bluuebunny/crossref_metadata_2025 huggingface dataset:
Hepatic steatosis in diabetic patients does not predict adverse liver‐related or cardiovascular outcomes
Authors: Dunn Michael A. , Behari Jaideep , Rogal Shari S. , O'Connell Michael R. , Furlan Alessandro , Aghayev Ayaz , Gumus Serter , Saul Melissa I. , Bae Kyongtae T.
Published: July 2013

Background & Aims

Steatosis is a defining feature of nonalcoholic fatty liver disease (NAFLD). However, evidence that severity of steatosis can predict adverse outcomes in NAFLD or nonalcoholic steatohepatitis (NASH) is lacking. The aim of this study was to determine whether steatosis assessed by computed tomography (CT) imaging predicts adverse outcomes in diabetic patients at risk for NAFLD/NASH.

Methods

We studied deaths, liver‐related and cardiovascular adverse outcomes in a 5‐year retrospective observational cohort of 2343 type 2 diabetic patients in a large care network who had noncontrast CT imaging for clinical indications. We measured steatosis by subtraction of spleen from liver attenuation, a method that showed low sensitivity (0.417) and high specificity (0.882) compared with histopathological scoring. We evaluated outcomes prediction using multivariate Cox proportional hazards modelling of steatosis both as a categorical (≥30%) and continuous variable.

Results

Steatosis ≥30% was present in 233 (9.9%) of the cohort at baseline. Over 5 years, there were 372 total deaths, 18 liver‐related and 99 cardiovascular deaths, 48 liver transplants, 51 occurrences of hepatic encephalopathy, 41 hepatocellular carcinomas, 653 myocardial infarctions, 66 strokes, 180 occurrences of angina, 735 occurrences of arrhythmia and 772 occurrences of congestive heart failure. Steatosis had no predictive value for any adverse outcome. Patients with steatosis averaged 8 years younger than those without it. Age had a strong covariate influence on occurrence of total deaths, cardiovascular deaths, myocardial infarctions, arrhythmias and congestive heart failure.

Conclusion

Although steatosis on imaging is often the abnormality that triggers diagnosis and assessment of NAFLD/NASH, it lacks predictive value for adverse clinical outcomes.
Financial Frictions and Inflation Differentials in a Monetary Union
Authors: Hristov Nikolay , Hülsewig Oliver , Wollmershäuser Timo
Published: July 2013

This paper presents a stylized New Keynesian dynamic stochastic general equilibrium (DSGE) model for a monetary union to analyze whether cyclical inflation differentials can be explained by cross‐country differences concerning the characteristics of financial markets. Our results suggest that empirically plausible degrees of heterogeneity with respect to two important credit market characteristics, i.e. the access to credit and the fraction of households holding debt, are a relevant source of inflation dispersion across European Monetary Union (EMU) member countries.
Mg and Si isotopic fractionation patterns in types B1 and B2 CAIs: Implications for formation under different nebular conditions
Authors: Bullock Emma S. , Knight Kim B. , Richter Frank M. , Kita Noriko T. , Ushikubo Takayuki , MacPherson Glenn J. , Davis Andrew M. , Mendybaev Ruslan A.
Published: July 2013

Magnesium and silicon isotopic profiles across melilite grains in two type B1 and two type B2 calcium‐aluminum‐rich inclusions (CAIs) reveal differing but constant enrichments in heavy isotopes everywhere except ≤1000 μm from the CAI margins. There is no close correlation in the B1s or the B2s between isotopic composition and åkermanite content of the melilite, a measure of progressive igneous crystallization, yet such a correlation might be expected in a type B2: without a melilite mantle (as in B1s) to seal the interior off and prevent further evaporation, the melt would have maintained communication with the external gas. These observations indicate a model in which B1s and B2s solidified under differing conditions. The B2s solidified under lower hydrogen pressures ( ≤ 10−4 – 10−5 bars) than did B1s ( > 10−4 bars), so surface volatilization was slower in the B2s and internal chemical and isotopic equilibrium was maintained over the interval of melilite crystallization. The outermost zones of the CAIs (≤1000 μm from the edge) are not consistently enriched in heavy isotopes relative to the interiors, as might be expected from diffusion‐limited surface evaporation of the melt. In all cases, the magnesium in the CAI margins is lighter than in the interiors. In one case, silicon in the margin also is lighter, but locally in some CAIs, it is isotopically heavier near the surface. If melt evaporation played a role in the formation of these outer zones, a later event in many cases caused isotopic re‐equilibration with an external and isotopically near‐normal reservoir.
Specificity and stability of the Acromyrmex–Pseudonocardia symbiosis
Authors: Andersen S. B. , Hansen L. H. , Sapountzis P. , Sørensen S. J. , Boomsma J. J.
Published: July 2013

