bluuebunny/crossref_metadata_2025 huggingface dataset:
Tectonic events, continental intraplate volcanism, and mantle plume activity in northern Arabia: Constraints from geochemistry and Ar‐Ar dating of Syrian lavas
Authors: Krienitz M.‐S. , Haase K. M. , Mezger K. , van den Bogaard P. , Thiemann V. , Shaikh‐Mashail M. A.
Published: April 2009

New 40Ar/39Ar ages combined with chemical and Sr, Nd, and Pb isotope data for volcanic rocks from Syria along with published data of Syrian and Arabian lavas constrain the spatiotemporal evolution of volcanism, melting regime, and magmatic sources contributing to the volcanic activity in northern Arabia. Several volcanic phases occurred in different parts of Syria in the last 20 Ma that partly correlate with different tectonic events like displacements along the Dead Sea Fault system or slab break‐off beneath the Bitlis suture zone, although the large volume of magmas and their composition suggest that hot mantle material caused volcanism. Low Ce/Pb (<20), Nb/Th (<10), and Sr, Nd, and Pb isotope variations of Syrian lavas indicate the role of crustal contamination in magma genesis, and contamination of magmas with up to 30% of continental crustal material can explain their 87Sr/86Sr. Fractionation‐corrected major element compositions and REE ratios of uncontaminated lavas suggest a pressure‐controlled melting regime in western Arabia that varies from shallow and high‐degree melt formation in the south to increasingly deeper regions and lower extents of the beginning melting process northward. Temperature estimates of calculated primary, crustally uncontaminated Arabian lavas indicate their formation at elevated mantle temperatures (Texcess ∼ 100–200°C) being characteristic for their generation in a plume mantle region. The Sr, Nd, and Pb isotope systematic of crustally uncontaminated Syrian lavas reveal a sublithospheric and a mantle plume source involvement in their formation, whereas a (hydrous) lithospheric origin of lavas can be excluded on the basis of negative correlations between Ba/La and K/La. The characteristically high 206Pb/204Pb (∼19.5) of the mantle plume source can be explained by material entrainment associated with the Afar mantle plume. The Syrian volcanic rocks are generally younger than lavas from the southern Afro‐Arabian region, indicating a northward progression of the commencing volcanism since the arrival of the Afar mantle plume beneath Ethiopia/Djibouti some 30 Ma ago. The distribution of crustally uncontaminated high 206Pb/204Pb lavas in Arabia indicates a spatial influence of the Afar plume of ∼2600 km in northward direction with an estimated flow velocity of plume material on the order of 22 cm/a.
Integrated archeomagnetic and micro–Raman spectroscopy study of pre‐Columbian ceramics from the Mesoamerican formative village of Cuanalan, Teotihuacan Valley, Mexico
Authors: Rodriguez Ceja Maria , Goguitchaichvili Avto , Morales Juan , Ostrooumov Mikhail , Manzanilla Linda R. , Aguilar Reyes Bertha , Urrutia‐Fucugauchi Jaime
Published: April 2009

We report a detailed archeomagnetic and micro–Raman spectroscopy investigation on pre‐Columbian pottery fragments from Cuanalan (a formative village in the valley of Teotihuacan, central Mexico). Available radiocarbon ages range from 2320 ± 80 to 2060 ± 90 B.P. Continuous low‐field susceptibility versus temperature curves performed in air indicate Ti‐poor titanomagnetites as magnetization carriers. Few samples, however, show two ferrimagnetic phases with Curie temperatures compatible with both Ti‐poor and Ti‐rich titanomagnetites. Hysteresis parameter ratios fall essentially in the pseudosingle‐domain region, which may indicate a mixture of multidomain and a significant amount of single‐domain grains. Mineralogical composition of the Teotihuacan ceramics has been investigated using micro–Raman spectroscopy. Samples are characterized by highly heterogeneous body matrix mineralogy due to the presence of a large variety of minerals with several mineralogical phases. Observed titanomagnetite and magnetite bands shift toward higher wave numbers, confirming a reducing atmosphere and a relatively high temperature (about 800–900°C) during the ceramic production. This definitively indicates the thermoremanent origin of magnetic magnetization. Archeointensity values have been determined from 7 pottery fragments (47 samples) out of 10 (70 samples) analyzed. Anisotropy of thermoremanent magnetization and the cooling rate effect upon thermoremanent magnetization intensity acquisition have been investigated in all the samples. The mean archeointensity values obtained in this study range from 24.2 ± 3.2 to 40.0 ± 1.7 μT, and corresponding virtual axial dipole moments range from 4.8 ± 0.6 to 8.0 ± 0.4 (1022 A m2). This corresponds to a mean virtual dipole moment value of 5.9 ± 1.1 × 1022 A m2, which is lower than the present‐day field strength and the predicted values by global models and the latest data compilation. However, our data agree well with currently available absolute intensity values from Mesoamerica. The archeointensity values uncorrected for cooling rate and anisotropy are systematically higher than the corrected values. These uncorrected values agree with the CALS7K model, which may be biased by the fact that such corrections were not applied to most of the previous data.
Surface freshening of the Canada Basin, 2003–2007: River runoff versus sea ice meltwater
Authors: Yamamoto‐Kawai M. , McLaughlin F. A. , Carmack E. C. , Nishino S. , Shimada K. , Kurita N.
Published: April 2009

