bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleeping arrangements and mass distribution of bed nets in six districts in central and northern Mozambique
Authors: Plucinski M. M. , Chicuecue S. , Macete E. , Chambe G. A. , Muguande O. , Matsinhe G. , Colborn J. , Yoon S. S. , Doyle T. J. , Kachur S. P. , Aide P. , Alonso P. L. , Guinovart C. , Morgan J. 
Published: September 2015

AbstractObjectiveUniversal coverage with insecticide‐treated bed nets is a cornerstone of modern malaria control. Mozambique has developed a novel bed net allocation strategy, where the number of bed nets allocated per household is calculated on the basis of household composition and assumptions about who sleeps with whom. We set out to evaluate the performance of the novel allocation strategy.MethodsA total of 1994 households were visited during household surveys following two universal coverage bed net distribution campaigns in Sofala and Nampula provinces in 2010–2013. Each sleeping space was observed for the presence of a bed net, and the sleeping patterns for each household were recorded. The observed coverage and efficiency were compared to a simulated coverage and efficiency had conventional allocation strategies been used. A composite indicator, the product of coverage and efficiency, was calculated. Observed sleeping patterns were compared with the sleeping pattern assumptions.ResultsIn households reached by the campaign, 93% (95% CI: 93–94%) of sleeping spaces in Sofala and 84% (82–86%) in Nampula were covered by campaign bed nets. The achieved efficiency was high, with 92% (91–93%) of distributed bed nets in Sofala and 93% (91–95%) in Nampula covering a sleeping space. Using the composite indicator, the novel allocation strategy outperformed all conventional strategies in Sofala and was tied for best in Nampula. The sleeping pattern assumptions were completely satisfied in 66% of households in Sofala and 56% of households in Nampula. The most common violation of the sleeping pattern assumptions was that male children 3–10 years of age tended not to share sleeping spaces with female children 3–10 or 10–16 years of age.ConclusionsThe sleeping pattern assumptions underlying the novel bed net allocation strategy are generally valid, and net allocation using these assumptions can achieve high coverage and compare favourably with conventional allocation strategies.
Dual effects of atmospheric pressure plasma jet on skin wound healing of mice
Authors: Xu Gui‐Min , Shi Xing‐Min , Cai Jing‐Fen , Chen Si‐Le , Li Ping , Yao Cong‐Wei , Chang Zheng‐Shi , Zhang Guan‐Jun 
Published: September 2015

ABSTRACTCold plasma has become an attractive tool for promoting wound healing and treating skin diseases. This article presents an atmospheric pressure plasma jet (APPJ) generated in argon gas through dielectric barrier discharge, which was applied to superficial skin wounds in BALB/c mice. The mice (n = 50) were assigned randomly into five groups (named A, B, C, D, E) with 10 animals in each group. Natural wound healing was compared with stimulated wound healing treated daily with APPJ for different time spans (10, 20, 30, 40, and 50 seconds) on 14 consecutive days. APPJ emission spectra, morphological changes in animal wounds, and tissue histological parameters were analyzed. Statistical results revealed that wound size changed over the duration of the experimental period and there was a significant interaction between experimental day and group. Differences between group C and other groups at day 7 were statistically significant (p < 0.05). All groups had nearly achieved closure of the untreated control wounds at day 14. The wounds treated with APPJ for 10, 20, 30, and 40 seconds showed significantly enhanced daily improvement compared with the control and almost complete closure at day 12, 10, 7, and 13, respectively. The optimal results of epidermal cell regeneration, granulation tissue hyperplasia, and collagen deposition in histological aspect were observed at day 7. However, the wounds treated for 50 seconds were less well healed at day 14 than those of the control. It was concluded that appropriate doses of cold plasma could inactivate bacteria around the wound, activate fibroblast proliferation in wound tissue, and eventually promote wound healing. Whereas, over doses of plasma suppressed wound healing due to causing cell death by apoptosis or necrosis. Both positive and negative effects may be related to the existence of reactive oxygen and nitrogen species (ROS and RNS) in APPJ.
Inhibition of Pseudomonas aeruginosa biofilm formation on wound dressings
Authors: Brandenburg Kenneth S. , Calderon Diego F. , Kierski Patricia R. , Brown Amanda L. , Shah Nihar M. , Abbott Nicholas L. , Schurr Michael J. , Murphy Christopher J. , McAnulty Jonathan F. , Czuprynski Charles J. 
Published: September 2015

