Genetics Techniques for Thermococcus kodakarensis

Thermococcus kodakarensis (T. kodakarensis) has emerged as a premier model system for studies of archaeal biochemistry, genetics, and hyperthermophily. This prominence is derived largely from the natural competence of T. kodakarensis and the comprehensive, rapid, and facile techniques available for manipulation of the T. kodakarensis genome. These genetic capacities are complemented by robust planktonic growth, simple selections, and screens, defined in vitro transcription and translation systems, replicative expression plasmids, in vivo reporter constructs, and an ever-expanding knowledge of the regulatory mechanisms underlying T. kodakarensis metabolism. Here we review the existing techniques for genetic and biochemical manipulation of T. kodakarensis. We also introduce a universal platform to generate the first comprehensive deletion and epitope/affinity tagged archaeal strain libraries

Social connectivity and adaptive capacity strategies in large-scale fisheries

Large-scale fisheries are important social-ecological systems that are increasingly being threatened by global climate change. Adaptive capacity is key for moving fisheries onto climate resilient pathways, however, implementing policies to improve adaptive capacity is challenging given the many diverse stakeholders involved in fisheries. Previous research suggests social networks are integral to adaptive capacity because social connectivity can enable, or constrain, knowledge and information sharing. We examine the network of communication among stakeholders in the Basque tropical tuna freezer purse seine fishery in the eastern Atlantic Ocean. We use cluster analysis, descriptive statistics, and exponential random graph models to assess whether different types of actors, occupying different network positions, value similar adaptive capacity strategies. The results indicate that many actor types are frequently connected within the fishery. Preferences for adaptive capacity strategies vary within and across actor types, and the preferences of highly central actors are generally more homogeneous and narrowly focused. All actors agree on the importance of the social organization domain from adaptive capacity, while fishing industry representatives tend to have the most holistic perspective on adaptive capacity overall. We discuss the implications of these findings as they relate to policies for supporting adaptive capacity and climate resilient fisheries. © 2021 by the author(s).This research was supported by the project CLOCK, under the European Horizon 2020 Program, ERC Starting Grant Agreement nº679812 funded by the European Research Council. It is also supported by the Basque Government through the BERC 2018-2021 program and by the Spanish Ministry of Economy and Competitiveness MINECO through the BC3 María de Maeztu excellence accreditation MDM-2017-0714. We thank, without implicating, Ö. Bodin, I. Fetzer, and J.Rocha for scientific advice, and all the participants of the study who made it possible

Robustness and the Paradox of Bridging Organizations: The Exit Problem in Regional Water Governance Networks in Central America

Bridging organizations facilitate a range of governance processes, including cooperation and social learning, and are theorized to be a key component of robust governance systems. In this article, we use node removal simulations to test structural hypotheses of robustness in a regional water governance network in Central America. We investigate the response of network measures supporting core governance processes to the targeted removal of bridging organizations and other actors, which we compare to random and centrality-based simulations. The results indicate removing bridging organizations has a greater impact on the network than any other type of actor, suggesting bridging organizations are critical to the robustness of the governance system. Furthermore, network structures supporting cooperation may be less robust than structures facilitating social learning. We conclude with policy implications of the research findings as they relate to the exit problem in governance systems with a large presence of international development actors

Recovery of Large Angular Scale CMB Polarization for Instruments Employing Variable-delay Polarization Modulators

Variable-delay Polarization Modulators (VPMs) are currently being implemented in experiments designed to measure the polarization of the cosmic microwave background on large angular scales because of their capability for providing rapid, front-end polarization modulation and control over systematic errors. Despite the advantages provided by the VPM, it is important to identify and mitigate any time-varying effects that leak into the synchronously modulated component of the signal. In this paper, the effect of emission from a $300$ K VPM on the system performance is considered and addressed. Though instrument design can greatly reduce the influence of modulated VPM emission, some residual modulated signal is expected. VPM emission is treated in the presence of rotational misalignments and temperature variation. Simulations of time-ordered data are used to evaluate the effect of these residual errors on the power spectrum. The analysis and modeling in this paper guides experimentalists on the critical aspects of observations using VPMs as front-end modulators. By implementing the characterizations and controls as described, front-end VPM modulation can be very powerful for mitigating $1/f$ noise in large angular scale polarimetric surveys. None of the systematic errors studied fundamentally limit the detection and characterization of B-modes on large scales for a tensor-to-scalar ratio of $r=0.01$. Indeed, $r<0.01$ is achievable with commensurately improved characterizations and controls.Comment: 13 pages, 13 figures, 1 table, matches published versio

