bluuebunny/crossref_metadata_2025 huggingface dataset:
Increase and decrease of sea ice area in the Sea of Okhotsk: Ice production in coastal polynyas and dynamic thickening in convergence zones
Authors: Kimura Noriaki , Wakatsuchi Masaaki
Published: June 2004

This paper examines the production and reduction of sea ice area in the Sea of Okhotsk. Analyses were carried out for 10 winters (December–April) from 1991/1992 to 2000/2001 using daily data of sea ice velocity and concentration, derived from images of the Defense Meteorological Satellite Program (DMSP) Special Sensor Microwave Imager (SSM/I). First, we mapped sea ice divergence, which was calculated from the daily ice velocity field. In the case of offshore winds, high divergence was observed along the coastline, while there existed a broad convergence area with inshore winds. Next, we examined local changes in an area of sea ice. As in the case of ice divergence, ice production and reduction are strongly controlled by wind direction. We found that a large amount of sea ice was produced in coastal areas under offshore wind conditions. The geographical distribution of the ice production area agrees well with that of the well‐known coastal polynya areas. Our estimation shows that 8.7 × 105 km2 yr−1 of sea ice is produced in the northern coastal area, and 3.7 × 105 km2 yr−1 in the Sakhalin coastal area. In contrast, 7.4 × 105 km2 yr−1 of the ice area disappeared in Shantarskiy Bay. This reduction of ice area is mainly caused by dynamic deformation of existing ice forming rafted ice or pressure ridges. This dynamic deformation plays an important role, not only in the reduction of Okhotsk sea ice area, but also in the thickening of ice.
Intraseasonal variations of water vapor and cirrus clouds in the tropical upper troposphere
Authors: Eguchi Nawo , Shiotani Masato
Published: June 2004

Space‐time variations of tropical upper tropospheric water vapor and cirrus clouds associated with the intraseasonal oscillation (ISO) are investigated using data from the Microwave Limb Sounder (MLS) and the Cryogenic Limb Array Etalon Spectrometer (CLAES) on board the Upper Atmosphere Research Satellite (UARS). Composite moisture and meteorological fields based on five ISO events selected in two boreal winters (1991–1993) are analyzed using 20–80 day band‐pass‐filtered data. At 215 and 146 hPa, wet anomalies with frequent appearance of cirrus clouds exist over the convective system and move eastward from the Indian Ocean to the central Pacific, suggesting a direct effect of convective activity up to this level. At 100 hPa, however, the moisture field seems to be indirectly affected by convective activity through the dynamical response to the convective heating. Dry anomalies are observed over the Indian Ocean around the developing stage and over the eastern Pacific around the mature‐to‐decaying stage of the ISO. Cirrus clouds are frequently found over the cold region located to the east of the convective system. These structures around the tropopause level are closely related to the eastward moving Kelvin and Rossby wave responses to the convective heating with the equatorial cold anomaly and with the subtropical anticyclonic gyres. Between the two gyres the easterly wind blowing through the equatorial cold region may cause dehydration through cirrus formation when the convective system develops over the Indian Ocean and the western Pacific. As the northern gyre intensifies, tropical dry air is transported to the subtropical Pacific and eventually to the equatorial eastern Pacific. It is suggested that the temperature and flow variations due to the coupled Kelvin‐Rossby wave structure play an important role in dehydrating air in the tropical and subtropical tropopause region.
A three‐dimensional regional modeling study of the impact of clouds on sulfate distributions during TRACE‐P
Authors: Kittaka C. , Pierce R. B. , Crawford J. H. , Hitchman M. H. , Johnson D. R. , Tripoli G. J. , Chin M. , Bandy A. R. , Weber R. J. , Talbot R. W. , Anderson B. E.
Published: June 2004

The University of Wisconsin Nonhydrostatic Modeling System (UWNMS) is combined with an aqueous sulfur chemistry module to simulate the sulfate transport in east Asia during the Transport and Chemical Evolution Over the Pacific (TRACE‐P) period. The simulated results are compared with in situ and satellite measurements collected during the TRACE‐P period. The comparisons showed overestimates of sulfate mixing ratios by 20% between 1 and 6 km and underestimates by 30% near the surface and by 50% above 6 km. The comparisons of the sulfate mixing ratios between the simulation and the measurements for a case study of a convective system showed an excellent agreement in the background sulfate mixing ratios. The simulated sulfate mixing ratios in cloudy regions, however, were underestimated by a factor of 2. Volume‐integrated sulfate mass in the model domain is calculated. Significant amounts of sulfate (volume‐integrated mass 1.5 × 106 to 7.5 × 106 kg) are released into air after being produced in clouds through the oxidation of sulfur dioxide by hydrogen peroxide. Instantaneous sulfate mass within clouds varies from 0.2 × 106 to 3.5 × 106 kg. Sulfate mass removed through precipitation is in the ranges between 0.01 × 106 and 1.8 × 106 kg. Sulfate mass in ice clouds was 2 orders of magnitude smaller than that in liquid clouds. This study shows that the sulfate input to the atmosphere exceeds the sulfate removed from the atmosphere through precipitation in the east Asian region during the TRACE‐P. Consequently, east Asia in spring can be an important source region of sulfate and thus can offset the sulfate loss through precipitation scavenging in other regions of the globe.
Aerosol particles from tropical convective systems: Cloud tops and cirrus anvils
Authors: Kojima Tomoko , Buseck Peter R. , Wilson James C. , Reeves J. Michael , Mahoney Michael J.
Published: June 2004

