bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lysobacter enzymogenes Uses Two Distinct Cell-Cell Signaling Systems for Differential Regulation of Secondary-Metabolite Biosynthesis and Colony Morphology
Authors: Qian Guoliang , Wang Yulan , Liu Yiru , Xu Feifei , He Ya-Wen , Du Liangcheng , Venturi Vittorio , Fan Jiaqin , Hu Baishi , Liu Fengquan 
Published: August 2013

ABSTRACT

Lysobacter enzymogenes
is a ubiquitous environmental bacterium that is emerging as a potentially novel biological control agent and a new source of bioactive secondary metabolites, such as the heat-stable antifungal factor (HSAF) and photoprotective polyene pigments. Thus far, the regulatory mechanism(s) for biosynthesis of these bioactive secondary metabolites remains largely unknown in
L. enzymogenes
. In the present study, the diffusible signal factor (DSF) and diffusible factor (DF)-mediated cell-cell signaling systems were identified for the first time from
L. enzymogenes
. The results show that both Rpf/DSF and DF signaling systems played critical roles in modulating HSAF biosynthesis in
L. enzymogenes
. Rpf/DSF signaling and DF signaling played negative and positive effects in polyene pigment production, respectively, with DF playing a more important role in regulating this phenotype. Interestingly, only Rpf/DSF, but not the DF signaling system, regulated colony morphology of
L. enzymgenes
. Both Rpf/DSF and DF signaling systems were involved in the modulation of expression of genes with diverse functions in
L. enzymogenes
, and their own regulons exhibited only a few loci that were regulated by both systems. These findings unveil for the first time new roles of the Rpf/DSF and DF signaling systems in secondary metabolite biosynthesis of
L. enzymogenes
.
Moderate Prevalence of Antimicrobial Resistance in Escherichia coli Isolates from Lettuce, Irrigation Water, and Soil
Authors: Holvoet Kevin , Sampers Imca , Callens Benedicte , Dewulf Jeroen , Uyttendaele Mieke 
Published: August 2013

ABSTRACT

Fresh produce is known to carry nonpathogenic epiphytic microorganisms. During agricultural production and harvesting, leafy greens can become contaminated with antibiotic-resistant pathogens or commensals from animal and human sources. As lettuce does not undergo any inactivation or preservation treatment during processing, consumers may be exposed directly to all of the (resistant) bacteria present. In this study, we investigated whether lettuce or its production environment (irrigation water, soil) is able to act as a vector or reservoir of antimicrobial-resistant
Escherichia coli
. Over a 1-year period, eight lettuce farms were visited multiple times and 738 samples, including lettuce seedlings (leaves and soil), soil, irrigation water, and lettuce leaves were collected. From these samples, 473 isolates of
Escherichia coli
were obtained and tested for resistance to 14 antimicrobials. Fifty-four isolates (11.4%) were resistant to one or more antimicrobials. The highest resistance rate was observed for ampicillin (7%), followed by cephalothin, amoxicillin-clavulanic acid, tetracycline, trimethoprim, and streptomycin, with resistance rates between 4.4 and 3.6%. No resistance to amikacin, ciprofloxacin, gentamicin, or kanamycin was observed. One isolate was resistant to cefotaxime. Among the multiresistant isolates (
n
= 37), ampicillin and cephalothin showed the highest resistance rates, at 76 and 52%, respectively.
E. coli
isolates from lettuce showed higher resistance rates than
E. coli
isolates obtained from soil or irrigation water samples. When the presence of resistance in
E. coli
isolates from lettuce production sites and their resistance patterns were compared with the profiles of animal-derived
E. coli
strains, they were found to be the most comparable with what is found in the cattle reservoir. This may suggest that cattle are a potential reservoir of antimicrobial-resistant
E. coli
strains in plant primary production.
Insertion of Endocellulase Catalytic Domains into Thermostable Consensus Ankyrin Scaffolds: Effects on Stability and Cellulolytic Activity
Authors: Cunha Eva S. , Hatem Christine L. , Barrick Doug 
Published: August 2013

