Article
Biophysics
Supravat Dey, Abhyudai Singh
Summary: Biomolecular clocks drive oscillatory dynamics in various biological processes, but their interactions with environmental factors like genomic decoys can impact their robustness and precision. Analysis of the Goodwin oscillator models in the presence of decoy binding reveals that stability of bound repressors affects oscillation emergence and precision. Degradation of bound repressors can enhance precision by reducing noise in amplitude and period of oscillations.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Shahar Rezenman, Maor Knafo, Ivgeni Tsigalnitski, Shiri Barad, Ghil Jona, Dikla Levi, Orly Dym, Ziv Reich, Ruti Kapon
Summary: Cellular lineage tracking is a valuable tool for studying heterogeneity, evolution, and fitness in populations. However, existing methods have limitations in terms of specificity, cost, and repeatability. To overcome these challenges, we developed gUMI-BEAR, a modular and cost-effective method for high-resolution population tracking.
Article
Multidisciplinary Sciences
Dheeraj Kanaparthi, Marko Lampe, Jan-Hagen Krohn, Baoli Zhu, Andreas Klingl, Tillmann Lueders
Summary: This study investigates the life cycle of bacterial protoplasts in their natural environment and discovers that their reproduction occurs in a defined sequence of steps, influenced by environmental conditions.
Article
Multidisciplinary Sciences
Jordan F. Hastings, Sharissa L. Latham, Alvin Kamili, Madeleine S. Wheatley, Jeremy Z. R. Han, Marie Wong-Erasmus, Monica Phimmachanh, Max Nobis, Chiara Pantarelli, Antonia L. Cadell, Yolande E. I. O'Donnell, King Ho Leong, Sophie Lynn, Fan-Suo Geng, Lujing Cui, Sabrina Yan, Joanna Achinger-Kawecka, Clare Stirzaker, Murray D. Norris, Michelle Haber, Toby N. Trahair, Frank Speleman, Katleen De Preter, Mark J. Cowley, Ozren Bogdanovic, Paul Timpson, Thomas R. Cox, Walter Kolch, Jamie I. Fletcher, Dirk Fey, David R. Croucher
Summary: Gene expression noise promotes stochastic drug resistance in rare cancer cells. However, when integrated across multiple components of an apoptotic signaling network, the influence of noise leads to a higher frequency of chemoresistant neuroblastoma cells. These cells are characterized by JNK impairment and retain a memory of their resistant state even after chemotherapy treatment.
Review
Genetics & Heredity
Abhishek Sarkar, Matthew Stephens
Summary: The Perspective suggests that a Poisson measurement model is sufficient for analyzing single-cell RNA sequencing data and could resolve current controversies. It argues against inconsistent terminology such as dropout and missing data. The development of methods should start with a simple Poisson model, as it is generally consistent with existing data.
Article
Biochemistry & Molecular Biology
Xiang Meng, Alan Reed, Sandie Lai, Juraj Szavits-Nossan, John E. G. McCarthy
Summary: Gene expression stochasticity is an inherent feature of biological systems, creating non-genetic cellular variation and influencing various processes. In this study, the researchers discovered a distinct form of non-transcriptional noise associated with the translation machinery and mRNA 5'UTR of the GCN4 gene in yeast. They characterized the heterogeneity of translation initiation mediated by GCN4-5'UTR using different techniques and found a subpopulation of cells that consistently exhibited enhanced GCN4 translation under non-starvation conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ales Varabyou, Steven L. Salzberg, Mihaela Pertea
Summary: RNA sequencing is commonly used to study gene expression, but simulations typically do not consider the impact of transcriptional noise. This study found that noise leads to systematic errors in computational methods, resulting in underestimation of transcript abundance and increased false-positive genes. Alignment-free methods may also struggle to detect transcripts expressed at low levels.
Article
Biology
Lucy Ham, Marcel Jackson, Michael P. H. Stumpf
Summary: Single-cell expression profiling reveals extensive cell-to-cell variability at the transcriptomic and proteomic level, posing challenges in inferring dynamics and causes of variability. New mathematical models and experimental set-ups are proposed to distinguish intrinsic and extrinsic noise, providing insights into understanding the origins and effects of cell-to-cell variability.
Article
Multidisciplinary Sciences
Najme Khorasani, Mehdi Sadeghi
Summary: This study proposes a computational model to investigate the internal mechanism of stem cells in producing different types of specialized cells. The results demonstrate that population geometries can disrupt spatial patterns, but the model with progenitor cells can restore the initial pattern after injury. The study also reveals the contradictory roles of stochasticity in breaking boundaries and providing non-genetic diversity.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Maria Douaihy, Rachel Topno, Mounia Lagha, Edouard Bertrand, Ovidiu Radulescu
Summary: Monitoring transcription in living cells reveals that it is discontinuous with active periods separated by inactive periods of distinct lifetimes. However, decoding temporal fluctuations and understanding the underlying transcriptional steps is challenging. BurstDECONV is a statistical inference method that can identify individual transcription initiation events and extract mechanistic features of transcription. Compared to alternative methods, BurstDECONV has advantages in terms of precision and flexibility, making it an ideal framework for live cell transcription imaging experiments. It is robust to noise and applicable to different biological contexts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Alena Klindziuk, Anatoly B. Kolomeisky
Summary: Transcription, a fundamental biological process, has been found to exhibit dynamic behavior of alternating between productive and inactive phases, known as transcriptional bursting. Despite significant attention from researchers, the microscopic origin and biological functions of transcriptional bursting remain unclear.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Asia Mendelevich, Saumya Gupta, Aleksei Pakharev, Athanasios Teodosiadis, Andrey A. Mironov, Alexander A. Gimelbrant
Summary: A new spike-in approach is developed to correct technical noise in allele-specific expression analysis, which is highly accurate and cost-effective. This approach involves adding a distinct RNA as a spike-in before library preparation, allowing for efficient analysis of allele-specific expression in large studies.
Article
Chemistry, Physical
Jakob Ruess, Guillaume Ballif, Chetan Aditya
Summary: Stochastic chemical kinetics is a method widely used in studying the random nature of chemical reactions within individual cells, however, the influence of the population context is often ignored. In this article, a modified master equation is proposed to track the time evolution of the expected population composition within a growing population. This approach allows for the classification of cell fate decision systems and the exploration of an important problem in biology.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Oriana Q. H. Zinani, Kemal Keseroglu, Supravat Dey, Ahmet Ay, Abhyudai Singh, Ertugrul M. Ozbudak
Summary: Fluctuations in gene expression can affect embryonic development, and the question of how pattern formation can be reproducibly executed despite these fluctuations is of interest. Studies on zebrafish segmentation clock genes have found that a negative feedback loop minimizes uncorrelated variability, while gene copy number affects RNA variability.
Article
Biochemical Research Methods
Jonathan R. Bowles, Caroline Hoppe, Hilary L. Ashe, Magnus Rattray
Summary: This study presents a scalable implementation of the cpHMM for fast inference of promoter activity and transcriptional kinetic parameters. The method can model genes of arbitrary length and accurately infer kinetic parameters within a computationally feasible timeframe.
