bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanism underlying selective regulation of G protein-gated inwardly rectifying potassium channels by the psychostimulant-sensitive sorting nexin 27
Authors: Balana Bartosz , Maslennikov Innokentiy , Kwiatkowski Witek , Stern Kalyn M. , Bahima Laia , Choe Senyon , Slesinger Paul A.
Published: March 2011

G protein-gated inwardly rectifying potassium (GIRK) channels are important gatekeepers of neuronal excitability. The surface expression of neuronal GIRK channels is regulated by the psychostimulant-sensitive sorting nexin 27 (SNX27) protein through a class I (-X-Ser/Thr-X-Φ, where X is any residue and Φ is a hydrophobic amino acid) PDZ-binding interaction. The G protein-insensitive inward rectifier channel (IRK1) contains the same class I PDZ-binding motif but associates with a different synaptic PDZ protein, postsynaptic density protein 95 (PSD95). The mechanism by which SNX27 and PSD95 discriminate these channels was previously unclear. Using high-resolution structures coupled with biochemical and functional analyses, we identified key amino acids upstream of the channel's canonical PDZ-binding motif that associate electrostatically with a unique structural pocket in the SNX27-PDZ domain. Changing specific charged residues in the channel's carboxyl terminus or in the PDZ domain converts the selective association and functional regulation by SNX27. Elucidation of this unique interaction site between ion channels and PDZ-containing proteins could provide a therapeutic target for treating brain diseases.
Primordial synthesis of amines and amino acids in a 1958 Miller H
2
S-rich spark discharge experiment
Authors: Parker Eric T. , Cleaves Henderson J. , Dworkin Jason P. , Glavin Daniel P. , Callahan Michael , Aubrey Andrew , Lazcano Antonio , Bada Jeffrey L.
Published: March 2011

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H
2
S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H
2
S, CH
4
, NH
3
, and CO
2
. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H
2
S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H
2
S may have played an important role in prebiotic reactions in early solar system environments.
Oxidation of NADPH on Kvβ1 inhibits ball-and-chain type inactivation by restraining the chain
Authors: Pan Yaping , Weng Jun , Levin Elena J. , Zhou Ming
Published: March 2011

The Kv1 family voltage-dependent K
+
channels assemble with cytosolic β subunits (Kvβ), which are composed of a flexible N terminus followed by a structured core domain. The N terminus of certain Kvβs inactivates the channel by blocking the ion conduction pore, and the core domain is a functional enzyme that uses NADPH as a cofactor. Oxidation of the Kvβ-bound NADPH inhibits inactivation and potentiates channel current, but the mechanism behind this effect is unknown. Here we show that after oxidation, the core domain binds to part of the N terminus, thus restraining it from blocking the channel. The interaction is partially mediated by two negatively charged residues on the core domain and three positively charged ones on the N terminus. These results provide a molecular basis for the coupling between the cellular redox state and channel activity, and establish Kvβ as a target for pharmacological control of Kv1 channels.
Broad-spectrum antiviral that interferes with de novo pyrimidine biosynthesis
Authors: Hoffmann Hans-Heinrich , Kunz Andrea , Simon Viviana A. , Palese Peter , Shaw Megan L.
Published: March 2011

Compound A3 was identified in a high-throughput screen for inhibitors of influenza virus replication. It displays broad-spectrum antiviral activity, and at noncytotoxic concentrations it is shown to inhibit the replication of negative-sense RNA viruses (influenza viruses A and B, Newcastle disease virus, and vesicular stomatitis virus), positive-sense RNA viruses (Sindbis virus, hepatitis C virus, West Nile virus, and dengue virus), DNA viruses (vaccinia virus and human adenovirus), and retroviruses (HIV). In contrast to mammalian cells, inhibition of viral replication by A3 is absent in chicken cells, which suggests species-specific activity of A3. Correspondingly, the antiviral activity of A3 can be linked to a cellular protein, dihydroorotate dehydrogenase (DHODH), which is an enzyme in the de novo pyrimidine biosynthesis pathway. Viral replication of both RNA and DNA viruses can be restored in the presence of excess uracil, which promotes pyrimidine salvage, or excess orotic acid, which is the product of DHODH in the de novo pyrimidine biosynthesis pathway. Based on these findings, it is proposed that A3 acts by depleting pyrimidine pools, which are crucial for efficient virus replication.
Heparan sulfate/heparin promotes transthyretin fibrillization through selective binding to a basic motif in the protein
Authors: Noborn Fredrik , O'Callaghan Paul , Hermansson Erik , Zhang Xiao , Ancsin John B. , Damas Ana M. , Dacklin Ingrid , Presto Jenny , Johansson Jan , Saraiva Maria J. , Lundgren Erik , Kisilevsky Robert , Westermark Per , Li Jin-Ping
Published: March 2011

