bluuebunny/crossref_metadata_2025 huggingface dataset:
INTER-RELATIONSHIPS OF INCOME, CHRONIC ENERGY DEFICIENCY, MORBIDITY AND HOSPITALIZATION AMONG ADULT MALE SLUM DWELLERS OF MIDNAPORE, WEST BENGAL, INDIA
Authors: BOSE KAUSHIK , BISAI SAMIRAN , DAS PRIYANKA , DIKSHIT SWAPAN , PRADHAN SAMPA
Published: November 2006

A cross-sectional study of 212 adult (>18 years) male slum dwellers (mean age=34·6±14·4 years) of Midnapore town, West Bengal, India, was undertaken to study the inter-relationships of chronic energy deficiency (CED), monthly family income (MFI), self-reported morbidity and hospitalization due to severe illness. The mean height, weight and body mass index (BMI) of the subjects were 160·0 cm, 50·8 kg and 19·9 kg/m2, respectively. The overall frequencies of CED (BMI<18·5 kg/m2), morbidity and hospitalization were 38·2%, 34·4% and 13·7%, respectively. Based on the WHO classification, the prevalence of CED among this population was high (20–39%), indicating a serious situation. Overall, MFI was significantly (p<0·01) positively correlated with BMI (r=0·21). Linear regression analyses showed that MFI had a significant impact (t=3·08; p<0·002) on BMI. Overall, MFI explained 3·9% variation in BMI. Subjects belonging to the lowest family income group (FIG I) had the lowest mean BMI (19·1 kg/m2) and the highest rate of CED (46·3%) and morbidity (36·6%). Those in the highest family income group (FIG III) had the largest mean BMI (20·8 kg/m2) and lowest rate of CED (30·2%) and morbidity (30·2%). The highest rate (18·9%) of hospitalization was found in this group. There were significant family income group differences in mean BMI (F=3·134, p<0·05). The frequency of morbidity (24·6%) and hospitalization (11·9%) was lowest among normal BMI individuals. Morbidity was significantly higher (χ2=11·92, p=0·0026) among CED (48·2%) subjects compared with normal BMI individuals (OR=2·85; CI=1·49–5·46). Similarly, compared with normal BMI subjects, morbidity was higher (38·5%; OR=1·92; 95% CI=0·50–7·18) among overweight subjects. Hospitalization was more common among CED subjects (16·1%; OR=1·42; CI=0·58–3·45) compared with normal BMI subjects. Similarly, the frequency of hospitalization was more among overweight individuals (15·4%; OR=1·35; 95% CI=0·0–7·59). In conclusion, this study provides evidence that the frequency of CED among this population is high, indicating a serious situation. Moreover there exists strong inter-relationships between BMI, CED, MFI and morbidity.
Advancing the Hexapole Cs-Corrector for
the Scanning Transmission Electron Microscope
Authors: Müller Heiko , Uhlemann Stephan , Hartel Peter , Haider Maximilian
Published: November 2006

Aberration correctors using hexapole fields have proven useful to
correct for the spherical aberration in electron microscopy. We
investigate the limits of the present design for the hexapole corrector
with respect to minimum probe size for the scanning transmission electron
microscope and discuss several ways in which the design could be improved
by rather small and incremental design changes for the next generation of
advanced probe-forming systems equipped with a gun monochromator.
SESAM: Exploring the Frontiers of Electron Microscopy
Authors: Koch Christoph T. , Sigle Wilfried , Höschen Rainer , Rühle Manfred , Essers Erik , Benner Gerd , Matijevic Marko
Published: November 2006

We report on the sub-electron-volt-sub-angstrom microscope (SESAM), a
high-resolution 200-kV FEG-TEM equipped with a monochromator and an
in-column MANDOLINE filter. We report on recent results obtained with this
instrument, demonstrating its performance (e.g., 87-meV energy resolution
at 10-s exposure time, or a transmissivity of the energy filter of
T1 eV = 11,000 nm2). New opportunities to
do unique experiments that may advance the frontiers of microscopy in
areas such as energy-filtered TEM, spectroscopy, energy-filtered electron
diffraction and spectroscopic profiling are also discussed.
Electron-Excited Energy Dispersive X-Ray Spectrometry at High Speed and at High Resolution: Silicon Drift Detectors and Microcalorimeters
Authors: Newbury Dale E.
Published: November 2006

Two recent developments in X-ray spectrometer technology provide dramatic improvements in analytical capabilities that impact the frontiers of electron microscopy. Silicon drift detectors (SDD) use the same physics as silicon (lithium) energy dispersive spectrometers [Si(Li) EDS] but differ in design: only 10% of the thickness of the Si(Li) EDS with an anode area below 0.1 mm2and a complex rear surface electrode pattern that creates a lateral internal charge collection field. The SDD equals or betters the Si(Li) EDS in most measures of performance. For output versus input count rate, the SDD exceeds the Si(Li) EDS by a factor of 5 to 10 for the same resolution. This high throughput can benefit analytical measurements that are count limited, such as X-ray mapping and trace measurements. The microcalorimeter EDS determines the X-ray energy by measuring the temperature rise in a metal absorber. Operating at 100 mK, the microcalorimeter EDS achieves resolution of 2–5 eV over a photon energy range of 200 eV to 10 keV in energy dispersive operation, eliminating most peak interference situations and providing high peak-to-background to detect low fluorescence yield peaks. Chemical bonding effects on low energy (<2 keV) peak shapes can be measured.
SONGS TO SHAPE A GERMAN NATION: HILLER’S COMIC OPERAS AND THE PUBLIC SPHERE
Authors: JOUBERT ESTELLE
Published: November 2006

