bluuebunny/crossref_metadata_2025 huggingface dataset:
A comparison of tracer methods for quantifying CO2sources in an urban region
Authors: Djuricin Sonja , Pataki Diane E. , Xu Xiaomei
Published: June 2010

The relative contribution of anthropogenic (natural gas and gasoline combustion) and biogenic (aboveground and belowground respiration) CO2sources has previously been quantified with the13C,18O, and14C isotopes of CO2. The unique combination of isotopic signatures of each source allows for top‐down attribution of sources using atmospheric measurements. Other tracers of CO2include carbon monoxide (CO), which is a direct tracer of fossil fuel combustion‐derived CO2as CO and CO2are evolved at specific ratios (RCO/CO2) during combustion depending on fuel source and combustion efficiency. We used the13C,18O, and14C tracers to partition between natural gas, gasoline, and aboveground and belowground respiration during four sampling events in the Los Angeles basin. Additionally, we compared the effectiveness of the independent CO tracer with the14C tracer to distinguish between anthropogenic and biogenic CO2. The three isotope tracer results showed that during the sampling period, fossil fuel combustion was not a dominant source of CO2and aboveground respiration contributed up to approximately 70% of CO2sources during the spring. However, the percent fossil fuel CO2calculated by the CO tracer was not entirely consistent with the fossil fuel CO2calculated by14C, which predicted up to ∼70% of winter CO2from fossil fuel sources. The CO tracer was useful for showing diurnal patterns of CO2sources. However, combustion RCO/CO2values vary significantly, which poses a challenge for accurately identifying CO2sources. Detailed local information about RCO/CO2is required to effectively utilize the CO tracer for quantifying sources of CO2.
Soluble mass, hygroscopic growth, and droplet activation of coated soot particles during LACIS Experiment in November (LExNo)
Authors: Henning S. , Wex H. , Hennig T. , Kiselev A. , Snider J. R. , Rose D. , Dusek U. , Frank G. P. , Pöschl U. , Kristensson A. , Bilde M. , Tillmann R. , Kiendler‐Scharr A. , Mentel T. F. , Walter S. , Schneider J. , Wennrich C. , Stratmann F.
Published: June 2010

The LACIS Experiment in November (LExNo) campaign was conducted in November 2005 at the Atmospheric Composition Change the European Network of Excellence (ACCENT) site Leipzig Aerosol Cloud Interaction Simulator (LACIS). The goal of LExNo was to provide deeper insight into the activation properties of coated soot particles imitating aged combustion aerosol particles. The aerosols were prepared by starting with spark‐generated soot particles. In some experiments the soot particles were compacted by exposure to propanol vapor; in others this step was bypassed. The soot was thermally coated with ammonium sulfate, levoglucosan, or a mixture of both ammonium sulfate and levoglucosan. The synthesized particles were investigated using aerosol mass spectrometry, a Hygroscopicity Tandem differential mobility analyzer, two Wyoming static diffusion cloud condensation nuclei (CCN) instruments, a Droplet Measurement Technologies continuous flow CCN instrument, and LACIS. A close correlation between the hygroscopic growth factor at 98% relative humidity and the critical supersaturation of CCN activation was observed. Closure between hygroscopic growth, CCN activation, and chemical composition of the investigated particles was achieved with two different single‐parameter Köhler model approaches and with a third approach, a standard Köhler model using as input parameter the soluble mass as determined by aerosol mass spectrometry.
Examination of laboratory‐generated coated soot particles: An overview of the LACIS Experiment in November (LExNo) campaign
Authors: Stratmann F. , Bilde M. , Dusek U. , Frank G. P. , Hennig T. , Henning S. , Kiendler‐Scharr A. , Kiselev A. , Kristensson A. , Lieberwirth I. , Mentel T. F. , Pöschl U. , Rose D. , Schneider J. , Snider J. R. , Tillmann R. , Walter S. , Wex H.
Published: June 2010

In the suite of laboratory measurements described here and in companion articles we deal with the hygroscopic growth and activation behavior of coated soot particles synthesized to mimic those of an atmospheric aerosol originating from biomass combustion. The investigations were performed during the measurement campaign LACIS Experiment in November (LExNo) which took place at the Leipzig Aerosol Cloud Interaction Simulator (LACIS). The specific goals of this campaign were (1) to perform a critical supersaturation measurement intercomparison using data sets from three different cloud condensation nucleus (CCN) instruments (two static thermal gradient type, one stream‐wise thermal gradient type) and LACIS, (2) to examine particle hygroscopic growth (hydrated particle size as function of relative humidity) for particle characteristics such as aerosol mass spectrometer (AMS) measured soluble mass and particle morphology, and (3) to relate critical supersaturations derived from both measurements of soluble mass and high‐humidity tandem differential mobility analyzer (HH‐TDMA) determined growth factors to critical supersaturations measured by means of the CCN instruments. This paper provides information on the particle synthesis techniques used during LExNo, an overview concerning the particle characterization measurements performed, and, by proving relations between measured composition, hygroscopic growth, and activation data, lay the foundations for the detailed investigations described in the companion studies. In the context of the present paper, excellent agreement of the critical supersaturations measured with three different CCN instruments and LACIS was observed. Furthermore, clear relations between coating masses determined with AMS and both hygroscopic growth factors at 98% RH and measured critical supersaturations could be seen. Also, a strong correlation between measured hygroscopic growth (growth factors at 98%) and measured critical supersaturation for all of the differently coated soot particles (coating substances being levoglucosan and/or ammonium (hydrogen) sulfate) was found. This is clearly indicative of the possibility of predicting the critical supersaturation of coated soot particles based on hygroscopic growth measurements using Köhler theory.
Origins of the Caribbean Rainfall Bimodal Behavior
Authors: Angeles Moisés E. , González Jorge E. , Ramírez‐Beltrán Nazario D. , Tepley Craig A. , Comarazamy Daniel E.
Published: June 2010