Transthyretin (TTR) is a homotetrameric protein that transports thyroxine and retinol. Tetramer destabilization and misfolding of the released monomers result in TTR aggregation, leading to its deposition as amyloid primarily in the heart and peripheral nervous system. Over 100 mutations of TTR have been linked to familial forms of TTR amyloidosis. Considerable effort has been devoted to the study of TTR aggregation of these mutants, although the majority of TTR-related amyloidosis is represented by sporadic cases due to the aggregation and deposition of the otherwise stable wild-type (WT) protein. Heparan sulfate (HS) has been found as a pertinent component in a number of amyloid deposits, suggesting its participation in amyloidogenesis. This study aimed to investigate possible roles of HS in TTR aggregation. Examination of heart tissue from an elderly cardiomyopathic patient revealed substantial accumulation of HS associated with the TTR amyloid deposits. Studies demonstrated that heparin/HS promoted TTR fibrillization through selective interaction with a basic motif of TTR. The importance of HS for TTR fibrillization was illustrated in a cell model; TTR incubated with WT Chinese hamster ovary cells resulted in fibrillization of the protein, but not with HS-deficient cells (pgsD-677). The effect of heparin on TTR fibril formation was further demonstrated in aDrosophilamodel that overexpresses TTR. Heparin was colocalized with TTR deposits in the head of the flies reared on heparin-supplemented medium, whereas no heparin was detected in the nontreated flies. Heparin of low molecular weight (Klexane) did not demonstrate this effect.
Malleability of folding intermediates in the homeodomain superfamily
Authors: Banachewicz Wiktor , Religa Tomasz L. , Schaeffer R. D. , Daggett Valerie , Fersht Alan R.
Published: March 2011

Members of the homeodomain superfamily are three-helix bundle proteins whose second and third helices form a helix-turn-helix motif (HTH). Their folding mechanism slides from the ultrafast, three-state framework mechanism for the engrailed homeodomain (EnHD), in which the HTH motif is independently stable, to an apparent two-state nucleation-condensation model for family members with an unstable HTH motif. The folding intermediate of EnHD has nearly native HTH structure, but it is not docked with helix1. The determinant of whether two- or three-state folding was hypothesized to be the stability of the HTH substructure. Here, we describe a detailed Φ-value analysis of the folding of the Pit1 homeodomain, which has similar ultrafast kinetics to that of EnHD. Formation of helix1 was strongly coupled with formation of HTH, which was initially surprising because they are uncoupled in the EnHD folding intermediate. However, we found a key difference between Pit1 and EnHD: The isolated peptide corresponding to the HTH motif in Pit1 was not folded in the absence of H1. Independent molecular dynamics simulations of Pit1 unfolding found an intermediate with H1 misfolded onto the HTH motif. The Pit1 folding pathway is the connection between that of EnHD and the slower folding homeodomains and provides a link in the transition of mechanisms from two- to three-state folding in this superfamily. The malleability of folding intermediates can lead to unstable substructures being stabilized by a variety of nonnative interactions, adding to the continuum of folding mechanisms.
Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH
Authors: Vila Jorge A. , Arnautova Yelena A. , Vorobjev Yury , Scheraga Harold A.
Published: March 2011

A method is proposed to determine the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH, provided that the observed

and

chemical shifts and the protein structure, or the fraction of H
+
form, are known. This method is based on the use of quantum chemical methods to compute the
13
C NMR shieldings of all the imidazole ring carbons (
13
C
γ
,

, and

) for each of the two tautomers, N

δ
1

-H and N

ϵ
2

-H, and the protonated form, H
+
, of histidine. This methodology enabled us (
i
) to determine the fraction of all the tautomeric forms of histidine for eight proteins for which the

and

chemical shifts had been determined in solution in the pH range of 3.2 to 7.5 and (
ii
) to estimate the fraction of tautomeric forms of eight histidine-containing dipeptide crystals for which the chemical shifts had been determined by solid-state
13
C NMR. Our results for proteins indicate that the protonated form is the most populated one, whereas the distribution of the tautomeric forms for the imidazole ring varies significantly among different histidines in the same protein, reflecting the importance of the environment of the histidines in determining the tautomeric forms. In addition, for ∼70% of the neutral histidine-containing dipeptides, the method leads to fairly good agreement between the calculated and the experimental tautomeric form. Coexistence of different tautomeric forms in the same crystal structure may explain the remaining 30% of disagreement.
Atomic-scale insight and design principles for turbine engine thermal barrier coatings from theory
Authors: Marino Kristen A. , Hinnemann Berit , Carter Emily A.
Published: March 2011

To maximize energy efficiency, gas turbine engines used in airplanes and for power generation operate at very high temperatures, even above the melting point of the metal alloys from which they are comprised. This feat is accomplished in part via the deposition of a multilayer, multicomponent thermal barrier coating (TBC), which lasts up to approximately 40,000 h before failing. Understanding failure mechanisms can aid in designing circumvention strategies. We review results of quantum mechanics calculations used to test hypotheses about impurities that harm TBCs and transition metal (TM) additives that render TBCs more robust. In particular, we discovered a number of roles that Pt and early TMs such as Hf and Y additives play in extending the lifetime of TBCs. Fundamental insight into the nature of the bonding created by such additives and its effect on high-temperature evolution of the TBCs led to design principles that can be used to create materials for even more efficient engines.
Recombinant immunotoxin against B-cell malignancies with no immunogenicity in mice by removal of B-cell epitopes
Authors: Onda Masanori , Beers Richard , Xiang Laiman , Lee Byungkook , Weldon John E. , Kreitman Robert J. , Pastan Ira
Published: March 2011

