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O’Connell AP, Moore JE, Hu AC. A Paratracheal Mass. JAMA Otolaryngol Head Neck Surg 2013; 139:959-60. [DOI: 10.1001/jamaoto.2013.4113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Nakanishi S, Rao JR, Matsuda M, Goldsmith CE, Coulter WA, Moore JE. Antibiotic resistance reversal (ARR) in Gram-negative and Gram-positive pathogens employing electric fields. Br J Biomed Sci 2013; 70:81-3. [PMID: 23888611 DOI: 10.1080/09674845.2013.11978265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bertram CD, Macaskill C, Davis MJ, Moore JE. Development of a model of a multi-lymphangion lymphatic vessel incorporating realistic and measured parameter values. Biomech Model Mechanobiol 2013; 13:401-16. [PMID: 23801424 DOI: 10.1007/s10237-013-0505-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/31/2013] [Indexed: 11/30/2022]
Abstract
Our published model of a lymphatic vessel consisting of multiple actively contracting segments between non-return valves has been further developed by the incorporation of properties derived from observations and measurements of rat mesenteric vessels. These included (1) a refractory period between contractions, (2) a highly nonlinear form for the passive part of the pressure-diameter relationship, (3) hysteretic and transmural-pressure-dependent valve opening and closing pressure thresholds and (4) dependence of active tension on muscle length as reflected in local diameter. Experimentally, lymphatic valves are known to be biased to stay open. In consequence, in the improved model, vessel pumping of fluid suffers losses by regurgitation, and valve closure is dependent on backflow first causing an adverse valve pressure drop sufficient to reach the closure threshold. The assumed resistance of an open valve therefore becomes a critical parameter, and experiments to measure this quantity are reported here. However, incorporating this parameter value, along with other parameter values based on existing measurements, led to ineffective pumping. It is argued that the published measurements of valve-closing pressure threshold overestimate this quantity owing to neglect of micro-pipette resistance. An estimate is made of the extent of the possible resulting error. Correcting by this amount, the pumping performance is improved, but still very inefficient unless the open-valve resistance is also increased beyond the measured level. Arguments are given as to why this is justified, and other areas where experimental data are lacking are identified. The model is capable of future adaptation as new experimental data appear.
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Richardson WJ, Wilson E, Moore JE. Altered phenotypic gene expression of 10T1/2 mesenchymal cells in nonuniformly stretched PEGDA hydrogels. Am J Physiol Cell Physiol 2013; 305:C100-10. [PMID: 23657569 DOI: 10.1152/ajpcell.00340.2012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Disease-related phenotype modulation of many cell types has been shown to be closely related to mechanical loading conditions; for example, vascular smooth muscle cell (SMC) phenotype shift from a mature, contractile state to a proliferative, synthetic state contributes to the formation of neointimal tissue during atherosclerosis and restenosis development and is related to SMC mechanical loading in vivo. The majority of past in vitro cell-stretching experiments have employed simplistic (uniform, uniaxial or biaxial) stretching environments to elucidate mechanobiological pathways involved in phenotypic shifts. However, the in vivo mechanics of the vascular wall consists of highly nonuniform stretch. Here we subjected 10T1/2 murine mesenchymal cells (an SMC precursor) to two- and three-dimensional nonuniform stretch environments. After 24 h of stretch, cells on an elastomeric membrane demonstrated varied proliferation [assessed by 5-bromo-2'-deoxyuridine (BrdU) incorporation] depending on location upon the membrane, with maximal proliferation occurring in a region of high, uniaxial stretch. Cells subjected to a nonuniform stretching regimen within three-dimensional polyethylene glycol diacrylate (PEGDA) hydrogel constructs demonstrated marked changes in mRNA expression of several phenotype-related proteins, indicating a sort of "hybrid" phenotype with contractile and synthetic markers being both upregulated and downregulated. Furthermore, expression levels of mRNAs were significantly different between various locations within the stretched gel. With the proliferation results, these data exhibit the capability of nonuniform stretching devices to induce heterogeneous cell responses, potentially indicative of spatial distributions of disease-related behaviors in vivo.