The annual precipitation pattern in the Caribbean basin shows a distinct bimodal behavior, where the first mode is called the Early Rainfall Season (April–July), and the second mode the Late Rainfall Season (August–November). The brief, relatively dry, period in July is usually referred to as the midsummer drought (MSD). It has been hypothesized that the migration through the Caribbean basin of the Intertropical Convergence Zone (ITCZ) and increases in aerosols due to the passing of Saharan Dust across the Caribbean in the summer months may result in the observed precipitation pattern. This paper focuses on determining the origins of the Caribbean MSD. Multiple regression analysis was carried‐out to determine if the ITCZ, the North Atlantic Oscillation (NAO) index, the Vertical Wind Shear (VWS), and different atmospheric particle (AP) concentrations transported from northern Africa correlate with the Caribbean MSD. It is shown that the ITCZ and NAO are weakly correlated with the Caribbean precipitation variability; however, the VWS and aerosol particles revealed an important contribution to rainfall during the summer months. Numerical experiments were then performed to quantify the influence of different VWS scenarios and different AP concentrations on the Caribbean precipitation bimodal behavior. The numerical approach uses the Regional Atmospheric Modeling System coupled with a new cloud microphysics module that allows discrimination between small and giant particles, as well as Cloud Concentration Nuclei (CCN) and Giant CCN activation. These numerical experiments support the statistical result that the VWS and the AP influence the rainfall production and pattern during the MSD. Results indicate that cloud microphysics play an important role in producing the observed climatological bimodal pattern, while variations in large‐scale atmospheric dynamics (like the VWS) help explain variations in the strength and pattern of the bimodal events and behavior.
Structural and geochronological evidence for Paleogene thrusting in the western Rhodopes, SW Bulgaria: Elements for a new tectonic model of the Rhodope Metamorphic Province
Authors: Jahn‐Awe Silke , Froitzheim Nikolaus , Nagel Thorsten J. , Frei Dirk , Georgiev Neven , Pleuger Jan
Published: June 2010

The Rhodope Metamorphic Province in the area around the Mesta Graben (SW Bulgaria) exposes a structurally lower complex, the Pangaion‐Pirin Complex of Variscan continental crust and its cover (mostly orthogneiss and marble), and a higher complex, the Rhodope Terrane of mixed oceanic and continental origin with metamorphosed Jurassic arc magmatites. The boundary between the two is the top‐to‐the‐southwest Nestos Shear Zone. The regional top‐to‐the‐southwest shearing of the two basement complexes is related to the emplacement of the Rhodope Terrane over the Pangaion‐Pirin Complex along this shear zone. Syntectonic and posttectonic Alpine intrusions within the basement can provide age limits for the thrusting. Zircons from the posttectonic Teshovo (south Pirin) Granitoid Pluton in the Pangaion‐Pirin Complex yielded crystallization ages of 32 ± 0.2 Ma (LA‐SF‐ICP‐MS U‐Pb method). Zircons from two syntectonic granite plutons in the Rhodope Terrane (Dolno Dryanovo and Spanchevo) have circa 143 to 145 Ma old inherited magmatic cores and circa 55 to 56 Ma old magmatic rims. These ages, especially the presence of the Upper Jurassic/Lower Cretaceous cores in the plutons from the Rhodope Terrane, and the structural relations indicate that the southwestward thrusting of the Rhodope Terrane over the Pangaion‐Pirin Complex took place in the Paleogene. A model is proposed in which the Pangaion‐Pirin Complex represents the margin of Apulia and the structure of the Rhodopes is explained by a switch of subduction polarity from SW dipping in the Jurassic and Early Cretaceous to NE dipping in the Late Cretaceous and Paleogene.
Mesospheric Ice Clouds as Indicators of Upper Atmosphere Climate Change: Workshop on Modeling Polar Mesospheric Cloud Trends; Boulder, Colorado, 10–11 December 2009
Authors: Thomas Gary , Marsh Dan , Lübken F.‐J.
Published: June 2010

The 20‐year‐old speculation that high‐altitude summertime ice clouds (polar mesospheric, or noctilucent, clouds, here denoted MC) are affected by anthropogenic activities has recently received support from a 30‐year time series of solar backscatter ultraviolet (SBUV) satellite measurements. SBUV data reveal a significant trend in bright MC properties. However, the robustness of the trend, extracted from interannual, local time, and solar cycle variability, and its underlying causes remains debatable.
Nine AGU Journals Rated Highly by Australian Evaluation System
Authors: Cook Bill
Published: June 2010

Nine AGU journals recently received high ratings from the Australian Research Council's Excellence in Research for Australia (ERA) initiative evaluation system. ERA evaluates and rates peer‐reviewed journals in a wide range of research fields on the basis of expert review and public consultation. For the 2010 ratings, released in February, ERA evaluated more than 20,000 peer‐reviewed journals.
Johnson Receives 2009 Early Career Tectonophysics Award
Authors: Hamburger Michael , Johnson Kaj M.
Published: June 2010

Kaj M. Johnson received the 2009 Early Career Tectonophysics Award at the 2009 AGU Fall Meeting, held 14–18 December in San Francisco, Calif. The award is for significant early career contributions to tectonophysics.
Reconstructing Climate Change: Not All Glaciers Suitable
Authors: Yde Jacob C. , Paasche Øyvind
Published: June 2010

