bluuebunny/crossref_metadata_2025 huggingface dataset:
Tectonomagmatic activity and ice dynamics in the Bransfield Strait back‐arc basin, Antarctica
Authors: Dziak Robert P. , Park Minkyu , Lee Won Sang , Matsumoto Haru , Bohnenstiehl DelWayne R. , Haxel Joseph H.
Published: January 2010

An array of moored hydrophones was used to monitor the spatiotemporal distribution of small‐ to moderate‐sized earthquakes and ice‐generated sounds within the Bransfield Strait, Antarctica. During a 2 year period, a total of 3900 earthquakes, 5925 icequakes and numerous ice tremor events were located throughout the region. The seismic activity included eight space‐time earthquake clusters, positioned along the central neovolcanic rift zone of the young Bransfield back‐arc basin. These sequences of small magnitude earthquakes, or swarms, suggest ongoing magmatic activity that becomes localized along isolated volcanic features and fissure‐like ridges in the southwest portion of the basin. A total of 122 earthquakes were located along the South Shetland trench, indicating continued deformation and possibly ongoing subduction along this margin. The large number of icequakes observed show a temporal pattern related to seasonal freeze‐thaw cycles and a spatial distribution consistent with channeling of sea ice along submarine canyons from glacier fronts. Several harmonic tremor episodes were sourced from a large (∼30 km2) iceberg that entered northeast portion of the basin. The spectral character of these signals suggests they were produced by either resonance of a small chamber of fluid within the iceberg, or more likely, due to periodicity of discrete stick‐slip events caused by contact of the moving iceberg with the seafloor. These pressure waves appear to have been excited by abrasion of the iceberg along the seafloor as it passed Clarence and Elephant Islands.
Linking hierarchical stratal architecture to plume spreading in a Lagrangian‐based transport model: 2. Evaluation using new data from the Borden site
Authors: Ramanathan Ramya , Ritzi Robert W. , Allen‐King Richelle M.
Published: January 2010

A new data set collected at the well‐documented Borden research site was used in order to evaluate a newly published but as yet untested idea for stochastic modeling (Ramanathan et al., 2008). The new data set reveals the stratal architecture of the Borden aquifer and allowed us to determine how the stratal architecture, at different scales, controlled the macrodispersion observed in the original natural gradient tracer test. The newly published idea for modeling uses a Lagrangian‐based model for the particle displacement variance developed from independent, physically based, quantifiable univariate statistics, including the proportions and mean length of the strata. The method for defining model parameters avoids the often equivocal step of fitting sample bivariate permeability statistics. The model parameters were developed from the new data from the Borden site. The new data included geologic data in much greater abundance than permeability data. There are two scales of unit types delineated in a hierarchy of stratal architecture. Their shapes are complex, not simple layers or lenses. The method facilitated the direct use of both geologic and permeability data, which need not be collocated. The dispersion model developed from these data represents the field‐measured particle displacement variance that occurred in the natural gradient tracer test well. The contributions to time‐dependent macrodispersion by strata at each scale were computed and analyzed independently. This analysis revealed that macrodispersion at the Borden site is primarily controlled by the proportions, and the mean and variance in length of larger‐scale strata of medium sand (M) and strata of fine sand and silt (FZ), with secondary contributions by smaller‐scale strata types occurring within the larger‐scale units. When sampling the pattern in the longitudinal direction, M and FZ couplets repeat at 10 m intervals on average, with a high length variance. To reach a time‐constant macrodispersivity, the stratal length variability must be fully sampled by the plume. The macrodispersivity becomes asymptotic beyond an advective distance of about 60 m, corresponding to about 12 longitudinal transitions between M and FZ unit types.
High-frequency phage-mediated gene transfer in freshwater environments determined at single-cell level
Authors: Kenzaka Takehiko , Tani Katsuji , Nasu Masao
Published: January 2010

Lateral gene transfer by phages has contributed significantly to the genetic diversity of bacteria. To accurately determine the frequency and range of phage-mediated gene transfer, it is important to understand the movement of DNA among microbes. Using an in situ DNA amplification technique (cycling primed in situ amplification-fluorescent in situ hybridization; CPRINS-FISH), we examined the propensity for phage-mediated gene transfer in freshwater environments at the single-cell level. Phage P1, T4 and isolated Escherichia coli phage EC10 were used as vectors. All E. coli phages mediated gene transfer from E. coli to both plaque-forming and non-plaque-forming Enterobacteriaceae strains at frequencies of 0.3–8 × 10−3 per plaque-forming unit (PFU), whereas culture methods using selective agar media could not detect transductants in non-plaque-forming strains. The DNA transfer frequencies through phage EC10 ranged from undetectable to 9 × 10−2 per PFU (undetectable to 2 × 10−3 per total direct count) when natural bacterial communities were recipients. Direct viable counting combined with CPRINS-FISH revealed that more than 20% of the cells carrying the transferred gene retained their viability in most cases. These results indicate that the exchange of DNA sequences among bacteria occurs frequently and in a wide range of bacteria, and may promote rapid evolution of the prokaryotic genome in freshwater environments.
Ecological and evolutionary factors underlying global and local assembly of denitrifier communities
Authors: Jones Christopher M , Hallin Sara
Published: January 2010

