bluuebunny/crossref_metadata_2025 huggingface dataset:
Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer
Authors: Casey Lachlan W. , Mark Alan E. , Kobe Bostjan
Published: September 2014

The role of small-angle X-ray scattering (SAXS) in structural biology is now well established, and its usefulness in combination with macromolecular crystallography is clear. However, the highly averaged SAXS data present a significant risk of over-interpretation to the unwary practitioner, and it can be challenging to frame SAXS results in a manner that maximises the reliability of the conclusions drawn. In this review, a series of recent examples are used to illustrate both the challenges for interpretation and approaches through which these can be overcome.
Evolution of
Drosophila
sex comb length illustrates the inextricable interplay between selection and variation
Authors: Malagón Juan N. , Ahuja Abha , Sivapatham Gabilan , Hung Julian , Lee Jiwon , Muñoz-Gómez Sergio A. , Atallah Joel , Singh Rama S. , Larsen Ellen
Published: September 2014

Significance

Not all possible biological shapes are actually seen in nature. Despite much experimental work, the developmental basis explaining the presence or absence of certain biological shapes remains poorly understood. We studied
Drosophila melanogaster
development using the sex comb, a group of modified bristles exhibiting spectacular morphological diversity among
Drosophila
species. We provide several lines of evidence suggesting that increasing
D. melanogaster
sex comb length produces a mechanical blockage, affecting comb shape and position. We infer that simple physical principles acting on tissues can influence the direction of evolution, and comparative studies of other fly species are consistent with this hypothesis. This work highlights the fundamental role of development for understanding biodiversity and evolution.
Connexin hemichannels contribute to spontaneous electrical activity in the human fetal cortex
Authors: Moore Anna R. , Zhou Wen-Liang , Sirois Carissa L. , Belinsky Glenn S. , Zecevic Nada , Antic Srdjan D.
Published: September 2014

Significance

Young neurons require occasional bursts of action-potential firing to maintain intracellular processes, to drive gene expression, to indicate their presence in a new location, and to attract and keep synaptic contacts. While in the adult cortex electrical activity is driven by synaptic inputs, during early cortical development these synaptic inputs are largely absent. In the absence of synaptic connections and sensory experience, human neurons use an energetically favorable membrane mechanism for generating and maintaining electrical activity: connexin hemichannels. The spontaneous flickering of connexin hemichannels produces depolarizing events (often crowned with bursts of action potentials) to help establish early electrical communication in young subplate neurons. This type of activity dominates the human cortical wall 5 months before birth.
Phospholipase D2 specifically regulates TREK potassium channels via direct interaction and local production of phosphatidic acid
Authors: Comoglio Yannick , Levitz Joshua , Kienzler Michael A. , Lesage Florian , Isacoff Ehud Y. , Sandoz Guillaume
Published: September 2014

Significance

Our work provides evidence for a mechanism for the formation of membrane microdomains in which the local concentration of a phospholipid can change independently of the bulk membrane to confer selectivity on membrane protein regulation. We found that, despite the fact that all TWIK-related K channel (TREK) family members are sensitive to phosphatidic acid (PA), only TREK1 and TREK2 are potentiated by phospholipase D2 (PLD2) (which produces PA), but not by PLD1. This surprising specificity is due to the direct binding of PLD2 to TREK. This binding allows a local PA production that tonically activates the channel. Furthermore, we found the local signaling via PA to have a secondary focusing effect for primary alcohols, which inhibit the channel by altering the PA microdomain.
Kinesin processivity is gated by phosphate release
Authors: Milic Bojan , Andreasson Johan O. L. , Hancock William O. , Block Steven M.
Published: September 2014

Significance

Kinesin-1 is a motor protein central to intracellular transport. Prevailing models of the kinesin mechanochemical cycle—which invoke docking of the neck linker domain upon ATP binding—fail to explain the remarkable processivity of kinesin, which represents a competition between dissociation from the microtubule and continuation of the stepping cycle. We show that kinesin dissociation, which characterizes the end of a processive run, is gated by phosphate release following ATP hydrolysis. The structural change driving kinesin motility, likely neck linker docking, is therefore completed only upon hydrolysis. Our results offer insights into gating mechanisms and necessitate revisions to existing models of the kinesin cycle.
Noncanonical SMC protein in
Mycobacterium smegmatis
restricts maintenance of
Mycobacterium fortuitum
plasmids
Authors: Panas Michael W. , Jain Paras , Yang Hui , Mitra Shimontini , Biswas Debasis , Wattam Alice Rebecca , Letvin Norman L. , Jacobs William R.
Published: September 2014