Glaciers are among the most trusted indicators of climate change, not just because they retreat due to the current rise in global temperatures but also because of their central role in reconstructing past climates. Glaciers come in many forms, and their sensitivity to climate change depends partly on the physics governing the individual glacier, implying that a response can be fast or slow, straightforward or complex, which in sum suggests that not all glaciers are equally suitable for reconstructing past and present climate conditions. In particular, surging and debris‐covered glaciers may especially yield misleading results (Figure 1).
Eruptions of Eyjafjallajökull Volcano, Iceland
Authors: Gudmundsson Magnús T. , Pedersen Rikke , Vogfjörd Kristín , Thorbjarnardóttir Bergthöra , Jakobsdóttir Steinunn , Roberts Matthew J.
Published: June 2010

The April 2010 eruption of Eyjafjallajökull volcano (Figure 1), located on Iceland's southern coast, created unprecedented disruptions to European air traffic during 15–20 April, costing the aviation industry an estimated $250 million per day (see the related news item in this issue). This cost brings into focus how volcanoes can affect communities thousands of miles away.

Eyjafjallajökull rises to 1666 meters above sea level and hosts agricultural land on its southern slopes, with farms located as close as 7 kilometers from the summit caldera. In the past 1500 years, Eyjafjallajökull has produced four comparatively small eruptions. The eruption previous to 2010 began in December 1821 and lasted for over a year, with intermittent explosive activity spreading a thin layer of tephra (ash and larger ejected clasts) over the surrounding region. In contrast, the explosive 2010 eruption, sourced within the ice‐capped summit of the volcano, so far is larger and characterized by magma of a slightly different composition. This may suggest that deep within the volcano, the 1821 magma source is mixing with new melt, or that residual melt from past intrusive events is being pushed out by new magma.
Nuclear Test Ban: Converting Political Visions to Reality
Authors: Suárez Gerardo
Published: June 2010

Negotiations to ban or at least restrict nuclear explosions began not long after the first test was conducted, in the Alamogordo desert of New Mexico on 16 July 1945. In August of that same year, the world witnessed the devastation of the Japanese cities of Hiroshima and Nagasaki and the horrifically destructive power that these weapons are capable of unleashing.

Almost 50 years later, the long and tortuous road to negotiating a treaty that comprehensively bans nuclear explosions, whether for alleged peaceful purposes or for weapons development, culminated on 24 September 1996 when the Comprehensive Nuclear‐Test‐Ban Treaty (CTBT) was opened for signature. In a surge of enthusiasm, that first day the treaty was signed by more than 70 nations, including the five acknowledged nuclear powers. Addressing the United Nations General Assembly, U.S. President Bill Clinton described the CTBT as “the longest‐sought, hardest‐fought prize in the history of arms control.”
Constraints on upper mantle viscosity from the flow‐induced pressure gradient across the Australian continental keel
Authors: Harig Christopher , Zhong Shijie , Simons Frederik J.
Published: June 2010

The thickness of continental lithosphere varies considerably from tectonically active to cratonic regions, where it can be as thick as 250–300 km. Embedded in the upper mantle like a ship, when driven to move by a velocity imposed at the surface, a continental keel is expected to induce a pressure gradient in the mantle. We hypothesize that the viscosity of the asthenosphere or the shear coupling between lower lithosphere and asthenosphere should control this pressure effect and thus the resulting dynamic topography. We perform three‐dimensional finite element calculations to examine the effects of forcing a continental keel by an imposed surface velocity, with the Australian region as a case study. When the upper mantle is strong but still weaker than the lower mantle, positive dynamic topography is created around the leading edge, and negative dynamic topography is created around the trailing edge of the keel, which is measurable by positive and negative geoid anomalies, respectively. For a weak upper mantle the effect is much reduced. We analyze geoidal and gravity anomalies in the Australian region by spatiospectral localization using Slepian functions. The method allows us to remove a best fit estimate of the geographically localized low spherical harmonic degree contributions. Regional geoid anomalies thus filtered are on the order of ±10 m across the Australian continent, with a spatial pattern similar to that predicted by the models. The comparison of modeled and observed geoid anomalies places constraints on mantle viscosity structure. Models with a two‐layer mantle cannot sufficiently constrain the ratio of viscosity between the upper and lower mantle. The addition of a third, weak, upper mantle layer, an asthenosphere, amplifies the effects of keels. Our three‐layer models, with lower mantle viscosity of 3 × 1022 Pa s, suggest that the upper mantle (asthenosphere) is 300 times weaker than the lower mantle, while the transition zone (400–670 km depths) has a viscosity varying between 1021 and 1022 Pa s.
Storm intensity and old‐growth forest disturbances in the Amazon region
Authors: Espírito‐Santo F. D. B. , Keller M. , Braswell B. , Nelson B. W. , Frolking S. , Vicente G.
Published: June 2010

We analyzed the pattern of large forest disturbances or blow‐downs apparently caused by severe storms in a mostly unmanaged portion of the Brazilian Amazon using 27 Landsat images and daily precipitation estimates from NOAA satellite data. For each Landsat a spectral mixture analysis (SMA) was applied. Based on SMA, we detected and mapped 279 patches (from 5 ha to 2,223 ha) characteristic of blow‐downs. A total of 21,931 ha of forest were disturbed. We found a strong correlation between occurrence of blow‐downs and frequency of heavy rainfall (Spearman's rank, r2 = 0.84, p < 0.0003). The recurrence intervals of large disturbances were estimated to be 90,000 yr for the eastern Amazon and 27,000 yr for the western Amazon. This suggests that weather patterns affect the frequency of large forest disturbances that may produce different rates of forest turnover in the eastern and western Amazon basin.
Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein
Authors: Sota Masahiro , Yano Hirokazu , M Hughes Julie , Daughdrill Gary W , Abdo Zaid , Forney Larry J , Top Eva M
Published: June 2010