In this article I assert that our modern understanding of the singspiel as a genre has been shaped not by eighteenth-century principles but rather by nineteenth-century notions of ‘romantic’ German opera. In contrast to a later through-composed ideal, Johann Adam Hiller’s comic operas, often viewed as the prototype of the German comic genre, were designed precisely in order that the songs might easily be detached from the spoken dialogue, disseminated outside of the public opera house and sung by audiences in various other contexts. The express purpose of these songs, as articulated by librettist Christian Felix Weisse, was to promote communal singing in social circles across Germany. The genre was thus designed for circulation within what Habermas describes as the public sphere: a conceptual space between the State and the private home in which texts, ideas and musical works were circulated and debated.

Composed in what was called the German Volkston (in the manner of the Volk), Hiller’s melodies are recorded as being sung and played throughout the streets and parks of major German cities and became so popular that they became known as folksongs. This idea of the Volk as a collective entity and of the Volkston, however, was rooted in a deeper sense of the public as nation. Inspired by Le devin du village and J. J. Rousseau’s writings on politics, language and the fine arts, Weisse and Hiller’s operas employ the pastoral mode, in which idealized peasants sing in the manner of a folksong. The idyllic simplicity of these early German-language comic operas appealed to a diversified German audience by affirming their roots, the public use of their language and their morally upright character as a nation. Thus comic opera as a genre was circulated within the public sphere with the intention of transcending the boundaries of social class to unite the German nation in song.
Estimation of interbasin transport using ocean bottom pressure: Theory and model for Asian marginal seas
Authors: Song Y. Tony
Published: November 2006

The Asian Marginal Seas are interconnected by a number of narrow straits, such as the Makassar Strait connecting the Pacific Ocean with the Indian Ocean, the Luzon Strait connecting the South China Sea with the Pacific Ocean, and the Korea/Tsushima Strait connecting the East China Sea with the Japan/East Sea. Here we propose a method, the combination of the “geostrophic control” formula of Garrett and Toulany (1982) and the “hydraulic control” theory of Whitehead et al. (1974), allowing the use of satellite‐observed sea‐surface‐height (SSH) and ocean‐bottom‐pressure (OBP) data for estimating interbasin transport. The new method also allows separating the interbasin transport into surface and bottom fluxes that play an important role in maintaining the mass balance of the regional oceans. Comparison with model results demonstrates that the combined method can estimate the seasonal variability of the strait transports and is significantly better than the method of using SSH or OBP alone.
General circulation model study on the green Sahara during the mid‐Holocene: An impact of convection originating above boundary layer
Authors: Chikira M. , Abe‐Ouchi A. , Sumi A.
Published: November 2006

The mechanism maintaining widespread vegetation over the Sahara, 6000 years before present (6kBP), is investigated with an atmospheric general circulation model (GCM) focusing on an impact of convection originating above the planetary boundary layer (PBL). The multiple cloud base Arakawa‐Schubert scheme (MCB) is implemented in the GCM, and it is shown that MCB significantly strengthens the impact of vegetation over the Sahara on precipitation in this region. If it is assumed that the whole Sahara was covered by vegetation at 6kBP, the total precipitation is sufficient to maintain vegetation over the south and northwest Sahara. High‐valued moist static energy air ranges from surface to the middle troposphere over the northern half of Intertropical Convergence Zone (ITCZ) in summer because of strong northward moisture transport in the lower troposphere. Convection originating above the PBL prevails in this region especially when the PBL top is lowered between night and early morning and strengthens the intrusion of the ITCZ into the Sahara. Then moisture is further transported northward by the African wave disturbances enhancing precipitation over the northwestern Sahara.
On the nature of meander instability
Authors: Lanzoni Stefano , Seminara Giovanni
Published: November 2006

