Publications
64 results found
Tang W, Bertaux F, Thomas P, et al., 2018, bayNorm: Bayesian gene expression recovery, imputation and normalisation for single cell RNA-sequencing data
<jats:p>Normalisation of single cell RNA sequencing (scRNA-seq) data is a prerequisite to their interpretation. The marked technical variability and high amounts of missing observations typical of scRNA-seq datasets make this task particularly challenging. Here, we introduce bayNorm, a novel Bayesian approach for scaling and inference of scRNA-seq counts. The method’s likelihood function follows a binomial model of mRNA capture, while priors are estimated from expression values across cells using an empirical Bayes approach. We demonstrate using publicly-available scRNA-seq datasets and simulated expression data that bayNorm allows robust imputation of missing values generating realistic transcript distributions that match single molecule FISH measurements. Moreover, by using priors informed by dataset structures, bayNorm improves accuracy and sensitivity of differential expression analysis and reduces batch effect compared to other existing methods. Altogether, bayNorm provides an efficient, integrated solution for global scaling normalisation, imputation and true count recovery of gene expression measurements from scRNA-seq data.</jats:p>
Uhia I, Priestman M, Joyce G, et al., 2018, Analysis of ParAB dynamics in mycobacteria shows active movement of ParB and differential inheritance of ParA, PLoS ONE, Vol: 13, Pages: 1-20, ISSN: 1932-6203
Correct chromosomal segregation, coordinated with cell division, is crucial for bacterial survival, but despite extensive studies, the mechanisms underlying this remain incompletely understood in mycobacteria. We report a detailed investigation of the dynamic interactions between ParA and ParB partitioning proteins in Mycobacterium smegmatis using microfluidics and time-lapse fluorescence microscopy to observe both proteins simultaneously. During growth and division, ParB presents as a focused fluorescent spot that subsequently splits in two. One focus moves towards a higher concentration of ParA at the new pole, while the other moves towards the old pole. We show ParB movement is in part an active process that does not rely on passive movement associated with cell growth. In some cells, another round of ParB segregation starts before cell division is complete, consistent with initiation of a second round of chromosome replication. ParA fluorescence distribution correlates with cell size, and in sister cells, the larger cell inherits a local peak of concentrated ParA, while the smaller sister inherits more homogeneously distributed protein. Cells which inherit more ParA grow faster than their sister cell, raising the question of whether inheritance of a local concentration of ParA provides a growth advantage. Alterations in levels of ParA and ParB were also found to disturb cell growth.
Bertaux F, Marguerat S, Shahrezaei V, 2018, Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits, ROYAL SOCIETY OPEN SCIENCE, Vol: 5, ISSN: 2054-5703
The cell division rate, size and gene expression programmes change in response to external conditions. These global changes impact on average concentrations of biomolecule and their variability or noise. Gene expression is inherently stochastic, and noise levels of individual proteins depend on synthesis and degradation rates as well as on cell-cycle dynamics. We have modelled stochastic gene expression inside growing and dividing cells to study the effect of division rates on noise in mRNA and protein expression. We use assumptions and parameters relevant to Escherichia coli, for which abundant quantitative data are available. We find that coupling of transcription, but not translation rates to the rate of cell division can result in protein concentration and noise homeostasis across conditions. Interestingly, we find that the increased cell size at fast division rates, observed in E. coli and other unicellular organisms, buffers noise levels even for proteins with decreased expression at faster growth. We then investigate the functional importance of these regulations using gene regulatory networks that exhibit bi-stability and oscillations. We find that network topology affects robustness to changes in division rate in complex and unexpected ways. In particular, a simple model of persistence, based on global physiological feedback, predicts increased proportion of persister cells at slow division rates. Altogether, our study reveals how cell size regulation in response to cell division rate could help controlling gene expression noise. It also highlights that understanding circuits' robustness across growth conditions is key for the effective design of synthetic biological systems.