The ability of bacterial plasmids to adapt to novel hosts and thereby shift their host range is key to their long-term persistence in bacterial communities. Promiscuous plasmids of the incompatibility group P (IncP)-1 can colonize a wide range of hosts, but it is not known if and how they can contract, shift or further expand their host range. To understand the evolutionary mechanisms of host range shifts of IncP-1 plasmids, an IncP-1β mini-replicon was experimentally evolved in four hosts in which it was initially unstable. After 1000 generations in serial batch cultures under antibiotic selection for plasmid maintenance (kanamycin resistance), the stability of the mini-plasmid dramatically improved in all coevolved hosts. However, only plasmids evolved in Shewanella oneidensis showed improved stability in the ancestor, indicating that adaptive mutations had occurred in the plasmid itself. Complete genome sequence analysis of nine independently evolved plasmids showed seven unique plasmid genotypes that had various kinds of single mutations at one locus, namely, the N-terminal region of the replication initiation protein TrfA. Such parallel evolution indicates that this region was under strong selection. In five of the seven evolved plasmids, these trfA mutations resulted in a significantly higher plasmid copy number. Evolved plasmids were found to be stable in four other naive hosts, but could no longer replicate in Pseudomonas aeruginosa. This study shows that plasmids can specialize to a novel host through trade-offs between improved stability in the new host and the ability to replicate in a previously permissive host.
Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis
Authors: Thomas Torsten , Rusch Doug , DeMaere Matt Z , Yung Pui Yi , Lewis Matt , Halpern Aaron , Heidelberg Karla B , Egan Suhelen , Steinberg Peter D , Kjelleberg Staffan
Published: June 2010

Sponges form close relationships with bacteria, and a remarkable phylogenetic diversity of yet-uncultured bacteria has been identified from sponges using molecular methods. In this study, we use a comparative metagenomic analysis of the bacterial community in the model sponge Cymbastela concentrica and in the surrounding seawater to identify previously unrecognized genomic signatures and functions for sponge bacteria. We observed a surprisingly large number of transposable insertion elements, a feature also observed in other symbiotic bacteria, as well as a set of predicted mechanisms that may defend the sponge community against the introduction of foreign DNA and hence contribute to its genetic resilience. Moreover, several shared metabolic interactions between bacteria and host include vitamin production, nutrient transport and utilization, and redox sensing and response. Finally, an abundance of protein–protein interactions mediated through ankyrin and tetratricopeptide repeat proteins could represent a mechanism for the sponge to discriminate between food and resident bacteria. These data provide new insight into the evolution of symbiotic diversity, microbial metabolism and host–microbe interactions in sponges.
Vascular Dysfunction in Obstructive Sleep Apnea and Type 2 Diabetes Mellitus
Authors: Yim‐Yeh Susie , Rahangdale Shilpa , Nguyen Anh Tu Duy , Stevenson Karen E. , Novack Victor , Veves Aristidis , Malhotra Atul
Published: June 2010

Despite the high prevalence of obstructive sleep apnea (OSA) in type 2 diabetes mellitus (DM), the attributable vascular risk from each condition is unknown. We hypothesize that OSA may have a similar effect on vascular function as type 2 diabetes does. Healthy normal‐weight subjects, healthy obese subjects, subjects with type 2 diabetes, and obese subjects with OSA were enrolled. Vascular function was assessed with brachial artery ultrasound for flow‐mediated dilatation (FMD) and in skin microcirculation by laser Doppler flowmetry. One hundred fifty‐three subjects were studied: healthy normal‐weight controls (NCs) (n = 14), healthy obese controls (OCs) (n = 33), subjects with DM (n = 68), and obese subjects with OSA (n = 38). The DM group did not undergo sleep study and thus may have had subclinical OSA. The OSA and type 2 diabetes groups had impaired FMD as compared to both the normal‐weight and OC groups (5.8 ± 3.8%, 5.4 ± 1.6% vs. 9.1 ± 2.5%, 8.3 ± 5.1%, respectively, P < 0.001, post hoc Fischer test). When referenced to the NC group, a multiple linear regression model adjusting for covariates found that baseline brachial artery diameter (β = −3.75, P < 0.001), OSA (β = −2.45, P = 0.02) and type 2 diabetes status (β = −2.31, P = 0.02), negatively predicted % FMD. OSA status did not seem to affect nitroglycerin‐induced vasodilation (endothelium‐independent) of the brachial artery or vascular function in the skin microcirculation. OSA impairs endothelial function in the brachial artery to a similar degree as type 2 diabetes does. OSA, however, does not appear to affect brachial endothelium‐independent vasodilation or skin microcirculatory function. Treatment of OSA in patients with concomitant type 2 diabetes, therefore, may be a potential therapeutic option to improve macro‐, but not microvascular outcomes.
12‐Month Outcomes and Process Evaluation of the SHED‐IT RCT: An Internet‐Based Weight Loss Program Targeting Men
Authors: Morgan Philip J. , Lubans David R. , Collins Clare E. , Warren Janet M. , Callister Robin
Published: June 2010

