bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors Affecting the Uptake and Retention of Vibrio vulnificus in Oysters
Authors: Froelich Brett A. , Noble Rachel T. 
Published: September 2014

ABSTRACT

Vibrio vulnificus
, a bacterium ubiquitous in oysters and coastal water, is capable of causing ailments ranging from gastroenteritis to grievous wound infections or septicemia. The uptake of these bacteria into oysters is often examined
in vitro
by placing oysters in seawater amended with
V. vulnificus
. Multiple teams have obtained similar results in studies where laboratory-grown bacteria were observed to be rapidly taken up by oysters but quickly eliminated. This technique, along with suggested modifications, is reviewed here. In contrast, the natural microflora within oysters is notoriously difficult to eliminate via depuration. The reason for the transiency of exogenous bacteria is that those bacteria are competitively excluded by the oyster's preexisting microflora. Evidence of this phenomenon is shown using
in vitro
oyster studies and a multiyear
in situ
case study. Depuration of the endogenous oyster bacteria occurs naturally and can also be artificially induced, but both of these events require extreme conditions, natural or otherwise, as explained here. Finally, the “viable but nonculturable” (VBNC) state of
Vibrio
is discussed. This bacterial torpor can easily be confused with a reduction in bacterial abundance, as bacteria in this state fail to grow on culture media. Thus, oysters collected from colder months may appear to be relatively free of
Vibrio
but in reality harbor VBNC cells that respond to exogenous bacteria and prevent colonization of oyster matrices. Bacterial-uptake experiments combined with studies involving cell-free spent media are detailed that demonstrate this occurrence, which could explain why the microbial community in oysters does not always mirror that of the surrounding water.
Campylobacter jejuni Motility Is Required for Infection of the Flagellotropic Bacteriophage F341
Authors: Baldvinsson Signe Berg , Sørensen Martine C. Holst , Vegge Christina S. , Clokie Martha R. J. , Brøndsted Lone 
Published: September 2014

ABSTRACT

Previous studies have identified a specific modification of the capsular polysaccharide as receptor for phages that infect
Campylobacter jejuni
. Using acapsular
kpsM
mutants of
C. jejuni
strains NCTC11168 and NCTC12658, we found that bacteriophage F341 infects
C. jejuni
independently of the capsule. In contrast, phage F341 does not infect
C. jejuni
NCTC11168 mutants that either lack the flagellar filaments (Δ
flaAB
) or that have paralyzed, i.e., nonrotating, flagella (Δ
motA
and Δ
flgP
). Complementing
flgP
confirmed that phage F341 requires rotating flagella for successful infection. Furthermore, adsorption assays demonstrated that phage F341 does not adsorb to these nonmotile
C. jejuni
NCTC11168 mutants. Taken together, we propose that phage F341 uses the flagellum as a receptor. Phage-host interactions were investigated using fluorescence confocal and transmission electron microscopy. These data demonstrate that F341 binds to the flagellum by perpendicular attachment with visible phage tail fibers interacting directly with the flagellum. Our data are consistent with the movement of the
C. jejuni
flagellum being required for F341 to travel along the filament to reach the basal body of the bacterium. The initial binding to the flagellum may cause a conformational change of the phage tail that enables DNA injection after binding to a secondary receptor.
A Highly Diastereoselective Oxidant Contributes to Ligninolysis by the White Rot Basidiomycete Ceriporiopsis subvermispora
Authors: Yelle Daniel J. , Kapich Alexander N. , Houtman Carl J. , Lu Fachuang , Timokhin Vitaliy I. , Fort Raymond C. , Ralph John , Hammel Kenneth E. 
Published: September 2014