The conversion of nitrite to nitric oxide in the denitrification pathway is catalyzed by at least two structurally dissimilar nitrite reductases, NirS and NirK. Although they are functionally equivalent, a genome with genes encoding both reductases has yet to be found. This exclusivity raises questions about the ecological equivalency of denitrifiers with either nirS or nirK, and how different ecological and evolutionary factors influence community assembly of nirS and nirK denitrifiers. Using phylogeny-based methods for analyzing community structure, we analyzed nirS and nirK data sets compiled from sequence repositories. Global patterns of phylogenetic community structure were determined using Unifrac, whereas community assembly processes were inferred using different community relatedness metrics. Similarities between globally distributed communities for both genes corresponded to similarities in habitat salinity. The majority of communities for both genes were phylogenetically clustered; however, nirK marine communities were more phylogenetically overdispersed than nirK soil communities or nirS communities. A more in-depth analysis was performed using three case studies in which a comparison of nirS and nirK community relatedness within the sites could be examined along environmental gradients. From these studies we observed that nirS communities respond differently to environmental gradients than nirK communities. Although it is difficult to attribute nonrandom patterns of phylogenetic diversity to specific niche-based or neutral assembly processes, our results indicate that coexisting nirS and nirK denitrifier communities are not under the same community assembly rules in different environments.
Bacterial community succession and chemical profiles of subtidal biofilms in relation to larval settlement of the polychaete Hydroides elegans
Authors: Chung Hong Chun , Lee On On , Huang Yi-Li , Mok Siu Yan , Kolter Roberto , Qian Pei-Yuan
Published: January 2010

Earlier studies have shown that biofilms can mediate the larval settlement of the polychaete Hydroides elegans and that changes in the bacterial community structure and density of biofilms often alter the larval settlement response. However, the chemical cues that mediate this response remain unknown. In this study, both successional changes in the bacterial community structure and the chemical profiles of subtidal biofilms are described and related to the larval settlement response. Multispecies biofilms were developed on polystyrene Petri dishes and granite rock in the subtidal zone over a period of 20 days. The effects of the substratum and age on the bacterial community structure and chemical profiles of the biofilms were evaluated with two molecular methods (microarray (PhyloChip) and denaturing gradient gel electrophoresis) and with gas chromatography–mass spectrometry, respectively. Both age and substratum altered the bacterial community structures and chemical profiles of the biofilms. Age had a greater effect in shaping the bacterial community structure than did the substratum. In contrast, the type of substratum more strongly affected the chemical profile. Extracts of biofilms of different ages, which developed on different substrata, were tested for the settlement of H. elegans larvae. The extracts induced larval settlement in a biofilm-age-dependent manner, and extracts originating from different substrata of the same age showed no differences in larval settlement. Our results suggest that the larval settlement response cannot be predicted by the overall chemical composition of the biofilm alone.
Changes in Circulating Satiety Hormones in Obese Children: A Randomized Controlled Physical Activity‐Based Intervention Study
Authors: Balagopal Prabhakaran (Babu) , Gidding Samuel S. , Buckloh Lisa M. , Yarandi Hossein N. , Sylvester James E. , George Donald E. , Funanage Vicky L.
Published: January 2010

The aims of this study are to examine in children: (i) obesity‐related alterations in satiety factors such as leptin, ghrelin, and obestatin; (ii) the link between satiety factors and cardiometabolic risk factors; and (iii) the impact of a physical activity‐based lifestyle intervention on the levels of these satiety factors in the obese. We studied a total of 21 adolescents (BMI percentile, 99.0 ± 0.6 for 15 obese and 56.2 ± 1.1 for 6 lean). The obese subjects underwent a 3‐month randomized controlled physical activity‐based lifestyle intervention. Leptin, soluble leptin receptor (sOB‐R), ghrelin, and obestatin levels were determined as the primary outcome measures. Other markers of cardiometabolic disease such as inflammation and insulin resistance were also determined. Body composition was measured by dual‐energy X‐ray absorptiometry. The concentrations of ghrelin, obestatin, and sOB‐R were significantly lower in the obese children compared to the lean controls, whereas that of leptin was higher (all P < 0.05). Although intervention led to a net increase in obestatin (P < 0.01) and no change in ghrelin levels, the balance between ghrelin and obestatin (ratio of ghrelin to obestatin, G/O) decreased (P < 0.02). Intervention reduced leptin and increased sOB‐R (P < 0.01 for both). Significant associations between satiety factors and other cardiometabolic risk factors were also observed. Taken together, alterations in the levels of satiety factors are evident early in the clinical course of obesity, but physical activity‐based lifestyle intervention either prevented their continued increase or normalized their levels. These beneficial effects appear to aid in the maintenance of body weight and reduction in cardiovascular risk.
Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes inMycobacterium tuberculosis
Authors: Gordon Blair R. G. , Li Yifei , Wang Linru , Sintsova Anna , van Bakel Harm , Tian Songhai , Navarre William Wiley , Xia Bin , Liu Jun
Published: January 2010

Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 ofMycobacterium tuberculosisis a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.
Molecular mimics can induce a nonautoaggressive repertoire that preempts induction of autoimmunity
Authors: Maverakis Emanual , Menezes Juscilene S. , Ametani Akio , Han Mei , Stevens David B. , He Yong , Wang Yan , Ono Yoko , Miyamura Yoshinori , Lam Kit S. , Ward E. Sally , Sercarz Eli E.
Published: January 2010

To determine the role that competition plays in a molecular mimic’s capacity to induce autoimmunity, we studied the ability of naïve encephalitogenic T cells to expand in response to agonist altered peptide ligands (APLs), some capable of stimulating both self-directed and exclusively APL-specific T cells. Our results show that although the APLs capable of stimulating exclusively APL-specific T cells are able to expand encephalitogenic T cells in vitro, the encephalitogenic repertoire is effectively outcompeted in vivo when the APL is used as the priming immunogen. Competition as a mechanism was supported by: (i) the demonstration of a population of exclusively APL-specific T cells, (ii) an experiment in which an encephalitogenic T cell population was successfully outcompeted by adoptively transferred naïve T cells, and (iii) demonstrating that the elimination of competing T cells bestowed an APL with the ability to expand naïve encephalitogenic T cells in vivo. In total, these experiments support the existence of a reasonably broad T cell repertoire responsive to a molecular mimic (e.g., a microbial agent), of which the exclusively mimic-specific component tends to focus the immune response on the invading pathogen, whereas the rare cross-reactive, potentially autoreactive T cells are often preempted from becoming involved.
Relational motivation for conformal operator ordering in quantum cosmology
Authors: Anderson Edward
Published: January 2010

Operator ordering in quantum cosmology is a major as-yet unsettled ambiguity with not only formal but also physical consequences. We determine the Lagrangian origin of the conformal invariance that underlies the conformal operator-ordering choice in quantum cosmology. This arises particularly naturally and simply from relationalist product-type actions (such as the Jacobi action for mechanics or Baierlein–Sharp–Wheeler-type actions for general relativity), for which all that is required is for the kinetic and potential factors to rescale in compensation to each other. These actions themselves mathematically sharply implement philosophical principles relevant to whole-universe modelling, so that the motivation for conformal operator ordering in quantum cosmology is thereby substantially strengthened. Relationalist product-type actions also give emergent times which amount to recovering Newtonian, proper and cosmic time in various contexts. The conformal scaling of these actions directly tells us how emergent time scales; if one follows suit with the Newtonian time or the lapse in the more commonly used difference-type Euler–Lagrange or Arnowitt–Deser–Misner-type actions, one sees how these too obey a more complicated conformal invariance. Moreover, our discovery of the conformal scaling of the emergent time permits relating how this simplifies equations of motion with how affine parametrization simplifies geodesics.
A Rap/Phosphatidylinositol 3-Kinase Pathway Controls Pseudopod Formation
Authors: Kortholt Arjan , Bolourani Parvin , Rehmann Holger , Keizer-Gunnink Ineke , Weeks Gerald , Wittinghofer Alfred , Van Haastert Peter J.M.
Published: January 2010

GbpD, a Dictyostelium discoideum guanine exchange factor specific for Rap1, has been implicated in adhesion, cell polarity, and chemotaxis. Cells overexpressing GbpD are flat, exhibit strongly increased cell-substrate attachment, and extend many bifurcated and lateral pseudopodia. Phg2, a serine/threonine-specific kinase, mediates Rap1-regulated cell-substrate adhesion, but not cell polarity or chemotaxis. In this study we demonstrate that overexpression of GbpD in pi3k1/2-null cells does not induce the adhesion and cell morphology phenotype. Furthermore we show that Rap1 directly binds to the Ras binding domain of PI3K, and overexpression of GbpD leads to strongly enhanced PIP3 levels. Consistently, upon overexpression of the PIP3-degradating enzyme PTEN in GbpD-overexpressing cells, the strong adhesion and cell morphology phenotype is largely lost. These results indicate that a GbpD/Rap/PI3K pathway helps control pseudopod formation and cell polarity. As in Rap-regulated pseudopod formation in Dictyostelium , mammalian Rap and PI3K are essential for determining neuronal polarity, suggesting that the Rap/PI3K pathway is a conserved module regulating the establishment of cell polarity.
Vav3-deficient Mice Exhibit a Transient Delay in Cerebellar Development
Authors: Quevedo Celia , Sauzeau Vincent , Menacho-Márquez Mauricio , Castro-Castro Antonio , Bustelo Xosé R.
Published: January 2010

Vav3 is a guanosine diphosphate/guanosine triphosphate exchange factor for Rho/Rac GTPases that has been involved in functions related to the hematopoietic system, bone formation, cardiovascular regulation, angiogenesis, and axon guidance. We report here that Vav3 is expressed at high levels in Purkinje and granule cells, suggesting additional roles for this protein in the cerebellum. Consistent with this hypothesis, we demonstrate using Vav3-deficient mice that this protein contributes to Purkinje cell dendritogenesis, the survival of granule cells of the internal granular layer, the timely migration of granule cells of the external granular layer, and to the formation of the cerebellar intercrural fissure. With the exception of the latter defect, the dysfunctions found in Vav3−/−mice only occur at well-defined postnatal developmental stages and disappear, or become ameliorated, in older animals. Vav2-deficient mice do not show any of those defects. Using primary neuronal cultures, we show that Vav3 is important for dendrite branching, but not for primary dendritogenesis, in Purkinje and granule cells. Vav3 function in the cerebellum is functionally relevant, because Vav3−/−mice show marked motor coordination and gaiting deficiencies in the postnatal period. These results indicate that Vav3 function contributes to the timely developmental progression of the cerebellum.
Regulators of Vps4 ATPase Activity at Endosomes Differentially Influence the Size and Rate of Formation of Intralumenal Vesicles
Authors: Nickerson Daniel P. , West Matthew , Henry Ryan , Odorizzi Greg
Published: January 2010