The stability of mutualistic interactions is likely to be affected by the genetic diversity of symbionts that compete for the same functional niche. Fungus‐growing (attine) ants have multiple complex symbioses and thus provide ample opportunities to address questions of symbiont specificity and diversity. Among the partners are Actinobacteria of the genus Pseudonocardia that are maintained on the ant cuticle to produce antibiotics, primarily against a fungal parasite of the mutualistic gardens. The symbiosis has been assumed to be a hallmark of evolutionary stability, but this notion has been challenged by culturing and sequencing data indicating an unpredictably high diversity. We used 454 pyrosequencing of 16S rRNA to estimate the diversity of the cuticular bacterial community of the leaf‐cutting ant Acromyrmex echinatior and other fungus‐growing ants from Gamboa, Panama. Both field and laboratory samples of the same colonies were collected, the latter after colonies had been kept under laboratory conditions for up to 10 years. We show that bacterial communities are highly colony‐specific and stable over time. The majority of colonies (25/26) had a single dominant Pseudonocardia strain, and only two strains were found in the Gamboa population across 17 years, confirming an earlier study. The microbial community on newly hatched ants consisted almost exclusively of a single strain of Pseudonocardia while other Actinobacteria were identified on older, foraging ants in varying but usually much lower abundances. These findings are consistent with recent theory predicting that mixtures of antibiotic‐producing bacteria can remain mutualistic when dominated by a single vertically transmitted and resource‐demanding strain.
Extending the Arabidopsis flowering paradigm to a mass flowering phenomenon in the tropics
Authors: Weston David J. , Wullschleger Stan D. , Tuskan Gerald A.
Published: July 2013

Flowering time is a critical life history trait, one that is shaped by evolution to maximize fecundity, reproductive success and fitness (Amasino ). This is especially true of annual plants where the cycle of floral initiation, pollination and seed production occur at regular intervals to ensure the survival of the species. In long‐lived perennials, however, flowering can be an intermittent phenomenon and thus a challenge to understand. In this issue of Molecular Ecology, Kobayashi et al. () tackle this particular challenge by applying modern‐day molecular techniques to the ‘spectacular and mysterious’ mass flowering that takes places in mixed dipterocarp forests of South‐East Asia. Here, amidst an almost unimaginable diversity of forbs, shrubs and trees, these authors used next‐generation sequencing technology to characterize what they refer to as the ‘ecological transcriptome’ in an attempt to glimpse into the functional genomic reprogramming of Shorea beccariana at pre‐ and postflowering developmental transitions. They encountered many of the challenges that are often underappreciated yet typical for tropical ecological research including sample collection within a ~40‐m high tree canopy, unpredictable flowering intervals and determining the most appropriate preflowering state for sampling. Despite these challenges, the authors were able to integrate gene ontology relationships with gene‐clustering algorithms and environmental data to support the hypothesis that drought is a key trigger for flowering in S. beccariana. The cloning and transgenic expression of selected S. beccariana genes to corroborate presumed protein function is a key feature of their work and seldom applied within an ecological framework. As illustrated by Kobayashi et al. (), the inclusion of molecular biology, genomics and bioinformatics has the potential to shed light on long‐standing questions of ecological concern.
Features governing symbiont persistence in the squid–vibrio association
Authors: Koch Eric J. , Miyashiro Tim , McFall‐Ngai Margaret J. , Ruby Edward G.
Published: July 2013

Experimental studies of the interaction between host and symbiont in a maturing symbiotic organ have presented a challenge for most animal–bacterial associations. Advances in the rearing of the host squid Euprymna scolopes have enabled us to explore the relationship between a defect in symbiont light production and late‐stage development (e.g. symbiont persistence and tissue morphogenesis) by experimental colonization with specific strains of the symbiont Vibrio fischeri. During the first 4 weeks postinoculation of juvenile squid, the population of wild‐type V. fischeri increased 100‐fold; in contrast, a strain defective in light production (Δlux) colonized normally the first day, but exhibited an exponential decline to undetectable levels over subsequent weeks. Co‐colonization of organs by both strains affected neither the trajectory of colonization by wild type nor the decline of Δlux levels. Uninfected animals retained the ability to be colonized for at least 2 weeks posthatch. However, once colonized by the wild‐type strain for 5 days, a subsequent experimentally induced loss of the symbionts could not be followed by a successful recolonization, indicating the host's entry into a refractory state. However, animals colonized by the Δlux before the loss of their symbionts were receptive to recolonization. Analyses of animals colonized with either a wild‐type or a Δlux strain revealed slight, if any, differences in the developmental regression of the ciliated light‐organ tissues that facilitate the colonization process. Thus, some other feature(s) of the Δlux strain's defect also may be responsible for its inability to persist, and its failure to induce a refractory state in the host.
Molecular analysis of the diets of snakes: changes in prey exploitation during development of the rare smooth snake Coronella austriaca
Authors: Brown David S. , Ebenezer Katie L. , Symondson William O. C.
Published: July 2013