Aerosol particles from the upper troposphere (UT) and lower stratosphere (LS) were collected during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers‐Florida Area Cirrus Experiment (CRYSTAL‐FACE) and studied by transmission electron microscopy (TEM). Samples were classified into three categories: (1) UT in‐cloud, (2) UT out‐of‐cloud, and (3) LS. Sulfate particles, including former H2SO4 droplets, are dominant in samples from all categories. The morphology of H2SO4 droplets indicates that they had been ammoniated to some extent at the time of collection. They are internally mixed with organic materials, metal sulfates, and solid particles of various compositions. K‐ and S‐bearing organic particles and Si‐Al‐rich particles are common to the three kinds of samples. In‐cloud samples contain abundant Zn‐rich particles. Their origin is unclear, but it seems likely that they are contaminants that originated through impact by ice cloud particles on the aircraft or sampling system. Ammoniation and internal mixing of H2SO4 in the UT aerosols may result in freezing at higher temperature than in pure H2SO4 aerosols. The relatively high extent of ammoniation in the UT in‐cloud samples may have resulted from vertical transport of ammonia by strong convection. Abundances of nonsulfate particles decrease with increasing altitudes. The nonsulfate particles originated from the lower troposphere and were transported to the UT and LS.
A new coupling algorithm for density‐driven flow in porous media
Authors: Ackerer Philippe , Younès Anis , Mancip Martial
Published: June 2004

We consider the numerical solution of coupled fluid flow and heat or mass transport in porous media. The aim of this work is to provide some new mathematical development and algorithm to reduce the CPU costs of the solution of these strongly non‐linear coupled equations widely used in geosciences and environmental sciences, without lost of accuracy. Usually, the flow equation is solved first. We show that, by solving the transport equation first, the CPU time can be significantly reduced. This new algorithm is not dependent on the numerical scheme and is quite easy to implement in a numerical code. The accuracy of this new way of coupling flow and transport equations is evaluated with 2D and 3D numerical tests.
Localization of self‐potential sources in volcano‐electric effect with complex continuous wavelet transform and electrical tomography methods for an active volcano
Authors: Saracco Ginette , Labazuy Philippe , Moreau Frédérique
Published: June 2004

This study concerns the fluid flow circulation associated with magmatic intrusion during volcanic eruptions from electrical tomography studies. The objective is to localize and characterize the sources responsible for electrical disturbances during a time evolution survey between 1993 and 1999 of an active volcano, the Piton de la Fournaise. We have applied a dipolar probability tomography and a multi‐scale analysis on synthetic and experimental SP data. We show the advantage of the complex continuous wavelet transform which allows to obtain directional information from the phase without a priori information on sources. In both cases, we point out a translation of potential sources through the upper depths during periods preceding a volcanic eruption around specific faults or structural features. The set of parameters obtained (vertical and horizontal localization, multipolar degree and inclination) could be taken into account as criteria to define volcanic precursors.
Delayed impact of the North Atlantic Oscillation on biosphere productivity in Asia
Authors: Wang Guiling , You Liangzhi
Published: June 2004

This study examines the relationship between the North Atlantic Oscillation (NAO) and vegetation productivity in Asia inferred from both provincial crop yields data in China and satellite‐derived Normalized Difference Vegetation Index data. Our finding suggests that vegetation productivity in northern Asia during the main growing season correlates significantly to NAO, with a surprising long delay of 1.5 years. Correlation at shorter time lags, which was the focus of previous studies, is weak and not significant between the NAO index and vegetation activities in Asia. This suggests the existence of a so‐far unrecognized mechanism that carries the NAO signal for multiple years. The lagged vegetation response also provides the potential for NAO to serve as a predictor for crop yields in China.
Use of Moderate‐Resolution Imaging Spectroradiometer bidirectional reflectance distribution function products to enhance simulated surface albedos
Authors: Roesch Andreas , Schaaf Crystal , Gao Feng
Published: June 2004

Moderate‐Resolution Imaging Spectroradiometer (MODIS) surface albedo at high spatial and spectral resolution is compared with other remotely sensed climatologies, ground‐based data, and albedos simulated with the European Center/Hamburg 4 (ECHAM4) global climate model at T42 resolution. The study demonstrates the importance of MODIS data in assessing and improving albedo parameterizations in weather forecast and climate models. The remotely sensed PINKER surface albedo climatology follows the MODIS estimates fairly well in both the visible and near‐infrared spectra, whereas ECHAM4 simulates high positive albedo biases over snow‐covered boreal forests and the Himalayas. In contrast, the ECHAM4 albedo is probably too low over the Sahara sand desert and adjacent steppes. The study clearly indicates that neglecting albedo variations within T42 grid boxes leads to significant errors in the simulated regional climate and horizontal fluxes, mainly in mountainous and/or snow‐covered regions. MODIS surface albedo at 0.05 resolution agrees quite well with in situ field measurements collected at Baseline Surface Radiation Network (BSRN) sites during snow‐free periods, while significant positive biases are found under snow‐covered conditions, mainly due to differences in the vegetation cover at the BSRN site (short grass) and the vegetation within the larger MODIS grid box. Black sky (direct beam) albedo from the MODIS bidirectional reflectance distribution function model captures the diurnal albedo cycle at BSRN sites with sufficient accuracy. The greatest negative biases are generally found when the Sun is low. A realistic approach for relating albedo and zenith angle has been proposed. Detailed evaluations have demonstrated that ignoring the zenith angle dependence may lead to significant errors in the surface energy balance.
The impact of aerosols and gravity waves on cirrus clouds at midlatitudes
Authors: Haag W. , Kärcher B.
Published: June 2004