Significance

A mutant strain of
Mycobacterium smegmatis
mc
2
155 provided the first plasmid transformation platform for any mycobacteria. It has since been used extensively as a surrogate host to study mycobacterial gene functions in
Mycobacterium tuberculosis
and
Mycobacterium leprae
. In this report, we discovered that the efficient plasmid transformation (ept) phenotype of mc
2
155 is caused by a loss-of-function mutation in a gene, namely
eptC
, which encodes a protein that shares homology with the structural maintenance of chromosomes (SMC) family. While SMCs generally promote DNA segregation to daughter cells, we show that EptC selectively inhibits plasmid segregation and thereby establish a new plasmid restrictive role of this mycobacterial SMC homolog.
Activation of iNKT cells by a distinct constituent of the endogenous glucosylceramide fraction
Authors: Brennan Patrick J. , Tatituri Raju V. V. , Heiss Christian , Watts Gerald F. M. , Hsu Fong-Fu , Veerapen Natacha , Cox Liam R. , Azadi Parastoo , Besra Gurdyal S. , Brenner Michael B.
Published: September 2014

Significance

Invariant natural killer T (iNKT) cells are a specialized subset of T cells that recognizes lipids, rather than peptides, as antigens. Recognition of both endogenous and exogenous lipids by iNKT cells contributes to immune responses during infection, cancer, autoimmune disease, and allergic disease. The endogenous lipids recognized by iNKT cells in most contexts, however, remain unclear. In this report, we characterize the lipid antigen activity found in mammalian milk and tissues. Our data suggest that activity is related to a minor component of the glucosylceramide fraction. Whether contributed from endogenous sources or from the diet, this rare, yet potent lipid activity may play an important role in driving immune responses.
Marijuana and Alcohol Use and Attempted Smoking Cessation in Adolescent Boys and Girls
Authors: Camenga Deepa R. , Kong Grace , Bagot Kara , Hoff Rani A. , Potenza Marc N. , Krishnan-Sarin Suchitra
Published: August 2014

Background

This study sought to determine the relationship between the frequency of current marijuana and alcohol use and cigarette quit attempts in male and female adolescent smokers.

Methods

Data from a cross-sectional survey of health behaviors in high-school-aged adolescents were analyzed. Current cigarette smokers ( n = 804) who reported use of at least 1 cigarette in the past month were divided into those with and without a history of at least 1 quit attempt (a self-reported episode of trying to “stop smoking”). Logistic regression models were fit to describe the association between the frequency of marijuana/alcohol use and a history of cigarette quit attempts.

Results

Among the total sample, higher-frequency marijuana use (more than 6 times in the past 30 days) and frequent binge drinking (more than 5 days of binge drinking in the past 30 days) decreased the odds of having a past cigarette quit attempt (higher-frequency marijuana: adjusted odds ratio [AOR] = 0.56, 95% confidence interval [CI] = 0.36–0.86; frequent binge drinking: AOR = 0.49, 95% CI = 0.29–0.83). A significant gender interaction was observed for the relationship between higher-frequency marijuana use and a history of cigarette quit attempts ( P = .03), with decreased odds in boys (AOR = 0.41, 95% CI = 0.22–0.77) but not in girls (AOR = 0.71, 95% CI = 0.37–1.33).

Conclusions

Adolescent smokers who report higher-frequency marijuana use or frequent binge drinking have a decreased likelihood of a history of a cigarette quit attempt. The gender-related association between higher-frequency marijuana use and a history of quit attempts suggests that boys with greater substance use may need particularly intensive support to initiate quit attempts.
Patient Focus Group Responses to Peer Mentoring in a High-Security Hospital
Authors: Böhm Bettina , Glorney Emily , Tapp James , Carthy John , Noak Jimmy , Moore Estelle
Published: August 2014

Peer mentoring programs in secure hospitals have attracted limited attention despite reported benefits of similar schemes within other mental health and prison services. High-secure hospital patient perspectives ( N = 17) on the concept of peer mentoring and the implications for establishing a peer support scheme were investigated via focus groups. Thematic analysis of discussions generated five themes: how to meet the adjustment and support needs of a peer; differences between mentoring and other relationships; mentoring by peers within a secure setting; expectations of a mentor's skills to meet the challenges of mentoring; and ownership of a mentoring scheme. The need to offset risk management against the potential benefits of peer support for a population excluded on the basis of risk is reviewed throughout.
A Therapeutic Approach to Jurisprudence: A Differential Thinking Model of Sanctions and Rewards
Authors: Barber-Rioja Virginia , Rotter Merrill
Published: August 2014

With the goal of decreasing violations and promoting compliance, Mental Health Courts (MHCs) apply behavior modification principles through the use of sanctions and rewards, including jail as punishment. However, unlike Drug Treatment Courts where this model originated, the use of sanctions for violations in MHCs is more complex as identifying, understanding and addressing compliance are more difficult in mental health treatment. Jail as a sanction may not have any clinical utility, but can have detrimental effects for offenders in general and for those with mental illness in particular. This paper proposes that a pure sanction-and-reward model is undesirable for individuals in the legal context, and proposes an alternative approach to court violations that is consistent with the biopsychosocial, problem-solving and recovery models. This proposed approach includes “thinking differentially” about defendants’ violations, identifying possible explanations for what underlies the problematic behavior and administering more situation-specific clinical and judicial interventions.
A Review and Analysis of Routine Outcome Measures for Forensic Mental Health Services
Authors: Shinkfield Gregg , Ogloff James
Published: August 2014

Considerable progress has been made in recent years towards implementing routine outcome measures within mental health services. However, the applicability of these tools for forensic-mental health populations has been questioned. A review and analysis was conducted to identify tools that could validly be applied in a forensic context, to provide a measure of functioning, recovery, risk, and placement pathways. Nineteen instruments were initially identified and evaluated against a hierarchy of criteria. While no tool assessed all domains of interest, six tools were ultimately considered to have potential utility as outcome measures for users of forensic mental health services.
Improving Compliance with Timely Intraoperative Redosing of Antimicrobials in Surgical Prophylaxis
Authors: Riggi Gina , Castillo Mayela , Fernandez Margaret , Wawrzyniak Andrew , Vigoda Michael , Eber Scott , Lubarsky David , Abbo Lilian M.
Published: September 2014

Background.