Reptiles are declining in many parts of the world, mainly due to habitat loss and environmental change. A major factor in this is availability of suitable food. For many animals, dietary requirements shift during developmental stages and a habitat will only be suitable for conserving a species if it supports all stages. Conventional methods for establishing diet often rely on visual recognition of morphologically identifiable features of prey in faeces, regurgitation or stomach contents, which suffer from biases and poor resolution of taxa. DNA‐based techniques facilitate noninvasive analysis of diet from faeces without these constraints. We tested the hypothesis that diet changes during growth stages of smooth snakes (Coronella austriaca), which have a highly restricted distribution in the UK but are widespread in continental Europe. Small numbers of the sympatric grass snake (Natrix natrix) were analysed for comparison. Faecal samples were collected from snakes and prey DNA analysed using PCR, targeting amphibians, reptiles, mammals and invertebrates. Over 85% of smooth snakes were found to have eaten reptiles and 28% had eaten mammals. Predation on mammals increased with age and was entirely absent among juveniles and subadults. Predation on reptiles did not change ontogenetically. Smooth snakes may, therefore, be restricted to areas of sufficiently high reptile densities to support young snakes.
The APSES transcription factor Efg1 is a global regulator that controls morphogenesis and biofilm formation in Candida parapsilosis
Authors: Connolly Leona A. , Riccombeni Alessandro , Grózer Zsuzsana , Holland Linda M. , Lynch Denise B. , Andes David R. , Gácser Attila , Butler Geraldine
Published: July 2013

Efg1 (a member of the APSES family) is an important regulator of hyphal growth and of the white‐to‐opaque transition in Candida albicans and very closely related species. We show that in Candida parapsilosis Efg1 is a major regulator of a different morphological switch at the colony level, from a concentric to smooth morphology. The rate of switching is at least 20‐fold increased in an efg1 knockout relative to wild type. Efg1 deletion strains also have reduced biofilm formation, attenuated virulence in an insect model, and increased sensitivity to SDS and caspofungin. Biofilm reduction is more dramatic in in vitro than in in vivo models. An Efg1 paralogue (Efh1) is restricted to Candida species, and does not regulate concentric‐smooth phenotype switching, biofilm formation or stress response. We used ChIP‐seq to identify the Efg1 regulon. A total of 931 promoter regions bound by Efg1 are highly enriched for transcription factors and regulatory proteins. Efg1 also binds to its own promoter, and negatively regulates its expression. Efg1 targets are enriched in binding sites for 93 additional transcription factors, including Ndt80. Our analysis suggests that Efg1 has an ancient role as regulator of development in fungi, and is central to several regulatory networks.
The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti
Authors: Pini Francesco , Frage Benjamin , Ferri Lorenzo , De Nisco Nicole J. , Mohapatra Saswat S. , Taddei Lucilla , Fioravanti Antonella , Dewitte Frederique , Galardini Marco , Brilli Matteo , Villeret Vincent , Bazzicalupo Marco , Mengoni Alessio , Walker Graham C. , Becker Anke , Biondi Emanuele G.
Published: July 2013

Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen‐fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.
Postprandial cardiac vagal tone and transient lower esophageal sphincter relaxation (TLESR)
Authors: Kuo P. , Bravi I. , Marreddy U. , Aziz Q. , Sifrim D.
Published: July 2013

Background

Transient lower esophageal sphincter relaxation (TLESR) is a vagally mediated reflex that occurs most frequently after a meal. Cardiac vagal tone (CVT) decreases after a meal, and correlates with changes in gastric electrical activity. Furthermore, decreased CVT has been reported in patients with gastro‐esophageal reflux disease. We therefore aimed to characterize the association between postprandial changes in CVT and the occurrence of TLESR and reflux.

Methods

Ten healthy volunteers underwent simultaneous autonomic nervous system, gastric myoelectric activity, lower esophageal‐sphincter pressure, and reflux monitoring for 30 min in the fasting state, followed by a standard meal, and a further 4 h postprandially. Results are in mean ± SEM.

Key Results

The number of TLESRs (P < 0.0001) and reflux episodes (P < 0.0001) increased after the meal, while CVT decreased (P < 0.01). Cardiac sensitivity to baroreceptor reflex (CSB) showed similar time course changes to CVT (P = 0.06). During the first postprandial hour there was a strong correlation between the number of TLESRs and reflux episodes with CVT (R2 = 0.51 and R2 = 0.50, respectively; P < 0.05). There was also an increase in the dominant power and power ratio on electrogastrography (P < 0.05) after the meal.

Conclusions & Inferences

In healthy volunteers, the increase in the number of TLESRs and reflux episodes after a meal occurred mostly at a time of reduced CVT. Further studies should explore whether modulation of CVT can modify frequency of TLESRs and also this relationship should be further explored in patients with reflux disease.
Davidson's Interpretations: The Step Not Taken
Authors: Dresner Eli
Published: July 2013

In the first section of this paper I follow an important trajectory in the development of Davidson's notion of radical interpretation: From being interpretationally concerned only with language, like Quine's radical translation that precedes it, through involving the ascription of belief in increasingly complex ways, to finally incorporating desire and preference. In the second section of the paper I show that Davidson falls short of incorporating non‐linguistic action in radical interpretation, I assess his motivations for doing so, and I criticize these motivations. In the third and final section I propose a unified interpretation scheme for language, action and mind.
Effects of local adaptation and interspecific competition on species’ responses to climate change
Authors: Bocedi Greta , Atkins Katherine E. , Liao Jishan , Henry Roslyn C. , Travis Justin M.J. , Hellmann Jessica J.
Published: July 2013

