bluuebunny/crossref_metadata_2025 huggingface dataset:
A statistical analysis of SuperDARN scattering volume electron densities and velocity corrections using a radar frequency shifting technique
Authors: Gillies R. G. , Hussey G. C. , Sofko G. J. , McWilliams K. A.
Published: July 2012

Ionospheric plasma drift velocities measured by High Frequency (HF) coherent scatter radars, such as the Super Dual Auroral Radar Network (SuperDARN), are typically underestimated, sometimes significantly, because the refractive index in the scattering volume is not known. Large‐scale or background estimates of ionospheric electron density and refractive index can be made by other instruments; however, these instruments both do not cover the large field‐of‐view of the SuperDARN radars and do not provide information about the small‐scale structures which may be very important for the scattering process. A method has been developed to use different operating frequencies of the SuperDARN radars to obtain the average scattering volume electron density. These electron density measurements provide an estimate of refractive index and allow for corrections to the SuperDARN velocity data to be made. A comprehensive analysis of all SuperDARN data since its inception almost 20 years ago has provided estimates of average electron density in the scattering volume of the radars for various magnetic latitudes, solar activities, local times, and seasons. The analysis indicates that the average electron density, and therefore refractive index, in the scattering volume can vary significantly with the various parameters. Densities ranging from less than 2 × 1011 m−3 to more than 8 × 1011 m−3, result in refractive index corrections from less than 5% (not very significant) to more than 50% (extremely significant). These results provide estimates of appropriate adjustments to the drift velocities assumed by SuperDARN for various conditions. Further, this research has provided substantial insight into the physics of the coherent scattering process and provides a method by which electron density of the scattering structures can be monitored. This will be tested using in situ high‐latitude ionospheric measurements from the upcoming enhanced Polar Outflow Probe (ePOP) satellite mission.
A two‐phase composite in simple shear: Effective mechanical anisotropy development and localization potential
Authors: Dabrowski M. , Schmid D. W. , Podladchikov Y. Y.
Published: July 2012

We present a combined shape and mechanical anisotropy evolution model for a two‐phase inclusion‐bearing rock subject to large deformation. A single elliptical inclusion embedded in a homogeneous but anisotropic matrix is used to represent a simplified shape evolution enforced on all inclusions. The mechanical anisotropy develops due to the alignment of elongated inclusions. The effective anisotropy is quantified using the differential effective medium (DEM) approach. The model can be run for any deformation path and an arbitrary viscosity ratio between the inclusion and host phase. We focus on the case of simple shear and weak inclusions. The shape evolution of the representative inclusion is largely insensitive to the anisotropy development and to parameter variations in the studied range. An initial hardening stage is observed up to a shear strain of γ = 1 irrespective of the inclusion fraction. The hardening is followed by a softening stage related to the developing anisotropy and its progressive rotation toward the shear direction. The traction needed to maintain a constant shear rate exhibits a fivefold drop at γ = 5 in the limiting case of an inviscid inclusion. Numerical simulations show that our analytical model provides a good approximation to the actual evolution of a two‐phase inclusion‐host composite. However, the inclusions develop complex sigmoidal shapes resulting in the formation of an S‐C fabric. We attribute the observed drop in the effective normal viscosity to this structural development. We study the localization potential in a rock column bearing varying fraction of inclusions. In the inviscid inclusion case, a strain jump from γ = 3 to γ = 100 is observed for a change of the inclusion fraction from 20% to 33%.
Compaction of porous rock by dissolution on discrete stylolites: A one‐dimensional model
Authors: Angheluta Luiza , Mathiesen Joachim , Aharonov Einat
Published: July 2012

Compaction of sedimentary porous rock by dissolution and precipitation is a complex deformation mechanism, that is often localized on stylolites and pressure solution seams. We consider a one‐dimensional model of compaction near a thin clay‐rich stylolite embedded in a porous rock. Under the assumption that the clay enhances solubility, the model predicts a reactive transport away from the clay layer followed by pore cementation. The evolution of the porosity, reactant transport, and compaction rate are studied as functions of model parameters and shown to reach a stationary state. We find good agreement between the porosity distribution predicted by the model and previously reported field measurements. The model provides quantitative estimates for compaction rates on stylolitic surfaces.
The benefit of modeled ozone data for the reconstruction of a 99‐year UV radiation time series
Authors: Junk J. , Feister U. , Helbig A. , Görgen K. , Rozanov E. , Krzyścin J. W. , Hoffmann L.
Published: July 2012

Solar erythemal UV radiation (UVER) is highly relevant for numerous biological processes that affect plants, animals, and human health. Nevertheless, long‐term UVER records are scarce. As significant declines in the column ozone concentration were observed in the past and a recovery of the stratospheric ozone layer is anticipated by the middle of the 21st century, there is a strong interest in the temporal variation of UVERtime series. Therefore, we combined ground‐based measurements of different meteorological variables with modeled ozone data sets to reconstruct time series of daily totals of UVER at the Meteorological Observatory, Potsdam, Germany. Artificial neural networks were trained with measured UVER, sunshine duration, the day of year, measured and modeled total column ozone, as well as the minimum solar zenith angle. This allows for the reconstruction of daily totals of UVERfor the period from 1901 to 1999. Additionally, analyses of the long‐term variations from 1901 until 1999 of the reconstructed, new UVER data set are presented. The time series of monthly and annual totals of UVERprovide a long‐term meteorological basis for epidemiological investigations in human health and occupational medicine for the region of Potsdam and Berlin. A strong benefit of our ANN‐approach is the fact that it can be easily adapted to different geographical locations, as successfully tested in the framework of the COSTAction 726.
Drainage network development in the Keanakāko‘i tephra, Kīlauea Volcano, Hawai‘i: Implications for fluvial erosion and valley network formation on early Mars
Authors: Craddock Robert A. , Howard Alan D. , Irwin Rossman P. , Tooth Stephen , Williams Rebecca M. E. , Chu Pao‐Shin
Published: July 2012