Appropriate use of antimicrobials for surgical prophylaxis is an important patient safety issue. Antimicrobial levels should be present during the duration of the surgical procedure until incision site closure. For prolonged surgical procedures in which the tissue concentration of the prophylactic antimicrobial may decrease to below the necessary minimum inhibitory concentration, intraoperative redosing of antimicrobials may be crucial

Objective.

To evaluate compliance of appropriate intraoperative antimicrobial surgical prophylaxis using real-time intraoperative antimicrobial dosing reminders at a large teaching hospital.

Methods.

A retrospective review of electronic records (March 2009–October 2012) was performed. Patients were included if they were at least 18 years of age and underwent a procedure requiring antimicrobial surgical prophylaxis. Compliance was determined by comparing 3 time intervals: baseline (March 2009–March 2010); intervention period 1 (IP-1; April 1, 2010–April 30, 2012), and intervention period 2 (IP-2; May 1, 2012–October 31, 2012). Interventions included a hospital-wide standardized protocol comprising an automated intraoperative paging system to notify when antimicrobials should be redosed.

Results.

A total of 7,461 of 75,230 surgical procedures required intraoperative redosing of antimicrobials and were analyzed. Patient mean age (± standard deviation) was 45 ± 19 years, and 62.6% were female. The most common procedures that required prophylaxis were solid organ transplantation, neurosurgical procedures, and orthopedic procedures. Baseline compliance (n = 2,183) was 15.8%; compliance significantly improved to 65.3% during IP-1 (n = 4,486; P < .001). The compliance rate improved to 76.7% during IP-2 (P > .001 compared with no reminder).

Conclusions.

Compliance with redosing of intraoperative antimicrobials was improved with the combined approach of guidelines, education to healthcare providers, and real-time automated paging system.
poRe: an R package for the visualization and analysis of nanopore sequencing data
Authors: Watson Mick , Thomson Marian , Risse Judith , Talbot Richard , Santoyo-Lopez Javier , Gharbi Karim , Blaxter Mark
Published: August 2014

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:  mick.watson@roslin.ed.ac.uk

Supplementary information : Supplementary data are available at Bioinformatics online.
Review and refinement of an existing qualitative risk assessment method for application within an ecosystem-based management framework
Authors: Fletcher Warrick (Rick) J.
Published: August 2014

The adoption of risk-based methodologies is considered essential for the successful implementation of an ecosystem approach to fisheries and broader aquatic management. To assist with these initiatives, one of the qualitative risk assessment methods adapted for fisheries management over a decade ago has been reviewed. This method was updated to ensure compliance with the revised international standards for risk management (ISO 31000) and to enable consideration of ecological, economic, social, and governance risks. The review also addressed the difficulties that have been encountered in stakeholder understanding of the underlying concepts and to increase the discipline in its application. The updates include simplifying the number of consequence and likelihood levels, adopting graphical techniques to represent different consequence levels, and discussing how changes in uncertainty can affect risk scores. Adopting an explicit “weight of evidence” approach has also assisted with determining which consequence scenarios are considered plausible and, where relevant, their specific likelihoods. The revised methods therefore incorporate the conceptual elements from a number of qualitative and quantitative approaches increasing their reliability and enabling a more seamless transition along this spectrum as more lines of evidence are collected. It is expected that with continued application of these methods, further refinements will be identified.
Total Serum Bilirubin Predicts Fat‐Soluble Vitamin Deficiency Better Than Serum Bile Acids in Infants With Biliary Atresia
Authors: Venkat Veena L. , Shneider Benjamin L. , Magee John C. , Turmelle Yumirle , Arnon Ronen , Bezerra Jorge A. , Hertel Paula M. , Karpen Saul J. , Kerkar Nanda , Loomes Kathleen M. , Molleston Jean , Murray Karen F. , Ng Vicky L. , Raghunathan Trivellore , Rosenthal Philip , Schwartz Kathleen , Sherker Averell H. , Sokol Ronald J. , Teckman Jeffrey , Wang Kasper , Whitington Peter F. , Heubi James E. ,   Childhood Liver Disease Research and Education Network (ChiLDReN)
Published: September 2014

Objective:

Fat‐soluble vitamin (FSV) deficiency is a well‐recognized consequence of cholestatic liver disease and reduced intestinal intraluminal bile acid. We hypothesized that serum bile acid (SBA) would predict biochemical FSV deficiency better than serum total bilirubin (TB) level in infants with biliary atresia.