Local adaptation and species interactions have been shown to affect geographic ranges; therefore, we need models of climate impact that include both factors. To identify possible dynamics of species when including these factors, we ran simulations of two competing species using an individual‐based, coupled map–lattice model using a linear climatic gradient that varies across latitude and is warmed over time. Reproductive success is governed by an individual's adaptation to local climate as well as its location relative to global constraints. In exploratory experiments varying the strength of adaptation and competition, competition reduces genetic diversity and slows range change, although the two species can coexist in the absence of climate change and shift in the absence of competitors. We also found that one species can drive the other to extinction, sometimes long after climate change ends. Weak selection on local adaptation and poor dispersal ability also caused surfing of cooler‐adapted phenotypes from the expanding margin backwards, causing loss of warmer‐adapted phenotypes. Finally, geographic ranges can become disjointed, losing centrally‐adapted genotypes. These initial results suggest that the interplay between local adaptation and interspecific competition can significantly influence species’ responses to climate change, in a way that demands future research.
MyD88 is essential for alveolar bone loss induced by Aggregatibacter actinomycetemcomitans lipopolysaccharide in mice
Authors: Madeira M.F.M. , Queiroz‐Junior C.M. , Cisalpino D. , Werneck S.M.C. , Kikuchi H. , Fujise O. , Ryffel B. , Silva T.A. , Teixeira M.M. , Souza D.G.
Published: July 2013

Aggregatibacter actinomycetemcomitans is a Gram‐negative bacteria highly associated with localized aggressive periodontitis. The recognition of microbial factors, such as lipopolysaccharide from A. actinomycetemcomitans (AaLPS), in the oral environment is made mainly by surface receptors known as Toll‐like receptors (TLR). TLR4 is the major LPS receptor. This interaction leads to the production of inflammatory cytokines by myeloid differentiation primary‐response protein 88 (MyD88) ‐dependent and ‐independent pathways, which may involve the adaptor Toll/interleukin‐1 receptor‐domain‐containing adaptor inducing interferon‐β (TRIF). The aim of this study was to assess the involvement of MyD88 in alveolar bone loss induced by AaLPS in mice. C57BL6/J wild‐type (WT) mice, MyD88, TRIF or TRIF/MyD88 knockout mice received 10 injections of AaLPS strain FDC Y4 (5 μg in 3 μl), in the palatal gingival tissue of the right first molar, every 48 h. Phosphate‐buffered saline was injected in the opposite side and used as control. Animals were sacrificed 24 h after the 10th injection and the maxillae were removed for macroscopic and biochemical analyses. The injections of AaLPS induced significant alveolar bone loss in WT mice. In the absence of MyD88 or TRIF/MyD88 no bone loss induced by AaLPS was observed. In contrast, responses in TRIF−/− mice were similar to those in WT mice. Diminished bone loss in the absence of MyD88 was associated with fewer TRAP‐positive cells and increased expression of osteoblast markers, RUNX2 and osteopontin. There was also reduced tumor necrosis factor‐α production in MyD88−/− mice. There was less osteoclast differentiation of hematopoietic bone marrow cells from MyD88−/− mice after AaLPS stimulation. Hence, the signaling through MyD88 is pivotal for AaLPS‐induced osteoclast formation and alveolar bone loss.
Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity
Authors: King Andrew J. , Montes Luis R. , Clarke Jasper G. , Affleck Julie , Li Yi , Witsenboer Hanneke , van der Vossen Edwin , van der Linde Piet , Tripathi Yogendra , Tavares Evanilda , Shukla Parul , Rajasekaran Thirunavukkarasu , van Loo Eibertus N. , Graham Ian A.
Published: July 2013

Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring ‘nontoxic’ provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F2 mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F2 plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker‐assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties.
Physical activity and working memory in healthy older adults: An ERP study
Authors: Chang Yu‐Kai , Huang Chung‐Ju , Chen Kuan‐Fu , Hung Tsung‐Min
Published: July 2013

This study examined the effects of physical activity on working memory in older adults using both behavioral and neuroelectric measures. Older adults were assigned to either a higher or lower physical activity group, and event‐related potentials were recorded during assessments of a modified Sternberg task. The results indicated that older adults in the higher physical activity group exhibited shorter response times, independent of the working memory load. Enhanced P3 and N1 amplitudes and a decreased P3 latency were observed in the higher physical activity group. These findings suggested that physical activity facilitates working memory by allocating more attentional resources and increasing the efficiency of evaluating the stimulus during the retrieval phase as well as engaging more attentional resources for the early discriminative processes during the encoding phase of a working memory task.
Structure and properties of the Adriatic crust in the central‐eastern Southern Alps (Italy) from local earthquake tomography
Authors: Viganò Alfio , Scafidi Davide , Martin Silvana , Spallarossa Daniele
Published: July 2013

