scholarly journals Escherichia coli’sphysiology can turn membrane voltage dyes into actuators

2019 ◽  
Author(s):  
L Mancini ◽  
G Terradot ◽  
T Tian ◽  
Y Pu ◽  
Y Li ◽  
...  
Keyword(s):  
Biological Membrane ◽  
Electrical Potential ◽  
Phospholipid Bilayer ◽  
Work Flow ◽  
Membrane Voltage ◽  
Cell Physiology ◽  
Cellular Processes ◽  
Nernst Potential ◽  
Trade Offs

ABSTRACTThe electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes, andVmalso plays a role in signal transduction. Therefore, measuring it is of great interest, and over the years a variety of techniques has been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favourite strategy, and their cytoplasmic accumulation depends onVmaccording to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the trade-offs between the ease with which the signal from the dye is observed, and the dyes’ interactions with cellular physiology, is rarely performed. Here we use a mathematical model to understand such trade-offs and, based on the knowledge gained, propose a general work-flow for the characterization of Nernstian dye candidates. We demonstrate the work-flow on the Thioflavin T dye inEscherichia coli, and identify conditions in which the dye turns from aVmprobe into an actuator.SIGNIFICANCE STATEMENTThe phospholipid bilayer of a biological membrane is virtually impermeable to charged molecules. Much like in a rechargeable battery, cells harness this property to store an electrical potential that fuels life reactions but also transduces signals. Measuring this electrical potential, also referred to as membrane voltage, is therefore of great interest and a variety of techniques have been employed for the purpose, starting as early as the 1930s. For the case of bacteria, which are smaller in size and possess a stiffer cell wall, arguably the most popular approach to measuring membrane voltage are Nernstian probes that accumulate across the bacterial membrane according to the Nernst potential. The present study characterizes the undesired effects Nernstian probes can have on cell physiology, which can be crucial for the accurate interpretation of experimental results. Using mathematical modelling and experiments, the study provides a general, simple workflow to characterise and minimise these effects.

dC/dV and CV Characterization of Gate Resistance Defects in eDRAM Circuits

2013 ◽  
Author(s):  
Sweta Pendyala ◽  
Dave Albert ◽  
Katherine Hawkins ◽  
Michael Tenney
Keyword(s):  
Deep Submicron ◽  
Work Flow ◽  
Localization Technique ◽  
Characterization Techniques ◽  
Capacitance Voltage ◽  
Gate Resistance

Abstract Resistive gate defects are unusual and difficult to detect with conventional techniques [1] especially on advanced devices manufactured with deep submicron SOI technologies. An advanced localization technique such as Scanning Capacitance Imaging is essential for localizing these defects, which can be followed by DC probing, dC/dV, CV (Capacitance-Voltage) measurements to completely characterize the defect. This paper presents a case study demonstrating this work flow of characterization techniques.

scholarly journals Noise and Breakdown Characterization of SPAD Detectors with Time-Gated Photon-Counting Operation

Sensors ◽  
2021 ◽  
Vol 21 (16) ◽  
pp. 5287
Author(s):  
Hiwa Mahmoudi ◽  
Michael Hofbauer ◽  
Bernhard Goll ◽  
Horst Zimmermann
Keyword(s):  
Breakdown Voltage ◽  
Single Photon ◽  
Photon Counting ◽  
Low Noise ◽  
Dark Count ◽  
Fully Integrated ◽  
Trade Offs ◽  
And Performance ◽  
Noise Models

Being ready-to-detect over a certain portion of time makes the time-gated single-photon avalanche diode (SPAD) an attractive candidate for low-noise photon-counting applications. A careful SPAD noise and performance characterization, however, is critical to avoid time-consuming experimental optimization and redesign iterations for such applications. Here, we present an extensive empirical study of the breakdown voltage, as well as the dark-count and afterpulsing noise mechanisms for a fully integrated time-gated SPAD detector in 0.35-μm CMOS based on experimental data acquired in a dark condition. An “effective” SPAD breakdown voltage is introduced to enable efficient characterization and modeling of the dark-count and afterpulsing probabilities with respect to the excess bias voltage and the gating duration time. The presented breakdown and noise models will allow for accurate modeling and optimization of SPAD-based detector designs, where the SPAD noise can impose severe trade-offs with speed and sensitivity as is shown via an example.

