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Linear Eyring Plots Conceal a Change in the Rate-Limiting Step in an Enzyme Reaction

Teresa F G Machado, Tracey M Gloster, Rafael G da Silva
2018 Biochemistry  
The temperature dependence of psychrophilic and mesophilic ( R)-3-hydroxybutyrate dehydrogenase steady-state rates yields nonlinear and linear Eyring plots, respectively.  ...  Whereas there is precedent for a change in the rate-limiting step in nonlinear Eyring plots of enzyme reactions, 26 PaHBDH Eyring plots are linear in the range of 283−308 K (Figure S7) , and the switch  ...  This indicates a temperature-dependent shift in the rate-limiting step giving rise to a linear Eyring plot.  ... 
doi:10.1021/acs.biochem.8b01099 pmid:30472832 pmcid:PMC6300308 fatcat:loyyxahjvfdvfmniulyzseueom

A Systematic Review of Metagenomic Sequencing as a Clinical Diagnostic Tool for Infectious Diseases [article]

Kumeren N Govender, Teresa L Street, Nicholas D Sanderson, David William Eyre
2020 medRxiv   pre-print
Metagenomics has the potential to revolutionise infectious diseases diagnostics, from rapid species and antimicrobial resistance prediction, to finding unrecognised and sometimes untreated infections. Our aim was to summarise all literature on culture-independent metagenomic sequencing to describe the accuracy of species and antimicrobial resistance prediction and, describe the challenges and progress in the field. Methods We conducted a systematic review with meta-analysis from eligible
more » ... retrieved from PubMed, Google Scholar and bioRxiv and, assessed risk of bias and quality using the QUADAS-2 tool. This study is registered with PROSPERO, number CRD42020163777. Findings We identified 36 studies, 22 of which used a species-agnostic approach to identify all possible pathogens. In these studies, the overall sensitivity and specificity of pathogen species detection were 88% (95%CI 81-92%) and 86% (95%CI 70-94%) respectively. Antimicrobial resistance prediction and comparison to phenotypic results was undertaken in six studies. Categorical agreement was 83% (95%CI 68-92%), very major (prediction sensitive, phenotype resistant) and major error (prediction resistant, phenotype sensitive) rates were 9% (95%CI 2-27%) and 1% (95%CI 0-20%) respectively. We report limited use of negative controls in studies 61% (22/36) which contribute to a major challenge of discriminating true pathogens from contamination, where there is no convergence on methodology. More efficient human DNA depletion methods are required as a median of 79% (IQR 62-96) [Range 7-98] of sequences were classified as human despite laboratory depletion techniques. The median time from sample to result was 23.5 hours (7-31) [4-144], with sequencing time accounting 10 hours (4.8-16) [1-16]. The average reported consumables cost per sample ranged from $128 to $685. Interpretation The science and regulatory environment are rapidly developing, and its role as a routine test or test of last resort still needs to be determined, however it is likely that clinical metagenomics will be an increasing part of the clinician′s armamentarium to diagnose infectious diseases in the near future.
doi:10.1101/2020.03.30.20043901 fatcat:wicim3txbzfsdklccpso4go5qe

Motivations for Sex Among Low-Income African American Young Women

Julianna Deardorff, Ahna Ballonoff Suleiman, Teresa S. Dal Santo, Michelle Flythe, J. Barry Gurdin, Stephen L. Eyre
2013 Health Education & Behavior  
Past qualitative research suggests that sexual relationships characterized by love are linked to parenthood desires, which have clear implications for condom use (Eyre & Millstein, 1999) .  ... 
doi:10.1177/1090198112473112 pmid:23372029 pmcid:PMC3880580 fatcat:mepw2sasurcvznevzfl7htgk5u

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing [article]

Nicholas D Sanderson, Jeremy Swann, Leanne Barker, James Kavanagh, Sarah Hoosdally, Derrick Crook, Teresa L Street, David W Eyre, the GonFast Investigators Group
2020 bioRxiv   pre-print
The rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhoea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance
more » ... rminants from error-prone Nanopore sequencing is a substantial bioinformatics challenge. Here we demonstrate an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20x reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.
doi:10.1101/2020.02.07.939322 fatcat:uymdumxe5jfxza4mmifn553ngy

Spurious thresholds in the relationship between species richness and vegetation cover

