keyword
MENU ▼
Read by QxMD icon Read
search

Stochastic gene regulation

keyword
https://www.readbyqxmd.com/read/29218900/single-subject-transcriptome-analysis-to-identify-functionally-signed-gene-set-or-pathway-activity
#1
Joanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A Lussier
Analysis of single-subject transcriptome response data is an unmet need of precision medicine, made challenging by the high dimension, dynamic nature and difficulty in extracting meaningful signals from biological or stochastic noise. We have proposed a method for single subject analysis that uses a mixture model for transcript fold-change clustering from isogenically paired samples, followed by integration of these distributions with Gene Ontology Biological Processes (GO-BP) to reduce dimension and identify functional attributes...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29177465/aminoglycoside-mediated-promotion-of-translation-readthrough-occurs-through-a-non-stochastic-mechanism-that-competes-with-translation-termination
#2
H M Chowdhury, M A Siddiqui, S Kanneganti, N Sharmin, M W Chowdhury, Talat Nasim
Attempts have been made to treat nonsense-associated genetic disorders by chemical agents and hence an improved mechanistic insight into the decoding of readthrough signals is essential for the identification and characterisation of factors for the treatment of these disorders. To identify either novel compounds or genes that modulate translation readthrough, we have employed dual reporter-based high-throughput screens that use enzymatic and fluorescence activities and screened bio-active NINDS compounds (n = 1000) and siRNA (n = 288) libraries...
November 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29175206/stochastic-simulation-of-multiscale-complex-systems-with-piskas-a-rule-based-approach
#3
Tomas Perez-Acle, Ignacio Fuenzalida, Alberto J M Martin, Rodrigo Santibañez, Rodrigo Avaria, Alejandro Bernardin, Alvaro M Bustos, Daniel Garrido, Jonathan Dushoff, James H Liu
Computational simulation is a widely employed methodology to study the dynamic behavior of complex systems. Although common approaches are based either on ordinary differential equations or stochastic differential equations, these techniques make several assumptions which, when it comes to biological processes, could often lead to unrealistic models. Among others, model approaches based on differential equations entangle kinetics and causality, failing when complexity increases, separating knowledge from models, and assuming that the average behavior of the population encompasses any individual deviation...
November 21, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29167445/stochastic-fluctuations-can-reveal-the-feedback-signs-of-gene-regulatory-networks-at-the-single-molecule-level
#4
Chen Jia, Peng Xie, Min Chen, Michael Q Zhang
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the analytical steady-state distribution of the protein copy number in a general kinetic model of stochastic gene expression with nonlinear feedback regulation, we reveal the relationship between stochastic fluctuations and feedback topology at the single-molecule level, which provides novel insights into how and to what extent a feedback loop can enhance or suppress molecular fluctuations...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29161860/modulation-of-first-passage-time-for-bursty-gene-expression-via-random-signals
#5
Qiuying Li, Lifang Huang, Jianshe Yu
The stochastic nature of cell-specific signal molecules (such as transcription factor, ribosome, etc.) and the intrinsic stochastic nature of gene expression process result in cell-to-cell variations at protein levels. Increasing experimental evidences suggest that cell phenotypic variations often depend on the accumulation of some special proteins. Hence, a natural and fundamental question is: How does input signal affect the timing of protein count up to a given threshold? To this end, we study effects of input signal on the first-passage time (FPT), the time at which the number of proteins crosses a given threshold...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29153325/genetic-and-epigenetic-strategies-potentiate-gal4-activation-to-enhance-fitness-in-recently-diverged-yeast-species
#6
Varun Sood, Jason H Brickner
Certain genes show more rapid reactivation for several generations following repression, a conserved phenomenon called epigenetic transcriptional memory. Following previous growth in galactose, GAL gene transcriptional memory confers a strong fitness benefit in Saccharomyces cerevisiae adapting to growth in galactose for up to 8 generations. A genetic screen for mutants defective for GAL gene memory revealed new insights into the molecular mechanism, adaptive consequences, and evolutionary history of memory...
November 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29130209/live-imaging-of-mrna-synthesis-in-drosophila
#7
Hernan G Garcia, Thomas Gregor
mRNA synthesis is one of the earliest readouts of the activity of a transcribed gene, which is of particular interest in the context of metazoan cell fate specification. These processes are intrinsically dynamic and stochastic, which makes in vivo single-cell measurements inevitable. Here, we present the application of a technology that has been widely used in single celled organisms to measure transcriptional activity in developing embryos of the fruit fly Drosophila melanogaster. The method allows for quantification of instantaneous polymerase occupancy of active gene loci and thereby enables the development and testing of models of gene regulation in development...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116032/single-cell-transcriptomics-suggest-that-human-adipocyte-progenitor-cells-constitute-a-homogeneous-cell-population
#8
Juan R Acosta, Simon Joost, Kasper Karlsson, Anna Ehrlund, Xidan Li, Myriam Aouadi, Maria Kasper, Peter Arner, Mikael Rydén, Jurga Laurencikiene
Regulation of adipose tissue stem cells (ASCs) and adipogenesis impact the development of excess body fat-related metabolic complications. Animal studies have suggested the presence of distinct subtypes of ASCs with different differentiation properties. In addition, ASCs are becoming the biggest source of mesenchymal stem cells used in therapies, which requires deep characterization. Using unbiased single cell transcriptomics we aimed to characterize ASC populations in human subcutaneous white adipose tissue (scWAT)...
