123 research outputs found
Dynamics of Genetic Circuits with Molecule Partitioning Errors in Cell Division and RNA-RNA Interactions
Many signaling and regulatory molecules within cells exist in very few copies per cell. Any process affecting even limited numbers of these molecules therefore has the potential to affect the dynamics of the biochemical networks of which they are a part. This sensitivity to small copy-number changes is what allows stochasticity in gene expression to introduce a degree of randomness in what cells do. While this randomness can be suppressed, it does not appear to be so in many biological systems, at least not to the maximum degree possible. This suggests that this randomness is not necessarily detrimental to cell populations, as it can produce qualitatively new behaviours in genetic networks which may be utilized by cells.In this thesis, two other mechanisms are investigated which, through their interaction with low copy-number molecules, are able to produce qualitatively different dynamics in genetic networks: the stochastic partitioning of molecules in cell division, and the direct interaction of two low copy-number molecules. For this, a novel simulator of chemical kinetics is first presented, designed to simulate the dynamics of genetic circuits inside growing populations of cells. It is then used to study a genetic switch where one repressive link is formed by direct interaction between RNA molecules. This arrangement was found to decouple the stability of the two noisy attractors of the network and the speeds of the state transitions. In other words, it allows the network to have two equally-stable noisy attractors, but differing state transition speeds.Next, the cell-to-cell diversity in RNA numbers (as quantified by the normalized variance) of a single gene over time in a growing model cell population was studied as a function of the division synchrony. In the model, synchronous cell divisions introduce transient increases in the cell-to-cell diversity in RNA numbers of the population, a prediction which was verified using single-molecule measurements of RNA numbers. Finally, the effects of the stochastic partitioning of regulatory molecules in cell division on the dynamics of two genetic circuits, a switch and a clock, were studied. Of these two circuits, the switch has the most dramatic changes in its dynamics, brought on by the inevitable negative correlation in molecule numbers that sister cells inherit. This negative correlation can allow a cell population to partition the phenotypes of the individual cells with less variance than a binomial distribution.These results advance our understanding of the different behaviours that can be produced in genetic circuits due to these two mechanisms. Since they produce unique behaviours, these mechanisms, and combinations thereof, are expected to be used for specialized purposes in natural genetic circuits. Further, since the downstream effects of these mechanisms may be more predictable than, e.g., modifying promoter sequences, they may also be useful in the design and implementation of future synthetic genetic circuits with specific behaviours.<br/
Stochastic sequence-level model of coupled transcription and translation in prokaryotes
<p>Abstract</p> <p>Background</p> <p>In prokaryotes, transcription and translation are dynamically coupled, as the latter starts before the former is complete. Also, from one transcript, several translation events occur in parallel. To study how events in transcription elongation affect translation elongation and fluctuations in protein levels, we propose a delayed stochastic model of prokaryotic transcription and translation at the nucleotide and codon level that includes the promoter open complex formation and alternative pathways to elongation, namely pausing, arrests, editing, pyrophosphorolysis, RNA polymerase traffic, and premature termination. Stepwise translation can start after the ribosome binding site is formed and accounts for variable codon translation rates, ribosome traffic, back-translocation, drop-off, and trans-translation.</p> <p>Results</p> <p>First, we show that the model accurately matches measurements of sequence-dependent translation elongation dynamics. Next, we characterize the degree of coupling between fluctuations in RNA and protein levels, and its dependence on the rates of transcription and translation initiation. Finally, modeling sequence-specific transcriptional pauses, we find that these affect protein noise levels.</p> <p>Conclusions</p> <p>For parameter values within realistic intervals, transcription and translation are found to be tightly coupled in <it>Escherichia coli</it>, as the noise in protein levels is mostly determined by the underlying noise in RNA levels. Sequence-dependent events in transcription elongation, e.g. pauses, are found to cause tangible effects in the degree of fluctuations in protein levels.</p
Mutual information in random Boolean models of regulatory networks
The amount of mutual information contained in time series of two elements
gives a measure of how well their activities are coordinated. In a large,
complex network of interacting elements, such as a genetic regulatory network
within a cell, the average of the mutual information over all pairs is a
global measure of how well the system can coordinate its internal dynamics. We
study this average pairwise mutual information in random Boolean networks
(RBNs) as a function of the distribution of Boolean rules implemented at each
element, assuming that the links in the network are randomly placed. Efficient
numerical methods for calculating show that as the number of network nodes
N approaches infinity, the quantity N exhibits a discontinuity at parameter
values corresponding to critical RBNs. For finite systems it peaks near the
critical value, but slightly in the disordered regime for typical parameter
variations. The source of high values of N is the indirect correlations
between pairs of elements from different long chains with a common starting
point. The contribution from pairs that are directly linked approaches zero for
critical networks and peaks deep in the disordered regime.Comment: 11 pages, 6 figures; Minor revisions for clarity and figure format,
one reference adde
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps
<p>Abstract</p> <p>Background</p> <p>In <it>Escherichia coli </it>the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-limiting steps that affect RNA production.</p> <p>Results</p> <p>We measured the <it>in vivo </it>kinetics of production of individual RNA molecules under the control of the lar promoter in <it>E. coli</it>. From the analysis of the distributions of intervals between transcription events in the regimes of weak and medium induction, we find that the process of transcription initiation of this promoter involves a sequential mechanism with two main rate-limiting steps, each lasting hundreds of seconds. Both steps become faster with increasing induction by IPTG and Arabinose.</p> <p>Conclusions</p> <p>The two rate-limiting steps in initiation are found to be important regulators of the dynamics of RNA production under the control of the lar promoter in the regimes of weak and medium induction. Variability in the intervals between consecutive RNA productions is much lower than if there was only one rate-limiting step with a duration following an exponential distribution. The methodology proposed here to analyze the <it>in vivo </it>dynamics of transcription may be applicable at a genome-wide scale and provide valuable insight into the dynamics of prokaryotic genetic networks.</p