Martine Maron, Michiala Bowen, Richard A. Fuller, Geoffrey C. Smith, Teresa J. Eyre, Michael Mathieson, James E. M. Watson, Clive A. McAlpine
2011 Global Ecology and Biogeography  
., 2009; Eyre et al., 2009) . Only surveys conducted since 2000 were used for this analysis.  ... 
doi:10.1111/j.1466-8238.2011.00706.x fatcat:pdzamtunhngnng4dhy6hhsu24a

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

Nicholas D. Sanderson, Jeremy Swann, Leanne Barker, James Kavanagh, Sarah Hoosdally, Derrick Crook, Teresa L. Street, David W. Eyre, The GonFast Investigators Group,
2020 Genome Research  
Illumina data were processed as described previously (De Silva et al. 2016; Eyre et al. 2017 ).  ...  This is in contrast to previous approaches using short-read data in which the different loci had to be analyzed together by mapping to a single copy of the gene (Eyre et al. 2017) .  ... 
doi:10.1101/gr.262865.120 pmid:32873606 pmcid:PMC7545138 fatcat:xdllawcwgbf3ljjqzo7bat5mhq

Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection [article]

Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick Crook, David W Eyre
2017 bioRxiv   pre-print
Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we compare direct-from-clinical-sample metagenomic Illumina sequencing with Nanopore sequencing, and report a real-time analytical pathway for Nanopore sequence data, designed for
more » ... ing bacterial composition of prosthetic joint infections. DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. A specific analysis pipeline was assembled to overcome the challenges of identifying the true infecting pathogen, given high levels of host contamination and unavoidable background lab and kit contamination. The majority of DNA classified (>90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological diagnosis and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within minutes from initiation of sequencing. We demonstrate initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data. The high proportion of human DNA in extracts prevents full genome analysis from complete coverage, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling.
doi:10.1101/220616 fatcat:am4rgs6h5ncmbcvpah7r76nvnm

Oleate Reverses Palmitate-induced Insulin Resistance and Inflammation in Skeletal Muscle Cells

Teresa Coll, Elena Eyre, Ricardo Rodríguez-Calvo, Xavier Palomer, Rosa M. Sánchez, Manuel Merlos, Juan Carlos Laguna, Manuel Vázquez-Carrera
2008 Journal of Biological Chemistry  
Here we report that in skeletal muscle cells the contribution to insulin resistance and inflammation of two common dietary long-chain fatty acids depends on the channeling of these lipids to distinct cellular metabolic fates. Exposure of cells to the saturated fatty acid palmitate led to enhanced diacylglycerol levels and the consequent activation of the protein kinase C/nuclear factor B pathway, finally resulting in enhanced interleukin 6 secretion and down-regulation of the expression of
more » ... involved in the control of the oxidative capacity of skeletal muscle (peroxisome proliferator-activated receptor (PPAR)␥-coactivator 1␣) and triglyceride synthesis (acyl-coenzyme A: diacylglycerol acyltransferase 2). In contrast, exposure to the monounsaturated fatty acid oleate did not lead to these changes. Interestingly, co-incubation of cells with palmitate and oleate reversed both inflammation and impairment of insulin signaling by channeling palmitate into triglycerides and by up-regulating the expression of genes involved in mitochondrial ␤-oxidation, thus reducing its incorporation into diacylglycerol. Our findings support a model of cellular lipid metabolism in which oleate protects against palmitate-induced inflammation and insulin resistance in skeletal muscle cells by promoting triglyceride accumulation and mitochondrial ␤-oxidation through PPAR␣-and protein kinase A-dependent mechanisms.
doi:10.1074/jbc.m708700200 pmid:18281277 fatcat:s5gol7firzauvd5mve6eqvi46e

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples [article]

Teresa Louise Street, Leanne Barker, Nicholas D Sanderson, James Kavanagh, Sarah Hoosdally, Kevin Cole, Robert Newnham, Mathyruban Selvaratnam, Monique Andersson, Martin Llewelyn, Justin O'Grady, Derrick W Crook (+1 others)
2019 bioRxiv   pre-print
Empirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. Methods: We investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N.
more » ... orrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA. Results: In simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections, but decreased yields in clinical samples. In ten urine samples from men with symptomatic urethral gonorrhoea, ≥87% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥92% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated Chlamydia co-infection.Conclusion: Using Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.
doi:10.1101/827485 fatcat:24u4fmezyjc5ldkfqsap6su6oy

Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing [article]