The extent of summer Arctic sea ice has reduced dramatically in recent years and, simultaneously, we have observed surface freshening over the Canada Basin in 2006 and 2007. In order to identify the source of this fresh water, either meteoric or sea ice meltwater, salinity, δ18O, and alkalinity were analyzed. Results show that sea ice meltwater increased in the surface water over the central part of the basin in 2006 and 2007, corresponding to the melting of an additional 2.7 m (1.3 m a−1) of sea ice. Anomalously fresh surface water observed in the southern part in 2007, however, was mostly attributed to Mackenzie River water extending into the basin interior, a source that was mainly absent in the early 2000s. Comparison with previous data shows that the meltwater component of surface water in the southern part of the Canada Basin has progressively increased at a mean rate of 0.27 m a−1 since 1987. This can be explained by a reduction of winter sea ice formation rate by 0.45 m or more during the past two decades. The runoff component showed larger variability in the southern basin but no obvious temporal trend. In the central basin, the river runoff component showed an increasing trend of 0.7 m a−1.
Reevaluation of long‐term Umkehr data and ozone profiles at Japanese stations
Authors: Miyagawa Koji , Sasaki Toru , Nakane Hideaki , Petropavlovskikh Irina , Evans Robert D.
Published: April 2009

Umkehr observations have been routinely conducted at Japanese stations, Sapporo, Tsukuba, Kagoshima, and Naha, and the Antarctic station, Syowa, for more than 50 years. Umkehr data are a valuable source of information on long‐term changes in the ozone vertical profile; however, the Umkehr record at Japanese stations has evident discontinuities. The majority of the discontinuities are related to the exchange of instruments for calibration (for total ozone measurements) and the replacement of instruments. These discontinuities may be related to the difference in instrument characteristics. In this article, reevaluation of the long‐term Umkehr data in Japanese network is done by assessment of instrument‐related changes in compared N values that exhibit solar zenith angle and total ozone dependence in addition to the step changes. The systematic errors are evaluated by simultaneous intercomparisons of each instrument with the reference instrument. Through this reevaluation, most discontinuities in a station's Umkehr time series are successfully corrected, and new sets of ozone vertical profiles are derived. The ozone profiles retrieved by two available Umkehr retrieval algorithms are compared with ozonesonde observations at every station and ozone lidar observations at Tsukuba. The results show that the revised Umkehr ozone profiles show improved consistency with both types of auxiliary ozone observations as compared to the old data sets, especially with regard to ozonesonde observations (difference of less than 5%). Trend analyses of the revised Umkehr ozone profile time series show a significant decrease in stratospheric ozone over Japan during the 1980s. It also varies between stations, with Naha showing the least significant trend among Japanese stations and Sapporo exhibiting as much as 6% of ozone decline per decade. In addition, a positive and statistically significant trend is detected in tropospheric ozone column at Naha (∼5.5% per decade) and Tsukuba (∼3.5% per decade) stations over the last 20 years, but no significant trend is observed over Sapporo.
Ground‐based observations of the slowdown in ozone decline and onset of ozone increase
Authors: Angell James K. , Free Melissa
Published: April 2009

This paper presents the evidence for a slowdown in ozone decline and subsequent ozone increase using ground‐based data, i.e., Dobson, Brewer, and Russian filter ozonometer total‐ozone data and Umkehr and ozonesonde‐derived layer‐ozone data. The impacts of quasi‐biennial oscillation (QBO) and 11‐year solar cycle were minimized by determining 5‐year trends based on 11‐year running means. On the basis of 50–60 total‐ozone stations, the global trends vary from a maximum negative value of −2.1 ± 0.6%/decade in 1988 to a value of 0.7 ± 0.5%/decade at the end of the record in 2000, where the confidence intervals are 2 standard deviations of the mean of the individual station trends. Because of the use of 5‐year trends and 11‐year running means, the actual year of slowdown in total‐ozone decline may be up to 7 years later than the year of maximum negative trend in our analysis, or close to the 1993–1995 peak in ozone‐depleting substances (ODS) in the atmosphere. Umkehr and ozonesonde‐derived layer‐ozone trends were determined for 32‐ to 53‐, 24‐ to 32‐, 19‐ to 24‐, 10‐ to 19‐, and 0‐ to 10‐km layers of the north temperate zone. On the basis of four Umkehr stations and about five ozonesonde stations, the integrated layer‐weighted Umkehr trends vary from a maximum negative value of −3.8 ± 0.3%/decade in 1989 to a value of 1.2 ± 2.1%/decade in 2000, while the integrated sonde trends vary from a maximum negative value of −4.8 ± 1.6%/decade in 1989 to a value of 1.8 ± 2.1/decade in 2000. Both Umkehr and sonde data show that nearly half of the increase in north temperate total‐ozone trend between 1989 and 2000 is due to trend increase in the low‐stratospheric 10‐ to 19‐km layer, with the troposphere contributing only about 5%.
Observed decadal variations in surface solar radiation and their causes
Authors: Ohmura Atsumu
Published: April 2009

