bluuebunny/crossref_metadata_2025 huggingface dataset:
UV climatology at McMurdo Station, Antarctica, based on version 2 data of the National Science Foundation's Ultraviolet Radiation Monitoring Network
Authors: Bernhard G. , Booth C. R. , Ehramjian J. C. , Nichol S. E.
Published: June 2006

Spectral ultraviolet (UV) and visible irradiance has been measured near McMurdo Station, Antarctica, between 1989 and 2004 with a SUV‐100 spectroradiometer. The instrument is part of the U.S. National Science Foundation's UV Monitoring Network. Here we present a UV climatology for McMurdo based on the recently produced “version 2” data edition. Compared to the previously published “version 0” data set, version 2 data differ by −5 to 12% in the UV, depending on wavelength, solar zenith angle (SZA), and year. A comparison with results of a radiative transfer model confirmed that measurements of different years are consistent to within ±5%. Clear‐sky spectra measured between October 1991 and March 1992 were significantly lower than spectra of other years because of the presence of volcanic aerosols. Total ozone column was calculated from UV spectra and was found in excellent agreement with collocated measurements of a Dobson spectrophotometer and satellite observations. Effective surface albedo was also estimated from clear‐sky spectra. Monthly average albedo ranges between 0.69 for March and 0.84 for October. Biologically effective UV radiation is largest in November and December when low total ozone amounts coincide with relatively small SZAs. During these months, the noon‐time UV Index typically varies between 2 and 5.5, but indices as high as 7.5 have been observed. The largest erythemal daily dose of 6.7 kJ/m2 was measured on 28 November 1998. Linear regression analyses did not indicate statistically significant trends in UV nor visible radiation for the months September to January. For February and March, we found large, statistically significant positive trends in the UV and visible as well as for short‐wave (0.3–3.0 μm) irradiance, ranging between 12 and 30% per decade. These trends are likely caused by changes in cloudiness and/or surface albedo, but the data do not allow unambiguous attribution of the increase to one of the two factors. On average, clouds reduce UV irradiance at 345 nm by 10% compared to clear‐sky levels. Reductions vary substantially by month and year, can exceed 60% on rare occasions, and generally increase with wavelength. Between September and November, the variability in UV introduced by changes in total ozone is about twice as high as the UV variability due to clouds.
Eddy covariance measurements of carbon exchange and latent and sensible heat fluxes over a boreal lake for a full open‐water period
Authors: Vesala Timo , Huotari Jussi , Rannik Üllar , Suni Tanja , Smolander Sampo , Sogachev Andrey , Launiainen Samuli , Ojala Anne
Published: June 2006

Long‐term measurements of sensible and latent heat and carbon dioxide fluxes were performed over a boreal lake in southern Finland using the direct micrometeorological eddy covariance (EC) technique. The water column was sampled weekly for dissolved carbon dioxide, and the CO2 flux was estimated also applying the concentration gradient method. Temperature and oxygen profiles of the lake were measured twice a week. The measurements covered one full open‐water period from April to November 2003, and it is the longest continuous CO2 record ever measured over a lake by EC. The sensible heat flux H was positive, that is, from the lake to the atmosphere, except in May, when it was >0 W/m2 at night and <0 W/m2 in daytime. The latent heat flux dominated clearly over H in spring and summer; that is, the Bowen ratio was less than 1. Higher‐moment turbulence statistics proved to be efficient in detection of frequent nonstationary situations. Applying the statistical criteria for CO2 concentration and vertical wind speed, averaging over a 5‐min period and selecting only the wind direction with longest fetch, we could obtain lake‐representative CO2 fluxes. Footprint analysis based on a closure model revealed that the source areas were relatively short because of the presence of turbulence generated by the surrounding forest, compared to a larger lake with an extended smooth surface. We observed a net CO2 source of 0.2–0.4 μmol m−2 s−1 excluding July, when the flux was closer to zero. The results are consistent with the gradient method, based on more infrequent sampling, and both methods gave the same average flux, 0.2 μmol m−2 s−1, over the whole open‐water period.
Comparison of ILAS‐II and ground‐based FTIR measurements of O3, HNO3, N2O, and CH4 over Kiruna, Sweden
Authors: Griesfeller A. , Griesfeller J. , Hase F. , Kramer I. , Loës P. , Mikuteit S. , Raffalski U. , Blumenstock T. , Nakajima H.
Published: June 2006

The Improved Limb Atmospheric Spectrometer‐II (ILAS‐II), a solar occultation instrument, was developed by the Ministry of the Environment (MOE) of Japan as a successor to ILAS. The ILAS‐II was launched on board the Advanced Earth Observing Satellite‐II (ADEOS‐II) satellite in December 2002 and took measurements between February and October 2003. Ground‐based Fourier transform infrared (FTIR) measurements were taken at Kiruna (northern Sweden, 68°N, 20°E) as part of ILAS‐II validation. These ground‐based observations of vertical profiles of O3, HNO3, N2O, and CH4 were compared to ILAS‐II measurements processed by the version 1.4 retrieval algorithm. Nineteen coincident FTIR and ILAS‐II observations were determined and analyzed. The ILAS‐II profiles had considerably better vertical resolution than the ground‐based profiles. The vertical resolution of the ILAS‐II profiles was therefore degraded to facilitate comparison between the two sets of profiles. Average relative differences were within 10 to 15% for all four gases. The ILAS‐II measurements of O3, N2O, and CH4 had a negative bias relative to the FTIR measurements. However, the bias of ILAS‐II measurements relative to the FTIR measurements was positive for HNO3.
Ice water content and precipitation rate as a function of equivalent radar reflectivity and temperature based on in situ observations
Authors: Boudala Faisal S. , Isaac George A. , Hudak David
Published: June 2006