This article reports the 12‐month follow‐up results and process evaluation of the SHED‐IT (Self‐Help, Exercise, and Diet using Information Technology) trial, an Internet‐based weight loss program exclusively for men. Sixty‐five overweight/obese male staff and students at the University of Newcastle (Callaghan, Australia) (mean (s.d.) age = 35.9 (11.1) years; BMI = 30.6 (2.8)) were randomly assigned to either (i) Internet group (n = 34) or (ii) Information only control group (n = 31). Both received one face‐to‐face information session and a program booklet. Internet group participants were instructed to use the study website for 3 months. Participants were assessed at baseline, 3‐, 6‐, and 12‐month follow‐up for weight, waist circumference, BMI, blood pressure, and resting heart rate. Retention at 3‐ and 12‐months was 85% and 71%, respectively. Intention‐to‐treat (ITT) analysis using linear mixed models revealed significant and sustained weight loss of −5.3 kg (95% confidence interval (CI): −7.5, −3.0) at 12 months for the Internet group and −3.1 kg (95% CI: −5.4, −0.7) for the control group with no group difference. A significant time effect was found for all outcomes (P < 0.001). Per‐protocol analysis revealed a significant group‐by‐time interaction for weight, waist circumference, BMI, and systolic blood pressure. Internet group compliers (who self‐monitored as instructed) maintained greater weight loss at 12 months (−8.8 kg; 95% CI −11.8, −5.9) than noncompliers (−1.9 kg; 95% CI −4.8, 1.0) and controls (−3.0 kg; 95% CI −5.2, −0.9). Qualitative analysis by questionnaire and interview highlighted the acceptability and satisfaction with SHED‐IT. Low‐dose approaches to weight loss are feasible, acceptable, and can achieve clinically important weight loss in men after 1‐year follow‐up.
Association of Common Polymorphisms in the Fractalkine Receptor (CX3CR1) With Obesity
Authors: Sirois‐Gagnon Dave , Chamberland Annie , Perron Stéphanie , Brisson Diane , Gaudet Daniel , Laprise Catherine
Published: June 2010

The inflammatory component in obesity is now well established. The CX3CR1 gene encodes the fractalkine (CX3CL1) receptor and has two coding single‐nucleotide polymorphisms, V249I and T280M, linked to a lower risk of other inflammatory diseases such as coronary artery disease (CAD) and asthma. To determine whether CX3CR1 is associated with obesity, we genotyped the V249I and T280M polymorphisms of the CX3CR1 gene in subjects with a BMI ≥30 kg/m2 and nonobese controls with a BMI <30 kg/m2. Binary logistic regression analyses revealed that the 280MM genotype was associated with obesity (P = 0.022). A gender‐specific one‐way ANOVA was also conducted to investigate mean BMI and waist circumference differences between genotypes of each polymorphism. For both polymorphisms independently, women carrying two copies of the minor allele had significant higher mean waist circumference than those carrying only one copy of the minor allele (MM > TM, P = 0.031; II > VI, P = 0.013) or those who were homozygous for the major allele (MM > TT, P = 0.005; II > VV, P = 0.006). We also observed significant higher mean waist circumference in men carrying one copy of the minor allele when compared to those who were homozygous for the major allele for the T280M polymorphism (TM > TT, P = 0.029). This study suggests that CX3CR1, a biomarker of obesity in this sample, constitutes a potential target for further investigation of the role of inflammation in the expression of obesity‐related phenotypes.
Regulation of plasma-membrane-associated sialidase NEU3 gene by Sp1/Sp3 transcription factors
Authors: Yamaguchi Kazunori , Koseki Koichi , Shiozaki Momo , Shimada Yukiko , Wada Tadashi , Miyagi Taeko
Published: June 2010

Gene expression of the human plasma membrane-associated sialidase (NEU3), a key enzyme for ganglioside degradation, is relatively high in brain and is modulated in response to many cellular processes, including neuronal cell differentiation and tumorigenesis. We demonstrated previously that NEU3 is markedly up-regulated in various human cancers and showed that NEU3 transgenic mice developed a diabetic phenotype and were susceptible to azoxymethane-induced aberrant crypt foci in their colon tissues. These results suggest that appropriate control of NEU3 gene expression is required for homoeostasis of cellular functions. To gain insights into regulation mechanisms, we determined the gene structure and assessed transcription factor involvement. Oligo-capping analysis indicated the existence of alternative promoters for the NEU3 gene. Transcription started from two clusters of multiple TSSs (transcription start sites); one cluster is preferentially utilized in brain and another in other tissues and cells. Luciferase reporter assays showed further that the region neighbouring the two clusters has promoter activity in the human cell lines analysed. The promoter lacks TATA, but contains CCAAT and CAAC, elements, whose deletions led to a decrease in promoter activity. Electrophoretic mobility-shift assays and chromatin immunoprecipitation demonstrated binding of transcription factors Sp (specificity protein) 1 and Sp3 to the promoter region. Down-regulation of the factors by siRNAs (short interfering RNAs) increased transcription from brain-type TSSs and decreased transcription from other TSSs, suggesting a role for Sp1 and Sp3 in selection of the TSSs. These results indicate that NEU3 expression is diversely regulated by Sp1/Sp3 transcription factors binding to alternative promoters, which might account for multiple modulation of gene expression.
One-carbon metabolism in plants: characterization of a plastid serine hydroxymethyltransferase
Authors: Zhang Yi , Sun Kehan , Sandoval Francisco J. , Santiago Katherine , Roje Sanja
Published: June 2010

