bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depth-Dependent Survival of Escherichia coli and Enterococci in Soil after Manure Application and Simulated Rainfall
Authors: Stocker M. D. , Pachepsky Y. A. , Hill R. L. , Shelton D. R. 
Published: May 2015

ABSTRACT

Once released, manure-borne bacteria can enter runoff via interaction with the thin mixing layer near the soil surface. The objectives of this work were to document temporal changes in profile distributions of manure-borne
Escherichia coli
and enterococci in the near-surface soil layers after simulated rainfalls and to examine differences in survival of the two fecal indicator bacteria. Rainfall simulations were performed in triplicate on soil-filled boxes with grass cover and solid manure application for 1 h with rainfall depths of 30, 60, and 90 mm. Soil samples were collected weekly from depth ranges of 0 to 1, 1 to 2, 2 to 5, and 5 to 10 cm for 1 month. Rainfall intensity was found to have a significant impact on the initial concentrations of fecal indicator bacteria in the soil. While total numbers of enterococci rapidly declined over time,
E. coli
populations experienced initial growth with concentration increases of 4, 10, and 25 times the initial levels at rainfall treatment depths of 30, 60, and 90 mm, respectively.
E. coli
populations grew to the approximately the same level in all treatments. The 0- to 1-cm layer contained more indicator bacteria than the layers beneath it, and survival of indicator bacteria was better in this layer, with decimation times between 12 and 18 days after the first week of growth. The proportion of bacteria in the 0- to 1-cm layer grew with time as the total number of bacteria in the 0- to 10-cm layer declined. The results of this work indicate the need to revisit the bacterial survival patterns that are assumed in water quality models.
Stoichiometric Assembly of the Cellulosome Generates Maximum Synergy for the Degradation of Crystalline Cellulose, as Revealed by
In Vitro
Reconstitution of the Clostridium thermocellum Cellulosome
Authors: Hirano Katsuaki , Nihei Satoshi , Hasegawa Hiroki , Haruki Mitsuru , Hirano Nobutaka 
Published: May 2015

ABSTRACT

The cellulosome is a supramolecular multienzyme complex formed by species-specific interactions between the cohesin modules of scaffoldin proteins and the dockerin modules of a wide variety of polysaccharide-degrading enzymes. Cellulosomal enzymes bound to the scaffoldin protein act synergistically to degrade crystalline cellulose. However, there have been few attempts to reconstitute intact cellulosomes due to the difficulty of heterologously expressing full-length scaffoldin proteins. We describe the synthesis of a full-length scaffoldin protein containing nine cohesin modules, CipA; its deletion derivative containing two cohesin modules, ΔCipA; and three major cellulosomal cellulases, Cel48S, Cel8A, and Cel9K, of the
Clostridium thermocellum
cellulosome. The proteins were synthesized using a wheat germ cell-free protein synthesis system, and the purified proteins were used to reconstitute cellulosomes. Analysis of the cellulosome assembly using size exclusion chromatography suggested that the dockerin module of the enzymes stoichiometrically bound to the cohesin modules of the scaffoldin protein. The activity profile of the reconstituted cellulosomes indicated that cellulosomes assembled at a CipA/enzyme molar ratio of 1/9 (cohesin/dockerin = 1/1) and showed maximum synergy (4-fold synergy) for the degradation of crystalline substrate and ∼2.4-fold-higher synergy for its degradation than minicellulosomes assembled at a ΔCipA/enzyme molar ratio of 1/2 (cohesin/dockerin = 1/1). These results suggest that the binding of more enzyme molecules on a single scaffoldin protein results in higher synergy for the degradation of crystalline cellulose and that the stoichiometric assembly of the cellulosome, without excess or insufficient enzyme, is crucial for generating maximum synergy for the degradation of crystalline cellulose.
Metabolism of Doubly
para
-Substituted Hydroxychlorobiphenyls by Bacterial Biphenyl Dioxygenases
Authors: Pham Thi Thanh My , Sondossi Mohammad , Sylvestre Michel 
Published: May 2015