Recruitment of endosomal sorting complexes required for transport (ESCRTs) to the cytosolic face of endosomes regulates selective inclusion of transmembrane proteins into the lumenal vesicles of multivesicular bodies (MVBs). ESCRT-0, -I, and -II bind directly to ubiquitinated transmembrane cargoes of the MVB pathway, whereas polymerization of ESCRT-III at endosomes is thought to bend the membrane and/or provide the energetic force that drives membrane scission and detachment of vesicles into the endosome lumen. Disassembly of the ESCRT-III polymer and dissociation of its subunits from endosomes requires the Vps4 ATPase, the activity of which is controlled in vivo by regulatory proteins. We identify distinct spatiotemporal roles for Vps4-regulating proteins through examinations of subcellular localization and endosome morphology. Did2 plays a unique role in the regulation of MVB lumenal vesicle size, whereas Vtal and Vps60 promote efficient membrane scission and delivery of membrane to the endosome lumen. These morphological effects probably result from Vps4-mediated manipulations of ESCRT-III, because we show dissociation of ESCRT-0, -I, and -II from endosomes is not directly dependent on Vps4 activity.
Role of the Second Cysteine-rich Domain and Pro275 in Protein Kinase D2 Interaction with ADP-Ribosylation Factor 1,Trans-Golgi Network Recruitment, and Protein Transport
Authors: Pusapati Ganesh Varma , Krndija Denis , Armacki Milena , von Wichert Götz , von Blume Julia , Malhotra Vivek , Adler Guido , Seufferlein Thomas
Published: January 2010

Protein kinase D (PKD) isoenzymes regulate the formation of transport carriers from the trans-Golgi network (TGN) that are en route to the plasma membrane. The PKD C1a domain is required for the localization of PKDs at the TGN. However, the precise mechanism of how PKDs are recruited to the TGN is still elusive. Here, we report that ADP-ribosylation factor (ARF1), a small GTPase of the Ras superfamily and a key regulator of secretory traffic, specifically interacts with PKD isoenzymes. ARF1, but not ARF6, binds directly to the second cysteine-rich domain (C1b) of PKD2, and precisely to Pro275 within this domain. Pro275 in PKD2 is not only crucial for the PKD2-ARF1 interaction but also for PKD2 recruitment to and PKD2 function at the TGN, namely, protein transport to the plasma membrane. Our data suggest a novel model in which ARF1 recruits PKD2 to the TGN by binding to Pro275 in its C1b domain followed by anchoring of PKD2 in the TGN membranes via binding of its C1a domain to diacylglycerol. Both processes are critical for PKD2-mediated protein transport.
Vesicular Calcium Regulates Coat Retention, Fusogenicity, and Size of Pre-Golgi Intermediates
Authors: Bentley Marvin , Nycz Deborah C. , Joglekar Ashwini , Fertschai Ismene , Malli Roland , Graier Wolfgang F. , Hay Jesse C.
Published: January 2010

The significance and extent of Ca2+regulation of the biosynthetic secretory pathway have been difficult to establish, and our knowledge of regulatory relationships integrating Ca2+with vesicle coats and function is rudimentary. Here, we investigated potential roles and mechanisms of luminal Ca2+in the early secretory pathway. Specific depletion of luminal Ca2+in living normal rat kidney cells using cyclopiazonic acid (CPA) resulted in the extreme expansion of vesicular tubular cluster (VTC) elements. Consistent with this, a suppressive role for vesicle-associated Ca2+in COPII vesicle homotypic fusion was demonstrated in vitro using Ca2+chelators. The EF-hand–containing protein apoptosis-linked gene 2 (ALG-2), previously implicated in the stabilization of sec31 at endoplasmic reticulum exit sites, inhibited COPII vesicle fusion in a Ca2+-requiring manner, suggesting that ALG-2 may be a sensor for the effects of vesicular Ca2+on homotypic fusion. Immunoisolation established that Ca2+chelation inhibits and ALG-2 specifically favors residual retention of the COPII outer shell protein sec31 on pre-Golgi fusion intermediates. We conclude that vesicle-associated Ca2+, acting through ALG-2, favors the retention of residual coat molecules that seem to suppress membrane fusion. We propose that in cells, these Ca2+-dependent mechanisms temporally regulate COPII vesicle interactions, VTC biogenesis, cargo sorting, and VTC maturation.
The Effects of a Fat Tax on French Households' Purchases: A Nutritional Approach
Authors: Allais Olivier , Bertail Patrice , Nichèle Véronique
Published: January 2010

