bluuebunny/crossref_metadata_2025_split huggingface dataset:
Denitrification and Nitrogen Fixation Dynamics in the Area Surrounding an Individual Ghost Shrimp (Neotrypaea californiensis) Burrow System
Authors: Bertics Victoria J. , Sohm Jill A. , Magnabosco Cara , Ziebis Wiebke 
Published: March 2012

ABSTRACT

Bioturbated sediments are thought of as areas of increased denitrification or fixed-nitrogen (N) loss; however, recent studies have suggested that not all N may be lost from these environments, with some N returning to the system via microbial dinitrogen (N
2
) fixation. We investigated denitrification and N
2
fixation in an intertidal lagoon (Catalina Harbor, CA), an environment characterized by bioturbation by thalassinidean shrimp (
Neotrypaea californiensis
). Field studies were combined with detailed measurements of denitrification and N
2
fixation surrounding a single ghost shrimp burrow system in a narrow aquarium (15 cm by 20 cm by 5 cm). Simultaneous measurements of both activities were performed on samples taken within a 1.5-cm grid for a two-dimensional illustration of their intensity and distribution. These findings were then compared with rate measurements performed on bulk environmental sediment samples collected from the lagoon. Results for the aquarium indicated that both denitrification and N
2
fixation have a patchy distribution surrounding the burrow, with no clear correlation to each other, sediment depth, or distance from the burrow. Field denitrification rates were, on average, lower in a bioturbated region than in a seemingly nonbioturbated region; however, replicates showed very high variability. A comparison of denitrification field results with previously reported N
2
fixation rates from the same lagoon showed that in the nonbioturbated region, depth-integrated (10 cm) denitrification rates were higher than integrated N
2
fixation rates (∼9 to 50 times). In contrast, in the bioturbated sediments, depending on the year and bioturbation intensity, some (∼6.2%) to all of the N lost via denitrification might be accounted for via N
2
fixation.
Intramolecular Regulation of the Sequence-Specific mRNA Interferase Activity of MazF Fused to a MazE Fragment with a Linker Cleavable by Specific Proteases
Authors: Park Jung-Ho , Yamaguchi Yoshihiro , Inouye Masayori 
Published: March 2012

ABSTRACT

The genomes of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) consist of single-stranded RNA encoding polyproteins, which are processed to individual functional proteins by virus-encoded specific proteases. These proteases have been used as targets for drug development. Here, instead of targeting these proteases to inhibit viral infection, we utilized the protease activity to activate a toxic protein to prevent viral infection. We engineered the MazE-MazF antitoxin-toxin system of
Escherichia coli
to fuse a C-terminal 41-residue fragment of antitoxin MazE to the N-terminal end of toxin MazF with a linker having a specific protease cleavage site for either HIV PR (HIV-1 protease), NS3 protease (HCV protease), or factor Xa. These fusion proteins formed a stable dimer (instead of the MazF
2
-MazE
2
-MazF
2
heterohexamer in nature) to inactivate the ACA (sequence)-specific mRNA interferase activity of MazF. When the fusion proteins were incubated with the corresponding proteases, the MazE fragment was cleaved from the fusion proteins, releasing active MazF, which then acted as an ACA-specific mRNA interferase cleaving single-stranded MS2 phage RNA. The intramolecular regulation of MazF toxicity by proteases as demonstrated may provide a novel approach for preventive and therapeutic treatments of infection by HIV-1, HCV, and other single-stranded RNA viruses.
Antimicrobial Resistance in Escherichia coli Isolates from Raccoons (Procyon lotor) in Southern Ontario, Canada
Authors: Jardine Claire M. , Janecko Nicol , Allan Mike , Boerlin Patrick , Chalmers Gabhan , Kozak Gosia , McEwen Scott A. , Reid-Smith Richard J. 
Published: March 2012