SHMT (serine hydroxymethyltransferase; EC 2.1.2.1) catalyses reversible hydroxymethyl group transfer from serine to H4PteGlun (tetrahydrofolate), yielding glycine and 5,10-methylenetetrahydrofolate. In plastids, SHMTs are thought to catalytically direct the hydroxymethyl moiety of serine into the metabolic network of H4PteGlun-bound one-carbon units. Genes encoding putative plastid SHMTs were found in the genomes of various plant species. SHMT activity was detected in chloroplasts in pea (Pisum sativum) and barley (Hordeum vulgare), suggesting that plastid SHMTs exist in all flowering plants. The Arabidopsis thaliana genome encodes one putative plastid SHMT (AtSHMT3). Its cDNA was cloned by reverse transcription–PCR and the encoded recombinant protein was produced in Escherichia coli. Evidence that AtSHMT3 is targeted to plastids was found by confocal microscopy of A. thaliana protoplasts transformed with proteins fused to enhanced green fluorescent protein. Characterization of recombinant AtSHMT3 revealed that substrate affinity for and the catalytic efficiency of H4PteGlu1-8 increase with n, and that H4PteGlu1-8 inhibit AtSHMT3. 5-Methyltetrahydrofolate and 5-formyltetrahydrofolate with one and five glutamate residues inhibited AtSHMT3-catalysed hydroxymethyl group transfer from serine to H4PteGlu6, with the pentaglutamylated inhibitors being more effective. Calculations revealed inhibition with 5-methyltetrahydrofolate or 5-formyltetrahydrofolate resulting in little reduction in AtSHMT3 activity under folate concentrations estimated for plastids.
Essential arginine residue of the Fo-a subunit in FoF1-ATP synthase has a role to prevent the proton shortcut without c-ring rotation in the Fo proton channel
Authors: Mitome Noriyo , Ono Sakurako , Sato Hiroki , Suzuki Toshiharu , Sone Nobuhito , Yoshida Masasuke
Published: June 2010

In FoF1 (FoF1-ATP synthase), proton translocation through Fo drives rotation of the oligomer ring of Fo-c subunits (c-ring) relative to Fo-a. Previous reports have indicated that a conserved arginine residue in Fo-a plays a critical role in the proton transfer at the Fo-a/c-ring interface. Indeed, we show in the present study that thermophilic FoF1s with substitution of this arginine (aR169) to other residues cannot catalyse proton-coupled reactions. However, mutants with substitution of this arginine residue by a small (glycine, alanine, valine) or acidic (glutamate) residue mediate the passive proton translocation. This translocation requires an essential carboxy group of Fo-c (cE56) since the second mutation (cE56Q) blocks the translocation. Rotation of the c-ring is not necessary because the same arginine mutants of the ‘rotation-impossible’ (c10-a)FoF1, in which the c-ring and Fo-a are fused to a single polypeptide, also exhibits the passive proton translocation. The mutant (aR169G/Q217R), in which the arginine residue is transferred to putatively the same topological position in the Fo-a structure, can block the passive proton translocation. Thus the conserved arginine residue in Fo-a ensures proton-coupled c-ring rotation by preventing a futile proton shortcut.
Molten Salts: Volume 3 Nitrates, Nitrites, and Mixtures: Electrical Conductance, Density, Viscosity, and Surface Tension Data
Authors: Janz G. J. , Krebs Ursula , Siegenthaler H. F. , Tomkins R. P. T.
Published: June 2010

Data on the electrical conductance, density, viscosity, and surface tension of nitrate—nitrate, nitrite—nitrite, and nitrite—nitrate mixtures have been systematically collected and evaluated. Results are given for some 71 binary mixtures over a range of compositions and temperatures. Values of the above properties for the single salts have been updated in accord with previously advanced recommendations.
The ‘Rotating Snakes’ in Smooth Motion do Not Appear to Rotate
Authors: Tomimatsu Erika , Ito Hiroyuki , Seno Takeharu , Sunaga Shoji
Published: June 2010

‘Rotating snakes’ is an illusory figure in which the ‘snakes’ are perceived to rotate. We report that when the image moves smoothly, the snakes do not appear to rotate, although the retinal images are continuously refreshed. Therefore, to produce the illusion, the image should remain stationary (without being refreshed) for some time on the same retinal position.
RGS inhibition at Gαi2selectively potentiates 5-HT1A–mediated antidepressant effects
Authors: Talbot Jeffery N. , Jutkiewicz Emily M. , Graves Steven M. , Clemans Crystal F. , Nicol Melanie R. , Mortensen Richard M. , Huang Xinyan , Neubig Richard R. , Traynor John R.
Published: June 2010

Elevating serotonin (5-HT) levels with selective serotonin reuptake inhibitors (SSRIs) is the most widely used treatment for depression. However, current therapies are ineffective, have delayed benefit, or cause side effects in many patients. Here, we define a mechanism downstream of 5-HT1A receptors that mediates antidepressant-like behavior and is profoundly and selectively enhanced by genetic disruption of regulators of G protein signaling (RGS) activity at Gαi2. Animals rendered insensitive to RGS protein regulation through a mutation in Gαi2 (G184S) exhibited spontaneous antidepressant- and anxiolytic-like behaviors. Mice expressing RGS-insensitive Gαi2 also exhibited increased cortical and hippocampal phosphorylation of glycogen synthase kinase-3β, a constitutively active proapoptotic kinase that is inhibited through phosphorylation in response to serotonin, SSRIs, and 5-HT1 receptor agonists. Both behavioral and biochemical phenotypes were blocked by treatment with WAY 100635, a 5-HT1A–selective antagonist. RGS-insensitive mice were also 5–10 times more responsive to the antidepressant-like effects of the SSRI fluvoxamine and 5-HT1A–selective agonist 8-hydroxy-2-dipropylaminotetralin. In contrast, the antidepressant potency of agents acting through nonserotonergic mechanisms was unchanged as was 5-HT1A action on body temperature. The findings point to a critical role for endogenous RGS proteins to suppress the antidepressant-like effects of 5-HT1A receptor activation. By selectively enhancing the beneficial effects of serotonin, inhibition of RGS proteins represents a therapeutic approach for the treatment of mood disorders.
FlhA provides the adaptor for coordinated delivery of late flagella building blocks to the type III secretion system
Authors: Bange Gert , Kümmerer Nico , Engel Christoph , Bozkurt Gunes , Wild Klemens , Sinning Irmgard
Published: June 2010