This article assesses the effects of a “fat tax” on the nutrients purchased by French households across different income groups. This is done by making a preliminary estimation of price elasticities using a complete demand system on household scanner data, and by calculating nutrient elasticities using estimated price elasticities. We find that a fat tax has small and ambiguous effects on nutrients purchased by French households, and a slight effect on body weight in the short run, with a greater effect in the long run. Such a tax generates substantial tax revenue, but is highly regressive.
On the (Mis)Use of Wealth as a Proxy for Risk Aversion
Authors: Bellemare Marc F. , Brown Zachary S.
Published: January 2010

Tests of risk sharing in the contracting literature often rely on wealth as a proxy for risk aversion. The intuition behind these tests is that since contract choice is monotonic in the coefficients of risk aversion, which are themselves assumed monotonic in wealth, the effect of a change in wealth on contract choice is clearly identified. We show that tests of risk sharing relying on wealth as a proxy for risk aversion are identified only insofar as the econometrician is willing to assume that (a) the principal is risk neutral or her preferences exhibit constant absolute risk aversion (CARA); and (b) the agent is risk neutral.
The Value of the Initial Payment of the Canadian Wheat Board as a Signaling Device
Authors: Tamini Lota D. , Gervais Jean‐Philippe , Larue Bruno
Published: January 2010

This paper analyzes the role of the initial payment used by the Canadian Wheat Board (CWB) in the determination of export prices and sales under the assumption that the CWB has better information about realized yields in Canada than its US competitor. In the separating equilibrium of the game, the initial payment of the CWB is larger than the initial payment under complete information. There exists an incentive under incomplete information to send a signal that realized yields are greater than expected to induce a reduction in the sales of foreign competitors. We illustrate the strategic value of the initial payment for Canadian wheat producers using a numerical simulation.
Optimal Control of Desensitizing Inputs: The Case of Paylean
Authors: Canchi Devendra , Li Ning , Foster Ken , Preckel Paul V. , Schinckel Allan , Richert Brian
Published: January 2010

We examine production economic implications of a specialized input to which a biological system (e.g., an animal) becomes desensitized over time, but its marginal productivity can be restored by increasing the dosage level. Optimal dosage levels and their timing become choice variables and may substitute or complement other inputs. This analysis is demonstrated for the case of Paylean in swine production. Use of a step‐up approach to optimal Paylean use is shown to return substantial value, especially in market structures that reward producers for lean carcass value, and in cases where the health status of the animals is compromised.
On the Measurement of Welfare for Market and Nonmarket Goods: A Numerical Approach
Authors: Ebert Udo
Published: January 2010

Extending Vartia's (1983) framework, the paper presents a simple numerical approach to the measurement of welfare for market and nonmarket goods on the basis of an incomplete (mixed) demand system. The method allows the determination of exact welfare measures. It provides a flexible and well‐founded alternative to ad hoc methods based on consumer surplus.
Successful Intracardiac Robotic Surgery Initial Results from Japan
Authors: Watanabe Go
Published: January 2010

Objective

The purpose of this study is to report our 2-year experience of performing endoscopic intracardiac procedures using the da Vinci Surgical System. Our teams at Kanazawa University and Tokyo Medical University groups began using the da Vinci Surgical System (Intuitive Surgical, Inc, Sunnyvale, CA) in 2005. This series represents the first Japanese application of robotic technology for totally endoscopic open-heart surgery.

Methods

From January 2008 to February 2009, 10 patients (mean age: 46.8 ± 16.3 years, 70% women) underwent endoscopic atrial septal defect closure and resection of the left atrial myxoma using the da Vinci Surgical System and peripheral cardiopulmonary bypass technique. Of the 10 patients, nine were classified as New York Heart Association class II and 1 patient exhibited atrial arrhythmias. In addition, two patients required mitral valve plasty (n = 2) and tricuspid annuloplasty (n = 1).

Results

Mean da Vinci Surgical System working time was 140.7 ± 57.4 minutes. Mean cardiopulmonary bypass and aortic cross clamp times were 103.1 ± 37.1 and 30.0 ± 16.9 minutes, respectively. There were no conversions to sternotomy or small thoracotomy. There were no hospital deaths. Mean intensive care unit and hospital stays were 1 day and 3.1 ± 0.3 days, respectively. All patients appreciated the cosmetic result and fast recovery.

Conclusions

Closed-chest atrial septal defect closure and myxoma resection performed using robotic techniques achieved excellent results and rapid postoperative recovery and provided an attractive cosmetic advantage over median sternotomy.
Percutaneous Aortic Valve Replacement
Authors: Bombien René , Lesche Claudia , Lozonschi Lucian , Feucker Max , Brinkmann Ralf , Dahmen Christian , Schünke Michael , Cremer Jochen , Lutter Georg
Published: January 2010

Objective

The feasibility of endovascular resection of highly calcified aortic valves has already been demonstrated by our group. Different endovascular and intracardiac tractability methods were applied. In this study, these technologies were analyzed comparing the tractability, the resection time, and the lesions in the surrounding tissue.

