bluuebunny/crossref_metadata_2025_split huggingface dataset:
The clinical severity score of chronic actinic dermatitis correlates with in vivo photoallergic reactions and the immunologic parameters related to a shift towards Th2 immunity from the Th2/Th1 balanced status in patients with chronic actinic dermatitis
Authors: Ko Dong‐Yeob , Choi Seung‐Hwan , Ha Seung‐Min , Kim Tae‐Hoon , Song Ki‐Hoon , Kim Kyeong Hee , Kim Ki‐Ho 
Published: April 2016

SummaryBackgroundChronic actinic dermatitis (CAD) has a more complicated pathogenetic basis than others. The clinical grading system and its correlations with the clinical and immunological parameters still remained to be investigated to define the nature of CAD in a more detailed manner.ObjectivesWe investigated correlations of the clinical severity score of CAD (CSS‐CAD) with the clinical and immunological parameters.MethodsWe evaluated 72 patients with CAD and classified them into three groups according to the CSS‐CAD. We analysed total IgE level, peripheral blood (PB) eosinophil count, the ratio of Th2cell (CCR4 + CD4 +) percentage over Th1 cell (CXCR3 + CD4 +) percentage (Th2/Th1) and/or the sum of suppressor/cytotoxic T cells.ResultsThe total IgE levels and the percentage of PB eosinophils were higher in the severer group than other groups. A shift towards Th2 from Th2/Th1 balanced status may be affected by total counts of suppressor T cells, and the patient with higher Th2/Th1 ratio than balanced status had the more proportion in the severer CSS‐CAD group than other groups.ConclusionThe CSS‐CAD correlates with total IgE level, PB eosinophil count and a shift towards Th2 immunity from Th2/Th1. So we suggest the Th1/Th2 dysbalance may be affected by the CSS‐CAD.
Craniofacial phenotyping for prediction of obstructive sleep apnoea in a Chinese population
Authors: Sutherland Kate , Lee Richard W. W. , Petocz Peter , Chan Tat On , Ng Susanna , Hui David S. , Cistulli Peter A. 
Published: April 2016

AbstractBackground and objectiveCraniofacial morphology is a risk factor for obstructive sleep apnoea (OSA). Facial photography has previously shown utility in predicting OSA in a Caucasian sleep clinic. However, ethnic differences in OSA risk factors may influence these facial predictors. Our aim was to assess phenotypical facial measurements for OSA prediction in a Chinese population.MethodsCalibrated frontal and profile facial photographs were taken before polysomnography. Photographs were analysed to derive head, face and neck measurements. Demographical, anthropometrical and facial photographical variables were considered in prediction models for OSA. OSA prediction models were derived using logistic regression and classification and regression tree techniques.ResultsTwo‐hundred subjects were recruited (146 OSA, 54 controls). The OSA group contained more men (77% vs 61%) and were more obese. Logistic regression modelling found cervicomental angle (OR 1.06/degree, 95% CI: 1.03–1.09, P < 0.001) and face width (OR 1.7/cm, 95% CI: 1.1–2.7, P = 0.02) predicted OSA (area under the receiver operating characteristics curve 0.76). Classification and regression tree analysis identified cricomental space area, mandibular width, mandibular plane angle and neck soft tissue area as predictors (area under receiver operating characteristics curve 0.81).ConclusionIn a Hong Kong Chinese sleep clinic, facial photographical measurements had predictive utility for OSA. Prediction models had similar accuracy and included variables to a previous Caucasian population.
Complete Sequences of
mcr-1
-Harboring Plasmids from Extended-Spectrum-β-Lactamase- and Carbapenemase-Producing Enterobacteriaceae
Authors: Li Aiqing , Yang Yong , Miao Minhui , Chavda Kalyan D. , Mediavilla José R. , Xie Xiaofang , Feng Ping , Tang Yi-Wei , Kreiswirth Barry N. , Chen Liang , Du Hong 
Published: April 2016