scholarly journals A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

2021 ◽  
Vol 22 (14) ◽  
pp. 7390
Author(s):  
Nicole Wesch ◽  
Frank Löhr ◽  
Natalia Rogova ◽  
Volker Dötsch ◽  
Vladimir V. Rogov
Keyword(s):  
Cellular Localization ◽  
Molecular Mechanisms ◽  
Biochemical Characterization ◽  
Effective Interaction ◽  
Regulatory Region ◽  
Titration Calorimetry ◽  
Enzymatic Reactions ◽  
Cellular Processes ◽  
Mechanism Of Interaction

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.

scholarly journals Axiomatization and Measurement of Quasi-Hyperbolic Discounting *

2014 ◽  
Vol 129 (3) ◽  
pp. 1449-1499 ◽  
Author(s):  
José Luis Montiel Olea ◽  
Tomasz Strzalecki
Keyword(s):  
Hyperbolic Discounting ◽  
Partial Identification ◽  
Axiomatic Characterization ◽  
Discount Factors ◽  
Elasticity Of Intertemporal Substitution ◽  
Trade Offs ◽  
Subject Pool ◽  
Identification Approach ◽  
The Subject

Abstract This article provides an axiomatic characterization of quasi-hyperbolic discounting and a more general class of semi-hyperbolic preferences. We impose consistency restrictions directly on the intertemporal trade-offs by relying on what we call “annuity compensations.” Our axiomatization leads naturally to an experimental design that disentangles discounting from the elasticity of intertemporal substitution. In a pilot experiment we use the partial identification approach to estimate bounds for the distributions of discount factors in the subject pool. Consistent with previous studies, we find evidence for both present and future bias.

An Investigation of the Distribution of Electric Potential and Space Charge in a Silicon Nanowire

2014 ◽  
Vol 69 (10-11) ◽  
pp. 597-605 ◽  
Author(s):  
A. Wesam Al-Mufti ◽  
Uda Hashim ◽  
Md. Mijanur Rahman ◽  
Tijjani Adam
Keyword(s):  
Finite Element Method ◽  
Space Charge ◽  
Electric Potential ◽  
Silicon Nanowire ◽  
Electrical Potential ◽  
Comsol Multiphysics ◽  
The Finite Element Method ◽  
Simulation Experiments ◽  
Different Dimensions

AbstractThe distribution of electric potential and space charge in a silicon nanowire has been investigated. First, a model of the nanowire is generated taking into consideration the geometry and physics of the nanowire. The physics of the nanowire was modelled by a set of partial differential equations (PDEs) which were solved using the finite element method (FEM). Comprehensive simulation experiments were performed on the model in order to compute the distribution of potential and space charge. We also determined, through simulation, how the characteristic of the nanowire is affected by its dimensions. The characterization of the resulting nanowire, calculated by COMSOL Multiphysics, shows different dimensions and their effect on space charge and electrical potential

Characterization of Myoelectric Signals Using System Identification Techniques

2004 ◽  
Author(s):  
Jeffrey T. Bingham ◽  
Marco P. Schoen
Keyword(s):  
System Identification ◽  
Motor Neurons ◽  
Current System ◽  
Electrical Potential ◽  
Computer Software ◽  
The Body ◽  
Myoelectric Signals ◽  
Hand Motion ◽  
The Central Nervous System

Human muscle motion is initiated in the central nervous system where a nervous signal travels through the body and the motor neurons excite the muscles to move. These signals, termed myoelectric signals, can be measured on the surface of the skin as an electrical potential. By analyzing these signals it is possible to determine the muscle actions the signals elicit, and thus can be used in manipulating smart prostheses and teleoperation of machinery. Due to the randomness of myoelectric signals, identification of the signals is not complete, therefore the goal of this project is to complete a study of the characterization of one set of hand motions using current system identification methods. The gripping motion of the hand and the corresponding myoelectric signals are measured and the data captured with a personal computer. Using computer software the captured data are processed and finally subjected to several system identification routines. Using this technique it is possible to construct a mathematical model that correlates the myoelectric signals with the matching hand motion.

scholarly journals Purification and Biochemical Characterization of the F1Fo-ATP Synthase from Thermoalkaliphilic Bacillus sp. Strain TA2.A1