ABSTRACT

The white rot basidiomycete
Ceriporiopsis subvermispora
delignifies wood selectively and has potential biotechnological applications. Its ability to remove lignin before the substrate porosity has increased enough to admit enzymes suggests that small diffusible oxidants contribute to delignification. A key question is whether these unidentified oxidants attack lignin via single-electron transfer (SET), in which case they are expected to cleave its propyl side chains between C
α
and C
β
and to oxidize the
threo
-diastereomer of its predominating β-O-4-linked structures more extensively than the corresponding
erythro
-diastereomer. We used two-dimensional solution-state nuclear magnetic resonance (NMR) techniques to look for changes in partially biodegraded lignin extracted from spruce wood after white rot caused by
C. subvermispora
. The results showed that (i) benzoic acid residues indicative of C
α
—C
β
cleavage were the major identifiable truncated structures in lignin after decay and (ii) depletion of β-O-4-linked units was markedly diastereoselective with a
threo
preference. The less selective delignifier
Phanerochaete chrysosporium
also exhibited this diastereoselectivity on spruce, and a
P. chrysosporium
lignin peroxidase operating in conjunction with the
P. chrysosporium
metabolite veratryl alcohol did likewise when cleaving synthetic lignin
in vitro
. However,
C. subvermispora
was significantly more diastereoselective than
P. chrysosporium
or lignin peroxidase-veratryl alcohol. Our results show that the ligninolytic oxidants of
C. subvermispora
are collectively more diastereoselective than currently known fungal ligninolytic oxidants and suggest that SET oxidation is one of the chemical mechanisms involved.
Anaerobic Activation of
p
-Cymene in Denitrifying Betaproteobacteria: Methyl Group Hydroxylation versus Addition to Fumarate
Authors: Strijkstra Annemieke , Trautwein Kathleen , Jarling René , Wöhlbrand Lars , Dörries Marvin , Reinhardt Richard , Drozdowska Marta , Golding Bernard T. , Wilkes Heinz , Rabus Ralf 
Published: September 2014

ABSTRACT

The betaproteobacteria “
Aromatoleum aromaticum
” pCyN1 and “
Thauera
” sp. strain pCyN2 anaerobically degrade the plant-derived aromatic hydrocarbon
p
-cymene (4-isopropyltoluene) under nitrate-reducing conditions. Metabolite analysis of
p
-cymene-adapted “
A. aromaticum
” pCyN1 cells demonstrated the specific formation of 4-isopropylbenzyl alcohol and 4-isopropylbenzaldehyde, whereas with “
Thauera
” sp. pCyN2, exclusively 4-isopropylbenzylsuccinate and tentatively identified (4-isopropylphenyl)itaconate were observed. 4-Isopropylbenzoate in contrast was detected with both strains. Proteogenomic investigation of
p
-cymene- versus succinate-adapted cells of the two strains revealed distinct protein profiles agreeing with the different metabolites formed from
p
-cymene. “
A. aromaticum
” pCyN1 specifically produced (i) a putative
p
-cymene dehydrogenase (CmdABC) expected to hydroxylate the benzylic methyl group of
p
-cymene, (ii) two dehydrogenases putatively oxidizing 4-isopropylbenzyl alcohol (Iod) and 4-isopropylbenzaldehyde (Iad), and (iii) the putative 4-isopropylbenzoate-coenzyme A (CoA) ligase (Ibl). The
p
-cymene-specific protein profile of “
Thauera
” sp. pCyN2, on the other hand, encompassed proteins homologous to subunits of toluene-activating benzylsuccinate synthase (termed [4-isopropylbenzyl]succinate synthase IbsABCDEF; identified subunits, IbsAE) and protein homologs of the benzylsuccinate β-oxidation (Bbs) pathway (termed BisABCDEFGH; all identified except for BisEF). This study reveals that two related denitrifying bacteria employ fundamentally different peripheral degradation routes for one and the same substrate,
p
-cymene, with the two pathways apparently converging at the level of 4-isopropylbenzoyl-CoA.
The Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Species Zobellia galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in the Vanadium Haloperoxidase Enzyme Family
Authors: Fournier Jean-Baptiste , Rebuffet Etienne , Delage Ludovic , Grijol Romain , Meslet-Cladière Laurence , Rzonca Justyna , Potin Philippe , Michel Gurvan , Czjzek Mirjam , Leblanc Catherine 
Published: September 2014

