bluuebunny/crossref_metadata_2025_split huggingface dataset:
A clinical trial of Integra Template for diabetic foot ulcer treatment
Authors: Driver Vickie R. , Lavery Lawrence A. , Reyzelman Alexander M. , Dutra Timothy G. , Dove Cyaandi R. , Kotsis Sandra V. , Kim Hyungjin Myra , Chung Kevin C. 
Published: August 2015

AbstractIndividuals with diabetes mellitus are at an increased risk of developing a diabetic foot ulcer (DFU). This study evaluated the safety and efficacy of Integra Dermal Regeneration Template (IDRT) for the treatment of nonhealing DFUs. The Foot Ulcer New Dermal Replacement Study was a multicenter, randomized, controlled, parallel group clinical trial conducted under an Investigational Device Exemption. Thirty‐two sites enrolled and randomized 307 subjects with at least one DFU. Consented patients were entered into the 14‐day run‐in phase where they were treated with the standard of care (0.9% sodium chloride gel) plus a secondary dressing and an offloading/protective device. Patients with less than 30% reepithelialization of the study ulcer after the run‐in phase were randomized into the treatment phase. The subjects were randomized to the control treatment group (0.9% sodium chloride gel; n = 153) or the active treatment group (IDRT, n = 154). The treatment phase was 16 weeks or until confirmation of complete wound closure (100% reepithelialization of the wound surface), whichever occurred first. Following the treatment phase, all subjects were followed for 12 weeks. Complete DFU closure during the treatment phase was significantly greater with IDRT treatment (51%) than control treatment (32%; p = 0.001) at sixteen weeks. The median time to complete DFU closure was 43 days for IDRT subjects and 78 days for control subjects in wounds that healed. The rate of wound size reduction was 7.2% per week for IDRT subjects vs. 4.8% per week for control subjects (p = 0.012). For the treatment of chronic DFUs, IDRT treatment decreased the time to complete wound closure, increased the rate of wound closure, improved components of quality of life and had less adverse events compared with the standard of care treatment. IDRT could greatly enhance the treatment of nonhealing DFUs.
The Ocean as a Global Reservoir of Antibiotic Resistance Genes
Authors: Hatosy Stephen M. , Martiny Adam C. 
Published: August 2015

ABSTRACT

Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g.,
Pelagibacter
,
Prochlorococcus
, and
Vibrio
). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.
Stability of Secondary and Tertiary Structures of Virus-Like Particles Representing Noroviruses: Effects of pH, Ionic Strength, and Temperature and Implications for Adhesion to Surfaces
Authors: Samandoulgou Idrissa , Hammami Riadh , Morales Rayas Rocio , Fliss Ismail , Jean Julie 
Published: August 2015

ABSTRACTLoss of ordered molecular structure in proteins is known to increase their adhesion to surfaces. The aim of this work was to study the stability of norovirus secondary and tertiary structures and its implications for viral adhesion to fresh foods and agrifood surfaces. The pH, ionic strength, and temperature conditions studied correspond to those prevalent in the principal vehicles of viral transmission (vomit and feces) and in the food processing and handling environment (pasteurization and refrigeration). The structures of virus-like particles representing GI.1, GII.4, and feline calicivirus (FCV) were studied using circular dichroism and intrinsic UV fluorescence. The particles were remarkably stable under most of the conditions. However, heating to 65°C caused losses of β-strand structure, notably in GI.1 and FCV, while at 75°C the α-helix content of GII.4 and FCV decreased and tertiary structures unfolded in all three cases. Combining temperature with pH or ionic strength caused variable losses of structure depending on the particle type. Regardless of pH, heating to pasteurization temperatures or higher would be required to increase GII.4 and FCV adhesion, while either low or high temperatures would favor GI.1 adhesion. Regardless of temperature, increased ionic strength would increase GII.4 adhesion but would decrease GI.1 adhesion. FCV adsorption would be greater at refrigeration, pasteurization, or high temperature combined with a low salt concentration or at a higher NaCl concentration regardless of temperature. Norovirus adhesion mediated by hydrophobic interaction may depend on hydrophobic residues normally exposed on the capsid surface at pH 3, pH 8, physiological ionic strength, and low temperature, while at pasteurization temperatures it may rely more on buried hydrophobic residues exposed upon structural rearrangement.
Pseudomonas aeruginosa and Achromobacter sp. Clonal Selection Leads to Successive Waves of Contamination of Water in Dental Care Units
Authors: Abdouchakour Fatima , Dupont Chloé , Grau Delphine , Aujoulat Fabien , Mournetas Patricia , Marchandin Hélène , Parer Sylvie , Gibert Philippe , Valcarcel Jean , Jumas-Bilak Estelle 
Published: August 2015

