bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methanogenic Paraffin Biodegradation: Alkylsuccinate Synthase Gene Quantification and Dicarboxylic Acid Production
Authors: Oberding Lisa K. , Gieg Lisa M. 
Published: October 2017

ABSTRACT

Paraffinic
n
-alkanes (>C
17
) that are solid at ambient temperature comprise a large fraction of many crude oils. The comparatively low water solubility and reactivity of these long-chain alkanes can lead to their persistence in the environment following fuel spills and pose serious problems for crude oil recovery operations by clogging oil production wells. However, the degradation of waxy paraffins under the anoxic conditions characterizing contaminated groundwater environments and deep subsurface energy reservoirs is poorly understood. Here, we assessed the ability of a methanogenic culture enriched from freshwater fuel-contaminated aquifer sediments to biodegrade the model paraffin
n
-octacosane (C
28
H
58
). Compared with that in controls, the consumption of
n
-octacosane was coupled to methane production, demonstrating its biodegradation under these conditions.
Smithella
was postulated to be an important C
28
H
58
degrader in the culture on the basis of its high relative abundance as determined by 16S rRNA gene sequencing. An identified
assA
gene (known to encode the α subunit of alkylsuccinate synthase) aligned most closely with those from other
Smithella
organisms. Quantitative PCR (qPCR) and reverse transcription qPCR assays for
assA
demonstrated significant increases in the abundance and expression of this gene in C
28
H
58
-degrading cultures compared with that in controls, suggesting
n
-octacosane activation by fumarate addition. A metabolite analysis revealed the presence of several long-chain α,ω-dicarboxylic acids only in the C
28
H
58
-degrading cultures, a novel observation providing clues as to how methanogenic consortia access waxy hydrocarbons. The results of this study broaden our understanding of how waxy paraffins can be biodegraded in anoxic environments with an application toward bioremediation and improved oil recovery.

IMPORTANCE
Understanding the methanogenic biodegradation of different classes of hydrocarbons has important applications for effective fuel-contaminated site remediation and for improved recovery from oil reservoirs. Previous studies have clearly demonstrated that short-chain alkanes (<C
17
) can be biodegraded anaerobically, but less is understood regarding the biodegradation of longer chain waxy alkanes (>C
17
) that comprise many fuel mixtures. Using an enrichment culture derived from a freshwater fuel-contaminated site, we demonstrate that the model waxy alkane
n
-octacosane can be biodegraded under methanogenic conditions by a presumed
Smithella
phylotype. Compared with that of controls, we show an increased abundance and expression of the
assA
gene, which is known to be important for anaerobic
n
-alkane metabolism. Metabolite analyses revealed the presence of a range of α,ω-dicarboxylic acids found only in
n
-octacosane-degrading cultures, a novel finding that lends insight as to how anaerobic communities may access waxes as growth substrates in anoxic environments.
Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production
Authors: Borrero Juan , Kelly Eoin , O'Connor Paula M. , Kelleher Philip , Scully Colm , Cotter Paul D. , Mahony Jennifer , van Sinderen Douwe 
Published: October 2017

ABSTRACT

Bacteriocins from lactic acid bacteria (LAB) are of increasing interest in recent years due to their potential as natural preservatives against food and beverage spoilage microorganisms. In a screening study for LAB, we isolated from olives a strain,
Lactobacillus plantarum
NI326, with activity against the beverage-spoilage bacterium
Alicyclobacillus acidoterrestris
. Genome sequencing of NI326 enabled the identification of a gene cluster (designated
plc
) encoding a putative circular bacteriocin and proteins involved in its modification, transport, and immunity. This novel bacteriocin, named plantaricyclin A (PlcA), was grouped into the circular bacteriocin subgroup II due to its high degree of similarity with other gassericin A-like bacteriocins. Purification of PlcA from the supernatant of
Lb. plantarum
NI326 resulted in an active peptide with a molecular mass of 5,570 Da, corresponding to that predicted from the (processed) PlcA amino acid sequence. The
plc
gene cluster was cloned and expressed in
Lactococcus lactis
NZ9000, resulting in the production of an active 5,570-Da bacteriocin in the supernatant. PlcA is believed to be produced as a 91-amino-acid precursor with a 33-amino-acid leader peptide, which is predicted to be removed, followed by joining of the N and C termini via a covalent linkage to form the mature 58-amino-acid circular bacteriocin PlcA. We report the characterization of a circular bacteriocin produced by
Lb. plantarum
. The inhibition displayed against
A. acidoterrestris
highlights its potential use as a preservative in food and beverages.