Flagella are the bacterial organelles of motility and can play important roles in pathogenesis. Flagella biosynthesis requires the coordinated export of huge protein amounts from the cytosol to the nascent flagellar structure at the cell surface and employs a type III secretion system (T3SS). Here we show that the integral membrane protein FlhA from the gram-positive bacterium
Bacillus subtilis
acts as an adaptor for late export substrates at the T3SS. The major filament protein (flagellin) and the filament-cap protein (FliD) bind to the FlhA cytoplasmic domain (FlhA-C) only in complex with their cognate chaperones (FliS and FliT). To understand the molecular details of these interactions we determined the FlhA-C crystal structure at 2.3 Å resolution. FlhA-C consists of an N-terminal linker region, three subdomains with a novel fold, and a disordered region essential for the adaptor function. We show that the export protein FliJ associates with the linker region and modulates the binding properties of FlhA-C. While the interaction of FliD/FliT is enhanced, flagellin/FliS is not affected. FliJ also keeps FliT associated with FlhA-C and excess of FliT inhibits binding of FliD/FliT, suggesting that empty FliT chaperones stay associated with FliJ after export of FliD. Taken together, these results allow to propose a model that explains how the T3SS may switch from the stoichiometric export of FliD to the high-throughput secretion of flagellin.
Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1
Authors: Pejchal Robert , Walker Laura M. , Stanfield Robyn L. , Phogat Sanjay K. , Koff Wayne C. , Poignard Pascal , Burton Dennis R. , Wilson Ian A.
Published: June 2010

Development of an effective vaccine against HIV-1 will likely require elicitation of broad and potent neutralizing antibodies against the trimeric surface envelope glycoprotein (Env). Monoclonal antibodies (mAbs) PG9 and PG16 neutralize ~80% of HIV-1 isolates across all clades with extraordinary potency and target novel epitopes preferentially expressed on Env trimers. As these neutralization properties are ideal for a vaccine-elicited antibody response to HIV-1, their structural basis was investigated. The crystal structure of the antigen-binding fragment (Fab) of PG16 at 2.5 Å resolution revealed its unusually long, 28-residue, complementarity determining region (CDR) H3 forms a unique, stable subdomain that towers above the antibody surface. A 7-residue “specificity loop” on the “hammerhead” subdomain was identified that, when transplanted from PG16 to PG9 and vice versa, accounted for differences in the fine specificity and neutralization of these two mAbs. The PG16 electron density maps also revealed that a CDR H3 tyrosine was sulfated, which was confirmed for both PG9 (doubly) and PG16 (singly) by mass spectral analysis. We further showed that tyrosine sulfation plays a role in binding and neutralization. An N-linked glycan modification is observed in the variable light chain, but not required for antigen recognition. Further, the crystal structure of the PG9 light chain at 3.0 Å facilitated homology modeling to support the presence of these unusual features in PG9. Thus, PG9 and PG16 use unique structural features to mediate potent neutralization of HIV-1 that may be of utility in antibody engineering and for high-affinity recognition of a variety of therapeutic targets.
A formula for the 𝑅-matrix using a system of weight preserving endomorphisms
Authors: Tingley Peter
Published: June 2010

We give a formula for the universal

R
R

-matrix of the quantized universal enveloping algebra

U
q

(

g

)
.

U_q(\mathfrak {g}).

This is similar to a previous formula due to Kirillov-Reshetikhin and Levendorskii-Soibelman, except that where they use the action of the braid group element

T

w
0

T_{w_0}

on each representation

V
V

, we show that one can instead use a system of weight preserving endomorphisms. One advantage of our construction is that it is well defined for all symmetrizable Kac-Moody algebras. However, we have only established that the result is equal to the universal

R
R

-matrix in finite type.
S100A4 Regulates Macrophage Chemotaxis
Authors: Li Zhong-Hua , Dulyaninova Natalya G. , House Reniqua P. , Almo Steven C. , Bresnick Anne R.
Published: June 2010

S100A4, a member of the S100 family of Ca2+-binding proteins, is directly involved in tumor metastasis. In addition to its expression in tumor cells, S100A4 is expressed in normal cells and tissues, including fibroblasts and cells of the immune system. To examine the contribution of S100A4 to normal physiology, we established S100A4-deficient mice by gene targeting. Homozygous S100A4−/−mice are fertile, grow normally and exhibit no overt abnormalities; however, the loss of S100A4 results in impaired recruitment of macrophages to sites of inflammation in vivo. Consistent with these observations, primary bone marrow macrophages (BMMs) derived from S100A4−/−mice display defects in chemotactic motility in vitro. S100A4−/−BMMs form unstable protrusions, overassemble myosin-IIA, and exhibit altered colony-stimulating factor-1 receptor signaling. These studies establish S100A4 as a regulator of physiological macrophage motility and demonstrate that S100A4 mediates macrophage recruitment and chemotaxis in vivo.
Phosphorylation Controls Autoinhibition of Cytoplasmic Linker Protein-170
Authors: Lee Ho-Sup , Komarova Yulia A. , Nadezhdina Elena S. , Anjum Rana , Peloquin John G. , Schober Joseph M. , Danciu Oana , van Haren Jeffrey , Galjart Niels , Gygi Steven P. , Akhmanova Anna , Borisy Gary G.
Published: June 2010