Teresa L Street, Nicholas D Sanderson, Bridget L Atkins, Andrew J Brent, Kevin Cole, Dona Foster, Martin A McNally, Sarah Oakley, Leon Peto, Adrian Taylor, Tim E A Peto, Derrick W Crook (+1 others)
2017 bioRxiv   pre-print
Eyre DW, Fawley WN, Best EL, Griffiths D, Stoesser NE, Crook DW, Peto TE, 506 Walker AS, Wilcox MH. 2013.  ...  Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson 517 JR, Walker AS, Peto TE, Crook DW. 2013.  ... 
doi:10.1101/118026 fatcat:3tzg5mapsvddblq7vcrltx5x2u

Produção científica sobre promoção da saúde nos cursos de pós-graduação brasileiros

Samira Valentim Gama Lira, Melina de Paiva Bezerra, Mirna Albuquerque Frota, Maria Teresa Moreno Valdés, Luiza Jane Eyre de Souza Vieira, Raimunda Magalhães da Silva
2009 Saúde e Sociedade  
Discutir a promoção de saúde no contexto da qualidade de vida dos indivíduos/coletividade e no meio acadêmico é uma articulação política, teórica e metodológica, portanto esta pesquisa teve por objetivo analisar a produção científica sobre promoção da saúde registrada na Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Capes). Foi realizada uma revisão sistemática no banco de teses da Capes e analisados 678 trabalhos registrados entre 2000 e 2004 e identificadas as categorias curso,
more » ... ano, região brasileira, área de conhecimento e resumo (tipo de estudo e coleta de dados). Constatou-se a predominância do curso de mestrado acadêmico com 531 (78,2%) pesquisas; entre os anos em que foram desenvolvidas as pesquisas sobre promoção da saúde, prevaleceu o ano de 2003, com 189 (27,8%) estudos, e entre as regiões brasileiras destacou-se a região Sudeste com 411 (60,5%) trabalhos. Na categoria área de conhecimento, preponderou a Saúde Coletiva com 138 (16%) pesquisas. No resumo do qual foi extraído o tipo de estudo, destacou-se a pesquisa qualitativa com 200 (29,4%) trabalhos. Conclui-se, portanto, que a produção científica na temática de promoção de saúde encontra-se progredindo, pois, no Brasil, a Política Nacional de Promoção de Saúde regularizou-se em 2004, sendo assim uma área em evidência para atuação interdisciplinar e descoberta de novas práticas e ações em saúde.
doi:10.1590/s0104-12902009000300008 fatcat:qakttfxv5vdhzea3wpjmhin74a

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

Nicholas D Sanderson, Teresa L Street, Dona Foster, Jeremy Swann, Bridget L Atkins, Andrew J Brent, Martin A McNally, Sarah Oakley, Adrian Taylor, Tim E A Peto, Derrick W Crook, David W Eyre
2018 BMC Genomics  
Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we report a real-time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections but potentially useful for any microbial
more » ... sequencing, and compare detection by direct-from-clinicalsample metagenomic nanopore sequencing with Illumina sequencing and standard microbiological diagnostic techniques. Results: DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. A specific analysis pipeline was assembled to overcome the challenges of identifying the true infecting pathogen, given high levels of host contamination and unavoidable background lab and kit contamination. The majority of DNA classified (> 90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological diagnosis and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within minutes from initiation of sequencing. Conclusions: We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data and use of this pipeline to show initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. The high proportion of human DNA in prosthetic joint infection extracts prevents full genome analysis from complete coverage, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling. The nine samples sequenced in this pilot study have shown a proof of concept for sequencing and analysis that will enable us to investigate further sequencing to improve specificity and sensitivity.
doi:10.1186/s12864-018-5094-y fatcat:nzjad7pwjjerzclraordkv34fq

Violência na escola pública: relatos de professores - doi:10.5020/18061230.2010.p34