Methods

All aortic valve resections (seven human hearts and 21 porcine hearts) were performed using a Thulium:YAG laser (continuous wave, wavelength of 2.01 μm, 20 watts power rating). In the first resection system, the laser fiber was controlled by a free in-lying flexible endoscope (Ø 2.5 mm, length of 600 mm). The distal part of the endoscope (40 mm) was moved in one plane by proximal manual control (three degrees of freedom). The resection system was separated into defined rooms assigning one room for one tool. The fiber was controlled by the above-mentioned endoscope (*) (three degrees of freedom). The third resection system was a mechanical microactuator carrying the laser fiber (three degrees of freedom). The fourth resection system contains a rotatable inlay with defined rooms and a newly designed nitinol (NiTi) microactuator that controlled the laser fiber (four degrees of freedom). The resection time per leaflet was measured in minutes. Gross anatomy and histology in the surrounding tissue were evaluated.

Results

The resection time in approaches 1, 2, 3, and 4 was 5.5 ± 2.3 minutes, 7.4 ± 2.7 minutes, ± 6.6 minutes, and2.3 ± 1.2 minutes, respectively. The gross anatomy and histology of collateral damages revealed only superficial lesions of the surrounding tissue. The amount of lesions and the resection time were lower in the fourth approach with four degrees of freedom.

Conclusions

This analysis demonstrated that a precise tractability with four degrees of freedom is necessary for a faster and safer endovascular resection of the aortic valve. The analysis will help to optimize the ongoing development of the endovascular and intra-cardiac resection technology.
The Active Tube Clearance System a Novel Bedside Chest-Tube Clearance Device
Authors: Shalli Shanaz , Boyle Edward M. , Saeed Diyar , Fukamachi Kiyotaka , Cohn William E. , Gillinov A. Marc
Published: January 2010

Objective

Chest-tube clogging can lead to complications after heart and lung surgery. Surgeons often choose large-diameter chest tubes or place more than one chest tube when concerned about the potential for clogging. The purpose of this report is to describe the design and function of a proprietary active tube clearance system, a novel device that clears clots and debris from chest tubes.

Device Description

The active tube clearance system is a novel chest tube clearance apparatus developed to maintain chest tube patency. Chest tube clearance is achieved by advancing the specially designed clearance member back and forth within the chest tube under sterile conditions, breaking down and pulling clots back toward the drainage receptacle, thereby leaving the inner portion of the chest tube clear of any obstructing material.

Conclusions

By maintaining chest tube patency, chest tube drainage can be performed more safely, and this apparatus may possibly lead to the use of smaller chest tubes and less invasive insertion techniques.
Off-pump Coronary Bypass Surgery in Patients with Low Ejection Fraction
Authors: Gorki Hagen , Patel Nirav C. , Panagopoulos Georgia , Jennings Joan , Balacumaraswami Lognathen , Plestis Konstadinos , Subramanian Valavanur A.
Published: January 2010

Objective

Long-term survival after off-pump surgery in patients with low ejection fraction was investigated.

Methods

Three hundred forty-six patients with ejection fraction 30% or less with isolated off-pump coronary artery bypass surgery (OPCAB) were compared with a propensity matched historical group operated on-pump (ONCAB) and with data from literature after percutaneous coronary intervention and OPCAB surgery.

Results

The lower invasiveness of OPCAB contributed to a significantly better 30-day survival, shorter postoperative length of stay, and fewer in-hospital complications. Incomplete revascularization of the posterior and lateral territories of the heart correlated with higher 1-year mortality. The probability of survival for 8 years after OPCAB was 50.1% (n = 76) versus 49.7% (n = 82) for ONCAB without comparable data from literature for OPCAB or percutaneous coronary intervention in these high-risk patients.

Conclusions

OPCAB surgery in patients with low ejection fraction is a viable alternative but so far without demonstrable long-term survival advantage to ONCAB.
Resizable Ventricular Patch Plasty in the Porcine Left Ventricle a Pilot Study
Authors: Huijgen Willemijn H. F. , Gründeman Paul F. , van der Spoel Tycho , Cramer Maarten-Jan , Steendijk Paul , Klautz Robert J. M. , van Herwerden Lex A.
Published: January 2010

Objective

Endoventricular circular patch plasty is a method used to reconstruct the ventricular cavity in patients with (post) ischemic left ventricular aneurysm or global dilatation. However, late redilatation with mitral regurgitation has been reported, in which postoperative apex shape seems to play an important role. We studied the feasibility of ventricular volume downsizing with a variably shaped patch in porcine hearts.

Methods

In five in vitro and two acute animal experiments, a dyskinetic aneurysm was simulated with a pericardial insert. Reducing patch surface by changing patch shape diminished end-diastolic volume. In vitro, static end-diastolic volume was determined for each patch shape using volumetry and echocardiography. In the acute animal experiments, preliminary observations of patch behavior in live material were made, and pressure/time relationship, dPdTmax, was registered.

Results

In vitro, bringing the convex patch into a flat plane reduced LV volume from 66 ± 7 mL (aneurysm) to 49 ± 5 mL. Four of 5 patch shapes further reduced volume to a mean of 38 ± 7 mL (P = 0.03). The in vitro echocardiographic measurements correlated with volumetry findings (r = 0.81). In the acute animal experiments, dPdTmax varied with patch shape, independent of volume changes.