Cytoplasmic linker protein (CLIP)-170 is a microtubule (MT) plus-end-tracking protein that regulates MT dynamics and links MT plus ends to different intracellular structures. We have shown previously that intramolecular association between the N and C termini results in autoinhibition of CLIP-170, thus altering its binding to MTs and the dynactin subunit p150Glued(J. Cell Biol. 2004: 166, 1003–1014). In this study, we demonstrate that conformational changes in CLIP-170 are regulated by phosphorylation that enhances the affinity between the N- and C-terminal domains. By using site-directed mutagenesis and phosphoproteomic analysis, we mapped the phosphorylation sites in the third serine-rich region of CLIP-170. A phosphorylation-deficient mutant of CLIP-170 displays an “open” conformation and a higher binding affinity for growing MT ends and p150Gluedas compared with nonmutated protein, whereas a phosphomimetic mutant confined to the “folded back” conformation shows decreased MT association and does not interact with p150Glued. We conclude that phosphorylation regulates CLIP-170 conformational changes resulting in its autoinhibition.
Identification of Three Distinct Functional Sites of Insulin-mediated GLUT4 Trafficking in Adipocytes Using Quantitative Single Molecule Imaging
Authors: Fujita Hideaki , Hatakeyama Hiroyasu , Watanabe Tomonobu M. , Sato Masaaki , Higuchi Hideo , Kanzaki Makoto
Published: June 2010

Insulin stimulation of glucose uptake is achieved by redistribution of insulin-responsive glucose transporters, GLUT4, from intracellular storage compartment(s) to the plasma membrane in adipocytes and muscle cells. Although GLUT4 translocation has been investigated using various approaches, GLUT4 trafficking properties within the cell are largely unknown. Our novel method allows direct analysis of intracellular GLUT4 dynamics at the single molecule level by using Quantum dot technology, quantitatively establishing the behavioral nature of GLUT4. Our data demonstrate the predominant mechanism for intracellular GLUT4 sequestration in the basal state to be “static retention” in fully differentiated 3T3L1 adipocytes. We also directly defined three distinct insulin-stimulated GLUT4 trafficking processes: 1) release from the putative GLUT4 anchoring system in storage compartment(s), 2) the speed at which transport GLUT4-containing vesicles move, and 3) the tethering/docking steps at the plasma membrane. Intriguingly, insulin-induced GLUT4 liberation from its static state appeared to be abolished by either pretreatment with an inhibitor of phosphatidylinositol 3-kinase or overexpression of a dominant-interfering AS160 mutant (AS160/T642A). In addition, our novel approach revealed the possibility that, in certain insulin-resistant states, derangements in GLUT4 behavior can impair insulin-responsive GLUT4 translocation.
Defects in the Secretory Pathway and High Ca2+Induce Multiple P-bodies
Authors: Kilchert Cornelia , Weidner Julie , Prescianotto-Baschong Cristina , Spang Anne
Published: June 2010

mRNA is sequestered and turned over in cytoplasmic processing bodies (PBs), which are induced by various cellular stresses. Unexpectedly, in Saccharomyces cerevisiae, mutants of the small GTPase Arf1 and various secretory pathway mutants induced a significant increase in PB number, compared with PB induction by starvation or oxidative stress. Exposure of wild-type cells to osmotic stress or high extracellular Ca2+mimicked this increase in PB number. Conversely, intracellular Ca2+-depletion strongly reduced PB formation in the secretory mutants. In contrast to PB induction through starvation or osmotic stress, PB formation in secretory mutants and by Ca2+required the PB components Pat1 and Scd6, and calmodulin, indicating that different stressors act through distinct pathways. Consistent with this hypothesis, when stresses were combined, PB number did not correlate with the strength of the translational block, but rather with the type of stress encountered. Interestingly, independent of the stressor, PBs appear as spheres of ∼40–100 nm connected to the endoplasmic reticulum (ER), consistent with the idea that translation and silencing/degradation occur in a spatially coordinated manner at the ER. We propose that PB assembly in response to stress occurs at the ER and depends on intracellular signals that regulate PB number.
Adenomatous Polyposis Coli Regulates Endothelial Cell Migration Independent of Roles in β-Catenin Signaling and Cell–Cell Adhesion
Authors: Harris Elizabeth S. , Nelson W. James
Published: June 2010

Adenomatous polyposis coli (APC), a tumor suppressor commonly mutated in cancer, is a cytoskeletal organizer for cell migration and a scaffold for GSK3β/CKI-mediated phosphorylation and degradation of the Wnt effector β-catenin. It remains unclear whether these different APC functions are coupled, or independently regulated and localized. In primary endothelial cells, we show that GSK3β/CKI-phosphorylated APC localizes to microtubule-dependent clusters at the tips of membrane extensions. Loss of GSK3β/CKI-phosphorylated APC from these clusters correlates with a decrease in cell migration. GSK3β/CKI-phosphorylated APC and β-catenin at clusters is degraded rapidly by the proteasome, but inhibition of GSK3β/CKI does not increase β-catenin–mediated transcription. GSK3β/CKI-phosphorylated and -nonphosphorylated APC also localize along adherens junctions, which requires actin and cell–cell adhesion. Significantly, inhibition of cell–cell adhesion results in loss of lateral membrane APC and a concomitant increase in GSK3β/CKI-phosphorylated APC in clusters. These results uncouple different APC functions and show that GSK3β/CKI phosphorylation regulates APC clusters and cell migration independently of cell–cell adhesion and β-catenin transcriptional activity.