IMPORTANCE
In this work, we describe the purification and characterization of an antimicrobial peptide, termed plantaricyclin A (PlcA), produced by a
Lactobacillus plantarum
strain isolated from olives. This peptide has a circular structure, and all genes involved in its production, circularization, and secretion were identified. PlcA shows antimicrobial activity against different strains, including
Alicyclobacillus acidoterrestris
, a common spoilage bacterium, which causes substantial economic losses in the beverage industry every year. In this study, we describe a circular antimicrobial peptide, PlcA, for a
Lactobacillus plantarum
strain.
Use of Comparative Genomics-Based Markers for Discrimination of Host Specificity in Fusarium oxysporum
Authors: van Dam Peter , de Sain Mara , ter Horst Anneliek , van der Gragt Michelle , Rep Martijn 
Published: October 2017

ABSTRACTThe polyphyletic nature of manyformae specialesofFusarium oxysporumprevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labor- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the sameforma specialis, which makes them potential markers for host-specific pathogenicity. We therefore compared candidate effector genes extracted from 60 existing and 22 newly generated genome assemblies, specifically targeting strains affecting cucurbit plant species. Based on these candidate effector genes, a total of 18 PCR primer pairs were designed to discriminate between each of the seven Cucurbitaceae-affectingformae speciales. When tested on a collection of strains encompassing different clonal lineages of theseformae speciales, nonpathogenic strains, and strains of otherformae speciales, they allowed clear recognition of the host range of each evaluated strain. WithinFusarium oxysporumf. sp.melonismore genetic variability exists than anticipated, resulting in threeF. oxysporumf. sp.melonismarker patterns that partially overlapped with the cucurbit-infectingFusarium oxysporumf. sp.cucumerinum,Fusarium oxysporumf. sp.niveum,Fusarium oxysporumf. sp.momordicae, and/orFusarium oxysporumf. sp.lagenariae. ForF. oxysporumf. sp.niveum, a multiplex TaqMan assay was evaluated and was shown to allow quantitative and specific detection of template DNA quantities as low as 2.5 pg. These results provide ready-to-use marker sequences for the mentionedF. oxysporumpathogens. Additionally, the method can be applied to find markers distinguishing other host-specific forms ofF. oxysporum.IMPORTANCEPathogenic strains ofFusarium oxysporumare differentiated intoformae specialesbased on their host range, which is normally restricted to only one or a few plant species. However, horizontal gene transfer between strains in the species complex has resulted in a polyphyletic origin of host specificity in many of theseformae speciales. This hinders accurate and rapid pathogen detection through molecular methods. In our research, we compared the genomes of 88 strains ofF. oxysporumwith each other, specifically targeting virulence-related genes that are typically highly similar within eachforma specialis. Using this approach, we identified marker sequences that allow the discrimination ofF. oxysporumstrains affecting various cucurbit plant species through different PCR-based methods.
Novel Metabolic Pathway for
N
-Methylpyrrolidone Degradation in Alicycliphilus sp. Strain BQ1
Authors: Solís-González Claudia Julieta , Domínguez-Malfavón Lilianha , Vargas-Suárez Martín , Gaytán Itzel , Cevallos Miguel Ángel , Lozano Luis , Cruz-Gómez M. Javier , Loza-Tavera Herminia 
Published: October 2017