Conclusions

In this pilot study, in vitro shape configuration of the resizable ventricular patch resulted in a calibrated end-diastolic volume reduction. The data of the two in vivo pilot experiments clearly indicate that change in patch configuration in the situation of more or less unchanged end-diastolic volume had impact on cardiac performance. Future studies must substantiate the results of this observation.
Cheaters in mutualism networks
Authors: Genini Julieta , Morellato L. Patrícia C. , Guimarães Paulo R. , Olesen Jens M.
Published: January 2010

Mutualism-network studies assume that all interacting species are mutualistic partners and consider that all links are of one kind. However, the influence of different types of links, such as cheating links, on network organization remains unexplored. We studied two flower-visitation networks (Malpighiaceae and Bignoniaceae and their flower visitors), and divide the types of link into cheaters (i.e. robbers and thieves of flower rewards) and effective pollinators. We investigated if there were topological differences among networks with and without cheaters, especially with respect to nestedness and modularity. The Malpighiaceae network was nested, but not modular, and it was dominated by pollinators and had much fewer cheater species than Bignoniaceae network (28% versus 75%). The Bignoniaceae network was mainly a plant–cheater network, being modular because of the presence of pollen robbers and showing no nestedness. In the Malpighiaceae network, removal of cheaters had no major consequences for topology. In contrast, removal of cheaters broke down the modularity of the Bignoniaceae network. As cheaters are ubiquitous in all mutualisms, the results presented here show that they have a strong impact upon network topology.
Noise-induced suppression of periodic travelling waves in oscillatory reaction–diffusion systems
Authors: Sieber Michael , Malchow Horst , Petrovskii Sergei V.
Published: January 2010

Ecological field data suggest that some species show periodic changes in abundance over time and in a specific spatial direction. Periodic travelling waves as solutions to reaction–diffusion equations have helped to identify possible scenarios, by which such spatio-temporal patterns may arise. In this paper, such solutions are tested for their robustness against an irregular temporal forcing, since most natural populations can be expected to be subject to erratic fluctuations imposed by the environment. It is found that small environmental noise is able to suppress periodic travelling waves in stochastic variants of oscillatory reaction–diffusion systems. Irregular spatio-temporal oscillations, however, appear to be more robust and persist under the same stochastic forcing.
Down-Regulation of the CSLF6 Gene Results in Decreased (1,3;1,4)-β-d-Glucan in Endosperm of Wheat
Authors: Nemeth Csilla , Freeman Jackie , Jones Huw D. , Sparks Caroline , Pellny Till K. , Wilkinson Mark D. , Dunwell Jim , Andersson Annica A.M. , Åman Per , Guillon Fabienne , Saulnier Luc , Mitchell Rowan A.C. , Shewry Peter R.
Published: January 2010

(1,3;1,4)-β-d-Glucan (β-glucan) accounts for 20% of the total cell walls in the starchy endosperm of wheat (Triticum aestivum) and is an important source of dietary fiber for human nutrition with potential health benefits. Bioinformatic and array analyses of gene expression profiles in developing caryopses identified the CELLULOSE SYNTHASE-LIKE F6 (CSLF6) gene as encoding a putative β-glucan synthase. RNA interference constructs were therefore designed to down-regulate CSLF6 gene expression and expressed in transgenic wheat under the control of a starchy endosperm-specific HMW subunit gene promoter. Analysis of wholemeal flours using an enzyme-based kit and by high-performance anion-exchange chromatography after digestion with lichenase showed decreases in total β-glucan of between 30% and 52% and between 36% and 53%, respectively, in five transgenic lines compared to three control lines. The content of water-extractable β-glucan was also reduced by about 50% in the transgenic lines, and the Mr distribution of the fraction was decreased from an average of 79 to 85 × 104 g/mol in the controls and 36 to 57 × 104 g/mol in the transgenics. Immunolocalization of β-glucan in semithin sections of mature and developing grains confirmed that the impact of the transgene was confined to the starchy endosperm with little or no effect on the aleurone or outer layers of the grain. The results confirm that the CSLF6 gene of wheat encodes a β-glucan synthase and indicate that transgenic manipulation can be used to enhance the health benefits of wheat products.
R2R3-NaMYB8 Regulates the Accumulation of Phenylpropanoid-Polyamine Conjugates, Which Are Essential for Local and Systemic Defense against Insect Herbivores inNicotiana attenuata
Authors: Kaur Harleen , Heinzel Nicolas , Schöttner Mathias , Baldwin Ian T. , GÁlis Ivan
Published: January 2010

