bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes
Authors: Chen Yi , Gonzalez-Escalona Narjol , Hammack Thomas S. , Allard Marc W. , Strain Errol A. , Brown Eric W. 
Published: August 2016

ABSTRACT

Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of
Listeria monocytogenes
, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak.

IMPORTANCE
Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study
L. monocytogenes
biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST schemes can be used for the simultaneous identification of clonal groups and the differentiation of individual outbreak strains and epidemiologically unrelated strains of the same clonal group. We further developed lineage-specific cgMLST schemes that targeted more genomic regions than the species-specific cgMLST schemes. Our data revealed the genome-level diversity of clonal groups defined by classic MLST schemes. Our identification of U.S. and international outbreaks caused by major clonal groups can contribute to further understanding of the global epidemiology of
L. monocytogenes
.
Heterologous Production of Cyanobacterial Mycosporine-Like Amino Acids Mycosporine-Ornithine and Mycosporine-Lysine in Escherichia coli
Authors: Katoch Meenu , Mazmouz Rabia , Chau Rocky , Pearson Leanne A. , Pickford Russell , Neilan Brett A. 
Published: August 2016

ABSTRACT

Mycosporine-like amino acids (MAAs) are an important class of secondary metabolites known for their protection against UV radiation and other stress factors. Cyanobacteria produce a variety of MAAs, including shinorine, the active ingredient in many sunscreen creams. Bioinformatic analysis of the genome of the soil-dwelling cyanobacterium
Cylindrospermum stagnale
PCC 7417 revealed a new gene cluster with homology to MAA synthase from
Nostoc punctiforme
. This newly identified gene cluster is unusual because it has five biosynthesis genes (
mylA
to
mylE
), compared to the four found in other MAA gene clusters. Heterologous expression of
mylA
to
mylE
in
Escherichia coli
resulted in the production of mycosporine-lysine and the novel compound mycosporine-ornithine. To our knowledge, this is the first time these compounds have been heterologously produced in
E. coli
and structurally characterized via direct spectral guidance. This study offers insight into the diversity, biosynthesis, and structure of cyanobacterial MAAs and highlights their amenability to heterologous production methods.

IMPORTANCE
Mycosporine-like amino acids (MAAs) are significant from an environmental microbiological perspective as they offer microbes protection against a variety of stress factors, including UV radiation. The heterologous expression of MAAs in
E. coli
is also significant from a biotechnological perspective as MAAs are the active ingredient in next-generation sunscreens.
Effect of Leaf Surface Chemical Properties on Efficacy of Sanitizer for Rotavirus Inactivation
Authors: Fuzawa Miyu , Ku Kang-Mo , Palma-Salgado Sindy Paola , Nagasaka Kenya , Feng Hao , Juvik John A. , Sano Daisuke , Shisler Joanna L. , Nguyen Thanh H. 
Published: August 2016

ABSTRACT

The use of sanitizers is essential for produce safety. However, little is known about how sanitizer efficacy varies with respect to the chemical surface properties of produce. To answer this question, the disinfection efficacies of an oxidant-based sanitizer and a new surfactant-based sanitizer for porcine rotavirus (PRV) strain OSU were examined. PRV was attached to the leaf surfaces of two kale cultivars with high epicuticular wax contents and one cultivar of endive with a low epicuticular wax content and then treated with each sanitizer. The efficacy of the oxidant-based sanitizer correlated with leaf wax content as evidenced by the 1-log
10
PRV disinfection on endive surfaces (low wax content) and 3-log
10
disinfection of the cultivars with higher wax contents. In contrast, the surfactant-based sanitizer showed similar PRV disinfection efficacies (up to 3 log
10
) that were independent of leaf wax content. A statistical difference was observed with the disinfection efficacies of the oxidant-based sanitizer for suspended and attached PRV, while the surfactant-based sanitizer showed similar PRV disinfection efficacies. Significant reductions in the entry and replication of PRV were observed after treatment with either disinfectant. Moreover, the oxidant-based-sanitizer-treated PRV showed sialic acid-specific binding to the host cells, whereas the surfactant-based sanitizer increased the nonspecific binding of PRV to the host cells. These findings suggest that the surface properties of fresh produce may affect the efficacy of virus disinfection, implying that food sanitizers should be carefully selected for the different surface characteristics of fresh produce.