Bend instability is the process whereby perturbations of the planform distribution of a channel relative to a straight configuration may grow, driven by erosion at concave banks and deposition at convex banks, leading to the development of a meandering pattern. Here we investigate the nature of this instability; that is, we ascertain under what conditions bend instability is convective or absolute. In the former case, an initial nonpersistent, small perturbation localized in space is convected away, eventually leaving the flow domain unperturbed. In the latter case, perturbations spread in both the upstream and downstream directions, eventually affecting the whole flow domain. In convective instabilities, the spatial‐temporal development of perturbations is somewhat dependent on the characteristics of the initial perturbation which is required to be persistent in time. On the contrary, absolute instabilities are able to amplify perturbations, even if triggered at some initial time and then ceased. If bend instability is convective, planform information migrates only in one direction, while in the absolute regime, information is propagated in both directions. We show that bend instability is most often, though not invariably, convective at both a linear and nonlinear level. Moreover, the group velocity of perturbations changes sign as the width to depth ratio of the channel crosses some threshold value (the resonant value of Blondeaux and Seminara (1985)): Below (above) resonance, information is propagated downstream (upstream). We discuss the implications that these findings have on the morphological characteristics of meandering rivers (in particular, the sense of skewing of meander bends and the direction of meander migration). We also clarify how the choice of appropriate boundary conditions in numerical simulations of planform evolution is crucially dependent on the nature of bend instability and on its subresonant or superresonant regime.
Discrimination between Jovian radio emissions and Saturn electrostatic discharges
Authors: Fischer G. , Macher W. , Gurnett D. A. , Desch M. D. , Lecacheux A. , Zarka P. , Kurth W. S. , Kaiser M. L.
Published: November 2006

Short vertical streaks in the dynamic spectrum of the Cassini/RPWS (Radio and Plasma Wave Science) receiver in the frequency range of a few MHz can be due to Jovian radio emissions or SEDs (Saturn electrostatic discharges). Although Jupiter is increasingly far from Cassini, the peaks of decametric Jovian arcs can still be detected a few dB above the galactic background, and in some cases they look very similar to the SEDs caused by lightning in Saturn's atmosphere. We show a method for discriminating between these two phenomena by using the ratio of the measured autocorrelations in case the receiver uses at least two antennas. We analyze the special event from July 22, 2003, which was interpreted as the first indication of SEDs at a time when the spacecraft was still at a distance of 1.08 AU from Saturn, and find that it originated from Jupiter.
Sea surface temperature variability in the tropical southeast Atlantic Ocean and West African rainfall
Authors: Reason C. J. C. , Rouault M.
Published: November 2006

Evidence is presented of a connection between sea surface temperature (SST) variability in the tropical southeast Atlantic Ocean off Angola and boreal summer rainfall over coastal West Africa. The strongest relationships exist between April–May SST in the Angola‐Benguela Frontal Zone area, May–June latent heat fluxes in this area, and July–August rainfall over the region 5°W–5°E, 5°N–10°N. Anomalously wet summers in this region are also characterised by a weaker African Easterly Jet, a stronger Tropical Easterly Jet and, in many cases, reduced rainfall further north over the Southern Sahel.
Seasonal change in anomalous WNPSH associated with the strong East Asian summer monsoon
Authors: Lee Eun‐Jeong , Yeh Sang‐Wook , Jhun Jong‐Ghap , Moon Byung‐Kwon
Published: November 2006

The most striking features observed in the strong East Asian summer monsoon (EASM) are the seasonal change in the anomalous western North Pacific subtropical high (WNPSH) and the accompanying convective activities over the tropical Pacific and the Indian Ocean. The seasonal change in the anomalous WNPSH associated with the strong EASM has been studied through model experiments. The results of numerical experiments indicate that the anomalous WNPSH associated with the strong EASM has a strong seasonality with respect to its intensity and location. This is due to the difference between the contributions of the remote and local sea surface temperature forcings in the tropical Pacific and the Indian Ocean. It is also found that the air‐sea interactions over the tropical western Pacific and the Indian Ocean are essential to appropriately simulate the intensity and location of the anomalous WNPSH, which in turn modulate the East Asian summer monsoon rainfall during the summer of the strong EASM years.
Occurrence dates of North Atlantic tropical storms and hurricanes: 2005 in perspective
Authors: Keim Barry D. , Robbins Kevin D.
Published: November 2006

This paper compares dates of the nth storm (1st, 2nd,…etc.) in sequence for all tropical storms and hurricanes in the North Atlantic Basin from 1851–2005. The year 2005 stands out as a season that got off to an early start, remained active throughout the season, and set many records for earliest occurrence dates for the nth named storm. Exceptionally warm sea surface temperatures may help explain the record breaking season of 2005. Other seasons with storms with early dates of occurrence include 1887, 1933, 1936, and 1995. All of these seasons are associated with a positive phase of the Atlantic Multidecadal Oscillation.
Extreme event dynamics in methane ebullition fluxes from tropical reservoirs
Authors: Ramos Fernando M. , Lima Ivan B. T. , Rosa Reinaldo R. , Mazzi Edmar A. , Carvalho João C. , Rasera Maria F. F. L. , Ometto Jean P. H. B. , Assireu Arcilan T. , Stech José L.
Published: November 2006

Tropical hydroelectric reservoirs generally constitute an appreciable source of CH4 (methane), a potent greenhouse gas. In this letter, we investigate the statistical characteristics of methane ebullition fluxes in hydroelectric reservoirs. To this end, we use CH4 flux measurements obtained in Manso (wet season, 2004) and Corumbá (dry and wet seasons, 2005) reservoirs, located respectively in Mato Grosso and Goiás, Brazil. Methane ebullition fluxes were measured using open dynamic chambers, connected to an infrared photo‐acoustic trace gas analyzer (TGA). Our main result indicates that when properly rescaled, all methane ebullition data collapse into a single statistic well described by a Generalized Pareto distribution, with shape parameter well above zero. The approach presented here, which combines high‐frequency CH4 ebullition data and Extreme Value theory analytical tools, shows that, although bubbling patterns appear to be highly complex and unpredictable, they may still be described by a rather simple (but non trivial) dynamics.
Floating bare tether as upper atmosphere probe
Authors: Sanmartin J. R. , Charro M. , Pelaez J. , Tinao I. , Elaskar S. , Hilgers A. , Martinez‐Sanchez M.
Published: November 2006