Methods:

Infants enrolled in the Trial of Corticosteroid Therapy in Infants with Biliary Atresia after hepatoportoenterostomy were the subjects of this investigation. Infants received standardized FSV supplementation and monitoring of TB, SBA, and vitamin levels at 1, 3, and 6 months. A logistic regression model was used with the binary indicator variable insufficient/sufficient as the outcome variable. Linear and nonparametric correlations were made between specific vitamin measurement levels and either TB or SBA.

Results:

The degree of correlation for any particular vitamin at a specific time point was higher with TB than with SBA (higher for TB in 31 circumstances vs 3 circumstances for SBA). Receiver operating characteristic curve shows that TB performed better than SBA (area under the curve 0.998 vs 0.821). Including both TB and SBA did not perform better than TB alone (area under the curve 0.998).

Conclusions:

We found that TB was a better predictor of FSV deficiency than SBA in infants with biliary atresia. The role of SBA as a surrogate marker of FSV deficiency in other cholestatic liver diseases, such as progressive familial intrahepatic cholestasis, α‐1‐antitrypsin deficiency, and Alagille syndrome in which the pathophysiology is dominated by intrahepatic cholestasis, warrants further study.
Extrahepatic Portal Vein Obstruction in Egyptian Children
Authors: El‐Karaksy Hanaa M. , El‐Koofy Nehal , Mohsen Nabil , Helmy Heba , Nabil Nevian , El‐Shabrawi Mortada
Published: September 2014

Background and Aim:

Extrahepatic portal vein obstruction (EHPVO) is an important cause of portal hypertension in children. The aim of this study was to describe the clinical presentation, possible risk factors, upper gastrointestinal endoscopic findings, and treatment modalities of children with EHPVO.

Methods:

After ethical approval of our study protocol by our institution review board, we analyzed available data from medical records of patients with EHPVO presenting to the Pediatric Hepatology Unit, Cairo University Pediatric Hospital, Egypt, for a period of 15 years from January 1996 to December 2010.

Results:

The study included 169 patients. Their ages at presentation ranged from 1 month to 12 years (median 2.5 years, interquartile range 5); 101 were boys. Hematemesis was a presenting symptom in 58%, splenomegaly was present in 87%, esophageal varices were present in 94%, and fundal varices were present in 23%. Possible risk factors, in the form of umbilical catheterization, umbilical sepsis, and exchange transfusion, were elicited in 18%. Propranolol was associated with reduction in bleeding episodes (P < 0.001), but was associated with increased chest symptoms (P < 0.01). Both injection sclerotherapy and band ligation were effective in the management of bleeding varices and for primary and secondary prophylaxis; however, injection sclerotherapy was associated with the development of secondary gastric varices (P = 0.03).

Conclusions:

This large study of children with EHPVO demonstrates the efficacy of propranolol in the reduction of gastrointestinal bleeding in children with EHPVO. Both injection sclerotherapy and band ligation were effective in the management of esophageal varices, although the former was associated with the development of secondary gastric varices. Randomized clinical trials to choose the best modalities for the management of portal hypertension in children are still lacking.
Instability of quantum equilibrium in Bohm's dynamics
Authors: Colin Samuel , Valentini Antony
Published: September 2014

We consider Bohm's second-order dynamics for arbitrary initial conditions in phase space. In principle, Bohm's dynamics allows for ‘extended’ non-equilibrium, with initial momenta not equal to the gradient of phase of the wave function (as well as initial positions whose distribution departs from the Born rule). We show that extended non-equilibrium does not relax in general and is in fact unstable. This is in sharp contrast with de Broglie's first-order dynamics, for which non-standard momenta are not allowed and which shows an efficient relaxation to the Born rule for positions. On this basis, we argue that, while de Broglie's dynamics is a tenable physical theory, Bohm's dynamics is not. In a world governed by Bohm's dynamics, there would be no reason to expect to see an effective quantum theory today (even approximately), in contradiction with observation.
Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genusSceloporus) in the southern Mexican highlands
Authors: Grummer Jared A. , Calderón-Espinosa Martha L. , Oca Adrián Nieto-Montes de , Smith Eric N. , Méndez-de la Cruz Fausto R. , Leaché Adam D.
Published: September 2014

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of theSceloporus spinosusgroup. The two species in this group,S. spinosusandS. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations ofS. spinosusandS. horridusowing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestralS. spinosusandS. horriduspopulations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.
Genetic Analysis ofDEFECTIVE KERNEL1Loop Function in Three-Dimensional Body Patterning inPhyscomitrella patens
Authors: Demko Viktor , Perroud Pierre-François , Johansen Wenche , Delwiche Charles F. , Cooper Endymion D. , Remme Pål , Ako Ako Eugene , Kugler Karl G. , Mayer Klaus F.X. , Quatrano Ralph , Olsen Odd-Arne
Published: September 2014