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Nakanishi S, Nakajima T, Tazumi A, Matsubara K, Moore JE, Millar BC, Matsuda M. Construction, expression and characterisation of recombinant molecules of the urease gene operon from a urease-positive thermophilic Campylobacter (UPTC) isolate. Br J Biomed Sci 2013; 70:15-21. [PMID: 23617093 DOI: 10.1080/09674845.2013.11669924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A recombinant molecule of the full-length urease gene operon was constructed in vitro from the Japanese urease-positive thermophilic Campylobacter (UPTC) CF89-12 isolate and expressed in Escherichia coli cells. Several large deletion recombinant variants of urease subunit genes were also constructed and expressed in E. coli cells. A positive urease reaction with the log-phase cultured E. coli JM109 cells in the NiCl2-containing medium transformed with pGEM-T vector carrying the recombinant molecule of the full-length operon was detected with isopropyl-beta-D-thiogalactoside. Among the several deletion recombinant variants, each ureA-, ureB-, ureE-, ureF-, ureG- and ureH-large deficient, only ureE-large deletion variant (63% deficient) showed a positive urease reaction (approximately 15-fold). In addition, a ureE-complete deletion recombinant variant (100% deficient) constructed also showed a positive reaction of urease (approximately 18-fold). Recombinant urease subunits A and B were immunologically identified by Western blot analysis with anti-urease alpha (A) and beta (B) raised against Helicobacter pylori.
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Bertram CD, Macaskill C, Moore JE. Incorporating measured valve properties into a numerical model of a lymphatic vessel. Comput Methods Biomech Biomed Engin 2013; 17:1519-34. [PMID: 23387996 DOI: 10.1080/10255842.2012.753066] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An existing lumped-parameter model of multiple lymphangions (lymphatic vascular segments) in series is adapted for the incorporation of recent physiological measurements of lymphatic vascular properties. The new data show very marked nonlinearity of the passive pressure-diameter relation during distension, relative to comparable blood vessels, and complex valve behaviour. Since lymph is transported as a result of either the active contraction or the passive squeezing of vascular segments situated between two one-way valves, the performance of these valves is of primary importance. The valves display hysteresis (the opening and closing pressure drop thresholds differ), a bias to staying open (both state changes occur when the trans-valve pressure drop is adverse) and pressure-drop threshold dependence on transmural pressure. These properties, in combination with the strong nonlinearity that valve operation represents, have in turn caused intriguing numerical problems in the model, and we describe numerical stratagems by which we have overcome the problems. The principal problem is also generalised into a relatively simple mathematical example, for which solution detail is provided using two different solvers.
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Nakajima T, Hayashi K, Nagatomi R, Matsubara K, Moore JE, Millar BC, Matsuda M. Molecular identification of an arsenic four-gene operon in Campylobacter lari. Folia Microbiol (Praha) 2012; 58:253-60. [PMID: 23132657 DOI: 10.1007/s12223-012-0207-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022]
Abstract
An arsenic (ars) four-gene operon, containing genes encoding a putative membrane permease (ArsP), a transcriptional repressor (ArsR), an arsenate reductase (ArsC) and an arsenical-resistance membrane transporter (Acr3) was first identified in urease-positive thermophilic Campylobacter (UPTC) isolate, CF89-12. UPTC CF89-12 and some other Campylobacter lari isolates contained their ars four-genes, similarly, differing from that in the reference C. lari RM2100 strain. Two putative promoters and a putative terminator were identified for the operon in UPTC CF89-12. In vivo transcription of the operon was confirmed in the UPTC cells. PCR experiments using two primer pairs designed in silico to amplify two arsR and arsC-acr3 segments, respectively, generated two amplicons, approximately 200 and 350 base pairs, with all 31 of 31 and 19 of 31 C. lari isolates (n = 17 for UPTC; n = 14 for UN C. lari), respectively. An inverted repeat forming a dyad structure, a potential binding site for a transcriptional repressor, was identified in the promoter region. Within the deduced 61 amino acids sequence of the putative arsR open reading frame from the UPTC CF89-12, a metal binding box and a DNA-binding helix-turn-helix motif were identified. The UPTC CF89-12 and some other UPTC isolates isolated from natural environment were resistant to arsenate.