ABSTRACTChronic nonhealing skin wounds often contain bacterial biofilms that prevent normal wound healing and closure and present challenges to the use of conventional wound dressings. We investigated inhibition of Pseudomonas aeruginosa biofilm formation, a common pathogen of chronic skin wounds, on a commercially available biological wound dressing. Building on prior reports, we examined whether the amino acid tryptophan would inhibit P. aeruginosa biofilm formation on the three‐dimensional surface of the biological dressing. Bacterial biomass and biofilm polysaccharides were quantified using crystal violet staining or an enzyme linked lectin, respectively. Bacterial cells and biofilm matrix adherent to the wound dressing were visualized through scanning electron microscopy. d‐/l‐tryptophan inhibited P. aeruginosa biofilm formation on the wound dressing in a dose dependent manner and was not directly cytotoxic to immortalized human keratinocytes although there was some reduction in cellular metabolism or enzymatic activity. More importantly, d‐/l‐tryptophan did not impair wound healing in a splinted skin wound murine model. Furthermore, wound closure was improved when d‐/l‐tryptophan treated wound dressing with P. aeruginosa biofilms were compared with untreated dressings. These findings indicate that tryptophan may prove useful for integration into wound dressings to inhibit biofilm formation and promote wound healing.
Long‐lasting effects of dexamethasone on immune cells and wound healing in the zebrafish
Authors: Sharif Faiza , Steenbergen Peter J. , Metz Juriaan R. , Champagne Danielle L. 
Published: September 2015

ABSTRACTThis study assessed the lasting impact of dexamethasone (DEX) exposure during early development on tissue repair capacity at later life stages (5, 14, and 24 days post fertilization [dpf]) in zebrafish larvae. Using the caudal fin amputation model, we show that prior exposure to DEX significantly delays but does not prevent wound healing at all life stages studied. DEX‐induced impairments on wound healing were fully restored to normal levels with longer post amputation recovery time. Further analyses revealed that DEX mainly exerted its detrimental effects in the early phase (0–5 hours) of wound‐healing process. Specifically, we observed the following events: (1) massive amount of cell death both by necrosis and apoptosis; (2) significant reduction in the number as well as misplacement of macrophages at the wound site; (3) aberrant migration and misplacement of neutrophils and macrophages at the wound site. These events were accompanied by significant (likely compensatory) changes in the expression of genes involved in tissue patterning, including up‐regulation of FKBP5 6 hours post DEX exposure and that of Wnt3a and RARγ at 24 hours post amputation. Taken together, this study provides evidence that DEX exposure during early sensitive periods of development appears to cause permanent alterations in the cellular/molecular immune processes that are involved in the early phase of wound healing in zebrafish. These findings are consistent with previous studies showing that antenatal course of DEX is associated with immediate and lasting alterations of the immune system in rodent models and humans. Therefore, the current findings support the use of the larval zebrafish model to study the impact of stress and stress hormone exposure in immature organisms on health risks in later life.
Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs
Authors: Munson-McGee Jacob H. , Field Erin K. , Bateson Mary , Rooney Colleen , Stepanauskas Ramunas , Young Mark J. 
Published: September 2015