Using ice particle spectra measured in stratiform ice clouds in midlatitude and Arctic regions, ice water content (IWC) and precipitation rate (Fm) retrieval algorithms as a function of temperature and radar reflectivity factor (Z) have been developed. These parameterizations were compared with (1) direct measurements of IWC using a Nevzorov probe, (2) precipitation retrieved using an X‐band Doppler scanning radar and a Precipitation Occurrence Sensor System (POSS), (3) the Canadian Global Environmental Multiscale (GEM) and High‐Resolution Model Application Project (HIMAP) models, and (4) derived IWC and precipitation from measured ice spectra during four field projects. The derived IWC and Fm from measured spectra have a correlation coefficient (r) better than 0.8. The IWC retrieved using the X‐band scanning radar during the First Alliance Icing Research Studies (AIRS I) agreed with IWC measured using the Nevzorov Probe much better than conventional IWC retrieval schemes. The retrieved precipitation rate based on the new algorithm using the POSS reflectivity measurements during the Second Alliance Icing Research Study (AIRS II) project agreed reasonably well with the precipitation rates predicted by the GEM and HIMAP models. This study clearly demonstrated that conventional IWC‐Ze relationships fail to replicate the IWC measured with Nevzorov probe. Furthermore, the Fm –Z relationship currently in use in the Canadian operational radar network appears to underestimate the ice precipitation rate. However, since there are some uncertainties in the direct measurements of IWC and no reliable direct measurements of precipitation, further studies are required to validate these parameterizations.
Assessment of the consistency of near‐infrared water vapor line intensities using high‐spectral‐resolution ground‐based Fourier transform measurements of solar radiation
Authors: Casanova Sophie E. B. , Shine Keith P. , Gardiner Tom , Coleman Marc , Pegrum Heather
Published: June 2006

Calculations of the absorption of solar radiation by atmospheric gases, and water vapor in particular, are dependent on the quality of databases of spectral line parameters. There has been increasing scrutiny of databases such as HITRAN in recent years, but this has mostly been performed on a band‐by‐band basis. We report nine high‐spectral‐resolution (0.03 cm−1) measurements of the solar radiation reaching the surface in southern England over the wave number range 2000 to 12,500 cm−1 (0.8 to 5 μm) that allow a unique assessment of the consistency of the spectral line databases over this entire spectral region. The data are assessed in terms of the modeled water vapor column that is required to bring calculations and observations into agreement; for an entirely consistent database, this water vapor column should be constant with frequency. For the HITRAN01 database, the spread in water vapor column is about 11%, with distinct shifts between different spectral regions. The HITRAN04 database is in significantly better agreement (about 5% spread) in the completely updated 3000 to 8000 cm−1 spectral region, but inconsistencies between individual spectral regions remain: for example, in the 8000 to 9500 cm−1 spectral region, the results indicate an 18% (±1%) underestimate in line intensities with respect to the 3000 to 8000 cm−1 region. These measurements also indicate the impact of isotopic fractionation of water vapor in the 2500 to 2900 cm−1 range, where HDO lines dominate over the lines of the most abundant isotope of H2O.
Role of boundary layer and cumulus convection on dust emission and transport over a midlatitude desert area
Authors: Takemi Tetsuya , Yasui Motoaki , Zhou Jixia , Liu Lichao
Published: June 2006

A series of high‐resolution simulations explicitly resolving diurnally varying convective motion is performed for investigating the dynamical processes of dust emission and transport induced by boundary layer and cumulus convection under fair‐weather conditions in a midlatitude desert area. The simulation set examines the sensitivity of the dust dynamics to vertical wind shear, upper level wind speed, and moist convection. The simulated results qualitatively capture the diurnal variation of the dust layer observed by lidar in a desert area in northern China. Dry convection plays a primary role in vertically mixing dust within the boundary layer. If cumulus convection also comes into play, mass concentration of dust increases not only within the boundary layer but also in the free troposphere. A coupled effect of dry and moist convection is important because convection is more enhanced with the coupled effect than without moist processes and in addition transports upper level higher momentum down to the surface, intensifying surface winds and hence dust emission. A wind speed exceeding the threshold for surface dust emission is necessary at the upper levels of the daytime boundary layer for the surface wind enhancement. Although the amount of dust lifted is much smaller during a single diurnal cycle of fair weather than is associated with a single case of synoptic disturbances, the total amount of dust emission due to fair‐weather processes may not be neglected in a longer timescale. This suggests that a proper parameterization for dry and moist convection in fair weather needs to be employed in large‐scale simulations.
Summer moisture availability across North America
Authors: van der Schrier G. , Briffa K. R. , Osborn T. J. , Cook E. R.
Published: June 2006