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Karrasch C, Bardarson JH, Moore JE. Finite-temperature dynamical density matrix renormalization group and the Drude weight of spin-1/2 chains. PHYSICAL REVIEW LETTERS 2012; 108:227206. [PMID: 23003649 DOI: 10.1103/physrevlett.108.227206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/27/2012] [Indexed: 06/01/2023]
Abstract
We propose an easily implemented approach to study time-dependent correlation functions of one-dimensional systems at finite-temperature T using the density matrix renormalization group. The entanglement growth inherent to any time-dependent calculation is significantly reduced if the auxiliary degrees of freedom which purify the statistical operator are time evolved with the physical Hamiltonian but reversed time. We exploit this to investigate the long-time behavior of current correlation functions of the XXZ spin-1/2 Heisenberg chain. This allows a direct extraction of the Drude weight D at intermediate to large T. We find that D is nonzero--and thus transport is dissipationless--everywhere in the gapless phase. At low temperatures we establish an upper bound to D by comparing with bosonization.
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Moore JE, Coulter WA, Goldsmith CE. Maintaining culturability of Streptococcus pneumoniae (pneumococci) during transportation. Br J Biomed Sci 2012; 69:34-5. [PMID: 22558803 DOI: 10.1080/09674845.2012.11669920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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85
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Hirayama J, Hayashi K, Goldsmith CE, Coulter WA, Millar BC, Dooley JSG, Matsuda M, Moore JE. Polymerase chain reaction amplification: effect of dyes and other staining agents employed in clinical microbiology laboratories. Br J Biomed Sci 2012; 69:35-7. [PMID: 22558804 DOI: 10.1080/09674845.2012.11978243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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86
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Nakajima T, Hirayama J, Tazumi A, Hayashi K, Tasaki E, Asakura M, Yamasaki S, Moore JE, Millar BC, Matsuda M. Comparative analysis of Campylobacter lari cytolethal distending toxin (CDT) effect on HeLa cells. J Basic Microbiol 2012; 52:559-65. [PMID: 22359318 DOI: 10.1002/jobm.201100297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/07/2011] [Indexed: 11/06/2022]
Abstract
We aimed to clarify if Campylobacter lari exerts a cytolethal distending toxin (CDT) effect on HeLa cells. Campylobacter cell lysates (CCLys) from C. jejuni 81-176 and urease-positive thermophilic Campylobacter (UPTC) CF89-12 and UPTC NCTC12893 isolates were shown to exert a CDT effect on HeLa cells with morphological changes examined by Giemsa staining and microscopy. However, Campylobacter lari JCM2530(T) isolate showed no effect. In addition, Campylobacter cell culture supernatant wash gave low or absent toxic effects with both C. jejuni and C. lari organisms. When western blot analysis was carried out to clarify if there was a CDTB effect in the CCLys and soluble fractions from Campylobacter isolates, which had a CDT effect on HeLa cells or did not have any effect, anti-recombinant CjCDTB antibodies identified an immunoreactively positive signal at around approximately 25 kDa on all the C. lari isolates examined, as well as the C. jejuni 81116 strain. Thus, all the Campylobacter isolates including those without any CDT effect were shown to express CDTB at the translational level.