ABSTRACT

Vanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species. Three putative VHPO genes were predicted in the genome of the flavobacterium
Zobellia galactanivorans
, a marine bacterium associated with macroalgae. In a phylogenetic analysis, these putative bacterial VHPO were closely related to other VHPO from diverse bacterial phyla but clustered independently from eukaryotic algal VBPO and fungal VCPO. Two of these bacterial VHPO, heterogeneously produced in
Escherichia coli
, were found to be strictly specific for iodide oxidation. The crystal structure of one of these vanadium-dependent iodoperoxidases, Zg-VIPO1, was solved by multiwavelength anomalous diffraction at 1.8 Å, revealing a monomeric structure mainly folded into α-helices. This three-dimensional structure is relatively similar to those of VCPO of the fungus
Curvularia inaequalis
and of
Streptomyces
sp. and is superimposable onto the dimeric structure of algal VBPO. Surprisingly, the vanadate binding site of Zg-VIPO1 is strictly conserved with the fungal VCPO active site. Using site-directed mutagenesis, we showed that specific amino acids and the associated hydrogen bonding network around the vanadate center are essential for the catalytic properties and also the iodide specificity of Zg-VIPO1. Altogether, phylogeny and structure-function data support the finding that iodoperoxidase activities evolved independently in bacterial and algal lineages, and this sheds light on the evolution of the VHPO enzyme family.
Dynamics of Gut Microbiota in Autoimmune Lupus
Authors: Zhang Husen , Liao Xiaofeng , Sparks Joshua B. , Luo Xin M. 
Published: September 2014

ABSTRACTGut microbiota has been recognized as an important environmental factor in health, as well as in metabolic and immunological diseases, in which perturbation of the host gut microbiota is often observed in the diseased state. However, little is known on the role of gut microbiota in systemic lupus erythematosus. We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model. In young, female lupus-prone mice resembling women at childbearing age, a population with the highest risk for lupus, we found marked depletion of lactobacilli, and increases inLachnospiraceaeand overall diversity compared to age-matched healthy controls. The predicted metagenomic profile in lupus-prone mice showed a significant enrichment of bacterial motility- and sporulation-related pathways. Retinoic acid as a dietary intervention restored lactobacilli that were downregulated in lupus-prone mice, and this correlated with improved symptoms. The predicted metagenomes also showed that retinoic acid reversed many lupus-associated changes in microbial functions that deviated from the control. In addition, gut microbiota of lupus-prone mice were different between sexes, and an overrepresentation ofLachnospiraceaein females was associated with an earlier onset of and/or more severe lupus symptoms.ClostridiaceaeandLachnospiraceae, both harboring butyrate-producing genera, were more abundant in the gut of lupus-prone mice at specific time points during lupus progression. Together, our results demonstrate the dynamics of gut microbiota in murine lupus and provide evidence to suggest the use of probiotic lactobacilli and retinoic acid as dietary supplements to relieve inflammatory flares in lupus patients.
Lactobacillus acidophilus ATCC 4356 Prevents Atherosclerosis via Inhibition of Intestinal Cholesterol Absorption in Apolipoprotein E-Knockout Mice
Authors: Huang Ying , Wang Jinfeng , Quan Guihua , Wang Xiaojun , Yang Longfei , Zhong Lili 
Published: September 2014

ABSTRACT

The objective of this study was to investigate the effect of
Lactobacillus acidophilus
ATCC 4356 on the development of atherosclerosis in apolipoprotein E-knockout (ApoE
−/−
) mice. Eight-week-old ApoE
−/−
mice were fed a Western diet with or without
L. acidophilus
ATCC 4356 daily for 16 weeks.
L. acidophilus
ATCC 4356 protected ApoE
−/−
mice from atherosclerosis by reducing their plasma cholesterol levels from 923 ± 44 to 581 ± 18 mg/dl, likely via a marked decrease in cholesterol absorption caused by modulation of Niemann-Pick C1-like 1 (NPC1L1). In addition, suppression of cholesterol absorption induced reverse cholesterol transport (RCT) in macrophages through the peroxisome proliferator-activated receptor/liver X receptor (PPAR/LXR) pathway. Fecal lactobacillus and bifidobacterium counts were significantly (
P
< 0.05) higher in the
L. acidophilus
ATCC 4356 treatment groups than in the control groups. Furthermore,
L. acidophilus
ATCC 4356 was detected in the rat small intestine, colon, and feces during the feeding trial. The bacterial levels remained high even after the administration of lactic acid bacteria had been stopped for 2 weeks. These results suggest that administration of
L. acidophilus
ATCC 4356 can protect against atherosclerosis through the inhibition of intestinal cholesterol absorption. Therefore,
L. acidophilus
ATCC 4356 may be a potential therapeutic material for preventing the progression of atherosclerosis.
Incidence of short stature at 3 years of age in late preterm infants: a population-based study
Authors: Nagasaka Miwako , Morioka Ichiro , Yokota Tomoyuki , Fujita Kaori , Kurokawa Daisuke , Koda Tsubasa , Shibata Akio , Yamada Hideto , Ito Yoshiya , Uchino Eiko , Shirai Chika , Iijima Kazumoto 
Published: September 2014

