scholarly journals Optimum Threshold Minimizes Noise in Timing of Intracellular Events

Author(s):  
Sherin Kannoly ◽  
Tianhui Gao ◽  
Supravat Dey ◽  
Ing-Nang Wang ◽  
Abhyudai Singh ◽  
...  

ABSTRACTHow the noisy expression of regulatory proteins affects timing of intracellular events is an intriguing fundamental problem that influences diverse cellular processes. Here we use the bacteriophage λ to study event timing in individual cells where cell lysis is the result of expression and accumulation of a single protein (holin) in the Escherchia coli cell membrane up to a critical threshold level. Site-directed mutagenesis of the holin gene was used to generate phage variants that vary in their timing of lysis from 30 to 190 min. Observation of the lysis times of single cells reveals an intriguing finding – the noise in lysis timing first decreases with increasing lysis time to reach a minimum, and then sharply increases at longer longer lysis times. A mathematical model with stochastic expression of holin together with dilution from cell growth was sufficient to explain the non-monotonic noise profile, and identify holin accumulation thresholds that generate precision in lysis timing.

2020 ◽  
Author(s):  
Supravat Dey ◽  
Sherin Kannoly ◽  
Pavol Bokes ◽  
John J Dennehy ◽  
Abhyudai Singh

AbstractTriggering of cellular events often relies on the level of a key gene product crossing a critical threshold. Achieving precision in event timing in spite of noisy gene expression facilitates high-fidelity functioning of diverse processes from biomolecular clocks, apoptosis and cellular differentiation. Here we investigate the role of an incoherent feedforward circuit in regulating the time taken by a bacterial virus (bacteriophage lambda) to lyse an infected Escherichia coli cell. Lysis timing is the result of expression and accumulation of a single lambda protein (holin) in the E. coli cell membrane up to a critical threshold level, which triggers the formation of membrane lesions. This easily visualized process provides a simple model system for characterizing event-timing stochasticity in single cells. Intriguingly, lambda’s lytic pathway synthesizes two functionally opposite proteins: holin and antiholin from the same mRNA in a 2:1 ratio. Antiholin sequesters holin and inhibits the formation of lethal membrane lesions, thus creating an incoherent feedforward circuit. We develop and analyze a stochastic model for this feedforward circuit that considers correlated bursty expression of holin/antiholin, and their concentrations are diluted from cellular growth. Interestingly, our analysis shows the noise in timing is minimized when both proteins are expressed at an optimal ratio, hence revealing an important regulatory role for antiholin. These results are in agreement with single cell data, where removal of antiholin results in enhanced stochasticity in lysis timing.


2008 ◽  
Vol 86 (10) ◽  
pp. 1095-1100 ◽  
Author(s):  
Steve C. Dinsmore ◽  
David L. Swanson

Freezing survival may differ among winters in chorus frogs ( Pseudacris triseriata (Wied-Neuwied, 1838)), and low freezing survival is associated with low hepatic glycogen stores. The pattern of prehibernation liver glycogen accumulation in chorus frogs is unknown. Frogs might accumulate hepatic glycogen stores until a threshold level sufficient for winter survival is attained, after which frogs enter hibernation (critical threshold hypothesis). According to this model, frogs active late in the season should only be those with low hepatic glycogen stores. Alternatively, hepatic glycogen levels might continue to increase throughout the fall as long as frogs remain active (continuous increase hypothesis). We tested these hypotheses by measuring liver and leg muscle glycogen, glucose, and glycogen phosphorylase activities in chorus frogs throughout the fall prehibernation period in southeastern South Dakota. Hepatic glycogen levels were significantly related to date and increased throughout the fall period, consistent with the continuous increase hypothesis. This suggests that hepatic glycogen levels do not serve as a cue for entrance into hibernation. Liver phosphorylase activity did not vary significantly with progression of the fall season and activity was lower than in winter, suggesting that the winter increment of phosphorylase activity requires some stimulus during hibernation (e.g., low temperatures).


2019 ◽  
Author(s):  
Khem Raj Ghusinga ◽  
Abhyudai Singh

AbstractAn important step in execution of several cellular processes is accumulation of a regulatory protein up to a specific threshold level. Since production of a protein is inherently stochastic, the time at which its level crosses a threshold exhibits cell-to-cell variation. A problem of interest is to characterize how the statistics of event timing is affected by various steps of protein expression. Our previous work studied this problem by considering a gene expression model where gene was always active. Here we extend our analysis to a scenario where gene stochastically switches between active and inactive states. We formulate event timing as the first-passage time for a protein’s level to cross a threshold and investigate how the rates of gene activation/inactivation affect the distribution and moments of the first-passage time. Our results show that both the time-scale of gene switching with respect to the protein degradation rate as well as the ratio of the gene inactivation to gene activation rates are important parameters in shaping the event-timing distribution.