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Maeda Y, Goldsmith CE, Coulter WA, Mason C, Dooley JSG, Lowery CJ, Millar BC, Moore JE. Comparasion of five gene loci (rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ) to aid the molecular identification of viridans-group streptococci and pneumococci. Br J Biomed Sci 2012; 68:190-6. [PMID: 22263433 DOI: 10.1080/09674845.2011.11730349] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Viridans-group streptococci (VGS) consist of several taxa which historically have been highly diverse. However, at times it may become necessary to have a reliable scheme for the identification of these organisms to the species level. The aim of this study is to compare the ability of five gene loci, namely rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ, to speciate such organisms through a sequence typing-based approach. Reference organisms consisting of six VGS species were compared based on sequence typing, followed by comparison of 31 wild-type respiratory isolates, and showed that employment of sequence typing using the rnpB gene locus was the most specific and reliable. Therefore, the use of rnpB sequencing for the identification of VGS to species level is a reliable and feasible option, based on a single gene target.
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Hayashi K, Tazumi A, Nakajima T, Endo A, Moore JE, Millar BC, Matsuda M. Reliability of a multiplex PCR assay for the identification of the major Campylobacter taxa. Br J Biomed Sci 2012; 68:185-9. [PMID: 22263432 DOI: 10.1080/09674845.2011.11730348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The primer pair (C412F/C1228R) constructed previously for the polymerase chain reaction (PCR) identification of the genus Campylobacter using an approximate 800 base pair (bp) 16S rRNA gene target segment proved to be useful for the identification of a total of 49 Campylobacter lari isolates including urease-positive thermophilic Campylobacter (UPTC) organisms (n=25). When the primer pair (CLF/R) developed previously for the PCR identification of C. lari species using an approximate 250 bp glyA segment was employed, 27 C. lari isolates, including all the UPTC isolates, were identified to be PCR-negative (55%). Therefore, this PCR procedure developed for the molecular identification of C. lari was shown to be unreliable for C. lari identification. Nucleotide sequencing analysis clarified the reason(s) why PCR-negative examples occurred in many C. lari isolates, including UPTC isolates. The primer pair target sequences in the C. lari-specific PCR-negative isolates apparently varied at the 3' end region, as compared with C. lari-specific PCR-positive isolates. Thus, the multiplex PCR assay developed previously was shown to be unreliable for the molecular identification of C. lari subspecies organisms.
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89
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Davies E, Wieboldt J, Stanley T, Maeda Y, Smyth M, Stanley S, McClean M, Evans W, Funston C, Millar BC, Goldsmith CE, Moore JE. Isolation and identification of 'Mycobacterium angelicum' from a patient with type II respiratory failure: suggested reporting guidelines to molecular clinical laboratories. Br J Biomed Sci 2012; 69:134-136. [PMID: 23057162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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90
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Moore JE, Millar BC, Coulter WA, Mason C, Rooney RJ, Loughrey A, Goldsmith CE. Mining the antibiogram: what more can it tell us? Br J Biomed Sci 2012; 69:76-80. [PMID: 22872932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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91
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Kakinuma Y, Maeda Y, Mason C, Goldsmith CE, Coulter WA, Matsuda M, Dooley JSG, Lowery CJ, Moore JE. Molecular characterisation of the quinolone resistance-determining regions (QRDR) including gyrA, gyrB, parC and parE genes in Streptococcus pneumoniae. Br J Biomed Sci 2012; 69:123-125. [PMID: 23057160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP). Currently, empirical treatment with quinolones is being used due to the emergence of beta-lactam and macrolide resistance in S. pneumonaie. Although the prevalence of quinolone-resistant S. pneumoniae remains low, increasing numbers of resistant isolates are being seen. Genetic mechanisms leading to fluoroquinolone resistance in pneumococci are complex. This study aims to use molecular methods to characterise all isolates through sequence analysis of their QRDR regions. Thirty-two S. pneumoniae isolates were obtained from nasal swabs from adult and paediatric patients attending local general practices in Northern Ireland. Phenotypic minimum inhibitory concentration (MIC) was determined for Clinical and Laboratory Standards Institute (CLSI) broth microdilution against ciprofloxacin, levofloxacin and norfloxacin. Simultaneously, the QRDR regions of gyrA, gyrB, parC and parE were analysed by sequence typing for all pneumococci obtained. Only one isolate (3.1%) showed reduced susceptibility to ciprofloxacin and levofloxacin. Two amino acid positions were discordant in the S. pneumoniae R6 strain and eight (25%) and 23 (71.9%) isolates contained the mutations Ile460Val in gyrA and Lys137Asn in parC (deposited in GenBank, accession numbers GQ999587-GQ999589), respectively. No mutations were found in either the gyrB or parE loci. In conclusion, the study demonstrated increased fluoroquinolone resistance which could not be accounted for simply through QRDR mutations, and, reciprocally, that mutations in the QRDR region do not necessarily result in overt phenotypic resistance.