Many nonhuman proteins have useful pharmacological activities, but are infrequently effective in humans because of their high immunogenicity. A recombinant immunotoxin (HA22, CAT8015, moxetumomab pasudotox) composed of an anti-CD22 antibody variable fragment fused to PE38, a 38-kDa portion of
Pseudomonas
exotoxin A, has produced many complete remissions in drug-resistant hairy-cell leukemia when several cycles of the agent can be given, but has much less activity when antibodies develop. We have pursued a strategy to deimmunize recombinant immunotoxins by identifying and removing B-cell epitopes. We previously reported that we could eliminate most B-cell epitopes using a combination of point mutations and deletions. Here we show the location and amino acid composition of all of the B-cell epitopes in the remaining 25-kDa portion of
Pseudomonas
exotoxin. Using this information, we eliminated these epitopes to produce an immunotoxin (HA22-LR-8M) that is fully cytotoxic against malignant B-cell lines, has high cytotoxic activity against cells directly isolated from patients with chronic lymphocytic leukemia, and has excellent antitumor activity in mice. HA22-LR-8M does not induce antibody formation in mice when given repeatedly by intravenous injection and does not induce a secondary antibody response when given to mice previously exposed to HA22. HA22-LR-8M also has greatly reduced antigenicity when exposed to sera from patients who have produced antibodies to HA22. The properties of HA22-LR-8M make it an excellent candidate for further clinical development.
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
Authors: Goodman Andrew L. , Kallstrom George , Faith Jeremiah J. , Reyes Alejandro , Moore Aimee , Dantas Gautam , Gordon Jeffrey I.
Published: March 2011

The proportion of the human gut bacterial community that is recalcitrant to culture remains poorly defined. In this report, we combine high-throughput anaerobic culturing techniques with gnotobiotic animal husbandry and metagenomics to show that the human fecal microbiota consists largely of taxa and predicted functions that are represented in its readily cultured members. When transplanted into gnotobiotic mice, complete and cultured communities exhibit similar colonization dynamics, biogeographical distribution, and responses to dietary perturbations. Moreover, gnotobiotic mice can be used to shape these personalized culture collections to enrich for taxa suited to specific diets. We also demonstrate that thousands of isolates from a single donor can be clonally archived and taxonomically mapped in multiwell format to create personalized microbiota collections. Retrieving components of a microbiota that have coexisted in single donors who have physiologic or disease phenotypes of interest and reuniting them in various combinations in gnotobiotic mice should facilitate preclinical studies designed to determine the degree to which tractable bacterial taxa are able to transmit donor traits or influence host biology.
Jasmonate signaling involves the abscisic acid receptor PYL4 to regulate metabolic reprogramming in
Arabidopsis
and tobacco
Authors: Lackman Petri , González-Guzmán Miguel , Tilleman Sofie , Carqueijeiro Inês , Pérez Amparo Cuéllar , Moses Tessa , Seo Mitsunori , Kanno Yuri , Häkkinen Suvi T. , Van Montagu Marc C. E. , Thevelein Johan M. , Maaheimo Hannu , Oksman-Caldentey Kirsi-Marja , Rodriguez Pedro L. , Rischer Heiko , Goossens Alain
Published: March 2011

The phytohormones jasmonates (JAs) constitute an important class of elicitors for many plant secondary metabolic pathways. However, JAs do not act independently but operate in complex networks with crosstalk to several other phytohormonal signaling pathways. Here, crosstalk was detected between the JA and abscisic acid (ABA) signaling pathways in the regulation of tobacco (
Nicotiana tabacum
) alkaloid biosynthesis. A tobacco gene from the PYR/PYL/RCAR family,
NtPYL4
, the expression of which is regulated by JAs, was found to encode a functional ABA receptor. NtPYL4 inhibited the type-2C protein phosphatases known to be key negative regulators of ABA signaling in an ABA-dependent manner. Overexpression of
NtPYL4
in tobacco hairy roots caused a reprogramming of the cellular metabolism that resulted in a decreased alkaloid accumulation and conferred ABA sensitivity to the production of alkaloids. In contrast, the alkaloid biosynthetic pathway was not responsive to ABA in control tobacco roots. Functional analysis of the
Arabidopsis
(
Arabidopsis thaliana
) homologs of
NtPYL4
,
PYL4
and
PYL5
, indicated that also in
Arabidopsis
altered
PYL
expression affected the JA response, both in terms of biomass and anthocyanin production. These findings define a connection between a component of the core ABA signaling pathway and the JA responses and contribute to the understanding of the role of JAs in balancing tradeoffs between growth and defense.
Electrostatic influences of charged inner pore residues on the conductance and gating of small conductance Ca
2+
activated K
+
channels
Authors: Li Weiyan , Aldrich Richard W.
Published: March 2011