Structure and properties of the Adriatic crust were determined from local earthquake tomography around the Giudicarie fault zone (central‐eastern Southern Alps, Italy). Tomographic results, based on well‐suited 436 revised earthquakes (period 1994–2007), have a resolution comparable to the scale of regional geological domains and tectonic structures. The observed strong velocity anomalies correlate well with lithological variations corresponding to different geological domains (particularly magmatic complexes at depth) and with high fracturing and/or presence of fluids along active fault systems (South Giudicarie and Valsugana–Bassano del Grappa–Montello thrusts).
Low‐dose acyclovir prophylaxis for the prevention of herpes simplex virus disease after allogeneic hematopoietic stem cell transplantation
Authors: Kawamura K. , Wada H. , Yamasaki R. , Ishihara Y. , Sakamoto K. , Ashizawa M. , Sato M. , Machishima T. , Terasako K. , Kimura S.‐I. , Kikuchi M. , Nakasone H. , Yamazaki R. , Kanda J. , Kako S. , Tanihara A. , Nishida J. , Kanda Y.
Published: July 2013

Background

Currently, acyclovir (ACV) at 1000 mg/day is widely used as prophylaxis in the early phase of hematopoietic stem cell transplant (HSCT) in Japan. However, low‐dose ACV (200 mg/day) has been shown to prevent varicella zoster virus reactivation in the middle and late phases of HSCT.

Methods

Therefore, in this study, we decreased the dose of ACV to 200 mg/day in the early phase after HSCT. We analyzed 93 consecutive herpes simplex virus (HSV)‐seropositive patients who underwent allogeneic HSCT for the first time in our center between June 2007 and December 2011.

Results

Before August 2009, 38 patients received oral ACV at 1000 mg/day (ACV1000) until day 35 after HSCT, whereas 55 patients received oral ACV at 200 mg/day (ACV200) after September 2009. We compared the cumulative incidence of HSV infection in the 2 groups. Oral ACV was changed to intravenous administration because of intolerance in 66% and 45% of the patients in the ACV1000 and ACV200 groups, respectively (P = 0.060). The probability of severe stomatitis (Bearman grade II–III) was 76% and 60% in the ACV1000 and ACV200 groups, respectively (P = 0.12). The number of patients who developed HSV disease before day 100 after HSCT was 0 in the ACV1000 group and 2 in the ACV200 group, with a cumulative incidence of 3.6% (P = 0.43). HSV disease in the latter 2 patients was limited to the lips and tongue and was successfully treated with ACV or valacyclovir at a treatment dose.

Conclusion

ACV at 200 mg/day appeared to be effective for preventing HSV disease in the early phase after HSCT.
Apical F‐actin‐regulated exocytic targeting of NtPPME1 is essential for construction and rigidity of the pollen tube cell wall
Authors: Wang Hao , Zhuang Xiaohong , Cai Yi , Cheung Alice Y. , Jiang Liwen
Published: July 2013

In tip‐confined growing pollen tubes, delivery of newly synthesized cell wall materials to the rapidly expanding apical surface requires spatial organization and temporal regulation of the apical F‐actin filament and exocytosis. In this study, we demonstrate that apical F‐actin is essential for the rigidity and construction of the pollen tube cell wall by regulating exocytosis of Nicotiana tabacum pectin methylesterase (NtPPME1). Wortmannin disrupts the spatial organization of apical F‐actin in the pollen tube tip and inhibits polar targeting of NtPPME1, which subsequently alters the rigidity and pectic composition of the pollen tube cell wall, finally causing growth arrest of the pollen tube. In addition to mechanistically linking cell wall construction and apical F‐actin, wortmannin can be used as a useful tool for studying endomembrane trafficking and cytoskeletal organization in pollen tubes.
‘Real time’ genetic manipulation: a new tool for ecological field studies
Authors: Schäfer Martin , Brütting Christoph , Gase Klaus , Reichelt Michael , Baldwin Ian , Meldau Stefan
Published: July 2013

Field experiments with transgenic plants often reveal the functional significance of genetic traits that are important for the performance of the plants in their natural environments. Until now, only constitutive overexpression, ectopic expression and gene silencing methods have been used to analyze gene‐related phenotypes in natural habitats. These methods do not allow sufficient control over gene expression for the study of ecological interactions in real time, of genetic traits that play essential roles in development, or of dose‐dependent effects. We applied the sensitive dexamethasone (DEX)‐inducible pOp6/LhGR expression system to the ecological model plant Nicotiana attenuata and established a lanolin‐based DEX application method to facilitate ectopic gene expression and RNA interference‐mediated gene silencing in the field and under challenging conditions (e.g. high temperature, wind and UV radiation). Fully established field‐grown plants were used to silence phytoene desaturase and thereby cause photobleaching only in specific plant sectors, and to activate expression of the cytokinin (CK) biosynthesis gene isopentenyl transferase (ipt). We used ipt expression to analyze the role of CKs in both the glasshouse and the field to understand resistance to the native herbivore Tupiocoris notatus, which attacks plants at small spatial scales. By spatially restricting ipt expression and elevating CK levels in single leaves, damage by T. notatus increased, demonstrating the role of CKs in this plant–herbivore interaction at a small scale. As the arena of most ecological interactions is highly constrained in time and space, these tools will advance the genetic analysis of dynamic traits that matter for plant performance in nature.
Use of 222radon as a simple tool for surface water–groundwater connectivity assessment: a case study in the arid Limarí basin, north‐central Chile
Authors: Oyarzún Ricardo , Jofré Elizabeth , Maturana Hugo , Oyarzún Jorge , Aguirre Evelyn
Published: July 2013

