scholarly journals The Semiotic Approach to Bacterial Chemotaxis

Biosemiotics ◽  
2021 ◽  
Author(s):  
Adam Kłóś ◽  
Przemysław Mieszko Płonka
Keyword(s):  
Molecular Level ◽  
Bacterial Chemotaxis ◽  
Population Level ◽  
General Process ◽  
E Coli ◽  
Bacterial Response ◽  
Semiotic Approach ◽  
Ultimate Nature ◽  
Cell Signaling Pathways

AbstractBacterial chemotaxis is often considered to be a textbook example of the rudimentary semiotic process. As such, it gives an excellent opportunity to better understand both semiosis and biology. Our study reviews this phenomenon in the light of up-to-date scientific knowledge to answer the most basic semiotic questions: what is the sign? What types of signs are there? What is the meaning understood on the molecular level, and by what means can it grow with time? As a case study, the bacterial chemotaxis toward glucose in E. coli species is chosen, and the semiotic framework of Charles Sanders Peirce applied. The analyses provide us with the following results: the sign, in its ultimate nature, is a general process. Bacterial chemotaxis can be understood in terms of Peircean type, symbol, and argument. The meaning on the molecular level is entirely pragmatic and, in this case, reduced to a bacterial response to glucose. A sign can grow through sign generalization, the emergence of different sign categories, the integration of these categories in functional cycles, and the introduction of contextuality. The sign of bacterial chemotaxis extends from the cell signaling pathways up to the population level. The presented results advance our knowledge of sign processing in the context of semiotic evolution.

scholarly journals A model-based approach to characterize enzyme-mediated response to antibiotic treatments: going beyond the SIR classification

2021 ◽  
Author(s):  
Virgile Andreani ◽  
Lingchong You ◽  
Philippe Glaser ◽  
Gregory Batt
Keyword(s):  
Bacterial Resistance ◽  
Molecular Level ◽  
Population Level ◽  
Cell Physiology ◽  
Quantitative Modelling ◽  
Bacterial Response ◽  
Antibiotic Degradation ◽  
Model Features ◽  
Population Resilience

To design appropriate treatments, one must be able to characterize accurately the response of bacteria to antibiotics. When exposed to β-lactam treatments, bacteria can be resistant and/or tolerant, and populations can exhibit resilience. Disentangling these phenomena is challenging and no consolidated understanding has been proposed so far. Because these responses involve processes happening at several levels, including the molecular level (e.g. antibiotic degradation), the cell physiology level (filamentation) and the population level (release of β-lactamases into the environment), quantitative modelling approaches are needed. Here, we propose a model of bacterial response to β-lactam treatments that accounts for bacterial resistance, tolerance, and population resilience. Our model can be calibrated solely based on optical density readouts, can predict the inoculum effect, and leads to a mechanistically relevant classification of bacterial response to treatments that goes beyond the classical susceptible / intermediate / resistant classification. Filamentation-mediated tolerance and collective enzyme-mediated antibiotic degradation are essential model features to explain the complex observed response of cell populations to antibiotic treatments.

RNA polymerase: Preparation and structural analysis of helical polymers

1984 ◽  
Vol 42 ◽  
pp. 152-153
Author(s):  
E. Loren Buhle ◽  
Pamela Rew ◽  
Ueli Aebi
Keyword(s):  
Structural Analysis ◽  
Rna Polymerase ◽  
Molecular Level ◽  
X Ray Diffraction ◽  
Helical Polymers ◽  
X Ray ◽  
E Coli ◽  
The Past ◽  
Ordered Arrays ◽  
Low Ionic Strength

While DNA-dependent RNA polymerase represents one of the key enzymes involved in transcription and ultimately in gene expression in procaryotic and eucaryotic cells, little progress has been made towards elucidation of its 3-D structure at the molecular level over the past few years. This is mainly because to date no 3-D crystals suitable for X-ray diffraction analysis have been obtained with this rather large (MW ~500 kd) multi-subunit (α2ββ'ζ). As an alternative, we have been trying to form ordered arrays of RNA polymerase from E. coli suitable for structural analysis in the electron microscope combined with image processing. Here we report about helical polymers induced from holoenzyme (α2ββ'ζ) at low ionic strength with 5-7 mM MnCl2 (see Fig. 1a). The presence of the ζ-subunit (MW 86 kd) is required to form these polymers, since the core enzyme (α2ββ') does fail to assemble into such structures under these conditions.

scholarly journals A Statistical Model for Assessing Sample Size for Bacterial Colony Selection: A Case Study of Escherichia Coli and Avian Cellulitis

2000 ◽  
Vol 12 (2) ◽  
pp. 118-125 ◽  
Author(s):  
Randall S. Singer ◽  
Wesley O. Johnson ◽  
Joan S. Jeffrey ◽  
Richard P. Chin ◽  
Tim E. Carpenter ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Statistical Model ◽  
Clinical Sample ◽  
Agar Plate ◽  
Sample Sizes ◽  
Simple Task ◽  
Single Strain ◽  
Bacterial Colony ◽  
E Coli

A general problem for microbiologists is determining the number of phenotypically similar colonies growing on an agar plate that must be analyzed in order to be confident of identifying all of the different strains present in the sample. If a specified number of colonies is picked from a plate on which the number of unique strains of bacteria is unknown, assigning a probability of correctly identifying all of the strains present on the plate is not a simple task. With Escherichia coli of avian cellulitis origin as a case study, a statistical model was designed that would delineate sample sizes for efficient and consistent identification of all the strains of phenotypically similar bacteria in a clinical sample. This model enables the microbiologist to calculate the probability that all of the strains contained within the sample are correctly identified and to generate probability-based sample sizes for colony identification. The probability of cellulitis lesions containing a single strain of E. coli was 95.4%. If one E. coli strain is observed out of three colonies randomly selected from a future agar plate, the probability is 98.8% that only one strain is on the plate. These results are specific for this cellulitis E. coli scenario. For systems in which the number of bacterial strains per sample is variable, this model provides a quantitative means by which sample sizes can be determined.