ABSTRACT

We conducted a cross-sectional study to determine the prevalence of antimicrobial resistance (AMR) in fecal
Escherichia coli
isolates from raccoons (
Procyon lotor
) living in Ontario, Canada. From June to October 2007, we trapped raccoons in three areas: one primarily urban site around Niagara, one primarily rural site north of Guelph, and one at the Toronto Zoo. In addition, we conducted a longitudinal study at the Toronto Zoo site to investigate the temporal dynamics of fecal
E. coli
and AMR in raccoons. Reduced susceptibility to ≥1 antimicrobial agent was detected in
E. coli
isolates from 19% of 16 raccoons at the urban site, 17% of 29 raccoons from the rural site, and 42% of 130 samples collected from 59 raccoons at the zoo site. Raccoons from the zoo site were significantly more likely to shed
E. coli
with reduced susceptibility to ≥1 antimicrobial agent than animals from the rural site (odds ratio [OR], 3.41; 95% confidence interval [CI], 1.17 to 12.09;
P
= 0.02). Resistance to expanded-spectrum cephalosporins (and the associated
bla
CMY-2
gene) was detected in two animals from the zoo site and one animal from the rural site. Serotyping and pulsed-field gel electrophoresis analysis show that raccoons on the zoo grounds harbor a diverse assemblage of
E. coli
, with rapid bacterial turnover within individuals over time. Our study indicates that raccoons may shed resistant bacteria of public health significance and that raccoons have the potential to disseminate these bacteria throughout their environment.
Production of
l
-Ribose from
l
-Ribulose by a Triple-Site Variant of Mannose-6-Phosphate Isomerase from Geobacillus thermodenitrificans
Authors: Lim Yu-Ri , Yeom Soo-Jin , Oh Deok-Kun 
Published: March 2012

ABSTRACT

A triple-site variant (W17Q N90A L129F) of mannose-6-phosphate isomerase from
Geobacillus thermodenitrificans
was obtained by combining variants with residue substitutions at different positions after random and site-directed mutagenesis. The specific activity and catalytic efficiency (
k
cat
/
K

m

) for
l
-ribulose isomerization of this variant were 3.1- and 7.1-fold higher, respectively, than those of the wild-type enzyme at pH 7.0 and 70°C in the presence of 1 mM Co
2+
. The triple-site variant produced 213 g/liter
l
-ribose from 300 g/liter
l
-ribulose for 60 min, with a volumetric productivity of 213 g liter
−1
h
−1
, which was 4.5-fold higher than that of the wild-type enzyme. The
k
cat
/
K

m

and productivity of the triple-site variant were approximately 2-fold higher than those of the
Thermus thermophilus
R142N variant of mannose-6-phosphate isomerase, which exhibited the highest values previously reported.
Novel Phakopsora pachyrhizi Extracellular Proteins Are Ideal Targets for Immunological Diagnostic Assays
Authors: Luster Douglas G. , McMahon Michael B. , Edwards H. Herb , Boerma Britney L. , Lewis Ivey Melanie L. , Miller Sally A. , Dorrance Anne E. 
Published: March 2012

ABSTRACTPhakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), continues to spread across the southeast and midsouth regions of the United States, necessitating the use of fungicides by producers. Our objective in this research was to identify ASR proteins expressed early during infection for the development of immunodiagnostic assays. We have identified and partially characterized a small gene family encoding extracellular proteins in theP. pachyrhiziurediniospore wall, termed PHEPs (forPhakopsoraextracellularprotein). Two highly expressed protein family members, PHEP 107 and PHEP 369, were selected as ideal immunodiagnostic targets for antibody development, after we detected PHEPs in plants as early as 3 days postinfection (dpi). Monoclonal antibodies (MAbs; 2E8E5-1 and 3G6H7-3) generated against recombinant PHEP 369 were tested for sensitivity against the recombinant protein and extracts from ASR-infected plants and for specificity against a set of common soybean pathogens. These antibodies should prove applicable in immunodiagnostic assays to detect infected soybeans and to identify ASR spores from sentinel surveillance plots.
New Sequence Types and Multidrug Resistance among Pathogenic Escherichia coli Isolates from Coastal Marine Sediments
Authors: Vignaroli C. , Luna G. M. , Rinaldi C. , Di Cesare A. , Danovaro R. , Biavasco F. 
Published: March 2012

ABSTRACT

The spread of antibiotic-resistant microorganisms is widely recognized, but data about their sources, presence, and significance in marine environments are still limited. We examined 109
Escherichia coli
strains from coastal marine sediments carrying virulence genes for antibiotic susceptibility, specific resistance genes, prevalence of class 1 and 2 integrons, and sequence type. Antibiotic resistance was found in 35% of strains, and multiple resistances were found in 14%; the resistances detected most frequently were against tetracycline (28%), ampicillin (16.5%), trimethoprim-sulfamethoxazole (13%), and streptomycin (7%). The highest prevalence of resistant strains was in phylogenetic group A, whereas phylogroup B2 exhibited a significantly lower frequency than all the other groups. Sixty percent of multiresistant strains harbored class 1 or 2 integrase genes, and about 50% carried resistance genes (particularly
dfrA
and
aadA
) linked to a class 1 integron. Multilocus sequence typing of 14 selected strains identified eight different types characteristic of extraintestinal pathogens and three new allelic combinations. Our data suggest that coastal marine sediment may be a suitable environment for the survival of pathogenic and antimicrobial-resistant
E. coli
strains capable of contributing to resistance spread via integrons among benthic bacteria, and they highlight a role for these strains in the emergence of new virulent genotypes.
CcrR, a TetR Family Transcriptional Regulator, Activates the Transcription of a Gene of the Ethylmalonyl Coenzyme A Pathway in Methylobacterium extorquens AM1
Authors: Hu Bo , Lidstrom Mary 
Published: March 2012

