Showing papers by "Ron Weiss published in 2008"

Temporal Logic Analysis of Gene Networks Under Parameter Uncertainty

Abstract: The lack of precise numerical information for the values of biological parameters severely limits the development and analysis of models of genetic regulatory networks. To deal with this problem, we propose a method for the analysis of genetic regulatory networks under parameter uncertainty. We consider models based on piecewise-multiaffine differential equations, dynamical properties expressed in temporal logic, and intervals for the values of uncertain parameters. The problem is then either to guarantee that the system satisfies the expected properties for every possible parameter value-the corresponding parameter set is then called valid-or to find valid subsets of a given parameter set. The proposed method uses discrete abstractions and model checking and allows for efficient search of the parameter space. However, the abstraction process creates spurious behaviors in the abstract systems, along which time does not progress. Consequently, the verification of liveness properties, expressing that something will eventually happen, and implicitly assuming progress of time, often fails. A solution to this second problem is proposed using the notion of transient regions. This approach has been implemented in a tool for robust verification of gene networks and applied to the tuning of a synthetic network built in E. coli.

A molecular noise generator

Abstract: Recent studies have demonstrated that intracellular variations in the rate of gene expression are of fundamental importance to cellular function and development. While such 'noise' is often considered detrimental in the context of perturbing genetic systems, it can be beneficial in processes such as species diversification and facilitation of evolution. A major difficulty in exploring such effects is that the magnitude and spectral properties of the induced variations arise from some intrinsic cellular process that is difficult to manipulate. Here, we present two designs of a molecular noise generator that allow for the flexible modulation of the noise profile of a target gene. The first design uses a dual-signal mechanism that enables independent tuning of the mean and variability of an output protein. This is achieved through the combinatorial control of two signals that regulate transcription and translation separately. We then extend the design to allow for DNA copy-number regulation, which leads to a wider tuning spectrum for the output molecule. To gain a deeper understanding of the circuit's functionality in a realistic environment, we introduce variability in the input signals in order to ascertain the degree of noise induced by the control process itself. We conclude by illustrating potential applications of the noise generator, demonstrating how it could be used to ascertain the robust or fragile properties of a genetic circuit.

Source separation based on binaural cues and source model constraints

Abstract: We describe a system for separating multiple sources from a two-channel recording based on interaural cues and known characteristics of the source signals. We combine a probabilistic model of the observed interaural level and phase differences with a prior model of the source statistics and derive an EM algorithm for finding the maximum likelihood parameters of the joint model. The system is able to separate more sound sources than there are observed channels. In simulated reverberant mixtures of three speakers the proposed algorithm gives a signalto-noise ratio improvement of 2.1 dB over a baseline algorithm using only interaural cues.

DySANA: dynamic speech and noise adaptation for voice activity detection.

Abstract: We describe a method of simultaneusly tracking noise and speech levels for signal-to-noise ratio adaptive speech endpoint detection. The method is based on the Kalman filter framework with switching observations and uses a dynamic distribution that 1) limits the rate of change of these levels 2) enforces a range on the values for the two levels and 3) enforces a ratio between the noise and the signal levels. We call this a Lombard dynamic distribution since it encodes the expectation that a speaker will increase his or her vocal intensity in noise. The method also employs a state transition matrix which encodes a prior on the states and provides a continuity constraint. The new method provides 46.1% relative improvement in WER over a baseline GMM based endpointer at 20 dB SNR.

Customized signaling with reconfigurable protein scaffolds.

Abstract: VOLUME 26 NUMBER 5 MAY 2008 NATURE BIOTECHNOLOGY dengue viruses. These candidate vaccines seem promising, but studies are still underway to determine whether they can confer a balanced immune response against all four dengue viruses and avoid immunological interference. For West Nile virus, the lead candidate vaccines—a DNA vaccine and a chimeric yellow fever 17D virus—also appear promising, but there is still no consensus on what constitutes a long-term protective immune response. Chang et al.5 build on earlier work by Kofler et al.9,10, who showed that the tick-borne encephalitis flavivirus still forms immunogenic virus particles even when much of the capsid gene sequence has been deleted. Using Kunjin, a subtype of West Nile virus found in Australia, Chang et al.5 have developed a ‘split-genome’ vaccine that generates two RNA species, one encoding the entire Kunjin virus genome except the capsid gene and the other encoding only the capsid gene. As both RNAs are encoded on the same DNA plasmid under the control of two cytomegalovirus promoters configured in a back-toback orientation, transfected cells transcribe and translate all the viral genes. The capsid protein acts as a helper to assemble virus particles containing the viral genomic RNA lacking the capsid gene. These so-called single-round infectious particles (SRIPs) then infect adjacent cells (Fig. 1), in contrast to DNA vaccines that produce viral antigens only in the cells initially infected. Because the viral genome transmitted to neighboring cells does not encode capsid protein, no further viral replication can occur. Chang et al.5 compare the immunogenicity of SRIPs in mice to a live virus, a traditional DNA vaccine (encoding the viral genome, with the exception of functional capsid) and a DNA vaccine that produces virus-like particles composed of the pre-membrane and envelope proteins. SRIPs confer a superior antibodymediated immune response in mice and horses, as well as protective immunity in mice, at lower doses of DNA compared with the traditional DNA vaccine. CD8+ T-cell responses elicited by SRIPs in mice were also significantly greater than those produced by the virus-like particle vaccine, although smaller than those following immunization with live virus. Neutralizing antibodies are considered critical for achieving protective immunity, but it is clear that a vaccine must elicit both antibodyand cell-mediated immunity to ensure long-term protection. Although these results represent an important proof of concept of a technology that should in theory be applicable to any flavivirus, a couple of important points should be considered. First, comparison of DNA-based vaccine strategies is very difficult given the many variables involved (e.g., viral strain, viral gene(s) selected, different parental virus strains and codon optimization). Second, it remains to be seen whether the present findings translate to primates. Several candidate DNA vaccines have performed impressively in lower animals only to disappoint in clinical trials. Prospects for using a SRIP-based approach in veterinary vaccines, such as those against Japanese encephalitis and West Nile virus infections of horses, seem more promising in the short term, especially as killed vaccines do not induce long-term protective immunity and booster doses are required to maintain immunity. The major issues surrounding new candidate vaccines always concern efficacy and safety. With regard to efficacy, we know that current licensed flavivirus vaccines have neutralizing antibody as the correlate of protection and that only low levels of neutralizing antibodies are required for protective immunity. We do not know whether this will be true for vaccines against dengue and West Nile viruses—and even if it is, as most investigators believe, it is unclear what level of neutralizing antibodies will be required. This question is particularly complicated for a dengue vaccine, as the disease is caused by four genetically and serologically related viruses. For a tetravalent vaccine, higher levels of neutralizing antibodies might be needed to control four viruses simultaneously. Candidate vaccines, such as those involving SRIPs, may help achieve this goal, possibly through a prime-boost regimen, although it remains to be shown that SRIP-based vaccines are effective over the long term. In the 21st century, safety has become the paramount attribute of a vaccine, even more so then efficacy, as society will not accept any adverse events associated with a vaccine. In this study, Chang et al.5 have boosted efficacy using viral particles that have clear safety advantages over live attenuated vaccines.