Costs and benefits of provocation in bacterial warfare.

Competition in animals involves a wide variety of aggressive behaviors. One of the most sophisticated strategies for a focal actor is to provoke a competitor into uncontrolled aggression toward other competitors. Like animals, bacteria rely on a broad spectrum of molecular weapons, some of which provoke potential rivals by triggering retaliation. While bacterial provocation is well documented, its potential adaptive value has received little attention. Here, we examine the costs and benefits of provocation using mathematical modeling and experiments with <i>Escherichia coli</i> strains encoding colicin toxins. We show that provocation is typically costly in one-to-one encounters because a provoking strain receives a strong reciprocal attack compared with nonprovoking strains. By contrast, provocation can be strongly beneficial in communities including more than two toxin-producing strains, especially when the provoker is shielded from, or resistant to, its opponents' toxins. In these scenarios, we demonstrate that the benefit of provocation derives from a "divide-and-conquer" effect by which aggression-provoking toxin producers force their competitors into increased reciprocal aggression, leading to their cross-elimination. Furthermore, we show that this effect can be mimicked by using antibiotics that promote warfare among strains in a bacterial community, highlighting the potential of provocation as an antimicrobial approach

The pUltra plasmid series: a robust and flexible tool for fluorescent labeling of Enterobacteria

Fluorescent labeling has been an invaluable tool for the study of living organisms and bacterial species are no exception to this. Here we present and characterize the pUltra plasmids which express constitutively a fluorescent protein gene (GFP, RFP, YFP or CFP) from a strong synthetic promoter and are suitable for the fluorescent labeling of a broad range of Enterobacteria. The amount of expressed fluorophore from these genetic constructs is such, that the contours of the cells can be delineated on the basis of the fluorescent signal only. In addition, labeling through the pUltra plasmids can be used successfully for fluorescence and confocal microscopy while unambiguous distinction of cells labeled with different colors can be carried out efficiently by microscopy or flow cytometry. We compare the labeling provided by the pUltra plasmids with that of another plasmid series encoding fluorescent proteins and we show that the pUltra constructs are vastly superior in signal intensity and discrimination power without having any detectable growth rate effects for the bacterial population. We also use the pUltra plasmids to produce mixtures of differentially labeled pathogenic Escherichia, Shigella and Salmonella species which we test during infection of mammalian cells. We find that even inside the host cell, different strains can be distinguished effortlessly based on their fluorescence. We, therefore, conclude that the pUltra plasmids are a powerful labeling tool especially useful for complex biological experiments such as the visualization of ecosystems of different bacterial species or of enteric pathogens in contact with their hosts

Multi-Phase Sub-Sampling Fractional-N PLL with soft loop switching for fast robust locking

This paper presents a low phase noise sub-sampling PLL (SSPLL) with multi-phase outputs. Automatic soft switching between the sub-sampling phase loop and frequency loop is proposed to improve robustness against perturbations and interferences that may cause a traditional SSPLL to lose lock. A quadrature LC oscillator with capacitive phase interpolation network is employed to generate multi-phase outputs, which are further utilized to achieve fractional-N frequency synthesis. Implemented in a 130nm CMOS technology, the SSPLL chip is able to achieve a measured in-band phase noise of -120 dBc/Hz and a measured integrated jitter of 209 fs at 2.4 GHz, while consuming 27.2 mW with 16 output phases. The measured reference spur and fractional spur level is -72 dBc and -49 dBc, respectively

Built-In Self-Test for Automatic Analog Frequency Response Measurement

Abstract-We present a Built-In Self-Test (BIST) approach based on direct digital synthesizer (DDS) for functional test of analog circuitry in mixed-signal systems. DDS with delta-sigma noise shaping is used to generate test signals with different frequencies and phases. The DDS-based BIST hardware implementation can sweep the frequencies through the interested bands and thus measure the frequency response of the analog circuit. The proposed BIST approach has been implemented in Verilog and synthesized into a Field Programmable Gate Array (FPGA). The actual device under test (DUT) was implemented using a Field Programmable Analog Array (FPAA) to form a complete BIST testbed for analog functional tests

A Comparative Analysis of STM Approaches to Reduction Operations in Irregular Applications

