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Incorporating prior knowledge improves detection of differences in bacterial growth rate
2015
BMC Systems Biology
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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
2022
Biosensors
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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
2019
MethodsX
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•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
2006
Antimicrobial Agents and Chemotherapy
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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
1996
Applied and Environmental Microbiology
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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
2014
Frontiers in Microbiology
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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
2022
Acta Scientific Veterinary Sciences
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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]
1992
Proceedings of the Ocean Drilling Program, 127/128 Part 1 Scientific Results
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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
2011
Antimicrobial Agents and Chemotherapy
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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
2021
Pharmaceutics
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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
2018
Journal of Bacteriology
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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
2008
Biogeosciences
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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
2007
Biogeosciences Discussions
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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]
1992
Proceedings of the Ocean Drilling Program, 127/128 Part 1 Scientific Results
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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
2020
Diagnostics
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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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