Towards synthetic biological approaches to resource utilization on space missions.

This paper demonstrates the significant utility of deploying non-traditional biological techniques to harness available volatiles and waste resources on manned missions to explore the Moon and Mars. Compared with anticipated non-biological approaches, it is determined that for 916 day Martian missions: 205 days of high-quality methane and oxygen Mars bioproduction with Methanobacterium thermoautotrophicum can reduce the mass of a Martian fuel-manufacture plant by 56%; 496 days of biomass generation with Arthrospira platensis and Arthrospira maxima on Mars can decrease the shipped wet-food mixed-menu mass for a Mars stay and a one-way voyage by 38%; 202 days of Mars polyhydroxybutyrate synthesis with Cupriavidus necator can lower the shipped mass to three-dimensional print a 120 m(3) six-person habitat by 85% and a few days of acetaminophen production with engineered Synechocystis sp. PCC 6803 can completely replenish expired or irradiated stocks of the pharmaceutical, thereby providing independence from unmanned resupply spacecraft that take up to 210 days to arrive. Analogous outcomes are included for lunar missions. Because of the benign assumptions involved, the results provide a glimpse of the intriguing potential of 'space synthetic biology', and help focus related efforts for immediate, near-term impact

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.Comment: v4: 12 pages, 5 figures, final accepted version. Error found and fixed in Appendi

Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm

There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.Comment: 15 pages, 9 figures, 2 table

Fast, cheap and somewhat in control

Efforts to manipulate living organisms have raised the question of whether engineering principles of hierarchy, abstraction and design can be applied to biological systems. Here, we consider the practical challenges to controlling living organisms that must be surmounted, or at least managed, if synthetic biology and cellular bioengineering are to be productive

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence

Global analysis of host response to induction of a latent bacteriophage

<p>Abstract</p> <p>Background</p> <p>The transition from viral latency to lytic growth involves complex interactions among host and viral factors, and the extent to which host physiology is buffered from the virus during induction of lysis is not known. A reasonable hypothesis is that the virus should be evolutionarily selected to ensure host health throughout induction to minimize its chance of reproductive failure. To address this question, we collected transcriptional profiles of <it>Escherichia coli </it>and bacteriophage lambda throughout lysogenic induction by UV light.</p> <p>Results</p> <p>We observed a temporally coordinated program of phage gene expression, with distinct early, middle and late transcriptional classes. Our study confirmed known host-phage interactions of induction of the heat shock regulon, escape replication, and suppression of genes involved in cell division and initiation of replication. We identified 728 <it>E. coli </it>genes responsive to prophage induction, which included pleiotropic stress response pathways, the Arc and Cpx regulons, and global regulators <it>crp </it>and <it>lrp</it>. Several hundred genes involved in central metabolism, energy metabolism, translation and transport were down-regulated late in induction. Though statistically significant, most of the changes in these genes were mild, with only 140 genes showing greater than two-fold change.</p> <p>Conclusion</p> <p>Overall, we observe that prophage induction has a surprisingly low impact on host physiology. This study provides the first global dynamic picture of how host processes respond to lambda phage induction.</p

Advancing the remote sensing of precipitation

Satellite-based global precipitation data has addressed the limitations of rain gauges and weather radar systems in forecasting applications and for weather and climate studies. Inspite of this ability, a number of issues that require the development of advanced concepts to address key challenges in satellite-based observations of precipitation were identified during the Advanced Concepts Workshop on Remote Sensing of Precipitation at Multiple Scales at the University of California. These include quantification of uncertainties of individual sensors and their propagation into multisensor products warrants a great deal of research. The development of metrics for validation and uncertainty analysis are of great importance. Bias removal, particularly probability distribution function (PDF)-based adjustment, deserves more in-depth research. Development of a near-real-time probabilistic uncertainty model for satellitebased precipitation estimates is highly desirable

Bounded-Angle Spanning Tree: Modeling Networks with Angular Constraints

We introduce a new structure for a set of points in the plane and an angle $\alpha$, which is similar in flavor to a bounded-degree MST. We name this structure $\alpha$-MST. Let $P$ be a set of points in the plane and let $0 < \alpha \le 2\pi$ be an angle. An $\alpha$-ST of $P$ is a spanning tree of the complete Euclidean graph induced by $P$, with the additional property that for each point $p \in P$, the smallest angle around $p$ containing all the edges adjacent to $p$ is at most $\alpha$. An $\alpha$-MST of $P$ is then an $\alpha$-ST of $P$ of minimum weight. For $\alpha < \pi/3$, an $\alpha$-ST does not always exist, and, for $\alpha \ge \pi/3$, it always exists. In this paper, we study the problem of computing an $\alpha$-MST for several common values of $\alpha$. Motivated by wireless networks, we formulate the problem in terms of directional antennas. With each point $p \in P$, we associate a wedge $W_p$ of angle $\alpha$ and apex $p$. The goal is to assign an orientation and a radius $r_p$ to each wedge $W_p$, such that the resulting graph is connected and its MST is an $\alpha$-MST. (We draw an edge between $p$ and $q$ if $p \in W_q$, $q \in W_p$, and $|pq| \le r_p, r_q$.) Unsurprisingly, the problem of computing an $\alpha$-MST is NP-hard, at least for $\alpha=\pi$ and $\alpha=2\pi/3$. We present constant-factor approximation algorithms for $\alpha = \pi/2, 2\pi/3, \pi$. One of our major results is a surprising theorem for $\alpha = 2\pi/3$, which, besides being interesting from a geometric point of view, has important applications. For example, the theorem guarantees that given any set $P$ of $3n$ points in the plane and any partitioning of the points into $n$ triplets, one can orient the wedges of each triplet {\em independently}, such that the graph induced by $P$ is connected. We apply the theorem to the {\em antenna conversion} problem