A number of studies have attempted to characterize Martian valley and channel networks. To date, however, little attention has been paid to the role of lithology, which could influence the rate of incision, morphology, and hydrology as well as the characteristics of transported materials. Here, we present an analysis of the physical and hydrologic characteristics of drainage networks (gullies and channels) that have incised the Keanakāko‘i tephra, a basaltic pyroclastic deposit that occurs mainly in the summit area of Kīlauea Volcano and in the adjoining Ka‘ū Desert, Hawai‘i. The Keanakāko‘i tephra is up to ∼10 m meters thick and largely devoid of vegetation, making it a good analog for the Martian surface. Although the scales are different, the Keanakāko‘i drainage networks suggest that several typical morphologic characteristics of Martian valley networks may be controlled by lithology in combination with ephemeral flood characteristics. Many gully headwalls and knickpoints within the drainage networks are amphitheater shaped, which results from strong‐over‐weak stratigraphy. Beds of fine ash, commonly bearing accretionary lapilli (pisolites), are more resistant to erosion than the interbedded, coarser weakly consolidated and friable tephra layers. Because the banks of the gullies and channels are easily eroded widths vary downslope, similar to Martian valley networks that have been characterized as “degraded.” The floors of the gullies and channels tend to be low‐relief with few prominent bed forms, reflecting the large proportion of sediment transported as bed load in high‐energy but short‐lived flood events. We calculate that the average flow velocities within the drainage networks are typically <10 cm/s, occurring during floods that probably last less than an hour. Analyses of sediment deposits that have overlain lava flows of known ages suggest that these ephemeral flood events are associated with large cold core winter cyclones, known locally as ‘kona storms’, that are capable of generating precipitation at rates >1 m/24 h. Given some recent modeling of the early Martian climate, our observations imply that rainfall on early Mars could also be associated with large intense events and that Martian valley network formation may be related to similar cyclonic storms.
Deformation associated with ghost craters and basins in volcanic smooth plains on Mercury: Strain analysis and implications for plains evolution
Authors: Klimczak Christian , Watters Thomas R. , Ernst Carolyn M. , Freed Andrew M. , Byrne Paul K. , Solomon Sean C. , Blair David M. , Head James W.
Published: July 2012

Since its insertion into orbit about Mercury in March 2011, the MESSENGER spacecraft has imaged most previously unseen regions of the planet in unprecedented detail, revealing extensive regions of contiguous smooth plains at high northern latitudes and surrounding the Caloris basin. These smooth plains, thought to be emplaced by flood volcanism, are populated with several hundred ghost craters and basins, nearly to completely buried impact features having rims for which the surface expressions are now primarily rings of deformational landforms. Associated with some ghost craters are interior groups of graben displaying mostly polygonal patterns. The origin of these graben is not yet fully understood, but comparison with numerical models suggests that the majority of such features are the result of stresses from local thermal contraction. In this paper, we highlight a previously unreported category of ghost craters, quantify extensional strains across graben‐bearing ghost craters, and make use of graben geometries to gain insights into the subsurface geology of smooth plains areas. In particular, the style and mechanisms of graben development imply that flooding of impact craters and basins led to substantial pooling of lavas, to thicknesses of ∼1.5 km. In addition, surface strains derived from groups of graben are generally in agreement with theoretically and numerically derived strains for thermal contraction.
The crystal fabric of ice from full‐waveform borehole sonic logging
Authors: Gusmeroli Alessio , Pettit Erin C. , Kennedy Joseph H. , Ritz Catherine
Published: July 2012

In an ice sheet, a preferred crystal orientation fabric affects deformation rates because ice crystals are strongly anisotropic: shear along the basal plane is significantly easier than shear perpendicular to the basal plane. The effect of fabric can be as important as temperature in defining deformation rates. Fabric is typically measured using analysis of thin sections under the microscope with co‐polarized light. Due to the time‐consuming and destructive nature of these measurements, however, it is difficult to capture the spatial variation in fabric necessary for evincing ice sheet flow patterns. Because an ice crystal is similarly elastically anisotropic, the speed of elastic waves through ice can be used as a proxy for quantify anisotropy. We use borehole sonic logging measurements and thin section data from Dome C, East Antarctica to define the relations between apparent fabric and borehole measured elastic speeds (compressionalVP and vertically polarized shear VSV). These relations, valid for single maximum fabrics, allow in‐situ, depth‐continuous fabric estimates of unimodal fabric strength from borehole sonic logging. We describe the single maximum fabric usinga1: the largest eigenvalue of the second‐order orientation tensor. For ice at −16°C anda1in the 0.7‐1 range the relations areVP = 248 a13.7 + 3755 m s−1 and VSV = −210a17.3 + 1968 m s−1.
Theory and numerical modeling of electrical self‐potential signatures of unsaturated flow in melting snow
Authors: Kulessa B. , Chandler D. , Revil A. , Essery R.
Published: July 2012