ABSTRACT

The ethylmalonyl coenzyme A (ethylmalonyl-CoA) pathway is one of the central methylotrophy pathways in
Methylobacterium extorquens
involved in glyoxylate generation and acetyl-CoA assimilation. Previous studies have elucidated the operation of the ethylmalonyl-CoA pathway in C
1
and C
2
assimilation, but the regulatory mechanisms for the ethylmalonyl-CoA pathway have not been reported. In this study, a TetR-type activator, CcrR, was shown to regulate the expression of crotonyl-CoA reductase/carboxylase, an enzyme of the ethylmalonyl-CoA pathway involved in the assimilation of C
1
and C
2
compounds in
Methylobacterium extorquens
AM1. A
ccrR
null mutant strain was impaired in its ability to grow on C
1
and C
2
compounds, correlating with the reduced activity of crotonyl-CoA reductase/carboxylase. Promoter fusion assays demonstrated that the activity of the promoter required for
ccr
expression (the
katA-ccr
promoter) decreased as much as 50% in the absence of
ccrR
compared to wild-type
M. extorquens
AM1. Gel mobility shift assays confirmed that CcrR directly binds to the region upstream of the
katA-ccr
promoter. A palindromic sequence upstream of
katA
at positions −334 to −321 with respect to the predicted translational start site was identified, and mutations in this region eliminated the gel retardation of the
katA-ccr
promoter region by CcrR. CcrR does not appear to regulate the expression of other ethylmalonyl-CoA pathway genes, suggesting the existence of additional regulators.
Analyses of MbtB, MbtE, and MbtF Suggest Revisions to the Mycobactin Biosynthesis Pathway in Mycobacterium tuberculosis
Authors: McMahon Matthew D. , Rush Jason S. , Thomas Michael G. 
Published: March 2012

ABSTRACT

The production of mycobactin (MBT) by
Mycobacterium tuberculosis
is essential for this bacterium to access iron when it is in an infected host. Due to this essential function, there is considerable interest in deciphering the mechanism of MBT assembly, with the goal of targeting select biosynthetic steps for antituberculosis drug development. The proposed scheme for MBT biosynthesis involves assembly of the MBT backbone by a hybrid nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS) megasynthase followed by the tailoring of this backbone by
N

6

acylation of the central
l
-Lys residue and subsequent
N

6

-hydroxylation of the central
N

6

-acyl-
l
-Lys and the terminal caprolactam. A complete testing of this hypothesis has been hindered by the inability to heterologously produce soluble megasynthase components. Here we show that soluble forms of the NRPS components MbtB, MbtE, and MbtF are obtained when these enzymes are coproduced with MbtH. Using these soluble enzymes we determined the amino acid specificity of each adenylation (A) domain. These results suggest that the proposed tailoring enzymes are actually involved in precursor biosynthesis since the A domains of MbtE and MbtF are specific for
N

6

-acyl-
N

6

-hydroxy-
l
-Lys and
N

6

-hydroxy-
l
-Lys, respectively. Furthermore, the preference of the A domain of MbtB for
l
-Thr over
l
-Ser suggests that the megasynthase produces MBT derivatives with β-methyl oxazoline rings. Since the most prominent form of MBT produced by
M. tuberculosis
lacks this β-methyl group, a mechanism for demethylation remains to be discovered. These results suggest revisions to the MBT biosynthesis pathway while also identifying new targets for antituberculosis drug development.
Functional Dissection of
N
-Acetylglutamate Synthase (ArgA) of Pseudomonas aeruginosa and Restoration of Its Ancestral
N
-Acetylglutamate Kinase Activity
Authors: Sancho-Vaello Enea , Fernández-Murga María L. , Rubio Vicente 
Published: March 2012