ABSTRACT

Dental care unit waterlines (DCUWs) consist of complex networks of thin tubes that facilitate the formation of microbial biofilms. Due to the predilection toward a wet environment, strong adhesion, biofilm formation, and resistance to biocides,
Pseudomonas aeruginosa
, a major human opportunistic pathogen, is adapted to DCUW colonization. Other nonfermentative Gram-negative bacilli, such as members of the genus
Achromobacter
, are emerging pathogens found in water networks. We reported the 6.5-year dynamics of bacterial contamination of waterlines in a dental health care center with 61 dental care units (DCUs) connected to the same water supply system. The conditions allowed the selection and the emergence of clones of
Achromobacter
sp. and
P. aeruginosa
characterized by multilocus sequence typing, multiplex repetitive elements-based PCR, and restriction fragment length polymorphism in pulsed-field gel electrophoresis, biofilm formation, and antimicrobial susceptibility. One clone of
P. aeruginosa
and 2 clones of
Achromobacter
sp. colonized successively all of the DCUWs: the last colonization by
P. aeruginosa
ST309 led to the closing of the dental care center. Successive dominance of species and clones was linked to biocide treatments.
Achromobacter
strains were weak biofilm producers compared to
P. aeruginosa
ST309, but the coculture of
P. aeruginosa
and
Achromobacter
enhanced
P. aeruginosa
ST309 biofilm formation. Intraclonal genomic microevolution was observed in the isolates of
P. aeruginosa
ST309 collected chronologically and in
Achromobacter
sp. clone A. The contamination control was achieved by a complete reorganization of the dental health care center by removing the connecting tubes between DCUs.
Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes
Authors: Wang Hang , Li Hongyi , Gilbert Jack A. , Li Haibo , Wu Longhua , Liu Meng , Wang Liling , Zhou Qiansheng , Yuan Junxiang , Zhang Zhijian 
Published: August 2015

ABSTRACT

Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (
Musca domestica
) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [
tet
(M),
tet
(O),
tet
(Q), and
tet
(W)] were reduced (
P
< 0.05), while those of genes encoding sulfonamide resistance (
sul1
and
sul2
) were increased (
P
< 0.05) when normalized to 16S rRNA. The abundances of tetracycline resistance genes were correlated (
P
< 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of
Flavobacteriaceae
spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family
Ruminococcaceae
, class
Bacilli
, or phylum
Proteobacteria
. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems.
Evolutionary Aspects of Emerging Lyme Disease in Canada
Authors: Ogden N. H. , Feil E. J. , Leighton P. A. , Lindsay L. R. , Margos G. , Mechai S. , Michel P. , Moriarty T. J. 
Published: August 2015

ABSTRACT

In North America, Lyme disease (LD) is a tick-borne zoonosis caused by the spirochete bacterium
Borrelia burgdorferi
sensu stricto
, which is maintained by wildlife. Tick vectors and bacteria are currently spreading into Canada and causing increasing numbers of cases of LD in humans and raising a pressing need for public health responses. There is no vaccine, and LD prevention depends on knowing who is at risk and informing them how to protect themselves from infection. Recently, it was found in the United States that some strains of
B. burgdorferi
sensu stricto
cause severe disease, whereas others cause mild, self-limiting disease. While many strains occurring in the United States also occur in Canada, strains in some parts of Canada are different from those in the United States. We therefore recognize a need to identify which strains specific to Canada can cause severe disease and to characterize their geographic distribution to determine which Canadians are particularly at risk. In this review, we summarize the history of emergence of LD in North America, our current knowledge of
B. burgdorferi
sensu stricto
diversity, its intriguing origins in the ecology and evolution of the bacterium, and its importance for the epidemiology and clinical and laboratory diagnosis of LD. We propose methods for investigating associations between
B. burgdorferi
sensu stricto
diversity, ecology, and pathogenicity and for developing predictive tools to guide public health interventions. We also highlight the emergence of
B. burgdorferi
sensu stricto
in Canada as a unique opportunity for exploring the evolutionary aspects of tick-borne pathogen emergence.
Experimental Evolution of Enhanced Growth by Bacillus subtilis at Low Atmospheric Pressure: Genomic Changes Revealed by Whole-Genome Sequencing
Authors: Waters Samantha M. , Zeigler Daniel R. , Nicholson Wayne L. 
Published: August 2015

