scholarly journals Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks

2021 ◽  
Author(s):  
Jacob Beal ◽  
Brian Teague ◽  
John T. Sexton ◽  
Sebastian Castillo-Hair ◽  
Nicholas A. DeLateur ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Regulatory Networks ◽  
Current Model ◽  
Genetic Regulatory Networks ◽  
Measurement Precision ◽  
Cellular Behavior ◽  
Flow Cytometry Data ◽  
Accuracy Measurement ◽  
The Relationship

Reliable, predictable engineering of cellular behavior is one of the key goals of synthetic biology. As the field matures, biological engineers will become increasingly reliant on computer models that allow for the rapid exploration of design space prior to the more costly construction and characterization of candidate designs. The efficacy of such models, however, depends on the accuracy of their predictions, the precision of the measurements used to parameterize the models, and the tolerance of biological devices for imperfections in modeling and measurement. To better understand this relationship, we have derived an Engineering Error Inequality that provides a quantitative mathematical bound on the relationship between predictability of results, model accuracy, measurement precision, and device characteristics. We apply this relation to estimate measurement precision requirements for engineering genetic regulatory networks given current model and device characteristics, recommending a target standard deviation of 1.5-fold. We then compare these requirements with the results of an interlaboratory study to validate that these requirements can be met via flow cytometry with matched instrument channels and an independent calibrant. Based on these results, we recommend a set of best practices for quality control of flow cytometry data and discuss how these might be extended to other measurement modalities and applied to support further development of genetic regulatory network engineering.

Pannexin channels increase propidium iodide permeability in frozen–thawed dog spermatozoa

2017 ◽  
Vol 29 (11) ◽  
pp. 2269 ◽  
Author(s):  
J. L. Torres ◽  
J. Palomino ◽  
R. D. Moreno ◽  
M. De los Reyes
Keyword(s):  
Flow Cytometry ◽  
Fluorescence Microscopy ◽  
Analysis Of Variance ◽  
Propidium Iodide ◽  
Membrane Channels ◽  
Flow Cytometry Data ◽  
Viable Cells ◽  
Head Segment ◽  
Relationship Of ◽  
The Relationship

Pannexins (Panx) are proteins that form functional single membrane channels, but they have not yet been described in dogs. The aim of the present study was to detect Panx1, Panx2 and Panx3 in frozen–thawed dog spermatozoa using flow cytometry and immunofluorescence analyses, evaluating the relationship of these proteins with propidium iodide (PI) in frozen–thawed spermatozoa. Fresh and frozen–thawed dog spermatozoa from eight dogs were preincubated with 3 μM PI with or without 15 μM carbenoxolone (CBX) or 1 mM probenecid (PBD), two Panx channel inhibitors, and then incubated with rabbit anti-Panx1, anti-Panx2 and anti-Panx3 antibodies (1 : 200). Panx immunolocalisation was assessed by fluorescence microscopy. Flow cytometry data were evaluated by analysis of variance. All three Panx proteins were found in dog spermatozoa: Panx1 was mostly localised to the acrosomal and equatorial segment, Panx2 was found in the posterior region of the head and tail and Panx3 was localised to the equatorial and posterior head segment. The percentage of PI-positive cells determined by flow cytometry was reduced (P < 0.05) in the presence of Panx inhibitors. These results show that Panx proteins are present in dog spermatozoa and increase PI permeability in frozen–thawed dog sperm, suggesting that the percentage of PI-positive spermatozoa used as an indicator of non-viable cells may lead to overestimation of non-viable cells.

DReSS: a method to quantitatively describe the influence of structural perturbations on state spaces of genetic regulatory networks

2020 ◽  
Author(s):  
Ziqiao Yin ◽  
Binghui Guo ◽  
Shuangge Ma ◽  
Yifan Sun ◽  
Zhilong Mi ◽  
...  
Keyword(s):  
Biological Networks ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Random Networks ◽  
Graph Distance ◽  
State Spaces ◽  
Biological Regulatory Networks ◽  
Structural Perturbations ◽  
The Relationship ◽  
Index Family

Abstract Structures of genetic regulatory networks are not fixed. These structural perturbations can cause changes to the reachability of systems’ state spaces. As system structures are related to genotypes and state spaces are related to phenotypes, it is important to study the relationship between structures and state spaces. However, there is still no method can quantitively describe the reachability differences of two state spaces caused by structural perturbations. Therefore, Difference in Reachability between State Spaces (DReSS) is proposed. DReSS index family can quantitively describe differences of reachability, attractor sets between two state spaces and can help find the key structure in a system, which may influence system’s state space significantly. First, basic properties of DReSS including non-negativity, symmetry and subadditivity are proved. Then, typical examples are shown to explain the meaning of DReSS and the differences between DReSS and traditional graph distance. Finally, differences of DReSS distribution between real biological regulatory networks and random networks are compared. Results show most structural perturbations in biological networks tend to affect reachability inside and between attractor basins rather than to affect attractor set itself when compared with random networks, which illustrates that most genotype differences tend to influence the proportion of different phenotypes and only a few ones can create new phenotypes. DReSS can provide researchers with a new insight to study the relation between genotypes and phenotypes.

scholarly journals Dynamical Criticality in Gene Regulatory Networks

Complexity ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Marco Villani ◽  
Luca La Rocca ◽  
Stuart Alan Kauffman ◽  
Roberto Serra
Keyword(s):  
Regulatory Networks ◽  
Single Gene ◽  
Biological Evolution ◽  
Boolean Networks ◽  
Genetic Regulatory Networks ◽  
Dynamical Regime ◽  
Random Boolean Networks ◽  
Statistical Framework ◽  
Gene Regulatory ◽  
The Relationship

A well-known hypothesis, with far-reaching implications, is that biological evolution should preferentially lead to states that are dynamically critical. In previous papers, we showed that a well-known model of genetic regulatory networks, namely, that of random Boolean networks, allows one to study in depth the relationship between the dynamical regime of a living being’s gene network and its response to permanent perturbations. In this paper, we analyze a huge set of new experimental data on single gene knockouts in S. cerevisiae, laying down a statistical framework to determine its dynamical regime. We find that the S. cerevisiae network appears to be slightly ordered, but close to the critical region. Since our analysis relies on dichotomizing continuous data, we carefully consider the issue of an optimal threshold choice.