Maps of the monthly self‐calibrating Palmer drought severity index (SCPDSI) have been calculated for the period 1901–2002 for the contiguous United States (20°–50°N and 130°–60°W) with a spatial resolution of 0.5° × 0.5°. The recently introduced SCPDSI improves upon the more common Palmer drought severity index by maintaining a more consistent behavior of the index and hence comparability over diverse climatological regions. Although the self‐calibrating PDSI and the “traditional” PDSI averaged over the contiguous United States correlate well, large differences were found for extensive areas. Over the area as whole the 1930s and 1950s stand out as times of persistent and exceptionally dry conditions, whereas the 1970s and the 1990s were generally wet. Over 55% of the Untied States saw moderate to extreme drought in 1934 and over 40% of the area was affected during the 1954–1956 drought. The wettest year, 1983, saw over 45% of the contiguous United States affected by moderate to extreme wet conditions. Three leading modes of coherent summer moisture variability are identified, and they have their largest loading over the northwestern United States, the southern plains, and the southwestern United States, respectively. No evidence is found for a statistically significant trend in the percentage area of the contiguous United States experiencing either moderate or extreme moisture availability conditions for the 1901–2002 period.
Kinematics of orocline tightening in the core of an arc: Paleomagnetic analysis of the Ponga Unit, Cantabrian Arc, northern Spain
Authors: Weil Arlo Brandon
Published: June 2006

Paleomagnetic and structural analyses of the Western European Variscan Belt (WEVB) suggest that the most viable kinematic model for Variscan deformation in northern Iberia is oroclinal bending of an originally linear belt in a two‐stage tectonic history. This history represents two regional compression phases (E‐W in the Late Carboniferous and N‐S in the Permian, both in present‐day coordinates), which resulted in the refolding (about steeply plunging axes) of initially north‐south trending thrusts and folds in the hinge zone, and oroclinal tightening due to vertical axis rotation of the belt's limbs. However, the orocline model has yet to be critically tested in the WEVB's core. This study reports new paleomagnetic, rock magnetic, and structural data from the inner core of the WEVB in order to test opposing kinematic models for the well‐documented fault and fold interference structures formed by late stage Variscan deformation and to better understand the overall development of the WEVB arc. Map‐scale structural features within the WEVB core have a highly sinuous geometry characterized by transverse and thrust‐parallel fold systems formed by fault bend folding over footwall ramps. The intersections of these two fold systems produce steeply plunging interference folds, which are best exposed in the Ponga thrust unit. A total of 67 paleomagnetic sites were collected in the Barcaliente Formation of the Ponga Unit, with emphasis placed on detailed spatial coverage of individual structural domains. A multicomponent paleomagnetic remanence was measured, which is interpreted to be composed of two components; a low unblocking temperature recent viscous magnetization and a high unblocking temperature ancient magnetization that was acquired in the latest Stephanian to Early Permian after initial D1 thrusting and folding bur prior to major secondary rotation. Rock magnetic experiments show that the characteristic remanence magnetization is carried by secondary authigenic pseudosingle‐domain magnetite. These paleomagnetic results are used to determine the kinematics and geometry of postmagnetization deformation by restoring in situ magnetic vectors back to a defined reference direction. On the basis of the restored Ponga Unit geometry, the steeply plunging interference folds found in the WEVB core are best described by a combination of secondary buckling of frontal‐ramp‐parallel hanging wall anticlines and modification of D1 lateral/oblique ramps as frontal ramps during late stage north‐south shortening. This combination of structural modification of the inner core of the WEVB was necessary to accommodate oroclinal bending during the final amalgamation of Pangea in the late Paleozoic.
Global auroral response to negative pressure impulses
Authors: Liou K. , Newell P. T. , Sotirelis T. , Meng C.‐I.
Published: June 2006

It is well known that sharp increases/decreases in the solar wind dynamic pressure can result in sudden compression/decompression of the magnetosphere and subsequent magnetic positive/negative impulses (SI+/SI−) detected on the ground magnetometers. While the large‐scale enhancement of aurora during an SI+ has been well established, the response of aurora to an SI− is still little known. This prompts an interesting question whether the response of the global aurora to an SI− mirrors the response to an SI+. This letter reports results from a study of auroral images, acquired from the ultraviolet imager (UVI) on board the Polar satellite, during 13 SI− events. It is found that, in most cases, the luminosity of the aurora indeed showed a clear decrease almost immediately after the decompression. In some cases, the luminosity decrease exhibits a day‐to‐night fading effect and is consistent with the tailward propagation of the magnetosphere decompression front. Auroral particle observations from DMSP indicate that reduction of CPS electron precipitation is the major cause of the large‐scale auroral dimming. We propose that an induction electric field triggered by the sudden expansion of the magnetosphere at the expansion front along with adiabatic decompression and magnetic reconfiguration are responsible for the observed effect.
Forest on the edge: Seasonal cloud forest in Oman creates its own ecological niche
Authors: Hildebrandt Anke , Eltahir Elfatih A. B.
Published: June 2006

