scholarly journals A biochemical logarithmic sensor with broad dynamic range

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 200 ◽  
Author(s):  
Steven A. Frank
Keyword(s):  
Dynamic Range ◽  
Mass Action ◽  
Output Response ◽  
Response Characteristics ◽  
Stochastic Fluctuations ◽  
Broad Dynamic Range ◽  
Biochemical Systems ◽  
Parameter Values ◽  
Kinetics Of ◽  
Input Level

Sensory perception often scales logarithmically with the input level. Similarly, the output response of biochemical systems sometimes scales logarithmically with the input signal that drives the system. How biochemical systems achieve logarithmic sensing remains an open puzzle. This article shows how a biochemical logarithmic sensor can be constructed from the most basic principles of chemical reactions. Assuming that reactions follow the classic Michaelis-Menten kinetics of mass action or the more generalized and commonly observed Hill equation response, the summed output of several simple reactions with different sensitivities to the input will often give an aggregate output response that logarithmically transforms the input. The logarithmic response is robust to stochastic fluctuations in parameter values. This model emphasizes the simplicity and robustness by which aggregate chemical circuits composed of sloppy components can achieve precise response characteristics. Both natural and synthetic designs gain from the power of this aggregate approach.

scholarly journals A biochemical logarithmic sensor with broad dynamic range

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 200 ◽  
Author(s):  
Steven A. Frank
Keyword(s):  
Dynamic Range ◽  
Mass Action ◽  
Output Response ◽  
Response Characteristics ◽  
Stochastic Fluctuations ◽  
Broad Dynamic Range ◽  
Biochemical Systems ◽  
Parameter Values ◽  
Kinetics Of ◽  
Input Level

Sensory perception often scales logarithmically with the input level. Similarly, the output response of biochemical systems sometimes scales logarithmically with the input signal that drives the system. How biochemical systems achieve logarithmic sensing remains an open puzzle. This article shows how a biochemical logarithmic sensor can be constructed from the most basic principles of chemical reactions. Assuming that reactions follow the classic Michaelis-Menten kinetics of mass action or the more generalized and commonly observed Hill equation response, the summed output of several simple reactions with different sensitivities to the input will often give an aggregate output response that logarithmically transforms the input. The logarithmic response is robust to stochastic fluctuations in parameter values. This model emphasizes the simplicity and robustness by which aggregate chemical circuits composed of sloppy components can achieve precise response characteristics. Both natural and synthetic designs gain from the power of this aggregate approach.

scholarly journals A biochemical logarithmic sensor with broad dynamic range

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 200 ◽  
Author(s):  
Steven A. Frank
Keyword(s):  
Dynamic Range ◽  
Mass Action ◽  
Output Response ◽  
Response Characteristics ◽  
Stochastic Fluctuations ◽  
Broad Dynamic Range ◽  
Biochemical Systems ◽  
Parameter Values ◽  
Kinetics Of ◽  
Input Level

Sensory perception often scales logarithmically with the input level. Similarly, the output response of biochemical systems sometimes scales logarithmically with the input signal that drives the system. How biochemical systems achieve logarithmic sensing remains an open puzzle. This article shows how a biochemical logarithmic sensor can be constructed from the most basic principles of chemical reactions. Assuming that reactions follow the classic Michaelis-Menton kinetics of mass action or the more generalized and commonly observed Hill equation response, the summed output of several simple reactions with different sensitivities to the input will often give an aggregate output response that logarithmically transforms the input. The logarithmic response is robust to stochastic fluctuations in parameter values. This model emphasizes the simplicity and robustness by which aggregate chemical circuits composed of sloppy components can achieve precise response characteristics. Both natural and synthetic designs gain from the power of this aggregate approach.

scholarly journals Homeostatic enhancement of sensory transduction

2017 ◽  
Vol 114 (33) ◽  
pp. E6794-E6803 ◽  
Author(s):  
Andrew R. Milewski ◽  
Dáibhid Ó Maoiléidigh ◽  
Joshua D. Salvi ◽  
A. J. Hudspeth
Keyword(s):  
Auditory System ◽  
Dynamic Range ◽  
Frequency Discrimination ◽  
Sensory Transduction ◽  
Tight Control ◽  
Homeostatic Mechanism ◽  
Broad Dynamic Range ◽  
Order Of Magnitude ◽  
System Robustness ◽  
Parameter Values

Our sense of hearing boasts exquisite sensitivity, precise frequency discrimination, and a broad dynamic range. Experiments and modeling imply, however, that the auditory system achieves this performance for only a narrow range of parameter values. Small changes in these values could compromise hair cells’ ability to detect stimuli. We propose that, rather than exerting tight control over parameters, the auditory system uses a homeostatic mechanism that increases the robustness of its operation to variation in parameter values. To slowly adjust the response to sinusoidal stimulation, the homeostatic mechanism feeds back a rectified version of the hair bundle’s displacement to its adaptation process. When homeostasis is enforced, the range of parameter values for which the sensitivity, tuning sharpness, and dynamic range exceed specified thresholds can increase by more than an order of magnitude. Signatures in the hair cell’s behavior provide a means to determine through experiment whether such a mechanism operates in the auditory system. Robustness of function through homeostasis may be ensured in any system through mechanisms similar to those that we describe here.