ObjectivesThis study aimed to investigate the incidence of short stature at 3 years of age in a Japanese cohort of late preterm infants who were born at 34–36 weeks’ gestational age (GA). We compared these late preterm infants with term infants (37–41 weeks’ GA), and evaluated the effect of birth weight on the incidence of short stature.MethodsA longitudinal population-based study of 26 970 neonates who were born between 34 weeks’ and 41 weeks’ GA in 2006–2008 was conducted in Kobe, Japan. Of these neonates, 1414 were late preterm and 25 556 were term infants. The late preterm infants were then divided into three subgroups based on birth weight as determined by Japanese neonatal anthropometric charts for GA at birth: large-for-GA (n=140), appropriate-for-GA (AGA, n=1083), and small-for-GA (SGA, n=191). The incidence of short stature at 3 years of age was calculated in the late preterm group and compared with that in the term group, and between the AGA and SGA groups with late preterm birth.ResultsThe incidence of short stature in the late preterm group was 2.9%, which was significantly higher than that in the term group (1.4%). Late preterm SGA infants developed short stature with a significantly higher (9.4%) incidence than that of late preterm AGA infants (2.1%).ConclusionsThe incidence of short stature in 3-year-old children who were late preterm infants has a 2-fold higher risk than that in term infants. The risk of developing short stature is increased 4.5-fold if they are SGA.
Exploring new avenues to assess the sharp end of patient safety: an analysis of nationally aggregated peer review data
Authors: Meeks Derek W , Meyer Ashley N D , Rose Barbara , Walker Yuri N , Singh Hardeep 
Published: September 2014

BackgroundMany healthcare organisations (HCOs) use peer review to evaluate clinical performance, but it is unclear whether these data provide useful insights for assessing the sharp end of patient safety.ObjectiveTo describe outcomes of peer review within the Department of Veterans Affairs (VA) healthcare system and identify opportunities to leverage peer review data for measurement and improvement of safety.DesignWe partnered with the VA's Risk Management Program Office to perform descriptive analyses of aggregated peer review data collected from 135 VA facilities between October 2011 and September 2012. We determined the frequency of screening factors used to initiate peer review and processes contributing to substandard care. We also evaluated peer review data for diagnosis-related performance concerns, an emerging area of interest in the patient safety field.ResultsDuring the study period, 23 287 cases were peer reviewed; 15 739 (68%) were sent to local peer review committees for final outcome determination after an initial review and 2320 cases were ultimately designated as substandard care (mean 17 cases/facility). In 20% of cases, the screening source was unspecified. The most common process contributing to substandard care was ‘timing and appropriateness of treatment’. Approximately 16% of committee reviewed cases had diagnosis-related performance concerns, which were estimated to occur in approximately 0.5% of total hospital admissions.ConclusionsPeer review may be a useful tool for HCOs to assess their sharp end clinical performance, particularly safety events related to diagnostic and treatment errors. To address these emerging and largely preventable events, HCOs could consider revamping their existing peer review programmes to enable self-assessment, feedback and improvement.
Conscious sedation versus general anaesthesia during mechanical thrombectomy for stroke: a propensity score analysis
Authors: McDonald Jennifer S , Brinjikji Waleed , Rabinstein Alejandro A , Cloft Harry J , Lanzino Giuseppe , Kallmes David F 
Published: September 2014