Cloud forests usually grow in the moist tropics where water is not a limiting factor to plant growth. Here, for the first time, we describe the hydrology of a water limited seasonal cloud forest in the Dhofar mountains of Oman. This ecosystem is under significant stress from camels feeding on tree canopies. The Dhofar forests are the remnants of a moist vegetation belt, which once spread across the Arabian Peninsula. According to our investigation the process of cloud immersion during the summer season creates within this desert a niche for moist woodland vegetation. Woodland vegetation survives in this ecosystem, sustained through enhanced capture of cloud water by their canopies (horizontal precipitation). Degraded land lacks this additional water source, which inhibits re‐establishment of trees. Our modeling results suggest that cattle feeding may lead to irreversible destruction of one of the most diverse ecosystems in Arabia.
Mobility, Housing Stress, and Neighborhood Contexts: Evidence from Los Angeles
Authors: Clark William A V , Ledwith Valerie
Published: June 2006

In this paper we examine, in two separate analyses, actual and planned residential moves. Although we now have robust models and substantive empirical analysis of residential mobility, especially of the role of housing consumption and the variables that trigger residential moves, we are less clear about how the model applies to minority households and in diverse ethnic settings. We use data from the Los Angeles Family and Neighborhood Study—a longitudinal study of mobility and neighborhood change in the Los Angeles region—to contrast the mobility outcomes for white and Latino households. In a separate analysis we examine planned mobility and extend the analysis of the role of neighborhood variables in explaining expected mobility. Through the incorporation of measures of neighborhood satisfaction and dissatisfaction we find, as hypothesized, that low levels of satisfaction and whether or not the neighborhood is perceived as ‘close-knit’ are modest predictors of the likelihood of future moves. However, the additive effect of neighborhood variables on intentions, beyond the structural effects of age and housing needs, is quite small.
Green Groups and Grey Areas: Scientific Boundary-Work, Nongovernmental Organisations, and Environmental Knowledge
Authors: Eden Sally , Donaldson Andrew , Walker Gordon
Published: June 2006

In this paper we examine the role of nongovernmental organisations (NGOs) in debates about environmental science and knowledge, using empirical evidence from in-depth interviews with a range of NGOs involved in the waste debate in the United Kingdom. We discuss theoretical issues of scientific boundary-work and the construction of expertise and socially distributed knowledge, and then apply these to our empirical evidence. Our conclusions are that NGOs continue to subscribe to the notion of the preeminent authority of science in environmental debates, but also work partly in a more diverse, highly networked world of knowledge production which requires them to be pragmatic and versatile in how they legitimate knowledge from various sources. Hence, scientific knowledge is highly contingent in its authority, and dependent upon continual (re)negotiation.
Expert Conceptualisations of the Role of Lay Knowledge in Environmental Decisionmaking: challenges for Deliberative Democracy
Authors: Petts Judith , Brooks Catherine
Published: June 2006

The authors draw upon survey evidence of expert conceptualisations of the value of public knowledge in environmental decisionmaking. In the context of local air quality management in particular, they consider how experts understand the potential benefits of technological citizenship, and what status they accord to lay knowledge relative to their own roles. Evidence suggests a continuing expert-deficit model of lay knowledge, with suspicions that the public misunderstand environmental issues. Although the need for public ‘buy-in’ to the solutions to problems such as air pollution is supported, this does not translate to a more proactive engagement of lay knowledge in the assessment of such issues. Experts seem to be personally challenged by such notions. The authors discuss the need for a cultural shift in expert understanding of the value of lay knowledge, supported by a move away from an oversimplification of the need for, and value of, public participation.
Democratization and Capacity Building for Environmental Governance: Managing Land Subsidence in Taiwan
Authors: Tang Ching-Ping , Tang Shui-Yan
Published: June 2006

A major challenge for any decentralizing regime is to develop more inclusive and participatory decisionmaking processes and to be responsive to conflicting demands from diverse constituencies while maintaining its governing capacity. Using Taiwan's experience in managing groundwater overextraction and land subsidence in its coastal areas, in this paper we demonstrate how democratization at its early stages may create added difficulties for the political system to face when trying to solve environmental problems. Yet in the long run, democratization may lead to an increase in participative and integrative governing capacities, bringing about more effective and equitable solutions to complex environmental problems.
Network Relations and Local Economic Development: Some Causes of Differentiated Network Structures and Intensities among Turkish Industrial Firms
Authors: Eraydın Ayda , Fingleton Bernard
Published: June 2006

The regional-growth literature emphasises the importance of positive network externalities as determinants of the long-run competitiveness of region, highlighting their role in reducing spatial transaction costs and facilitating collective learning and innovation. In this paper we contribute to this literature by presenting new evidence from a firm-based survey within three Turkish industrial centres about the causes of differentiated network activity. Using multivariate analysis, we show that locational rather than sectoral differences explain local-linkage intensities, but this is not the case for global links. Second, there is an important relationship between firm size and local-linkage and global-linkage densities; the density of local networks decreases with increasing firm size, whereas the density of global networks increases with firm size. Third, there is a positive relation between globalnetwork density and firm productivity. We argue that the comparative and quantitative analysis we employ is a useful adjunct to case-study analysis, which could help avoid misconceptions and lead to a more realistic theory.
‘Adref’: Theoretical Contexts of Attachment to Place for Mature and Older People in Rural North Wales
Authors: Burholt Vanessa
Published: June 2006