IMPORTANCE
Food sanitizer efficacies are affected by the surface properties of vegetables. This study evaluated the disinfection efficacies of two food sanitizers, an oxidant-based sanitizer and a surfactant-based sanitizer, on porcine rotavirus strain OSU adhering to the leaf epicuticular surfaces of high- and low-wax-content cultivars. The disinfection efficacy of the oxidant-based sanitizer was affected by the surface properties of the vegetables, while the surfactant-based sanitizer was effective for both high- and low-wax leafy vegetable cultivars. This study suggests that the surface properties of vegetables may be an important factor that interacts with disinfection with food sanitizers of rotaviruses adhering to fresh produce.
Copper Resistance of the Emerging Pathogen Acinetobacter baumannii
Authors: Williams Caitlin L. , Neu Heather M. , Gilbreath Jeremy J. , Michel Sarah L. J. , Zurawski Daniel V. , Merrell D. Scott 
Published: August 2016

ABSTRACT

Acinetobacter baumannii
is an important emerging pathogen that is capable of causing many types of severe infection, especially in immunocompromised hosts. Since
A. baumannii
can rapidly acquire antibiotic resistance genes, many infections are on the verge of being untreatable, and novel therapies are desperately needed. To investigate the potential utility of copper-based antibacterial strategies against
Acinetobacter
infections, we characterized copper resistance in a panel of recent clinical
A. baumannii
isolates. Exposure to increasing concentrations of copper in liquid culture and on solid surfaces resulted in dose-dependent and strain-dependent effects; levels of copper resistance varied broadly across isolates, possibly resulting from identified genotypic variation among strains. Examination of the growth-phase-dependent effect of copper on
A. baumannii
revealed that resistance to copper increased dramatically in stationary phase. Moreover,
A. baumannii
biofilms were more resistant to copper than planktonic cells but were still susceptible to copper toxicity. Exposure of bacteria to subinhibitory concentrations of copper allowed them to better adapt to and grow in high concentrations of copper; this copper tolerance response is likely achieved via increased expression of copper resistance mechanisms. Indeed, genomic analysis revealed numerous putative copper resistance proteins that share amino acid homology to known proteins in
Escherichia coli
and
Pseudomonas aeruginosa
. Transcriptional analysis revealed significant upregulation of these putative copper resistance genes following brief copper exposure. Future characterization of copper resistance mechanisms may aid in the search for novel antibiotics against
Acinetobacter
and other highly antibiotic-resistant pathogens.

IMPORTANCE
Acinetobacter baumannii
causes many types of severe nosocomial infections; unfortunately, some isolates have acquired resistance to almost every available antibiotic, and treatment options are incredibly limited. Copper is an essential nutrient but becomes toxic at high concentrations. The inherent antimicrobial properties of copper give it potential for use in novel therapeutics against drug-resistant pathogens. We show that
A. baumannii
clinical isolates are sensitive to copper
in vitro
, both in liquid and on solid metal surfaces. Since bacterial resistance to copper is mediated though mechanisms of efflux and detoxification, we identified genes encoding putative copper-related proteins in
A. baumannii
and showed that expression of some of these genes is regulated by the copper concentration. We propose that the antimicrobial effects of copper may be beneficial in the development of future therapeutics that target multidrug-resistant bacteria.
Minor Coat and Heat Shock Proteins Are Involved in the Binding of Citrus Tristeza Virus to the Foregut of Its Aphid Vector, Toxoptera citricida
Authors: Killiny N. , Harper S. J. , Alfaress S. , El Mohtar C. , Dawson W. O. 
Published: August 2016