We use a Lagrangian microphysical aerosol‐cloud model to simulate cirrus clouds along trajectories at northern hemisphere midlatitudes. The model is constrained by recent in situ observations in terms of aerosol size distributions, freezing relative humidities, cooling rates, and cirrus particle sedimentation rates. Key features include competition between insoluble and volatile aerosol particles and temperature perturbations induced by high‐frequency gravity waves. Recent analyses of field measurements have revealed the crucial roles both factors play in cirrus formation. We show that most cirrus form in synoptic cold pools, but with microphysical properties determined by mesoscale variability in vertical velocities. Heterogeneous ice nuclei (IN) present in concentrations probably typical for northern midlatitude background conditions (<0.01–0.03 cm−3) significantly modify cirrus properties but do not control cirrus formation. The key effect of IN on cirrus clouds is a reduction of the number of ice crystals. This indirect aerosol effect results in reduced cloud albedo due to increased effective radii and decreased ice water contents, as well as in nonlinear changes of cirrus occurrence, optical extinction, and fraction of clouds that are subvisible. The nonlinear dependence of the three latter quantities appears when IN concentrations rise above a threshold concentration of some 0.01 cm−3, the exact value depending on the cloud formation temperature, cooling rate, and IN freezing relative humidity. In such conditions, IN become the controlling factor in cirrus formation, diminishing the role of homogeneous freezing. Ice nuclei with freezing thresholds near ice saturation are capable of introducing strong changes of cloud properties, even at low concentrations. Optically thin and subvisible cirrus are particularly susceptible to IN. The presence of a small number of IN (0.001 cm−3) can significantly increase their occurrence frequencies. If such clouds predominantly form on IN, they might be affected by anthropogenic activities. Changes in upper tropospheric cooling rates and ice‐forming aerosols in a future climate may induce changes in cirrus occurrence that are comparable in magnitude to observed decadal trends in global cirrus cover.
Restriction of BMP4 activity domains in the developing neural tube of the mouse embryo
Authors: Hu Qiyong , Ueno Naoto , Behringer Richard R
Published: June 2004

Bone morphogenetic protein (BMP) signals pattern the dorsal neural tube, defining distinct neuronal progenitor cell domains along the dorsoventral axis of the developing spinal cord. These dorsally expressed BMPs appear to have a limited range of action. The mechanisms that regulate this range of action are unclear. We created a GAL4/UAS bigenic mouse system to overexpress BMP4 or a mutant form of BMP4 (mutBMP4), which lacks a subset of amino‐terminal basic amino acids that limits its range of action, in the dorsal neural tube. UAS‐Bmp4 and UAS‐mutBmp4 responder genes were activated in the dorsal neural tube by a Wnt1‐GAL4 transgene. Analysis of the spinal cords of bigenic embryos that expressed comparable levels of transgenic transcripts revealed that mutBMP4 acted more ventrally in the neural tube than BMP4. This suggests that the amino‐terminal basic amino‐acid motif of mature BMP4 controls long‐range activity for dorsoventral patterning of the vertebrate neural tube.
Plexin‐B3 is a functional receptor for semaphorin 5A
Authors: Artigiani Stefania , Conrotto Paolo , Fazzari Pietro , Gilestro Giorgio F , Barberis Davide , Giordano Silvia , Comoglio Paolo M , Tamagnone Luca
Published: June 2004

Semaphorins are a large family of molecular cues implicated in neural development and in a variety of functions outside the nervous system. Semaphorin 5A (Sema5A) is a transmembrane semaphorin, containing seven thrombospondin type‐1 repeats, which was recently found to control axon guidance. Here we show that plexin‐B3 is a high‐affinity receptor specific for Sema5A. We further demonstrate that plexin‐B3 activation by Sema5A mediates functional responses in plexin‐B3‐expressing cells (either fibroblasts, epithelial and primary endothelial cells). In addition, Sema5A can trigger the intracellular signalling of the hepatocyte growth factor/scatter factor receptor, Met, associated in a complex with plexin‐B3. We thus conclude that Sema5A is able to elicit multiple functional responses through its receptor plexin‐B3.
14-3-3 Proteins and photoneuroendocrine transduction: role in controlling the daily rhythm in melatonin
Authors: Klein D. C. , Ganguly S. , Coon S. , Weller J. L. , Obsil T. , Hickman A. , Dyda F.
Published: June 2004

This paper describes the role 14-3-3 proteins play in vertebrate photoneuroendocrine transduction. 14-3-3 proteins form a complex with arylalkylamine N-acetyltransferase (AANAT), the enzyme which turns melatonin production on during the day and off at night. Complex formation is triggered at night by cAMP-dependent phosphorylation of the enzyme, and results in activation and protection against proteolysis. This enhances melatonin production > 10-fold. Light exposure results in dephosphorylation of the enzyme and disassociation from 14-3-3, leading to destruction and a rapid drop in melatonin production and release and circulating levels.
Plant 14-3-3 protein families: evidence for isoform-specific functions?
Authors: Roberts M. R. , de Bruxelles G. L.
Published: June 2004