ABSTRACT

Nanoarchaeota
are obligate symbionts with reduced genomes first described from marine thermal vent environments. Here, both community metagenomics and single-cell analysis revealed the presence of
Nanoarchaeota
in high-temperature (∼90°C), acidic (pH ≈ 2.5 to 3.0) hot springs in Yellowstone National Park (YNP) (United States). Single-cell genome analysis of two cells resulted in two nearly identical genomes, with an estimated full length of 650 kbp. Genome comparison showed that these two cells are more closely related to the recently proposed
Nanobsidianus stetteri
from a more neutral YNP hot spring than to the marine
Nanoarchaeum equitans
. Single-cell and catalyzed reporter deposition-fluorescence
in situ
hybridization (CARD-FISH) analysis of environmental hot spring samples identified the host of the YNP
Nanoarchaeota
as a
Sulfolobales
species known to inhabit the hot springs. Furthermore, we demonstrate that
Nanoarchaeota
are widespread in acidic to near neutral hot springs in YNP. An integrated viral sequence was also found within one
Nanoarchaeota
single-cell genome and further analysis of the purified viral fraction from environmental samples indicates that this is likely a virus replicating within the YNP
Nanoarchaeota
.
Eradication of Methicillin-Resistant Staphylococcus aureus and of Enterobacteriaceae Expressing Extended-Spectrum Beta-Lactamases on a Model Pig Farm
Authors: Schmithausen Ricarda Maria , Kellner Sophia Ricarda , Schulze-Geisthoevel Sophia Veronika , Hack Sylvia , Engelhart Steffen , Bodenstein Isabel , Al-Sabti Nahed , Reif Marion , Fimmers Rolf , Körber-Irrgang Barbara , Harlizius Jürgen , Hoerauf Achim , Exner Martin , Bierbaum Gabriele , Petersen Brigitte , Bekeredjian-Ding Isabelle 
Published: September 2015

ABSTRACT

Colonization of livestock with bacteria resistant to antibiotics is considered a risk for the entry of drug-resistant pathogens into the food chain. For this reason, there is a need for novel concepts to address the eradication of drug-resistant commensals on farms. In the present report, we evaluated the decontamination measures taken on a farm contaminated with methicillin-resistant
Staphylococcus aureus
(MRSA) and
Enterobacteriaceae
expressing extended-spectrum β-lactamases (ESBL-E). The decontamination process preceded the conversion from piglet breeding to gilt production. Microbiological surveillance showed that the decontamination measures eliminated the MRSA and ESBL-E strains that were detected on the farm before the complete removal of pigs, cleaning and disinfection of the stable, and construction of an additional stable meeting high-quality standards. After pig production was restarted, ESBL-E remained undetectable over 12 months, but MRSA was recovered from pigs and the environment within the first 2 days. However,
spa
(
Staphylococcus aureus
protein A gene) typing revealed acquisition of an MRSA strain (type t034) that had not been detected before decontamination. Interestingly, we observed that a farmworker who had been colonized with the prior MRSA strain (t2011) acquired the new strain (t034) after 2 months. In summary, this report demonstrates that decontamination protocols similar to those used here can lead to successful elimination of contaminating MRSA and ESBL-E in pigs and the stable environment. Nevertheless, decontamination protocols do not prevent the acquisition of new MRSA strains.
Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits
Authors: Reith Frank , Zammit Carla M. , Pohrib Rebecca , Gregg Adrienne L. , Wakelin Steven A. 
Published: September 2015

ABSTRACT

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (
P
< 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (
P
< 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (
P
< 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly
Acidobacteria
,
Bacilli
,
Betaproteobacteria
, and
Epsilonproteobacteria
. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity.
Positive Regulation of Staphylococcal Enterotoxin H by Rot (Repressor of Toxin) Protein and Its Importance in Clonal Complex 81 Subtype 1 Lineage-Related Food Poisoning
Authors: Sato'o Yusuke , Hisatsune Junzo , Nagasako Yuria , Ono Hisaya K. , Omoe Katsuhiko , Sugai Motoyuki 
Published: September 2015