ABSTRACT

Degradation of cellulose for biofuels production holds promise in solving important environmental and economic problems. However, the low activities (and thus high enzyme-to-substrate ratios needed) of hydrolytic cellulase enzymes, which convert cellulose into simple sugars, remain a major barrier. As a potential strategy to stabilize cellulases and enhance their activities, we have embedded cellulases of extremophiles into hyperstable α-helical consensus ankyrin domain scaffolds. We found the catalytic domains CelA (CA, GH8;
Clostridium thermocellum
) and Cel12A (C12A, GH12;
Thermotoga maritima
) to be stable in the context of the ankyrin scaffold and to be active against both soluble and insoluble substrates. The ankyrin repeats in each fusion are folded, although it appears that for the C12A
c
atalytic
d
omain (CD; where the N and C termini are distant in the crystal structure), the two flanking ankyrin domains are independent, whereas for CA (where termini are close), the flanking ankyrin domains stabilize each other. Although the activity of CA is unchanged in the context of the ankyrin scaffold, the activity of C12A is increased between 2- and 6-fold (for regenerated amorphous cellulose and carboxymethyl cellulose substrates) at high temperatures. For C12A, activity increases with the number of flanking ankyrin repeats. These results showed ankyrin arrays to be a promising scaffold for constructing designer cellulosomes, preserving or enhancing enzymatic activity and retaining thermostability. This modular architecture will make it possible to arrange multiple cellulase domains at a precise spacing within a single polypeptide, allowing us to search for spacings that may optimize reactivity toward the repetitive cellulose lattice.
bZIP Transcription Factors in the Oomycete Phytophthora infestans with Novel DNA-Binding Domains Are Involved in Defense against Oxidative Stress
Authors: Gamboa-Meléndez Heber , Huerta Apolonio I. , Judelson Howard S. 
Published: August 2013

ABSTRACT

Transcription factors of the basic leucine zipper (bZIP) family control development and stress responses in eukaryotes. To date, only one bZIP has been described in any oomycete; oomycetes are members of the stramenopile kingdom. In this study, we describe the identification of 38 bZIPs from the
Phytophthora infestans
genome. Half contain novel substitutions in the DNA-binding domain at a site that in other eukaryotes is reported to always be Asn. Interspecific comparisons indicated that the novel substitutions (usually Cys, but also Val and Tyr) arose after oomycetes diverged from other stramenopiles. About two-thirds of
P. infestans
bZIPs show dynamic changes in mRNA levels during the life cycle, with many of the genes being upregulated in sporangia, zoospores, or germinated zoospore cysts. One bZIP with the novel Cys substitution was shown to reside in the nucleus throughout growth and development. Using stable gene silencing, the functions of eight bZIPs with the Cys substitution were tested. All but one were found to play roles in protecting
P. infestans
from hydrogen peroxide-induced injury, and it is proposed that the novel Cys substitution serves as a redox sensor. A ninth bZIP lacking the novel Asn-to-Cys substitution, but having Cys nearby, was also shown through silencing to contribute to defense against peroxide. Little effect on asexual development, plant pathogenesis, or resistance to osmotic stress was observed in transformants silenced for any of the nine bZIPs.
Novel Feature of Mycobacterium avium subsp. paratuberculosis, Highlighted by Characterization of the Heparin-Binding Hemagglutinin Adhesin
Authors: Lefrancois Louise H. , Bodier Christelle C. , Cochard Thierry , Canepa Sylvie , Raze Dominique , Lanotte Philippe , Sevilla Iker A. , Stevenson Karen , Behr Marcel A. , Locht Camille , Biet Franck 
Published: August 2013