We have developed a new theory and numerical model of electrical self‐potential (SP) signals associated with unsaturated flow in melting snow. The model is applicable to continuous natural melt as well as transient flow phenomena such as meltwater pulses and is tested using laboratory column experiments. SP signals fundamentally depend on the temporal evolution of snow porosity and meltwater flux, electrical conductivity (EC), and pH. We infer a reversal of the sign of the zeta potential (a fundamental electrical property of grain surfaces in porous media) consistent with well‐known elution sequences of ions that cause progressive increases and decreases in meltwater pH and EC, respectively. Injection of fully melted snow samples, containing the entire natural range of ions, into melting snow columns caused additional temporary reversals of the sign of the zeta potential. Widely used empirical relationships between effective saturation, meltwater fraction, EC, and pH, as well as snow porosity, grain size, and permeability, are found to be robust for modeling purposes. Thus nonintrusive SP measurements can serve as proxies for snow meltwater fluxes and the temporal evolution of fundamental snow textural, hydraulic, or water quality parameters. Adaptation of automated multisensor SP acquisition technology from other environmental applications thus promises to bridge the widely acknowledged gap in spatial scales between satellite remote sensing and point measurements of snow properties. SP measurements and modeling may therefore contribute to solving a wide range of problems related to the assessment of water resource availability, avalanche or flood risk, or the amplification of climatic forcing of ice shelf, ice sheet, or glacier dynamics.
Targeted recovery of novel phylogenetic diversity from next-generation sequence data
Authors: Lynch Michael D J , Bartram Andrea K , Neufeld Josh D
Published: July 2012

Next-generation sequencing technologies have led to recognition of a so-called ‘rare biosphere’. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts. Here, we test this hypothesis by combining molecular and bioinformatic approaches for targeted retrieval of phylogenetic novelty within rare biosphere OTUs. We combined BLASTN network analysis, phylogenetics and targeted primer design to amplify 16S rRNA gene sequences from unique potential bacterial lineages, comprising part of the rare biosphere from a multi-million sequence data set from an Arctic tundra soil sample. Demonstrating the feasibility of the protocol developed here, three of seven recovered phylogenetic lineages represented extremely divergent taxonomic entities. These divergent target sequences correspond to (a) a previously unknown lineage within the BRC1 candidate phylum, (b) a sister group to the early diverging and currently recognized monospecific Cyanobacteria Gloeobacter, a genus containing multiple plesiomorphic traits and (c) a highly divergent lineage phylogenetically resolved within mitochondria. A comparison to twelve next-generation data sets from additional soils suggested persistent low-abundance distributions of these novel 16S rRNA genes. The results demonstrate this sequence analysis and retrieval pipeline as applicable for exploring underrepresented phylogenetic novelty and recovering taxa that may represent significant steps in bacterial evolution.
Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank
Authors: Jungbluth Sean P , Grote Jana , Lin Huei-Ting , Cowen James P , Rappé Michael S
Published: July 2012

Despite its immense size, logistical and methodological constraints have largely limited microbiological investigations of the subseafloor basement biosphere. In this study, a unique sampling system was used to collect fluids from the subseafloor basaltic crust via a Circulation Obviation Retrofit Kit (CORK) observatory at Integrated Ocean Drilling Program borehole 1301A, located at a depth of 2667 m in the Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Here, a fluid delivery line directly accesses a 3.5 million years old basalt-hosted basement aquifer, overlaid by 262 m of sediment, which serves as a barrier to direct exchange with bottom seawater. At an average of 1.2 × 104 cells ml−1, microorganisms in borehole fluids were nearly an order of magnitude less abundant than in surrounding bottom seawater. Ribosomal RNA genes were characterized from basement fluids, providing the first snapshots of microbial community structure using a high-integrity fluid delivery line. Interestingly, microbial communities retrieved from different CORKs (1026B and 1301A) nearly a decade apart shared major community members, consistent with hydrogeological connectivity. However, over three sampling years, the dominant gene clone lineage changed from relatives of Candidatus Desulforudis audaxviator within the bacterial phylum Firmicutes in 2008 to the Miscellaneous Crenarchaeotic Group in 2009 and a lineage within the JTB35 group of Gammaproteobacteria in 2010, and statistically significant variation in microbial community structure was observed. The enumeration of different phylogenetic groups of cells within borehole 1301A fluids supported our observation that the deep subsurface microbial community was temporally dynamic.
Unique nucleocytoplasmic dsDNA and +ssRNA viruses are associated with the dinoflagellate endosymbionts of corals
Authors: Correa Adrienne M S , Welsh Rory M , Vega Thurber Rebecca L
Published: July 2012