In this paper I examine older people's attachment to place in rural Wales. The sample includes 406 people aged 70 years and over living in diverse rural communities of North Wales. Respondents were asked to divulge the main reason for wanting to stay in their present community. 522 individual verbatim statements were examined and seven key areas of attachment to place were identified: general locational satisfaction, historical perspective, aesthetic and emotional components of location, social support, social integration, appropriateness of the environment, and relocation constraints. Each of these areas is explored with reference to different theoretical perspectives. I conclude that the multifaceted nature of place attachment requires a multidisciplinary approach to the study of people and their environments. A four-domain conceptual scheme of attachment to place is developed that takes into account the interrelationship between physical, social, temporal, and psychological factors. These domains of place attachment are closely intertwined, and strongly related to each other.
Dynamics of clusters: From elementary to biological structures
Authors: Cheng Po-Yuan , Baskin J. Spencer , Zewail Ahmed H.
Published: June 2006

Between isolated atoms or molecules and bulk materials there lies a class of unique structures, known as clusters, that consist of a few to hundreds of atoms or molecules. Within this range of “nanophase,” many physical and chemical properties of the materials evolve as a function of cluster size, and materials may exhibit novel properties due to quantum confinement effects. Understanding these phenomena is in its own rights fundamental, but clusters have the additional advantage of being controllable model systems for unraveling the complexity of condensed-phase and biological structures, not to mention their vanguard role in defining nanoscience and nanotechnology. Over the last two decades, much progress has been made, and this short overview highlights our own involvement in developing cluster dynamics, from the first experiments on elementary systems to model systems in the condensed phase, and on to biological structures.
Electron and boson clusters in confined geometries: Symmetry breaking in quantum dots and harmonic traps
Authors: Yannouleas Constantine , Landman Uzi
Published: June 2006

We discuss the formation of crystalline electron clusters in semiconductor quantum dots and of crystalline patterns of neutral bosons in harmonic traps. In a first example, we use calculations for two electrons in an elliptic quantum dot to show that the electrons can localize and form a molecular dimer. The calculated singlet–triplet splitting (
J
) as a function of the magnetic field (
B
) agrees with cotunneling measurements with its behavior reflecting the effective dissociation of the dimer for large
B
. Knowledge of the dot shape and of
J
(
B
) allows determination of the degree of entanglement. In a second example, we study strongly repelling neutral bosons in two-dimensional harmonic traps. Going beyond the Gross–Pitaevskii (GP) mean-field approximation, we show that bosons can localize and form polygonal-ring-like crystalline patterns. The total energy of the crystalline phase saturates in contrast to the GP solution, and its spatial extent becomes smaller than that of the GP condensate.
Ultrafast dynamics in atomic clusters: Analysis and control
Authors: Bonačić-Koutecký Vlasta , Mitrić Roland , Werner Ute , Wöste Ludger , Berry R. Stephen
Published: June 2006

We present a study of dynamics and ultrafast observables in the frame of pump–probe negative-to-neutral-to-positive ion (NeNePo) spectroscopy illustrated by the examples of bimetallic trimers Ag
2
Au
−
/Ag
2
Au/Ag
2
Au
+
and silver oxides Ag
3
O
2
−
/Ag
3
O
2
/Ag
3
O
2
+
in the context of cluster reactivity. First principle multistate adiabatic dynamics allows us to determine time scales of different ultrafast processes and conditions under which these processes can be experimentally observed. Furthermore, we present a strategy for optimal pump–dump control in complex systems based on the
ab initio
Wigner distribution approach and apply it to tailor laser fields for selective control of the isomerization process in Na
3
F
2
.
The shapes of pulses can be assigned to underlying processes, and therefore control can be used as a tool for analysis.
Multiple self-localized electronic states in
trans
-polyacetylene
Authors: Lin Xi , Li Ju , Först Clemens J. , Yip Sidney
Published: June 2006

Electronic structure calculations on a conjugated polymer chain by Hartree–Fock and density functional theory show a sequence of self-localized states, which stand in contrast to the single self-localized soliton state described by the Su–Schrieffer–Heeger model Hamiltonian. An extended Hubbard model, which treats electron–electron interactions up to second neighbors, is constructed to demonstrate that the additional states arise from a strong band-bending effect due to the presence of localized electric fields of charged solitons. We suggest the optical response of these electronic states may be associated with the near-edge oscillations observed in photo-induced absorption spectra. Our calculations indicate further that in the presence of counterions, the additional localized states continue to exist. Implications regarding soliton mobility and high-resolution ion sensing are briefly discussed.
Influence of the hinge region on complement activation, C1q binding, and segmental flexibility in chimeric human immunoglobulins.
Authors: Tan L K , Shopes R J , Oi V T , Morrison S L
Published: June 2006