The Influence of Characterization of Metallic Gasket Rough Surface on Gas Sealing Performance in Seal Structure

2015 ◽  
Vol 723 ◽  
pp. 162-166
Author(s):  
Wen Jian Yang ◽  
Xiao Ming Huang ◽  
Guo Liang Xu ◽  
Xiang Kui Lv
Keyword(s):  
Rough Surface ◽  
Current Model ◽  
Geometrical Model ◽  
Leakage Rate ◽  
Roughness Parameters ◽  
Gas Leakage ◽  
Sealing Performance ◽  
Auto Correlation Function ◽  
The Relationship

To investigate the influence of the roughness characteristics of the metallic gasket on the gas leakage rate, a mathematical model of a rough surface based on the Gauss distribution function and exponential auto-correlation function was built. According to this model, a 3D geometrical model of a sealing clearance with two rough surfaces was configured. Effect of the roughness parameters on the gas sealing performance was numerical analyzed, and through the comparison with the classical smooth parallel plate leakage model, the relationship between the leakage rate and the roughness parameters of the sealing surfaces was built. Furthermore, the relationship between contact pressure and the leakage rate for the different roughness surfaces was studied based on the current model. The results show the methodology proposed in current work is effective in predicting the actual sealing performance of static seal structure.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Microstructural Characterization of Au-Ge-Ni based ohmic contacts to GaAs/AlGaAs modfet device

1987 ◽  
Vol 45 ◽  
pp. 326-327
Author(s):  
A.K. Rai ◽  
A.K. Petford-Long ◽  
A. Ezis ◽  
D.W. Langer
Keyword(s):  
Contact Resistance ◽  
Ohmic Contact ◽  
Ohmic Contacts ◽  
Microstructural Characterization ◽  
Almost Everywhere ◽  
Spacer Layer ◽  
Good Contact ◽  
The Relationship ◽  
Lower Contact

Considerable amount of work has been done in studying the relationship between the contact resistance and the microstructure of the Au-Ge-Ni based ohmic contacts to n-GaAs. It has been found that the lower contact resistivity is due to the presence of Ge rich and Au free regions (good contact area) in contact with GaAs. Thus in order to obtain an ohmic contact with lower contact resistance one should obtain a uniformly alloyed region of good contact areas almost everywhere. This can possibly be accomplished by utilizing various alloying schemes. In this work microstructural characterization, employing TEM techniques, of the sequentially deposited Au-Ge-Ni based ohmic contact to the MODFET device is presented.The substrate used in the present work consists of 1 μm thick buffer layer of GaAs grown on a semi-insulating GaAs substrate followed by a 25 Å spacer layer of undoped AlGaAs.

Modeling Genetic Regulatory Networks Using First-Order Probabilistic Logic

2013 ◽  
Author(s):  
Nand Kishore ◽  
Radhakrishnan Balu ◽  
Shashi P. Karna
Keyword(s):  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
Probabilistic Logic ◽  
First Order

Characterization of Auditory Disability and Its Relation to the Resilience

2018 ◽  
Vol 5 (2) ◽  
pp. 15
Author(s):  
Bibian Bibeca Bumbila García ◽  
Hernán Andrés Cedeño Cedeño ◽  
Tatiana Moreira Chica ◽  
Yaritza Rossana Parrales Ríos
Keyword(s):  
Social Integration ◽  
Conceptual Analysis ◽  
Disabled People ◽  
Disabled Students ◽  
Hearing Disability ◽  
Technical University ◽  
The Relationship ◽  
Made In

The objective of the work is to establish the characterization of the auditory disability and its relationship with resilience at the Technical University of Manabí. The article shows a conceptual analysis related to the inclusion and social integration of disabled students. Based on the fact that the person with disabilities grows and develops in the same way as that of people without disabilities and what usually happens is that disabled people are rejected and discriminated against based on a prefabricated and erroneous conceptualization of these people. The results associated with the application of the SV-RES test prepared by the researchers are shown (Saavedra & Villalta, 2008b). Characterization of the auditory deficit is made in the students, and the limitations that derive from it are pointed out. We analyze the particularities related to communication with students who have a hearing disability and resilience in this type of student, where some personal highlights that in this sense constitute an example of resilience. Finally, the results related to the study of the relationship between students' hearing disability and the level of resilience dimensions are shown.

The Problem of Divine Hiddenness

2018 ◽  
Author(s):  
Michael C. Rea
Keyword(s):  
Problem Of Evil ◽  
Philosophical Discussion ◽  
Detailed Characterization ◽  
The Past ◽  
Divine Hiddenness ◽  
The Problem Of Evil ◽  
The Relationship

This chapter provides a detailed characterization of the various meanings of the term “divine hiddenness,” carefully and rigorously articulates the version of the problem of divine hiddenness that has dominated contemporary philosophical discussion for the past twenty-five years, and then explains the relationship between that problem and the problem of evil.

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