Long‐term variations of global solar irradiance at the Earth's surface from the beginning of the observations to 2005 are analyzed for more than 400 sites. Further, likely causes for the variations, an estimation of the magnitudes of aerosol direct and indirect effects, and the temperature sensitivity of the climate system due to radiation changes are evaluated. The record of observed global radiation begins with an increasing phase from 1920s to late 1940s/early 1960s. This brightening period (first brightening phase) is followed by the decreasing trend lasting to late 1980s, known as the global dimming, which finally translates into the second brightening phase in many regions of the world. These decadal variations are to great extent caused by aerosol and cloud fluctuations. The total aerosol effect as well as its direct and indirect effects were evaluated mainly on the basis of the observations. To meet this goal, simultaneous observations of global solar radiation and zenith transmittance are necessary. Five such regions/sites in Europe and Japan satisfy these conditions. By using the 20‐year dimming phase from 1960 to 1980 and the 15‐year brightening phase from 1990 to 2005, it was found that the aerosol direct and indirect effects played about an equal weight in changing global solar radiation. The temperature sensitivity due to radiation change is estimated at 0.05 to 0.06 K/(W m−2). The first brightening phase lasting to 1940s/early 1960s does not show a compatibility with the variation of transmittance of the atmosphere and originated probably from a different cause.
Testing evidence of recent hydration state change in sulfates on Mars
Authors: Roach L. H. , Mustard J. F. , Murchie S. L. , Bibring J.‐P. , Forget F. , Lewis K. W. , Aharonson O. , Vincendon M. , Bishop J. L.
Published: April 2009

The East Candor Interior Layered Deposit (ILD) has signatures of mono‐ and polyhydrated sulfate in alternating layers that give insight into the processes which formed these layered deposits and on the environmental conditions acting on them since then. We use orbital data to explore multiple hypotheses for how these deposits formed: (1) sulfate‐bearing ILDs experience hydration changes on seasonal to a few years timescales under current Mars environmental conditions; (2) the deposits experience hydration under recent Mars conditions but require the wetter climate of high obliquity; and (3) the kieserite could be an original or diagenetic part of a complex evaporite mineral assemblage. Modeled climatology shows recent Mars environmental conditions might pass between multiple sulfate fields. However, comparison of Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité (OMEGA) and Compact Reconnaissance Imaging Spectrometer (CRISM) observations of the same ILD do not show changes in hydration over 2 Mars years. Low temperatures might slow the kinetics of that transition; it is likely that more clement conditions during periods of high obliquity are needed to overcome mineral metastability and hydrate kieserite‐bearing deposits. We find the alternate model, that the deposit is a cyclic evaporite sequence of mono‐ and polyhydrated sulfates, also plausible but with an unexplained dearth of Fe sulfates.
Production of glycolipid biosurfactants by basidiomycetous yeasts
Authors: Morita Tomotake , Fukuoka Tokuma , Imura Tomohiro , Kitamoto Dai
Published: April 2009

BSs (biosurfactants) produced by various micro‐organisms show unique properties (e.g. mild production conditions, lower toxicity, higher biodegradability and environmental compatibility) compared with chemically synthesized surfactants. The numerous advantages of BSs have prompted applications not only in the food, cosmetic and pharmaceutical industries but also in environmental protection and energy‐saving technology. Among BSs, glycolipid types are the most promising, owing to their high productivity from renewable resources and versatile biochemical properties. MELs (mannosylerythritol lipids), which are glycolipid BSs abundantly produced by basidiomycetous yeasts such as strains of Pseudozyma, exhibit not only excellent interfacial properties, but also remarkable differentiation‐inducing activities against human leukaemia cells. MELs also show high binding affinity towards different immunoglobulins and lectins. Recently, a cationic liposome bearing MEL has been demonstrated to increase dramatically the efficiency of gene transfection into mammalian cells. These features of BSs should broaden their application in new advanced technologies. In the present review the current status of research and development on glycolipid BSs, especially their production by Pseudozyma yeasts, is described.
Electromechanical coupling in the membranes of
Shaker
-transfected HEK cells
Authors: Beyder Arthur , Sachs Frederick
Published: April 2009

Membranes flex with changes in transmembrane potential as a result of changes in interfacial tension, the Lippman effect. We studied the membrane electromotility of
Shaker
K
+
-transfected HEK-293 cells in real time by using combined patch-clamp atomic force microscopy. In the voltage range where the channels were closed,
Shaker
expression had little effect on electromotility relative to wild-type cells. Depolarization between −120 and −40 mV resulted in a linear upward cantilever deflection equivalent to an increase in membrane tension. However, when depolarized sufficiently for channel opening, the electromotility saturated and only recovered over 10 s of milliseconds. This remarkable loss of motility was associated with channel opening, not ionic flux or movement of the voltage sensors. The IL mutant of
Shaker
, in which the voltage dependence of channel opening but not sensor movement is shifted to more positive potentials, caused the loss of electromotility saturation also to shift to more positive potentials. The temporary loss of electromotility associated with channel opening is probably caused by local buckling of the bilayer as the inner half of the channel expands as expected from X-ray structural data.
Insulin receptor tyrosine kinase substrate links theE. coliO157:H7 actin assembly effectors Tir and EspFUduring pedestal formation
Authors: Vingadassalom Didier , Kazlauskas Arunas , Skehan Brian , Cheng Hui-Chun , Magoun Loranne , Robbins Douglas , Rosen Michael K. , Saksela Kalle , Leong John M.
Published: April 2009