We have characterized a series of genetically engineered chimeric human IgG3 and IgG4 anti-dansyl (DNS) antibodies with identical antibody-combining sites but different hinge region amino acid compositions to determine how the hinge region influences Fab fragment segmental flexibility, C1q binding, and complement activation. Our data support the correlation between "upper hinge" length and Fab segmental flexibility; moreover, we confirm that a hinge region is essential for C1q binding and complement activation. However, the hinge length by itself is not sufficient for complement activity in IgG molecules. We have demonstrated that the IgG4 hinge, which imparts restricted segmental flexibility, reduces the ability of IgG3 molecules to activate complement. We also find that the IgG3 hinge region, which imparts greater segmental motion, is not sufficient to create complement activation activity in IgG4 anti-DNS antibodies. Finally, we conclude that (i) segmental motion is correlated with "upper hinge" length, (ii) hinge length and segmental flexibility is not enough to alter complement binding and activation, and (iii) segmental flexibility does not correlate with proficiency to activate the complement cascade.
gamma-Preprotachykinin-(72-92)-peptide amide: an endogenous preprotachykinin I gene-derived peptide that preferentially binds to neurokinin-2 receptors.
Authors: Dam T V , Takeda Y , Krause J E , Escher E , Quirion R
Published: June 2006

The presence of N-terminally extended forms of neurokinin A has recently been reported in the mammalian brain. Among them, gamma-preprotachykinin-(72-92)-peptide amide [gamma-PPT-(72-92)-NH2], a peptide derived by posttranslational processing of gamma-preprotachykinin, is most prominent. We report here that this peptide most likely acts on neurokinin-2 receptor sites since neurokinin A (a putative neurokinin-2 agonist) and gamma-PPT-(72-92)-NH2 are potent competitors of 125I-labeled gamma-PPT-(72-92)-NH2 binding whereas selective neurokinin-1 and -3 agonists are not. Moreover, the distribution of 125I-labeled gamma-PPT-(72-92)-NH2 and 125I-labeled neurokinin A binding sites are very similar in rat brain. On the other hand, 125I-labeled Bolton-Hunter-substance P (a neurokinin-1 ligand) and 125I-labeled Bolton-Hunter-eledoisin (a neurokinin-3 ligand) binding sites are differentially located in this tissue. Thus, it appears that gamma-PPT-(72-92)-NH2 binds to neurokinin-2 receptors and should be considered as a putative endogenous ligand for this receptor class.
Unusual molecular characteristics of a repeat sequence island within a Giemsa-positive band on the mouse X chromosome.
Authors: Nasir J , Fisher E M , Brockdorff N , Disteche C M , Lyon M F , Brown S D
Published: June 2006

The mouse genome contains 50 copies of a long complex repeat unit localized as a repeat sequence island to the A3 Giemsa-positive (dark) band on the mouse X chromosome. The repeat units are not tandemly arranged but are juxtaposed and inserted by unrelated sequences of high repetition. The repeat sequence island possesses two notable features that have been suggested as diagnostic features of mammalian Giemsa-positive bands. First, the repeat sequence island encompasses a 1-megabase region devoid of CpG islands; second, it features a high concentration of L1 long interspersed repeat sequences.
Evolutionary changes in influenza B are not primarily governed by antibody selection.
Authors: Air G M , Gibbs A J , Laver W G , Webster R G
Published: June 2006

Influenza B viruses evolve more slowly than human influenza A, but no reasons for the difference have been established. We have analyzed sequence changes in the hemagglutinin and neuraminidase of influenza B viruses (and have determined four hemagglutinin sequences, of B/Bonn/43, B/USSR/100/83, B/Victoria/3/85, and B/Memphis/6/86) in relation to antigenic properties and compared these with similar analyses of variation in influenza A antigens. Independent of the slower rate of change in influenza B antigens, only approximately 30% of nucleotide changes in either the hemagglutinin or neuraminidase gene sequence result in amino acid changes in the protein, whereas in influenza A 50% of nucleotide changes result in altered amino acids. Thus, there is less selection for change, or less tolerance to change, in the influenza B antigens. This is similar to findings with influenza C and findings with influenza A viruses that replicate in lower animals and birds and is closer to the type of variation found in other RNA viruses. We propose that human influenza A is unique in that it is the only virus group in which antibody selection dominates evolutionary change.
A yeast artificial chromosome containing the mouse homeobox cluster Hox-2.
Authors: Rubock M J , Larin Z , Cook M , Papalopulu N , Krumlauf R , Lehrach H
Published: June 2006

We have isolated two genes, Hox-2.8 and Hox-2.9, from the mouse homeobox cluster Hox-2, located on chromosome 11. A 120-kilobase yeast artificial chromosome (YAC) containing a large region of the murine Hox-2 cluster, including 45 kilobases of sequence upstream of the most 5' gene, was cloned. The DNA sequence of the YAC is unrearranged relative to the genomic map. We have subcloned from the YAC insert a homeobox gene, Hox-2.8, whose homeodolmain is highly related to that of the Drosophila homeotic gene proboscopedia (pb). The expression pattern of Hox-2.8 during embryogenesis extends the trend established by genes from Hox-2.5 to -2.7 of successively anterior domains of expression in the neural tube. We have also subcloned and sequenced from a cosmid the labial (lab)-related Hox-2.9, the most 3' member of the cluster to date. These data lend further support to the idea of a common evolutionary origin of the mouse Hox and Drosophila HOM clusters. The YAC will enable us to construct modified forms of the Hox-2 cluster in yeast and to identify their effect on the phenotype of the animal in transgenic mouse strains.
Molecular cloning of a member of a third class of Shaker-family K+ channel genes in mammals.
Authors: McCormack T , Vega-Saenz de Miera E C , Rudy B
Published: June 2006