2020 ◽  
Vol 295 (52) ◽  
pp. 18105-18121
Author(s):  
Andrew C. Hedman ◽  
Dean E. McNulty ◽  
Zhigang Li ◽  
Laëtitia Gorisse ◽  
Roland S. Annan ◽  
...  

IQGAP1 is a key scaffold protein that regulates numerous cellular processes and signaling pathways. Analogous to many other cellular proteins, IQGAP1 undergoes post-translational modifications, including phosphorylation. Nevertheless, very little is known about the specific sites of phosphorylation or the effects on IQGAP1 function. Here, using several approaches, including MS, site-directed mutagenesis, siRNA-mediated gene silencing, and chemical inhibitors, we identified the specific tyrosine residues that are phosphorylated on IQGAP1 and evaluated the effect on function. Tyr-172, Tyr-654, Tyr-855, and Tyr-1510 were phosphorylated on IQGAP1 when phosphotyrosine phosphatase activity was inhibited in cells. IQGAP1 was phosphorylated exclusively on Tyr-1510 under conditions with enhanced MET or c-Src signaling, including in human lung cancer cell lines. This phosphorylation was significantly reduced by chemical inhibitors of MET or c-Src or by siRNA-mediated knockdown of MET. To investigate the biological sequelae of phosphorylation, we generated a nonphosphorylatable IQGAP1 construct by replacing Tyr-1510 with alanine. The ability of hepatocyte growth factor, the ligand for MET, to promote AKT activation and cell migration was significantly greater when IQGAP1-null cells were reconstituted with IQGAP1 Y1510A than when cells were reconstituted with WT IQGAP1. Collectively, our data suggest that phosphorylation of Tyr-1510 of IQGAP1 alters cell function. Because increased MET signaling is implicated in the development and progression of several types of carcinoma, IQGAP1 may be a potential therapeutic target in selected malignancies.


2020 ◽  
Vol 6 (39) ◽  
pp. eabc2648
Author(s):  
Marc Hippler ◽  
Kai Weißenbruch ◽  
Kai Richler ◽  
Enrico D. Lemma ◽  
Masaki Nakahata ◽  
...  

Many essential cellular processes are regulated by mechanical properties of their microenvironment. Here, we introduce stimuli-responsive composite scaffolds fabricated by three-dimensional (3D) laser lithography to simultaneously stretch large numbers of single cells in tailored 3D microenvironments. The key material is a stimuli-responsive photoresist containing cross-links formed by noncovalent, directional interactions between β-cyclodextrin (host) and adamantane (guest). This allows reversible actuation under physiological conditions by application of soluble competitive guests. Cells adhering in these scaffolds build up initial traction forces of ~80 nN. After application of an equibiaxial stretch of up to 25%, cells remodel their actin cytoskeleton, double their traction forces, and equilibrate at a new dynamic set point within 30 min. When the stretch is released, traction forces gradually decrease until the initial set point is retrieved. Pharmacological inhibition or knockout of nonmuscle myosin 2A prevents these adjustments, suggesting that cellular tensional homeostasis strongly depends on functional myosin motors.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Emma L. Howard ◽  
Paul Cool ◽  
Gillian L. Cribb

Abstract The aim of this study was to investigate if the risk of pathological fracture can be predicted with the proportion of body weight that can be put through the affected leg in patients with metastatic bone disease of the lower limb. A prospective observational study was conducted in patients with metastatic disease in the lower limb. Receiver Operator Characteristic curves were used to identify the optimum threshold level of single stance weight bearing to predict fracture and compared to the Mirels score. Patients who underwent surgery could weight bear significantly less than those who did not have surgical intervention. The optimum threshold to predict pathological fracture was 85% of total body weight. No patient below the threshold level of 85% single stance body weight sustained a pathological fracture. The use of single stance body weight can be a useful in conjunction with the Mirels score to predict pathological fracture. If less than 85% of total body weight can be put through the affected limb, the risk of fracture increases, and consideration of treatment is suggested.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexander Thiemicke ◽  
Hossein Jashnsaz ◽  
Guoliang Li ◽  
Gregor Neuert