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
comprises two genotypically defined groups, known as the cattle (C) and sheep (S) groups. Recent studies have reported phenotypic differences between
M. avium
subsp.
paratuberculosis
groups C and S, including growth rates, infectivity for macrophages, and iron metabolism. In this study, we investigated the genotypes and biological properties of the virulence factor heparin-binding hemagglutinin adhesin (HBHA) for both groups. In
Mycobacterium tuberculosis
, HBHA is a major adhesin involved in mycobacterium-host interactions and extrapulmonary dissemination of infection. To investigate HBHA in
M. avium
subsp.
paratuberculosis
, we studied
hbhA
polymorphisms by fragment analysis using the GeneMapper technology across a large collection of isolates genotyped by mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) and IS
900
restriction fragment length polymorphism (RFLP-IS
900
) analyses. Furthermore, we analyzed the structure-function relationships of recombinant HBHA proteins of types C and S by heparin-Sepharose chromatography and surface plasmon resonance (SPR) analyses.
In silico
analysis revealed two forms of HBHA, corresponding to the prototype genomes for the C and S types of
M. avium
subsp.
paratuberculosis
. This observation was confirmed using GeneMapper on 85
M. avium
subsp.
paratuberculosis
strains, including 67 strains of type C and 18 strains of type S. We found that HBHAs from all type C strains contain a short C-terminal domain, while those of type S present a long C-terminal domain, similar to that produced by
Mycobacterium avium
subsp.
avium
. The purification of recombinant HBHA from
M. avium
subsp.
paratuberculosis
of both types by heparin-Sepharose chromatography highlighted a correlation between their affinities for heparin and the lengths of their C-terminal domains, which was confirmed by SPR analysis. Thus, types C and S of
M. avium
subsp.
paratuberculosis
may be distinguished by the types of HBHA they produce, which differ in size and adherence properties, thereby providing new evidence that strengthens the genotypic differences between the C and S types of
M. avium
subsp.
paratuberculosis
.
Assessment of the impact on time to complete medical record using an electronic medical record versus a paper record on emergency department patients: a study
Authors: Perry Jeffrey J , Sutherland Jane , Symington Cheryl , Dorland Katie , Mansour Marlene , Stiell Ian G 
Published: August 2013

BackgroundElectronic medical records are becoming an integral part of healthcare delivery.ObjectiveThe goal of this study was to compare paper documentation versus electronic medical record for non-traumatic chest pain to determine differences in time for physicians to complete medical records using paper versus electronic mediums. We also assessed physician satisfaction with the electronic format.MethodsWe conducted this before-after study in a single large tertiary care academic emergency department. In the ‘Before Period’, stopwatches determined the time for paper medical recording. In the ‘After Period’, a template-based electronic medical record was introduced and the time for electronic recording was measured. The time to record in the before and after periods were compared using a two-sided t test. We surveyed physicians to assess satisfaction.ResultsWe enrolled 100 non-traumatic patients with chest pain in the before period and 73 in the after period. The documentation time was longer using electronic charting, (9.6±5.9 min vs 6.1±2.5 min; p<0.001). 18 of 20 physicians participating in the after period completed surveys. Physicians were not satisfied with the electronic patient recording for non-traumatic chest pain.ConclusionsThis is the first study that we are aware of which compared paper versus electronic medical records in the emergency department. Electronic recording took longer than paper records. Physicians were not satisfied using this electronic record. Given the time pressures on emergency physicians, a solution to minimise the charting time using electronic medical records must be found before widespread uptake of electronic charting will be possible.
Waveform Analysis–Guided Treatment Versus a Standard Shock-First Protocol for the Treatment of Out-of-Hospital Cardiac Arrest Presenting in Ventricular Fibrillation
Authors: Freese John P. , Jorgenson Dawn B. , Liu Ping-Yu , Innes Jennifer , Matallana Luis , Nammi Krishnakant , Donohoe Rachael T. , Whitbread Mark , Silverman Robert A. , Prezant David J. 
Published: August 2013

Background—
Ventricular fibrillation (VF) waveform properties have been shown to predict defibrillation success and outcomes among patients treated with immediate defibrillation. We postulated that a waveform analysis algorithm could be used to identify VF unlikely to respond to immediate defibrillation, allowing selective initial treatment with cardiopulmonary resuscitation in an effort to improve overall survival.