We report the cloning of RKShIIIA, a cDNA encoding a K+ channel sequence expressed in rat brain. This cDNA encodes K+ channel subunits that express in Xenopus oocytes a slow, 4-aminopyridine- and tetraethylammonium-sensitive, delayed rectifier-type K+ channel activated by large membrane depolarizations. This gene belongs to the Shaker (Sh) family of K+ channel genes, since the predicted protein has the same overall structure and shows significant homology to other members of this family. However, RKShIIIA cannot be assigned to either of the two known classes of Sh-family genes in mammals based on sequence analysis. Notable features of the RKShIIIA protein product include a probable cytoplasmic loop rich in prolines and a stretch very homologous to the Drosophila Shaw protein, both near the amino terminus.
Numbers of "blobs" in the primary visual cortex of neonatal and adult monkeys.
Authors: Purves D , LaMantia A S
Published: June 2006

We have examined the number of "blobs" (cytochrome oxidase-positive cortical modules) in the primary visual cortex (area 17) of infant and adult rhesus monkeys. The density of these iterated circuits--about five per mm2--was not significantly different in three newborn and three mature animals. Measurement of the surface of area 17 in serial sections, however, showed that the total area occupied by the primary visual cortex increases by about 50% during maturation. Based on these measurements, the number of blobs in this species is about 8000 at birth and about 12,000 in maturity. Evidently, these complex functional units are added gradually to the developing primate brain over a period that extends into postnatal life.
TGA1a, a tobacco DNA-binding protein, increases the rate of preinitiation complex formation in a plant in vitro transcription system [corrected]
Authors: Yamazaki K , Katagiri F , Imaseki H , Chua N H
Published: June 2006

We describe here a plant in vitro transcription system for class II promoters using wheat germ extract. In this system transcription is stimulated by TGA1a, a tobacco DNA-binding protein, and the stimulation is dependent on the presence of its cognate binding site upstream of the TATA box. Titration experiments showed that transcription initiation is more sensitive than transcription elongation to low concentrations of sarkosyl (N-lauroylsarcosine). At 0.07% sarkosyl, the formation of initiated complex is inhibited but transcription elongation is not. Under these conditions, events associated with a single round of transcription can be studied. We demonstrate that the time required for completing transcription of a 380-base-pair template is about 10 min. Addition of TGA1a increases the number of preinitiation complexes by approximately 3-fold with no significant effect on the frequency of transcription initiation from a single complex or on the rate of RNA elongation. We anticipate that this in vitro system will be valuable for the elucidation of mechanisms that regulate transcription in plants.
Chemical synthesis of the thymidylate synthase gene.
Authors: Climie S , Santi D V
Published: June 2006

A 978-base-pair gene that encodes thymidylate synthase (TS; 5,10-methylenetetrahydrofolate:dUMP C-methyltransferase, EC 2.1.1.45) from Lactobacillus casei has been synthesized and inserted into Escherichia coli expression vectors. The DNA sequence contains 35 unique restriction sites that are located an average of 28 base pairs apart throughout the entire length of the gene. A ribosome binding site was included 9 base pairs upstream from the translation start site and codon usage was adjusted to ensure efficient translation in E. coli. The TS gene is flanked by unique EcoRI and HindIII restriction sites that render the gene portable to any of several E. coli expression vectors. Catalytically active TS encoded by the synthetic gene is expressed in large amounts (10-20% of the soluble protein) and is indistinguishable from that isolated from L. casei. The utility of the synthetic gene for mutagenesis is demonstrated by a single experiment in which His-199 was replaced with 14 different amino acids. Analysis of the mutants by genetic complementation indicates that TS can tolerate a number of amino acid substitutions at that position and shows that His-199 is not strictly required for catalytic activity.
Tension in secretory granule membranes causes extensive membrane transfer through the exocytotic fusion pore.
Authors: Monck J R , Alvarez de Toledo G , Fernandez J M
Published: June 2006

For fusion to occur the repulsive forces between two interacting phospholipid bilayers must be reduced. In model systems, this can be achieved by increasing the surface tension of at least one of the membranes. However, there has so far been no evidence that the secretory granule membrane is under tension. We have been studying exocytosis by using the patch-clamp technique to measure the surface area of the plasma membrane of degranulating mast cells. When a secretory granule fuses with the plasma membrane there is a step increase in the cell surface area. Some fusion events are reversible, in which case we have found that the backstep is larger than the initial step, indicating that there is a net decrease in the area of the plasma membrane. The decrease has the following properties: (i) the magnitude is strongly dependent on the lifetime of the fusion event and can be extensive, representing as much as 40% of the initial granule surface area; (ii) the rate of decrease is independent of granule size; and (iii) the decrease is not dependent on swelling of the secretory granule matrix. We conclude that the granule membrane is under tension and that this tension causes a net transfer of membrane from the plasma membrane to the secretory granule, while they are connected by the fusion pore. The high membrane tension in the secretory granule may be the critical stress necessary for bringing about exocytotic fusion.
Extracellular ATP in T-lymphocyte activation: possible role in effector functions.
Authors: Filippini A , Taffs R E , Sitkovsky M V
Published: June 2006