Use of a conductive bare tape electrically floating in low Earth orbit as an effective electron beam source to produce artificial auroral effects, free of problems that mar standard beams, is considered. Ambient ions impacting the tape with keV energies over most of its length liberate secondary electrons that race down the magnetic field, excite neutrals in the E layer, and result in auroral emissions. The tether would operate with both a power supply and a plasma contactor off at nighttime; power and contactor would be on at daytime for reboost. Tomographic analysis of auroral emissions from the footprint of the beam, as observed from the spacecraft, can provide density profiles of dominant neutral species in the E layer. A characteristic tether system, at altitude ∼300 km and moderate orbital inclination, would involve an aluminum tape with a length of ∼20 km, a width of ∼15 mm, and a thickness of ∼0.2 mm for a full‐system mass around 1200 kg, with two thirds going into the power subsystem.
Role of mixing in the structure and evolution of a buoyant discharge plume
Authors: Chen Fei , MacDonald Daniel G.
Published: November 2006

A field study to examine the near‐field structure of a buoyant discharge plume, and the turbulent mixing associated with its evolution, was conducted in Mount Hope Bay near Somerset, Massachusetts. The study focused on a 50 m3/s thermal discharge, approximately 5° C warmer than ambient waters, emanating from an electrical generating facility. The discharge enters the Bay through a 10 m wide surface canal creating a plume that has many attributes in common with larger scale river plumes. At a distance of 200 m, the plume was characterized by a core with high velocity and 2 ∼ 3°C higher temperature than ambient water. At this location the core of the plume was observed with a width of approximately 150 m during ebb tide, remaining bottom attached along the plume centerline. Analysis of the temperature budget with respect to specific isotherms yielded values of Reynolds temperature flux , on the order of 10−2°C m/s, suggesting buoyancy flux values (B = gα) of order 10−5 m2/s3. These values are consistent with the turbulent energy expected to enter the system as a result of bottom stress, implying that mixing across the first 200 m is driven by bottom friction and is most active along the edges of the plume where thermal gradients are strong. The industrial plume studied here is dynamically similar to larger geophysical plumes, such as river plumes. However, the aspect ratio is critical in determining whether mixing driven by bottom friction is important in the overall evolution of the plume.
Variability and trends in the global tropopause estimated from radiosonde data
Authors: Seidel Dian J. , Randel William J.
Published: November 2006

This study examines global tropopause variability on synoptic, monthly, seasonal, and multidecadal timescales using 1980–2004 radiosonde data. On synoptic and monthly timescales, tropopause height variations are anticorrelated with stratospheric temperature variations and positively correlated with tropospheric temperature variations. Correlations are stronger in the extratropics than in the tropics, for the upper troposphere (500–300 hPa) than for the lower troposphere, and for the lower stratosphere than for the middle stratosphere. The extratropical tropopause is more sensitive to temperature changes than the tropical tropopause, and in both regions, monthly anomalies of tropopause height are more sensitive to stratospheric temperature change than tropospheric, rising 2–3 km per degree cooling of the lower stratosphere. Tropopause height trends over 1980–2004 are upward at almost all of the (predominantly extratropical) stations analyzed, yielding an estimated global trend of 64 ± 21 m/decade, a corresponding tropopause pressure trend of −1.7 ± 0.6 hPa/decade, and tropopause temperature decrease of 0.41 ± 0.09 K/decade. These tropopause trends are accompanied by significant stratospheric cooling and smaller tropospheric warming. However, the tropopause trends are spatially correlated with stratospheric temperature trends and uncorrelated with tropospheric temperature trends. This association of tropopause height and stratospheric temperature trends, together with the presence of a significant quasi‐biennial oscillation signal in tropopause height, suggests that at these lowest frequencies the tropopause is primarily coupled with stratospheric temperatures. Therefore, as an indicator of climate change, long‐term changes in the tropopause may carry less information about changes throughout the vertical temperature profile than has been suggested by previous studies using reanalyses and global climate models.
The chemoattractant decoy receptor D6 as a negative regulator of inflammatory responses
Authors: Borroni E.M. , Buracchi C. , de la Torre Y. Martinez , Galliera E. , Vecchi A. , Bonecchi R. , Mantovani A. , Locati M.
Published: November 2006