The residence of dinoflagellate algae (genus: Symbiodinium) within scleractinian corals is critical to the construction and persistence of tropical reefs. In recent decades, however, acute and chronic environmental stressors have frequently destabilized this symbiosis, ultimately leading to coral mortality and reef decline. Viral infection has been suggested as a trigger of coral–Symbiodinium dissociation; knowledge of the diversity and hosts of coral-associated viruses is critical to evaluating this hypothesis. Here, we present the first genomic evidence of viruses associated with Symbiodinium, based on the presence of transcribed +ss (single-stranded) RNA and ds (double-stranded) DNA virus-like genes in complementary DNA viromes of the coral Montastraea cavernosa and expressed sequence tag (EST) libraries generated from Symbiodinium cultures. The M. cavernosa viromes contained divergent viral sequences similar to the major capsid protein of the dinoflagellate-infecting +ssRNA Heterocapsa circularisquama virus, suggesting a highly novel dinornavirus could infect Symbiodinium. Further, similarities to dsDNA viruses dominated (∼69%) eukaryotic viral similarities in the M. cavernosa viromes. Transcripts highly similar to eukaryotic algae-infecting phycodnaviruses were identified in the viromes, and homologs to these sequences were found in two independently generated Symbiodinium EST libraries. Phylogenetic reconstructions substantiate that these transcripts are undescribed and distinct members of the nucleocytoplasmic large DNA virus (NCLDVs) group. Based on a preponderance of evidence, we infer that the novel NCLDVs and RNA virus described here are associated with the algal endosymbionts of corals. If such viruses disrupt Symbiodinium, they are likely to impact the flexibility and/or stability of coral–algal symbioses, and thus long-term reef health and resilience.
Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties
Authors: Dohrmann Anja B , Küting Meike , Jünemann Sebastian , Jaenicke Sebastian , Schlüter Andreas , Tebbe Christoph C
Published: July 2012

Ribosomal 16S rRNA gene pyrosequencing was used to explore whether the genetically modified (GM) Bt-maize hybrid MON 89034 × MON 88017, expressing three insecticidal recombinant Cry proteins of Bacillus thuringiensis, would alter the rhizosphere bacterial community. Fine roots of field cultivated Bt-maize and three conventional maize varieties were analyzed together with coarse roots of the Bt-maize. A total of 547 000 sequences were obtained. Library coverage was 100% at the phylum and 99.8% at the genus rank. Although cluster analyses based on relative abundances indicated no differences at higher taxonomic ranks, genera abundances pointed to variety specific differences. Genera-based clustering depended solely on the 49 most dominant genera while the remaining 461 rare genera followed a different selection. A total of 91 genera responded significantly to the different root environments. As a benefit of pyrosequencing, 79 responsive genera were identified that might have been overlooked with conventional cloning sequencing approaches owing to their rareness. There was no indication of bacterial alterations in the rhizosphere of the Bt-maize beyond differences found between conventional varieties. B. thuringiensis-like phylotypes were present at low abundance (0.1% of Bacteria) suggesting possible occurrence of natural Cry proteins in the rhizospheres. Although some genera indicated potential phytopathogenic bacteria in the rhizosphere, their abundances were not significantly different between conventional varieties and Bt-maize. With an unprecedented sensitivity this study indicates that the rhizosphere bacterial community of a GM maize did not respond abnormally to the presence of three insecticidal proteins in the root tissue.
Factors affecting antler investment in Iberian red deer
Authors: Gómez J. A. , Ceacero F. , Landete-Castillejos T. , Gaspar-López E. , García A. J. , Gallego L.
Published: July 2012

Antler constitutes such a costly trait that the skeleton of the deer undergoes a process similar to osteoporosis to meet the high demands of mineral deposition in the antler. The allometric relationship between antler and body size is one of the oldest known. However, no study has assessed the proportion that antlers constitute with regard to the skeleton (from which most of the material is drawn), nor which factors influence this investment. To assess this, we studied 171 males (aged 1–5 years), determined their antler and bodyweights and scored their body condition. Then we calculated antler investment as antler weight relative to estimated skeletal weight. Results showed that antler investment in males ≥2 years old (i.e. excluding yearlings) depended on age rather than the whole bodyweight or body condition. Antler investment increased from 6% in yearlings to 35% in 5-year-old males, with a mean of 19%. A GLMM showed that in males ≥2 years old, within age, the heavier the male and the better the body condition at the start of antler growth, the greater the investment in antlers. In yearlings, antler investment did not depend on bodyweight or body condition. In conclusion, antler weight relative to skeleton weight is a good method to assess antler investment. This investment is influenced by age and, in males ≥2 years old, also by bodyweight or condition at the start of antler growth.
Systematically Bridging the Gap Between Novae and Supernovae
Authors: Kasliwal M. M.
Published: July 2012

The venerable study of cosmic explosions is over a century old. However, until recently, there has existed a glaring six-magnitude luminosity gap between the brightest novae and faintest supernovae. Serendipitous discoveries, archival searches and ongoing systematic surveys are yielding optical transients that are fainter, faster and rarer than supernovae. Theorists predict a variety of mechanisms to produce transients in the gap and observers have the best chance of finding them in the local Universe. Here I review the discoveries and the unique physics of cosmic explosions that bridge this gap between novae and supernovae.
Social science research related to wildfire management: an overview of recent findings and future research needs
Authors: McCaffrey Sarah , Toman Eric , Stidham Melanie , Shindler Bruce
Published: July 2012

