scholarly journals Experimental Validation of Stability and Applicability of Start Growth Time Method For High-Throughput Bacterial Ecotoxicity Assessment.

2021 ◽  
Author(s):  
Siang Chen Wu ◽  
Chang-Chun Shih
Keyword(s):  
High Throughput ◽  
Copper Ions ◽  
Shewanella Oneidensis ◽  
Model Organisms ◽  
Growth Time ◽  
Dead Cell ◽  
Bacterial Cells ◽  
Growth Phases ◽  
Time Saving ◽  
Non Linear

Abstract Ecotoxicity assessments based on bacteria as model organisms is widely used for routine toxicity screening because it has advantages of time-saving, high sensitivity, cost-effectiveness, and less ethical responsibility. Determination of ecotoxicity effect via bacterial growth can avoid the restriction of model bacteria selection and unique equipment requirement, but traditional viable cell count methods are relatively labor- and time-intensive. The Start Growth Method (SGT) is a high-throughput and time-conserving method to determine the amount of viable bacterial cells. However, its usability and stability for ecotoxicity assessment are rarely studied. This study confirmed its applicability in terms of bacterial types (gram-positive and gram-negative), growth phases (middle exponential and early stationary phases), and simultaneous existence of dead cells (adjustment by flow cytometry). Our results verified that the stability of establishing SGT correlation is independent of the bacterial type and dead-cell portion. Moreover, we only observed the effect of growth phases on the slope value of established SGT correlation in Shewanella oneidensis, which suggests that preparing inoculum for the SGT method should be consistent in keeping its stability. Our results also elucidate that the SGT values and the live cell percentages meet the non-linear exponential correlation with high correlation coefficients from 0.97 to 0.99 for all the examined bacteria. The non-linear exponential correlation facilitates the application of the SGT method on the ecotoxicity assessment. Finally, applying the exponential SGT correlation to evaluate the ecotoxicity effect of copper ions on E. coli was experimentally validated. The SGT-based method would require about 6 to 7 hours to finish the assessment and obtained an estimated EC50 at 2.27 ± 0.04 mM. This study demonstrates that the exponential SGT correlation can be a high-throughput, time-conversing, and wide-applicable method for bacterial ecotoxicity assessment.

Combination of Free Software, Light Microscopy and Non-specific Dyes for a High-throughput Analysis in Live/Dead Cell Count

2015 ◽  
Vol 11 (4) ◽  
pp. 233-238 ◽  
Author(s):  
Luciano Cardoso ◽  
Suellen Cordeiro ◽  
Marcio Fronza ◽  
Denise Endringer ◽  
Tadeu de Andrade ◽  
...  
Keyword(s):  
Light Microscopy ◽  
Cell Count ◽  
High Throughput ◽  
Free Software ◽  
Dead Cell ◽  
High Throughput Analysis ◽  
Throughput Analysis

High-throughput target validation in model organisms

2004 ◽  
Vol 3 (5) ◽  
pp. 191-197 ◽  
Author(s):  
Thanh N. Doan ◽  
Carmen D. Eilertson ◽  
Amy L. Rubinstein
Keyword(s):  
High Throughput ◽  
Model Organisms ◽  
Target Validation

scholarly journals Organismal view of a plant and a plant cell.

2001 ◽  
Vol 48 (2) ◽  
pp. 443-451 ◽  
Author(s):  
P Wojtaszek
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Growth Time ◽  
Dead Cell ◽  
Plant Body ◽  
The Status ◽  
A Cell ◽  
Plant Form ◽  
Biological Organisation

Cell walls are at the basis of a structural, four-dimensional framework of plant form and growth time. Recent rapid progress of cell wall research has led to the situation where the old, long-lasting juxtaposition: "living" protoplast--"dead" cell wall, had to be dropped. Various attempts of re-interpretation cast, however, some doubts over the very nature of plant cell and the status of the walls within such a cell. Following a comparison of exocellular matrices of plants and animals, their position in relation to cells and organisms is analysed. A multitude of perspectives of the biological organisation of living beings is presented with particular attention paid to the cellular and organismal theories. Basic tenets and resulting corollaries of both theories are compared, and evolutionary and developmental implications are considered. Based on these data, "The Plant Body"--an organismal concept of plants and plant cells is described.

scholarly journals Adaptation of the Start-Growth-Time Method for High-Throughput Biofilm Quantification

2021 ◽  
Vol 12 ◽  
Author(s):  
Lara Thieme ◽  
Anita Hartung ◽  
Kristina Tramm ◽  
Julia Graf ◽  
Riccardo Spott ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Growth Curves ◽  
Antimicrobial Effect ◽  
Growth Time ◽  
Colony Forming Unit ◽  
Resazurin Assay ◽  
Unspecific Binding ◽  
Biofilm Quantification ◽  
Doubling Times

Colony forming unit (CFU) determination by agar plating is still regarded as the gold standard for biofilm quantification despite being time- and resource-consuming. Here, we propose an adaption of the high-throughput Start-Growth-Time (SGT) method from planktonic to biofilm analysis, which indirectly quantifies CFU/mL numbers by evaluating regrowth curves of detached biofilms. For validation, the effect of dalbavancin, rifampicin and gentamicin against mature biofilms of Staphylococcus aureus and Enterococcus faecium was measured by accessing different features of the viability status of the cell, i.e., the cultivability (conventional agar plating), growth behavior (SGT) and metabolic activity (resazurin assay). SGT correlated well with the resazurin assay for all tested antibiotics, but only for gentamicin and rifampicin with conventional agar plating. Dalbavancin treatment-derived growth curves showed a compared to untreated controls significantly slower increase with reduced cell doubling times and reduced metabolic rate, but no change in CFU numbers was observed by conventional agar plating. Here, unspecific binding of dalbavancin to the biofilm interfered with the SGT methodology since the renewed release of dalbavancin during detachment of the biofilms led to an unintended antimicrobial effect. The application of the SGT method for anti-biofilm testing is therefore not suited for antibiotics which stick to the biofilm and/or to the bacterial cell wall. Importantly, the same applies for the well-established resazurin method for anti-biofilm testing. However, for antibiotics which do not bind to the biofilm as seen for gentamicin and rifampicin, the SGT method presents a much less labor-intensive method suited for high-throughput screening of anti-biofilm compounds.