Other than signalling receptors sustaining leucocyte recruitment during inflammatory reactions, the chemokine system includes ‘silent’ receptors with distinct specificity and tissue distribution. The best-characterized molecule of this subgroup is the CC chemokine receptor D6, which binds most inflammatory CC chemokines and targets them to degradation via constitutive ligand-independent internalization. Structure–function analysis and recent results with gene-targeted animals indicate that D6 has unique functional and structural features, which make it ideally adapted to act as a chemokine decoy and scavenger receptor, strategically located on lymphatic endothelium and placenta to dampen inflammation in tissues and draining lymph nodes.
Negative regulation of leucocyte functions by CD33-related siglecs
Authors: Avril T. , Attrill H. , Zhang J. , Raper A. , Crocker P.R.
Published: November 2006

The siglecs (sialic acid-binding Ig-like lectins) are a family of transmembrane receptors expressed in the haemopoietic, immune and nervous systems. The CD33-related siglecs are a distinct subset mostly expressed in the innate immune system where they can function as inhibitory receptors by suppressing the signalling mediated by receptors coupled with ITAMs (immunoreceptor tyrosine-based activation motifs). CD33-related siglecs contain ITIMs (immunoreceptor tyrosine-based inhibitory motifs) that recruit and activate SHP-1 [SH2 (Src homology 2) domain-containing phosphatase-1] and SHP-2. In addition, the ITIMs of CD33-related siglecs can suppress siglec-dependent adhesion of sialylated ligands and mediate endocytosis. Siglec-H is a recently characterized murine CD33-related endocytic receptor that lacks intrinsic tyrosine-based signalling motifs and is expressed selectively on PDCs (plasmacytoid dendritic cells). Siglec-H depends on DAP12 (DNAX-activating protein of 12 kDa) for surface expression and cross-linking with anti-siglec-H antibodies can selectively inhibit interferon-α production by PDCs following TLR9 (Toll-like receptor 9) ligation. Thus CD33-related siglecs are able to mediate diverse inhibitory functions of leucocytes in the innate immune system via both ITIM-dependent and -independent pathways.
The therapeutic potential of positive and negative immune cell co-stimulation during inflammation
Authors: Gwyer E. , Snelgrove R. , Hussell T.
Published: November 2006

Inflammatory cascades are initiated in response to alarm signals that may result from infection, malignant transformation or trauma. Immunity, however, must be controlled; otherwise damage may occur to otherwise healthy tissue within the same microenvironment. Similarly, peripheral tolerance mechanisms must ensure that autoreactive thymic or bone marrow emigrants do not respond upon encounter with the autoantigen. Organized lymphoid structures such as lymph nodes, spleen and Peyer's patches appear to regulate inflammation successfully, displaying controlled expansion and contraction. However, when immune cells flood into effector sites, the organization of T- and B-lymphocytes is lacking. What controls inflammatory cascades in lymph nodes but rarely in effector sites is not clear. We believe the difference lies in the Toll-like receptor ligand load, which is high in effector sites and drives uncontrolled inflammation. Similarly, we believe that initiation of autoimmune inflammation is initiated by the liberation of inflammatory signals due to infection or trauma. In this review, we highlight some of the molecules responsible for maintaining an activated T-cell phenotype, strategies to interrupt these therapeutically and the impact of ligating inhibitory receptors on antigen-presenting cells.
Perspectives on the RNA polymerase II core promoter
Authors: Juven-Gershon T. , Hsu J.-Y. , Kadonaga J.T.
Published: November 2006

The RNA polymerase II core promoter is a critical yet often overlooked component in the transcription process. The core promoter is defined as the stretch of DNA, which encompasses the RNA start site and is typically approx. 40–50 nt in length, that directs the initiation of gene transcription. In the past, it has been generally presumed that core promoters are general in function and that transcription initiation occurs via a common shared mechanism. Recent studies have revealed, however, that there is considerable diversity in core promoter structure and function. There are a number of DNA elements that contribute to core promoter activity, and the specific properties of a given core promoter are dictated by the presence or absence of these core promoter motifs. The known core promoter elements include the TATA box, Inr (initiator), BREu {BRE [TFIIB (transcription factor for RNA polymerase IIB) recognition element] upstream of the TATA box} and BREd (BRE downstream of the TATA box), MTE (motif ten element), DCE (downstream core element) and DPE (downstream core promoter element). In this paper, we will provide some perspectives on current and future issues that pertain to the RNA polymerase II core promoter.
The regulatory roles and mechanism of transcriptional pausing
Authors: Landick R.
Published: November 2006

The multisubunit RNAPs (RNA polymerases) found in all cellular life forms are remarkably conserved in fundamental structure, in mechanism and in their susceptibility to sequence-dependent pausing during transcription of DNA in the absence of elongation regulators. Recent studies of both prokaryotic and eukaryotic transcription have yielded an increasing appreciation of the extent to which gene regulation is accomplished during the elongation phase of transcription. Transcriptional pausing is a fundamental enzymatic mechanism that underlies many of these regulatory schemes. In some cases, pausing functions by halting RNAP for times or at positions required for regulatory interactions. In other cases, pauses function by making RNAP susceptible to premature termination of transcription unless the enzyme is modified by elongation regulators that programme efficient gene expression. Pausing appears to occur by a two-tiered mechanism in which an initial rearrangement of the enzyme's active site interrupts active elongation and puts RNAP in an elemental pause state from which additional rearrangements or regulator interactions can create long-lived pauses. Recent findings from biochemical and single-molecule transcription experiments, coupled with the invaluable availability of RNAP crystal structures, have produced attractive hypotheses to explain the fundamental mechanism of pausing.
Liver X receptors and cholesterol homoeostasis: spotlight on the adrenal gland
Authors: Cummins C.L. , Mangelsdorf D.J.
Published: November 2006