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Moore RJ, Rao JR, Nelson D, McCollum G, Ballard LM, Millar BC, Nakanishi S, Tasaki E, Nakajima T, Matsuda M, Goldsmith CE, Coulter WA, Loughrey A, Rooney RJ, O'Sullivan JT, Moore JE. Examination of the antibacterial properties of sphagnum moss (Sphagnum spp.) and its significance with turf burning in Ireland. Br J Biomed Sci 2012; 69:178-180. [PMID: 23304795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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93
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Walb MC, Moore JE, Attia A, Wheeler KT, Miller MS, Munley MT. A technique for murine irradiation in a controlled gas environment. BIOMEDICAL SCIENCES INSTRUMENTATION 2012; 48:470-7. [PMID: 22846321 PMCID: PMC3709974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
NASAs extra-vehicular activities (EVAs) involve exposure to high energy photons while breathing 100% oxygen. Using previously verified mouse models, our laboratory is studying whether low dose irradiation under these hyperoxic conditions could lead to an increase in carcinogenic potential. To simulate the environment astronauts encounter during an EVA, enclosed chambers were constructed that allowed for mouse movement, controlled gas conditions, and uniform radiation dose delivery. Custom-built gas chambers with input/output gas valves and dividers that allowed for uniform gas flow were used to keep 6 unanesthetized mice separated while they were irradiated. The chambers were supplied with 100% oxygen or air using ball valves linked together with T-splitters. A calibrated ion chamber was used to verify the radiation dose distribution across an entire chamber. Mice were placed in the gas environments for 0.5 h, irradiated with a 10 or 18 MV photon beam from a medical linear accelerator, and left in their gas environment for 2 h post-irradiation. We irradiated 200 mice (5 different doses between 0-1000 mGy) under normoxic or 100% oxygen conditions. For the next step of this research, these mice will be euthanized 9 months post-irradiation, and lung tumors will be counted and sized to determine if hyperoxia increases the carcinogenic effect for this model.
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Hayashi K, Hirayama J, Goldsmith CE, Coulter WA, Millar BC, Dooley JSG, Loughrey A, Rooney PJ, Matsuda M, Moore JE. Exposure to clinical X-ray radiation does not alter antibiotic susceptibility or genotype profile in gram-negative and gram-positive clinical pathogens. Br J Biomed Sci 2012; 69:119-122. [PMID: 23057159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Inadvertent exposure of bacterial pathogens to X-ray radiation may be an environmental stress, where the bacterium may respond by increasing mutational events, thereby potentially resulting in increased antibiotic resistance and alteration to genotypic profile. In order to examine this, four clinical pathogens, including the Gram-negative organisms Escherichia coli O157:H7 NCTC12900 and Pseudomonas aeruginosa NCTC10662, as well as the Gram-positive organisms Staphylococcus aureus NCTC6571 and Enterococcus faecium were exposed to X-rays (35,495 cGy/cm2) over a seven-day period. Antibiotic susceptibility was assessed before, during and after exposure by examining susceptibility, as quantified by E-test with six antibiotics, as well as to a further 11 antibiotics by measurement of susceptibility zone sizes (mm). Additionally, the DNA profile of each organism was compared before, during and after exposure employing the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC PCR). Results indicated that exposure of these organisms to this amount of X-ray radiation did not alter their antibiotic susceptibility, nor their genomic DNA profile. Overall, these data indicate that exposure of bacteria to X-ray radiation does not alter the test organisms' antibiotic susceptibility profiles, nor alter genomic DNA profiles of bacteria, which therefore does not compromise molecular epidemiological tracking of bacteria within healthcare environments in which patients have been exposed to X-ray radiation.