ABSTRACT

Knowledge of how microorganisms respond and adapt to low-pressure (LP) environments is limited. Previously,
Bacillus subtilis
strain WN624 was grown at the near-inhibitory LP of 5 kPa for 1,000 generations and strain WN1106, which exhibited increased relative fitness at 5 kPa, was isolated. Genomic sequence differences between ancestral strain WN624 and LP-evolved strain WN1106 were identified using whole-genome sequencing. LP-evolved strain WN1106 carried amino acid-altering mutations in the coding sequences of only seven genes (
fliI
,
parC
,
ytoI
,
bacD
,
resD
,
walK
, and
yvlD
) and a single 9-nucleotide in-frame deletion in the
rnjB
gene that encodes RNase J2, a component of the RNA degradosome. By using a collection of frozen stocks of the LP-evolved culture taken at 50-generation intervals, it was determined that (i) the fitness increase at LP occurred rapidly, while (ii) mutation acquisition exhibited complex kinetics. A knockout mutant of
rnjB
was shown to increase the competitive fitness of
B. subtilis
at both LP and standard atmospheric pressure.
FleQ Coordinates Flagellum-Dependent and -Independent Motilities in Pseudomonas syringae pv. tomato DC3000
Authors: Nogales Joaquina , Vargas Paola , Farias Gabriela A. , Olmedilla Adela , Sanjuán Juan , Gallegos María-Trinidad 
Published: August 2015

ABSTRACT

Motility plays an essential role in bacterial fitness and colonization in the plant environment, since it favors nutrient acquisition and avoidance of toxic substances, successful competition with other microorganisms, the ability to locate the preferred hosts, access to optimal sites within them, and dispersal in the environment during the course of transmission. In this work, we have observed that the mutation of the flagellar master regulatory gene,
fleQ
, alters bacterial surface motility and biosurfactant production, uncovering a new type of motility for
Pseudomonas syringae
pv. tomato DC3000 on semisolid surfaces. We present evidence that
P. syringae
pv. tomato DC3000 moves over semisolid surfaces by using at least two different types of motility, namely, swarming, which depends on the presence of flagella and syringafactin, a biosurfactant produced by this strain, and a flagellum-independent surface spreading or sliding, which also requires syringafactin. We also show that FleQ activates flagellum synthesis and negatively regulates syringafactin production in
P. syringae
pv. tomato DC3000. Finally, it was surprising to observe that mutants lacking flagella or syringafactin were as virulent as the wild type, and only the simultaneous loss of both flagella and syringafactin impairs the ability of
P. syringae
pv. tomato DC3000 to colonize tomato host plants and cause disease.
Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease
Authors: Lopez-Siles Mireia , Martinez-Medina Margarita , Abellà Carles , Busquets David , Sabat-Mir Miriam , Duncan Sylvia H. , Aldeguer Xavier , Flint Harry J. , Garcia-Gil L. Jesús 
Published: August 2015

ABSTRACT

Faecalibacterium prausnitzii
depletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associated
F. prausnitzii
populations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprint
F. prausnitzii
populations in biopsy specimens from 31 healthy control (H) subjects and 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness of
F. prausnitzii
subtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [OTU99]), which were shared by all groups of patients. Their distribution and the presence of some disease-specific
F. prausnitzii
phylotypes allowed us to differentiate the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (
P
= 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (
P
= 0.005). This study reveals that even though the main members of the
F. prausnitzii
population are present in both H subjects and individuals with gut diseases, richness is reduced in the latter and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability of
F. prausnitzii
phylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.
Light-Dependent Sulfide Oxidation in the Anoxic Zone of the Chesapeake Bay Can Be Explained by Small Populations of Phototrophic Bacteria
Authors: Findlay Alyssa J. , Bennett Alexa J. , Hanson Thomas E. , Luther George W. 
Published: August 2015