scholarly journals Multiplex Assays of Luminex for Identification of COVID-19 Antibodies in Patient Serum: Performance Evaluation and Comparison to ELISA

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S92-S92
Author(s):  
M S Shapiro ◽  
X Wang ◽  
D R Mendu ◽  
A Firpo
Keyword(s):  
Dynamic Range ◽  
High Titer ◽  
Mount Sinai Hospital ◽  
Antibody Testing ◽  
Luminex Assay ◽  
Multiplex Assays ◽  
Negative Results ◽  
Broad Dynamic Range ◽  
Circulating Antibodies ◽  
Mount Sinai

Abstract Introduction/Objective Mount Sinai Hospital has received emergency use authorization (EUA) from the FDA for Coronavirus Disease 2019 (COVID-19) antibody testing using ELISA. This serological assay detects and titrates the presence of circulating antibodies to COVID-19. Other platforms have aimed to achieve the credentials of the ELISA instrument, including the multiplex assays of Luminex. The platform is known to have a greater throughput (384 wells vs. 96 wells per microplate) and faster processing speed (8 hours vs. 17 hours). Methods Luminex utilizes beads that couple to the same COVID-19 antigens (mRBD and mSpike) which were utilized for the ELISA assay. The beads are read determining the mean fluorescence intensity (MFI). In order to compare the two methods, our study included 61 patients with COVID-19 at Mount Sinai Hospital, to screen and titrate their sera using Luminex, and to correspond the MFI values with the ELISA titers. Results The Luminex assay has achieved the same level of confidence as ELISA. The 61 patients, representing 30 negatives and 31 positives, are consistently identified as such on both platforms. Our data highlights 32% of patients with a low titer (<1:160), 42% of patients with a high titer (1:160 ~ 1:320), and 26% of patients with a very high titer level (>1:320). These titers correlated well with the MFI values. Based on a cutoff of 80,000 MFI, the sensitivity and specificity of the assay is 98% and 85%, respectively, with no overlapping of MFI between positive and negative results. Conclusion Overall, the study has demonstrated that the Luminex is a strong alternative for the ELISA platform. The Luminex highlights the broad dynamic range with no overlapping between positives and negatives. Migration from ELISA to Luminex, a platform with faster and greater throughput, is therefore, highly desirable.

scholarly journals Training an asymmetric signal perceptron through reinforcement in an artificial chemistry

2014 ◽  
Vol 11 (93) ◽  
pp. 20131100 ◽  
Author(s):  
Peter Banda ◽  
Christof Teuscher ◽  
Darko Stefanovic
Keyword(s):  
State Of The Art ◽  
Chemical Species ◽  
Mass Action ◽  
Mass Action Kinetics ◽  
Dna Strand Displacement ◽  
Autonomous Adaptation ◽  
Biochemical Systems ◽  
Dna Strand ◽  
Logic Functions ◽  
Application Specific

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible.

scholarly journals A tandem giant magnetoresistance assay for one-shot quantification of clinically relevant concentrations of N-terminal pro-B-type natriuretic peptide in human blood

2021 ◽  
Author(s):  
Fanda Meng ◽  
Weisong Huo ◽  
Jie Lian ◽  
Lei Zhang ◽  
Xizeng Shi ◽  
...  
Keyword(s):  
Detection Limit ◽  
Giant Magnetoresistance ◽  
Dynamic Range ◽  
Point Of Care ◽  
Sample Volume ◽  
Small Sample ◽  
Broad Dynamic Range ◽  
Gmr Sensors ◽  
Gmr Sensor ◽  
Sample Volume Requirement

AbstractWe report a microfluidic sandwich immunoassay constructed around a dual-giant magnetoresistance (GMR) sensor array to quantify the heart failure biomarker NT-proBNP in human plasma at the clinically relevant concentration levels between 15 pg/mL and 40 ng/mL. The broad dynamic range was achieved by differential coating of two identical GMR sensors operated in tandem, and combining two standard curves. The detection limit was determined as 5 pg/mL. The assay, involving 53 plasma samples from patients with different cardiovascular diseases, was validated against the Roche Cobas e411 analyzer. The salient features of this system are its wide concentration range, low detection limit, small sample volume requirement (50 μL), and the need for a short measurement time of 15 min, making it a prospective candidate for practical use in point of care analysis.

scholarly journals Engineering Cyanobacterial Cell Morphology for Enhanced Recovery and Processing of Biomass

