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Incorporating prior knowledge improves detection of differences in bacterial growth rate

Lydia M Rickett, Nick Pullen, Matthew Hartley, Cyril Zipfel, Sophien Kamoun, József Baranyi, Richard J. Morris
2015 BMC Systems Biology  
Conclusions: We have demonstrated that by making use of existing experimental knowledge, it is possible to significantly improve detection of differences in bacterial growth rate.  ...  Robust statistical detection of differences in the bacterial growth rate can be challenging, particularly when dealing with small differences or noisy data.  ...  We thank Brian Morris for the computational evaluation of various growth curve and Bayesian analysis functions. Author details  ... 
doi:10.1186/s12918-015-0204-9 pmid:26391452 pmcid:PMC4578766 fatcat:xuosjzremnd2jgpkbntildrq2e

Strategies for Improving Small-Molecule Biosensors in Bacteria

Corwin A. Miller, Joanne M. L. Ho, Matthew R. Bennett
2022 Biosensors  
Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters.  ...  and strategies for incorporating additional genetic modules.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/bios12020064 pmid:35200325 pmcid:PMC8869690 fatcat:uusbz7mtwrgpnb6jvgoc732u5q

An efficient, cost-effective method for determining the growth rate of sulfate-reducing bacteria using spectrophotometry

J.L. Wood, A. Osman, S.A. Wade
2019 MethodsX  
•Our results allay theoretical concerns that acidification may distort growth rate analysis by impacting cells differently depending on their metabolic state.  ...  its applicability to growth rate studies.  ...  Acknowledgments We would like to acknowledge the financial support of DST Group for this work (project MyIP: 8009). Appendix A.  ... 
doi:10.1016/j.mex.2019.09.036 pmid:31667126 pmcid:PMC6812320 fatcat:og5mfso2xzdkfdpgvjmwt2ihva

Semimechanistic Pharmacokinetic/Pharmacodynamic Model for Assessment of Activity of Antibacterial Agents from Time-Kill Curve Experiments

E. I. Nielsen, A. Viberg, E. Lowdin, O. Cars, M. O. Karlsson, M. Sandstrom
2006 Antimicrobial Agents and Chemotherapy  
In conclusion, for all drugs, the final PK/PD model successfully described bacterial growth and killing kinetics when the bacteria were exposed to different antibiotic concentrations.  ...  The drug effect was included as an increase of the killing rate of bacteria in the susceptible state, according to a maximum-effect (E max ) model.  ...  Incorporating prior knowledge of and experience with the system studied into the model-building process, and thereby creating mechanistically based PK/PD models, may increase the predictability of the  ... 
doi:10.1128/aac.00604-06 pmid:17060524 pmcid:PMC1797646 fatcat:xqhwlvqyv5fnliommgetvtzqe4

Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization

A Alfreider, J Pernthaler, R Amann, B Sattler, F Glockner, A Wille, R Psenner
1996 Applied and Environmental Microbiology  
The bacterial assemblage varied considerably between and within different habitats (snow, slush, and lake water) but was in most cases dominated by members of the beta subclass (6.5 to 116% of bacteria  ...  the different slush and pelagic layers, detectability with the fluorescent probe EUB was constantly high.  ...  Bacterial in situ growth rates and protein production were estimated from all but the snow layers via dual labeling with In pelagic samples incorporation rates were so low that reliable measurements required  ... 
pmid:16535341 pmcid:PMC1388879 fatcat:g3kypnrfgnf5zptntozv2yl5cm

Detecting rare gene transfer events in bacterial populations

Kaare M. Nielsen, Thomas Bøhn, Jeffrey P. Townsend
2014 Frontiers in Microbiology  
We aim to improve the knowledge of how bacteria utilize horizontally transferred DNA and the factors that regulate genetic recombination processes in natural environments.  ...  Leader of the MMPE research group since 2009 (www.uit.no/forskning/mmpe).  ...  Nielsen acknowledge financial support from GenØk-Center for Biosafety, the Research Council of Norway and the University of Tromsø. Kaare M. Nielsen acknowledges EU COST Action network FP0905.  ... 
doi:10.3389/fmicb.2013.00415 pmid:24432015 pmcid:PMC3882822 fatcat:ythph4oznbdellhinyddchmyf4