14-3-3 proteins regulate a wide range of target proteins via direct protein-protein interactions. The target-binding domain in 14-3-3 proteins is highly conserved, suggesting similar biochemical properties for all 14-3-3s. However, higher eukaryotes possess multiple 14-3-3 genes, and these genes exhibit diverse patterns of gene expression within any one organism. This tends to suggest specific functions for particular genes. Some biochemical data suggest 14-3-3 isoform-specific protein-protein interactions, whereas other studies conclude that apparent isoform-specificity is the result of differences in expression patterns rather than in the biochemical properties of 14-3-3 isoforms. Here we discuss evidence that demonstrates that the expression levels of 14-3-3 proteins in cells are important for regulating the activity of their target proteins, and further that the elimination of individual 14-3-3 isoforms can result in detectable phenotypes. We also examine evidence that 14-3-3 isoform specificity can in some cases reflect differing biochemical properties as well as differential transcriptional regulation.
Affinity purification of diverse plant and human 14-3-3-binding partners
Authors: Milne F. C. , Moorhead G. , Rubio M. Pozuelo , Wong B. , Kulma A. , Harthill J. E. , Villadsen D. , Cotelle V. , MacKintosh C.
Published: June 2004

Many proteins that bind to a 14-3-3 column in competition with a 14-3-3-binding phospho-peptide have been purified from plant and mammalian cells and tissues. New 14-3-3 targets include enzymes of biosynthetic metabolism, vesicle trafficking, cell signalling and chromatin function. These findings indicate central regulatory roles for 14-3-3s in partitioning carbon among the pathways of sugar, amino acid, nucleotide and protein biosynthesis in plants. Our results also suggest that the current perception that 14-3-3s bind predominantly to signalling proteins in mammalian cells is incorrect, and has probably arisen because of the intensity of research on mammalian signalling and for technical reasons.
Use of 14-3-3 in the diagnosis of Creutzfeldt-Jakob disease
Authors: Green A. J. E.
Published: June 2004

The transmissible spongiform encephalopathies include human diseases such as Creutzfeldt-Jakob disease (CJD) and kuru as well as animal diseases such as scrapie and bovine spongiform encephalopathy (BSE). The emergence of variant CJD, which is causally related to BSE, has generated much interest in the development of rapid and sensitive diagnostic tests for the pre-mortem diagnosis of CJD. In 1986 two proteins were detected in the cerebrospinal fluid (CSF) of patients with sporadic CJD. These proteins were later demonstrated to be members of the 14-3-3 family, and tests for the detection of CSF 14-3-3 were developed. A number of studies have shown that the detection of CSF 14-3-3 is an accurate test for sporadic CJD, although the results with variant CJD are less promising.
Plant 14-3-3 proteins assist ion channels and pumps
Authors: de Boer A. H.
Published: June 2004

Turgor pressure is a cellular parameter, important for a range of physiological processes in plants, like cell elongation, gas exchange and gravitropic/phototropic bending. Regulation of turgor pressure involves ion and water transport at the expense of metabolic energy (ATP). The primary pump in the plasma membrane (the H+-ATPase) is a key player in turgor regulation since it provides the driving force for ion uptake, followed by water influx through osmosis. Using the phytotoxin fusicoccin (a well-known activator of the ATPase) as a tool, 14-3-3 proteins were identified as regulators of the H+-ATPase. Since fusicoccin has a dramatic effect on K+ accumulation and cellular respiration as well, we studied whether 14-3-3 proteins play a role in the regulation of the mitochondrial F0F1-ATP synthase and ion channels in the vacuolar and plasma membranes. Besides the plasma membrane H+-ATPase, we have identified thus far at least four other transport proteins that are regulated by 14-3-3 proteins. The mechanism of regulation will be described and the possibility that 14-3-3 proteins act as coordinators of ion transporters with varied but interdependent functions will be discussed.
Transcriptional regulation of the calcitonin receptor gene
Authors: Pondel M. D. , Jagger C. , Hebden C. , Partington G. , Mould R.
Published: June 2004

Calcitonin is a 32-amino-acid peptide hormone that is produced by parafollicular cells of the thyroid gland in response to increased levels of extracellular calcium. In this article we review our previous and current research on the transcriptional regulation of the pig and human calcitonin receptor (CTR) gene. Initially, our experiments on the transcriptional analysis of the pig CTR gene in transgenic mice are examined, followed by our studies on the cloning of the human CTR (hCTR) gene promoter and its transcriptional activity in hCTR-positive cell lines. We further describe the activity of the hCTR promoter in transgenic mice and review current experiments to identify transcriptional regulatory elements and the transcription factors they interact with, which direct the tissue-specific expression pattern of hCTR promoter activity.
Corticotropin-releasing hormone receptors
Authors: Hillhouse E. W. , Randeva H. , Ladds G. , Grammatopoulos D.
Published: June 2004

Corticotropin-releasing hormone (CRH) and related peptides (urocortins, sauvagine, urotensin) play a central role in the co-ordination of autonomic, behavioural, cardiovascular, immune and endocrine responses to stressful stimuli. Their actions are mediated through activation of two types of G-protein-coupled receptors encoded by separate genes. In this review we focus on the diverse structural and functional characteristics of the family of CRH-like peptides and their receptors.
Additional signals from VPAC/PAC family receptors
Authors: McCulloch D. A. , MacKenzie C. J. , Johnson M. S. , Robertson D. N. , Holland P. J. , Ronaldson E. , Lutz E. M. , Mitchell R.
Published: June 2004