As a recently consolidated paradigm for optimistic concurrency in modern multicore architectures, Transactional Memory (TM) can help to the exploitation of parallelism in irregular applications when data dependence information is not available up to run- time. This paper presents and discusses how to leverage TM to exploit parallelism in an important class of irregular applications, the class that exhibits irregular reduction patterns. In order to test and compare our techniques with other solutions, they were implemented in a software TM system called ReduxSTM, that acts as a proof of concept. Basically, ReduxSTM combines two major ideas: a sequential-equivalent ordering of transaction commits that assures the correct result, and an extension of the underlying TM privatization mechanism to reduce unnecessary overhead due to reduction memory updates as well as unnecesary aborts and rollbacks. A comparative study of STM solutions, including ReduxSTM, and other more classical approaches to the parallelization of reduction operations is presented in terms of time, memory and overhead.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

PROMPT Observations of the Early-Time Optical Afterglow of GRB 060607A

PROMPT (Panchromatic Robotic Optical Monitoring and Polarimetry Telescopes) observed the early-time optical afterglow of GRB 060607A and obtained a densely sampled multiwavelength light curve that begins only tens of seconds after the GRB. Located at Cerro Tololo Inter-American Observatory in Chile, PROMPT is designed to observe the afterglows of gamma-ray bursts using multiple automated 0.4-m telescopes that image simultaneously in many filters when the afterglow is bright and may be highly variable. The data span the interval from 44 seconds after the GRB trigger to 3.3 hours in the Bgri filters. We observe an initial peak in the light curve at approximately three minutes, followed by rebrightenings peaking around 40 minutes and again at 66 minutes. Although our data overlap with the early Swift gamma-ray and x-ray light curves, we do not see a correlation between the optical and high-energy flares. We do not find evidence for spectral evolution throughout the observations. We model the variations in the light curves and find that the most likely cause of the rebrightening episodes is a refreshment of the forward shock preceded by a rapidly fading reverse shock component, although other explanations are plausible.Comment: 23 pages, 3 figures, accepted to Ap

A 5 GHz Direct Digital Synthesizer MMIC with Direct Modulation and Spur Randomization

Abstract-This paper presents a low power, ultra high speed and high resolution SiGe DDS MMIC with 24-bit phase and 10-bit amplitude resolution. The DDS MMIC has the capabilities of direct frequency and phase modulations with 24 bit and 12 bit resolution, respectively. It is the first reported mm-wave DDS with direct digital frequency and phase modulation capabilities. Utilizing a 13-bit built-in ultra high speed pseudorandom binary sequence (PRBS) generator, the DDS MMIC can perform least significant bit (LSB) dithering for spur randomization. With more than twenty thousand transistors, the DDS MMIC includes a 24-bit ripple carry accumulator for phase accumulation, a 12-bit ripple carry adder for phase modulation, an LSB dithering block for spur randomization and a 10-bit segmented sine-weighted DAC for phase to amplitude mapping and digital to analog conversion. The DDS core occupies 3.0×2.5 mm 2 and consumes 4.7 W power under a single 3.3 V power supply. The Nyquist band SFDR is measured as 38 dBc with 469.360351 MHz output under 5.0 GHz maximum clock (FCW = 0x180800). With 1.246258914 GHz output frequency (FCW = 0x3FCFE7), the narrow band SFDR is measured as 82 dBc. The DDS MMIC is packaged and tested in LCC-68 cavity. Index Terms-digital-to-analog converter (DAC), direct digital synthesizer (DDS), direct digital frequency synthesizer (DDFS), sine-weighted digital-to-analog converter, Rom-less DDS, frequency modulation (FM), phase modulation (PM

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

A growing body of experimental evidence supports the hypothesis that the 3D structure of chromatin in the nucleus is closely linked to important functional processes, including DNA replication and gene regulation. In support of this hypothesis, several research groups have examined sets of functionally associated genomic loci, with the aim of determining whether those loci are statistically significantly colocalized. This work presents a critical assessment of two previously reported analyses, both of which used genome-wide DNA–DNA interaction data from the yeast Saccharomyces cerevisiae, and both of which rely upon a simple notion of the statistical significance of colocalization. We show that these previous analyses rely upon a faulty assumption, and we propose a correct non-parametric resampling approach to the same problem. Applying this approach to the same data set does not support the hypothesis that transcriptionally coregulated genes tend to colocalize, but strongly supports the colocalization of centromeres, and provides some evidence of colocalization of origins of early DNA replication, chromosomal breakpoints and transfer RNAs