ABSTRACT

Here we completely sequenced four
mcr-1
-haboring plasmids, isolated from two extended-spectrum-β-lactamase (ESBL)-producing
Escherichia coli
and two carbapenemase-producing
Klebsiella pneumoniae
clinical isolates. The
mcr-1
-harboring plasmids from an
E. coli
sequence type 2448 (ST2448) isolate and two
K. pneumoniae
ST25 isolates were identical (all pMCR1-IncX4), belonging to the IncX4 incompatibility group, while the plasmid from an
E. coli
ST2085 isolate (pMCR1-IncI2) belongs to the IncI2 group. A nearly identical 2.6-kb
mcr-1-pap2
element was found to be shared by all
mcr-1
-carrying plasmids.
Synthesis and Antimicrobial Evaluation of Amixicile-Based Inhibitors of the Pyruvate-Ferredoxin Oxidoreductases of Anaerobic Bacteria and Epsilonproteobacteria
Authors: Kennedy Andrew J. , Bruce Alexandra M. , Gineste Catherine , Ballard T. Eric , Olekhnovich Igor N. , Macdonald Timothy L. , Hoffman Paul S. 
Published: April 2016

ABSTRACT

Amixicile is a promising derivative of nitazoxanide (an antiparasitic therapeutic) developed to treat systemic infections caused by anaerobic bacteria, anaerobic parasites, and members of the
Epsilonproteobacteria
(
Campylobacter
and
Helicobacter
). Amixicile selectively inhibits pyruvate-ferredoxin oxidoreductase (PFOR) and related enzymes by inhibiting the function of the vitamin B
1
cofactor (thiamine pyrophosphate) by a novel mechanism. Here, we interrogate the amixicile scaffold, guided by docking simulations, direct PFOR inhibition assays, and MIC tests against
Clostridium difficile
,
Campylobacter jejuni
, and
Helicobacter pylori
. Docking simulations revealed that the nitro group present in nitazoxanide interacts with the protonated N4′-aminopyrimidine of thiamine pyrophosphate (TPP). The
ortho
-propylamine on the benzene ring formed an electrostatic interaction with an aspartic acid moiety (B456) of PFOR that correlated with improved PFOR-inhibitory activity and potency by MIC tests. Aryl substitution with electron-withdrawing groups and substitutions of the propylamine with other alkyl amines or nitrogen-containing heterocycles both improved PFOR inhibition and, in many cases, biological activity against
C. difficile
. Docking simulation results correlate well with mechanistic enzymology and nuclear magnetic resonance (NMR) studies that show members of this class of antimicrobials to be specific inhibitors of vitamin B
1
function by proton abstraction, which is both novel and likely to limit mutation-based drug resistance.
Identification of a Third Mn(II) Oxidase Enzyme in Pseudomonas putida GB-1
Authors: Geszvain Kati , Smesrud Logan , Tebo Bradley M. 
Published: April 2016

ABSTRACT

The oxidation of soluble Mn(II) to insoluble Mn(IV) is a widespread bacterial activity found in a diverse array of microbes. In the Mn(II)-oxidizing bacterium
Pseudomonas putida
GB-1, two Mn(II) oxidase genes, named
mnxG
and
mcoA
, were previously identified; each encodes a multicopper oxidase (MCO)-type enzyme. Expression of these two genes is positively regulated by the response regulator MnxR. Preliminary investigation into putative additional regulatory pathways suggested that the flagellar regulators FleN and FleQ also regulate Mn(II) oxidase activity; however, it also revealed the presence of a third, previously uncharacterized Mn(II) oxidase activity in
P. putida
GB-1. A strain from which both of the Mn(II) oxidase genes and
fleQ
were deleted exhibited low levels of Mn(II) oxidase activity. The enzyme responsible was genetically and biochemically identified as an animal heme peroxidase (AHP) with domain and sequence similarity to the previously identified Mn(II) oxidase MopA. In the Δ
fleQ
strain,
P. putida
GB-1 MopA is overexpressed and secreted from the cell, where it actively oxidizes Mn. Thus, deletion of
fleQ
unmasked a third Mn(II) oxidase activity in this strain. These results provide an example of an Mn(II)-oxidizing bacterium utilizing both MCO and AHP enzymes.