As with other aspects of natural-resource management, the approach to managing wildland fires has evolved over time as scientific understanding has advanced and the broader context surrounding management decisions has changed. Prior to 2000 the primary focus of most fire research was on the physical and ecological aspects of fire; social science research was limited to a small number of studies. However, as more people moved into fire-prone areas interest grew in understanding relevant social dynamics. This growing interest was supported by increased funding for fire research overall with the creation of the Joint Fire Science Program in 1998 and the National Fire Plan in 2000. In subsequent years, a significant body of research has developed on the human dimensions of wildland fire covering diverse topics including: attitudes towards pre-fire mitigation, social acceptability of fire and fuels management, community preparedness, public response during fires, citizen–agency communications and post-fire recovery. This paper reports on two aspects of a Joint Fire Science Program project intended to take stock of the key social science lessons provided to date: a basic review of findings in the non-economic fire social science literature and identification of future research needs.
Catalytic hydrogen evolution from a covalently linked dicobaloxime
Authors: Valdez Carolyn N. , Dempsey Jillian L. , Brunschwig Bruce S. , Winkler Jay R. , Gray Harry B.
Published: July 2012

A dicobaloxime in which monomeric Co(III) units are linked by an octamethylene bis(glyoxime) catalyzes the reduction of protons from
p
-toluenesulfonic acid as evidenced by electrocatalytic waves at -0.4 V vs. the saturated calomel electrode (SCE) in acetonitrile solutions. Rates of hydrogen evolution were determined from catalytic current peak heights (
k
app
 = 1100 ± 70 M
-1
 s
-1
). Electrochemical experiments reveal no significant enhancement in the rate of H
2
evolution from that of a monomeric analogue: The experimental rate law is first order in catalyst and acid consistent with previous findings for similar mononuclear cobaloximes. Our work suggests that H
2
evolution likely occurs by protonation of reductively generated Co
II
H rather than homolysis of two Co
III
H units.
Speed, dissipation, and error in kinetic proofreading
Authors: Murugan Arvind , Huse David A. , Leibler Stanislas
Published: July 2012

Proofreading mechanisms increase specificity in biochemical reactions by allowing for the dissociation of intermediate complexes. These mechanisms disrupt and reset the reaction to undo errors at the cost of increased time of reaction and free energy expenditure. Here, we draw an analogy between proofreading and microtubule growth which share some of the features described above. Our analogy relates the statistics of growth and shrinkage of microtubules in physical space to the cycling of intermediate complexes in the space of chemical states in proofreading mechanisms. Using this analogy, we find a new kinetic regime of proofreading in which an exponential speed-up of the process can be achieved at the cost of a somewhat larger error rate. This regime is analogous to the transition region between two known growth regimes of microtubules (bounded and unbounded) and is sharply defined in the limit of large proofreading networks. We find that this advantageous regime of speed-error tradeoff might be present in proofreading schemes studied earlier in the charging of tRNA by tRNA synthetases, in RecA filament assembly on ssDNA, and in protein synthesis by ribosomes.
One-electron oxidation of an oxoiron(IV) complex to form an [O═Fe
V
═NR]
+
center
Authors: Van Heuvelen Katherine M. , Fiedler Adam T. , Shan Xiaopeng , De Hont Raymond F. , Meier Katlyn K. , Bominaar Emile L. , Münck Eckard , Que Lawrence
Published: July 2012

Oxoiron(V) species are postulated to be involved in the mechanisms of the arene
cis
-dihydroxylating Rieske dioxygenases and of bioinspired nonheme iron catalysts for alkane hydroxylation, olefin
cis
-dihydroxylation, and water oxidation. In an effort to obtain a synthetic oxoiron(V) complex, we report herein the one-electron oxidation of the
S
 = 1 complex [Fe
IV
(O)(TMC)(NCCH
3
)]
2+
(
1
, where TMC is tetramethylcyclam) by treatment with
tert
-butyl hydroperoxide and strong base in acetonitrile to generate a metastable

complex
2
at -44 °C, which has been characterized by UV-visible, resonance Raman, Mössbauer, and EPR methods. The defining spectroscopic characteristic of
2
is the unusual
x
/
y
anisotropy observed for the
57
Fe and
17
O A tensors associated with the high-valent Fe═O unit and for the
14
N A tensor of a ligand derived from acetonitrile. As shown by detailed density functional theory (DFT) calculations, the unusual
x
/
y
anisotropy observed can only arise from an iron center with substantially different spin populations in the d

xz

and d

yz

orbitals, which cannot correspond to an Fe
IV
═O unit but is fully consistent with an

Fe
V
center, like that found for [Fe
V
(O)(TAML)]
-
(where TAML is tetraamido macrocyclic ligand), the only well-characterized oxoiron(V) complex reported. Mass spectral analysis shows that the generation of
2
entails the addition of an oxygen atom to
1
and the loss of one positive charge. Taken together, the spectroscopic data and DFT calculations support the formulation of
2
as an iron(V) complex having axial oxo and acetylimido ligands, namely [Fe
V
(O)(TMC)(NC(O)CH
3
)]
+
.
An essential novel component of the noncanonical mitochondrial outer membrane protein import system of trypanosomatids
Authors: Pusnik Mascha , Mani Jan , Schmidt Oliver , Niemann Moritz , Oeljeklaus Silke , Schnarwiler Felix , Warscheid Bettina , Lithgow Trevor , Meisinger Chris , Schneider André
Published: July 2012