November 7, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29098989/an-application-of-the-krylov-fsp-ssa-method-to-parameter-fitting-with-maximum-likelihood
#9
Khanh N Dinh, Roger B Sidje
Monte Carlo methods such as the stochastic simulation algorithm (SSA) have traditionally been employed in gene regulation problems. However, there has been increasing interest to directly obtain the probability distribution of the molecules involved by solving the chemical master equation (CME). This requires addressing the curse of dimensionality that is inherent in most gene regulation problems. The finite state projection (FSP) seeks to address the challenge and there have been variants that further reduce the size of the projection or that accelerate the resulting matrix exponential...
November 3, 2017: Physical Biology
https://www.readbyqxmd.com/read/29084263/a-plasmid-based-escherichia-coli-gene-expression-system-with-cell-to-cell-variation-below-the-extrinsic-noise-limit
#10
Zach Hensel
Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription...
2017: PloS One
https://www.readbyqxmd.com/read/29080679/sfrp2-dpp4-and-fmo1-lsp1-define-major-fibroblast-populations-in-human-skin
#11
Tracy Tabib, Christina Morse, Ting Wang, Wei Chen, Robert Lafyatis
Fibroblasts produce matrix, regulate inflammation, mediate reparative processes, and serve as pluripotent mesenchymal cells. Analyzing digested normal human skin by single cell RNA-seq (scRNA-seq), we explored different fibroblast populations. T-distributed stochastic neighbor embedding and clustering of scRNA-seq data from six biopsies revealed two major fibroblast populations, defined by distinct genes, including SFRP2 and FMO1, expressed exclusively by these two major fibroblast populations. Further subpopulations were defined within each of the SFRP2 and FMO1 populations, as well as five minor fibroblast populations, each expressing discrete genes: CRABP1, COL11A1, FMO2, PRG4 or C2ORF40...
October 25, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29058744/hybrid-deterministic-stochastic-simulation-of-complex-biochemical-systems
#12
Paola Lecca, Fabio Bagagiolo, Marina Scarpa
In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects...
November 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#13
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29030469/single-cell-gene-expression-analysis-reveals-regulators-of-distinct-cell-subpopulations-among-developing-human-neurons
#14
Jiaxu Wang, Piroon Jenjaroenpun, Akshay Bhinge, Vladimir Espinosa Angarica, Antonio Del Sol, Intawat Nookaew, Vladimir A Kuznetsov, Lawrence W Stanton
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29025390/partitioning-of-functional-gene-expression-data-using-principal-points
#15
Jaehee Kim, Haseong Kim
BACKGROUND: DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data since they are considered as independent realizations of a stochastic process. This process requires appropriate models to identify patterns of gene functions. The partitioning of the functional data can find homogeneous subgroups of entities for the massive genes within the inherent biological networks...
October 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28977492/dna-residence-time-is-a-regulatory-factor-of-transcription-repression
#16
Karen Clauß, Achim P Popp, Lena Schulze, Johannes Hettich, Matthias Reisser, Laura Escoter Torres, N Henriette Uhlenhaut, J Christof M Gebhardt
Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28968704/sincerities-inferring-gene-regulatory-networks-from-time-stamped-single-cell-transcriptional-expression-profiles
#17
Nan Papili Gao, S M Minhaz Ud-Dean, Olivier Gandrillon, Rudiyanto Gunawan
Motivation: Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired...
September 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28947742/noise-reduction-as-an-emergent-property-of-single-cell-aging
#18
Ping Liu, Ruijie Song, Gregory L Elison, Weilin Peng, Murat Acar
Noise-induced heterogeneity in gene expression is an inherent reality for cells. However, it is not well understood how noise strength changes for a single gene while the host cell is aging. Using a state-of-the-art microfluidic platform, we measure noise dynamics in aging yeast cells by tracking the generation-specific activity of the canonical GAL1 promoter. We observe noise reduction during normal aging of a cell, followed by a short catastrophe phase in which noise increased. We hypothesize that aging-associated increases in chromatin state transitions are behind the observed noise reduction and a stochastic model provides quantitative support to the proposed mechanism...
September 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28938803/hybrid-models-for-chemical-reaction-networks-multiscale-theory-and-application-to-gene-regulatory-systems
#19
Stefanie Winkelmann, Christof Schütte
Well-mixed stochastic chemical kinetics are properly modeled by the chemical master equation (CME) and associated Markov jump processes in molecule number space. If the reactants are present in large amounts, however, corresponding simulations of the stochastic dynamics become computationally expensive and model reductions are demanded. The classical model reduction approach uniformly rescales the overall dynamics to obtain deterministic systems characterized by ordinary differential equations, the well-known mass action reaction rate equations...
September 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28878283/rate-limiting-steps-in-transcription-dictate-sensitivity-to-variability-in-cellular-components
#20
Jarno Mäkelä, Vinodh Kandavalli, Andre S Ribeiro
Cell-to-cell variability in cellular components generates cell-to-cell diversity in RNA and protein production dynamics. As these components are inherited, this should also cause lineage-to-lineage variability in these dynamics. We conjectured that these effects on transcription are promoter initiation kinetics dependent. To test this, first we used stochastic models to predict that variability in the numbers of molecules involved in upstream processes, such as the intake of inducers from the environment, acts only as a transient source of variability in RNA production numbers, while variability in the numbers of a molecular species controlling transcription of an active promoter acts as a constant source...
September 6, 2017: Scientific Reports
keyword
keyword
79106
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"