We report the results from a pilot study on the use of 222Rn (222radon) for river–aquifer interaction assessment in the Limarí watershed, north‐central Chile. Previous studies on this tool for such applications are not abundant at international level, and no records exist for Chile. The lowest 222Rn levels (less than 1000 Bq/m3) were found in water reservoirs, thus indicating that this isotope is easily lost (and therefore usually absent) in surface waters. Conversely, the highest levels of 222Rn were found in groundwater, with maxima activities around 20 000 Bq/m3. This remarkable contrast allowed clear identification of zones of surface water–groundwater connectivity in the searched watershed domain.
Patterning of silicon nitride for CMOS gate spacer technology. I. Mechanisms involved in the silicon consumption in CH3F/O2/He high density plasmas
Authors: Blanc Romuald , Leverd François , David Thibaut , Joubert Olivier
Published: July 2013

A loss of silicon in active source/drain regions of CMOS transistors can be observed during nitride spacer etch processes, employing CH3F/O2/He based chemistries in high density plasmas. This phenomenon, the so-called “silicon recess”, is a key criterion for the subsequent steps involved in the transistor fabrication process. In this work, the authors compare two CH3F/O2/He spacer etch processes typically used in industry. The mechanism for high Si3N4/Si selectivity is identified as the creation of a SiOxFy passivation layer, generated at the silicon surface. Using in situ ellipsometry and angle resolved x-ray photoelectron spectroscopy, the authors demonstrate that the oxidized layer which leads to silicon recess is driven by the ion energy. Moreover, in the case of high ion energy processes, implanted carbon has been identified under the SiOxFy passivation layer.
The Chemokine CXCL12 Generates Costimulatory Signals in T Cells to Enhance Phosphorylation and Clustering of the Adaptor Protein SLP-76
Authors: Smith Xin , Schneider Helga , Köhler Karsten , Liu Hebin , Lu Yuning , Rudd Christopher E.
Published: July 2013

Chemokine and antigen signals converge on an adaptor protein to enhance T cell activation.
PTEN Variations
Authors: Ray L. Bryan
Published: July 2013

The phosphatase PTEN works as a lipid phosphatase in the cytoplasm and a protein phosphatase in the nucleus.
Viral Hypoxia Response
Authors: Gough Nancy R.
Published: July 2013

Even under normoxic conditions, vaccinia virus uses the protein C16 to activate the hypoxic response in infected cells.
Pharmacokinetics and Pharmacodynamics of Once-Daily Administration of Intravenous Tobramycin in Adult Patients with Cystic Fibrosis Hospitalized for an Acute Pulmonary Exacerbation
Authors: Butterfield Jill M. , Lodise Thomas P. , Beegle Scott , Rosen Jonathan , Farkas Joshua , Pai Manjunath P.
Published: July 2013

The serum pharmacokinetic profile of intravenous (i.v.) tobramycin administration was characterized for a sample of nine adult patients with cystic fibrosis (CF) who were hospitalized for an acute pulmonary exacerbation. Current recommended i.v. tobramycin dosing protocols are predicted through modeling and simulation to be suboptimal. Empirical tobramycin regimens of ≥15 mg/kg of body weight administered i.v. once daily should be evaluated for adult patients with CF to optimize outcomes.
Dried Blood Spot Analysis Suitable for Therapeutic Drug Monitoring of Voriconazole, Fluconazole, and Posaconazole
Authors: van der Elst Kim C. M. , Span Lambert F. R. , van Hateren Kai , Vermeulen Karin M. , van der Werf Tjip S. , Greijdanus Ben , Kosterink Jos G. W. , Uges Donald R. A. , Alffenaar Jan-Willem C.
Published: July 2013

Invasive aspergillosis and candidemia are important causes of morbidity and mortality in immunocompromised and critically ill patients. The triazoles voriconazole, fluconazole, and posaconazole are widely used for the treatment and prophylaxis of these fungal infections. Due to the variability of the pharmacokinetics of the triazoles among and within individual patients, therapeutic drug monitoring is important for optimizing the efficacy and safety of antifungal treatment. A dried blood spot (DBS) analysis was developed and was clinically validated for voriconazole, fluconazole, and posaconazole in 28 patients. Furthermore, a questionnaire was administered to evaluate the patients' opinions of the sampling method. The DBS analytical method showed linearity over the concentration range measured for all triazoles. Results for accuracy and precision were within accepted ranges; samples were stable at room temperature for at least 12 days; and different hematocrit values and blood spot volumes had no significant influence. The ratio of the drug concentration in DBS samples to that in plasma was 1.0 for voriconazole and fluconazole and 0.9 for posaconazole. Sixty percent of the patients preferred DBS analysis as a sampling method; 15% preferred venous blood sampling; and 25% had no preferred method. There was significantly less perception of pain with the DBS sampling method (
P
= 0.021). In conclusion, DBS analysis is a reliable alternative to venous blood sampling and can be used for therapeutic drug monitoring of voriconazole, fluconazole, and posaconazole. Patients were satisfied with DBS sampling and had less pain than with venous sampling. Most patients preferred DBS sampling to venous blood sampling.
Trimethoprim Resistance of Dihydrofolate Reductase Variants from Clinical Isolates of Pneumocystis jirovecii
Authors: Queener S. F. , Cody V. , Pace J. , Torkelson P. , Gangjee A.
Published: July 2013