The LXRs (liver X receptors) (LXRα and LXRβ) are nuclear hormone receptors that are activated by oxysterols, endogenous oxidative metabolites of cholesterol. These receptors regulate an integrated network of genes that control whole body cholesterol and lipid homoeostasis. A brief overview of the mechanism of this regulation by LXRs in the liver, macrophage and intestine will be outlined, followed by data from our recent work demonstrating that LXRα is crucial in maintaining adrenal cholesterol homoeostasis. In the adrenal gland, oxysterols are formed as intermediates in the conversion of cholesterol into steroid hormones and can act as endogenous activators of LXR. We have found using both gain- and loss-of-function models that LXR acts to maintain free cholesterol below toxic levels in the adrenal gland, through the co-ordinated regulation of genes involved in cholesterol efflux [ABCA1 (ATP-binding-cassette transporter A1)], storage (sterol-regulatory-element-binding protein-1c and apolipoprotein E) and metabolism to steroid hormones (steroidogenic acute regulatory protein). Furthermore, we show that under chronic dietary stress, the adrenal glands of LXR-null mice (and not wild-type mice) accumulate free cholesterol. These results support the role of LXR as a global regulator of cholesterol homoeostasis, where LXR provides a safety valve to limit free cholesterol in tissues experiencing high cholesterol flux.
The impact of pregnane X receptor activation on liver fibrosis
Authors: Wright M.C.
Published: November 2006

The PXR (pregnane X receptor) is a nuclear receptor transcription factor that is activated by a range of endobiotics and xenobiotics. The activated PXR modulates the transcription of genes in hepatocytes (the main functional cell of the liver) associated with endobiotic and xenobiotic uptake, metabolism and excretion. However, activation of the PXR also inhibits a deleterious response of the liver to chronic damage – that of fibrosis. The antifibrogenic mode of action is mediated through changes in the expression of genes in hepatic stellate cells and liver macrophages (Kupffers). These results suggest an additional function for the PXR.
Confronting an influenza pandemic: ethical and scientific issues
Authors: Schuklenk U. , Gartland K.M.A.
Published: November 2006

The prolonged concern over the potential for a global influenza pandemic to cause perhaps many millions of fatalities is a chilling one. After the SARS (severe acute respiratory syndrome) scares [1], attention has turned towards the possibility of an avian influenza virus hybridizing with a human influenza virus to create a highly virulent, as yet unknown, killer, on a scale unseen since the Spanish flu outbreak of 1918, which produced more fatalities than the Great War. In deciding how countries should react to this potential pandemic, individually and collectively, a reasonable and practical balance must be struck between the rights and obligations of individual citizens and protection of the wider community and, indeed, society as a whole. In this communication, ethical issues are discussed in the context of some of the scientific questions relating to a potential influenza pandemic. Among these issues are the rights and obligations of healthcare professionals, difficulties surrounding resource allocation, policies that have an impact on liberty and trade, when and how to introduce any vaccine or other form of mass treatment, global governance questions and the role of health policies in contemporary society. By considering these issues and questions in advance of an influenza, or indeed any other, pandemic commencing, countries can be better prepared to deal with the inevitably difficult decisions required during such events, rather than dusting down outdated previous plans, or making and implementing policy in an ad hoc manner with a resultant higher risk of adverse consequences.
P450ome of the white rot fungus Phanerochaete chrysosporium: structure, evolution and regulation of expression of genomic P450 clusters
Authors: Yadav J.S. , Doddapaneni H. , Subramanian V.
Published: November 2006

The model white rot fungus Phanerochaete chrysosporium has the extraordinary ability to degrade (to CO2) lignin and detoxify a variety of chemical pollutants. Whole genome sequencing of this fungus has revealed the presence of the largest P450ome in fungi comprising approx. 150 P450 genes, most of which have unknown function. On the basis of our genome-wide structural and evolutionary analysis, these P450 genes could be classified into 12 families and 23 subfamilies and under 11 fungal P450 clans. The analysis further revealed an extensive gene clustering with a total of 16 P450 clusters constituted of up to 11 members per cluster. In particular, evidence and role of gene duplications and horizontal gene transfer in the evolution of these P450 clusters have been discussed using two of the P450 families [CYP63 and CYP505 (where CYP is cytochrome P450)] as examples. In addition, the observed differential transcriptional induction of the clustered members of the CYP63 gene family, in response to different xenobiotic chemicals and carbon sources, indicated functional divergence within the P450 clusters, of this basidiomycete fungus.
Protein dynamics and imidazole binding in cytochrome P450 enzymes
Authors: Verras A. , Ortiz de Montellano P.R.
Published: November 2006