ABSTRACT

The molecular mechanisms underlying the biodegradation of
N
-methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans and is teratogenic in rats, are unknown.
Alicycliphilus
sp. strain BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (
nmpABCDEF
) that is transcribed as a polycistronic mRNA and encodes enzymes involved in NMP biodegradation.
nmpA
and the transposon-affected gene
nmpB
encode an
N
-methylhydantoin amidohydrolase that transforms NMP to γ-
N
-methylaminobutyric acid; this is metabolized by an amino acid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA) or by deamination to produce succinate semialdehyde (SSA). If GABA is produced, the activity of a GABA aminotransferase (GABA-AT), not encoded in the
nmp
gene cluster, is needed to generate SSA. SSA is transformed by a succinate semialdehyde dehydrogenase (SSDH) (NMPF) to succinate, which enters the Krebs cycle. The abilities to consume NMP and to utilize it for growth were complemented in the transposon-tagged mutant by use of the
nmpABCD
genes. Similarly,
Escherichia coli
MG1655, which has two SSDHs but is unable to grow in NMP, acquired these abilities after functional complementation with these genes. In wild-type (wt) BQ1 cells growing in NMP, GABA was not detected, but SSA was present at double the amount found in cells growing in Luria-Bertani medium (LB), suggesting that GABA is not an intermediate in this pathway. Moreover,
E. coli
GABA-AT deletion mutants complemented with
nmpABCD
genes retained the ability to grow in NMP, supporting the possibility that γ-
N
-methylaminobutyric acid is deaminated to SSA instead of being demethylated to GABA.

IMPORTANCE
N
-Methylpyrrolidone is a cyclic amide reported to be biodegradable. However, the metabolic pathway and enzymatic activities for degrading NMP are unknown. By developing molecular biology techniques for
Alicycliphilus
sp. strain BQ1, an environmental bacterium able to grow in NMP, we identified a six-gene cluster encoding enzymatic activities involved in NMP degradation. These findings set the basis for the study of new enzymatic activities and for the development of biotechnological processes with potential applications in bioremediation.
Improving the ability to review preoperative radiographs intraoperatively in trauma and orthopaedic theatres at Lancashire teaching hospitals
Authors: Jump Christopher 
Published: October 2017

BackgroundThe ability to review preoperative radiographs during trauma and orthopaedic surgery is essential for the surgeon to provide optimum treatment to the patient. However, due to current information technology (IT) systems, screen-savers frequently interrupt the ability to review images and theatre staff are not routinely available to deactivate the screen-saver. This prolongs theatre time for the patient and affects the quality of care provided. The aim of this quality improvement project was to improve the availability of radiographs for the surgeon to review intraoperatively.Method/resultsData were collected from all trauma and orthopaedic theatres at two hospital sites covering all subspecialties and including emergency and elective cases. Baseline measurements showed that the frequency of preoperative radiographs not interrupted during an operation was 0% (0/50). Following this the Trust’s IT systems were improved to prevent activation of the screen-saver on the theatre computers using the generic theatre login details. After the first-cycle intervention, data were collected showing 52% (14/27) of preoperative radiographs were not interrupted by a screen-saver. The cause for this result being less than expected was investigated and found to be due to an alternative computer login being used on the theatre computers at one of the hospital sites. Education of theatre staff was then undertaken to ensure the correct theatre login was used and notices to remind staff placed on the theatre computers. After the second-cycle intervention, data were collected showing that 100% (26/26) of preoperative radiographs were not interrupted during operative time allowing the surgeon to review images when required.Conclusion/implicationsThis quality improvement project has made changes to theatre IT systems and practices of theatre staff which has resulted in a significant improvement in the ability for the operating surgeon to review preoperative radiographs intraoperatively.
Long-term outcomes of patients with pulmonary arteriovenous malformations considered for lung transplantation, compared with similarly hypoxaemic cohorts
Authors: Shovlin Claire L , Buscarini Elisabetta , Hughes J Michael B , Allison David J , Jackson James E 
Published: October 2017