Applications of Supercomputers in Sequence Analysis and Genome Annotation

2015 ◽  
pp. 149-175
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Sequence Analysis ◽  
High Throughput ◽  
Genome Annotation ◽  
Critical Role ◽  
Time Saving ◽  
Genetic Causes ◽  
Modern Era

In the modern era of science, bioinformatics play a critical role in unraveling the potential genetic causes of various diseases. Two of the most important areas of bioinformatics today, sequence analysis and genome annotation, are essential for the success of identifying the genes responsible for different diseases. These two emerging areas utilize highly intensive mathematical calculations in order to carry out the processes. Supercomputers facilitate such calculations in an efficient and time-saving manner generating high-throughput images. Thus, this chapter thoroughly discusses the applications of supercomputers in the areas of sequence analysis and genome annotation. This chapter also showcases sophisticated software and algorithms utilized by the two mentioned areas of bioinformatics.

scholarly journals Comparative toxicity assessment of novel Si quantum dots and their traditional Cd-based counterparts using bacteria models Shewanella oneidensis and Bacillus subtilis

2018 ◽  
Vol 5 (8) ◽  
pp. 1890-1901 ◽  
Author(s):  
Sunipa Pramanik ◽  
Samantha K. E. Hill ◽  
Bo Zhi ◽  
Natalie V. Hudson-Smith ◽  
Jeslin J. Wu ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Bacillus Subtilis ◽  
Shewanella Oneidensis ◽  
Toxicity Assessment ◽  
Bacterial Cells ◽  
Environment Friendly ◽  
Comparative Toxicity ◽  
Si Quantum Dots

The investigated Si quantum dots do not affect the viability of bacterial cells, and could potentially prove to be a more environment-friendly, sustainable, and cheaper alternative to traditional Cd-based quantum dots.

scholarly journals Non-Linear Instability of Stars With M > 100 M⊙

1974 ◽  
Vol 59 ◽  
pp. 77-79
Author(s):  
J. C. B. Papaloizou ◽  
R. J. Tayler
Keyword(s):  
Main Sequence ◽  
Finite Amplitude ◽  
Linear Instability ◽  
Growth Time ◽  
Transfer Time ◽  
Main Sequence Stars ◽  
Small Perturbations ◽  
Non Linear ◽  
Linear Effects ◽  
Low Amplitude

Massive main sequence stars are vibrationally unstable to small perturbations excited in the region of nuclear energy generation. This instability may, however, be limited at finite amplitude. Only the fundamental radial mode is unstable with an e-folding time of 105 to 106 pulsation periods; in contrast the overtones have damping times short compared with the growth time of the fundamental. Non-linear effects couple the linear modes. At very low amplitude the energy transfer time between modes is long compared with both growth and damping times and, as the overtones decay, a pure fundamental should result. However, as the amplitude increases, the transfer time becomes less than the growth and damping times. Energy can then be transferred from the fundamental to the overtones and damping can lead to a limitation of amplitude.

scholarly journals Copper Complexation Screen Reveals Compounds with Potent Antibiotic Properties against Methicillin-Resistant Staphylococcus aureus

2014 ◽  
Vol 58 (7) ◽  
pp. 3727-3736 ◽  
Author(s):  
Mehri Haeili ◽  
Casey Moore ◽  
Christopher J. C. Davis ◽  
James B. Cochran ◽  
Santosh Shah ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
High Throughput ◽  
Copper Ions ◽  
Antibacterial Properties ◽  
Rare Event ◽  
Innate Immune ◽  
Release Mechanism ◽  
Immune Functions ◽  
Methicillin Resistant ◽  
Copper Complexation

ABSTRACTMacrophages take advantage of the antibacterial properties of copper ions in the killing of bacterial intruders. However, despite the importance of copper for innate immune functions, coordinated efforts to exploit copper ions for therapeutic interventions against bacterial infections are not yet in place. Here we report a novel high-throughput screening platform specifically developed for the discovery and characterization of compounds with copper-dependent antibacterial properties toward methicillin-resistantStaphylococcus aureus(MRSA). We detail how one of the identified compounds, glyoxal-bis(N4-methylthiosemicarbazone) (GTSM), exerts its potent strictly copper-dependent antibacterial properties on MRSA. Our data indicate that the activity of the GTSM-copper complex goes beyond the general antibacterial effects of accumulated copper ions and suggest that, in contrast to prevailing opinion, copper complexes can indeed exhibit species- and target-specific activities. Based on experimental evidence, we propose that copper ions impose structural changes upon binding to the otherwise inactive GTSM ligand and transfer antibacterial properties to the chelate. In turn, GTSM determines target specificity and utilizes a redox-sensitive release mechanism through which copper ions are deployed at or in close proximity to a putative target. According to our proof-of-concept screen, copper activation is not a rare event and even extends to already established drugs. Thus, copper-activated compounds could define a novel class of anti-MRSA agents that amplify copper-dependent innate immune functions of the host. To this end, we provide a blueprint for a high-throughput drug screening campaign which considers the antibacterial properties of copper ions at the host-pathogen interface.

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