ABSTRACT

In this work, we examined the profile of metabolites produced from the doubly
para
-substituted biphenyl analogs 4,4′-dihydroxybiphenyl, 4-hydroxy-4′-chlorobiphenyl, 3-hydroxy-4,4′-dichlorobiphenyl, and 3,3′-dihydroxy-4,4′-chlorobiphenyl by biphenyl-induced
Pandoraea pnomenusa
B356 and by its biphenyl dioxygenase (BPDO). 4-Hydroxy-4′-chlorobiphenyl was hydroxylated principally through a 2,3-dioxygenation of the hydroxylated ring to generate 2,3-dihydro-2,3,4-trihydroxy-4′-chlorobiphenyl and 3,4-dihydroxy-4′-chlorobiphenyl after the removal of water. The former was further oxidized by the biphenyl dioxygenase to produce ultimately 3,4,5-trihydroxy-4′-chlorobiphenyl, a dead-end metabolite. 3-Hydroxy-4,4′-dichlorobiphenyl was oxygenated on both rings. Hydroxylation of the nonhydroxylated ring generated 2,3,3′-trihydroxy-4′-chlorobiphenyl with concomitant dechlorination, and 2,3,3′-trihydroxy-4′-chlorobiphenyl was ultimately metabolized to 2-hydroxy-4-chlorobenzoate, but hydroxylation of the hydroxylated ring generated dead-end metabolites. 3,3′-Dihydroxy-4,4′-dichlorobiphenyl was principally metabolized through a 2,3-dioxygenation to generate 2,3-dihydro-2,3,3′-trihydroxy-4,4′-dichlorobiphenyl, which was ultimately converted to 3-hydroxy-4-chlorobenzoate. Similar metabolites were produced when the biphenyl dioxygenase of
Burkholderia xenovorans
LB400 was used to catalyze the reactions, except that for the three substrates used, the BPDO of LB400 was less efficient than that of B356, and unlike that of B356, it was unable to further oxidize the initial reaction products. Together the data show that BPDO oxidation of doubly
para
-substituted hydroxychlorobiphenyls may generate nonnegligible amounts of dead-end metabolites. Therefore, biphenyl dioxygenase could produce metabolites other than those expected, corresponding to dihydrodihydroxy metabolites from initial doubly
para
-substituted substrates. This finding shows that a clear picture of the fate of polychlorinated biphenyls in contaminated sites will require more insights into the bacterial metabolism of hydroxychlorobiphenyls and the chemistry of the dihydrodihydroxylated metabolites derived from them.
Liposome-Encapsulated Bacteriophages for Enhanced Oral Phage Therapy against Salmonella spp
Authors: Colom Joan , Cano-Sarabia Mary , Otero Jennifer , Cortés Pilar , Maspoch Daniel , Llagostera Montserrat 
Published: May 2015

ABSTRACT

Bacteriophages UAB_Phi20, UAB_Phi78, and UAB_Phi87 were encapsulated in liposomes, and their efficacy in reducing
Salmonella
in poultry was then studied. The encapsulated phages had a mean diameter of 309 to 326 nm and a positive charge between +31.6 and +35.1 mV (pH 6.1). In simulated gastric fluid (pH 2.8), the titer of nonencapsulated phages decreased by 5.7 to 7.8 log units, whereas encapsulated phages were significantly more stable, with losses of 3.7 to 5.4 log units. The liposome coating also improved the retention of bacteriophages in the chicken intestinal tract. When cocktails of the encapsulated and nonencapsulated phages were administered to broilers, after 72 h the encapsulated phages were detected in 38.1% of the animals, whereas the nonencapsulated phages were present in only 9.5%. The difference was significant. In addition, in an
in vitro
experiment, the cecal contents of broilers promoted the release of the phages from the liposomes. In broilers experimentally infected with
Salmonella
, the daily administration of the two cocktails for 6 days postinfection conferred similar levels of protection against
Salmonella
colonization. However, once treatment was stopped, protection by the nonencapsulated phages disappeared, whereas that provided by the encapsulated phages persisted for at least 1 week, showing the enhanced efficacy of the encapsulated phages in protecting poultry against
Salmonella
over time. The methodology described here allows the liposome encapsulation of phages of different morphologies. The preparations can be stored for at least 3 months at 4°C and could be added to the drinking water and feed of animals.
Generation of a Novel Staphylococcus aureus Ghost Vaccine and Examination of Its Immunogenicity against Virulent Challenge in Rats
Authors: Vinod Nagarajan , Oh Sung , Park Hyun Jung , Koo Jung Mo , Choi Chang Won , Kim Sei Chang 
Published: May 2015