IntroductionPulmonary arteriovenous malformations (PAVMs) may not be amenable to treatment by embolisation or surgical resection, and many patients are left with significant hypoxaemia. Lung transplantation has been undertaken. There is no guidance on selection criteria.MethodsTo guide transplantation listing assessments, the outcomes of the six patients who had been considered for transplantation were compared with a similarly hypoxaemic patient group recruited prospectively between 2005 and 2016 at the same UK institution.ResultsSix patients had been formally considered for lung transplantation purely for PAVMs. One underwent a single lung transplantation for diffuse PAVMs and died within 4 weeks of surgery. The other five were not transplanted, in four cases at the patients’ request. Their current survival ranges from 16 to 27 (median 21) years post-transplant assessment.Of 444 consecutive patients with PAVMs recruited between 2005 and 2016, 42 were similarly hypoxaemic to the ‘transplant-considered’ cohort (SaO2<86.5%). Hypoxaemic cohorts maintained arterial oxygen content (CaO2) through secondary erythrocytosis and higher haemoglobin. The ‘transplant-considered’ cohort had similar CaO2to the hypoxaemic comparator group, but higher Medical Research Council (MRC) dyspnoea scores (p=0.023), higher rates of cerebral abscesses (p=0.0043) and higher rates of venous thromboemboli (p=0.0009) that were evident before and after the decision to list for transplantation.ConclusionsThe non-transplanted patients demonstrated marked longevity. Symptoms and comorbidities were better predictors of health than oxygen measurements. While a case-by-case decision, weighing survival estimates and quality of life will help patients in their decision making, the data suggest a very strong case must be made before lung transplantation is considered.
Burden of bacterial upper respiratory tract pathogens in school children of Nepal
Authors: Thapa Sangita , Gokhale Shishir , Sharma Annavarapu Laxminarasimha , Sapkota Lokendra Bahadur , Ansari Shamshul , Gautam Rajendra , Shrestha Sony , Neopane Puja 
Published: October 2017

IntroductionRespiratory tract infections are one of the most common human infections in all age group and important cause of mortality and morbidity worldwide. Most bacterial upper respiratory tract infections are vaccine preventable. This study aimed to determine the prevalence of carrier state of bacterial upper respiratory tract pathogens among school children. It also aimed to study their antibiograms.MethodsThe specimen from posterior pharyngeal wall and tonsils were collected from 204 participants on calcium alginate coated swabs (HiMedia). Isolates were identified by standard microbiological methods and tested for in vitro antibiotic susceptibility testing by modified Kirby-Bauer disc diffusion method.ResultsIn this study,Streptococcus pneumoniae(16.6%) was the most common bacterial pathogen recovered, followed byStaphylococcus aureus(14.7%), β-haemolytic streptococci (non-Group A) (8.8%),Streptococcus pyogenes(5.3%) andCorynebacterium diphtheriae(3.4%). The Gram negative bacteria wereKlebsiella pneumoniae(4.9%),Haemophilus influenzae(3.4%) andNeisseria meningitidis(1.4%). Important findings in antibiogram include high resistance ofStreptococcus pneumoniaeto penicillin (91.17%) and resistance ofS. aureusto oxacillin (23.3%).ConclusionPharyngeal colonisation byS. pneumoniaewas found high among school children and this calls for an urgent need to include pneumococcal vaccine in routine national immunisation schedule of Nepal given the high burden of invasive pneumococcal disease. Despite expected universal vaccination, pharyngeal colonisation byC. diphtheriaeis possible and there is possibility of transmission of these respiratory pathogens to other healthy children.
Alcohol drinking and cigarette smoking in relation to risk of active tuberculosis: prospective cohort study
Authors: Soh Avril Zixin , Chee Cynthia Bin Eng , Wang Yee-Tang , Yuan Jian-Min , Koh Woon-Puay 
Published: October 2017

IntroductionHeavy alcohol consumption increases the risk of active tuberculosis (TB). However, the relation between lower levels of alcohol intake and TB risk remains unclear. We aimed to evaluate the association between alcohol intake and risk of active TB and assess whether the associations were modified by smoking status, which is another risk factor for active TB.MethodsThe Singapore Chinese Health Study is a prospective cohort of 63 257 adults aged 45–74 years recruited from 1993 to 1998. Information on alcohol intake and smoking history was collected at recruitment. Active TB cases were identified via linkage with National TB Notification Registry.ResultsDuring a mean follow-up of 16.8 years, 1249 incident cases of active TB were identified. Among non-smokers, compared with total abstinence, participants who had monthly to weekly intake of alcohol had reduced TB risk (HR 0.70, 95% CI 0.55 to 0.89), but this reduction in risk with low-dose drinking was not observed among current smokers (HR 0.96, 95% CI 0.77 to 1.18; p for interaction=0.02). Comparatively, drinking 2+ drinks daily was associated with increased TB risk among current smokers (HR 1.51, 95% CI 1.11 to 2.05). This increased risk was not observed among non-smokers (HR 0.93, 95% CI 0.49 to 1.77) and the interaction between alcohol intake and smoking status was of borderline significance (p for interaction=0.08). In joint effect, compared with those who neither smoked nor drank, the risk of active TB increased from 1.82 (95% CI 1.57 to 2.10) in current smokers who were non-drinkers to 3.16 (95% CI 2.35 to 4.24) in current smokers who also drank 2+ drinks daily.ConclusionWhile low intake of alcohol may protect against active TB among non-smokers, drinking 2+ drinks daily could act synergistically with smoking to increase the risk of active TB in current smokers.
New biomarker for acute ischaemic stroke: plasma glycogen phosphorylase isoenzyme BB
Authors: Park Kwang-Yeol , Ay Ilknur , Avery Ross , Caceres Juan Alfredo , Siket Matthew S , Pontes-Neto Octavio M , Zheng Hui , Rost Natalia S , Furie Karen L , Sorensen Alma Gregory , Koroshetz Walter J , Ay Hakan 
Published: October 2017