The receptors for the neuropeptides vasoactive intestinal polypeptide and pituitary adenylate cyclase-activating polypeptide are strong activators of adenylate cyclase, but recent evidence suggests that they can elicit a number of additional intracellular signals. Some of these are likely to be downstream of the conventional adenylate cyclase pathway, but it is now clear that others reflect novel primary coupling events of the receptors.
A small sequence in the third intracellular loop of the VPAC1 receptor is responsible for its efficient coupling to the calcium effector
Authors: Langer I. , Vertongen P. , Perret J. , Waelbroeck M. , Robberecht P.
Published: June 2004

The stimulatory effect of vasoactive intestinal peptide (VIP) on the intracellular calcium concentration ([Ca2+]i) has been investigated in Chinese hamster ovary cells stably transfected with the reporter gene aequorin, and expressing human VPAC1, VPAC2, chimaeric VPAC1/VPAC2 or mutated receptors. The VIP-induced increase in [Ca2+]i was linearly correlated with receptor density, and was higher in cells expressing VPAC1 receptors than in cells expressing a similar density of VPAC2 receptors. The study was performed to establish the receptor sequence responsible for this difference. VPAC1/VPAC2 chimaeric receptors were first used for broad positioning: those receptors having the third intracellular loop (IC3) of the VPAC1 or the VPAC2 receptor behaved, in this respect, phenotypically like VPAC1 and VPAC2 receptors respectively. Replacement in the VPAC2 receptor of the sequence comprising residues 315–318 (VGGN) within IC3 by its VPAC1 receptor counterpart (residues 328–331; IRKS) and the introduction of VGGN instead of IRKS into VPAC1 was sufficient to mimic VPAC1 and VPAC2 receptor characteristics respectively. Thus a small sequence in the IC3 domain of the VPAC1 receptor is responsible for the efficient agonist-stimulated increase in [Ca2+]i.
Receptor component protein (RCP): a member of a multi-protein complex required for G-protein-coupled signal transduction
Authors: Prado M. A. , Evans-Bain B. , Dickerson I. M.
Published: June 2004

The calcitonin-gene-related peptide (CGRP) receptor component protein (RCP) is a 148-amino-acid intracellular protein that is required for G-protein-coupled signal transduction at receptors for the neuropeptide CGRP. RCP works in conjunction with two other proteins to constitute a functional CGRP receptor: calcitonin-receptor-like receptor (CRLR) and receptor-activity-modifying protein 1 (RAMP1).CRLR has the stereotypical seven-transmembrane topology of a G-protein-coupled receptor; it requires RAMP1 for trafficking to the cell surface and for ligand specificity, and requires RCP for coupling to the cellular signal transduction pathway. We have made cell lines that expressed an antisense construct of RCP and determined that CGRP-mediated signal transduction was reduced, while CGRP binding was unaffected. Furthermore, signalling at two other endogenous G-protein-coupled receptors was unaffected, suggesting that RCP was specific for a limited subset of receptors.
X-ray crystallographic studies of IgG-Fcγ receptor interactions
Authors: Sondermann P. , Oosthuizen V.
Published: June 2004

Human Fcγ receptors (FcγRs) for the Fc portion of IgG are major mediators of the adaptive immune response. Crystal structures of their extracellular domains were recently solved and shown to obey a common fold, resulting in a heart-shaped structure. Together with the multifunctional Fc fragment, whose structure was deciphered in the 1970s, the complex of an FcγR with Fc was recently crystallized. Its crystal structure indicates that despite the dimeric character of the Fc fragment, only one FcγR can bind to Fc, due to an introduced asymmetry within the homodimeric Fc, as well as by binding to symmetrically related residues of both Fc chains. Homology modelling suggested that the other FcγRs bind the Fc in a similar manner. The resolved complex structure can be regarded as a paradigm for Ig binding to Fc receptors and serves as a solid base for the design of compounds interfering with complex formation. Such molecules would be of invaluable benefit for the therapy of immunological disorders.
Engineering therapeutic antibodies for improved function
Authors: Presta L. G. , Shields R. L. , Namenuk A. K. , Hong K. , Meng Y. G.
Published: June 2004

The binding sites on human IgG1 for human Fcγ receptor (FcγR) I, FcγRIIa, FcγRIIb, FcγRIIIa and neonatal FcR have been mapped. A common set of IgG1 residues is involved in binding to all FcγRs, while FcγRII and FcγRIII utilize distinct sites outside this common set. In addition to residues which abrogated binding to the FcγR, several positions were found which improved binding only to specific FcγRs or simultaneously improved binding to one type of FcγR and reduced binding to another type. Selected IgG1 variants with improved binding to FcγRIIIa were then tested in an in vitro antibody-dependent cellular cytotoxicity (ADCC) assay and showed an enhancement in ADCC when either peripheral blood mononuclear cells or natural killer cells were used.
Bispecific antibodies targeting cancer cells
Authors: Peipp M. , Valerius T.
Published: June 2004