IMPORTANCE
The identity of the Mn(II) oxidase enzyme in
Pseudomonas putida
GB-1 has been a long-standing question in the field of bacterial Mn(II) oxidation. In the current work, we demonstrate that
P. putida
GB-1 employs both the multicopper oxidase- and animal heme peroxidase-mediated pathways for the oxidation of Mn(II), rendering this model organism relevant to the study of both types of Mn(II) oxidase enzymes. The presence of three oxidase enzymes in
P. putida
GB-1 deepens the mystery of why microorganisms oxidize Mn(II) while providing the field with the tools necessary to address this question. The initial identification of MopA as a Mn(II) oxidase in this strain required the deletion of FleQ, a regulator involved in both flagellum synthesis and biofilm synthesis in
Pseudomonas aeruginosa
. Therefore, these results are also an important step toward understanding the regulation of Mn(II) oxidation.
Metrics Proposed To Prevent the Harvest of Leafy Green Crops Exposed to Floodwater Contaminated with Escherichia coli
Authors: Callahan Mary Theresa , Micallef Shirley A. , Sharma Manan , Millner Patricia D. , Buchanan Robert L. 
Published: April 2016

ABSTRACT

The California Leafy Green Products Handler Marketing Agreement (LGMA) requires leafy green crops within 9 m of the edge of a flooded field not be harvested due to potential contamination (California Leafy Green Products Handler Marketing Board,
Commodity Specific Flood Safety Guidelines for the Production and Harvest of Lettuce and Leafy Greens
, 2012). Further, previously flooded soils should not be replanted for 60 days. In this study, the suitability of the LGMA metrics for farms in the Mid-Atlantic region of the United States was evaluated. The upper end of a spinach bed (in Beltsville, MD) established on a −5% grade was flooded with water containing 6 log CFU/ml
Escherichia coli
to model a worst-case scenario of bacterial movement through soil.
Escherichia coli
prevalence in soil and on foliar tissue was determined by most probable number (MPN) analysis at distances up to 9 m from the edge of the flood for 63 days. While
E. coli
was quickly detected at the 9-m distance within 1 day in the spring trial and within 3 days in the fall trial, no
E. coli
was detected on plants outside the flood zone after 14 days. On day 63 for the two trials,
E. coli
populations in the flood zone soil were higher in the fall than in the spring. Regression analysis predicted that the time required for a 3-log MPN/g (dry weight) decrease in
E. coli
populations inside the flood zone was within the 60-day LGMA guideline in the spring but would require 90 days in the fall. Overall, data suggest that the current guidelines should be revised to include considerations of field and weather conditions that may promote bacterial movement and survival.

IMPORTANCE
This study tracked the movement of
Escherichia coli
from floodwater across a horizontal plane of soil and the potential for the contamination of distant leafy green produce. The purpose of this study was to address the validity of the California Leafy Green Products Handler Marketing Agreement recommendations for the harvest of leafy green crops after a flooding event. These recommendations were based on the turning radius of farming equipment but did not take into consideration the potential subsurface movement of pathogens in the water through soil. This research shows that further considerations of field slope, temperature, and additional rainfall events may be necessary to provide appropriate guidelines to prevent the harvest of leafy green crops contaminated by enteric pathogens in floodwaters. This study may be used to provide a framework for comprehensive recommendations to growers for good harvesting practices after a flooding event.
Polymorphisms, Chromosomal Rearrangements, and Mutator Phenotype Development during Experimental Evolution of Lactobacillus rhamnosus GG
Authors: Douillard François P. , Ribbera Angela , Xiao Kun , Ritari Jarmo , Rasinkangas Pia , Paulin Lars , Palva Airi , Hao Yanling , de Vos Willem M. 
Published: April 2016