DEFECTIVE KERNEL1 (DEK1) of higher plants plays an essential role in position-dependent signaling and consists of a large transmembrane domain (MEM) linked to a protease catalytic domain and a regulatory domain. Here, we show that the postulated sensory Loop of the MEM domain plays an important role in the developmental regulation of DEK1 activity in the moss Physcomitrella patens. Compared with P. patens lacking DEK1 (∆dek1), the dek1∆loop mutant correctly positions the division plane in the bud apical cell. In contrast with an early developmental arrest of ∆dek1 buds, dek1∆loop develops aberrant gametophores lacking expanded phyllids resulting from misregulation of mitotic activity. In contrast with the highly conserved sequence of the protease catalytic domain, the Loop is highly variable in land plants. Functionally, the sequence from Marchantia polymorpha fully complements the dek1∆loop phenotype, whereas sequences from maize (Zea mays) and Arabidopsis (Arabidopsis thaliana) give phenotypes with retarded growth and affected phyllid development. Bioinformatic analysis identifies MEM as a member of the Major Facilitator Superfamily, membrane transporters reacting to stimuli from the external environment. Transcriptome analysis comparing wild-type and ∆dek1 tissues identifies an effect on two groups of transcripts connected to dek1 mutant phenotypes: transcripts related to cell wall remodeling and regulation of the AINTEGUMENTA, PLETHORA, and BABY BOOM2 (APB2) and APB3 transcription factors known to regulate bud initiation. Finally, sequence data support the hypothesis that the advanced charophyte algae that evolved into ancestral land plants lost cytosolic calpains, retaining DEK1 as the sole calpain in the evolving land plant lineage.
Voltage-Sensor Transitions of the Inward-Rectifying K+ Channel KAT1 Indicate a Latching Mechanism Biased by Hydration within the Voltage Sensor
Authors: Lefoulon Cécile , Karnik Rucha , Honsbein Annegret , Gutla Paul Vijay , Grefen Christopher , Riedelsberger Janin , Poblete Tomás , Dreyer Ingo , Gonzalez Wendy , Blatt Michael R.
Published: September 2014

The Kv-like (potassium voltage-dependent) K+ channels at the plasma membrane, including the inward-rectifying KAT1 K+ channel of Arabidopsis (Arabidopsis thaliana), are important targets for manipulating K+ homeostasis in plants. Gating modification, especially, has been identified as a promising means by which to engineer plants with improved characteristics in mineral and water use. Understanding plant K+ channel gating poses several challenges, despite many similarities to that of mammalian Kv and Shaker channel models. We have used site-directed mutagenesis to explore residues that are thought to form two electrostatic countercharge centers on either side of a conserved phenylalanine (Phe) residue within the S2 and S3 α-helices of the voltage sensor domain (VSD) of Kv channels. Consistent with molecular dynamic simulations of KAT1, we show that the voltage dependence of the channel gate is highly sensitive to manipulations affecting these residues. Mutations of the central Phe residue favored the closed KAT1 channel, whereas mutations affecting the countercharge centers favored the open channel. Modeling of the macroscopic current kinetics also highlighted a substantial difference between the two sets of mutations. We interpret these findings in the context of the effects on hydration of amino acid residues within the VSD and with an inherent bias of the VSD, when hydrated around a central Phe residue, to the closed state of the channel.
In Vivo 31P-Nuclear Magnetic Resonance Studies of Glyphosate Uptake, Vacuolar Sequestration, and Tonoplast Pump Activity in Glyphosate-Resistant Horseweed
Authors: Ge Xia , d’Avignon D. André , Ackerman Joseph J.H. , Sammons R. Douglas
Published: September 2014

Horseweed (Conyza canadensis) is considered a significant glyphosate-resistant (GR) weed in agriculture, spreading to 21 states in the United States and now found globally on five continents. This laboratory previously reported rapid vacuolar sequestration of glyphosate as the mechanism of resistance in GR horseweed. The observation of vacuole sequestration is consistent with the existence of a tonoplast-bound transporter. 31P-Nuclear magnetic resonance experiments performed in vivo with GR horseweed leaf tissue show that glyphosate entry into the plant cell (cytosolic compartment) is (1) first order in extracellular glyphosate concentration, independent of pH and dependent upon ATP; (2) competitively inhibited by alternative substrates (aminomethyl phosphonate [AMPA] and N-methyl glyphosate [NMG]), which themselves enter the plant cell; and (3) blocked by vanadate, a known inhibitor/blocker of ATP-dependent transporters. Vacuole sequestration of glyphosate is (1) first order in cytosolic glyphosate concentration and dependent upon ATP; (2) competitively inhibited by alternative substrates (AMPA and NMG), which themselves enter the plant vacuole; and (3) saturable. 31P-Nuclear magnetic resonance findings with GR horseweed are consistent with the active transport of glyphosate and alternative substrates (AMPA and NMG) across the plasma membrane and tonoplast in a manner characteristic of ATP-binding cassette transporters, similar to those that have been identified in mammalian cells.
On the calibration of high-energy X-ray diffraction setups. II. Assessing the rotation axis and residual strains
Authors: Borbély Andras , Renversade Loïc , Kenesei Peter
Published: September 2014