BackgroundGlycogen phosphorylase is the key enzyme that breaks down glycogen to yield glucose-1-phosphate in order to restore depleted energy stores during cerebral ischaemia. We sought to determine whether plasma levels of glycogen phosphorylase BB (GPBB) isoform increased in patients with acute ischaemic stroke (AIS).MethodsWe studied plasma GPBB levels within 12 hours and again at 48±24 hours of symptom onset in 172 patients with imaging-confirmed AIS and 133 stroke-free individuals. We determined the ability of plasma GPBB to discriminate between cases and controls and examined the predictive value of plasma GPBB for 90-day functional outcome, 90-day survival and acute lesion volumes on neuroimaging.ResultsThe mean (SD) GPBB levels were higher in cases (46.3±38.6 ng/mL at first measurement and 38.6±36.5 ng/mL at second measurement) than in controls (4.1±7.6 ng/mL, p<0.01 for both). The area under the receiver operating characteristic (ROC) curve for case–control discrimination based on first GPBB measurement was 0.96 (95% CI 0.93 to 0.98). The sensitivity and specificity based on optimal operating point on the ROC curve (7.0 ng/mL) were both 93%. GPBB levels increased in 90% of patients with punctate infarcts (<1.5 mL) and in all patients admitted within the first 4.5 hours of onset. There was no correlation between GPBB concentration and either clinical outcome or acute infarct volume.ConclusionGPBB demonstrates robust response to acute ischaemia and high sensitivity for small infarcts. If confirmed in more diverse populations that also include stroke mimics, GPBB could find utility as a stand-alone marker for acute brain ischaemia.
Short delay to initiate plasma exchange is the strongest predictor of outcome in severe attacks of NMO spectrum disorders
Authors: Bonnan Mickael , Valentino Rudy , Debeugny Stéphane , Merle Harold , Fergé Jean-Louis , Mehdaoui Hossein , Cabre Philippe 
Published: October 2017

IntroductionSevere attacks of neuromyelitis optica spectrum disorder (NMO-SD) are improved by plasma exchange (PLEX) given as an adjunctive therapy. Initial studies failed to demonstrate a delay of PLEX treatment influenced clinical outcome; however PLEX was always used late. We examine the clinical consequences of delay in PLEX initiation on severe optic neuritis and spinal cord attacks in NMO-SD.MethodsAll of our patients who suffered attacks of NMO-SD, treated in our centre by PLEX, were retrospectively considered for inclusion. Primary outcome was defined as complete improvement. Secondary poor/good outcomes were respectively defined to be the higher/lower third of Delta-Expanded Disability Status Scale (EDSS) (late minus baseline EDSS). Delays from clinical onset to PLEX initiation were categorised for multivariate analysis.ResultsOf the 60 patients included, NMO-SD criteria (2015) were fulfilled in 92%. One hundred and fifteen attacks were included and received PLEX with a median of 7 days (0–54) after clinical onset. The probability to regain complete improvement continuously decreased from 50% for PLEX given at day 0 to 1%–5% after day 20. Through multivariate analysis, the baseline impairment and PLEX delay were associated with the probability to complete improvement (OR 5.3; 95% CI 1.8 to 15.9). Reducing the PLEX delay also influenced the good secondary outcome but not the poor secondary outcome.ConclusionsThese results confirm an improved clinical benefit of early initiation of PLEX during severe attacks of NMO-SD. Perceiving PLEX as a rescue therapy only after steroid failure could be deleterious.