ABSTRACT

Vector transmission is a critical stage in the viral life cycle, yet for most plant viruses how they interact with their vector is unknown or is explained by analogy with previously described relatives. Here we examined the mechanism underlying the transmission of citrus tristeza virus (CTV) by its aphid vector,
Toxoptera citricida
, with the objective of identifying what virus-encoded proteins it uses to interact with the vector. Using fluorescently labeled virions, we demonstrated that CTV binds specifically to the lining of the cibarium of the aphid. Through
in vitro
competitive binding assays between fluorescent virions and free viral proteins, we determined that the minor coat protein is involved in vector interaction. We also found that the presence of two heat shock-like proteins, p61 and p65, reduces virion binding
in vitro
. Additionally, treating the dissected mouthparts with proteases did not affect the binding of CTV virions. In contrast, chitinase treatment reduced CTV binding to the foregut. Finally, competition with glucose,
N
-acetyl-β-
d
-glucosamine, chitobiose, and chitotriose reduced the binding. These findings together suggest that CTV binds to the sugar moieties of the cuticular surface of the aphid cibarium, and the binding involves the concerted activity of three virus-encoded proteins.

IMPORTANCE
Limited information is known about the specific interactions between citrus tristeza virus and its aphid vectors. These interactions are important for the process of successful transmission. In this study, we localized the CTV retention site as the cibarium of the aphid foregut. Moreover, we demonstrated that the nature of these interactions is protein-carbohydrate binding. The viral proteins, including the minor coat protein and two heat shock proteins, bind to sugar moieties on the surface of the foregut. These findings will help in understanding the transmission mechanism of CTV by the aphid vector and may help in developing control strategies which interfere with the CTV binding to its insect vector to block the transmission.
Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating
Authors: Cusick Kathleen D. , Lin Baochuan , Malanoski Anthony P. , Strycharz-Glaven Sarah M. , Cockrell-Zugell Allison , Fitzgerald Lisa A. , Cramer Jeffrey A. , Barlow Daniel E. , Boyd Thomas J. , Biffinger Justin C. 
Published: August 2016

ABSTRACTThe effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth ofThermus scotoductusSA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response ofT. scotoductusSA-01 to dielectric heating during growth.IMPORTANCEThe residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating usingThermus scotoductusSA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation.
Peptidoglycan Acetylation of Campylobacter jejuni Is Essential for Maintaining Cell Wall Integrity and Colonization in Chicken Intestines
Authors: Iwata Taketoshi , Watanabe Ayako , Kusumoto Masahiro , Akiba Masato 
Published: August 2016

ABSTRACT

Peptidoglycan (PG) acetylation of Gram-positive bacteria confers lysozyme resistance and contributes to survival in the host. However, the importance of PG acetylation in Gram-negative bacteria has not been fully elucidated. The genes encoding putative PG acetyltransferase A (PatA) and B (PatB) are highly conserved in
Campylobacter jejuni
, the predominant cause of bacterial diarrhea worldwide. To evaluate the importance of PatA and PatB of
C. jejuni
, we constructed
patA
and
patB
isogenic mutants and compared their phenotypes with those of the parental strains. Although transmission electron microscopy did not reveal morphological changes, both mutants exhibited decreased motility and biofilm formation
in vitro
. The extent of acetylation of the PG purified from the
patA
and
patB
mutants was significantly lower than the PG acetylation in the parental strains. Both mutants exhibited decreased lysozyme resistance and intracellular survival in macrophage cells. In a chick colonization experiment, significant colonization deficiency was observed for both mutants. These results suggest that PatA and PatB of
C. jejuni
play important roles in maintaining cell wall integrity by catalyzing PG
O
-acetylation and that the loss of these enzymes causes decreased motility and biofilm formation, thus leading to colonization deficiency in chicken infection.