ABSTRACT

In many microorganisms, the first step of arginine biosynthesis is catalyzed by the classical
N
-acetylglutamate synthase (NAGS), an enzyme composed of N-terminal amino acid kinase (AAK) and C-terminal histone acetyltransferase (GNAT) domains that bind the feedback inhibitor arginine and the substrates, respectively. In NAGS, three AAK domain dimers are interlinked by their N-terminal helices, conforming a hexameric ring, whereas each GNAT domain sits on the AAK domain of an adjacent dimer. The arginine inhibition of
Pseudomonas aeruginosa
NAGS was strongly hampered, abolished, or even reverted to modest activation by changes in the length/sequence of the short linker connecting both domains, supporting a crucial role of this linker in arginine regulation. Linker cleavage or recombinant domain production allowed the isolation of each NAGS domain. The AAK domain was hexameric and inactive, whereas the GNAT domain was monomeric/dimeric and catalytically active although with ∼50-fold-increased and ∼3-fold-decreased

K
m

glutamate
and
k
cat
values, respectively, with arginine not influencing its activity. The deletion of N-terminal residues 1 to 12 dissociated NAGS into active dimers, catalyzing the reaction with substrate kinetics and arginine insensitivity identical to those for the GNAT domain. Therefore, the interaction between the AAK and GNAT domains from different dimers modulates GNAT domain activity, whereas the hexameric architecture appears to be essential for arginine inhibition. We proved the closeness of the AAK domains of NAGS and
N
-acetylglutamate kinase (NAGK), the enzyme that catalyzes the next arginine biosynthesis step, shedding light on the origin of classical NAGS, by showing that a double mutation (M26K L240K) in the isolated NAGS AAK domain elicited NAGK activity.
Checking pregnancy status in adolescent girls before procedures under general anaesthesia
Authors: Donaldson J F , Napier S J , Ward-Jones M , Wheeler R A , Spargo P M 
Published: March 2012

ObjectiveSurgery, ionising radiation and anaesthesia in the presence of an undetected pregnancy could be harmful. British guidelines state that female patients of 'childbearing age' should have their pregnancy status established before surgery. Approaching this topic with an adolescent girl can be challenging.DesignThe authors conducted an observational study and a survey in their institution and a national survey of Association of Paediatric Anaesthetists (APA) linkmen.SettingLocal: Southampton. National: UK.ResultsBoth surveys demonstrate widespread concerns about inconsistent and informal practices. Only 45% of respondents in the authors' institution stated they ask adolescent girls if they could be pregnant. 40% of APA linkmen were unaware of national guidelines.ConclusionsThis work illustrates the need for consistent national guidance. We propose that all girls who have reached menarche should be routinely offered a urine pregnancy test before any procedure under general anaesthesia.
Restless legs syndrome and risk of incident cardiovascular disease in women and men: prospective cohort study
Authors: Winter Anke C , Schürks Markus , Glynn Robert J , Buring Julie E , Gaziano J Michael , Berger Klaus , Kurth Tobias 
Published: March 2012

ObjectivesTo evaluate the association between restless legs syndrome (RLS) and incident cardiovascular disease (CVD).DesignProspective cohort study.SettingWomen's Health Study (WHS) and Physicians' Health Study (PHS), USA.Participants29 756 female health professionals aged ≥45 years and 19 182 male physicians aged ≥40 years at baseline.Main outcome measuresMain outcome was incidence of major CVD; secondary outcomes were first incidence of myocardial infarction, stroke, death due to CVD or coronary revascularisation.Results3487 (11.7%) women and 1373 (7.2%) men met International Restless Legs Study Group criteria for RLS. In the WHS 450 major CVD events occurred and 1064 major CVD events were confirmed in the PHS. In both cohorts, RLS was not associated with increased risk of major CVD, stroke, myocardial infarction, CVD death or coronary revascularisation. After adjustment for major vascular risk factors, the HRs (95% CI) for major CVD were 1.15 (0.88 to 1.50) in women and 1.01 (0.81 to 1.25) in men. Highest multivariable-adjusted HRs were 1.29 (0.91 to 1.82) for total stroke in women and 1.22 (0.87 to 1.70) for CVD death in men. Excluding participants with comorbidities potentially leading to RLS did not substantially change the effect estimates.ConclusionsIn these large prospective studies of female and male health professionals, RLS was not associated with an increased risk of any incident CVD event. The data do not support the hypothesis that RLS is a marker of increased risk of vascular disease.
Building information for systematic improvement of the prevention of hospital-acquired pressure ulcers with statistical process control charts and regression
Authors: Padula William V , Mishra Manish K , Weaver Christopher D , Yilmaz Taygan , Splaine Mark E 
Published: March 2012