Shahrezaei V, Robertson B, Thomas P, et al., 2017, Mycobacteria modify their cell size control under sub-optimal carbon sources, Frontiers in Cell and Developmental Biology, Vol: 5, ISSN: 2296-634X
The decision to divide is the most important one that any cell must make. Recent single cell studies suggest that most bacteria follow an “adder” model of cell size control, incorporating a fixed amount of cell wall material before dividing. Mycobacteria, including the causative agent of tuberculosis Mycobacterium tuberculosis, are known to divide asymmetrically resulting in heterogeneity in growth rate, doubling time, and other growth characteristics in daughter cells. The interplay between asymmetric cell division and adder size control has not been extensively investigated. Moreover, the impact of changes in the environment on growth rate and cell size control have not been addressed for mycobacteria. Here, we utilize time-lapse microscopy coupled with microfluidics to track live Mycobacterium smegmatis cells as they grow and divide over multiple generations, under a variety of growth conditions. We demonstrate that, under optimal conditions, M. smegmatis cells robustly follow the adder principle, with constant added length per generation independent of birth size, growth rate, and inherited pole age. However, the nature of the carbon source induces deviations from the adder model in a manner that is dependent on pole age. Understanding how mycobacteria maintain cell size homoeostasis may provide crucial targets for the development of drugs for the treatment of tuberculosis, which remains a leading cause of global mortality.
Sturrock M, Li S, Shahrezaei V, 2017, The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression, Journal of Theoretical Biology, Vol: 424, Pages: 55-72, ISSN: 0022-5193
Gene expression is an inherently noisy process. This noise is generally thought to be deleterious as precise internal regulation of biochemical reactions is essential for cell growth and survival. Self-repression of gene expression, which is the simplest form of a negative feedback loop, is commonly believed to be employed by cellular systems to decrease the stochastic fluctuations in gene expression. When there is some delay in autoregulation, it is also believed that this system can generate oscillations. In eukaryotic cells, mRNAs that are synthesised in the nucleus must be exported to the cytoplasm to function in protein synthesis, whereas proteins must be transported into the nucleus from the cytoplasm to regulate the expression levels of genes. Nuclear transport thus plays a critical role in eukaryotic gene expression and regulation. Some recent studies have suggested that nuclear retention of mRNAs can control noise in mRNA expression. However, the effect of nuclear transport on protein noise and its interplay with negative feedback regulation is not completely understood. In this paper, we systematically compare four different simple models of gene expression. By using simulations and applying the linear noise approximation to the corresponding chemical master equations, we investigate the influence of nuclear import and export on noise in gene expression in a negative autoregulatory feedback loop. We first present results consistent with the literature, i.e., that negative feedback can effectively buffer the variability in protein levels, and nuclear retention can decrease mRNA noise levels. Interestingly we find that when negative feedback is combined with nuclear retention, an amplification in gene expression noise can be observed and is dependant on nuclear translocation rates. Finally, we investigate the effect of nuclear compartmentalisation on the ability of self-repressing genes to exhibit stochastic oscillatory dynamics.
Archer N, Walsh MD, Shahrezaei V, et al., 2016, Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways, Cell Systems, Vol: 3, Pages: 467-479.E12, ISSN: 2405-4712
Experimental procedures for preparing RNA-seq and single-cell (sc) RNA-seq libraries are based on assumptions regarding their underlying enzymatic reactions. Here, we show that the fairness of these assumptions varies within libraries: coverage by sequencing reads along and between transcripts exhibits characteristic, protocol-dependent biases. To understand the mechanistic basis of this bias, we present an integrated modeling framework that infers the relationship between enzyme reactions during library preparation and the characteristic coverage patterns observed for different protocols. Analysis of new and existing (sc)RNA-seq data from six different library preparation protocols reveals that polymerase processivity is the mechanistic origin of coverage biases. We apply our framework to demonstrate that lowering incubation temperature increases processivity, yield, and (sc)RNA-seq sensitivity in all protocols. We also provide correction factors based on our model for increasing accuracy of transcript quantification in existing samples prepared at standard temperatures. In total, our findings improve our ability to accurately reflect in vivo transcript abundances in (sc)RNA-seq libraries.