ABSTRACT

Lactobacillus rhamnosus
GG is a lactic acid bacterium widely marketed by the food industry. Its genomic analysis led to the identification of a gene cluster encoding mucus-binding SpaCBA pili, which is located in a genomic island enriched in insertion sequence (IS) elements. In the present study, we analyzed by genome-wide resequencing the genomic integrity of
L. rhamnosus
GG in four distinct evolutionary experiments conducted for approximately 1,000 generations under conditions of no stress or salt, bile, and repetitive-shearing stress. Under both stress-free and salt-induced stress conditions, the GG population (excluding the mutator lineage in the stress-free series [see below]) accumulated only a few single nucleotide polymorphisms (SNPs) and no frequent chromosomal rearrangements. In contrast, in the presence of bile salts or repetitive shearing stress, some IS elements were found to be activated, resulting in the deletion of large chromosomal segments that include the
spaCBA-srtC1
pilus gene cluster. Remarkably, a high number of SNPs were found in three strains obtained after 900 generations of stress-free growth. Detailed analysis showed that these three strains derived from a founder mutant with an altered DNA polymerase subunit that resulted in a mutator phenotype. The present work confirms the stability of the pilus production phenotype in
L. rhamnosus
GG under stress-free conditions, highlights the possible evolutionary scenarios that may occur when this probiotic strain is extensively cultured, and identifies external factors that affect the chromosomal integrity of GG. The results provide mechanistic insights into the stability of GG in regard to its extensive use in probiotic and other functional food products.

IMPORTANCE
Lactobacillus rhamnosus
GG is a widely marketed probiotic strain that has been used in numerous clinical studies to assess its health-promoting properties. Hence, the stability of the probiotic functions of
L. rhamnosus
GG is of importance, and here we studied the impact of external stresses on the genomic integrity of
L. rhamnosus
GG. We studied three different stresses that are relevant for understanding its robustness and integrity under both
ex vivo
conditions, i.e., industrial manufacturing conditions, and
in vivo
conditions, i.e., intestinal tract-associated stress. Overall, our findings contribute to predicting the genomic stability of
L. rhamnosus
GG and its ecological performance.
Nitrous Oxide Reduction Kinetics Distinguish Bacteria Harboring Clade I NosZ from Those Harboring Clade II NosZ
Authors: Yoon Sukhwan , Nissen Silke , Park Doyoung , Sanford Robert A. , Löffler Frank E. 
Published: April 2016

ABSTRACT

Bacteria capable of reduction of nitrous oxide (N
2
O) to N
2
separate into clade I and clade II organisms on the basis of
nos
operon structures and
nosZ
sequence features. To explore the possible ecological consequences of distinct
nos
clusters, the growth of bacterial isolates with either clade I (
Pseudomonas stutzeri
strain DCP-Ps1,
Shewanella loihica
strain PV-4) or clade II (
Dechloromonas aromatica
strain RCB,
Anaeromyxobacter
dehalogenans
strain 2CP-C)
nosZ
with N
2
O was examined. Growth curves did not reveal trends distinguishing the clade I and clade II organisms tested; however, the growth yields of clade II organisms exceeded those of clade I organisms by 1.5- to 1.8-fold. Further, whole-cell half-saturation constants (

K
s

s) for N
2
O distinguished clade I from clade II organisms. The apparent

K
s

values of 0.324 ± 0.078 μM for
D. aromatica
and 1.34 ± 0.35 μM for
A. dehalogenans
were significantly lower than the values measured for
P. stutzeri
(35.5 ± 9.3 μM) and
S. loihica
(7.07 ± 1.13 μM). Genome sequencing demonstrated that
Dechloromonas denitrificans
possessed a clade II
nosZ
gene, and a measured

K
s

of 1.01 ± 0.18 μM for N
2
O was consistent with the values determined for the other clade II organisms tested. These observations provide a plausible mechanistic basis for why the relative activity of bacteria with clade I
nos
operons compared to that of bacteria with clade II
nos
operons may control N
2
O emissions and determine a soil's N
2
O sink capacity.