The mitochondrial outer membrane protein Tom40 is the general entry gate for imported proteins in essentially all eukaryotes. Trypanosomatids lack Tom40, however, and use instead a protein termed the archaic translocase of the outer mitochondrial membrane (ATOM). Here we report the discovery of pATOM36, a novel essential component of the trypanosomal outer membrane protein import system that interacts with ATOM. pATOM36 is not related to known Tom proteins from other organisms and mediates the import of matrix proteins. However, there is a group of precursor proteins whose import is independent of pATOM36. Domain-swapping experiments indicate that the N-terminal presequence-containing domain of the substrate proteins at least in part determines the dependence on pATOM36. Secondary structure profiling suggests that pATOM36 is composed largely of α-helices and its assembly into the outer membrane is independent of the sorting and assembly machinery complex. Taken together, these results show that pATOM36 is a novel component associated with the ATOM complex that promotes the import of a subpopulation of proteins into the mitochondrial matrix.
Collagen/β1 integrin signaling up-regulates the ABCC1/MRP-1 transporter in an ERK/MAPK-dependent manner
Authors: El Azreq Mohammed-Amine , Naci Dalila , Aoudjit Fawzi
Published: July 2012

The mechanisms by which β1 integrins regulate chemoresistance of cancer cells are still poorly understood. In this study, we report that collagen/β1 integrin signaling inhibits doxorubicin-induced apoptosis of Jurkat and HSB2 leukemic T-cells by up-regulating the expression and function of the ATP-binding cassette C 1 (ABCC1) transporter, also known as multidrug resistance–associated protein 1. We find that collagen but not fibronectin reduces intracellular doxorubicin content and up-regulates the expression levels of ABCC1. Inhibition and knockdown studies show that up-regulation of ABCC1 is necessary for collagen-mediated reduction of intracellular doxorubicin content and collagen-mediated inhibition of doxorubicin-induced apoptosis. We also demonstrate that activation of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase signaling pathway is involved in collagen-induced reduction of intracellular doxorubicin accumulation, collagen-induced up-regulation of ABCC1 expression levels, and collagen-mediated cell survival. Finally, collagen-mediated up-regulation of ABCC1 expression and function also requires actin polymerization. Taken together, our results indicate for the first time that collagen/β1 integrin/ERK signaling up-regulates the expression and function of ABCC1 and suggest that its activation could represent an important pathway in cancer chemoresistance. Thus simultaneous targeting of collagen/β1 integrin and ABCC1 may be more efficient in preventing drug resistance than targeting each pathway alone.
Cdc28–Cln3 phosphorylation of Sla1 regulates actin patch dynamics in different modes of fungal growth
Authors: Zeng Guisheng , Wang Yan-Ming , Wang Yue
Published: July 2012

A dynamic balance between targeted transport and endocytosis is critical for polarized cell growth. However, how actin-mediated endocytosis is regulated in different growth modes remains unclear. Here we report differential regulation of cortical actin patch dynamics between the yeast and hyphal growth in Candida albicans. The mechanism involves phosphoregulation of the endocytic protein Sla1 by the cyclin-dependent kinase (CDK) Cdc28–Cln3 and the actin-regulating kinase Prk1. Mutational studies of the CDK phosphorylation sites of Sla1 revealed that Cdc28–Cln3 phosphorylation of Sla1 enhances its further phosphorylation by Prk1, weakening Sla1 association with Pan1, an activator of the actin-nucleating Arp2/3 complex. Sla1 is rapidly dephosphorylated upon hyphal induction and remains so throughout hyphal growth. Consistently, cells expressing a phosphomimetic version of Sla1 exhibited markedly reduced actin patch dynamics, impaired endocytosis, and defective hyphal development, whereas a nonphosphorylatable Sla1 had the opposite effect. Taken together, our findings establish a molecular link between CDK and a key component of the endocytic machinery, revealing a novel mechanism by which endocytosis contributes to cell morphogenesis.
Yeast vacuoles fragment in an asymmetrical two-phase process with distinct protein requirements
Authors: Zieger Martin , Mayer Andreas
Published: July 2012

Yeast vacuoles fragment and fuse in response to environmental conditions, such as changes in osmotic conditions or nutrient availability. Here we analyze osmotically induced vacuole fragmentation by time-lapse microscopy. Small fragmentation products originate directly from the large central vacuole. This happens by asymmetrical scission rather than by consecutive equal divisions. Fragmentation occurs in two distinct phases. Initially, vacuoles shrink and generate deep invaginations that leave behind tubular structures in their vicinity. Already this invagination requires the dynamin-like GTPase Vps1p and the vacuolar proton gradient. Invaginations are stabilized by phosphatidylinositol 3-phosphate (PI(3)P) produced by the phosphoinositide 3-kinase complex II. Subsequently, vesicles pinch off from the tips of the tubular structures in a polarized manner, directly generating fragmentation products of the final size. This phase depends on the production of phosphatidylinositol-3,5-bisphosphate and the Fab1 complex. It is accelerated by the PI(3)P- and phosphatidylinositol 3,5-bisphosphate–binding protein Atg18p. Thus vacuoles fragment in two steps with distinct protein and lipid requirements.
Owen Martin Phillips. 30 December 1930 — 13 October 2010
Authors: Turner J. Stewart , Olson Peter L.
Published: July 2012