Methods and Results—

In a multicenter, double-blind, randomized study, out-of-hospital cardiac arrest patients in 2 urban emergency medical services systems were treated with automated external defibrillators using either a VF waveform analysis algorithm or the standard shock-first protocol. The VF waveform analysis used a predefined threshold value below which return of spontaneous circulation (ROSC) was unlikely with immediate defibrillation, allowing selective treatment with a 2-minute interval of cardiopulmonary resuscitation before initial defibrillation. The primary end point was survival to hospital discharge. Secondary end points included ROSC, sustained ROSC, and survival to hospital admission. Of 6738 patients enrolled, 987 patients with VF of primary cardiac origin were included in the primary analysis. No immediate or long-term survival benefit was noted for either treatment algorithm (ROSC, 42.5% versus 41.2%,
P
=0.70; sustained ROSC, 32.4% versus 33.4%,
P
=0.79; survival to admission, 34.1% versus 36.4%,
P
=0.46; survival to hospital discharge, 15.6% versus 17.2%,
P
=0.55, respectively).

Conclusions—
Use of a waveform analysis algorithm to guide the initial treatment of out-of-hospital cardiac arrest patients presenting in VF did not improve overall survival compared with a standard shock-first protocol. Further study is recommended to examine the role of waveform analysis for the guided management of VF.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00535106.
Influences of the Pacific–Japan Teleconnection Pattern on Synoptic-Scale Variability in the Western North Pacific
Authors: Li Richard C. Y. , Zhou Wen , Li Tim 
Published: August 2013

Abstract
This study investigates the influences of the Pacific–Japan (PJ) teleconnection pattern on synoptic-scale variability (SSV) in the western North Pacific (WNP). The PJ pattern exhibits salient intraseasonal variations, with a dominant peak at 10–50 days. During positive PJ phases, strengthened SSV is found in the WNP, with a much stronger and better organized synoptic wave train structure. Such a synoptic-scale wave train, however, is greatly weakened during negative PJ phases. Examination of the vertical profiles of the observational data suggests that environmental parameters are generally more (less) favorable for the growth of synoptic disturbances under positive (negative) PJ conditions.
Observational results are further verified with an anomaly atmospheric general circulation model, which reveals faster (slower) growth of the synoptic-scale wave train when the environmental anomalies associated with positive (negative) PJ phases are incorporated into the summer mean state of the model. In addition, sensitivity experiments indicate that thermodynamic parameters of the planetary boundary layer (PBL) play a determining role in controlling the development of synoptic disturbances in the WNP. The increase (decrease) in background PBL moisture during positive (negative) PJ phases enhances (suppresses) perturbation moisture convergence and thus the convective heating associated with SSV, leading to strengthened (weakened) synoptic-scale activity in the WNP. Serving as potential seed disturbances for cyclogenesis, the strengthened (weakened) synoptic-scale activity may also contribute to the enhancement (suppression) in intraseasonal TC frequency during positive (negative) PJ phases.
Small-Scale Variability in Sea Surface Salinity and Implications for Satellite-Derived Measurements
Authors: Vinogradova Nadya T. , Ponte Rui M. 
Published: August 2013

Abstract
Calibration and validation efforts of the Aquarius and Soil Moisture and Ocean Salinity (SMOS) satellite missions involve comparisons of satellite and in situ measurements of sea surface salinity (SSS). Such estimates of SSS can differ by the presence of small-scale variability, which can affect the in situ point measurement, but be averaged out in the satellite retrievals because of their large footprint. This study quantifies how much of a difference is expected between in situ and satellite SSS measurements on the basis of their different sampling of spatial variability. Maps of sampling error resulting from small-scale noise, defined here as the root-mean-square difference between “local” and footprint-averaged SSS estimates, are derived using a solution from a global high-resolution ocean data assimilation system. The errors are mostly &lt;0.1 psu (global median is 0.05 psu), but they can be &gt;0.2 psu in several regions, particularly near strong currents and outflows of major rivers. To examine small-scale noise in the context of other errors, its values are compared with the overall expected differences between monthly Aquarius SSS and Argo-based estimates. Results indicate that in several ocean regions, small-scale variability can be an important source of sampling error for the in situ measurements.
mRNA-engineered mesenchymal stem cells for targeted delivery of interleukin-10 to sites of inflammation
Authors: Levy Oren , Zhao Weian , Mortensen Luke J. , LeBlanc Sarah , Tsang Kyle , Fu Moyu , Phillips Joseph A. , Sagar Vinay , Anandakumaran Priya , Ngai Jessica , Cui Cheryl H. , Eimon Peter , Angel Matthew , Lin Charles P. , Yanik Mehmet Fatih , Karp Jeffrey M. 
Published: August 2013