EnterohemorrhagicEscherichia coliO157:H7 translocates 2 effectors to trigger localized actin assembly in mammalian cells, resulting in filamentous actin “pedestals.” One effector, the translocated intimin receptor (Tir), is localized in the plasma membrane and clustered upon binding the bacterial outer membrane protein intimin. The second, the proline-rich effector EspFU(aka TccP) activates the actin nucleation-promoting factor WASP/N-WASP, and is recruited to sites of bacterial attachment by a mechanism dependent on an Asn-Pro-Tyr (NPY458) sequence in the Tir C-terminal cytoplasmic domain. Tir, EspFU, and N-WASP form a complex, but neither EspFUnor N-WASP bind Tir directly, suggesting involvement of another protein in complex formation. Screening of the mammalian SH3 proteome for the ability to bind EspFUidentified the SH3 domain of insulin receptor tyrosine kinase substrate (IRTKS), a factor known to regulate the cytoskeleton. Derivatives of WASP, EspFU, and the IRTKS SH3 domain were capable of forming a ternary complex in vitro, and replacement of the C terminus of Tir with the IRTKS SH3 domain resulted in a fusion protein competent for actin assembly in vivo. A second domain of IRTKS, the IRSp53/MIM homology domain (IMD), bound to Tir in a manner dependent on the C-terminal NPY458sequence, thereby recruiting IRTKS to sites of bacterial attachment. Ectopic expression of either the IRTKS SH3 domain or the IMD, or genetic depletion of IRTKS, blocked pedestal formation. Thus, enterohemorrhagicE. colitranslocates 2 effectors that bind to distinct domains of a common host factor to promote the formation of a complex that triggers robust actin assembly at the plasma membrane.
Re-emergence of hand-muscle representations in human motor cortex after hand allograft
Authors: Vargas Claudia D. , Aballéa Antoine , Rodrigues Érika C. , Reilly Karen T. , Mercier Catherine , Petruzzo Palmina , Dubernard Jean M. , Sirigu Angela
Published: April 2009

The human primary motor cortex (M1) undergoes considerable reorganization in response to traumatic upper limb amputation. The representations of the preserved arm muscles expand, invading portions of M1 previously dedicated to the hand, suggesting that former hand neurons are reassigned to the control of remaining proximal upper limb muscles. Hand allograft offers a unique opportunity to study the reversibility of such long-term cortical changes. We used transcranial magnetic stimulation in patient LB, who underwent bilateral hand transplantation 3 years after a traumatic amputation, to longitudinally track both the emergence of intrinsic (from the donor) hand muscles in M1 as well as changes in the representation of stump (upper arm and forearm) muscles. The same muscles were also mapped in patient CD, the first bilateral hand allograft recipient. Newly transplanted intrinsic muscles acquired a cortical representation in LB's M1 at 10 months postgraft for the left hand and at 26 months for the right hand. The appearance of a cortical representation of transplanted hand muscles in M1 coincided with the shrinkage of stump muscle representations for the left but not for the right side. In patient CD, transcranial magnetic stimulation performed at 51 months postgraft revealed a complete set of intrinsic hand-muscle representations for the left but not the right hand. Our findings show that newly transplanted muscles can be recognized and integrated into the patient's motor cortex.
Kinetic laws, phase–phase expansions, renormalization group, and INR calibration
Authors: Vlad Marcel O. , Corlan Alexandru D. , Morán Federico , Spang Rainer , Oefner Peter , Ross John
Published: April 2009

We introduce systematic approaches to chemical kinetics based on the use of phase–phase (log–log) representations of the rate equations. For slow processes, we obtain a corrected form of the mass-action law, where the concentrations are replaced by kinetic activities. For fast reactions, delay expressions are derived. The phase–phase expansion is, in general, applicable to kinetic and transport processes. A mechanism is introduced for the occurrence of a generalized mass-action law as a result of self-similar recycling. We show that our self-similar recycling model applied to prothrombin assays reproduces the empirical equations for the International Normalized Ratio calibration (
INR
), as well as the Watala, Golanski, and Kardas relation (WGK) for the dependence of the
INR
on the concentrations of coagulation factors. Conversely, the experimental calibration equation for the
INR
, combined with the experimental WGK relation, without the use of theoretical models, leads to a generalized mass-action type kinetic law.
The radiocarbon signature of microorganisms in the mesopelagic ocean
Authors: Hansman Roberta L. , Griffin Sheila , Watson Jordan T. , Druffel Ellen R. M. , Ingalls Anitra E. , Pearson Ann , Aluwihare Lihini I.
Published: April 2009

Several lines of evidence indicate that microorganisms in the meso- and bathypelagic ocean are metabolically active and respiring carbon. In addition, growing evidence suggests that archaea are fixing inorganic carbon in this environment. However, direct quantification of the contribution from deep ocean carbon sources to community production in the dark ocean remains a challenge. In this study, carbon flow through the microbial community at 2 depths in the mesopelagic zone of the North Pacific Subtropical Gyre was examined by exploiting the unique radiocarbon signatures (Δ14C) of the 3 major carbon sources in this environment. The radiocarbon content of nucleic acids, a biomarker for viable cells, isolated from size-fractionated particles (0.2–0.5 μm and >0.5 μm) showed the direct incorporation of carbon delivered by rapidly sinking particles. Most significantly, at the 2 mesopelagic depths examined (670 m and 915 m), carbon derived from in situ autotrophic fixation supported a significant fraction of the free-living microbial community (0.2–0.5 μm size fraction), but the contribution of chemoautotrophy varied markedly between the 2 depths. Results further showed that utilization of the ocean's largest reduced carbon reservoir,14C-depleted, dissolved organic carbon, was negligible in this environment. This isotopic portrait of carbon assimilation by the in situ, free-living microbial community, integrated over >50,000 L of seawater, implies that recent, photosynthetic carbon is not always the major carbon source supporting microbial community production in the mesopelagic realm.
PKCγ-induced trafficking of AMPA receptors in embryonic zebrafish depends on NSF and PICK1
Authors: Patten Shunmoogum A. , Ali Declan W.
Published: April 2009

