scholarly journals Modeling and analysis of the macronutrient signaling network in budding yeast

2021 ◽  
Vol 32 (21) ◽  
Author(s):  
Amogh P. Jalihal ◽  
Pavel Kraikivski ◽  
T. M. Murali ◽  
John J. Tyson

A computational model of the underlying regulatory mechanisms is proposed to study nutrient signaling. The model’s predictions are consistent with literature-curated experimental measurements. Using this model, novel, testable predictions are made in genetic mutant strains undergoing complex nutrient shifts.

2020 ◽  
Author(s):  
Amogh P. Jalihal ◽  
Pavel Kraikivski ◽  
T. M. Murali ◽  
John J. Tyson

AbstractIn eukaryotes, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks. The function of these networks is to govern robust cellular responses to unpredictable changes in the nutritional environment of the cell. In the budding yeast, Saccharomyces cerevisiae, these nutrient signaling pathways and their interconnections have been well characterized. However the complexity of the signaling network confounds the interpretation of the overall regulatory ‘logic’ of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model’s kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.


2018 ◽  
Vol 69 (10) ◽  
pp. 2948-2939 ◽  
Author(s):  
Carmen Moldovan ◽  
Lidia Dobrescu ◽  
Violeta Ristoiu ◽  
Bogdan Firtat ◽  
Silviu Dinulescu ◽  
...  

This article presents experimental measurements performed in order to connect a neuronal cell culture to an exoprosthesis. The experiments focused on the biosignals� acquisition from the cell culture. A special gold-plated glass plate device was realized and several constructive variants were analyzed. A Olympus microscope with fluorescence and photo system was used. The acquisition of bio signals from the neuron culture is realized and described in the paper. The measurements were made in the sterile environment within the laboratory of Institute of Cellular Biology and Pathology. The measurements have been made for the pair of electrodes 1-1 at the edge of the glass plate.


2017 ◽  
Vol 9 (2) ◽  
pp. 156-166 ◽  
Author(s):  
Adriana T. Dawes ◽  
David Wu ◽  
Karley K. Mahalak ◽  
Edward M. Zitnik ◽  
Natalia Kravtsova ◽  
...  

Alterations to only specific parameters in a model including EGF, Wnt and Notch lead to cell behavior differences.


1977 ◽  
Vol 233 (5) ◽  
pp. F464-F480 ◽  
Author(s):  
L. P. Sullivan ◽  
D. J. Welling ◽  
D. G. Deeds ◽  
J. H. Simone

Techniques have been developed for studying the distribution and the rates of exchange of K among urine, the tubular cells, and the circulation in the isolated, pump-perfused, bullfrog kidney. Tubular cells were loaded with 42K via the portal circulation, and the subsequent washout of the tracer into the vena cava and into urine was measured. Analysis of the data indicated the existence of at least three cellular pools of K. Pools a and b have half times of exchange of 1.1 and 4.1 min and contain about 25 and 40% of tissue K, respectively. The remainder of cellular K is contained in one or more very slowly exchanging pools. The rate of exchange of K at the basolateral surface of tubular cells is 50-fold greater than at the luminal surface. A pulse-washout method was also devised to permit control and experimental measurements to be made in the same kidney. With this technique, we found that portal perfusion with 10 mM K increased the rate of uptake into pools a and b from the circulation and the rate constants for efflux into the urine from both pools, Acetazolamide increased uptake into pool a and the rate constants for efflux into the urine from both pools.


1998 ◽  
Vol 120 (04) ◽  
pp. 66-68 ◽  
Author(s):  
Klaus-Ju¨rgen Bathe

This article reviews finite element methods that are widely used in the analysis of solids and structures, and they provide great benefits in product design. In fact, with today’s highly competitive design and manufacturing markets, it is nearly impossible to ignore the advances that have been made in the computer analysis of structures without losing an edge in innovation and productivity. Various commercial finite-element programs are widely used and have proven to be indispensable in designing safer, more economical products. Applications of acoustic-fluid/structure interactions are found whenever the fluid can be modeled to be inviscid and to undergo only relatively small particle motions. The interplay between finite-element modeling and analysis with the recognition and understanding of new physical phenomena will advance the understanding of physical processes. This will lead to increasingly better simulations. Based on current technology and realistic expectations of further hardware and software developments, a tremendous future for fluid–structure interaction applications lies ahead.


2014 ◽  
Vol 1020 ◽  
pp. 25-30
Author(s):  
Marianna Šuštiaková ◽  
Pavol Ďurica ◽  
Radoslav Ponechal ◽  
Marek Cangár

The paper evaluated thermo-technical characteristics of the experimental walls, consisting of five different tracks in three different color surfaces at different base material. The hygrothermal behavior of the structures and layers is monitored year-round. The computational model of the laboratory room and tested samples is compiled and debugged on the basis of experimental measurements. The dynamic simulations of temperature and humidity parameters were realized.


1999 ◽  
Vol 19 (12) ◽  
pp. 7983-7994 ◽  
Author(s):  
Aparna Sreenivasan ◽  
Douglas Kellogg

ABSTRACT In budding yeast, the Clb2 mitotic cyclin initiates a signaling network that negatively regulates polar bud growth during mitosis. This signaling network appears to require the function of a Clb2-binding protein called Nap1, the Cdc42 GTPase, and two protein kinases called Gin4 and Cla4. In this study, we demonstrate that the Elm1 kinase also plays a role in the control of bud growth during mitosis. Cells carrying a deletion of the ELM1 gene undergo a prolonged mitotic delay, fail to negatively regulate polar bud growth during mitosis, and show defects in septin organization. In addition, Elm1 is required in vivo for the proper regulation of both the Cla4 and Gin4 kinases and interacts genetically with Cla4, Gin4, and the mitotic cyclins. Previous studies have suggested that Elm1 may function to negatively regulate the Swe1 kinase. To further understand the functional relationship between Elm1 and Swe1, we have characterized the phenotype of Δelm1 Δswe1 cells. We found that Δelm1 Δswe1 cells are inviable at 37°C and that a large proportion of Δelm1Δswe1 cells grown at 30°C contain multiple nuclei, suggesting severe defects in cytokinesis. In addition, we found that Elm1 is required for the normal hyperphosphorylation of Swe1 during mitosis. We propose a model in which the Elm1 kinase functions in a mitotic signaling network that controls events required for normal bud growth and cytokinesis, while the Swe1 kinase functions in a checkpoint pathway that delays nuclear division in response to defects in these events.


2015 ◽  
Vol 9 (1) ◽  
Author(s):  
Sushil Tripathi ◽  
Åsmund Flobak ◽  
Konika Chawla ◽  
Anaïs Baudot ◽  
Torunn Bruland ◽  
...  

Cytoskeleton ◽  
2015 ◽  
Vol 72 (10) ◽  
pp. 517-533 ◽  
Author(s):  
Haosu Tang ◽  
Tamara C. Bidone ◽  
Dimitrios Vavylonis

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