Shahrezaei V, Marguerat S, 2015, Connecting growth with gene expression: of noise and numbers., Current Opinion in Microbiology, Vol: 25, Pages: 127-135, ISSN: 1879-0364
Growth is a dynamic process whereby cells accumulate mass. Growth rates of single cells are connected to RNA and protein synthesis rates, and therefore with biomolecule numbers. Noise in gene expression depends on these numbers, and is thus linked with cellular growth. Whether these global attributes of the cell participate in gene regulation is still largely unexplored. New experimental and modelling studies suggest that systemic variations in biomolecule numbers can coordinate cellular processes, including growth itself, through global regulatory feedback that acts in addition to genetic regulatory networks. Here, we review these findings and speculate on possible implications of this less appreciated layer of gene regulation for cellular physiology and adaptation to changing environments.
Smith S, Shahrezaei V, 2015, General transient solution of the one-step master equation in one dimension, Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, Vol: 91, Pages: 062119-1-062119-6, ISSN: 1063-651X
Exact analytical solutions of the master equation are limited to special cases and exact numerical methods areinefficient. Even the generic one-dimensional, one-step master equation has evaded exact solution, aside fromthe steady-state case. This type of master equation describes the dynamics of a continuous-time Markov processwhose range consists of positive integers and whose transitions are allowed only between adjacent sites. Thesolution of any master equation can be written as the exponential of a (typically huge) matrix, which requiresthe calculation of the eigenvalues and eigenvectors of the matrix. Here we propose a linear algebraic methodfor simplifying this exponential for the general one-dimensional, one-step process. In particular, we prove thatthe calculation of the eigenvectors is actually not necessary for the computation of exponential, thereby wedramatically cut the time of this calculation. We apply our new methodology to examples from birth-deathprocesses and biochemical networks. We show that the computational time is significantly reduced compared toexisting methods
Smith S, Shahrezaei V, 2015, General transient solution of the one-step master equation in one dimension., Phys Rev E Stat Nonlin Soft Matter Phys, Vol: 91
Exact analytical solutions of the master equation are limited to special cases and exact numerical methods are inefficient. Even the generic one-dimensional, one-step master equation has evaded exact solution, aside from the steady-state case. This type of master equation describes the dynamics of a continuous-time Markov process whose range consists of positive integers and whose transitions are allowed only between adjacent sites. The solution of any master equation can be written as the exponential of a (typically huge) matrix, which requires the calculation of the eigenvalues and eigenvectors of the matrix. Here we propose a linear algebraic method for simplifying this exponential for the general one-dimensional, one-step process. In particular, we prove that the calculation of the eigenvectors is actually not necessary for the computation of exponential, thereby we dramatically cut the time of this calculation. We apply our new methodology to examples from birth-death processes and biochemical networks. We show that the computational time is significantly reduced compared to existing methods.
Uhia I, Williams KJ, Shahrezaei V, et al., 2015, Mycobacterial growth, Cold Spring Harbor Perspectives in Medicine, Vol: 5, ISSN: 2157-1422
In this work, we review progress made in understanding the molecular underpinnings of growth and division in mycobacteria, concentrating on work published since the last comprehensive review ( Hett and Rubin 2008). We have focused on exciting work making use of new time-lapse imaging technologies coupled with reporter-gene fusions and antimicrobial treatment to generate insights into how mycobacteria grow and divide in a heterogeneous manner. We try to reconcile the different observations reported, providing a model of how they might fit together. We also review the topic of mycobacterial spores, which has generated considerable discussion during the last few years. Resuscitation promoting factors, and regulation of growth and division, have also been actively researched, and we summarize progress in these areas.
Robb ML, Shahrezaei V, 2014, Stochastic Cellular Fate Decision Making by Multiple Infecting Lambda Phage, PLOS ONE, Vol: 9, ISSN: 1932-6203
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- Citations: 10
Dushek O, Lellouch AC, Vaux DJ, et al., 2014, Biosensor Architectures for High-Fidelity Reporting of Cellular Signaling, Biophysical Journal, Vol: 107, Pages: 773-782, ISSN: 1542-0086
Understanding mechanisms of information processing in cellular signaling networks requires quantitative measurements of protein activities in living cells. Biosensors are molecular probes that have been developed to directly track the activity of specific signaling proteins and their use is revolutionizing our understanding of signal transduction. The use of biosensors relies on the assumption that their activity is linearly proportional to the activity of the signaling protein they have been engineered to track. We use mechanistic mathematical models of common biosensor architectures (single-chain FRET-based biosensors), which include both intramolecular and intermolecular reactions, to study the validity of the linearity assumption. As a result of the classic mechanism of zero-order ultrasensitivity, we find that biosensor activity can be highly nonlinear so that small changes in signaling protein activity can give rise to large changes in biosensor activity and vice versa. This nonlinearity is abolished in architectures that favor the formation of biosensor oligomers, but oligomeric biosensors produce complicated FRET states. Based on this finding, we show that high-fidelity reporting is possible when a single-chain intermolecular biosensor is used that cannot undergo intramolecular reactions and is restricted to forming dimers. We provide phase diagrams that compare various trade-offs, including observer effects, which further highlight the utility of biosensor architectures that favor intermolecular over intramolecular binding. We discuss challenges in calibrating and constructing biosensors and highlight the utility of mathematical models in designing novel probes for cellular signaling.