The trafficking of AMPA receptors (Rs) to and from synaptic membranes is a key component underlying synaptic plasticity mechanisms such as long-term potentiation (LTP) and long-term depression (LTD), and is likely important for synaptic development in embryonic organisms. However, some of the key biochemical components required for receptor trafficking in embryos are still unknown. Here, we report that in embryonic zebrafish, the activation of PKCγ by phorbol 12-myristate 13-acetate, strongly potentiates the amplitude of AMPAR-mediated miniature excitatory postsynaptic currents (AMPA-mEPSCs) via a N-ethylmaleimide-sensitive fusion (NSF) and protein interacting with C-kinase-1 (PICK1)-dependent process. We found that the mEPSC potentiation is DAG- and Ca
2+
-dependent, and occurs on application of active PKCγ. Peptides that prevent the association of NSF and PICK1 with the GluR2 subunit, and the actin-polymerization blocker, latrunculin B, prevented the increase in mEPSC amplitude. Also, application of tetanus toxin (TeTx), which cleaves SNARE proteins, also blocked the increase in mEPSC amplitude. Last, application of a 5 mM K
+
medium led to an enhancement in mEPSC amplitude that was prevented by addition of the PKCγ and NSF-blocking peptides, and the NMDA receptor blocker, 2-amino-5-phosphonovaleric acid (APV). Thus, activation of PKCγ is necessary for the activity-dependent trafficking of AMPARs in embryonic zebrafish. This process is NMDA and SNARE-dependent and requires AMPARs to associate with both NSF and PICK1. The present data further our understanding of AMPAR trafficking, and have important implications for synaptic development and synaptic plasticity.
Flow-induced clustering and alignment of vesicles and red blood cells in microcapillaries
Authors: McWhirter J. Liam , Noguchi Hiroshi , Gompper Gerhard
Published: April 2009

The recent development of microfluidic devices allows the investigation and manipulation of individual liquid microdroplets, capsules, and cells. The collective behavior of several red blood cells (RBCs) or microcapsules in narrow capillaries determines their flow-induced morphology, arrangement, and effective viscosity. Of fundamental interest here is the relation between the flow behavior and the elasticity and deformability of these objects, their long-range hydrodynamic interactions in microchannels, and thermal membrane undulations. We study these mechanisms in an
in silico
model, which combines a particle-based mesoscale simulation technique for the fluid hydrodynamics with a triangulated-membrane model. The 2 essential control parameters are the volume fraction of RBCs (the tube hematocrit,

H
T

), and the flow velocity. Our simulations show that already at very low

H
T

, the deformability of RBCs implies a flow-induced cluster formation above a threshold flow velocity. At higher

H
T

values, we predict 3 distinct phases: one consisting of disordered biconcave-disk-shaped RBCs, another with parachute-shaped RBCs aligned in a single file, and a third with slipper-shaped RBCs arranged as 2 parallel interdigitated rows. The deformation-mediated clustering and the arrangements of RBCs and microcapsules are relevant for many potential applications in physics, biology, and medicine, such as blood diagnosis and cell sorting in microfluidic devices.
Desorption electrospray ionization mass spectrometry reveals surface-mediated antifungal chemical defense of a tropical seaweed
Authors: Lane Amy L. , Nyadong Leonard , Galhena Asiri S. , Shearer Tonya L. , Stout E. Paige , Parry R. Mitchell , Kwasnik Mark , Wang May D. , Hay Mark E. , Fernandez Facundo M. , Kubanek Julia
Published: April 2009

Organism surfaces represent signaling sites for attraction of allies and defense against enemies. However, our understanding of these signals has been impeded by methodological limitations that have precluded direct fine-scale evaluation of compounds on native surfaces. Here, we asked whether natural products from the red macroalga
Callophycus serratus
act in surface-mediated defense against pathogenic microbes. Bromophycolides and callophycoic acids from algal extracts inhibited growth of
Lindra thalassiae
, a marine fungal pathogen, and represent the largest group of algal antifungal chemical defenses reported to date. Desorption electrospray ionization mass spectrometry (DESI-MS) imaging revealed that surface-associated bromophycolides were found exclusively in association with distinct surface patches at concentrations sufficient for fungal inhibition; DESI-MS also indicated the presence of bromophycolides within internal algal tissue. This is among the first examples of natural product imaging on biological surfaces, suggesting the importance of secondary metabolites in localized ecological interactions, and illustrating the potential of DESI-MS in understanding chemically-mediated biological processes.
The bacteriophage T4 AsiA protein contacts the β-flap domain of RNA polymerase
Authors: Yuan Andy H. , Nickels Bryce E. , Hochschild Ann
Published: April 2009