Luiza Jane Eyre de Souza Vieira, Carlos Alberto Pereira de Abreu, Maria Teresa Moreno Valdês, Eliany Nazaré de Oliveira, Renata Carneiro Ferreira, Ana Maria Fontenelle Catrib
2012 Revista Brasileira em Promoção da Saúde  
Objetivo: Analisar a percepção de violência a partir dos relatos de professores do Ensino Fundamental e Médio de uma escola pública estadual, em Fortaleza, Ceará. Método: Estudo descritivo, qualitativo, realizado com 26 professores, no período de janeiro a maio de 2006. Para a coleta de dados adotaram-se os seguintes procedimentos: discussão sobre violência na escola durante as reuniões da semana pedagógica; leitura do regimento escolar e distribuição de um instrumento com questão norteadora
more » ... re a concepção de violência, a partir da realidade escolar, entre os participantes do estudo. Posteriormente foi feita a análise temática dos relatos. Resultados: Através dos relatos dos professores emergiram as seguintes categorias: agressões físicas, verbais e brigas como as mais citadas; esconder objetos pessoais, palavrões, empurrões, desrespeito ao professor e brincadeiras de mau gosto também foram mencionados. Conclusão: A partir dos relatos conclui-se que a violência é percebida nas dimensões física, moral e simbólica e essas "tipologias" corroboram as denominações encontradas na literatura como bullying ou incivilidades, que predominam no contexto escolar.
doi:10.5020/1169 doaj:b916dec1095648ed8478da576b627337 fatcat:viczslghfvad5f2n7dbxbwrmwu

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

Teresa L. Street, Leanne Barker, Nicholas D. Sanderson, James Kavanagh, Sarah Hoosdally, Kevin Cole, Robert Newnham, Mathyruban Selvaratnam, Monique Andersson, Martin J. Llewelyn, Justin O'Grady, Derrick W. Crook (+1 others)
2019 Journal of Clinical Microbiology  
Background. Empirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. Methods. We investigated if Nanopore sequencing can detect sufficient N. gonorrhoeae DNA to reconstruct whole genomes directly from urine samples.
more » ... used N. gonorrhoeae spiked urine samples and samples from gonorrhoea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced whilst minimizing contaminating host DNA. Results. In simulated infections the Qiagen UCP Pathogen Mini kit provided the highest ratio N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections, but decreased yields in clinical samples. In ten urine samples from men with symptomatic urethral gonorrhoea, ≥92.8% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥93.8% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR Media tubes and from urethral swabs, and in the presence of simulated Chlamydia co-infection. Conclusion. Using Nanopore sequencing of urine samples from men with urethral gonorrhoea sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture.
doi:10.1128/jcm.01822-19 pmid:31852766 pmcid:PMC7041563 fatcat:dg3x2opyajcalj2rqmeljnnvyy

An Approach to Mapping Forest Growth Stages in Queensland, Australia through Integration of ALOS PALSAR and Landsat Sensor Data

Daniel Clewley, Richard Lucas, Arnon Accad, John Armston, Michiala Bowen, John Dwyer, Sandy Pollock, Peter Bunting, Clive McAlpine, Teresa Eyre, Annie Kelly, João Carreiras (+1 others)
2012 Remote Sensing  
Whilst extensive clearance of forests in the eastern Australian Brigalow Belt Bioregion (BBB) has occurred since European settlement, appropriate management of those that are regenerating can facilitate restoration of biomass (carbon) and biodiversity Remote Sens. 2012, 4 2237 to levels typical of relatively undisturbed or remnant formations. However, maps of forests are different stages of regeneration are needed to facilitate restoration planning, including prevention of further re-clearing.
more » ... ocusing on the Tara Downs subregion of the BBB and on forests with brigalow (Acacia harpophylla) as a component, this research establishes a method for differentiating and mapping early, intermediate and remnant growth stages from Japan Aerospace Exploration Agency (JAXA) Advanced Land Observing Satellite (ALOS) Phased-Array L-band Synthetic Aperture Radar (PALSAR) Fine Beam Dual (FBD) L-band HH-and HV-polarisation backscatter and Landsat-derived Foliage Projective Cover (FPC). Using inventory data collected from 74 plots, located in the Tara Downs subregion, forests were assigned to one of three regrowth stages based on their height and cover relative to that of undisturbed stands. The image data were then segmented into objects with each assigned to a growth stage by comparing the distributions of L-band HV and HH polarisation backscatter and FPC to that of reference distributions using a z-test. Comparison with independent assessments of growth stage, based on time-series analysis of aerial photography and SPOT images, established an overall accuracy of >70%, with this increasing to 90% when intermediate regrowth was excluded and only early-stage regrowth and remnant classes were considered. The proposed method can be adapted to respond to amendments to user-definitions of growth stage and, as regional mosaics of ALOS PALSAR and Landsat FPC are available for Queensland, has application across the state.
doi:10.3390/rs4082236 fatcat:w2kybh6wbzgb3hfigxax5l2j6a
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