Delaney KR, Shahrezaei V, 2013, Uncaging calcium in neurons., Cold Spring Harb Protoc, Vol: 2013, Pages: 1115-1124
Changes in intracellular free calcium concentration (Δ[Ca(2+)]i) driving physiological events such as neurotransmitter release or Ca(2+)-dependent currents can be monitored using Ca(2+)-sensitive fluorescent dyes. Although these dyes can correlate Δ[Ca(2+)]i with a physiological event, they cannot directly test for causality between changes in [Ca(2+)]i and that event. Photolabile Ca(2+) chelators are Ca(2+)-binding molecules that can alter and, to a certain extent, control [Ca(2+)]i in an inducible manner and with temporal and spatial resolution that surpasses microinjection or ionophore application. Here we discuss the properties of caged Ca(2+) compounds as well as some practical considerations for their use in neuronal cells, where they have proven particularly effective.
Joyce G, Williams KJ, Robb M, et al., 2012, Cell Division Site Placement and Asymmetric Growth in Mycobacteria, PLOS One, Vol: 7, ISSN: 1932-6203
Mycobacteria are members of the actinomycetes that grow by tip extension and lack apparent homologues of the known cell division regulators found in other rod-shaped bacteria. Previous work using static microscopy on dividing mycobacteria led to the hypothesis that these cells can grow and divide asymmetrically, and at a wide range of sizes, in contrast to the cell growth and division patterns observed in the model rod-shaped organisms. In this study, we test this hypothesis using live-cell time-lapse imaging of dividing Mycobacterium smegmatis labelled with fluorescent PBP1a, to probe peptidoglycan synthesis and label the cell septum. We demonstrate that the new septum is placed accurately at mid-cell, and that the asymmetric division observed is a result of differential growth from the cell tips, with a more than 2-fold difference in growth rate between fast and slow growing poles. We also show that the division site is not selected at a characteristic cell length, suggesting this is not an important cue during the mycobacterial cell cycle.
Szomolay B, Shahrezaei V, 2012, Bell-shaped and ultrasensitive dose-response in phosphorylation-dephosphorylation cycles: the role of kinase-phosphatase complex formation, BMC Systems Biology, Vol: 6, Pages: 1-14, ISSN: 1752-0509
BackgroundPhosphorylation-dephosphorylation cycles (PDCs) mediated by kinases and phosphatases are common in cellular signalling. Kinetic modelling of PDCs has shown that these systems can exhibit a variety of input-output (dose-response) behaviors including graded response, ultrasensitivity and bistability. In addition to proteins, there are a class of lipids known as phosphoinositides (PIs) that can be phosphorylated. Experimental studies have revealed the formation of an antagonistic kinase-phosphatase complex in regulation of phosphorylation of PIs. However, the functional significance of this type of complex formation is not clear.ResultsWe first revisit the basic PDC and show that partial asymptotic phosphorylation of substrate limits ultrasensitivity. Also, substrate levels are changed one can obtain non-monotonic bell-shaped dose-response curves over a narrow range of parameters. Then we extend the PDC to include kinase-phosphatase complex formation. We report the possibility of robust bell-shaped dose-response for a specific class of the model with complex formation. Also, we show that complex formation can produce ultrasensitivity outside the Goldbeter-Koshland zero-order ultrasensitivity regime through a mechanism similar to competitive inhibition between an enzyme and its inhibitor.ConclusionsWe conclude that the novel PDC module studied here exhibits new dose-response behaviour. In particular, we show that the bell-shaped response could result in transient phosphorylation of substrate. We discuss the relevance of this result in the context of experimental observations on PI regulation in endosomal trafficking.