Metatranscriptome of human faecal microbial communities in a cohort of adult men
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms\u27 ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic \u27core\u27 universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a \u27variable\u27 metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological interaction network reconstruction, which remained stable over the six-month timespan, as did strain tracking within and between participants. These results provide an initial characterization of human faecal microbial ecology into core, subject-specific, microorganism-specific and temporally variable transcription, and they differentiate metagenomically versus metatranscriptomically informative aspects of the human faecal microbiome
Stability of the human faecal microbiome in a cohort of adult men
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samplesâone pair collected 24â72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation. Metagenomic instability accounted for ~74% of corresponding metatranscriptomic instability. The rest was probably attributable to sources such as regulation. Among the pathways that were differentially regulated, most were consistently over- or under-transcribed at each time point. Together, these results suggest that a single measurement of the faecal microbiome can provide long-term information regarding organismal composition and functional potential, but repeated or short-term measures may be necessary for dynamic features identified by metatranscriptomics
Information propagation within the Genetic Network of Saccharomyces cerevisiae
Background: A gene network's capacity to process information, so as to bind past events to future actions, depends on its structure and logic. From previous and new microarray measurements in Saccharomyces cerevisiae following gene deletions and overexpressions, we identify a core gene regulatory network (GRN) of functional interactions between 328 genes and the transfer functions of each gene. Inferred connections are verified by gene enrichment. Results: We find that this core network has a generalized clustering coefficient that is much higher than chance. The inferred Boolean transfer functions have a mean p-bias of 0.41, and thus similar amounts of activation and repression interactions. However, the distribution of p-biases differs significantly from what is expected by chance that, along with the high mean connectivity, is found to cause the core GRN of S. cerevisiae's to have an overall sensitivity similar to critical Boolean networks. In agreement, we find that the amount of information propagated between nodes in finite time series is much higher in the inferred core GRN of S. cerevisiae than what is expected by chance. Conclusions: We suggest that S. cerevisiae is likely to have evolved a core GRN with enhanced information propagation among its genes.Peer reviewe
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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men
Background & Aims: Sulfur-metabolizing microbes, which convert dietary sources of sulfur into genotoxic hydrogen sulfide (H2S), have been associated with development of colorectal cancer (CRC). We identified a dietary pattern associated with sulfur-metabolizing bacteria in stool and then investigated its association with risk of incident CRC using data from a large prospective study of men.
Methods: We collected data from 51,529 men enrolled in the Health Professionals Follow-up Study since 1986 to determine the association between sulfur-metabolizing bacteria in stool and risk of CRC over 26 years of follow-up. First, in a subcohort of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet using semiquantitative food frequency questionnaires to identify food groups associated with 43 bacterial species involved in sulfur metabolism. We used these data to develop a sulfur microbial dietary score. We then used Cox proportional hazards modeling to evaluate adherence to this pattern among eligible individuals (n = 48,246) from 1986 through 2012 with risk for incident CRC.
Results: Foods associated with higher sulfur microbial diet scores included increased consumption of processed meats and low-calorie drinks and lower consumption of vegetables and legumes. Increased sulfur microbial diet scores were associated with risk of distal colon and rectal cancers, after adjusting for other risk factors (multivariable relative risk, highest vs lowest quartile, 1.43; 95% confidence interval 1.14â1.81; P-trend = .002). In contrast, sulfur microbial diet scores were not associated with risk of proximal colon cancer (multivariable relative risk 0.86; 95% CI 0.65â1.14; P-trend = .31).
Conclusions: In an analysis of participants in the Health Professionals Follow-up Study, we found that long-term adherence to a dietary pattern associated with sulfur-metabolizing bacteria in stool was associated with an increased risk of distal CRC. Further studies are needed to determine how sulfur-metabolizing bacteria might contribute to CRC pathogenesis
LSST: from Science Drivers to Reference Design and Anticipated Data Products
(Abridged) We describe here the most ambitious survey currently planned in
the optical, the Large Synoptic Survey Telescope (LSST). A vast array of
science will be enabled by a single wide-deep-fast sky survey, and LSST will
have unique survey capability in the faint time domain. The LSST design is
driven by four main science themes: probing dark energy and dark matter, taking
an inventory of the Solar System, exploring the transient optical sky, and
mapping the Milky Way. LSST will be a wide-field ground-based system sited at
Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m
effective) primary mirror, a 9.6 deg field of view, and a 3.2 Gigapixel
camera. The standard observing sequence will consist of pairs of 15-second
exposures in a given field, with two such visits in each pointing in a given
night. With these repeats, the LSST system is capable of imaging about 10,000
square degrees of sky in a single filter in three nights. The typical 5
point-source depth in a single visit in will be (AB). The
project is in the construction phase and will begin regular survey operations
by 2022. The survey area will be contained within 30,000 deg with
, and will be imaged multiple times in six bands, ,
covering the wavelength range 320--1050 nm. About 90\% of the observing time
will be devoted to a deep-wide-fast survey mode which will uniformly observe a
18,000 deg region about 800 times (summed over all six bands) during the
anticipated 10 years of operations, and yield a coadded map to . The
remaining 10\% of the observing time will be allocated to projects such as a
Very Deep and Fast time domain survey. The goal is to make LSST data products,
including a relational database of about 32 trillion observations of 40 billion
objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures
available from https://www.lsst.org/overvie
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