ObjectivesTo demonstrate complementary results of regression and statistical process control (SPC) chart analyses for hospital-acquired pressure ulcers (HAPUs), and identify possible links between changes and opportunities for improvement between hospital microsystems and macrosystems.MethodsOrdinary least squares and panel data regression of retrospective hospital billing data, and SPC charts of prospective patient records for a US tertiary-care facility (2004–2007). A prospective cohort of hospital inpatients at risk for HAPUs was the study population.ResultsThere were 337 HAPU incidences hospital wide among 43 844 inpatients. A probit regression model predicted the correlation of age, gender and length of stay on HAPU incidence (pseudo R2=0.096). Panel data analysis determined that for each additional day in the hospital, there was a 0.28% increase in the likelihood of HAPU incidence. A p-chart of HAPU incidence showed a mean incidence rate of 1.17% remaining in statistical control. A t-chart showed the average time between events for the last 25 HAPUs was 13.25 days. There was one 57-day period between two incidences during the observation period. A p-chart addressing Braden scale assessments showed that 40.5% of all patients were risk stratified for HAPUs upon admission.ConclusionSPC charts complement standard regression analysis. SPC amplifies patient outcomes at the microsystem level and is useful for guiding quality improvement. Macrosystems should monitor effective quality improvement initiatives in microsystems and aid the spread of successful initiatives to other microsystems, followed by system-wide analysis with regression. Although HAPU incidence in this study is below the national mean, there is still room to improve HAPU incidence in this hospital setting since 0% incidence is theoretically achievable. Further assessment of pressure ulcer incidence could illustrate improvement in the quality of care and prevent HAPUs.
Withdrawal of artificial nutrition and hydration in the Neonatal Intensive Care Unit: parental perspectives
Authors: Hellmann Jonathan , Williams Constance , Ives-Baine Lori , Shah Prakesh S 
Published: March 2012

ObjectiveTo review the experience of the practice of withdrawal of artificial nutrition and hydration (WANH) and to describe parental perspectives on the process.DesignA retrospective chart review and parental survey.SettingTertiary level Neonatal Intensive Care Unit (NICU).ParticipantsInfants who had WANH after withdrawal of other life-sustaining treatment, and their parents.Main outcome measureParental perspectives on the care and process were obtained through a survey administered 1 to 4 years after the death of their infant.ResultsFifteen cases (5.5% of all mortality and 0.5% of all admissions) of WANH were identified, and 10 parents participated in the survey. The median (range) gestational age was 40 weeks (31–42) and birth weight was 3409 g (2000–4640). The reason for WANH was predicted poor outcome due to severe neurological injury/disease. The median (range) time between WANH and death was 16 days (2–37). All parents reported favourable perceptions of preparation, support, communication and care. Seven parents reported concerns regarding pain experienced by their infant. Parents reported the ability to spend quality time, creating tangible memories and the virtues and professional qualities of the caregivers to be helpful, but identified that consistency and continuity of care could be improved.ConclusionWithin the spectrum of palliative care in neonates, WANH can be a tenable, justifiable and humane practice in the NICU.
Activation procedures in the electroencephalograms of healthy and epileptic cats under propofol anaesthesia
Authors: Brauer C. , Kästner S. B. R. , Kulka A. M. , Tipold A. 
Published: March 2012

The current study evaluated the diagnostic value of electroencephalographic recordings (EEG) in cats with epilepsy under special consideration of photic stimulation and hyperventilation. EEGs in six healthy cats were recorded under light (mean dose of 0.23 mg/kg/min) and deep (mean dose of 0.7 mg/kg/min) propofol anaesthesia, whereas EEGs in 13 diseased cats were recorded under a propofol anaesthesia which was kept as light as possible (mean dose of 0.39 mg/kg/min). Paroxysmal discharges were detected in six of 13 cats suffering from seizures (two cats with idiopathic epilepsy and four cats with symptomatic epilepsy). Activation techniques did not enhance the diagnostic value of the EEGs. Photic driving was detected in one of six healthy cats under light, in five of six healthy cats under deep propofol anaesthesia and in 11 of 13 cats with seizures. Systematic use of activation techniques does not seem to increase the diagnostic yield of the recorded EEGs and should not be used in a clinical setting until future studies indicate value. Further investigations into the origin of photic driving under propofol anaesthesia are needed and could lead to the development of a reliable animal model to research into drug effects on the EEG.