scholarly journals Spread of Antibiotic Resistance in Aquatic Environments: E. coli as a Case Study

Proceedings ◽  
2018 ◽  
Vol 2 (11) ◽  
pp. 693 ◽  
Author(s):  
Maria Adamantia Efstratiou ◽  
Marina Bountouni ◽  
Efthimios Kefalas
Keyword(s):  
Escherichia Coli ◽  
Drinking Water ◽  
Antibiotic Resistance ◽  
Rural Communities ◽  
Ground Water ◽  
Aquatic Environments ◽  
Multiple Resistance ◽  
E Coli ◽  
Of Greece

The aim of this study was to gather information on the spread of antibiotic resistance in Escherichia coli isolates from wells, boreholes and untreated drinking water in islands of Greece. We analyzed for antibiotic resistance 235 E. coli strains isolated from untreated drinking water of small rural communities, and ground water from 4 islands. Resistance was tested against Norfloxacin, Ciprofloxacin, Levofloxacin, Amoxicillin and Cefaclor. More than half (54.9%) were resistant to at least one of the antibiotics tested. Of these 26.3% showed multiple resistance (to two or more antibiotics). Strains from drinking water sources were overall more sensitive. Frequent resistance was observed for Amoxicillin (38.3%) and Levofloxacin (28.5%), low for Norfloxacin (5.5%).

scholarly journals Molecular level characterization of diatom‐associated biopolymers that bind234Th,233Pa,210Pb, and7Be in seawater: A case study withPhaeodactylum tricornutum

2015 ◽  
Vol 120 (9) ◽  
pp. 1858-1869 ◽  
Author(s):  
Chia‐Ying Chuang ◽  
Peter H. Santschi ◽  
Chen Xu ◽  
Yuelu Jiang ◽  
Yi‐Fang Ho ◽  
...  
Keyword(s):  
Molecular Level

scholarly journals A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free Systems

2020 ◽  
Author(s):  
Vipul Singhal ◽  
Zoltan A. Tuza ◽  
Zachary Z. Sun ◽  
Richard M. Murray
Keyword(s):  
Reaction Rate ◽  
Behavior Prediction ◽  
Genetic Circuits ◽  
Matlab Toolbox ◽  
Parameter Inference ◽  
Batch Mode ◽  
E Coli ◽  
Entire Duration ◽  
Resource Loading

AbstractWe introduce a MATLAB based simulation toolbox, called txtlsim, for an E. coli based Transcription-Translation (TX-TL) system. This toolbox accounts for several cell-free related phenomena, such as resource loading, consumption, and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire duration of batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protien expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

scholarly journals A semiotic approach to language ideologies: Modelling the changing Icelandic languagescape

2020 ◽  
Vol 48 (2-4) ◽  
pp. 271-296
Author(s):  
Stephen Pax Leonard
Keyword(s):  
Language Policy ◽  
Language Ideologies ◽  
Speech Community ◽  
Policy Makers ◽  
E Coli ◽  
Semiotic Model ◽  
Semiotic Approach ◽  
Ethnographic Data ◽  
Linguistic Purism

Attempts have been made to examine how speakers frame linguistic varieties by employing social semiotic models. Using ethnographic data collected over many years, this article applies such a model to Iceland, once described as the ‘e-coli of linguistics’ – its size, historical isolation and relative linguistic homogeneity create conditions akin to a sociolinguistic laboratory. This semiotic model of language ideologies problematizes the prevailing discourse of linguistic purism at a time of sociolinguistic upheaval. The analysis shows how an essentializing scheme at the heart of Icelandic language policy ensured that linguistic “anomalies” such as “dative disease” and “genitive phobia” indexed essential differences. “Impure” language was indicative of un-Icelandicness. Once monolingual (indeed monodialectal), the Icelandic speech community is increasingly characterized by innovative linguistic transgressions which thus far have not been instrumentalized by language policy makers. It is shown how a semiotic model can help us analyse the function of language ideologies more generally.

scholarly journals WATER QUALITY ANALYSIS: A CASE STUDY IN BYRAMANGALA LAKE WATER AND SURROUNDING GROUND WATER

2017 ◽  
Vol 5 (4RASM) ◽  
pp. 71-77
Author(s):  
Babitha Rani ◽  
Dimple Bahri ◽  
Prabin Neupane ◽  
Kunal Kothari ◽  
Vishal Gadgihalli ◽  
...  
Keyword(s):  
Water Quality ◽  
Ground Water ◽  
Lake Water ◽  
Suspended Solids ◽  
Quality Analysis ◽  
Total Hardness ◽  
Water Quality Analysis ◽  
E Coli

A study was carried out to find out the water quality ofByramangala lake of Ramanagara district. The water quality of Byramangala lake water and ground water from bore wells situated in the area within 600 meters surrounding the lake was analyzed. The quality analysis of various parameters such as BODs, COD, DO, E-Coli, and pH, Total Dissolved Solids, Total Suspended Solids and Total Hardness were tested. In addition, the presence of metals such as Cadmium (Cd), Chromium (Cr), Lead (Pb), and Iron (Fe) in the lake water and ground water samples were tested. Results for the various tests conducted showed similar trends for both lake water and ground water. It was observed that certain parameters such as BOD5, and COD were beyond permissible limits as per the BIS standards for drinking water. A few remedial measures have been proposed that may help in mitigating the pollution in the selected project area Byramangala Lake.

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