To initiate transcription from specific promoters, the bacterial RNA polymerase (RNAP) core enzyme must associate with the initiation factor σ, which contains determinants that allow sequence-specific interactions with promoter DNA. Most bacteria contain several σ factors, each of which directs recognition of a distinct set of promoters. A large and diverse family of proteins known as “anti-σ factors” regulates promoter utilization by targeting specific σ factors. The founding member of this family is the AsiA protein of bacteriophage T4. AsiA specifically targets the primary σ factor in
Escherichia coli
, σ
70
, and inhibits transcription from the major class of σ
70
-dependent promoters. AsiA-dependent transcription inhibition has been attributed to a well-documented interaction between AsiA and conserved region 4 of σ
70
. Here, we establish that efficient AsiA-dependent transcription inhibition also requires direct protein–protein contact between AsiA and the RNAP core. In particular, we demonstrate that AsiA contacts the flap domain of the RNAP β-subunit (the β-flap). Our findings support the emerging view that the β-flap is a target site for regulatory proteins that affect RNAP function during all stages of the transcription cycle.
Red death in
Caenorhabditis elegans
caused by
Pseudomonas aeruginosa
PAO1
Authors: Zaborin Alexander , Romanowski Kathleen , Gerdes Svetlana , Holbrook Christopher , Lepine Francois , Long Jason , Poroyko Valeriy , Diggle Stephen P. , Wilke Andreas , Righetti Karima , Morozova Irina , Babrowski Trissa , Liu Donald C. , Zaborina Olga , Alverdy John C.
Published: April 2009

During host injury,
Pseudomonas aeruginosa
can be cued to express a lethal phenotype within the intestinal tract reservoir—a hostile, nutrient scarce environment depleted of inorganic phosphate. Here we determined if phosphate depletion activates a lethal phenotype in
P. aeruginosa
during intestinal colonization. To test this, we allowed
Caenorhabditis elegans
to feed on lawns of
P. aeruginosa
PAO1 grown on high and low phosphate media. Phosphate depletion caused PAO1 to kill 60% of nematodes whereas no worms died on high phosphate media. Unexpectedly, intense redness was observed in digestive tubes of worms before death. Using a combination of transcriptome analyses, mutants, and reporter constructs, we identified 3 global virulence systems that were involved in the “red death” response of
P. aeruginosa
during phosphate depletion; they included phosphate signaling (PhoB), the MvfR–PQS pathway of quorum sensing, and the pyoverdin iron acquisition system. Activation of all 3 systems was required to form a red colored PQS+Fe
3+
complex which conferred a lethal phenotype in this model. When pyoverdin production was inhibited in
P. aeruginosa
by providing excess iron, red death was attenuated in
C. elegans
and mortality was decreased in mice intestinally inoculated with
P. aeruginosa
. Introduction of the red colored PQS+Fe
3+
complex into the digestive tube of
C. elegans
or mouse intestine caused mortality associated with epithelial disruption and apoptosis. In summary, red death in
C. elegans
reveals a triangulated response between PhoB, MvfR–PQS, and pyoverdin in response to phosphate depletion that activates a lethal phenotype in
P. aeruginosa
.
Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs
Authors: Prilusky Jaime , Bibi Eitan
Published: April 2009

Posttranscriptional processes often involve specific signals in mRNAs. Because mRNAs of integral membrane proteins across evolution are usually translated at distinct locations, we searched for universally conserved specific features in this group of mRNAs. Our analysis revealed that codons of very hydrophobic amino acids, highly represented in integral membrane proteins, are composed of 50% uracils (U). As expected from such a strong U bias, the calculated U profiles of mRNAs closely resemble the hydrophobicity profiles of their encoded proteins and may designate genes encoding integral membrane proteins, even in the absence of information on ORFs. We also show that, unexpectedly, the U-richness phenomenon is not merely a consequence of the codon composition of very hydrophobic amino acids, because counterintuitively, the relatively hydrophilic serine and tyrosine, also encoded by U-rich codons, are overrepresented in integral membrane proteins. Interestingly, although the U-richness phenomenon is conserved, there is an evolutionary trend that minimizes usage of U-rich codons. Taken together, the results suggest that U-richness is an evolutionarily ancient feature of mRNAs encoding integral membrane proteins, which might serve as a physiologically relevant distinctive signature to this group of mRNAs.
Skin adhesive versus subcuticular suture for perineal skin repair after episiotomy – a randomized controlled trial
Authors: MOTA RAQUEL , COSTA FERNANDA , AMARAL ALEXANDRA , OLIVEIRA FÁTIMA , SANTOS CRISTINA COSTA , AYRES‐DE‐CAMPOS DIOGO
Published: April 2009

Objective. Surgical repair of perineal lesions after delivery is frequently associated with pain and discomfort, interfering with the normal activities of the puerperium. The aim of this study was to compare perineal skin repair after episiotomy with adhesive glue versus a subcuticular suture, regarding the incidence of pain and wound complications. Study design. Randomized clinical trial. Setting. Tertiary care university hospital. Material and methods. One hundred women having mediolateral episiotomy at vaginal delivery were enrolled. They were randomized to receive skin adhesive (n = 53) or subcuticular suture (n = 47) for closure of perineal skin. The main outcome measure was self‐evaluated pain in the 30 days following delivery. Secondary outcome measures were technical difficulties reported with the procedure, duration of surgical repair, wound complications observed at 42–68 hours post‐partum and re‐initiation of sexual activity by 30 days post‐partum. Results. No significant differences were observed between the two groups in incidence of technical difficulties and failed procedures, pain during the procedure, wound complications at hospital discharge, self‐evaluated measures of pain at 7 and 30 days or re‐initiation of sexual activity by 30 days post‐partum. The skin adhesive group had a significantly shorter mean duration of the procedure (four minutes less). Conclusion. Perineal skin closure using adhesive glue is faster than subcuticular suture, and associated with a similar incidence of complications and pain in the first 30 days.
Maternal deaths in Denmark 2002–2006
Authors: BØDKER BIRGIT , HVIDMAN LONE , WEBER TOM , MØLLER MARGRETHE , AARRE ANNETTE , NIELSEN KAREN MARIE , SØRENSEN JETTE LED
Published: April 2009