IMPORTANCE
Anthropogenic activities, in particular fertilizer application for agricultural production, increase N
2
O emissions to the atmosphere. N
2
O is a strong greenhouse gas with ozone destruction potential, and there is concern that nitrogen may become the major driver of climate change. Microbial N
2
O reductase (NosZ) catalyzes N
2
O reduction to environmentally benign dinitrogen gas and represents the major N
2
O sink process. The observation that bacterial groups with clade I
nosZ
versus those with clade II
nosZ
exhibit distinct affinities to N
2
O has implications for N
2
O flux models, and these distinct characteristics may provide opportunities to curb N
2
O emissions from relevant soil ecosystems.
Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities
Authors: Sheng Yizhi , Bibby Kyle , Grettenberger Christen , Kaley Bradley , Macalady Jennifer L. , Wang Guangcai , Burgos William D. 
Published: April 2016

ABSTRACT

Two acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration.
Acidithiobacillus
,
Ferrovum
,
Gallionella
,
Leptospirillum
,
Ferrimicrobium
,
Acidiphilium
, and
Acidocella
were all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup.

IMPORTANCE
This study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites.
Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes
Authors: Mus Florence , Crook Matthew B. , Garcia Kevin , Garcia Costas Amaya , Geddes Barney A. , Kouri Evangelia D. , Paramasivan Ponraj , Ryu Min-Hyung , Oldroyd Giles E. D. , Poole Philip S. , Udvardi Michael K. , Voigt Christopher A. , Ané Jean-Michel , Peters John W. 
Published: April 2016

ABSTRACT

Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N
2
to NH
3
, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
Occurrence and Spread of Quinolone-Resistant Escherichia coli on Dairy Farms
Authors: Duse Anna , Persson Waller Karin , Emanuelson Ulf , Ericsson Unnerstad Helle , Persson Ylva , Bengtsson Björn 
Published: April 2016

ABSTRACT

Quinolone-resistant
Escherichia coli
(QREC) is common in feces from young calves, but the prevalence and genetic diversity of QREC in groups of cattle of other ages and the farm environment are unknown. The aims of the study were to obtain knowledge about the occurrence of QREC on dairy farms, the genetic diversity of QREC within and between farms, and how these relate to the number of purchased animals and geographic distances between farms. We analyzed the within-sample prevalence of QREC in individual fecal samples from preweaned dairy calves and postpartum cows and in environmental samples from 23 Swedish dairy farms. The genetic diversity of the QREC isolates on 10 of these farms was assessed. In general, QREC was more prevalent in the dairy farm environment and in postpartum cows if QREC was commonly found in calves than if QREC was rare in calves. In particular, we found more QREC organisms in feed and water troughs and in environments that may come into contact with young calves. Thus, the results suggest that QREC circulates between cattle and the farm environment and that calves are important for the maintenance of QREC. Some genotypes of QREC were widespread both within and between farms, indicating that QREC has spread within the farms and likely also between farms, possibly through purchased animals. Farms that had purchased many animals over the years had greater within-farm diversity than farms with more closed animal populations. Finally, animals on more closely located farms were more likely to share the same genotype than animals on farms located far apart.

IMPORTANCE
This study investigates the occurrence of a specific type of antimicrobial-resistant bacterium on dairy farms. It contributes to increased knowledge about the occurrence and spread of these bacteria, and the results pave the way for actions or further studies that could help mitigate the spread of these bacteria on dairy farms and in the community as a whole.