Although phenylpropanoid-polyamine conjugates (PPCs) occur ubiquitously in plants, their biological roles remain largely unexplored. The two major PPCs of Nicotiana attenuata plants, caffeoylputrescine (CP) and dicaffeoylspermidine, increase dramatically in local and systemic tissues after herbivore attack and simulations thereof. We identified NaMYB8, a homolog of NtMYBJS1, which in BY-2 cells regulates PPC biosynthesis, and silenced its expression by RNA interference in N. attenuata (ir-MYB8), to understand the ecological role(s) of PPCs. The regulatory role of NaMYB8 in PPC biosynthesis was validated by a microarray analysis, which revealed that transcripts of several key biosynthetic genes in shikimate and polyamine metabolism accumulated in a NaMYB8-dependent manner. Wild-type N. attenuata plants typically contain high levels of PPCs in their reproductive tissues; however, NaMYB8-silenced plants that completely lacked CP and dicaffeoylspermidine showed no changes in reproductive parameters of the plants. In contrast, a defensive role for PPCs was clear; both specialist (Manduca sexta) and generalist (Spodoptera littoralis) caterpillars feeding on systemically preinduced young stem leaves performed significantly better on ir-MYB8 plants lacking PPCs compared with wild-type plants expressing high levels of PPCs. Moreover, the growth of M. sexta caterpillars was significantly reduced when neonates were fed ir-MYB8 leaves sprayed with synthetic CP, corroborating the role of PPCs as direct plant defense. The spatiotemporal accumulation and function of PPCs in N. attenuata are consistent with the predictions of the optimal defense theory: plants preferentially protect their most fitness-enhancing and vulnerable parts, young tissues and reproductive organs, to maximize their fitness.
Regulation of Plant Glycine Decarboxylase byS-Nitrosylation and Glutathionylation
Authors: Palmieri M. Cristina , Lindermayr Christian , Bauwe Hermann , Steinhauser Clara , Durner Joerg
Published: January 2010

Mitochondria play an essential role in nitric oxide (NO) signal transduction in plants. Using the biotin-switch method in conjunction with nano-liquid chromatography and mass spectrometry, we identified 11 candidate proteins that were S-nitrosylated and/or glutathionylated in mitochondria of Arabidopsis (Arabidopsis thaliana) leaves. These included glycine decarboxylase complex (GDC), a key enzyme of the photorespiratory C2 cycle in C3 plants. GDC activity was inhibited by S-nitrosoglutathione due to S-nitrosylation/S-glutathionylation of several cysteine residues. Gas-exchange measurements demonstrated that the bacterial elicitor harpin, a strong inducer of reactive oxygen species and NO, inhibits GDC activity. Furthermore, an inhibitor of GDC, aminoacetonitrile, was able to mimic mitochondrial depolarization, hydrogen peroxide production, and cell death in response to stress or harpin treatment of cultured Arabidopsis cells. These findings indicate that the mitochondrial photorespiratory system is involved in the regulation of NO signal transduction in Arabidopsis.
Free and ATP-bound structures of Ap4A hydrolase fromAquifex aeolicusV5
Authors: Jeyakanthan Jeyaraman , Kanaujia Shankar Prasad , Nishida Yuya , Nakagawa Noriko , Praveen Surendran , Shinkai Akeo , Kuramitsu Seiki , Yokoyama Shigeyuki , Sekar Kanagaraj
Published: January 2010

Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16 kDa) fromAquifex aeolicushas been determined in free and ATP-bound forms at 1.8 and 1.95 Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an αβα-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase fromCaenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.
Expansion of the aspartate β-semialdehyde dehydrogenase family: the first structure of a fungal ortholog
Authors: Arachea Buenafe T. , Liu Xuying , Pavlovsky Alexander G. , Viola Ronald E.
Published: January 2010

The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a critical transformation that produces the first branch-point intermediate in an essential microbial amino-acid biosynthetic pathway. The first structure of an ASADH isolated from a fungal species (Candida albicans) has been determined as a complex with its pyridine nucleotide cofactor. This enzyme is a functional dimer, with a similar overall fold and domain organization to the structurally characterized bacterial ASADHs. However, there are differences in the secondary-structural elements and in cofactor binding that are likely to cause the lower catalytic efficiency of this fungal enzyme. Alterations in the dimer interface, through deletion of a helical subdomain and replacement of amino acids that participate in a hydrogen-bonding network, interrupt the intersubunit-communication channels required to support an alternating-site catalytic mechanism. The detailed functional information derived from this new structure will allow an assessment of ASADH as a possible target for antifungal drug development.
Retraction of articles by H. M. Krishna Murthyet al.
Authors:   International Union of Crystallography
Published: January 2010

Two papers by H. M. Krishna Murthyet al.are retracted.
QTL for resistance to summer mortality and OsHV‐1 load in the Pacific oyster (Crassostrea gigas)
Authors: Sauvage C. , Boudry P. , De Koning D.‐J. , Haley C. S. , Heurtebise S. , Lapègue S.
Published: January 2010

Summer mortality is a phenomenon severely affecting the aquaculture production of the Pacific oyster (Crassostrea gigas). Although its causal factors are complex, resistance to mortality has been described as a highly heritable trait, and several pathogens including the virus Ostreid Herpes virus type 1 (OsHV‐1) have been associated with this phenomenon. A QTL analysis for survival of summer mortality and OsHV‐1 load, estimated using real‐time PCR, was performed using five F2 full‐sib families resulting from a divergent selection experiment for resistance to summer mortality. A consensus linkage map was built using 29 SNPs and 51 microsatellite markers. Five significant QTL were identified and assigned to linkage groups V, VI, VII and IX. Analysis of single full‐sib families revealed differential QTL segregation between families. QTL for the two‐recorded traits presented very similar locations, highlighting the interest of further study of their respective genetic controls. These QTL show substantial genetic variation in resistance to summer mortality, and present new opportunities for selection for resistance to OsHV‐1.