Engineering synthetic spatial patterns in microbial populations and communities.

Spatial pattern formation is an important feature of almost all biological systems. Thanks to the advances in synthetic biology, we can engineer microbial populations and communities to display sophisticated spatial patterns. This bottom-up approach can be used to elucidate the general principles underlying pattern formation. Moreover, it is of interest for a plethora of applications, from the production of novel living materials to medical diagnostics. In this short review, we comment on the recent experimental advances in engineering the spatial patterns formed by microbes. We classify the synthetic patterns based on the input signals provided and the biological processes deployed. We highlight some applications of microbial pattern formation and discuss the challenges and potential future directions

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g., being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges. First, we encapsulate single bacteria into microfluidic agarose gel beads. After incubation, they harbor monoclonal bacterial microcolonies (e.g., expressing a synthetic construct) and can be sorted according their fluorescence by fluorescence activated cell sorting (FACS). We determine enrichment rates and demonstrate that we can measure the average fluorescent signals of microcolonies containing phenotypically heterogeneous cells, obviating the problem of cell-to-cell variability. Finally, we apply this method to sort a pBAD promoter library at ON and OFF states

Trade, transboundary pollution, and foreign lobbying

In this paper, we explore the use of trade policy in addressing transboundary stock pollution problems such as acid rain and water pollution. We show that a tariff determined by the current level of accumulated pollution can induce the time path of emissions optimal for the downstream (polluted) country. But if the upstream (polluting) country can lobby the downstream government to impose lower tariffs, distortions brought by corruption and foreign lobbying lead to a rise in the upstream country's social welfare, and to a decrease in social welfare in the downstream country. Thus, the usefulness of trade policy as a tool for encouraging cooperation and internalizing transboundary externalities depends critically on the degree of governments' susceptibility to foreign political influence

Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch.

The formation of spatiotemporal patterns of gene expression is frequently guided by gradients of diffusible signaling molecules. The toggle switch subnetwork, composed of two cross-repressing transcription factors, is a common component of gene regulatory networks in charge of patterning, converting the continuous information provided by the gradient into discrete abutting stripes of gene expression. We present a synthetic biology framework to understand and characterize the spatiotemporal patterning properties of the toggle switch. To this end, we built a synthetic toggle switch controllable by diffusible molecules in Escherichia coli. We analyzed the patterning capabilities of the circuit by combining quantitative measurements with a mathematical reconstruction of the underlying dynamical system. The toggle switch can produce robust patterns with sharp boundaries, governed by bistability and hysteresis. We further demonstrate how the hysteresis, position, timing, and precision of the boundary can be controlled, highlighting the dynamical flexibility of the circuit

Signals of sneutrino-antisneutrino mixing in an e−γe^- \gamma collider in anomaly-mediated supersymmetry breaking

Sneutrino-antisneutrino mixing occurs in a supersymmetric model where neutrinos have nonzero Majorana masses. This can lead to the sneutrino decaying into a final state with a "wrong-sign charged lepton". Hence, in an $e^- \gamma$ collider, the signal of the associated production of an electron-sneutrino and the lighter chargino and their subsequent decays can be e^- \gamma \to e^+ {\tilde \tau}_1^- {\tilde \tau}_1^- + \mpT where the ${\tilde \tau}_1$s are long-lived and can produce heavily ionizing charged tracks. This signal is free of any Standard Model background and the supersymmetric backgrounds are small. Such a signal can be experimentally observable under certain conditions which are possible to obtain in an anomaly-mediated supersymmetry breaking scenario. Information on a particular combination of the neutrino masses and mixing angles can also be extracted through the observation of this signal. Possible modifications in the signal event and the accompanying Standard Model background have been discussed when the ${\tilde \tau}_1$s decay promptly.Comment: 26 pages, 6 figures, RevTeX4. Discussion and references added. Typos corrected. To appear in Phys. Rev.

The phase diagram of the lattice Calogero-Sutherland model

We introduce a {\it lattice} version of the Calogero Sutherland model adapted to describe $1/d^2$ pairwise interacting steps with discrete positions on a vicinal surface. The configurational free energy is obtained within a transfer matrix method. The full phase diagram for attractive and for repulsive interaction is deduced. For attraction, critical temperatures of faceting transitions are found to depend on step density.Comment: latex PRBCalogSuth.tex, 6 files, 4 pages [SPEC-S00/900

Geochemical and Thermodinamic Modeling of Segara Anak Lake and the 2009 Eruption of Rinjani Volcano, Lombok, Indonesia