SK channels underlie important physiological functions by linking calcium signaling with neuronal excitability. Potassium currents through SK channels demonstrate inward rectification, which further reduces their small outward conductance. Although it has been generally attributed to block of outward current by intracellular divalent ions, we find that inward rectification is in fact an intrinsic property of SK channels independent of intracellular blockers. We identified three charged residues in the S6 transmembrane domain of SK channels near the inner mouth of the pore that collectively control the conductance and rectification through an electrostatic mechanism. Additionally, electrostatic contributions from these residues also play an important role in determining the intrinsic open probability of SK channels in the absence of Ca
2+
, affecting the apparent Ca
2+
affinity for activation.
Hepatic insulin resistance in mice with hepatic overexpression of diacylglycerol acyltransferase 2
Authors: Jornayvaz François R. , Birkenfeld Andreas L. , Jurczak Michael J. , Kanda Shoichi , Guigni Blas A. , Jiang Debbie C. , Zhang Dongyan , Lee Hui-Young , Samuel Varman T. , Shulman Gerald I.
Published: March 2011

Mice overexpressing acylCoA:diacylglycerol (DAG) acyltransferase 2 in the liver (Liv-
DGAT2
) have been shown to have normal hepatic insulin responsiveness despite severe hepatic steatosis and increased hepatic triglyceride, diacylglycerol, and ceramide content, demonstrating a dissociation between hepatic steatosis and hepatic insulin resistance. This led us to reevaluate the role of DAG in causing hepatic insulin resistance in this mouse model of severe hepatic steatosis. Using hyperinsulinemic-euglycemic clamps, we studied insulin action in Liv-
DGAT2
mice and their wild-type (WT) littermate controls. Here, we show that Liv-
DGAT2
mice manifest severe hepatic insulin resistance as reflected by decreased suppression of endogenous glucose production (0.8 ± 41.8 vs. 87.7 ± 34.3% in WT mice,
P
< 0.01) during the clamps. Hepatic insulin resistance could be attributed to an almost 12-fold increase in hepatic DAG content (
P
< 0.01) resulting in a 3.6-fold increase in protein kinase Cε (PKCε) activation (
P
< 0.01) and a subsequent 52% decrease in insulin-stimulated insulin receptor substrate 2 (IRS-2) tyrosine phosphorylation (
P
< 0.05), as well as a 64% decrease in fold increase pAkt/Akt ratio from basal conditions (
P
< 0.01). In contrast, hepatic insulin resistance in these mice was not associated with increased endoplasmic reticulum (ER) stress or inflammation. Importantly, hepatic insulin resistance in Liv-
DGAT2
mice was independent of differences in body composition, energy expenditure, or food intake. In conclusion, these findings strengthen the link between hepatic steatosis and hepatic insulin resistance and support the hypothesis that DAG-induced PKCε activation plays a major role in nonalcoholic fatty liver disease (NAFLD)-associated hepatic insulin resistance.
Rapport management in air traffic control in Malaysian aviation discourse
Authors: Paramasivam Shamala
Published: March 2011

Oral communication is documented as the weakest link in air traffic control interactions and one of the primary causes of aviation accidents and incidents. The language of air traffic control communication is characterised by the use of prescribed phraseologies, and when these are missing, plain language becomes a dominant feature. During plain language use mitigation is recorded as a feature of communication and described as an attribute of communication in crews classified as high in safety performance. The present study departs from this observation and seeks to examine the linguistic features for rapport management in air traffic control in non-routine situations in the Malaysian context. Managing the pilot–controller relationship is categorised as one of the dominant communicative functions in air traffic control and a category that is associated with the use of politeness markers. An examination of the language functions in this category and their associated forms vis-à-vis features of politeness are considered useful for training in air traffic communication. Pragmatics is used in this study as the approach to discourse analysis and Spencer-Oatey’s (2000b) understanding of politeness as ‘rapport management’ is employed as the framework for data analysis. The study draws on both audio-recordings of radiotelephony communication in role-play situations involving expert Malaysian controllers taking on roles as pilot and controller, as well as transcripts of real-life radiotelephony communication between Malaysian controllers and international pilots. The findings show that the interactions are primarily oriented to rapport-maintenance. The linguistic devices for rapport management include justifications, terms of address, conventionally polite expressions such as ‘please’, modals, and conditional language use. Rapport management is shown to help foster shared mindfulness and team thinking between controllers and pilots.
Japanese sojourners’ attitudes toward Americans
Authors: Imamura Makiko , Zhang Yan Bing , Harwood Jake
Published: March 2011