ABSTRACTStaphylococcus aureusis a Gram-positive pathogen that causes a wide range of infections in humans and animals. Bacterial ghosts are nonliving, empty cell envelopes and are well represented as novel vaccine candidates. In this study, we examined the immunogenicity and protective efficacy ofS. aureusghosts (SAGs) against a virulent challenge in rats. Nonliving SAGs were generated by using the MIC of sodium hydroxide. The formation of a transmembrane lysis tunnel structure in SAGs was visualized by scanning electron microscopy. To investigate these SAGs as a vaccine candidate, rats were divided into four groups, A (nonimmunized control), B (orally immunized), C (subcutaneously immunized), and D (intravenously immunized). The IgG antibody responses were significantly stronger in the SAG-immunized groups than in the nonimmunized control group (P< 0.05). Moreover, a significant increase in the populations of CD4+and CD8+T cells was observed in all three immunized groups (P< 0.05). We also found that serum bactericidal antibodies were significantly elicited in the SAG-immunized groups (P< 0.05). Most importantly, the bacterial loads in the immunized groups were significantly lower than those in the nonimmunized control group (P< 0.01). These results suggest that immunization with SAGs induces immune responses and provides protection against a virulentS. aureuschallenge.
Comparative Roles of the Two Helicobacter pylori Thioredoxins in Preventing Macromolecule Damage
Authors: Kuhns Lisa G. , Wang Ge , Maier Robert J. 
Published: May 2015

ABSTRACT

Thioredoxins are highly conserved throughout a wide range of organisms, and they are essential for the isurvival of oxygen-sensitive cells. The gastric pathogen
Helicobacter pylori
uses the thioredoxin system to maintain its thiol/disulfide balance. There are two thioredoxins present in
H. pylori
, Trx1 and Trx2 (herein referred to as TrxA and TrxC). TrxA has been shown to be important as an electron donor for some antioxidant enzymes, but the function of TrxC remains unknown (L. M. Baker, A. Raudonikiene, P. S. Hoffman, and L. B. Poole, J Bacteriol 183:1961–1973, 2001; P. Alamuri and R. J. Maier, J Bacteriol 188:5839–5850, 2006). We demonstrate that both TrxA and TrxC are important in protecting
H. pylori
from oxidative stress. Individual Δ
trxA
and Δ
trxC
deletion mutant strains each show a greater abundance of lipid peroxides and suffer more DNA damage and more protein carbonylation than the parent. Both deletion mutants were much more sensitive to O
2
-mediated viability loss than the parent. Unexpectedly, the oxidative DNA damage and protein carbonylation was more severe in the Δ
trxC
mutant than in the Δ
trxA
mutant; it had 20-fold- and 4-fold-more carbonylated protein content than the wild type and the Δ
trxA
strain, respectively, after 4 h of atmospheric O
2
stress.
trx
transcript abundance was altered by the deletion of the heterologous
trx
gene. The Δ
trxC
mutant lacked mouse colonization ability, while the ability to colonize mouse stomachs was significantly reduced in the Δ
trxA
mutant.
The PduL Phosphotransacylase Is Used To Recycle Coenzyme A within the Pdu Microcompartment
Authors: Liu Yu , Jorda Julien , Yeates Todd O. , Bobik Thomas A. 
Published: May 2015

ABSTRACT

In
Salmonella enterica
, 1,2-propanediol (1,2-PD) utilization (Pdu) is mediated by a bacterial microcompartment (MCP). The Pdu MCP consists of a multiprotein shell that encapsulates enzymes and cofactors for 1,2-PD catabolism, and its role is to sequester a reactive intermediate (propionaldehyde) to minimize cellular toxicity and DNA damage. For the Pdu MCP to function, the enzymes encapsulated within must be provided with a steady supply of substrates and cofactors. In the present study, Western blotting assays were used to demonstrate that the PduL phosphotransacylase is a component of the Pdu MCP. We also show that the N-terminal 20-residue-long peptide of PduL is necessary and sufficient for targeting PduL and enhanced green fluorescent protein (eGFP) to the lumen of the Pdu MCP. We present the results of genetic tests that indicate that PduL plays a role in the recycling of coenzyme A internally within the Pdu MCP. However, the results indicate that some coenzyme A recycling occurs externally to the Pdu MCP. Hence, our results support a model in which a steady supply of coenzyme A is provided to MCP lumen enzymes by internal recycling by PduL as well as by the movement of coenzyme A across the shell by an unknown mechanism. These studies expand our understanding of the Pdu MCP, which has been linked to enteric pathogenesis and which provides a possible basis for the development of intracellular bioreactors for use in biotechnology.