BackgroundDebate exists as to whether patients with acute ischemic stroke who are undergoing mechanical thrombectomy should receive general anaesthesia or conscious sedation during the procedure. Using a multihospital administrative database, we compared outcomes and complications of patients receiving mechanical thrombectomy, who were receiving general anaesthesia and conscious sedation, and studied trends in usage over time.Materials and methodsPremier database patients who underwent mechanical thrombectomy from 2006 to 2013 for acute ischemic stroke were identified. Using propensity score analysis, recipients of general anaesthesia and conscious sedation underwent 1:1 matching. Outcomes including usage trends, discharge status, mortality, length of stay, haemorrhage and pneumonia were examined.ResultsA total of 2512 patients receiving mechanical thrombectomy were identified. 1999 (80%) received general anaesthesia and 513 (20%) received conscious sedation. Following 1:1 matching by the propensity score matching, 507 general anaesthesia and 507 conscious sedation patients were matched. Patients who received general anaesthesia during their procedure had significantly higher rates of in-hospital mortality (25% vs 12%, OR=2.37 95% CI 1.68 to 3.37, p<0.0001), and pneumonia (17.0% vs 9.3%, OR=2.0, 95% CI 1.35 to 2.96, p=0.0005) compared with patients of thrombectomy who received conscious sedation. ICH/SAH rates were similar between patients receiving general anaesthesia and patients receiving conscious sedation (11% vs 12%, p=0.62). Usage rate of general anaesthesia decreased from 83.8% in 2006 and 74.0% in 2013.ConclusionsIn our cohort, thrombectomy patients receiving conscious sedation have decreased in-hospital mortality, decreased rates of pneumonia, and lower hospital costs and lengths of stay when compared with patients who received general anaesthesia. However, most practitioners continue to use general anaesthesia in the setting of acute stroke interventions.
British Pennsylvanian (Carboniferous) coal-bearing sequences: where is the time?
Authors: Scott Andrew C. , Stephens Rosemary S. 
Published: September 2014

Abstract
The Lower and Middle Coal Measures of Langsettian (Westphalian A) and Duckmantian (Westphalian B) age (together equals Bashkirian in part) in Britain comprise an alternation of clastic sediments and coal deposited on coastal and alluvial plains over a period of 2–3.5 million years, depending on which time scale is accepted. In both the Pennine and South Wales Basins there are no obvious unconformities. Many of the clastic sequences show evidence of rapid sedimentation (burial of trees, bivalve escape burrows) that may suggest that a significant amount of time is taken up during the peat-forming intervals. Thickness data from a range of boreholes that record continuous sections through this time period were collated. Coal and sediment thicknesses, as well as coal to sediment ratios, are compared both within and across the basins. Data on the coals has allowed consideration of the time taken to deposit the peats. This work considers the compaction of the peat to coal, as well as a range of peat accumulation rates. Assuming the largest de-compaction rates and slowest accumulation rates of the coal formation, less than 50% of the allocated time can be accounted for. In addition however, calculations suggest that peat formation accounts for less than 25% of the total time taken for sediment accumulation. It is suspected that there are major time gaps in the sequences, most probably occurring between seat-earths and coal and within the coals, and it is believed that this finding has significance for the debate over short-term climate changes in the Carboniferous and the causes of peat and sediment alternations.

Supplementary material:

Borehole thickness data and references are available at
http://www.geolsoc.org.uk/SUP18788
XXIX. The Microscopical Examination of Rocks
Authors: Thompson George R. 
Published: September 2014

I
n
the course of his remarks the writer pointed out the province of the microscope in the study of rocks, and that through its use a vast field, which was otherwise hid away from our unaided senses, was opened out for investigation. In many instances, of course, the component parts of rocks could be identified by the naked eye—granite, for example, and the coarser grits—but very little could be made of the finer igneous rocks, such as basalt, without the use of the lens. In the case of many of the fine Silurian greywackés, it was almost impossible to distinguish them from igneous rocks without microscopic aid, but when it was invoked the component particles were at once seen to be of a clastic nature.

The author then proceeded to examine the composition of the clastic and crystalline rocks, which were shown to have a definite structure or arrangement of their substances, as might be seen from the regular shape of the crystals where they have had free space to grow. The genesis of crystals as shown in glassy rocks was explained, as also the formation of crystallites, microliths, skeleton crystals, &c.
Mr. Thompson next pointed out how the different minerals could be recognised in microscopic sections by means of their physical and crystalline properties, such as shape, cleavage, colour, refracting index, and others. He ended his paper by giving a full and lucid description of the form of microscope best adapted for petrological work, with the production and use