2003 ◽  
Vol 185 (15) ◽  
pp. 4442-4449 ◽  
Author(s):  
Gregory M. Cook ◽  
Stefanie Keis ◽  
Hugh W. Morgan ◽  
Christoph von Ballmoos ◽  
Ulrich Matthey ◽  
...  
Keyword(s):  
Atp Synthase ◽  
Biochemical Characterization ◽  
Atp Hydrolysis ◽  
Sodium Dodecyl ◽  
Electrical Potential ◽  
Atp Synthesis ◽  
Intrinsic Property ◽  
Protein Sequencing ◽  
Hydrolysis Activity

ABSTRACT We describe here purification and biochemical characterization of the F1Fo-ATP synthase from the thermoalkaliphilic organism Bacillus sp. strain TA2.A1. The purified enzyme produced the typical subunit pattern of an F1Fo-ATP synthase on a sodium dodecyl sulfate-polyacrylamide gel, with F1 subunits α, β, γ, δ, and ε and Fo subunits a, b, and c. The subunits were identified by N-terminal protein sequencing and mass spectroscopy. A notable feature of the ATP synthase from strain TA2.A1 was its specific blockage in ATP hydrolysis activity. ATPase activity was unmasked by using the detergent lauryldimethylamine oxide (LDAO), which activated ATP hydrolysis >15-fold. This activation was the same for either the F1Fo holoenzyme or the isolated F1 moiety, and therefore latent ATP hydrolysis activity is an intrinsic property of F1. After reconstitution into proteoliposomes, the enzyme catalyzed ATP synthesis driven by an artificially induced transmembrane electrical potential (Δψ). A transmembrane proton gradient or sodium ion gradient in the absence of Δψ was not sufficient to drive ATP synthesis. ATP synthesis was eliminated by the electrogenic protonophore carbonyl cyanide m-chlorophenylhydrazone, while the electroneutral Na+/H+ antiporter monensin had no effect. Neither ATP synthesis nor ATP hydrolysis was stimulated by Na+ ions, suggesting that protons are the coupling ions of the ATP synthase from strain TA2.A1, as documented previously for mesophilic alkaliphilic Bacillus species. The ATP synthase was specifically modified at its c subunits by N,N′-dicyclohexylcarbodiimide, and this modification inhibited ATP synthesis.

scholarly journals Study of Osteocyte Behavior by High-Resolution Intravital Imaging Following Photo-Induced Ischemia

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2874
Author(s):  
Hengfeng Yuan ◽  
Wen Jiang ◽  
Yuanxin Chen ◽  
Betty Kim
Keyword(s):  
Imaging Techniques ◽  
Avascular Osteonecrosis ◽  
Functional Changes ◽  
Cellular Processes ◽  
Non Invasive ◽  
Behavioral Dynamics ◽  
Bony Anatomy ◽  
Magnetic Resonance Imaging Mri

Ischemic injuries and local hypoxia can result in osteocytes dysfunction and play a key role in the pathogenesis of avascular osteonecrosis. Conventional imaging techniques including magnetic resonance imaging (MRI) and computed tomography (CT) can reveal structural and functional changes within bony anatomy; however, characterization of osteocyte behavioral dynamics in the setting of osteonecrosis at the single cell resolution is limited. Here, we demonstrate an optical approach to study real-time osteocyte functions in vivo. Using nicotinamide adenine dinucleotide (NADH) as a biomarker for metabolic dynamics in osteocytes, we showed that NADH level within osteocytes transiently increase significantly after local ischemia through non-invasive photo-induced thrombosis of afferent arterioles followed by a steady decline. Our study presents a non-invasive optical approach to study osteocyte behavior through the modulation of local environmental conditions. Thus it provides a powerful toolkit to study cellular processes involved in bone pathologies in vivo.

scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

scholarly journals Characterization of Poldip2 knockout mice: avoiding incorrect gene targeting

2021 ◽  
Author(s):  
Bernard Lassègue ◽  
Sandeep Kumar ◽  
Rohan Mandavilli ◽  
Keke Wang ◽  
Michelle Tsai ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Cell Clone ◽  
Gene Trap ◽  
Rna Seq ◽  
Multifunctional Protein ◽  
Cellular Processes ◽  
Depth Study ◽  
Perinatal Lethality ◽  
Knockout Line

AbstractPOLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from two limitations: perinatal lethality in homozygotes and constitutive Poldip2 inactivation. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, an RNA-seq experiment was performed in constitutive knockout carotid arteries. Results support the involvement of POLDIP2 in multiple cellular processes and provide new opportunities for future in-depth study of its functions.

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