The calibration of high-energy X-ray diffraction setups using an area detector and a rotation axis is discussed. The characterization of the tilt and spatial distortions of an area detector was discussed in part one of this series [Borbély, Renversade, Kenesei & Wright (2014).J. Appl. Cryst.47, 1042–1053]. Part II links the detector frame to the laboratory frame comprising an additional rotation axis and introduces a general diffractometer equation accounting for all sources of misalignment. Additionally, an independent high-accuracy method for the evaluation of the crystallographic orientation and cell parameters of the undeformed reference crystal is presented. Setup misalignments are mainly described in terms of a residual strain tensor, considered as a quality label of the diffractometer. The method is exemplified using data sets acquired at beamlines ID11 (European Synchrotron Radiation Facility) and 1-ID (Advanced Photon Source) on Al and W single crystals, respectively. The results show that the residual strain tensor is mainly determined by the detector spatial distortion, and values as small as 1–2 × 10−4can be practically achieved.
processPIXEL: a program to generate energy-vector models from Gavezzotti'sPIXELcalculations
Authors: Bond Andrew D.
Published: September 2014

A command-line program is presented to convert the output from Gavezzotti'sPIXELcalculations to Shishkin's energy-vector models representing the intermolecular interaction topology. The output models comprise sets of vectors joining the centres of the molecules in a crystal structure, scaled so that the vector representing the most stabilizing pairwise interaction has length equal to half of the corresponding intermolecular separation. When the energy-vector model is packed, the most stabilizing pairwise interaction is represented as a continuous line between interacting molecules, while the other intermolecular interactions are shown as discontinuous lines, with a smaller gap representing a more stabilizing interaction. The energy-vector models can be overlaid on the crystal structure using theMercuryvisualizer to enable convenient visualization of structural motifs that contribute significantly to the overall crystal packing energy.
Mass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering study
Authors: Besselink Rogier , ten Elshof Johan E.
Published: September 2014

The nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data.
An Investigation of PCR Inhibition Using Plexor®‐Based Quantitative PCR and Short Tandem Repeat Amplification
Authors: Thompson Robyn E. , Duncan George , McCord Bruce R.
Published: September 2014

A common problem in forensic DNA typing is PCR inhibition resulting in allele dropout and peak imbalance. In this paper, we have utilized the Plexor® real‐time PCR quantification kit to evaluate PCR inhibition. This is performed by adding increasing concentrations of various inhibitors and evaluating changes in melt curves and PCR amplification efficiencies. Inhibitors examined included calcium, humic acid, collagen, phenol, tannic acid, hematin, melanin, urea, bile salts, EDTA, and guanidinium thiocyanate. Results were plotted and modeled using mathematical simulations. In general, we found that PCR inhibitors that bind DNA affect melt curves and CT takeoff points while those that affect the Taq polymerase tend to affect the slope of the amplification curve. Mixed mode effects were also visible. Quantitative PCR results were then compared with subsequent STR amplification using the PowerPlex® 16 HS System. The overall results demonstrate that real‐time PCR can be an effective method to evaluate PCR inhibition and predict its effects on subsequent STR amplifications.
Ultrasound‐guided block of the suprascapular nerve – a volunteer study of a new proximal approach
Authors: ROTHE C. , STEEN‐HANSEN C. , LUND J. , JENSTRUP M. T. , LANGE K. H. W.
Published: September 2014

Background

The standard approach for the suprascapular nerve block is deep in the supraspinous fossa. However, with this approach, the suprascapular nerve is difficult to visualize by ultrasound. The aim of this study was to describe a new method to visualize and selectively block the suprascapular nerve in a more superficial and proximal location.

Methods

Twelve healthy volunteers were included. We located the brachial plexus in transverse section with ultrasound, and by longitudinal slide, we identified the departure of the suprascapular nerve from the superior trunk. The suprascapular nerve was followed under ultrasound visualization into the subclavian triangle under the inferior belly of the omohyoid muscle. We performed in‐plane ultrasound‐guided selective suprascapular nerve block by injecting 1 ml of lidocaine, 20 mg/ml close to the nerve. Nerve identification was aided by nerve stimulation. We assessed sensory and motor block of the suprascapular, axillary, radial, median, and ulnar nerves before, 15 and 30 min after performing the block.

Results

Eight volunteers demonstrated a selective suprascapular nerve block. Three had block failure and one volunteer did not receive the intervention.

Conclusions

We describe a new ultrasound‐guided low‐volume local anaesthetic technique to selectively block the suprascapular nerve. The potential clinical role of this new approach remains to be determined.
Ethanol sclerotherapy for venous malformation
Authors: Steiner Frederica , FitzJohn Trevor , Tan Swee T.
Published: September 2014

Background

Ethanol sclerotherapy (ES) is the preferred treatment for venous malformation (VM) with surgery playing an adjunctive role. Results of ES, however, are not well documented in the literature.

Methods

VM patients were identified from our vascular anomalies database from 1996 to 2011. After treatment completion, patients completed questionnaires evaluating symptoms and their severity and effect on appearance, function and overall quality of life (QoL), before and >6 months after treatment, using visual analogue scales of 0–10. Patients rated their overall satisfaction with ES using a scale of 0–10.