IMPORTANCE
The importance of peptidoglycan (PG) acetylation in Gram-negative bacteria has not been fully elucidated. The genes encoding putative PG acetyltransferase A (PatA) and B (PatB) are highly conserved in
Campylobacter jejuni
, the predominant cause of bacterial diarrhea worldwide. We evaluated the importance of these enzymes using isogenic mutants. The results of this study suggest that PatA and PatB of
C. jejuni
play important roles in maintaining cell wall integrity. The loss of these factors caused multiple phenotypic changes, leading to colonization deficiency in chicken infection. These data should be useful in developing novel control measures to prevent chicken colonization by
C. jejuni
. Inhibitors of the PG acetylation enzymes PatA and PatB might serve as potent anti-
C. jejuni
agents.
Introducing Vibro-Acupuncture: A Psychophysical Study
Authors: Wang Kelun , Larsen Dennis Boye , Jensen Tanja Kim , Liu Tiejun , Liu Zhuxuan , Arendt-Nielsen Lars 
Published: August 2016

Background/aim To potentially enhance the effects of conventional acupuncture, a novel acu-vibrator (prototype) has been developed to perform vibro-acupuncture (VA). The aim of this psychophysical study was to investigate the subjective sensations of VA compared with conventional manual acupuncture (MA) and non-penetrating sham acupuncture (SA). Methods 30 young healthy volunteers (21 men and 9 women) received VA, MA, and SA at LI4 and LI10 in a randomised, single-blind, placebo-controlled, cross-over manner. After 25 min of treatment, the Massachusetts General Hospital (MGH) acupuncture sensation scale (MASS), McGill pain questionnaire (MPQ), and numerical rating scale (NRS; 0–10) were employed followed by the acupuncture credibility and indication scale. Adverse events were investigated after treatment. Data were analysed using Friedman's test for repeated measures on ranks and post hoc Wilcoxon signed-rank tests with Bonferroni correction. Results The MASS scores were significantly higher during MA and VA compared with SA at both LI4 and LI10 (p<0.017). Treatment with VA evoked significantly higher vibration sensations compared with MA and SA (p<0.005). Treatment with SA yielded significantly lower NRS and MPQ scores compared with MA and VA (p<0.001) with no difference between MA and VA (p>0.05). Blinding of participants was achieved for SA and MA; however, VA was correctly identified in 29 of 30 subjects due to the characteristic vibrational stimulation. No serious adverse events were recorded for any of the treatments. Conclusions Subjective sensations were influenced by treatment mode, with MA and VA yielding higher stimulation responses compared with SA. VA evoked specific vibrational sensations beyond MA, which might have specific effects in various disorders.
Nocturnal emergency department visits, duration of symptoms and risk of hospitalisation among adults with asthma exacerbations: a multicentre observational study
Authors: Yasuda Hideto , Hagiwara Yusuke , Watase Hiroko , Hasegawa Kohei 
Published: August 2016

ObjectivesWe sought to compare the characteristics of patients with asthma presenting to the emergency department (ED) during the night-time with those of patients presenting at other times of the day, and to determine whether the time of ED presentation is associated with the risk of hospitalisation.Design and settingA multicentre chart review study of 23 EDs across Japan.ParticipantsPatients aged 18–54 years with a history of physician-diagnosed asthma, presented to the ED between January 2009 and December 2011Outcome measuresThe outcome of interest was hospitalisation, including admissions to an observation unit, inpatient unit and intensive care unit.ResultsAmong the 1354 patients (30.1% in the night-time group vs 69.9% in the other time group) included in this study, the median age was 34 years and ∼40% were male. Overall 145 patients (10.7%) were hospitalised. Patients in the night-time group were more likely to have a shorter duration of symptoms (≤3 hours) before ED presentation than those in the other time group (25.9% in night-time vs 13.4% in other times; p<0.001). In contrast, there were no significant differences in respiratory rate, initial peak expiratory flow or ED asthma treatment between the two groups (p>0.05). Similarly, the risk of hospitalisation did not differ between the two groups (11.3% in night-time vs 10.5% in other times; p=0.65). In a multivariable model adjusting for potential confounders, the risk of hospitalisation in the night-time group was not statistically different from the other time group (OR, 1.10; 95% CI 0.74 to 1.61; p=0.63).ConclusionsThis multicentre study in Japan demonstrated no significant difference in the risk of hospitalisations according to the time of ED presentation.