In recent years, antibody therapy has become a new treatment modality for tumour patients, although the majority of responses are only partial and not long lasting. Based on evidence that effector-cell-mediated mechanisms significantly contribute to antibody efficacy in vivo, several approaches are currently persued to improve the interaction between Fc receptor-expressing effector cells and tumour target antigens. These approaches include application of Fc receptor-directed bispecific antibodies, which contain one specificity for a tumour-related antigen and another for a cytotoxic Fc receptor on immune effector cells. Thereby, bispecific antibodies selectively engage cytotoxic trigger molecules on killer cells, avoiding, for example, interaction with inhibitory Fc receptors. In vitro, chemically linked bispecific antibodies directed against the Fcγ receptors FcγRIII (CD16) and FcγRI (CD64), and the Fc α receptor FcαRI (CD89), were significantly more effective than conventional IgG antibodies. Recent animal studies confirmed the therapeutic potential of these constructs. However, results from clinical trials have been less promising so far and have revealed clear limitations of these molecules, such as short plasma half-lives compared with conventional antibodies. In this review, we briefly summarize the scientific background for bispecific antibodies, and describe the rationale for the generation of novel recombinant molecules. These constructs may allow us to more specifically tailor pharmacokinetic properties to the demands of clinical applications.
Formatting antibody fragments to mediate specific therapeutic functions
Authors: Weir A. N. C. , Nesbitt A. , Chapman A. P. , Antoniw A. G. Popplewell P. , Lawson A. D. G.
Published: June 2004

Monoclonal antibodies are increasingly being used as therapeutic agents in a wide range of indications, including oncology, inflammation and infectious disease. In most cases the basis of the therapeutic function is the high degree of specificity and affinity the antibody-based drug has for its target antigen. However, the mechanism of action (MOA), the way the drug takes advantage of this specificity to mediate a therapeutic effect, varies considerably from drug to drug. Three basic potential categories of MOAs exist: antagonists, agonists and specific delivery mechanisms to target an active function to a particular cell type. The latter functions include selective cell killing, based on Fc-mediated events, recruitment of effector cells, and drug or radioisotope delivery. The majority of these mechanisms are not necessarily optimally mediated by an IgG structure; clearly, in the case of antibody-dependent cellular cytotoxicity or complement-mediated lysis, Fc is required. However, Fab fragments (the fragment comprising one antigen-binding arm of the Y-shaped IgG molecule) can be formatted to mediate most mechanisms and have the advantage that valency and half-life can be controlled to simplify the drug and address only the mechanism required. Moreover, Fab fragments can be produced in microbial expression systems which address manufacturing issues such as scale of supply and cost of goods.
Amino acid sequence requirements in the human IgAI hinge for cleavage by streptococcal IgAI proteases
Authors: Senior B. W. , Batten M. R. , Kilian M. , Woof J. M.
Published: June 2004

All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the α chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were constructed. The mutations were found to be without major effect upon the structure or functional abilities of the antibodies. However, they had a major effect upon their sensitivity to cleavage by some of the IgA1 proteases.
Amyloid fibril formation by human stefin B: influence of the initial pH-induced intermediate state
Authors: Žerovnik E. , Turk V. , Waltho J. P.
Published: June 2004

The amyloid fibril field is briefly described, with some stress put on differences between various proteins and possible role for domain swapping. In the main body of the text, first, a short review is given of the folding properties of both human stefins, α/β-type globular proteins of 53% identity with a known three-dimensional fold. Second, in vitro study of amyloid fibril formation by human stefin B (type I cystatin) is described. Solvents of pH 4.8 and pH 3.3 with and without 2,2,2-trifluoroethanol (TFE) were probed, as it has been shown previously that stefin B forms acid intermediates, a native-like and molten globule intermediate, respectively. The kinetics of fibrillation were measured by thioflavin T fluorescence and CD. At pH 3.3, the protein is initially in the molten globule state. The fibrillation is faster than at pH 4.8; however, there is more aggregation observed. On adding TFE at each pH, the fibril formation is further accelerated.
Therapeutics in Alzheimer's and Prion Diseases
Authors: Wisniewski T. , Brown D. R. , Sigurdsson E. M.
Published: June 2004

There is increasing recognition that numerous neurodegenerative conditions have the same underlying pathogenetic mechanism, namely a change in protein conformation, where the β-sheet content is increased. In Alzheimer's disease, amyloid deposition in the form of neuritic plaques and congophilic angiopathy is driven by the conversion of normal soluble amyloid-β peptide (sAβ) to Aβ plaques; while in the prionoses the critical event is the conversion of normal prion protein, PrPc, to the disease-associated form, PrPsc. This common theme in the pathogenesis of these disorders and the extracellular localization of the accumulating abnormal protein make them highly amenable to therapeutic approaches based on experimental manipulation of protein conformation and clearance. A number of different approaches under current development include drugs which affect the processing of the precursor proteins drugs the clearance of the amyloidogenic protein, and which inhibit or prevent the conformation change and immunological approaches. Particularly interesting are compounds termed ‘β-sheet breakers’ that directly target the abnormal conformational change both for Aβ- and PrPsc-related deposits. In addition, immune system activation can serve as β-sheet breakers and/or to increase the clearance of the disease-associated proteins. These conformation-based approaches appear to hold the best promise for therapies for this devastating group of disorders.
Terminal steps of haem biosynthesis
Authors: Dailey H. A.
Published: June 2004