Guided by the intergroup contact hypothesis, the authors examined the associations among Japanese sojourners’ (N = 94) perceived linguistic competence with English, communication accommodation of their most frequent American contact, relational solidarity with the contact, and their attitudes toward Americans as a cultural group. Results indicated that participants’ linguistic competence with English and perceptions of Americans’ communication accommodation positively predicted their relational solidarity with their most frequent American contact. In addition, relational solidarity mediated the relationships between both linguistic competence and communication accommodation and cognitive and behavioral attitudes. Results were discussed in light of communication accommodation theory, the contact hypothesis and prior literature in intergroup and intercultural communication.
A circle is not the generalized inverse limit of a subset of [0,1]²
Authors: Illanes Alejandro
Published: March 2011

In this paper we show that the simple closed curve cannot be obtained as the inverse limit of an upper semi-continuous multivalued function from

[
0
,
1
]

[0,1]

into

[
0
,
1
]

[0,1]

.
A restriction theorem for the H-type groups
Authors: Liu Heping , Wang Yingzhan
Published: March 2011

We prove that the restriction operator for the H-type groups is bounded from

L
p

L^p

to

L

p
′

L^{p’}

for

p
p

near to

1
1

when the dimension of the center is larger than one, and the range of

p
p

depends on the dimension of the center. This is different from the Heisenberg group, on which the restriction operator is not bounded from

L
p

L^p

to

L

p
′

L^{p’}

unless

p
=
1

p=1

.
anota: analysis of differential translation in genome-wide studies
Authors: Larsson Ola , Sonenberg Nahum , Nadon Robert
Published: March 2011

Summary: Translational control of gene expression has emerged as a major mechanism that regulates many biological processes and shows dysregulation in human diseases including cancer. When studying differential translation, levels of both actively translating mRNAs and total cytosolic mRNAs are obtained where the latter is used to correct for a possible contribution of differential cytosolic mRNA levels to the observed differential levels of actively translated mRNAs. We have recently shown that analysis of partial variance (APV) corrects for cytosolic mRNA levels more effectively than the commonly applied log ratio approach. APV provides a high degree of specificity and sensitivity for detecting biologically meaningful translation changes, especially when combined with a variance shrinkage method for estimating random error. Here we describe the anota (analysis of translational activity) R-package which implements APV, allows scrutiny of associated statistical assumptions and provides biologically motivated filters for analysis of genome wide datasets. Although the package was developed for analysis of differential translation in polysome microarray or ribosome-profiling datasets, any high-dimensional data that result in paired controls, such as RNP immunoprecipitation-microarray (RIP-CHIP) datasets, can be successfully analyzed with anota.

Availability: The anota Bioconductor package, www.bioconductor.org.

Contact:  ola.larsson@ki.se; robert.nadon@mcgill.ca
PvRACK1 Loss-of-Function Impairs Cell Expansion and Morphogenesis in Phaseolus vulgaris L. Root Nodules
Authors: Islas-Flores Tania , Guillén Gabriel , Alvarado-Affantranger Xóchitl , Lara-Flores Miguel , Sánchez Federico , Villanueva Marco A.
Published: March 2011

Receptor for activated C kinase (RACK1) is a highly conserved, eukaryotic protein of the WD-40 repeat family. Its peculiar β-propeller structure allows its interaction with multiple proteins in various plant signal-transduction pathways, including those arising from hormone responses, development, and environmental stress. During Phaseolus vulgaris root development, RACK1 (PvRACK1) mRNA expression was induced by auxins, abscissic acid, cytokinin, and gibberellic acid. In addition, during P. vulgaris nodule development, PvRACK1 mRNA was highly accumulated at 12 to 15 days postinoculation, suggesting an important role after nodule meristem initiation and Rhizobium nodule infection. PvRACK1 transcript accumulation was downregulated by a specific RNA interference construct which was expressed in transgenic roots of composite plants of P. vulgaris inoculated with Rhizobium tropici. PvRACK1 downregulated transcript levels were monitored by quantitative reverse-transcription polymerase chain reaction analysis in individual transgenic roots and nodules. We observed a clear phenotype in PvRACK1-knockdown nodules, in which nodule number and nodule cell expansion were impaired, resulting in altered nodule size. Microscopic analysis indicated that, in PvRACK1-knockdown nodules, infected and uninfected cells were considerably smaller (80 and 60%, respectively) than in control nodules. In addition, noninfected cells and symbiosomes in silenced nodules showed significant defects in membrane structure under electron microscopy analysis. These findings indicate that PvRACK1 has a pivotal role in cell expansion and in symbiosome and bacteroid integrity during nodule development.
Validation of a Real-Time Polymerase Chain Reaction Assay for the Identification of Meloidogyne arenaria
Authors: Agudelo Paula , Lewis Stephen A. , Fortnum Bruce A.
Published: March 2011