Owen Phillips made outstanding contributions to the understanding of the ocean, notably through the diverse research topics incorporated in his monograph
The dynamics of the upper ocean
. He also contributed significantly to the understanding of geological processes in books on subsurface flows and reactions in permeable rocks. Owen was born and attended school and university in Sydney, Australia, winning scholarships to Cambridge in 1952 to do his PhD under the supervision of George Batchelor (FRS 1957). In 1957 he moved to the USA to join the faculty of Johns Hopkins University, returning to Cambridge four years later as Assistant Director of Research in the new Department of Applied Mathematics and Theoretical Physics. In 1964 Owen returned to Johns Hopkins, where he stayed until retirement in 1998: first as Professor of Geophysical Mechanics and later as Professor of Geophysics in the Department of Earth and Planetary Sciences, a department that he subsequently chaired.
Accelerated simulation of unfolding and refolding of a large single chain globular protein
Authors: Seddon Gavin M. , Bywater Robert P.
Published: July 2012

We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs C
oncoord
and D
arvols
. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work.
Inactivation and reactivation of ribonuclease A studied by computer simulation
Authors: Seddon Gavin M. , Bywater Robert P.
Published: July 2012

The year 2011 marked the half-centenary of the publication of what came to be known as the Anfinsen postulate, that the tertiary structure of a folded protein is prescribed fully by the sequence of its constituent amino acid residues. This postulate has become established as a
credo
, and, indeed, no contradictions seem to have been found to date. However, the experiments that led to this postulate were conducted on only a single protein, bovine ribonuclease A (RNAse). We conduct molecular dynamics (MD) simulations on this protein with the aim of mimicking this experiment as well as making the methodology available for use with basically any protein. There have been many attempts to model denaturation and refolding processes of globular proteins
in silico
using MD, but only a few examples where disulphide-bond containing proteins were studied. We took the view that if the reductive deactivation and oxidative reactivation processes of RNAse could be modelled
in silico,
this would provide valuable insights into the workings of the classical Anfinsen experiment.
Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
Authors: Rolfe Matthew D. , Ocone Andrea , Stapleton Melanie R. , Hall Simon , Trotter Eleanor W. , Poole Robert K. , Sanguinetti Guido , Green Jeffrey
Published: July 2012

Understanding gene regulation requires knowledge of changes in transcription factor (TF) activities. Simultaneous direct measurement of numerous TF activities is currently impossible. Nevertheless, statistical approaches to infer TF activities have yielded non-trivial and verifiable predictions for individual TFs. Here, global statistical modelling identifies changes in TF activities from transcript profiles of
Escherichia coli
growing in stable (fixed oxygen availabilities) and dynamic (changing oxygen availability) environments. A core oxygen-responsive TF network, supplemented by additional TFs acting under specific conditions, was identified. The activities of the cytoplasmic oxygen-responsive TF, FNR, and the membrane-bound terminal oxidases implied that, even on the scale of the bacterial cell, spatial effects significantly influence oxygen-sensing. Several transcripts exhibited asymmetrical patterns of abundance in aerobic to anaerobic and anaerobic to aerobic transitions. One of these transcripts,
ndh
, encodes a major component of the aerobic respiratory chain and is regulated by oxygen-responsive TFs ArcA and FNR. Kinetic modelling indicated that ArcA and FNR behaviour could not explain the
ndh
transcript profile, leading to the identification of another TF, PdhR, as the source of the asymmetry. Thus, this approach illustrates how systematic examination of regulatory responses in stable and dynamic environments yields new mechanistic insights into adaptive processes.
Rehydroxylation (RHX) dating of archaeological pottery
Authors: Wilson Moira A. , Hamilton Andrea , Ince Ceren , Carter Margaret A. , Hall Christopher
Published: July 2012

We show that the rehydroxylation (RHX) method can be used to date archaeological pottery, and give the first RHX dates for three disparate items of excavated material. These are in agreement with independently assigned dates. We define precisely the mass components of the ceramic material before, during and after dehydroxylation. These include the masses of three types of water present in the sample: capillary water, weakly chemisorbed molecular water and chemically combined RHX water. We describe the main steps of the RHX dating process: sample preparation, drying, conditioning, reheating and measurement of RHX mass gain. We propose a statistical criterion for isolating the RHX component of the measured mass gain data after reheating and demonstrate how to calculate the RHX age. An effective lifetime temperature (ELT) is defined, and we show how this is related to the temperature history of a sample. The ELT is used to adjust the RHX rate constant obtained at the measurement temperature to the effective lifetime value used in the RHX age calculation. Our results suggest that RHX has the potential to be a reliable and technically straightforward method of dating archaeological pottery, thus filling a long-standing gap in dating methods.
Synergistic Interactions between Carotene Ring Hydroxylases Drive Lutein Formation in Plant Carotenoid Biosynthesis
Authors: Quinlan Rena F. , Shumskaya Maria , Bradbury Louis M.T. , Beltrán Jesús , Ma Chunhui , Kennelly Edward J. , Wurtzel Eleanore T.
Published: July 2012