Modulation of CMB polarization with a warm rapidly-rotating half-wave plate on the Atacama B-Mode Search (ABS) instrument

We evaluate the modulation of Cosmic Microwave Background (CMB) polarization using a rapidly-rotating, half-wave plate (HWP) on the Atacama B-Mode Search (ABS). After demodulating the time-ordered-data (TOD), we find a significant reduction of atmospheric fluctuations. The demodulated TOD is stable on time scales of 500-1000 seconds, corresponding to frequencies of 1-2 mHz. This facilitates recovery of cosmological information at large angular scales, which are typically available only from balloon-borne or satellite experiments. This technique also achieves a sensitive measurement of celestial polarization without differencing the TOD of paired detectors sensitive to two orthogonal linear polarizations. This is the first demonstration of the ability to remove atmospheric contamination at these levels from a ground-based platform using a rapidly-rotating HWP.Comment: 8 pages, 8 figures, Published in RSI under the title "Modulation of cosmic microwave background polarization with a warm rapidly rotating half-wave plate on the Atacama B-Mode Search instrument.

Systematic effects from an ambient-temperature, continuously-rotating half-wave plate

We present an evaluation of systematic effects associated with a continuously-rotating, ambient-temperature half-wave plate (HWP) based on two seasons of data from the Atacama B-Mode Search (ABS) experiment located in the Atacama Desert of Chile. The ABS experiment is a microwave telescope sensitive at 145 GHz. Here we present our in-field evaluation of celestial (CMB plus galactic foreground) temperature-to-polarization leakage. We decompose the leakage into scalar, dipole, and quadrupole leakage terms. We report a scalar leakage of ~0.01%, consistent with model expectations and an order of magnitude smaller than other CMB experiments have reported. No significant dipole or quadrupole terms are detected; we constrain each to be <0.07% (95% confidence), limited by statistical uncertainty in our measurement. Dipole and quadrupole leakage at this level lead to systematic error on r<0.01 before any mitigation due to scan cross-linking or boresight rotation. The measured scalar leakage and the theoretical level of dipole and quadrupole leakage produce systematic error of r<0.001 for the ABS survey and focal-plane layout before any data correction such as so-called deprojection. This demonstrates that ABS achieves significant beam systematic error mitigation from its HWP and shows the promise of continuously-rotating HWPs for future experiments.Comment: 11 pages, 8 figures; revision to submitted version, Fig. 5 and Eqs. (14) and (15) corrected; added Fig. 9 and description, text revisions for clarification, Fig. 5 revised for better calibration, corrected labeling errors and plotting bugs in Fig. 3, 4, and Eq. (14) and (15

Characterizing Atacama B-mode Search Detectors with a Half-Wave Plate

The Atacama B-Mode Search (ABS) instrument is a cryogenic ($\sim$10 K) crossed-Dragone telescope located at an elevation of 5190 m in the Atacama Desert in Chile that observed for three seasons between February 2012 and October 2014. ABS observed the Cosmic Microwave Background (CMB) at large angular scales ($40<\ell<500$) to limit the B-mode polarization spectrum around the primordial B-mode peak from inflationary gravity waves at $\ell \sim100$. The ABS focal plane consists of 480 transition-edge sensor (TES) bolometers. They are coupled to orthogonal polarizations from a planar ortho-mode transducer (OMT) and observe at 145 GHz. ABS employs an ambient-temperature, rapidly rotating half-wave plate (HWP) to mitigate systematic effects and move the signal band away from atmospheric $1/f$ noise, allowing for the recovery of large angular scales. We discuss how the signal at the second harmonic of the HWP rotation frequency can be used for data selection and for monitoring the detector responsivities.Comment: 7 pages, 3 figures, conference proceedings submitted to the Journal of Low Temperature Detector