Pneumocystis jirovecii
is an opportunistic pathogen that causes serious pneumonia in immunosuppressed patients. Standard therapy and prophylaxis include trimethoprim (TMP)-sulfamethoxazole; trimethoprim in this combination targets dihydrofolate reductase (DHFR). Fourteen clinically observed variants of
P. jirovecii
DHFR were produced recombinantly to allow exploration of the causes of clinically observed failure of therapy and prophylaxis that includes trimethoprim. Six DHFR variants (S31F, F36C, L65P, A67V, V79I, and I158V) showed resistance to inhibition by trimethoprim, with

K
i

values for trimethoprim 4-fold to 100-fold higher than those for the wild-type
P. jirovecii
DHFR. An experimental antifolate with more conformational flexibility than trimethoprim showed strong activity against one trimethoprim-resistant variant. The two variants that were most resistant to trimethoprim (F36C and L65P) also had increased

K
m

values for dihydrofolic acid (DHFA). The catalytic rate constant (
k
cat
) was unchanged for most variant forms of
P. jirovecii
DHFR but was significantly lowered in F36C protein; one naturally occurring variant with two amino acid substitutions (S106P and E127G) showed a doubling of
k
cat
, as well as a

K
m

for NADPH half that of the wild type. The strongest resistance to trimethoprim occurred with amino acid changes in the binding pocket for DHFA or trimethoprim, and the strongest effect on binding of NADPH was linked to a mutation involved in binding the phosphate group of the cofactor. This study marks the first confirmation that naturally occurring mutations in the gene for DHFR from
P. jirovecii
produce variant forms of DHFR that are resistant to trimethoprim and may contribute to clinically observed failures of standard therapy or prophylaxis.
A Novel, Broad-Spectrum Inhibitor of Enterovirus Replication That Targets Host Cell Factor Phosphatidylinositol 4-Kinase IIIβ
Authors: van der Schaar Hilde M. , Leyssen Pieter , Thibaut Hendrik J. , de Palma Armando , van der Linden Lonneke , Lanke Kjerstin H. W. , Lacroix Céline , Verbeken Erik , Conrath Katja , MacLeod Angus M. , Mitchell Dale R. , Palmer Nicholas J. , van de Poël Hervé , Andrews Martin , Neyts Johan , van Kuppeveld Frank J. M.
Published: July 2013

Despite their high clinical and socioeconomic impacts, there is currently no approved antiviral therapy for the prophylaxis or treatment of enterovirus infections. Here we report on a novel inhibitor of enterovirus replication, compound 1, 2-fluoro-4-(2-methyl-8-(3-(methylsulfonyl)benzylamino)imidazo[1,2-
a
]pyrazin-3-yl)phenol. This compound exhibited a broad spectrum of antiviral activity, as it inhibited all tested species of enteroviruses and rhinoviruses, with 50% effective concentrations ranging between 4 and 71 nM. After a lengthy resistance selection process, coxsackievirus mutants resistant to compound 1 were isolated that carried substitutions in their 3A protein. Remarkably, the same substitutions were recently shown to provide resistance to inhibitors of phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ), a lipid kinase that is essential for enterovirus replication, suggesting that compound 1 may also target this host factor. Accordingly, compound 1 directly inhibited PI4KIIIβ in an
in vitro
kinase activity assay. Furthermore, the compound strongly reduced the PI 4-phosphate levels of the Golgi complex in cells. Rescue of coxsackievirus replication in the presence of compound 1 by a mutant PI4KIIIβ carrying a substitution in its ATP-binding pocket revealed that the compound directly binds the kinase at this site. Finally, we determined that an analogue of compound 1, 3-(3-fluoro-4-methoxyphenyl)-2-methyl-
N
-(pyridin-4-ylmethyl)imidazo[1,2-
a
]pyrazin-8-amine, is well tolerated in mice and has a dose-dependent protective activity in a coxsackievirus serotype B4-induced pancreatitis model.
Complete Nucleotide Sequence of a
bla
KPC
-Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals
Authors: Chen Liang , Chavda Kalyan D. , Al Laham Nahed , Melano Roberto G. , Jacobs Michael R. , Bonomo Robert A. , Kreiswirth Barry N.
Published: July 2013