Objective. To describe a method for identification, classification and assessment of maternal deaths in Denmark and to identify substandard care. Design. Register study and case audit based on data from the Registers of the Danish Medical Health Board, death certificates and hospital records. Setting. Denmark 2002–2006. Population. Women who died during a pregnancy or within 42 days after a pregnancy. Methods. Maternal deaths were identified by notification from maternity wards and data from the Danish National Board of Health. A national audit committee assessed hospital records of direct and indirect deaths. Main outcome measures. Maternal mortality ratio, causes of death and suboptimal care. Results. In the study period, 26 women died during pregnancy or within 42 days from direct or indirect causes, leading to a maternal mortality ratio of 8.0/100,000 live births. Causes of death were cardiac disease, thromboembolism, hypertensive disorders of pregnancy, Streptococcus A infections, suicide, amniotic fluid embolism, cerebrovascular hemorrhage, asthma and diabetes. Conclusion. Our method proved valid and can be used for future research. Causes of death could be identified and learning points from the assessments could form the basis of focused education and guidelines. Future complementary ‘near miss’ studies and cooperation with other countries with comparable health systems are expected to improve the benefits of the enquiries, contributing to improved management of life‐threatening conditions in pregnancy and childbirth.
Cone-beam computed tomography: A new method for imaging of the temporal bone
Authors: Peltonen L. I. , Aarnisalo A. A. , Käser Y. , Kortesniemi M. K. , Robinson S. , Suomalainen A. , Jero J.
Published: April 2009

Background: Clinical cone-beam computed tomography (CBCT), used in diagnostics of dental and maxillofacial radiology for almost 10 years, allows three-dimensional (3D) imaging of a focused area, with reasonable radiation dose.

Purpose: To clarify the applicability of CBCT in imaging of the temporal bone.

Material and Methods: We imaged cadaver temporal bones, one non-operated and five postmortem operated, with CBCT to evaluate the accuracy of this method in showing clinically important landmarks and the positions of middle-ear implants. In addition, to clarify the imaging protocols for the best possible result, we conducted a contrast-to-noise ratio (CNR) analysis by imaging a specially built phantom insert with different protocols.

Results: For all the temporal bones, image quality was good and of diagnostic value, and the surgical landmarks as well as positions and details of the implants could be accurately observed. Based on measurements conducted with the phantom, the best possible clarity of the images with the machine used (3D Accuitomo; Morita Co., Kyoto, Japan) was achieved with a tube voltage of 80 kVp and a current of 4 mA.

Conclusion: Cone-beam CT is a promising new method for otologic imaging, based on its accuracy and relatively low radiation exposure per investigation.
Three-dimensional double-echo steady-state (3D-DESS) magnetic resonance imaging of the knee: Contrast optimization by adjusting flip angle
Authors: Moriya S. , Miki Y. , Yokobayashi T. , Ishikawa M.
Published: April 2009

Background: The three-dimensional double-echo steady-state (3D-DESS) sequence is being used to investigate sequence parameters for the assessment of knee cartilage by magnetic resonance imaging (MRI). With the flip angle (FA) values that are commonly used, contrast between cartilage and synovial fluid may be too low to delineate minor lesions of the cartilage surface.

Purpose: To investigate the value of FA maximizing contrast between cartilage and synovial fluid using the 3D-DESS sequence.

Material and Methods: In 10 healthy volunteers (five men, five women; age range 23–48 years), 3D-DESS imaging was performed to capture median sagittal sections of the knee by adjusting FA from 10° to 90°. Cartilage–synovial fluid contrast-to-noise ratio (CNR) was measured to determine the value of FA maximizing CNR. Water-excitation pulse was used to suppress fat signals. MRI was performed at 1.0T using a circular polarization flex coil.

Results: Cartilage–synovial fluid CNR was highest with 90° FA, yielding images with good contrast between cartilage and synovial fluid.

Conclusion: Simply by increasing FA to 90° in 3D-DESS imaging, the contrast between cartilage and synovial fluid increased substantially. Subtle cartilage lesions may thus be detectable using 3D-DESS sequences.
Evaluation of patient radiation dose during cardiac interventional procedures: What is the most effective method?
Authors: Chida K. , Kagaya Y. , Saito H. , Ishibashi T. , Takahashi S. , Zuguchi M.
Published: April 2009

Cardiac interventional radiology has lower risks than surgical procedures. This is despite the fact that radiation doses from cardiac intervention procedures are the highest of any commonly performed general X-ray examination. Maximum radiation skin doses (MSDs) should be determined to avoid radiation-associated skin injuries in patients undergoing cardiac intervention procedures. However, real-time evaluation of MSD is unavailable for many cardiac intervention procedures. This review describes methods of determining MSD during cardiac intervention procedures. Currently, in most cardiac intervention procedures, real-time measuring of MSD is not feasible. Thus, we recommend that physicians record the patient's total entrance skin dose, such as the dose at the interventional reference point when it can be monitored, in order to estimate MSD in intervention procedures.
Evaluation of genome-wide association study results through development of ontology fingerprints
Authors: Tsoi Lam C. , Boehnke Michael , Klein Richard L. , Zheng W. Jim
Published: April 2009

Motivation: Genome-wide association (GWA) studies may identify multiple variants that are associated with a disease or trait. To narrow down candidates for further validation, quantitatively assessing how identified genes relate to a phenotype of interest is important.

