scholarly journals Minimal intervening control of biomolecular networks leading to a desired cellular state

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sang-Mok Choo ◽  
Sang-Min Park ◽  
Kwang-Hyun Cho
Keyword(s):  
State Transition ◽  
Basin Of Attraction ◽  
Boolean Networks ◽  
Cell Phenotype ◽  
General Control ◽  
Attractor State ◽  
Biomolecular Networks ◽  
Control Framework ◽  
A Cell ◽  
Network States

Abstract A cell phenotype can be represented by an attractor state of the underlying molecular regulatory network, to which other network states eventually converge. Here, the set of states converging to each attractor is called its basin of attraction. A central question is how to drive a particular cell state toward a desired attractor with minimal interventions on the network system. We develop a general control framework of complex Boolean networks to provide an answer to this question by identifying control targets on which one-time temporary perturbation can induce a state transition to the boundary of a desired attractor basin. Examples are shown to illustrate the proposed control framework which is also applicable to other types of complex Boolean networks.

scholarly journals Author response: A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation

2017 ◽  
Author(s):  
Meng Amy Li ◽  
Paulo P Amaral ◽  
Priscilla Cheung ◽  
Jan H Bergmann ◽  
Masaki Kinoshita ◽  
...  
Keyword(s):  
Dna Methylation ◽  
State Transition ◽  
De Novo ◽  
Author Response ◽  
Cell State ◽  
A Cell

scholarly journals Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Ana J. Chucair-Elliott ◽  
Sarah R. Ocañas ◽  
David R. Stanford ◽  
Victor A. Ansere ◽  
Kyla B. Buettner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Affinity Purification ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Tissue Level ◽  
Cell Phenotype ◽  
Specific Gene ◽  
Cell Type ◽  
A Cell ◽  
Cell Type Specific

AbstractEpigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

BOOLEAN NETWORKS WITH MEMORY

2008 ◽  
Vol 18 (12) ◽  
pp. 3799-3814 ◽  
Author(s):  
RAMÓN ALONSO-SANZ ◽  
LARRY BULL
Keyword(s):  
Boolean Networks ◽  
Time Step ◽  
Different Types ◽  
A Cell ◽  
With Memory ◽  
In Cells

In standard Boolean Networks (BN) the new state of a cell depends upon the neighborhood configuration only at the preceding time step. The effect of implementing memory of different types in cells of BN with different degrees of random rewiring is studied in this article.

scholarly journals Effect of memory in non-Markovian Boolean networks illustrated with a case study: A cell cycling process

2016 ◽  
Vol 116 (3) ◽  
pp. 30004 ◽  
Author(s):  
H. Ebadi ◽  
M. Saeedian ◽  
M. Ausloos ◽  
G. R. Jafari
Keyword(s):  
Boolean Networks ◽  
Cycling Process ◽  
A Cell ◽  
Cell Cycling

scholarly journals Tetrahymena POT1a Regulates Telomere Length and Prevents Activation of a Cell CycleCheckpoint

2006 ◽  
Vol 27 (5) ◽  
pp. 1592-1601 ◽  
Author(s):  
Naduparambil K. Jacob ◽  
Rachel Lescasse ◽  
Benjamin R. Linger ◽  
Carolyn M. Price
Keyword(s):  
Telomere Length ◽  
Binding Proteins ◽  
Growth Arrest ◽  
Cell Cycle Checkpoint ◽  
Cell Phenotype ◽  
Ssdna Binding ◽  
Cycle Checkpoint ◽  
Length Regulation ◽  
A Cell ◽  
Ssdna Binding Proteins

ABSTRACT The POT1/TEBP telomere proteins are a group of single-stranded DNA (ssDNA)-binding proteins that have long been assumed to protect the G overhang on the telomeric 3′ strand. We have found that the Tetrahymena thermophila genome contains two POT1 gene homologs, POT1a and POT1b. The POT1a gene is essential, but POT1b is not. We have generated a conditional POT1a cell line and shown that POT1a depletion results in a monster cell phenotype and growth arrest. However, G-overhang structure is essentially unchanged, indicating that POT1a is not required for overhang protection. In contrast, POT1a is required for telomere length regulation. After POT1a depletion, most telomeres elongate by 400 to 500 bp, but some increase by up to 10 kb. This elongation occurs in the absence of further cell division. The growth arrest caused by POT1a depletion can be reversed by reexpression of POT1a or addition of caffeine. Thus, POT1a is required to prevent a cell cycle checkpoint that is most likely mediated by ATM or ATR (ATM and ATR are protein kinases of the PI-3 protein kinase-like family). Our findings indicate that the essential function of POT1a is to prevent a catastrophic DNA damage response. This response may be activated when nontelomeric ssDNA-binding proteins bind and protect the G overhang.