Klebsiella pneumoniae
carbapenemase (KPC)-producing
K. pneumoniae
strains have spread worldwide and become a significant public health threat.
bla
KPC
, the plasmid-borne KPC gene, was frequently identified on numerous transferable plasmids in different incompatibility replicon groups. Here we report the complete nucleotide sequence of a novel
bla
KPC-3
-harboring IncI2 plasmid, pBK15692, isolated from a multidrug-resistant
K. pneumoniae
ST258 strain isolated from a New Jersey hospital in 2005. pBK15692 is 78 kb in length and carries a backbone that is similar to those of other IncI2 plasmids (pR721, pChi7122-3, pHN1122-1, and pSH146-65), including the genes encoding type IV pili and shufflon regions. Comparative genomics analysis of IncI2 plasmids reveals that they possess a conserved plasmid backbone but are divergent with respect to the integration sites of resistance genes. In pBK15692, the
bla
KPC-3
-harboring Tn
4401
was inserted into a Tn
1331
element and formed a nested transposon. A PCR scheme was designed to detect the prevalence of IncI2 and pBK15692-like plasmids from a collection of clinical strains from six New Jersey and New York hospitals isolated between 2007 and 2011. IncI2 plasmids were found in 46.2% isolates from 318 clinical
K. pneumoniae
strains. Notably, 59 pBK15692-like plasmids (23%) have been identified in 256 KPC-bearing
K. pneumoniae
strains, and all carried KPC-3 and belong to the epidemic ST258 clone. Our study revealed that the prevalence of IncI2 plasmids has been considerably underestimated. Further studies are needed to understand the distribution of this plasmid group in other health care regions and decipher the association between IncI2 plasmids and
bla
KPC-3
-bearing ST258 strains.
Analysis of Antibodies to Newly Described Plasmodium falciparum Merozoite Antigens Supports MSPDBL2 as a Predicted Target of Naturally Acquired Immunity
Authors: Tetteh Kevin K. A. , Osier Faith H. A. , Salanti Ali , Kamuyu Gathoni , Drought Laura , Failly Marilyne , Martin Christophe , Marsh Kevin , Conway David J.
Published: July 2013

Prospective studies continue to identify malaria parasite genes with particular patterns of polymorphism which indicate they may be under immune selection, and the encoded proteins require investigation. Sixteen new recombinant protein reagents were designed to characterize three such polymorphic proteins expressed in
Plasmodium falciparum
schizonts and merozoites: MSPDBL1 (also termed MSP3.4) and MSPDBL2 (MSP3.8), which possess Duffy binding-like (DBL) domains, and SURFIN4.2, encoded by a member of the surface-associated interspersed (
surf
) multigene family. After testing the antigenicities of these reagents by murine immunization and parasite immunofluorescence, we analyzed naturally acquired antibody responses to the antigens in two cohorts in coastal Kenya in which the parasite was endemic (Chonyi [
n
= 497] and Ngerenya [
n
= 461]). As expected, the prevalence and levels of serum antibodies increased with age. We then investigated correlations with subsequent risk of clinical malaria among children <11 years of age during 6 months follow-up surveillance. Antibodies to the polymorphic central region of MSPDBL2 were associated with reduced risk of malaria in both cohorts, with statistical significance remaining for the 3D7 allelic type after adjustment for individuals' ages in years and antibody reactivity to whole-schizont extract (Chonyi, risk ratio, 0.51, and 95% confidence interval [CI], 0.28 to 0.93; Ngerenya, risk ratio, 0.38, and 95% CI, 0.18 to 0.82). For the MSPDBL1 Palo Alto allelic-type antigen, there was a protective association in one cohort (Ngerenya, risk ratio, 0.53, and 95% CI, 0.32 to 0.89), whereas the other antigens showed no protective associations after adjustment. These findings support the prediction that antibodies to the polymorphic region of MSPDBL2 contribute to protective immunity.
LuxR Homologue SmcR Is Essential for Vibrio vulnificus Pathogenesis and Biofilm Detachment, and Its Expression is Induced by Host Cells
Authors: Kim Seung Min , Park Jin Hwan , Lee Hyun Sung , Kim Won Bin , Ryu Jung Min , Han Ho Jae , Choi Sang Ho
Published: July 2013

Quorum sensing is a cell-to-cell communication system known to control many bacterial processes. In the present study, the functions of quorum sensing in the pathogenesis of
Vibrio vulnificus
, a food-borne pathogen, were assessed by evaluating the virulence of a mutant deficient in SmcR, a quorum-sensing regulator and homologue of LuxR. When biofilms were used as an inoculum, the
smcR
mutant was impaired in virulence and colonization capacity in the infection of mice. The lack of SmcR also resulted in decreased histopathological damage in mouse jejunum tissue. These results indicated that SmcR is essential for
V. vulnificus
pathogenesis. Moreover, the
smcR
mutant exhibited significantly reduced biofilm detachment. Upon exposure to INT-407 host cells, the wild type, but not the
smcR
mutant, revealed accelerated biofilm detachment. The INT-407 cells increased
smcR
expression by activating the expression of LuxS, an autoinducer-2 synthase, indicating that host cells manipulate the cellular level of SmcR through the quorum-sensing signaling of
V. vulnificus
. A whole-genome microarray analysis revealed that the genes primarily involved in biofilm detachment and formation are up- and downregulated by SmcR, respectively. Among the SmcR-regulated genes,
vvpE
encoding an elastolytic protease was the most upregulated, and the purified VvpE appeared to dissolve established biofilms directly in a concentration-dependent manner
in vitro
. These results suggest that the host cell-induced SmcR enhances the detachment of
V. vulnificus
biofilms entering the host intestine and thereby may promote the dispersal of the pathogen to new colonization loci, which is crucial for pathogenesis.