We hypothesized that cytolytic T lymphocytes (CTL) may utilize extracellular ATP (ATPo) during the effector phase of the CTL-target cell interactions and that CTL could be the source of ATPo. It is demonstrated here that incubation of CTL with activating ligands [Con A or monoclonal antibody (mAb) to the T-cell antigen receptor (TCR)] results in the extracellular Ca2(+)-independent accumulation of the ATPo. The addition of the ATP-degrading enzymes into the mixture of CTL and target cells results in a strong inhibition of the CTL-mediated, TCR-triggered lethal-hit delivery to the target cell. In a parallel control experiment, the employed enzymes did not affect target cell-induced, TCR-triggered exocytosis of granules from CTL. Thus, the removal of ATPo with enzymes does not interfere with the activation of CTL by the target cell but does block lytic events. Cloned helper T lymphocytes also accumulate ATPo after incubation with anti-TCR mAb or Con A, suggesting the possibility that ATPo, which acts in concert with ectoprotein kinases and/or purinergic receptors, may be of general use as a messenger in cellular interactions of T lymphocytes.
Host genes that influence transposition in yeast: the abundance of a rare tRNA regulates Ty1 transposition frequency.
Authors: Xu H , Boeke J D
Published: June 2006

Genetic screening of a yeast genomic library in a high-copy-number vector identified the normally single copy tRNA(CCU Arg) gene as one of the genes and reduces Ty1 transposition frequency when overexpressed. Immunoblot analyses of Ty1-encoded proteins indicate an inverse correlation between the copy number of the tRNA gene and the production of the TYB protein. Thus, Ty1 transposition frequency is apparently regulated by the level of tRNA(CCU Arg) in yeast cells.
Immunocytology on microwave-fixed cells reveals rapid and agonist-specific changes in subcellular accumulation patterns for cAMP or cGMP.
Authors: Barsony J , Marx S J
Published: June 2006

We developed a method for cAMP and cGMP immunocytology based upon fixation by microwave irradiation. Fixation by microwave irradiation prevented three problems found with other fixation methods: nucleotide loss from cells, nucleotide diffusion within cells, and chemical modification of immunologic epitopes. Six agonists (four that stimulate adenylate cyclase and two that stimulate guanylate cyclase) produced cAMP or cGMP accumulation patterns that were agonist-specific, dose-dependent, detectable at physiologic concentrations of hormone, and time-dependent within 15 sec to 30 min. cAMP accumulation after 1 mM forskolin was greatest in the nucleus. Isoproterenol, prostaglandin E2, or calcitonin caused initial accumulation of cAMP along the plasma membrane, but later accumulation was greater in the cytoplasm. With calcitonin the later accumulation of cAMP was selectively perinuclear and along the nuclear membrane. Sodium nitroprusside stimulated cGMP accumulation diffusely throughout the cytoplasm. Atrial natriuretic peptide initiated cGMP accumulation near the plasma membrane, and cGMP accumulation moved from there into the cytoplasm. In conclusion, microwave irradiation preserved cell structure and allowed visualization of expected as well as unsuspected changes in intracellular accumulation patterns of cAMP and cGMP.
RETRACTED: Amino acid variations at a single residue in an autoimmune peptide profoundly affect its properties: T-cell activation, major histocompatibility complex binding, and ability to block experimental allergic encephalomyelitis.
Authors: Kumar V , Urban J L , Horvath S J , Hood L
Published: June 2006

Myelin basic protein (MBP) or helper T cells reactive against MBP induce an autoimmune disease, experimental allergic encephalomyelitis, in B10.PL and PL/J inbred mice. In both strains, virtually the entire repertoire of MBP-specific T cells recognize an N-terminal peptide fragment in the context of the I-Au molecule encoded by the major histocompatibility complex (MHC) and utilize a very limited set of T-cell receptor genes. To delineate the nature of the trimolecular complex, consisting of the T-cell receptor, MBP-peptide fragment, and MHC molecule (I-Au), we have synthesized 13 variants of the 9-mer N-terminal immunodominant peptide differing at residue 4 and studied their immune recognition in vitro and in vivo. These substitutions have a striking range of effects on T-cell activation, ability to bind to the MHC molecule, and initiation of immune responses in vivo. An understanding of the autoimmune peptide/MHC/T-cell receptor interactions allowed us to design variant 9-mer peptides that have high affinity for an MHC molecule and are effective in blocking experimental allergic encephalomyelitis, possibly through two distinct mechanisms, peripheral T-cell tolerance and the inhibition of binding of the encephalitogenic peptide to the MHC molecules.
Sequencing of peptides and proteins with blocked N-terminal amino acids: N-acetylserine or N-acetylthreonine.
Authors: Wellner D , Panneerselvam C , Horecker B L
Published: June 2006

Many proteins cannot be directly sequenced by Edman degradation because they have a blocked N-terminal residue. A method is presented for deblocking such proteins when the N-terminal residue is N-acetylserine (which occurs frequently in eukaryotic proteins) or N-acetylthreonine. The method has been applied successfully to the determination of the N-terminal amino acid sequence of human, bovine, and rat parathymosins. Prothymosin alpha and other blocked proteins and peptides were also readily deblocked and sequenced by this procedure. It is proposed that the mechanism of the deblocking reaction involves an acid-catalyzed N----O shift of the acetyl group followed by a beta-elimination.