2018 ◽  
Vol 32 (32) ◽  
pp. 202-221
Author(s):  
Agnieszka Sałek-Imińska

In the modern world an undoubted increase in the economic factor of maintaining the security of states is observed. Economic security is an important element of the functioning of national economies, including the states of the eastern flank of NATO. Perceiving economic security as a balance of development needs of these states we can identify several areas of activity of its quantifiers, which can include development, infrastructure and balance opportunities and needs. To determine the levels of these quantifiers, we must use a carefully selected set of meters. One of them is Gross Domestic Product (GDP) which clearly describes the measurable features present in the analyzed national economies. The objective of this article is to attempt to indicate the level of the economic security of NATO’s eastern flank states in terms of the level of economic growth measured by GDP. From an autonomous perspective, this meter does not give grounds for expressing value judgments in the context of the widely understood level of economic security, but it constitutes their necessary component and basis for further analyzes and evaluations. For the needs of the elaboration, an assumption was made, being a simplification of the economic reality, indicating that changes in annual GDP will show the level of the economic security of NATO’s eastern flank states. Hence, an increase in GDP growth lower than 1.9% in a period, which the analysis refers to, is a sign of a decrease in the level of economic security of a given state and vice versa. In all the states of NATO’s eastern flank, an improvement in its level was observed, where in 2017 in all the states of NATO’s eastern flank the rate of GDP growth was higher than the assumed critical threshold level of 1.9%. Years 2014–2016 also constitute a period of improvement in the level of the economic security of the analyzed states, except for Bulgaria in 2014, Estonia and Lithuania in 2015 and Estonia in 2016. While the period from 2008 to 2013 is a period when the level of the economic security of the states of NATO’s eastern flank is diverse and there are no indications that it improved. In the context of the analyzed problem, the best years were 2008 and 2011, for which GDP growth was the highest. In 2008 Estonia, Latvia and Hungary were those that did not reach the critical threshold (decline in economic security). The other six states were characterized by an increase in the level of economic security. The following year is a period when all the states (except for Poland) did not register any improvement. This resulted from a general economic recession, which was observed in the region of Central and Eastern Europe. Considering the number of years for which the assumed critical threshold level of 1.9% was not reached, we can claim that the economy of Poland (2 periods: 2012–2013), and then Czech Republic, Lithuania, Latvia and Slovakia (3 periods), Romania (4 years) and Bulgaria, Estonia and Hungary (5 years) were characterized by the highest level of economic security in the analyzed period.


2007 ◽  
Vol 12 (5) ◽  
pp. 653-671 ◽  
Author(s):  
LUCA BOLZONI ◽  
GIULIO A. DE LEO

In the epidemiological literature, the eradication of a wildlife disease through culling is usually described in terms of a constant hunting rate to simulate the selective removal of animals from the population. By using simple SI (susceptible–infected) models, it is easy to prove that, if the hunting rate is high enough, the population eventually drops below a critical threshold level under which the pathogen is deemed to be extinct. However, hunting costs as well as the monetary benefits of disease control are almost systematically neglected. Moreover, the hunting rate is usually assumed to be constant over time, while in reality health authorities can implement more flexible culling policies. In this work we examine a class of more realistic time-variant culling strategies in a cost–benefit framework. Culling strategies differ in the way decisions are made about when and how much to cull; that is, whether hunting occurs when disease prevalence, host population density, or the number of carcasses exceeds (or is below) a given threshold. For each culling strategy, the optimal value of the control parameters and the hunting rate are those that minimize the sum of the culling costs and the sanitary costs associated with infection over a specific period of time. Classical swine fever (CSF) in wild boar populations has been taken as a reference example because of its potential economic impact on industrialized and developing countries.We show that the optimal time-flexible culling strategy is invariably more efficient than the best traditional strategy in which the hunting rate is held constant through time. We also show that the type of hunting strategy that is selected as optimal depends on the shape of the cost functions.


1998 ◽  
Vol 111 (2) ◽  
pp. 257-269 ◽  
Author(s):  
Amy B. Harkins ◽  
Aaron P. Fox

The functional effect of activating Ca2+-permeable neuronal nicotinic acetylcholine receptors (nAChRs) on vesicle secretion was studied in PC12 cells. Single cells were patch-clamped in the whole-cell configuration and stimulated with either brief pulses of nicotine to activate the Ca2+-permeable nAChRs or with voltage steps to activate voltage-dependent Ca2+ channels. Membrane capacitance was used as a measure of vesicle secretion. Activation of nAChRs by nicotine application to cells voltage clamped at −80 mV evoked secretion. This secretion was completely abolished by nicotinic antagonists. When the cells were voltage clamped at +20 mV in the presence of Cd2+ to block voltage-activated Ca2+ channels, nicotine elicited a small amount of secretion. Most interestingly, when the nAChRs were activated coincidentally with voltage-dependent Ca2+ channels, secretion was augmented approximately twofold over the secretion elicited with voltage-dependent Ca2+ channels alone. Our data suggest that Ca2+ influx via nAChRs affects Ca2+-dependent cellular functions, including vesicle secretion. In addition to the secretion evoked by nAChR activation at hyperpolarized potentials, we demonstrate that even at depolarized potentials, nAChRs provide an important Ca2+ entry pathway underlying Ca2+-dependent cellular processes such as exocytosis.


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