The terminal three steps in haem biosynthesis are the oxidative decarboxylation of coproporphyrinogen III to protoporphyrinogen IX, followed by the six-electron oxidation of protoporphyrinogen to protoporphyrin IX, and finally the insertion of ferrous iron to form haem. Interestingly, Nature has evolved distinct enzymic machinery to deal with the antepenultimate (co-proporphyrinogen oxidase) and penultimate (protoporphyrinogen oxidase) steps for aerobic compared with anaerobic organisms. The terminal step is catalysed by the enzyme ferrochelatase. This enzyme is clearly conserved with regard to a small set of essential catalytic residues, but varies significantly with regard to size, subunit composition, cellular location and the presence or absence of a [2Fe-2S] cluster. Coproporphyrinogen oxidase and protoporphyrinogen oxidase are reviewed with regard to their enzymic and physical characteristics. Ferrochelatase, which is the best characterized of these three enzymes, will be described with particular emphasis paid to what has been learned from the crystal structure of the Bacillus subtilis and human enzymes.
Structural diversity in metal ion chelation and the structure of uroporphyrinogen III synthase
Authors: Schubert H. L. , Raux E. , Matthews M. A. A. , Phillips J. D. , Wilson K. S. , Hill C. P. , Warren M. J.
Published: June 2004

All tetrapyrroles are synthesized through a branched pathway, and although each tetrapyrrole receives unique modifications around the ring periphery, they all share the unifying feature of a central metal ion. Each pathway maintains a unique metal ion chelatase, and several tertiary structures have been determined, including those of the protoporphyrin ferrochelatase from both human and Bacillus subtilus, and the cobalt chelatase CbiK. These enzymes exhibit strong structural similarity and appear to function by a similar mechanism. Met8p, from Saccharomyces cerevisiae, catalyses ferrochelation during the synthesis of sirohaem, and the structure reveals a novel chelatase architecture whereby both ferrochelation and NAD+-dependent dehydrogenation take place in a single bifunctional active site. Asp-141 appears to participate in both catalytic reactions. The final common biosynthetic step in tetrapyrrole biosynthesis is the generation of uroporphyrinogen by uroporphyrinogen III synthase, whereby the D ring of hydroxymethylbilane is flipped during ring closure to generate the asymmetrical structure of uroporphyrinogen III. The recently derived structure of uroporphyrinogen III synthase reveals a bi-lobed structure in which the active site lies between the domains.
Controlling the reactivity of radical intermediates by coenzyme B12-dependent methylmalonyl-CoA mutase
Authors: Banerjee R. , Vlasie M.
Published: June 2004

Adenosylcobalamin or coenzyme B12-dependent enzymes are members of the still relatively small group of radical enzymes and catalyse 1,2-rearrangement reactions. A member of this family is methylmalonyl-CoA mutase, which catalyses the isomerization of methylmalonyl-CoA to succinyl-CoA and, unlike the others, is present in both bacteria and animals. Enzymes that catalyse some of the most chemically challenging reactions are the ones that tend to deploy radical chemistry. The use of radical intermediates in an active site lined with amino acid side chains that threaten to extinguish the reaction by presenting alternative groups for abstraction poses the conundrum of how the enzymes control their reactivity. In this review, insights into this issue that have emerged from kinetic, mutagenesis and structural studies are described for methylmalonyl-CoA mutase.
Haem degradation in animals and plants
Authors: Mantle T. J.
Published: June 2004

Two enzyme systems have evolved for the reduction of linear tetrapyrroles: one family, found in plants, algae and cyanobacteria, uses ferredoxin and catalyses the reduction of the terminal pyrrole rings (A and D) and one of the vinyl side chains to form various light-harvesting and light-sensing chromophores. The other group (biliverdin reductases A and B) utilize NAD(P)H and catalyse reduction at C10 (hydride addition) to form the ‘bile’ pigments bilirubin-IXα and bilirubin-IX.
Novel domain packing in the crystal structure of a thiosulphate-oxidizing enzyme
Authors: Bamford V. A. , Berks B. C. , Hemmings A. M.
Published: June 2004

A key component of the oxidative biogeochemical sulphur cycle involves the utilization by bacteria of reduced inorganic sulphur compounds as electron donors to photosynthetic or respiratory electron transport chains. The SoxAX protein of the photosynthetic bacterium Rhodovulum sulfidophilum is a heterodimeric c-type cytochrome that is involved in the oxidation of thiosulphate and sulphide. The recently solved crystal structure of the SoxAX complex represents the first structurally characterized example of a productive electron transfer complex between haemoproteins where both partners adopt the c-type cytochrome fold. The packing of c-type cytochrome domains both within SoxA and at the interface between the subunits of the complex has been compared with other examples and found to be unique.
Current understanding of the function of magnesium chelatase
Authors: Reid J. D. , Hunter C. N.
Published: June 2004

Despite the global significance of chlorophylls and other modified tetrapyrroles, many aspects of their biosynthetic pathways are poorly understood. A key enzyme at the branch point between the haem and chlorophyll pathways, magnesium chelatase, couples the free energy of ATP hydrolysis to the insertion of magnesium into porphyrin, a process that is likely to be mediated through protein conformational changes. Conclusions from recent structural and functional studies of individual subunits are combined to provide a mechanistic outline of the full magnesium chelatase complex. Gathering further information presents a considerable challenge, and recent steps towards this goal will be introduced.
The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella
Authors: Schwalb C. , Chapman S. K. , Reid G. A.
Published: June 2004