IMPORTANCE
Bacterial MCPs are widespread organelles that play important roles in pathogenesis and global carbon fixation. Here we show that the PduL phosphotransacylase is a component of the Pdu MCP. We also show that PduL plays a key role in cofactor homeostasis by recycling coenzyme A internally within the Pdu MCP. Further, we identify a potential N-terminal targeting sequence using a bioinformatic approach and show that this short sequence extension is necessary and sufficient for directing PduL as well as heterologous proteins to the lumen of the Pdu MCP. These findings expand our general understanding of bacterial MCP assembly and cofactor homeostasis.
Bacillus anthracis Overcomes an Amino Acid Auxotrophy by Cleaving Host Serum Proteins
Authors: Terwilliger Austen , Swick Michelle C. , Pflughoeft Kathryn J. , Pomerantsev Andrei , Lyons C. Rick , Koehler Theresa M. , Maresso Anthony 
Published: May 2015

ABSTRACT

Bacteria sustain an infection by acquiring nutrients from the host to support replication. The host sequesters these nutrients as a growth-restricting strategy, a concept termed “nutritional immunity.” Historically, the study of nutritional immunity has centered on iron uptake because many bacteria target hemoglobin, an abundant circulating protein, as an iron source. Left unresolved are the mechanisms that bacteria use to attain other nutrients from host sources, including amino acids. We employed a novel medium designed to mimic the chemical composition of human serum, and we show here that
Bacillus anthracis
, the causative agent of anthrax disease, proteolyzes human hemoglobin to liberate essential amino acids which enhance its growth. This property can be traced to the actions of InhA1, a secreted metalloprotease, and extends to at least three other serum proteins, including serum albumin. The results suggest that we must also consider proteolysis of key host proteins to be a way for bacterial pathogens to attain essential nutrients, and we provide an experimental framework to determine the host and bacterial factors involved in this process.

IMPORTANCE
The mechanisms by which bacterial pathogens acquire nutrients during infection are poorly understood. Here we used a novel defined medium that approximates the chemical composition of human blood serum, blood serum mimic (BSM), to better model the nutritional environment that pathogens encounter during bacteremia. Removing essential amino acids from BSM revealed that two of the most abundant proteins in blood—hemoglobin and serum albumin—can satiate the amino acid requirement for
Bacillus anthracis
, the causative agent of anthrax. We further demonstrate that hemoglobin is proteolyzed by the secreted protease InhA1. These studies highlight that common blood proteins can be a nutrient source for bacteria. They also challenge the historical view that hemoglobin is solely an iron source for bacterial pathogens.
Importance of Real-Time Assays To Distinguish Multidrug Efflux Pump-Inhibiting and Outer Membrane-Destabilizing Activities in Escherichia coli
Authors: Misra Rajeev , Morrison Keith D. , Cho Hyun Jae , Khuu Thanh 
Published: May 2015

ABSTRACTThe constitutively expressed AcrAB multidrug efflux system ofEscherichia colishows a high degree of homology with the normally silent AcrEF system. Exposure of a strain withacrABdeleted to antibiotic selection pressure frequently leads to the insertion sequence-mediated activation of the homologous AcrEF system. In this study, we used strains constitutively expressing either AcrAB or AcrEF from their normal chromosomal locations to resolve a controversy about whether phenylalanylarginine β-naphthylamide (PAβN) inhibits the activities of AcrAB and AcrEF and/or acts synergistically with antibiotics by destabilizing the outer membrane permeability barrier. Real-time efflux assays allowed a clear distinction between the efflux pump-inhibiting activity of PAβN and the outer membrane-destabilizing action of polymyxin B nonapeptide (PMXBN). When added in equal amounts, PAβN, but not PMXBN, strongly inhibited the efflux activities of both AcrAB and AcrEF pumps. In contrast, when outer membrane destabilization was assessed by the nitrocefin hydrolysis assay, PMXBN exerted a much greater damaging effect than PAβN. Strong action of PAβN in inhibiting efflux activity compared to its weak action in destabilizing the outer membrane permeability barrier suggests that PAβN acts mainly by inhibiting efflux pumps. We concluded that at low concentrations, PAβN acts specifically as an inhibitor of both AcrAB and AcrEF efflux pumps; however, at high concentrations, PAβN in the efflux-proficient background not only inhibits efflux pump activity but also destabilizes the membrane. The effects of PAβN on membrane integrity are compounded in cells unable to extrude PAβN.IMPORTANCEThe increase in multidrug-resistant bacterial pathogens at an alarming rate has accelerated the need for implementation of better antimicrobial stewardship, discovery of new antibiotics, and deeper understanding of the mechanism of drug resistance. The work carried out in this study highlights the importance of employing real-time fluorescence-based assays in differentiating multidrug efflux-inhibitory and outer membrane-destabilizing activities of antibacterial compounds.
Access all areas? An area-level analysis of accessibility to general practice and community pharmacy services in England by urbanity and social deprivation
Authors: Todd Adam , Copeland Alison , Husband Andy , Kasim Adetayo , Bambra Clare 
Published: May 2015