ABSTRACT

Microbial sulfide oxidation in aquatic environments is an important ecosystem process, as sulfide is potently toxic to aerobic organisms. Sulfide oxidation in anoxic waters can prevent the efflux of sulfide to aerobic water masses, thus mitigating toxicity. The contribution of phototrophic sulfide-oxidizing bacteria to anaerobic sulfide oxidation in the Chesapeake Bay and the redox chemistry of the stratified water column were investigated in the summers of 2011 to 2014. In 2011 and 2013, phototrophic sulfide-oxidizing bacteria closely related to
Prosthecochloris
species of the phylum
Chlorobi
were cultivated from waters sampled at and below the oxic-anoxic interface, where measured light penetration was sufficient to support populations of low-light-adapted photosynthetic bacteria. In 2012, 2013, and 2014, light-dependent sulfide loss was observed in freshly collected water column samples. In these samples, extremely low light levels caused 2- to 10-fold increases in the sulfide uptake rate over the sulfide uptake rate under dark conditions. An enrichment, CB11, dominated by
Prosthecochloris
species, oxidized sulfide with a

K
s

value of 11 μM and a
V
max
value of 51 μM min
−1
(mg protein
−1
). Using these kinetic values with
in situ
sulfide concentrations and light fluxes, we calculated that a small population of
Chlorobi
similar to those in enrichment CB11 can account for the observed anaerobic light-dependent sulfide consumption activity in natural water samples. We conclude that
Chlorobi
play a far larger role in the Chesapeake Bay than currently appreciated. This result has potential implications for coastal anoxic waters and expanding oxygen-minimum zones as they begin to impinge on the photic zone.
Quantitative Microbial Ecology through Stable Isotope Probing
Authors: Hungate Bruce A. , Mau Rebecca L. , Schwartz Egbert , Caporaso J. Gregory , Dijkstra Paul , van Gestel Natasja , Koch Benjamin J. , Liu Cindy M. , McHugh Theresa A. , Marks Jane C. , Morrissey Ember M. , Price Lance B. 
Published: August 2015

ABSTRACT

Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to
s
table
i
sotope
p
robing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in
18
O and
13
C composition after exposure to [
18
O]water or [
13
C]glucose. The addition of glucose increased the assimilation of
18
O into DNA from [
18
O]water. However, the increase in
18
O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
Cerium Regulates Expression of Alternative Methanol Dehydrogenases in Methylosinus trichosporium OB3b
Authors: Farhan Ul Haque Muhammad , Kalidass Bhagyalakshmi , Bandow Nathan , Turpin Erick A. , DiSpirito Alan A. , Semrau Jeremy D. 
Published: August 2015

ABSTRACT

Methanotrophs have multiple methane monooxygenases that are well known to be regulated by copper, i.e., a “copper switch.” At low copper/biomass ratios the soluble methane monooxygenase (sMMO) is expressed while expression and activity of the particulate methane monooxygenase (pMMO) increases with increasing availability of copper. In many methanotrophs there are also multiple methanol dehydrogenases (MeDHs), one based on Mxa and another based on Xox. Mxa-MeDH is known to have calcium in its active site, while Xox-MeDHs have been shown to have rare earth elements in their active site. We show here that the expression levels of Mxa-MeDH and Xox-MeDH in
Methylosinus trichosporium
OB3b significantly decreased and increased, respectively, when grown in the presence of cerium but the absence of copper compared to the absence of both metals. Expression of sMMO and pMMO was not affected. In the presence of copper, the effect of cerium on gene expression was less significant, i.e., expression of Mxa-MeDH in the presence of copper and cerium was slightly lower than in the presence of copper alone, but Xox-MeDH was again found to increase significantly. As expected, the addition of copper caused sMMO and pMMO expression levels to significantly decrease and increase, respectively, but the simultaneous addition of cerium had no discernible effect on MMO expression. As a result, it appears Mxa-MeDH can be uncoupled from methane oxidation by sMMO in
M. trichosporium
OB3b but not from pMMO.