Shewanella spp. demonstrate great variability in the use of terminal electron acceptors in anaerobic respiration; these include nitrate, fumarate, DMSO, trimethylamine oxide, sulphur compounds and metal oxides. These pathways open up possible applications in bioremediation. The wide variety of respiratory substrates for Shewanella is correlated with the evolution of several multi-haem membrane-bound, periplasmic and outer-membrane c-type cytochromes. The 21 kDa c-type cytochrome CymA of the freshwater strain Shewanella oneidensis MR-1 has an N-terminal membrane anchor and a globular tetrahaem periplasmic domain. According to sequence alignments, CymA is a member of the NapC/NirT family. This family of redox proteins is responsible for electron transfer from the quinone pool to periplasmic and outer-membrane-bound reductases. Prior investigations have shown that the absence of CymA results in loss of the ability to respire with Fe(III), fumarate and nitrate, indicating that CymA is involved in electron transfer to several terminal reductases. Here we describe the expression, purification and characterization of a soluble, truncated CymA (‘CymA). Potentiometric studies suggest that there are two pairs of haems with potentials of -175 and -261 mV and that ‘CymA is an efficient electron donor for the soluble fumarate reductase, flavocytochrome c3.
Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases
Authors: de Vries S. , Schröder I.
Published: June 2004

The denitrification pathway has been studied in the hyperthermophilic archaeon Pyrobaculum aerophilum. In contrast with Gram-negative bacteria, all four denitrification enzymes are membrane-bound. P. aerophilum is also the only denitrifyer identified so far in which menaquinol is the electron donor to all four denitrification reductases. The NO reductase (NOR) of P. aerophilum belongs to the superfamily of haem-copper oxidases and is of the qNOR (quinol-dependent) type. Three types of NOR have been purified so far: cNOR (cytochrome c/pseudoazurin-dependent), qNOR and qCuANOR (qNOR that contains CuA at the electron entry site). It is proposed that the NORs and the various cytochrome oxidases have evolved by modular evolution, in view of the structure of their electron donor sites. qNOR is further proposed to be the ancestor of all NORs and cytochrome oxidases belonging to the superfamily of haem-copper oxidases.
Mechanisms of mercury bioremediation
Authors: Essa A. M. M. , Macaskie L. E. , Brown N. L.
Published: June 2004

Mercury is one of the most toxic heavy metals, and has significant industrial and agricultural uses. These uses have led to severe localized mercury pollution. Mercury volatilization after its reduction to the metallic form by mercury-resistant bacteria has been reported as a mechanism for mercury bioremediation [Brunke, Deckwer, Frischmuth, Horn, Lunsdorf, Rhode, Rohricht, Timmis and Weppen (1993) FEMS Microbiol. Rev. 11, 145–152; von Canstein, Timmis, Deckwer and Wagner-Dobler (1999) Appl. Environ. Microbiol. 65, 5279–5284]. The reduction/volatilization system requires to be studied further, in order to eliminate the escape of the metallic mercury into the environment. Recently we have demonstrated three different mechanisms for mercury detoxification in one organism, Klebsiella pneumoniae M426, which may increase the capture efficiency of mercury.
Metal insertion into NiFe-hydrogenases
Authors: Blokesch M. , Paschos A. , Theodoratou E. , Bauer A. , Hube M. , Huth S. , Böck A.
Published: June 2004

The synthesis and the insertion of the metallo-centre of NiFe-hydrogenases is a complex process, in which seven maturation enzymes plus ATP, GTP and carbamoyl phosphate are involved. The review summarizes what is known about the properties and activities of these auxiliary proteins, and postulates a pathway along which maturation may take place.
Sulfolobus aconitase, a regulator of iron metabolism?
Authors: Uhrigshardt H. , Zoske S. , Anemüller S.
Published: June 2004

The aconitase of Sulfolobus solfataricus, a hyperthermophilic crenarchaeon, was cloned and heterologously expressed in Escherichia coli. Enzymic analyses and EPR measurements indicated clearly that the iron-sulphur cluster of the thermophilic aconitase was already inserted in the mesophilic host. The enzyme was purified to a specific activity of approx.44 units/mg and to 90% homogeneity. The enzymic parameters of the recombinant aconitase turned out to be in the same range as the respective values for the previously characterized native enzyme from the closely related S. acidocaldarius. Based on its primary sequence, the recombinant aconitase is closely related to bacterial A-like and to eukaryotic iron regulatory protein-like proteins. Specific aconitase activities in cytosolic extracts of S. acidocaldarius were found to be decreased markedly in iron-starved compared with iron-repleted cells. However, no differences in aconitase levels between iron-starved and iron-supplemented cells could be detected by immunostaining.
A new mechanism for membrane iron transport in Pseudomonas aeruginosa
Authors: Schalk I.J. , Abdallah M. A. , Pattus F.
Published: June 2004

Various biochemical and biophysical studies have demonstrated the existence of a novel iron-uptake mechanism in Pseudomonas aeruginosa, different from that generally described for ferrichrome and ferric-enterobactin in Escherichia coli. This new iron-uptake mechanism involves all the proteins generally reported to be involved in the uptake of ferric-siderophore complexes in Gram-negative bacteria (i.e. the outer membrane receptor, periplasmic binding protein and ATP-binding-cassette transporter), but differs in the behaviour of the siderophore. One of the key features of this process is the binding of iron-free pyoverdin to the outer membrane receptor FpvA in conditions of iron deficiency.