2017 ◽  
Vol 83 (9) ◽  
Author(s):  
Adam Jordan ◽  
Jenna Chandler ◽  
Joshua S. MacCready ◽  
Jingcheng Huang ◽  
Katherine W. Osteryoung ◽  
...  
Keyword(s):  
Cell Division ◽  
Cell Morphology ◽  
Dynamic Range ◽  
Enhanced Recovery ◽  
Downstream Processing ◽  
Crop Species ◽  
Content Type ◽  
Alternative Crop ◽  
Cell Harvesting ◽  
Broad Dynamic Range

ABSTRACT Cyanobacteria are emerging as alternative crop species for the production of fuels, chemicals, and biomass. Yet, the success of these microbes depends on the development of cost-effective technologies that permit scaled cultivation and cell harvesting. Here, we investigate the feasibility of engineering cell morphology to improve biomass recovery and decrease energetic costs associated with lysing cyanobacterial cells. Specifically, we modify the levels of Min system proteins in Synechococcus elongatus PCC 7942. The Min system has established functions in controlling cell division by regulating the assembly of FtsZ, a tubulin-like protein required for defining the bacterial division plane. We show that altering the expression of two FtsZ-regulatory proteins, MinC and Cdv3, enables control over cell morphology by disrupting FtsZ localization and cell division without preventing continued cell growth. By varying the expression of these proteins, we can tune the lengths of cyanobacterial cells across a broad dynamic range, anywhere from an ∼20% increased length (relative to the wild type) to near-millimeter lengths. Highly elongated cells exhibit increased rates of sedimentation under low centrifugal forces or by gravity-assisted settling. Furthermore, hyperelongated cells are also more susceptible to lysis through the application of mild physical stress. Collectively, these results demonstrate a novel approach toward decreasing harvesting and processing costs associated with mass cyanobacterial cultivation by altering morphology at the cellular level. IMPORTANCE We show that the cell length of a model cyanobacterial species can be programmed by rationally manipulating the expression of protein factors that suppress cell division. In some instances, we can increase the size of these cells to near-millimeter lengths with this approach. The resulting elongated cells have favorable properties with regard to cell harvesting and lysis. Furthermore, cells treated in this manner continue to grow rapidly at time scales similar to those of uninduced controls. To our knowledge, this is the first reported example of engineering the cell morphology of cyanobacteria or algae to make them more compatible with downstream processing steps that present economic barriers to their use as alternative crop species. Therefore, our results are a promising proof-of-principle for the use of morphology engineering to increase the cost-effectiveness of the mass cultivation of cyanobacteria for various sustainability initiatives.

scholarly journals Plasmonic substrates for multiplexed protein microarrays with femtomolar sensitivity and broad dynamic range

2011 ◽  
Vol 2 (1) ◽  
Author(s):  
Scott M. Tabakman ◽  
Lana Lau ◽  
Joshua T. Robinson ◽  
Jordan Price ◽  
Sarah P. Sherlock ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Protein Microarrays ◽  
Broad Dynamic Range

A FRET based pH probe with a broad working range applicable to referenced ratiometric dual wavelength and luminescence lifetime read out

2015 ◽  
Vol 51 (28) ◽  
pp. 6145-6148 ◽  
Author(s):  
Robert J. Meier ◽  
Johann M. B. Simbürger ◽  
Tero Soukka ◽  
Michael Schäferling
Keyword(s):  
Dynamic Range ◽  
Dual Wavelength ◽  
Luminescence Lifetime ◽  
Ph Sensing ◽  
Ph Probe ◽  
Broad Dynamic Range ◽  
Europium Chelate ◽  
Ratiometric Ph Sensing

A FRET system composed of a europium chelate and carboxynaphthofluorescein enables ratiometric pH sensing with an exceptionally broad dynamic range.

scholarly journals A Logistic Approach for Kinetics of Isothermal Pyrolysis of Cellulose

Processes ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 551
Author(s):  
Jorge López-Beceiro ◽  
Ana María Díaz-Díaz ◽  
Ana Álvarez-García ◽  
Javier Tarrío-Saavedra ◽  
Salvador Naya ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Time Derivative ◽  
Inert Atmosphere ◽  
Second Step ◽  
Rate Parameter ◽  
Thermogravimetric Data ◽  
Different Temperatures ◽  
Parameter Values ◽  
Kinetics Of ◽  
Logistic Functions

A kinetic model is proposed to fit isothermal thermogravimetric data obtained from cellulose in an inert atmosphere at different temperatures. The method used here to evaluate the model involves two steps: (1) fitting of single time-derivative thermogravimetric curves (DTG) obtained at different temperatures versus time, and (2) fitting of the rate parameter values obtained at different temperatures versus temperature. The first step makes use of derivative of logistic functions. For the second step, the dependence of the rate factor on temperature is evaluated. That separation of the curve fitting from the analysis of the rate factor resulted to be very flexible since it proved to work for previous crystallization studies and now for thermal degradation of cellulose.

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