Plant carotenoids play essential roles in photosynthesis, photoprotection, and as precursors to apocarotenoids. The plastid-localized carotenoid biosynthetic pathway is mediated by well-defined nucleus-encoded enzymes. However, there is a major gap in understanding the nature of protein interactions and pathway complexes needed to mediate carotenogenesis. In this study, we focused on carotene ring hydroxylation, which is performed by two structurally distinct classes of enzymes, the P450 CYP97A and CYP97C hydroxylases and the nonheme diiron HYD enzymes. The CYP97A and HYD enzymes both function in the hydroxylation of β-rings in carotenes, but we show that they are not functionally interchangeable. The formation of lutein, which involves hydroxylation of both β- and ε-rings, was shown to require the coexpression of CYP97A and CYP97C enzymes. These enzymes were also demonstrated to interact in vivo and in vitro, as determined using bimolecular fluorescence complementation and a pull-down assay, respectively. We discuss the role of specific hydroxylase enzyme interactions in promoting pathway flux and preventing the formation of pathway dead ends. These findings will facilitate efforts to manipulate carotenoid content and composition for improving plant adaptation to climate change and/or for enhancing nutritionally important carotenoids in food crops.
Bcl‐2, Bcl‐6, and the International Prognostic Index are prognostic indicators in patients with diffuse large B‐cell lymphoma treated with rituximab‐containing chemotherapy
Authors: Maeshima Akiko Miyagi , Taniguchi Hirokazu , Fukuhara Suguru , Morikawa Noriyuki , Munakata Wataru , Maruyama Dai , Kim Sung‐Won , Watanabe Takashi , Kobayashi Yukio , Tobinai Kensei , Tsuda Hitoshi
Published: July 2012

This study aimed to clarify the clinicopathological prognostic parameters of de novo diffuse large B‐cell lymphoma (DLBCL) in the rituximab era. We examined the correlation of 22 clinicopathological parameters with progression‐free survival (PFS), overall survival (OS), and primary refractory disease in 285 DLBCL patients treated with rituximab‐containing chemotherapy. Complete response rate was 87%, overall response rate was 91%, 5‐year PFS rate was 72%, and 5‐year OS rate was 91%. By log–rank test, higher International Prognostic Index (IPI) (P < 0.0001), Bcl‐2 positivity (P = 0.0013), Bcl‐6 negativity (P = 0.0112), and no irradiation (P = 0.0371) were significantly correlated with shorter PFS; higher IPI (P = 0.0107), starry sky pattern (P = 0.0466), and no irradiation (P = 0.0264) correlated with shorter OS. In multivariate analyses, higher IPI (P = 0.0006), Bcl‐2 positivity (P = 0.0015), and Bcl‐6 negativity (P = 0.04) were significantly correlated with shorter PFS; higher IPI (P = 0.0045) correlated with shorter OS. Bcl‐2 (P = 0.0029), Bcl‐6 (P = 0.002), and IPI (P < 0.0001) were significantly correlated with primary refractory disease. In conclusion, Bcl‐2 positivity, Bcl‐6 negativity, and higher IPI were indicators of shorter PFS and OS plus primary refractory disease in patients with DLBCL in the rituximab era.
Comparison of the oestrogen and progesterone receptor status in primary breast carcinomas as evaluated by immunohistochemistry and immunocytochemistry: a consecutive series of 267 patients
Authors: Domanski A. M. , Monsef N. , Domanski H. A. , Grabau D. , Fernö M.
Published: July 2012

A.M. Domanski, N. Monsef, H.A. Domanski, D. Grabau and M. Fernö Comparison of the oestrogen and progesterone receptor status in primary breast carcinomas as evaluated by immunohistochemistry and immunocytochemistry: a consecutive series of 267 patients

Objective:  The use of cytological specimens to evaluate tumour biomarkers in metastatic breast cancer lesions has attracted increased interest because of the considerable number of reports that have shown discordance between the primary tumour and metastatic lesion. Oestrogen receptor (ER) and progesterone receptor (PgR) assays are crucial for the management of patients with breast cancer, in both adjuvant and palliative settings. The aim of this study was to compare the ER and PgR immunocytochemical analysis of fine needle aspiration (FNA) samples with the immunohistochemistry (IHC) of surgical specimens and core biopsies from primary breast cancers.

Methods:  The FNA specimens were prepared as cell blocks (n = 25) or ThinPreps (n = 258) for the immunocytochemistry (IC) ER and PgR analyses. Sixteen patients were excluded because of lack of follow‐up (n = 1), neoadjuvant therapy (n = 3) or cell counts in their fine needle aspirates that were too low (n = 12). The results of IC on 25 cell blocks and 242 ThinPreps were compared with IHC on the corresponding core needle biopsies (n = 16) or excised tumours (n = 251). The ER and PgR status was defined as negative (when less than 10% of the nuclei were stained) or positive (when equal or more than 10% of the nuclei were stained). Kappa statistics were used to evaluate the concordance.

Results:  The ER concordance was 98% with ThinPrep (κ = 0.93) and 92% with cell block (κ = 0.82). The corresponding values for PgR were 96% (κ = 0.91) and 96% (κ = 0.92).

Conclusions:  Our results confirm that, in cases in which biopsies or surgical specimens are not available, IC (with either cell block or ThinPrep techniques) is a reliable method for the determination of the ER and PgR status performed under strict conditions using primary breast carcinomas, and is therefore potentially useful in metastatic settings.