Schley D, Tanaka RJ, Leungchavaphongse K, et al., 2012, Modelling the influence of foot-and-mouth disease vaccine antigen stability and dose on the bovine immune response, PLOS One, Vol: 7, ISSN: 1932-6203
Dushek O, van der Merwe PA, Shahrezaei V, 2011, Ultrasensitivity in Multisite Phosphorylation of Membrane-Anchored Proteins, BIOPHYSICAL JOURNAL, Vol: 100, Pages: 1189-1197, ISSN: 0006-3495
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- Citations: 44
Ollivier JF, Shahrezaei V, Swain PS, 2010, Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks, PLOS COMPUTATIONAL BIOLOGY, Vol: 6
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- Citations: 36
Malleshaiah MK, Shahrezaei V, Swain PS, et al., 2010, The scaffold protein Ste5 directly controls a switch-like mating decision in yeast, NATURE, Vol: 465, Pages: 101-105, ISSN: 0028-0836
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- Citations: 138
Shahrezaei V, Swain PS, 2009, Analytical distributions for stochastic gene expression (vol 105, pg 17256, 2008), PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 106, Pages: 346-346, ISSN: 0027-8424
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- Citations: 1
Shahrezaei V, Swain PS, 2008, Analytical distributions for stochastic gene expression, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 17256-17261, ISSN: 0027-8424
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- Citations: 540
Shahrezaei V, Swain PS, 2008, The stochastic nature of biochemical networks, CURRENT OPINION IN BIOTECHNOLOGY, Vol: 19, Pages: 369-374, ISSN: 0958-1669
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- Citations: 138
Shahrezaei V, Ollivier JF, Swain PS, 2008, Colored extrinsic fluctuations and stochastic gene expression, MOLECULAR SYSTEMS BIOLOGY, Vol: 4, ISSN: 1744-4292
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- Citations: 190
Shahrezaei V, Cao A, Delaney KR, 2006, Ca<SUP>2+</SUP> from one or two channels controls fusion of a single vesicle at the frog neuromuscular junction, JOURNAL OF NEUROSCIENCE, Vol: 26, Pages: 13240-13249, ISSN: 0270-6474
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- Citations: 51
Shahrezaei V, Delaney KR, 2005, Brevity of the Ca<SUP>2+</SUP> microdomain and active zone geometry prevent Ca<SUP>2+</SUP>-sensor saturation for neurotransmitter release, JOURNAL OF NEUROPHYSIOLOGY, Vol: 94, Pages: 1912-1919, ISSN: 0022-3077
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- Citations: 20
Shahrezaei V, Delaney KR, 2004, Consequences of molecular-level Ca<SUP>2+</SUP> channel and synaptic vesicle colocalization for the Ca<SUP>2+</SUP> microdomain and neurotransmitter exocytosis:: A Monte Carlo study, BIOPHYSICAL JOURNAL, Vol: 87, Pages: 2352-2364, ISSN: 0006-3495
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- Citations: 42
Otsu Y, Shahrezaei V, Li B, et al., 2004, Competition between phasic and asynchronous release for recovered synaptic vesicles at developing hippocampal autaptic synapses, JOURNAL OF NEUROSCIENCE, Vol: 24, Pages: 420-433, ISSN: 0270-6474
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- Citations: 130
Shahrezaei V, Delaney K, 2004, Effects of brief calcium transients and non-equilibrium binding to the exocytotic machinery in modulating fast neurotransmitter release., 48th Annual Meeting of the Biophysical Society, Publisher: BIOPHYSICAL SOCIETY, Pages: 548A-548A, ISSN: 0006-3495
Shahrezaei V, Ejtehadi MR, 2000, Geometry selects highly designable structures, JOURNAL OF CHEMICAL PHYSICS, Vol: 113, Pages: 6437-6442, ISSN: 0021-9606
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- Citations: 13
Shahrezaei V, Hamedani N, Ejtehadi MR, 1999, Protein ground state candidates in a simple model: An enumeration study, PHYSICAL REVIEW E, Vol: 60, Pages: 4629-4636, ISSN: 1539-3755
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- Citations: 12
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