Objectives(1) To determine the percentage of the population in England that has access to a general practitioner (GP) premises within a 20 min walk (the accessibility); (2) explore the relationship between the walking distance to a GP premises and urbanity and social deprivation and (3) compare accessibility of a GP premises to that of a community pharmacy—and how this may vary by urbanity and social deprivation.DesignThis area-level analysis spatial study used postcodes for all GP premises and community pharmacies in England. Each postcode was assigned to a population lookup table and Lower Super Output Area (LSOA). The LSOA was then matched to urbanity (urban, town and fringe, or village, hamlet and isolated dwellings) and deprivation decile (using the Index of Multiple Deprivation score 2010).Primary outcome measureLiving within a 20 min walk of a GP premises.ResultsOverall, 84.8% of the population is estimated to live within a 20 min walk of a GP premises: 81.2% in the most affluent areas, 98.2% in the most deprived areas, 94.2% in urban and 19.4% in rural areas. This is consistently lower when compared with the population living within a 20 min walk of a community pharmacy.ConclusionsOur study shows that the vast majority of the population live within a 20 min walk of a GP premises, with higher proportions in the most deprived areas—a positive primary care law. However, more people live within a 20 min walk of a community pharmacy compared with a GP premises, and this potentially has implications for the commissioning of future services from these healthcare providers in England.
Is a haptic simulation interface more effective than computer mouse-based interface for neonatal intubation skills training?
Authors: Agarwal Anup , Leviter Julie , Mannarino Candace , Levit Orly , Johnston Lindsay , Auerbach Marc 
Published: May 2015

ObjectiveTo compare the efficacy of a three-dimensional (3D) haptic interface to a two-dimensional (2D) mouse interface for a screen-based simulation (SBS) neonatal intubation (NI) training intervention. Primary hypothesis: a haptic interface is more effective than a mouse interface for SBS training intervention for NI. Secondary hypothesis: SBS training, regardless of interface, will result in improved NI performance on a neonatal airway simulator.Methods45 participants were randomised to either a haptics or a mouse interface to complete an identical SBS training intervention for NI over a five-month period. Participants completed pre- and post-training surveys to assess demographics, experience, knowledge and attitudes. The primary outcome of participants’ NI skills performance was assessed on a neonatal manikin simulator. Skills were measured pre- and post- training by number of attempts and time to successfully intubate, and airway visualization.ResultsThe demographics, training and experience were similar between groups. There was no difference in the improvement in skills, knowledge, attitudes or satisfaction ratings pre- and post-training between the groups. There was a significant decrease in number of attempts to intubate a neonatal airway simulator (2.89 vs 1.96, p<0.05) and improvement in the percent of subjects intubating in <30 seconds (22% vs 27%, p=0.02) from pre- to post-training in the study population overall.ConclusionUsing a haptic interface did not have an advantage over a mouse interface in improving NI skills, knowledge, attitudes, or satisfaction. Overall, a SBS training intervention for NI improved skills measured on a neonatal airway simulator.
A review of RST
VOLC
, an original algorithm for automatic detection and near-real-time monitoring of volcanic hotspots from space
Authors: Pergola N. , Coviello I. , Filizzola C. , Lacava T. , Marchese F. , Paciello R. , Tramutoli V. 
Published: May 2015

Abstract

The observation of volcanic thermal activity from space dates back to the late 1960s. Several methods have been proposed to improve detection and monitoring capabilities of thermal volcanic features, and to characterize them to improve our understanding of volcanic processes, as well as to inform operational decisions. In this paper we review the RST
VOLC
algorithm, which has been designed and implemented for automated detection and near-real-time monitoring of volcanic hotspots. The algorithm is based on the general Robust Satellite Techniques (RST) approach, representing an original strategy for satellite data analysis in the space–time domain. It has proven to be a useful tool for investigating volcanoes worldwide, by means of different satellite sensors, onboard polar orbiting and geostationary platforms. The RST
VOLC
rationale, its requirements and main operational capabilities are described here, together with the advantages of the tool and the known limitations. Results achieved through the study of two past eruptive events are shown, together with some recent examples demonstrating the near-continuous monitoring capability offered by RST
VOLC
. A summary is also made of the type products that the method is able to generate and provide. Lastly, the future perspectives, in terms of its possible implementation on the new generation of satellite systems, are briefly discussed.