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Macoon B, Sollenberger LE, Staples CR, Portier KM, Fike JH, Moore JE. Grazing management and supplementation effects on forage and dairy cow performance on cool-season pastures in the southeastern United States. J Dairy Sci 2011; 94:3949-59. [PMID: 21787931 DOI: 10.3168/jds.2010-3947] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/25/2011] [Indexed: 11/19/2022]
Abstract
Cool-season annual forages provide high-quality herbage for up to 5 mo in the US Gulf Coast states, but their management in pasture-based dairy systems has received little attention. Objectives of this study were to evaluate pasture and animal responses when lactating Holstein cows (n=32, mean DIM=184±21) grazed either N-fertilized rye (Secale cereale L.)-annual ryegrass (Lolium multiflorum Lam.) mixed pastures or rye-annual ryegrass-crimson clover (Trifolium incarnatum L.)-red clover (Trifolium pratense L.) pastures at 2 stocking rates (5 vs. 2.5 cows/ha) and 2 rates of concentrate supplementation [0.29 or 0.40 kg of supplement (as is)/kg of daily milk production]. Two cows paired by parity (one multiparous and one primiparous) were assigned randomly to each pasture. The 2 × 2 × 2 factorial arrangement of treatments was replicated twice in a completely randomized design. Forage mixture and supplementation rate did not affect milk production during three 28-d periods. Greater milk production occurred at the low (19.7 kg/d) than the high (14.7 kg/d) stocking rate during periods 2 and 3, but production was similar during period 1. Despite lower production per cow, milk production per hectare was generally greater at the high stocking rate (81.6 vs. 49.5 kg/ha). Generally, greater pregraze herbage mass on pastures at the lower stocking rate (1,400 vs. 1,150 kg/ha) accounted for greater herbage allowance. Both forage (8.0 vs. 5.9 kg/d) and total (14.1 vs. 11.6) organic matter intake were greater at the low stocking rate. Cows fed less supplement had greater forage organic matter intake (8.0 vs. 6.1 kg/d). Greater herbage mass was associated with the greater intake and subsequent greater milk production. Differences in forage nutritive value, blood metabolites and milk composition, although showing some response to treatments, may not be of sufficient magnitude to affect choice of pasture species or other management practices. Animal performance was not improved by adding clovers to mixed cool-season grass pastures like those in this study. Stocking rate had a major effect on pasture and animal performance. During the cool season, supplementation with concentrates should be planned based on estimated energy intake from forages to achieve optimum milk production and ensure maintenance of body condition.
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Murayama M, Maeda Y, Goldsmith CE, Coulter WA, Masons C, Millar BC, Matsuda M, Moore JE. Molecular characterisation of the quinolone resistance-determining region (QRDR) of the parC gene locus in viridans-group streptococci. Br J Biomed Sci 2011; 68:109-11. [PMID: 21950200 DOI: 10.1080/09674845.2011.11730335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Forty-eight isolates of viridans-group streptococci (VGS) from adults and children in the community are examined for their resistance to ciprofloxacin phenotypically by determination of the minimum inhibitory concentration (MIC). In addition, the parC gene locus is amplified and sequenced in all isolates and mutations noted. Overall, 44 VGS organisms were found to be susceptible to ciprofloxacin by the broth microdilution method, and the remaining four strains had intermediate susceptibility. Reduced MICs were observed with intermediate strains when reserpine was added to the broth, inhibiting any efflux activity. Overall, the effect of adding reserpine to the broth medium was to add one doubling dilution to the MIC in the case of Streptococcus mitis, S. oralis and S. salivarius, as well as to increase the MIC by two doubling dilutions in two of the three S. parasanguinis isolates. Amino acid sequence analysis of the quinolone resistance-determining region (QRDR) of the parC gene locus showed good correlation to the phenotypic resistance to ciprofloxacin, where no confirmed mutation conferring quinolone resistance was found. Eleven amino acid positions showed discordance with S. pneumoniae R6 and eight (S52, F55, S58, N91, E135, K137, F141 and S167) were common in the VGS species examined. In addition, minor substitutions were found at three positions (D51, T54 and V86). In conclusion, this study demonstrates the low occurrence of ciprofloxacin resistance in a population of VGS isolated from the community. In addition, several silent mutations were noted in VGS organisms without any increase in MIC against ciprofloxacin.