Bacterial Recovery from Canine Eyes with Complicated Corneal Ulcerations: Comparison of Direct Plating Versus Culturette Submission: A Pilot Study

Haley E Jost, Christine C Lim, Leslie Sharkey, Julia L Sharp, Michael L Creutzinger, Michala de Linde Henriksen
2022 Acta Scientific Veterinary Sciences  
This study suggests that submitting a culturette does not result in different bacterial growth than direct plating.  ...  There was not sufficient evidence to suggest bacterial detection differed between the two culture methods (p = 1.00).  ...  There was not sufficient evidence to suggest a difference between bacterial growth or no growth when the use of topical antibiotics versus no use of topical antibiotics prior to culture were evaluated  ... 
doi:10.31080/asvs.2022.04.0322 fatcat:dh4o2qlljzfnhhtpsoqam7jbca

Bacterial Biomass and Activity in the Deep Sediment Layers of the Japan Sea, Hole 798B [chapter]

B.A. Cragg, S.M. Harvey, J.C. Fry, R.A. Herbert, R.J. Parkes
1992 Proceedings of the Ocean Drilling Program, 127/128 Part 1 Scientific Results  
Rates of thymidine incorporation into bacterial DNA and anaerobic sulfate reduction are high in the surface sediments and decrease rapidly down to 3 mbsf.  ...  in the top 6 mbsf, with high but rapidly decreasing bacterial populations (total and dividing bacteria, and concentrations of different types of viable heterotrophic bacteria) and potential bacterial  ...  Rates of thymidine incorporation into DNA have been used as a quantitative measure of bacterial growth (Moriarty, 1990) .  ... 
doi:10.2973/odp.proc.sr.127128-1.184.1992 fatcat:7mvlp2uafnhztglfiz5pk2lvae

Quantitative Impact of Neutrophils on Bacterial Clearance in a Murine Pneumonia Model

Beining Guo, Kamilia Abdelraouf, Kimberly R. Ledesma, Kai-Tai Chang, Michael Nikolaou, Vincent H. Tam
2011 Antimicrobial Agents and Chemotherapy  
In this study, the impact of neutrophils on bacterial clearance was quantitatively assessed in a murine pneumonia model.In vitrotime-growth studies were performed to determine the growth rate constants  ...  A simple mathematical model was proposed to quantify the contribution of neutrophils to bacterial clearance and predict the bacterial growth/suppression in animals.  ...  The rate of change of 145 bacteria over time was expressed as the difference between the intrinsic bacterial growth rate 146 and the kill rate provided by the neutrophils.  ... 
doi:10.1128/aac.00508-11 pmid:21807974 pmcid:PMC3186951 fatcat:zzqs4gpihncmxo6zx6vgiigjvy

The Use of Translational Modelling and Simulation to Develop Immunomodulatory Therapy as an Adjunct to Antibiotic Treatment in the Context of Pneumonia

Robin Michelet, Moreno Ursino, Sandrine Boulet, Sebastian Franck, Fiordiligie Casilag, Mara Baldry, Jens Rolff, Madelé van Dyk, Sebastian G Wicha, Jean-Claude Sirard, Emmanuelle Comets, Sarah Zohar (+1 others)
2021 Pharmaceutics  
The resulting workflow combines expert and prior knowledge on the compound with the in vitro and in vivo data generated during exploratory studies in order to construct high-dimensional models considering  ...  The treatment of respiratory tract infections is threatened by the emergence of bacterial resistance.  ...  Acknowledgments: The publication of this article was funded by Freie Universität Berlin. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pharmaceutics13050601 pmid:33922017 pmcid:PMC8143524 fatcat:7jlmzr7hqrh53pnbzlvqxtn7dy

Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum

Cajetan Neubauer, Ajay S. Kasi, Nora Grahl, Alex L. Sessions, Sebastian H. Kopf, Roberta Kato, Deborah A. Hogan, Dianne K. Newman, Victor J. DiRita
2018 Journal of Bacteriology  
The microbial community composition was determined by counting rRNA with NanoString DNA analysis, and growth rates were obtained by incubating CF sputum with heavy water and tracing incorporation of deuterium  ...  A promising tool to better understand the physiology of microorganisms in a patient is stable-isotope probing, which we previously developed to estimate the growth rates of S. aureus in cystic fibrosis  ...  Keens for their guidance with our study, the CHLA CF center team, and patients of the CHLA CF clinic for participating in this study. We thank the anonymous reviewers for their comments.  ... 
doi:10.1128/jb.00365-18 pmid:30249710 fatcat:aaa7ye3mfnb3rcmtfgjsr6kc3y

Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

I. Obernosterer, P. Catala, R. Lami, J. Caparros, J. Ras, A. Bricaud, C. Dupuy, F. van Wambeke, P. Lebaron
2008 Biogeosciences  
Even a short residence in the surface microlayer influences leucine incorporation by different bacterial groups, probably as a response to the differences in the physical and chemical nature of the two  ...  By contrast, bacterial heterotrophic production ( 3 H-leucine incorporation) was consistently lower in the surface microlayer than in surface waters.  ...  Two anonymous reviewers helped improve an earlier version of the manuscript. Financial support for this work came from the French National program PROOF (INSU/CNRS). Edited by: A. Boetius  ... 
doi:10.5194/bg-5-693-2008 fatcat:5a5w4vlddnhybpakhprtrgg44q

Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

I. Obernosterer, P. Catala, R. Lami, J. Caparros, J. Ras, A. Bricaud, C. Dupuy, F. van Wambeke, P. Lebaron
2007 Biogeosciences Discussions  
Even a short residence in the surface microlayer influences leucine incorporation by different bacterial groups, probably as a response to the differences in the physical and chemical nature of the two  ...  By contrast, bacterial heterotrophic production ( 3 H-leucine incorporation) was consistently lower in the surface microlayer than in surface waters.  ...  Two anonymous reviewers helped improve an earlier version of the manuscript. Financial support for this work came from the French National program PROOF (INSU/CNRS). Edited by: A. Boetius  ... 
doi:10.5194/bgd-4-2809-2007 fatcat:r73sids6vbdzpbyvphogewozmy

The Potential for Bacteria Growth in Deep Sediment Layers of the Japan Sea, Hole 798B-Leg 128 [chapter]

J.M. Getliff, J.C. Fry, B.A. Cragg, R.J. Parkes
1992 Proceedings of the Ocean Drilling Program, 127/128 Part 1 Scientific Results  
The frequency of dividing and divided cells (FDDC) increased, and FDDC values were maximal in the midlogarithmic growth phase, as were bacterial productivity estimates calculated from 3 H-thymidine incorporation  ...  Direct evidence of in-situ growth, as shown by dividing cells, was found in the upper sediments but not below 10 mbsf. Growth was stimulated in all samples except at 9.75 mbsf.  ...  ACKNOWLEDGMENTS We thank the Ocean Drilling Program for allowing us to take samples from Leg 128 and an anonymous referee for suggested improvements to the manuscript.  ... 
doi:10.2973/odp.proc.sr.127128-1.183.1992 fatcat:fhngbthiwrgqhngj55pf3dydy4

Routine Fluorescence Imaging to Detect Wound Bacteria Reduces Antibiotic Use and Antimicrobial Dressing Expenditure While Improving Healing Rates: Retrospective Analysis of 229 Foot Ulcers

Nadine Price
2020 Diagnostics  
rates within 12-weeks (48% vs. 39%), likely due to earlier bacterial detection and improved wound hygiene.  ...  To aid point-of-care detection of bacterial burden, a fluorescence imaging device (MolecuLight i:X) was introduced to the Whipps Cross Hospital Podiatry clinic.  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/diagnostics10110927 pmid:33182630 fatcat:ig3supgc4nay3jbynap2tljms4
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