. We present a sequence of evidence that, taken together, suggest that arsenic may be released in the near surface and then transported to depth. We establish that (
i
) the only portion of the sediment profile with conditions destabilizing to arsenic in our analysis is in the surface or near-surface environment; (
ii
) a consistent input of arsenic via sediment deposition exists; (
iii
) retardation of arsenic transport is limited in the aquifers; and (
iv
) groundwater recharge occurs at a rate sufficient to necessitate continued input of arsenic to maintain observed concentrations. Our analyses thus lead to the premise that arsenic is liberated in surface and near-surface sediments through cyclic redox conditions and is subsequently transported to well depth. Influx of sediment and redox cycling provide a long-term source of arsenic that when liberated in the near surface is only weakly partitioned onto sediments deeper in the profile and is transported through aquifers by groundwater recharge.
Stereotypic and random patterns of connectivity in the larval mushroom body calyx of
Drosophila
Authors: Masuda-Nakagawa Liria M. , Tanaka Nobuaki K. , O'Kane Cahir J.
Published: December 2005

The larval brain of
Drosophila
is a useful model to study olfactory processing because of its cellular simplicity. The early stages of central olfactory processing involve the detection of odor features, but the coding mechanisms that transform them into a representation in higher brain centers is not clear. Here we examine the pattern of connectivity of the main neurons that process olfactory information in the calyx (dendritic region) of the mushroom bodies, a higher brain center essential for associative olfactory learning. The larval calyx has a glomerular organization. We generated a map of calyx glomeruli, using both anatomical criteria and the pattern of innervation by subsets of its input neurons (projection neurons), molecularly identified by GAL4 markers. Thus, we show that projection neurons innervate calyx glomeruli in a stereotypic manner. By contrast, subsets of mushroom body neurons (Kenyon cells) that are labeled by GAL4 markers show no clear preference for specific glomeruli. Clonal subsets of Kenyon cells show some preference for subregions of the calyx, implying that they receive distinct input. However, at the level of individual glomeruli, dendritic terminals of larval-born Kenyon cells innervate about six glomeruli, apparently randomly. These results are consistent with a model in which Kenyon cells process olfactory information by integrating different inputs from several calyx glomeruli in a combinatorial manner.
Ridom TraceEdit: a DNA trace editor and viewer
Authors: Rothgänger Jörg , Weniger Markus , Weniger Thomas , Mellmann Alexander , Harmsen Dag
Published: December 2005

Summary: Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved.

Availability: TraceEdit is freely available via the Internet at . TraceEdit has been designed to operate on Windows, MacOS X and UNIX platforms.

Contact:  info@ridom.de
HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana
Authors: Yang Guojun , Hall Timothy C.
Published: December 2005

Summary: Determination of transgene location is essential for investigating the effects of position on transgene expression levels and facilitates cloning of the resident gene affected by insertion. Currently used PCR-based approaches for determination of transgene location are relatively complicated and often fail when the transgene is duplicated, rearranged or fragmented. HideNseek is a new bioinformatics tool that allows computation of transgene locations, provided that a suitable genomic restriction enzyme digestion profile is available. Since the new approach is not based on the terminal sequences of the transgene insert, it is less sensitive to transgene duplication, rearrangement or fragmentation. HideNseek has been tested experimentally and by in silico simulation. The experimental example provided here shows that this simple approach is feasible, permitting rapid location of transgenes with little bench work.

Availability: available on request from the authors.

Contact:  tim@idmb.tamu.edu

Supplementary data: HideNseek input and output examples, experimental procedures and figures showing experimental results are provided as supplementary files: Supplementary material 1, 2, 3 and Supplementary figures (Figs 1 and 2), respectively. Supplementary data is available at Bioinformatics online.
SEAN: SNP prediction and display program utilizing EST sequence clusters
Authors: Huntley Derek , Baldo Angela , Johri Saurabh , Sergot Marek
Published: December 2005

Summary: SEAN is an application that predicts single nucleotide polymorphisms (SNPs) using multiple sequence alignments produced from expressed sequence tag (EST) clusters. The algorithm uses rules of sequence identity and SNP abundance to determine the quality of the prediction. A Java viewer is provided to display the EST alignments and predicted SNPs.

Availability: SEAN is freely available from

Contact:  d.huntley@imperial.ac.uk
CMfinder—a covariance model based RNA motif finding algorithm
Authors: Yao Zizhen , Weinberg Zasha , Ruzzo Walter L.
Published: December 2005

Motivation: The recent discoveries of large numbers of non-coding RNAs and computational advances in genome-scale RNA search create a need for tools for automatic, high quality identification and characterization of conserved RNA motifs that can be readily used for database search. Previous tools fall short of this goal.

Results: CMfinder is a new tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way.

Extensive tests show that our method works well on datasets with either low or high sequence similarity, is robust to inclusion of lengthy extraneous flanking sequence and/or completely unrelated sequences, and is reasonably fast and scalable. In testing on 19 known ncRNA families, including some difficult cases with poor sequence conservation and large indels, our method demonstrates excellent average per-base-pair accuracy—79% compared with at most 60% for alternative methods. More importantly, the resulting probabilistic model can be directly used for homology search, allowing iterative refinement of structural models based on additional homologs. We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species.

Availability: Results and web server version are available at

Contact:  yzizhen@cs.washington.edu

Supplementary information: Supplementary technical details are available at