Meloidogyne arenaria is an economically important parasite of many crops worldwide. Identification and detection of this species in soil samples is necessary for the design of crop rotation systems, selection of resistant cultivars, and potential use of biological control options. The objective of this study was to develop and validate a real-time polymerase chain reaction (PCR) assay, using species-specific primers and SYBR Green I Dye, for identification of M. arenaria. The specificity of the assay was confirmed by testing for amplification of DNA from other Meloidogyne spp. and from M. arenaria populations of different geographic origins. Field soil samples containing a mixture of M. arenaria and M. incognita were used to compare identification by the real-time PCR assay with identification by esterase phenotype analysis of mature females and by morphometrics of juveniles. The real-time PCR assay provided an accurate and sensitive means for the identification of single juveniles from soil samples.
Assessing the Adequacy of the Simulation Model LATEBLIGHT Under Nicaraguan Conditions
Authors: Blandón-Díaz Jorge Ulises , Forbes Gregory A. , Andrade-Piedra Jorge L. , Yuen Jonathan E.
Published: March 2011

In this study, the adequacy of the late blight simulation model LATEBLIGHT (version LB2004) was evaluated under Nicaraguan conditions. During 2007 to 2008, five field experiments were conducted in three potato-production regions in northern Nicaragua. Two susceptible (‘Cal White’ and ‘Granola’) and one resistant (‘Jacqueline Lee’) potato cultivars were evaluated without use of fungicides and with three application intervals (4, 7, and 14 days) of the fungicide chlorothalonil. The simulation model was considered adequate because it accurately predicted high disease severity in susceptible cultivars without fungicide protection, and demonstrated a decrease in the disease progress curves with additional fungicide applications, similar to that observed in the plots. The model also generally predicted inadequate fungicide control, even with a 4-day spray interval, which also occurred in the field. Lack of adequate fungicide protection would indicate the need for cultivars with higher levels of durable resistance, and that farmers should consider more effective fungicides applications (higher dosages or different chemistries) if susceptible cultivars are used.
Spatiotemporal Colonization of Xylella fastidiosa in its Vector Supports the Role of Egestion in the Inoculation Mechanism of Foregut-Borne Plant Pathogens
Authors: Backus Elaine A. , Morgan David J. W.
Published: March 2011

The pathogen that causes Pierce's disease of grapevine, Xylella fastidiosa, is the only known bacterial, arthropod-transmitted plant pathogen that does not circulate in the vector's hemolymph. Instead, bacteria are foregut-borne, persistent in adult vectors but semipersistent in immatures (i.e., bacteria colonize cuticular surfaces of the anterior foregut, are retained for hours to days, but are lost during molting). Yet, exactly how a sharpshooter vector inoculates bacteria from foregut acquisition sites is unknown. The present study used confocal laser-scanning microscopy to identify locations in undissected, anterior foreguts of the glassy-winged sharpshooter colonized by green fluorescent protein-expressing X. fastidiosa. Spatial and temporal distributions of colonizing X. fastidiosa were examined daily over acquisition access periods of 1 to 6 days for both contaminated field-collected and clean laboratory-reared Homalodisca vitripennis. Results provide the first direct, empirical evidence that established populations of X. fastidiosa can disappear from vector foreguts over time. When combined with existing knowledge on behavior, physiology, and functional anatomy of sharpshooter feeding, present results support the idea that the disappearance is caused by outward fluid flow (egestion) not inward flow (ingestion) (i.e., swallowing). Thus, results support the hypothesis that egestion is a critical part of the X. fastidiosa inoculation mechanism. Furthermore, results suggest a cyclical, spatiotemporal pattern of microbial colonization, disappearance, and recolonization in the precibarium. Colonization patterns also support two types of egestion, termed rinsing and discharging egestion herein. Finally, comparison of acquisition results for field-collected versus laboratory-reared sharpshooters suggest that there may be competitive binding for optimum acquisition sites in the foregut. Therefore, successful inoculation of X. fastidiosa may depend, in large part, on vector load in the precibarium.
Sequence Variability, Recombination Analysis, and Specific Detection of the W Strain of Plum pox virus
Authors: Glasa Miroslav , Malinowski Tadeusz , Predajňa Lukáš , Pupola Neda , Dekena Dzintra , Michalczuk Lech , Candresse Thierry
Published: March 2011

Plum pox virus (PPV), a member of the genus Potyvirus, is the causal agent of Sharka, the most detrimental disease of stone-fruit trees worldwide. PPV isolates are grouped into seven distinct strains. The minor PPV-W strain was established recently for the divergent W3174 isolate found in Canada. Here, the partial or complete genomic sequences of four PPV-W isolates from Latvia have been determined. The completely sequenced isolates LV-141pl and LV-145bt share 93.1 and 92.1% nucleotide identity, respectively, with isolate W3174, with two regions of higher (>20%) divergence in the P1/HC-Pro and NIa (VPg) regions. Further analyses demonstrated that these two regions correspond to two independent recombination events in the W3174 genome, one involving PPV-M (approximate genome positions 692 to 1424) and the other PPV-D (nucleotides 5672 to 5789). The LV-141pl and LV-145bt isolates appear to be representatives of the “ancestral” PPV-W strain, not affected by recombination. The PPV-W intrastrain variability is substantially higher than that of all other PPV strains, with potential implications for the serological detection of PPV-W isolates. A PPV-W-specific primer pair has been developed, allowing the specific reverse-transcription polymerase chain reaction detection of all five presently available W isolates. The characterization of these new PPV-W isolates sheds light on PPV-W evolutionary history, further supports the hypothesis of its East-European origin, and opens the way for the biological and epidemiological characterization of this poorly known PPV strain.
Pilot of a National Inpatient Medication Chart in Australia: improving prescribing safety and enabling prescribing training
Authors: Coombes Ian D. , Reid Carol , McDougall David , Stowasser Danielle , Duiguid Margaret , Mitchell Charles
Published: March 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Prescribing errors are common and are caused by multiple factors. Standard medication charts have been recommended by British and Australian Health services. A study of a standard medication chart in five hospitals in one state of Australia significantly reduced prescribing errors.