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Tasaki E, Hirayama J, Tazumi A, Hayashi K, Hara Y, Ueno H, Moore JE, Millar BC, Matsuda M. Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC). World J Microbiol Biotechnol 2011; 28:713-20. [PMID: 22806867 DOI: 10.1007/s11274-011-0867-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 08/20/2011] [Indexed: 11/24/2022]
Abstract
Novel clustered regularly-interspaced short palindromic repeats (CRISPRs) locus [7,500 base pairs (bp) in length] occurred in the urease-positive thermophilic Campylobacter (UPTC) Japanese isolate, CF89-12. The 7,500 bp gene loci consisted of the 5'-methylaminomethyl-2-thiouridylate methyltransferase gene, putative (P) CRISPR associated (p-Cas), putative open reading frames, Cas1 and Cas2, leader sequence region (146 bp), 12 CRISPRs consensus sequence repeats (each 36 bp) separated by a non-repetitive unique spacer region of similar length (26-31 bp) and the phosphatidyl glycerophosphatase A gene. When the CRISPRs loci in the UPTC CF89-12 and five C. jejuni isolates were compared with one another, these six isolates contained p-Cas, Cas1 and Cas2 within the loci. Four to 12 CRISPRs consensus sequence repeats separated by a non-repetitive unique spacer region occurred in six isolates and the nucleotide sequences of those repeats gave approximately 92-100% similarity with each other. However, no sequence similarity occurred in the unique spacer regions among these isolates. The putative σ(70) transcriptional promoter and the hypothetical ρ-independent terminator structures for the CRISPRs and Cas were detected. No in vivo transcription of p-Cas, Cas1 and Cas2 was confirmed in the UPTC cells.
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Maeda Y, Goldsmith CE, Coulter WA, Mason C, Dooley JSG, Lowery CJ, Snelling WJ, Moore JE. Prevalence of clustered regulatory interspaced short palindromic repeat (CRISPR)-like sequences in mitis-group streptococci. Br J Biomed Sci 2011; 68:65-8. [PMID: 21706916 DOI: 10.1080/09674845.2011.11730325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPRs) have been discovered in many bacteria and archaea. Many CRISPR-like sequences have been identified in an increasing number of studies on the function of CRISPRs. One CRISPR-like sequence of approximately 240 base pairs has been found to be highly conserved within 11 genome sequences of Streptococcus pneumoniae. A specific CRISPR-like polymerase chain reaction (PCR) assay was designed with the novel primers CRISPR 5F (forward primer) 5'-CTA ATY TCA TAA CCA TAR GAA TC-3' and CRISPR 3R (reverse primer) 5'-GAT AAR ATC CTY TAA WCT TCT AG-3' to detect the presence of this CRISPR-like sequence in pneumococci, as well as in viridans-group streptococci (VGS). This study investigates the prevalence of this CRISPR-like sequence in S. pneumoniae and 12 viridans-group streptococcal species and shows its existence to be shared by the majority of S. pneumoniae and, to a lesser extent, S. mitis. This CRISPR-like sequence was also found in S. australis and it is highly conserved among these strains, suggesting possible biological functional differences from true CRISPR because this CRISPR-like sequence has relatively few repeat numbers, and adjacent homology of CRISPR-associated (cas) genes was absent. The sharing of this CRISPR-like sequence between pneumococci, the mitis group and other VGS, as well as its high sequence homology, may suggest close evolutionary emergence of this sequence between these species.