P450 (cytochrome P450) enzymes have major roles in the biosynthesis of endogenous factors such as steroids and eicosanoids, in the termination of the action of endogenous factors such as retinoic acid, in the metabolism of most drugs and xenobiotics and in the generation of toxic and carcinogenic products. Understanding the determinants of the substrate and inhibitor specificities of these enzymes is important for drug design. The crystallographic analysis of the deformability of two bacterial P450 active sites associated with the binding of azole (a class of inhibitors with an imidazole or triazole ring that co-ordinates to the haem iron) inhibitors described in the present study illustrates the importance of protein conformational malleability in the binding of imidazole derivatives.
Flavocytochrome P450 BM3 and the origin of CYP102 fusion species
Authors: Girvan H.M. , Waltham T.N. , Neeli R. , Collins H.F. , McLean K.J. , Scrutton N.S. , Leys D. , Munro A.W.
Published: November 2006

Flavocytochrome P450 (cytochrome P450) BM3 is an intensively studied model system within the P450 enzyme superfamily, and is a natural fusion of a P450 to its P450 reductase redox partner. The fusion arrangement enables efficient electron transfer within the enzyme and a catalytic efficiency that cannot be matched in P450 systems from higher organisms. P450 BM3's potential for industrially relevant chemical transformations is now recognized, and variants with biotechnological applications have been constructed. Simultaneously, structural and mechanistic studies continue to reveal the intricate mechanistic details of this enzyme, including its dimeric organization and the relevance of this quaternary structure to catalysis. Homologues of BM3 have been found in several bacteria and fungi, indicating important physiological functions in these microbes and enabling first insights into evolution of the enzyme family. This short paper deals with recent developments in our understanding of structure, function, evolution and biotechnological applications of this important P450 system.
CYP121, CYP51 and associated redox systems in Mycobacterium tuberculosis: towards deconvoluting enzymology of P450 systems in a human pathogen
Authors: McLean K.J. , Dunford A.J. , Sabri M. , Neeli R. , Girvan H.M. , Balding P.R. , Leys D. , Seward H.E. , Marshall K.R. , Munro A.W.
Published: November 2006

An extraordinary array of P450 (cytochrome P450) enzymes are encoded on the genome of the human pathogen Mycobacterium tuberculosis (Mtb) and in related mycobacteria and actinobacteria. These include the first characterized sterol 14α-demethylase P450 (CYP51), a known target for azole and triazole drugs in yeasts and fungi. To date, only two Mtb P450s have been characterized in detail: CYP51 and CYP121. The CYP121 P450 shows structural relationships with P450 enzymes involved in synthesis of polyketide antibiotics. Both P450s exhibit tight binding to a range of azole drugs (e.g. clotrimazole and fluconazole) and the same drugs also have potent effects on growth of mycobacteria (but not of e.g. Escherichia coli). Atomic structures are available for both Mtb CYP51 and CYP121, revealing modes of azole binding and intriguing mechanistic and structural aspects. This paper reviews our current knowledge of these and the other P450 systems in Mtb including recent data relating to the reversible conversion of the CYP51 enzyme between P450 (thiolate-co-ordinated) and P420 (thiol-co-ordinated) species on reduction of the haem iron in the absence of a P450 substrate. The accessory flavoprotein and iron–sulfur proteins required to drive P450 catalysis are also discussed, providing an overview of the current state of knowledge of Mtb P450 redox systems.
Understanding electron transport systems of Streptomyces cytochrome P450
Authors: Chun Y.-J. , Shimada T. , Waterman M.R. , Guengerich F.P.
Published: November 2006

Streptomyces spp. are known to produce various types of biologically active compounds including antibiotics, antiparasitic agents, herbicides and immunosuppressants. P450 (cytochrome P450) enzymes may have key roles in these biosynthetic and biotransformation reactions. Recent genomic analysis of Streptomyces coelicolor A3(2) indicates that S. coelicolor may have six ferredoxins (Fdxs), four putative Fdx reductases (FdRs) and 18 P450 genes. However, there are few clues to explain the mechanisms and functions of Streptomyces P450 systems. To solve these questions, we have expressed and purified five S. coelicolor P450s, four FdRs and six Fdxs in Escherichia coli. Of the purified P450s, CYP105D5 has fatty acid hydroxylation activity in a system reconstituted with putidaredoxin reductase and Fdx4 or with spinach FdR and spinach Fdx, although the reconstitutions with FdR2 or FdR3 and any of the Fdxs did not support CYP105D5-catalysed oleic acid hydroxylation. Elucidation of the detailed mechanisms of electron transport system for Streptomyces P450 may provide the perspective for usefulness of P450s as a biocatalyst.
Biochemical analysis of mutations in P450 oxidoreductase
Authors: Pandey A.V.
Published: November 2006