ABSTRACT

We previously demonstrated the clonal complex 81 (CC81) subtype 1 lineage is the major staphylococcal food poisoning (SFP)-associated lineage in Japan (Y. Sato'o et al., J Clin Microbiol
52:
2637–2640, 2014,
http://dx.doi.org/10.1128/JCM.00661-14
). Strains of this lineage produce staphylococcal enterotoxin H (SEH) in addition to SEA. However, an evaluation of the risk for the recently reported SEH has not been sufficiently conducted. We first searched for staphylococcal enterotoxin (SE) genes and SE proteins in milk samples that caused a large SFP outbreak in Japan. Only SEA and SEH were detected, while there were several SE genes detected in the samples. We next designed an experimental model using a meat product to assess the productivity of SEs and found that only SEA and SEH were detectably produced
in situ
. Therefore, we investigated the regulation of SEH production using a CC81 subtype 1 isolate. Through mutant analysis of global regulators, we found the repressor of toxin (Rot) functioned oppositely as a stimulator of SEH production. SEA production was not affected by Rot.
seh
mRNA expression correlated with
rot
both in media and on the meat product, and the Rot protein was shown to directly bind to the
seh
promoter. The
seh
promoter sequence was predicted to form a loop structure and to hide the RNA polymerase binding sequences. We propose Rot binds to the promoter sequence of
seh
and unfolds the secondary structure that may lead the RNA polymerase to bind the promoter, and then
seh
mRNA transcription begins. This alternative Rot regulation for SEH may contribute to sufficient toxin production by the CC81 subtype 1 lineage in foods to induce SFP.
Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence
Authors: Sun Hui , Santalahti Minna , Pumpanen Jukka , Köster Kajar , Berninger Frank , Raffaello Tommaso , Jumpponen Ari , Asiegbu Fred O. , Heinonsalo Jussi 
Published: September 2015

ABSTRACTForest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the generaCortinariusandPilodermadominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics.
High-Level Heterologous Production of
d
-Cycloserine by Escherichia coli
Authors: Kumagai Takanori , Ozawa Tomoki , Tanimoto Momoko , Noda Masafumi , Matoba Yasuyuki , Sugiyama Masanori 
Published: September 2015

ABSTRACT

Previously, we successfully cloned a
d
-cycloserine (
d
-CS) biosynthetic gene cluster consisting of 10 open reading frames (designated
dcsA
to
dcsJ
) from
d
-CS-producing
Streptomyces lavendulae
ATCC 11924. In this study, we put four
d
-CS biosynthetic genes (
dcsC
,
dcsD
,
dcsE
, and
dcsG
) in tandem under the control of the T7 promoter in an
Escherichia coli
host. SDS-PAGE analysis demonstrated that the 4 gene products were simultaneously expressed in host cells. When
l
-serine and hydroxyurea (HU), the precursors of
d
-CS, were incubated together with the
E. coli
resting cell suspension, the cells produced significant amounts of
d
-CS (350 ± 20 μM). To increase the productivity of
d
-CS, the
dcsJ
gene, which might be responsible for the
d
-CS excretion, was connected downstream of the four genes. The
E. coli
resting cells harboring the five genes produced
d
-CS at 660 ± 31 μM. The
dcsD
gene product, DcsD, forms
O
-ureido-
l
-serine from
O
-acetyl-
l
-serine (OAS) and HU, which are intermediates in
d
-CS biosynthesis. DcsD also catalyzes the formation of
l
-cysteine from OAS and H
2
S. To repress the side catalytic activity of DcsD, the
E. coli
chromosomal
cysJ
and
cysK
genes, encoding the sulfite reductase α subunit and OAS sulfhydrylase, respectively, were disrupted. When resting cells of the double-knockout mutant harboring the four
d
-CS biosynthetic genes, together with
dcsJ
, were incubated with
l
-serine and HU, the
d
-CS production was 980 ± 57 μM, which is comparable to that of
d
-CS-producing
S. lavendulae
ATCC 11924 (930 ± 36 μM).
Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment
Authors: Stellato Giuseppina , De Filippis Francesca , La Storia Antonietta , Ercolini Danilo 
Published: September 2015

ABSTRACT

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of
Streptococcus thermophilus
and possible spoilage-associated bacteria, including
Pseudomonas
,
Acinetobacter
, and
Psychrobacter
, with a relative abundance above 50%. The most abundant yeasts were
Kluyveromyces marxianus
,
Yamadazyma triangularis
,
Trichosporon faecale
, and
Debaryomyces hansenii
. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.
Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius
Authors: Guinane Caitriona M. , Piper Clare , Draper Lorraine A. , O'Connor Paula M. , Hill Colin , Ross R. Paul , Cotter Paul D. 
Published: September 2015

ABSTRACT

Bacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of
Lactobacillus salivarius
, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the
L. salivarius
bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in
L. salivarius
. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize
in vivo
and
in vitro
production of these antimicrobials.