WHAT THIS STUDY ADDS

• A standard medication chart developed in one area can be adopted through a collaborative process and successfully implemented across a diverse country resulting in similar reductions in prescribing errors. Three of the four stages of the prescribing process (information gathering, decision making and communication of instructions) can be improved by the use of an improved standard medication chart. The introduction of a standard medication chart has enabled development of standard prescribing education programmes.

AIMS To establish whether a standard national inpatient medication chart (NIMC) could be implemented across a range of sites in Australia and reduce frequency of prescribing errors and improve the completion of adverse drug reaction (ADR) and warfarin documentation.

METHODS A medication chart, which had previously been implemented in one state, was piloted in 22 public hospitals across Australia. Prospective before and after observational audits of prescribing errors were undertaken by trained nurse and pharmacist teams. The introduction of the chart was accompanied by local education of prescribers and presentation of baseline audit findings.

RESULTS After the introduction of the NIMC, prescribing errors decreased by almost one‐third, from 6383 errors in 15 557 orders, a median (range) of 3 (0–48) per patient to 4293 in 15 416 orders, 2 (0–45) per patient (Wilcoxon Rank Sum test, P < 0.001). The documentation of drugs causing previous ADRs increased significantly from 81.9% to 88.9% of drugs (χ2 test, P < 0.001). The documentation of the indication for warfarin increased from 12.1 to 34.3% (χ2 test, P= 0.001) and the documentation of target INR increased from 10.8 to 70.0% (χ2 test, P < 0.001) after implementation of the chart.

CONCLUSIONS National implementation of a standard medication chart is possible. Similar reduction in the rate of prescribing errors can be achieved in multiple sites across one country. The consequent benefits for patient care and training of staff could be significant.
Proton pump inhibitors and the risk of overanticoagulation during acenocoumarol maintenance treatment
Authors: Teichert Martina , van Noord Charlotte , Uitterlinden Andrė G. , Hofman Albert , Buhre Peter N. , De Smet Peter A. G. M. , Straus Sabine , Stricker Bruno H. Ch. , Visser Loes E.
Published: March 2011

In the Netherlands, several reports have described a potentiation of acenocoumarol‐induced anticoagulation by co‐medication of omeprazole or esomeprazole and competitive inhibition of CYP2C19 has been suggested as a possible mechanism for this interaction. We conducted an observational cohort study to investigate the effects of various proton pump inhibitors (PPIs) on acenocoumarol effectiveness. All 2755 subjects from the Rotterdam Study who received acenocoumarol maintenance treatment between April 1st, 1991 and September 9th, 2009 were followed for events of an international normalized ratio (INR) ≥ 6, until death, end of treatment, or end of the study period. The Andersen–Gill extension of the Cox proportional hazards model was used to calculate risks for repeated events of overanticoagulation in relation to concomitant PPI use. The risk for overanticoagulation was most pronounced for esomeprazole (HR 1·99, 95% CI 1·55–2·55) and lansoprazole (HR 1·49, 95% CI 1·05–2·10). There was also a lower and non‐significant risk increase for the other PPIs. We did not detect a modification of these results by CYP2C19*2 genotype. Caution should be paid to co‐medication with esomeprazole and lansoprazole during acenocoumarol treatment and possibly also with other PPIs.
Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples
Authors: Antonangelo L. , Vargas F. S. , Acencio M. M. P. , Corá A. P. , Teixeira L. R. , Genofre E. H. , Sales R. K. B.
Published: March 2011

L. Antonangelo, F. S. Vargas, M. M. P. Acencio, A. P. Corá, L. R. Teixeira, E. H. Genofre and R. K. B. Sales  Effect of temperature and storage time on cellular analysis of fresh pleural fluid samples

Objective:  Despite the methodological variability in preparation techniques for pleural fluid cytology, it is fundamental that the cells should be preserved, permitting adequate morphological classification. We evaluated numerical and morphological changes in pleural fluid specimens processed after storage at room temperature or under refrigeration.

Methods:  Aliquots of pleural fluid from 30 patients, collected in ethylenediaminetetraacetic acid‐coated tubes and maintained at room temperature (21 °C) or refrigeration (4 °C) were evaluated after 2 and 6 hours and 1, 2, 3, 4, 7 and 14 days. Evaluation of cytomorphology and global and percentage counts of leucocytes, macrophages and mesothelial cells were included.