Key Points
mRNA transfection is an effective tool to simultaneously engineer MSCs for enhanced homing and improved secretome. MSCs can be systemically targeted to sites of inflammation to achieve therapeutically relevant concentrations of biological agents.
A novel method to assess collagen architecture in skin
Authors: Osman Osman S , Selway Joanne L , Harikumar Parvathy E , Stocker Claire J , Wargent Edward T , Cawthorne Michael A , Jassim Sabah , Langlands Kenneth 
Published: August 2013

Abstract

Background
Texture within biological specimens may reveal critical insights, while being very difficult to quantify. This is a particular problem in histological analysis. For example, cross-polar images of picrosirius stained skin reveal exquisite structure, allowing changes in the basketweave conformation of healthy collagen to be assessed. Existing techniques measure gross pathological changes, such as fibrosis, but are not sufficiently sensitive to detect more subtle and progressive pathological changes in the dermis, such as those seen in ageing. Moreover, screening methods for cutaneous therapeutics require accurate, unsupervised and high-throughput image analysis techniques.

Results
By analyzing spectra of images post Gabor filtering and Fast Fourier Transform, we were able to measure subtle changes in collagen fibre orientation intractable to existing techniques. We detected the progressive loss of collagen basketweave structure in a series of chronologically aged skin samples, as well as in skin derived from a model of type 2 diabetes mellitus.

Conclusions
We describe a novel bioimaging approach with implications for the evaluation of pathology in a broader range of biological situations.
Genetic variation in brown trout Salmo truttaacross the Danube, Rhine, and Elbe headwaters: a failure of the phylogeographic paradigm?
Authors: Lerceteau-Köhler Estelle , Schliewen Ulrich , Kopun Theodora , Weiss Steven 
Published: August 2013

AbstractBackgroundBrown troutSalmo truttahave been described in terms of five major mtDNA lineages, four of which correspond to major ocean basins, and one, according to some authors, to a distinct taxon, marbled troutSalmo marmoratus. The Atlantic and Danubian lineages of brown trout meet in a poorly documented contact zone in Central Europe. The natural versus human mediated origin of the Atlantic lineage in the upper Danube is a question of both theoretical and practical importance with respect to conservation management. We provide a comprehensive population genetic analysis of brown trout in the region with the aim of evaluating the geographic distribution and genetic integrity of these two lineages in and around their contact zone.ResultsGenetic screening of 114 populations of brown trout across the Danube/Rhine/Elbe catchments revealed a counter-intuitive phylogeographic structure with near fixation of the Atlantic lineage in the sampled portions of the Bavarian Danube. Along the Austrian Danube, phylogeographic informative markers revealed increasing percentages of Danube-specific alleles with downstream distance. Pure Danube lineage populations were restricted to peri-alpine isolates within previously glaciated regions. Both empirical data and simulated hybrid comparisons support that trout in non-glaciated regions north and northeast of the Alps have an admixed origin largely based on natural colonization. In contrast, the presence of Atlantic basin alleles south and southeast of the Alps stems from hatchery introductions and subsequent introgression. Despite extensive stocking of the Atlantic lineage, little evidence of first generation stocked fish or F1hybrids were found implying that admixture has been established over time.ConclusionsA purely phylogeographic paradigm fails to describe the distribution of genetic lineages ofSalmoin Central Europe. The distribution pattern of the Atlantic and Danube lineages is extremely difficult to explain without invoking very strong biological mechanisms.The peri-alpine distribution of relict populations of pure Danubian lineage brown trout implies that they colonized headwater river courses post-glacially ahead of the expansion of the Atlantic lineage. The recognition of natural as opposed to anthropogenic introgression of the Atlantic lineage into Danubian gene pools is of fundamental importance to management strategies.