All microsomal P450s require POR (cytochrome P450 reductase) for catalytic activity. Most of the clinically used drugs are metabolized by a small number of P450s and polymorphisms in the cytochrome P450s are known to cause changes in drug metabolism. We have recently found a number of POR missense mutations in the patients with disordered steroidogenesis. Our initial report described five missense mutations (A284P, R454H, V489E, C566Y and V605F) identified in four patients. We built bacterial expression vectors for each POR variant, purified the membranes expressing normal or variant POR and characterized their activities with cytochrome c and P450c17 assays. We have recently completed an extensive study of the range of POR mutations and characterized the mutants/polymorphisms A112V, T139A, M260V, Y456H, A500V, G536R, L562P, R613X, V628I and F643del from sequencing of patient DNA. We also studied POR variants Y179D, P225L, R313W, G410S and G501R that were available in databases or the published literature. We analysed the mutations with a three-dimensional model of human POR that was based on an essentially similar rat POR with known crystal structure. The missense mutations found in patients with disordered steroidogenesis mapped to functionally important domains of POR and the apparent polymorphisms mapped to less crucial regions. Since a variation in POR can alter the activity of all microsomal P450s, it can also affect the drug metabolism even with a normal P450. Understanding the genetic and biochemical basis of POR-mediated drug metabolism will provide valuable information about possible differences in P450-mediated reactions among the individuals carrying a variant or polymorphic form of POR.
Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine
Authors: Hamberger B. , Bohlmann J.
Published: November 2006

Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in conifers.
Impact of changes in the target P450 CYP51 enzyme associated with altered triazole-sensitivity in fungal pathogens of cereal crops
Authors: Cools H.J. , Fraaije B.A. , Kim S.H. , Lucas J.A.
Published: November 2006

Control of diseases caused by fungi in both medicine and agriculture is heavily dependent on the use of triazoles. As a consequence, resistance to triazoles is a threat to both human health and the sustainability of agricultural production systems. In human pathogens, particularly Candida albicans, mutations encoding alterations in the target cytochrome P450 sterol 14α-demethylase (CYP51; where CYP is cytochrome P450) enzyme are the primary determinants of triazole resistance. In fungal pathogens of cereals, CYP51A1 modifications, some at positions known to contribute to a resistant phenotype in human pathogens, have also been identified in isolates with altered triazole-sensitivity. However, unlike medicine where resistance to triazoles is a major clinical problem, failures of triazoles to control crop diseases in the field are rare with mean population sensitivities generally remaining low, perhaps due to differences in the selection pressures imposed on human and cereal pathogen populations. Nonetheless, the biological potential for resistance exists, and the question remains as to whether widespread triazole resistance can develop in an important cereal pathogen.
The involvement of cytochrome P450 system in the fate of 2,4,6-trinitrotoluene (TNT) in European eel [Anguilla anguilla (Linnaeus, 1758)]
Authors: Torre C. Della , Corsi I. , Alcaro L. , Amato E. , Focardi S.
Published: November 2006

TNT (2,4,6-trinitrotoluene) was the most common nitro aromatic explosive available in World War II ammunitions. The presence of ordnance dumped at sea might represent a great concern for marine species living close to dumping sites and the toxicological properties of the chemicals released into the marine environments need to be evaluated. The aim of the present study is to investigate the involvement of CYP (cytochrome P450) system in the metabolism of TNT in marine organisms by using the European eel [Anguilla anguilla (Linnaeus, 1758)] as model species. In vivo exposure to sublethal concentration of TNT (0.5, 1 and 2.5 mg/l) leads to a significant decrease in the phase I CYP1A catalytic activities such as EROD (7-ethoxyresorufin-O-de-ethylase) and MROD (7-methoxyresorufin-O-de-ethylase). On the opposite, a significant increase in NADPH cytochrome c reductase activity as well as phase II UDP-glucuronosyltransferase activity is observed. An inhibition at enzyme level is hypothesized for both CYP1A enzymes, also confirmed by a similar decrease observed after in vitro exposure. An active role of NADPH cytochrome c reductase and phase II enzymes in the TNT metabolism may also be hypothesized.
Biocatalytic conversion of avermectin into 4″-oxo-avermectin: discovery, characterization, heterologous expression and specificity improvement of the cytochrome P450 enzyme
Authors: Molnár I. , Jungmann V. , Stege J. , Trefzer A. , Pachlatko J.P.
Published: November 2006

4″-Oxo-avermectin is a key intermediate in the manufacture of the insecticide emamectin benzoate from the natural product avermectin. Seventeen Streptomyces strains with the ability to oxidize avermectin to 4″-oxo-avermectin in a regioselective manner have been discovered, and the enzymes responsible for this reaction were found to be CYPs (cytochrome P450 mono-oxygenases). The genes for these enzymes have been cloned, sequenced and compared to reveal a new subfamily of CYPs. The biocatalytic enzymes have been overexpressed in Escherichia coli, Streptomyces lividans and solvent-tolerant Pseudomonas putida strains using different promoters and vectors. FDs (ferredoxins) and FREs (ferredoxin:NADP+ reductases) were also cloned from Streptomyces coelicolor and biocatalytic Streptomyces strains, and tested in co-expression systems to optimize the electron transport. Subsequent studies showed that increasing the biocatalytic conversion levels to commercial relevance results in the production of several side products in significant amounts. Chimaeric Ema CYPs were created by sequential rounds of GeneReassembly™, a proprietary directed evolution method, and selected for improved substrate specificity by high-throughput screening.