DOI: 10.17014/ijog.v5i4.106Rinjani is the second highest volcano in Indonesia with an elevation of 3726 m above sea level. The steep and highest cone of Rinjani consists mainly of loose pyroclastic ejecta and contains a crater with a few solfataras. The West of this cone is Segara Anak caldera. The western side of the caldera is occupied by a 230 m deep lake, covering an area of 11 km² and its volume was (before the 2009 eruption) estimated 1.02 km3. This is probably the largest hot volcanic lake in the world.The lake water is neutral (pH: 7-8) and its chemistry dominated by chlorides and sulfates with a relatively high TDS (Total Dissolved Solids: 2640 mg/l). This unusual TDS as well as the lake surface temperatures (20 - 22°C) well above ambient temperatures (14 - 15°C) for this altitude, reflect a strong input of hydrothermal fluids. Numerous hot springs are located along the shore at the foot of Barujari volcanic cone. Bathymetric profiles show also several areas with columns of gas bubbles escaping from the lake floor indicating a significant discharge of CO gas into the lake. The mass and energy balance model of Rinjani Crater Lake produce total heat lost value on the average of 1700 MW. Most of the heating periods of the lake occurred when the heat released by the surface of the lake to the atmosphere was lower than the heat supplied from the hydrothermal system. Peaks of heat losses correspond to period of strong winds. Crater lake monitoring can provide a basic information about deep magmatic activity and surface processes that occur in the volcano. The monitoring also contributes to predict the next eruption in order to improve mitigation of volcanic eruption. Precursory signals of the May 2009 eruption can be seen from significant changes in the temperature and chemistry of some of the hot springs, the increase of Fe concentrations in spring #54, chemical plume of low pH and dissolved oxygen, acidification of Segara Anak Lake, and increasing of lake surface temperatures. The new lava flow from May - August 2009 eruption covers an area of 650,000 m2. The shoreline was significantly modified by the entry of lava into Segara Anak Lake. The area of the lake is reduced by 460,000 m2

Coupling potential of ICESat/GLAS and SRTM for the discrimination of forest landscape types in French Guiana

The Shuttle Radar Topography Mission (SRTM) has produced the most accurate nearly global elevation dataset to date. Over vegetated areas, the measured SRTM elevations are the result of a complex interaction between radar waves and tree crowns. In this study, waveforms acquired by the Geoscience Laser Altimeter System (GLAS) were combined with SRTM elevations to discriminate the five forest landscape types (LTs) in French Guiana. Two differences were calculated: (1) penetration depth, defined as the GLAS highest elevations minus the SRTM elevations, and (2) the GLAS centroid elevations minus the SRTM elevations. The results show that these differences were similar for the five LTs, and they increased as a function of the GLAS canopy height and of the SRTM roughness index. Next, a Random Forest (RF) classifier was used to analyze the coupling potential of GLAS and SRTM in the discrimination of forest landscape types in French Guiana. The parameters used in the RF classification were the GLAS canopy height, the SRTM roughness index, the difference between the GLAS highest elevations and the SRTM elevations and the difference between the GLAS centroid elevations and the SRTM elevations. Discrimination of the five forest landscape types in French Guiana was possible, with an overall classification accuracy of 81.3% and a kappa coefficient of 0.75. All forest LTs were well classified with an accuracy varying from 78.4% to 97.5%. Finally, differences of near coincident GLAS waveforms, one from the wet season and one from the dry season, were analyzed. The results showed that the open forest LT (LT12), in some locations, contains trees that lose leaves during the dry season. These trees allow LT12 to be easily discriminated from the other LTs that retain their leaves using the following three criteria: (1) difference between the GLAS centroid elevations and the SRTM elevations, (2) ratio of top energy in the wet season to top energy in the dry season, or (3) ratio of ground energy in the wet season to ground energy in the dry season

In memoriam two distinguished participants of the Bregenz Symmetries in Science Symposia: Marcos Moshinsky and Yurii Fedorovich Smirnov

Some particular facets of the numerous works by Marcos Moshinsky and Yurii Fedorovich Smirnov are presented in these notes. The accent is put on some of the common interests of Yurii and Marcos in physics, theoretical chemistry, and mathematical physics. These notes also contain some more personal memories of Yurii Smirnov.Comment: Submitted for publication in Journal of Physics: Conference Serie

Regional scale rain-forest height mapping using regression-kriging of spaceborne and airborne lidar data : application on French Guiana

LiDAR data has been successfully used to estimate forest parameters such as canopy heights and biomass. Major limitation of LiDAR systems (airborne and spaceborne) arises from their limited spatial coverage. In this study, we present a technique for canopy height mapping using airborne and spaceborne LiDAR data (from the Geoscience Laser Altimeter System (GLAS)). First, canopy heights extracted from both airborne and spaceborne LiDAR were extrapolated from available environmental data. The estimated canopy height maps using Random Forest (RF) regression from airborne or GLAS calibration datasets showed similar precisions (~6 m). To improve the precision of canopy height estimates, regression-kriging was used. Results indicated an improvement in terms of root mean square error (RMSE, from 6.5 to 4.2 m) using the GLAS dataset, and from 5.8 to 1.8 m using the airborne LiDAR dataset. Finally, in order to investigate the impact of the spatial sampling of future LiDAR missions on canopy height estimates precision, six subsets were derived from the initial airborne LiDAR dataset. Results indicated that using the regression-kriging approach a precision of 1.8 m on the canopy height map was achievable with a flight line spacing of 5 km. This precision decreased to 4.8 m for flight line spacing of 50 km