Results:  The samples had quantitative cellular variations from day 3 or 4 onwards, depending on the storage conditions. Morphological alterations occurred earlier in samples maintained at room temperature (day 2) than in those under refrigeration (day 4).

Conclusions:  This study confirms that storage time and temperature are potential pre‐analytical causes of error in pleural fluid cytology.
Host size selection and sex allocation behaviour among parasitoid trophic levels
Authors: HEINZ KEVIN M.
Published: March 2011

Abstract.

Sex ratio in the ectoparasitoid Chrysocharis nephereus, when attacking larvae of the lepidopteran leafminer Cameraria jacintoensis inhabiting the scrub oak Quercus dumosa, varies as a function of host size.

Female progeny are overproduced on large hosts and male progeny are overproduced on small hosts. Whether a host is perceived as large or small depends on the distribution of sizes of hosts encountered. Lastly, the primary sex ratio is consistently male biased. These patterns are not due to variation in progeny sex specific mortality, but are probably a result of maternal choice.

Female wasp size increases at a greater rate than does male wasp size with an equivalent increase in C.jacintoensis larval size. Although the average adult longevity of female C.nephereus is significantly greater than the average longevity of male C.nephereus, male wasp longevity increases at a greater rate than does female wasp longevity with an equivalent increase in C.jacintoensis larval size.

Chrysocharis nephereus developing on large C.jacintoensis are more likely to be hyperparasitized by Closterocerus sp. than are C.nephereus developing on smaller sized C.jacintoensis. Closterocerus sp. hyperparasitize female C.nephereus progeny with significantly greater frequency than male progeny.

Female C.nephereus overproducing daughters on large hosts and sons on small hosts may experience fitness trade‐offs between the benefits associated with producing offspring on large hosts and costs associated with these offspring becoming hyperparasitized.
Influence of feeding guild on insect response to host plant fertilization
Authors: MEYER GRETCHEN A. , ROOT RICHARD B.
Published: March 2011

Abstract.

The densities of insect herbivores in fertilized and unfertilized field plots of goldenrods, Solidago altissima (Compositae), were monitored over a period of 4 years.

A total of seventeen insect taxa occurred on the plots over the course of the study, including sap feeders, leaf chewers, leaf miners, leaf gallers and stem gallers with multiple representatives in each of these feeding guilds.

Nine of the seventeen taxa significantly increased in density on fertilized plots in at least one year of the study, two taxa showed marginally significant increases on fertilized plots, two significantly decreased in density on fertilized plots in at least one year, and the remaining taxa were unaffected by the fertilizer treatment.

The effects of fertilization on the insects were not strongly related to feeding guild; the group of insects that increased on fertilized plots was functionally diverse, and for the most part members of the same guild did not respond to the fertilizer treatment in consistent ways.

Differences between fertilized and unfertilized plots were greatest in the fourth year. The insects that showed delayed responses to fertilizer treatment may have been affected by changes in microclimate that developed slowly over the course of the study, suggesting that long‐term studies may be necessary to detect effects of host plant stress on insect herbivores.
Potential for host range expansion in Ceratitis capitata flies: impact of proximity of adult food to egg‐laying sites
Authors: PROKOPY RONALD J. , DUAN JIAN JUN , VARGAS ROGER I.
Published: March 2011

Abstract.

In field cage and field tests, female Mediterranean fruit flies, Ceratitis capitata (Wiedemann), in trees alighted in significantly greater numbers upon sticky‐coated (non‐odour‐emitting) kumquats, Fortunella japonica, that were in the vicinity of odorous natural proteinaceous food (bird faeces) or synthetic food odour than on similar kumquats distant from bird faeces or synthetic food odour.

In field cage tests, oviposition in non‐sticky kumquats nearby bird faeces was significantly greater than in non‐sticky kumquats distant from bird faeces.

In field tests, medflies laid significantly more eggs in host kumquat and non‐host hawthorn, Crataegus mollis, fruit adjacent to bird faeces and synthetic food odour than in fruit of these types distant from food‐type stimuli.

These findings suggest that odour of natural food of medflies could lure flies to plants whose fruit emit little or no attractive odour and are not permanent hosts but which are nonetheless susceptible to egg‐laying and larval development, resulting in temporary expansion of host range.
Impact of mass movements in the Kocaeli Province, Turkey
Authors: Karakaş Ahmet , Coruk Özkan
Published: March 2011

Recent mass movements in the Kocaeli Province, Turkey in 2010 caused damage to people, property and infrastructure, especially in Izmit and its vicinity. The causes and impact of these mass movements are outlined, so as to increase awareness of their dangerous aspects. Some of these mass movement events took place in urban areas, bringing attention to the need for better and more effective land use practices. The impact of these movements indicates the benefit there would be from geology and engineering geology in the planning of any property development and land use.