Results

Fifty‐four (23.9%) of the 226 VM patients underwent a total of 90 ES sessions (average 1.7 sessions per patient). Complications occurred in 12 (22.2%) patients in 12 (13.3%) ES sessions. Minor complications occurred in nine (16.7%) patients including transient paraesthesia (n = 3), transient weakness of facial nerve branch(es) (n = 3), skin blistering (n = 2) and spontaneously healing ulceration (n = 1). Major complications occurred in three (5.6%) patients in three (3.3%) ES sessions including skin necrosis (n = 1), Horner's syndrome (n = 1) and finger paraesthesia with joint stiffness (n = 1). ES improved the severity of background pain, episodic pain, contour deformity and skin discoloration in 86.0%, 72.4%, 83.0% and 72.2% of patients respectively. It reduced the effect of VM on appearance, function and overall QoL in 69.8%, 73.0% and 64.3% of patients. Mean treatment satisfaction was 7.9 (range, 0–10).

Conclusion

ES reduces pain, contour deformity and skin discoloration, and improves appearance, function and QoL. Our complication rates are consistent with the literature.
The effect of M‐phase stage‐dependent kinase inhibitors on inositol 1,4,5‐trisphosphate receptor 1 (IP3R1) expression and localization in pig oocytes
Authors: Sathanawongs Anucha , Fujiwara Katsuyoshi , Kato Tsubasa , Hirose Masahiko , Kamoshita Maki , Wojcikiewicz Richard J. H. , Parys Jan B. , Ito Junya , Kashiwazaki Naomi
Published: September 2014

At fertilization, inositol 1,4,5‐trisphosphate receptor type 1 (IP3R1) has a crucial role in Ca2+ release in mammals. Expression levels, localization and phosphorylation of IP3R1 are important for its function, but it still remains unclear which molecule(s) regulates IP3R1 behavior in pig oocytes. We examined whether there was a difference in localization of IP3R1 after in vitro or in vivo maturation of pig oocytes. In mouse oocytes, large clusters of IP3R1 were formed in the cortex of the oocyte except in a ring‐shaped band of cortex adjacent to the spindle. However, no such clusters of IP3R1 were observed in pig oocytes and there was no difference in its localization between in vitro and in vivo matured oocytes. We next tried to clarify which factor(s) regulates IP3R1 localization, phosphorylation and expression using M‐phase stage‐dependent kinase inhibitors. Our results show that treatments with roscovitine (p34cdc2 kinase inhibitor) or U0126 (mitogen‐activated protein kinase inhibitor) did not affect IP3R1 expression or localization in pig oocytes, although the latter strongly inhibited phosphorylation. However, treatment with BI‐2536, an inhibitor of polo‐like kinase 1 (Plk1), dramatically decreased the expression level of IP3R1 in pig oocytes in a dose‐dependent manner. From these results, it is suggested that Plk1 is involved in the regulation of IP3R1 expression in pig oocytes.
Influence of corpus luteum and ovarian volume on the number and quality of bovine oocytes
Authors: Penitente‐Filho Jurandy Mauro , Jimenez Carolina Rodrigues , Zolini Adriana Moreira , Carrascal Erly , Azevedo Jovana Luiza , Silveira Camila Oliveira , Oliveira Fabrício Albani , Torres Ciro Alexandre Alves
Published: September 2014

In order to evaluate whether ovarian volume, presence and diameter of the corpus luteum (CL) have effects on the number and quality of bovine recovered oocytes, 110 ovaries were obtained from the slaughterhouse. Cumulus oocytes complex were aspirated and evaluated under stereomicroscope. Oocytes were counted and classified according to their quality (Grades I, II, III and IV). Ovarian volume was weakly correlated to the number of good quality oocytes (P < 0.05). Ovaries with CL showed greater numbers of good quality oocytes than ovaries without CL (P < 0.05). Further, presence of CL and its diameter positively influenced the probability of recovering good quality oocytes (P < 0.05). In conclusion, ovarian volume is not a good parameter itself to predict important ovarian characteristics; moreover, analysis of CL, its presence and diameter, may be a good tool to improve efficiency on in vitro embryo production programs.
Glomerular filtration rate in cows estimated by a prediction formula
Authors: Murayama Isao , Miyano Anna , Sato Tsubasa , Iwama Ryosuke , Satoh Hiroshi , Ichijyo Toshihiro , Sato Shigeru , Furuhama Kazuhisa
Published: September 2014

To testify the relevance of Jacobsson's equation for estimating bovine glomerular filtration rate (GFR), we prepared an integrated formula based on its equation using clinically healthy dairy (n = 99) and beef (n = 63) cows, and cows with reduced renal function (n = 15). The isotonic, nonionic, contrast medium iodixanol was utilized as a test tracer. The GFR values estimated from the integrated formula were well consistent with those from the standard multisample method in each cow strain, and the Holstein equation prepared by a single blood sample in Holstein dairy cows. The basal reference GFR value in healthy dairy cows was significantly higher than that in healthy beef cows, presumably due to a breed difference or physiological state difference. It is concluded that the validity for the application of Jacobsson's equation to estimate bovine GFR is proven and it can be used in bovine practices.
Bioethics and the Framing of Climate Change's Health Risks
Authors: Valles Sean A.
Published: September 2014