Results: We describe an approach to characterize genes or biological concepts (phenotypes, pathways, diseases, etc.) by ontology fingerprint—the set of Gene Ontology (GO) terms that are overrepresented among the PubMed abstracts discussing the gene or biological concept together with the enrichment p-value of these terms generated from a hypergeometric enrichment test. We then quantify the relevance of genes to the trait from a GWA study by calculating similarity scores between their ontology fingerprints using enrichment p-values. We validate this approach by correctly identifying corresponding genes for biological pathways with a 90% average area under the ROC curve (AUC). We applied this approach to rank genes identified through a GWA study that are associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block. We found that the genes with highest scores were: ABCA1, lipoprotein lipase (LPL) and cholesterol ester transfer protein, plasma for high-density lipoprotein; low-density lipoprotein receptor, APOE and APOB for low-density lipoprotein; and LPL, APOA1 and APOB for triglyceride. In addition, we identified genes relevant to lipid metabolism from the literature even in cases where such knowledge was not reflected in current annotation of these genes. These results demonstrate that ontology fingerprints can be used effectively to prioritize genes from GWA studies for experimental validation.

Contact:  zhengw@musc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Diversity, Virulence, and 2,4-Diacetylphloroglucinol Sensitivity of Gaeumannomyces graminis var. tritici Isolates from Washington State
Authors: Kwak Youn-Sig , Bakker Peter A. H. M. , Glandorf Debora C. M. , Rice Jennifer T. , Paulitz Timothy C. , Weller David M.
Published: April 2009

We determined whether isolates of the take-all pathogen Gaeumannomyces graminis var. tritici become less sensitive to 2,4-diacetylphloroglucinol (2,4-DAPG) during wheat monoculture as a result of exposure to the antibiotic over multiple growing seasons. Isolates of G. graminis var. tritici were baited from roots of native grasses collected from noncropped fields and from roots of wheat from fields with different cropping histories near Lind, Ritzville, Pullman, and Almota, WA. Isolates were characterized by using morphological traits, G. graminis variety-specific polymerase chain reaction and pathogenicity tests. The sensitivity of G. graminis var. tritici isolates to 2,4-DAPG was determined by measuring radial growth of each isolate. The 90% effective dose value was 3.1 to 4.4 μg ml–1 for 2,4-DAPG-sensitive isolates, 4.5 to 6.1 μg ml–1 for moderately sensitive isolates, and 6.2 to 11.1 μg ml–1 for less sensitive isolates. Sensitivity of G. graminis var. tritici isolates to 2,4-DAPG was normally distributed in all fields and was not correlated with geographic origin or cropping history of the field. There was no correlation between virulence on wheat and geographical origin, or virulence and sensitivity to 2,4-DAPG. These results indicate that G. graminis var. tritici does not become less sensitive to 2,4-DAPG during extended wheat monoculture.
Seed Treatment with 2,4-Diacetylphloroglucinol-Producing Pseudomonads Improves Crop Health in Low-pH Soils by Altering Patterns of Nutrient Uptake
Authors: Raudales Rosa E. , Stone Erica , McSpadden Gardener Brian B.
Published: April 2009

Seed treatment with a 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas strain ameliorated abiotic stress disorder in corn caused by growth in a low-pH soil. In two consecutive growing seasons, Wood1R-treated seed gave rise to plants that grew taller (P ≤ 0.05), had fewer foliar lesions (P ≤ 0.10), and provided greater yields (P ≤ 0.1) than the negative controls when grown in soil with a pH < 5.0. Under controlled conditions, seed treatment with Wood1R also reduced foliar lesion severity (P ≤ 0.05 in two of three experiments) but failed to increase shoot or root growth in young seedlings grown in acidic soil. Significant (P ≤ 0.05) patterns of altered mineral nutrient uptake (i.e., generally increasing P and Mg while reducing Al) were observed to occur as a result of Wood1R seed treatment under both sets of growing conditions. In contrast, suppression of seedling damping-off disease was not indicated in this low-pH soil, because no difference in crop stand was observed for any experiment. Additionally, Wood1R-mediated growth inhibition of seedling pathogens was reduced in vitro at pH < 5.0, indicating that secretion of antifungal metabolites may not occur in low-pH soils. This is the first report of an abiotic stress amelioration of acid soil stress-related symptoms by a DAPG-producing pseudomonad.
Role of Recombination in the Evolution of Host Specialization Within Bean yellow mosaic virus
Authors: Wylie S. J. , Jones R. A. C.
Published: April 2009

Seven complete genomes and 64 coat protein gene sequences belonging to Bean yellow mosaic virus (BYMV) isolates from different continents were examined for evidence of genetic recombination using six different recombination-detection programs. In the seven complete genomes and a single complete genome of the related virus Clover yellow vein virus (ClYVV), evidence for eight recombination patterns was found by four or more programs, giving firm evidence of their presence, and five additional recombination patterns were detected by three or fewer programs, giving tentative evidence of their occurrence. When the nucleotide sequences of 64 BYMV and one ClYVV coat protein genes were analyzed, three firm recombination patterns were detected in 21 isolates (32%). With another six isolates (9%), tentative evidence was found for three further recombination patterns. Of the 19 firm or tentative recombination patterns detected within and between strain groups of BYMV, and with ClYVV, 12 involved a generalist group of isolates as a parent but none of the other BYMV groups acted as parents more than six times. These findings suggest that recombination played an important role in the evolution of BYMV strain groups that specialize in infecting particular groups of domesticated plants.