scholarly journals Surface modification of uniaxial cyclic strain cell culture platform with temperature-responsive polymer for cell sheet detachment

2015 ◽  
Vol 3 (40) ◽  
pp. 7899-7902 ◽  
Author(s):  
E. L. Lee ◽  
H. H. Bendre ◽  
A. Kalmykov ◽  
J. Y. Wong
Keyword(s):  
Cell Culture ◽  
Intact Cell ◽  
Cell Sheet ◽  
Cyclic Strain ◽  
Cell Phenotype ◽  
Temperature Responsive ◽  
Current Cell ◽  
Responsive Polymer ◽  
Smooth Muscle Cell Phenotype ◽  
A Cell

Because current cell sheet-based blood vessels lack biomimetic structure and require excessively long culture times that may compromise smooth muscle cell phenotype, we modified a cell culture platform with thermoresponsive copolymers to allow intact cell sheet detachment after uniaxial conditioning.

scholarly journals Serine-204 in the linker region of Smad3 mediates the collagen-I response to TGF-β in a cell phenotype-specific manner

2013 ◽  
Vol 319 (19) ◽  
pp. 2928-2937 ◽  
Author(s):  
J.A. Browne ◽  
X. Liu ◽  
H.W. Schnaper ◽  
T. Hayashida
Keyword(s):  
Collagen I ◽  
Cell Phenotype ◽  
Linker Region ◽  
Specific Manner ◽  
A Cell

scholarly journals PERAN TEKNOLOGI INFORMASI DALAM MENGANTISIPASI KECURANGAN AKUNTANSI (Studi Kasus pada PT Bangkit Berkah)

2021 ◽  
Vol 6 (1) ◽  
pp. 57-66
Author(s):  
Debi Novalia ◽  
Hidayatul Kahfi ◽  
Rika Lidya
Keyword(s):  
Information Technology ◽  
Internal Control ◽  
Primary Data ◽  
Accounting Fraud ◽  
General Control ◽  
Study Approach ◽  
Control Framework ◽  
Role Of Information

ABSTRACTThe aim of this research is to find out the role of information technology of PT Bangkit Berkah. in anticipating occurrences of accounting fraud by focusing on the adequacy of the application of IT Control with the COSO Internal Control Framework. The data used to support this research are primary data obtained from interviews and observations. This research is a descriptive qualitative research with the case study approach. The results of the study showed that information technology implemented by PT Bangkit Berkah. is capable of anticipating occurrences of accounting fraud through both general control and application control. This also supports the reduction of accounting fraud experienced by PT Bangkit Berkah. However, the information system is still unintegrated because the data backup procedure is manually conducted. This deficiency results in several risks and threats for the company in maintaining the principle of data security in risk management.Keywords: Information Technology, Fraud in Accounting, Internal Control Systems. АBSTRАKPenelitian ini bertujuan untuk mengetahui peran teknologi informasi PT Bangkit Berkah dalam mengantisipasi kecurangan akuntansi. Penelitian ini berfokus pada kecukupan penerapan teknologi informasi PT Bangkit Berkah dengan IT Control yang telah dipopulerkan oleh COSO. Data yang digunakan untuk mendukung penelitian ini adalah data primer hasil wawancara dan observasi. Penelitian ini mengikuti desain penelitian studi kasus dengan pendekatan kualitatif deskriptif. Hasil penelitian menunjukkan bahwa teknologi informasi yang diimplementasikan oleh PT Bangkit Berkah dapat mengantisipasi kecurangan akuntansi baik yang dilakukan melalui pengendalian umum (general control) maupun pengendalian aplikasi (application control). Hal tersebut telah mengurangi terjadinya fraud yang telah dialami oleh PT Bangkit Berkah. Namun sebagai kelemahan yang masih ada, PT Bangkit Berkah masih menggunakan sistem yang tidak terintegrasi dan penyimpanan data secara manual. Kekurangan ini menimbulkan beberapa risiko dan ancaman bagi perusahaan dalam mempertahankan prinsip keamanan data dalam manajemen ris

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