Cheryl Cox MacPherson recently argued, in an article for this journal, that ‘Climate Change is a Bioethics Problem’. This article elaborates on that position, particularly highlighting bioethicists' potential ability to help reframe the current climate change discourse to give more attention to its health risks. This reframing process is especially important because of the looming problem of climate change skepticism. Recent empirical evidence from science framing experiments indicates that the public reacts especially positively to climate change messages framed in public health terms, and bioethicists are particularly well positioned to contribute their expertise to the process of carefully developing and communicating such messages. Additionally, as climate framing research and practice continue, it will be important for bioethicists to contribute to the creation of that project's nascent ethical standards. The discourse surrounding antibiotic resistance is posited as an example that can lend insight into how communicating a public health‐framed message, including the participation of bioethicists, can help to override public skepticism about the findings of politically contentious scientific fields.
Structure‐Based Grafting, Mutation, and Optimization of Peptide Inhibitors to Fit in the Active Pocket of Human Secreted Phospholipase A2: Find New Use of Old Peptide Agents with Anti‐Inflammatory Activity
Authors: Zhan Chengye , Li Shusheng , Zhong Qiang , Zhou Daixing
Published: September 2014

Phospholipase A2 (PLA2) is a key enzyme in the production of diverse mediators of inflammatory conditions, which possesses an open active pocket that is physicochemically compatible with a variety of small‐molecule substrates and peptide inhibitors. Although various peptides and peptide analogues have been identified to have inhibitory activity against PLA2 originated from animals and plants, only very few were designed for human secreted PLA2 (hsPLA2), an attractive target of inflammatory arthritis. Considering that the catalytic domains of PLA2 family members across different species are highly conserved in primary sequence, advanced structure, and biological function, in this study, we proposed a synthetic pipeline to implement structure‐based grafting, mutation, and optimization of peptide ligands from the snake PLA2–peptide complex crystal structures into the active pocket of apo hsPLA2 structure to computationally generate a large number of potential peptide inhibitors for hsPLA2, and the hsPLA2 inhibitory potency of few highly promising candidates arising from the theoretical analysis was determined. As might be expected, three peptides FLSFK, FLVYK, and FISYR showed relatively high inhibitory capability against hsPLA2, and other three ALSYK, LVFYA, and KGAILGFM were also modestly potent as they can suppress the enzymatic activity with observable doses. Further, the designed peptide FLVYK with highest potency was carried out with structure‐guided modification based on its atomic interactions with hsPLA2 using the computationally modeled structure data, consequently resulting in a dual‐point mutant ELIYK with significantly increased activity.
In vitro Antiviral Effects and 3D QSAR Study of Resveratrol Derivatives as Potent Inhibitors of Influenza H1N1 Neuraminidase
Authors: Li Chao , Fang Jian‐Song , Lian Wen‐Wen , Pang Xiao‐Cong , Liu Ai‐Lin , Du Guan‐Hua
Published: September 2014

The anti‐influenza virus activities of 50 resveratrol (RV: 3, 5, 4′‐trihydroxy‐trans‐stilbene) derivatives were evaluated using a neuraminidase (NA) activity assay. The results showed that 35 compounds exerted an inhibitory effect on the NA activity of the influenza virus strain A/PR/8/34 (H1N1) with 50% inhibitory concentration (IC50) values ranging from 3.56 to 186.1 μm. Next, the 35 RV derivatives were used to develop 3D quantitative structure–activity relationship (3D QSAR) models for understanding the chemical–biological interactions governing their activities against NA. The comparative molecular field analysis (CoMFA r2 = 0.973, q2 = 0.620, qtest2 = 0.661) and the comparative molecular similarity indices analysis (CoMSIA r2 = 0.956, q2 = 0.610, qtest2 = 0.531) were applied. Afterward, molecular docking was performed to study the molecular interactions between the RV derivatives and NA. Finally, a cytopathic effect (CPE) reduction assay was used to evaluate the antiviral effects of the RV derivatives in vitro. Time‐of‐addition studies demonstrated that the RV derivatives might have a direct effect on viral particle infectivity. Our results indicate that the RV derivatives are potentially useful antiviral compounds for new drug design and development for influenza treatment.
The Effect of Ontario's Greenbelt on the Price of Vacant Farmland
Authors: Deaton B. James , Vyn Richard J.
Published: September 2014

A hedonic property regression estimates a difference‐in‐differences coefficient to assess the effect of Ontario's Greenbelt zoning on vacant farmland prices around the Greater Toronto Area. In our analysis on over five hundred property sales between 2002 and 2009 we find some evidence that the Greenbelt legislation negatively influenced vacant farmland values located in close proximity to urban areas. However, the statistical significance of this result is sensitive to the exclusion of smaller parcels and to assumptions regarding endogeneity.