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Kan J, Chellamuthu P, Obraztsova A, Moore JE, Nealson KH. Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV). J Appl Microbiol 2011; 111:329-37. [PMID: 21599813 DOI: 10.1111/j.1365-2672.2011.05055.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS This study applied culture-dependent and molecular approaches to examine the bacterial communities at corrosion sites at Granite Mountain Record Vault (GMRV) in Utah, USA, with the goal of understanding the role of microbes in these unexpected corrosion events. METHODS AND RESULTS Samples from corroded steel chunks, rock particles and waters around the corrosion pits were collected for bacterial isolation and molecular analyses. Bacteria cultivated from these sites were identified as members of Alphaproteobacteria, Gammaproteobacteria, Firmicutes and Actinobacteria. In addition, molecular genetic characterization of the communities via nested-polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) indicated the presence of a broad spectrum of bacterial groups, including Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. However, neither cultivation nor molecular approaches identified sulfate-reducing bacteria (SRB), the bacteria commonly implicated as causative organisms were found associated with corrosive lesions in a process referred to as microbially influenced corrosion (MIC). The high diversity of bacterial groups at the corrosion sites in comparison with that seen in the source waters suggested to us a role for the microbes in corrosion, perhaps being an expression of a redox-active group of microbes transferring electrons, harvesting energy and producing biomass. CONCLUSIONS The corrosion sites contained highly diverse microbial communities, consistent with the involvement of microbial activities along the redox gradient at corrosion interface. We hypothesize an electron transport model for MIC, involving diverse bacterial groups such as acid-producing bacteria (APB), SRB, sulfur-oxidizing bacteria (SOB), metal-reducing bacteria (MRB) and metal-oxidizing bacteria (MOB). SIGNIFICANCE AND IMPACT OF THE STUDY The characterization of micro-organisms that influence metal-concrete corrosion at GMRV has significant implications for corrosion control in high-altitude freshwater environments. MIC provides a potential opportunity to further our understandings of extracellular electron transfer and interspecies communications.
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Nakanishi S, Tazumi A, Moore JE, Millar BC, Matsuda M. Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene operon and its adjacent genetic loci from urease-positive thermophilic Campylobacter (UPTC) organisms. Br J Biomed Sci 2011; 67:208-15. [PMID: 21294449 DOI: 10.1080/09674845.2010.11730321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular and comparative analyses of the full-length cytolethal distending toxin (cdt) gene operon and its adjacent genetic loci (2.7-9.4 kilo base pairs in length) are carried out with 12 urease-positive thermophilic Campylobacter (UPTC) isolates using several polymerase chain reaction (PCR) primer pairs. Three putative open reading frames (ORFs) for cdtA, cdtB and cdtC, two putative promoters and a hypothetically intrinsic rho-independent transcription terminator were identified in all the operons of the 12 UPTC isolates examined. Although the number of amino acid residues slightly varied for the putative cdtA and cdtC ORFs, those for the cdtB were similar among all the UPTC isolates, as well as the six urease-negative (UN) C. lari examined previously. Regarding the cdt genes in UPTC CF89-12, each ORF commenced with an ATG start codon and terminated with a TAG stop codon for cdtA and cdtB and a TAA for cdtC. Start and stop codons of the three ORFs for the other 11 UPTC isolates were identical to those from the UPTC CF89-12 isolate except for the TTG start codon for cdtC in the two isolates (NCTC12892 and 12893) and the TGA stop codon for cdtA in five isolates (A1, A2, A3, 89049 and 92251). Two putative promoter structures, consisting of sequences at the -35-like (TTAATA) and -10-like (TATTAA) regions, as well as the start codon (ATG), were identified for the transcriptional promoter, immediately upstream of the cdtA gene in all the 12 isolates, Although the genetic heterogeneity of the cdtB gene locus occurred in all 28 C. lari isolates (n = 16 UN C. lari; n = 12 UPTC) examined, all nine amino acid-specific DNase residues were completely conserved in all their cdtB genes. Variable gene insertions with heterogeneous order and combinations occurred between cdtC and lpxB genes in the all UPTC organisms examined.
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