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For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary time....

By Brendan C. Barry--Public Library of Science--2016-01-04
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Social insect colonies use interactions among workers to regulate collective behavior. Harvester ant foragers interact in a chamber just inside the nest entrance, here called the 'entrance chamber'. Previous studies of the activation of foragers in red harvester ants show that an outgoing forager inside the nest experiences an increase in brief antennal contacts before ....

By Evlyn Pless,Jovel Queirolo,Noa Pinter-Wollman,Sam Crow,Maya B. Mathur,Deborah M. Gordon,Kelsey Rebe A--Public Library of Science--2016-01-04
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Aberrant chromatin regulation is a frequent driver of leukemogenesis. Mutations in chromatin regulators often result in more stem-like cells that seed a bulk leukemic population. Inhibitors targeting these proteins represent an emerging class of therapeutics, and identifying further chromatin regulators that promote disease progression may result in additional drug targ....

By Jennifer R. Shingleton,Michael Hemann--Public Library of Science--2016-01-04
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Cuttlefish are cephalopods capable of rapid camouflage responses to visual stimuli. However, it is not always clear to what these animals are responding. Previous studies have found cuttlefish to be more responsive to lateral stimuli rather than substrate. However, in previous works, the cuttlefish were allowed to settle next to the lateral stimuli. In this study, we ex....

By Yakir Gagnon,Benjamin R. Wheeler,Jules S. Jaffe,Darcy Taniguchi,Sonke Johnsen--Public Library of Science--2016-01-04
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More than 90% of common variants associated with complex traits do not affect proteins directly, but instead the circuits that control gene expression. This has increased the urgency of understanding the regulatory genome as a key component for translating genetic results into mechanistic insights and ultimately therapeutics. To address this challenge, we developed Hapl....

By Lucas D. Ward,Manolis Kellis--Oxford University Press--2016-01-04
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The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and pr....

By Ka-Chun Wong,Yue Li,Chengbin Peng,Alan M. Moses,Zhaolei Zhang--Oxford University Press--2016-01-04
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Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advanc....

By Hui Zhou,Brenda Vonk,Johannes A. Roubos,Christopher A. Voigt,Roel A. L. Bovenberg--Oxford University Press--2016-01-04
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We present a time-variability study of young stellar objects (YSOs) in the cluster IRAS 20050+2720, performed at 3.6 and 4.5 μm with the Spitzer Space Telescope; this study is part of the Young Stellar Object VARiability (YSOVAR) project. We have collected light curves for 181 cluster members over 60 days. We find a high variability fraction among embedded cluster memb....

By K. Poppenhaeger,A. M. Cody,K. R. Covey,L. A. Hillenbrand,P. Plavchan,L. M. Rebul--IOP Publishing--2016-01-04
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Models are developed to simulate light curves of stars dimmed by transiting exoplanets with and without rings. These models are then applied to Kepler photometry to search for planetary rings in a sample of 21 exoplanets, mostly hot Jupiters, chosen to offer the best observational opportunity for discovering potential rings. We also examine what kinds of rings might be ....

By Matthew Z. Heising,Geoffrey W. Marcy,Hilke Schlichting--IOP Publishing--2016-01-04
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We present a detailed abundance analysis of 23 elements for a newly discovered carbon-enhanced metal-poor (CEMP) star, HE 0414−0343, from the Chemical Abundances of Stars in the Halo Project. Its spectroscopic stellar parameters are T[subscript eff] = 4863 K, log g = 1.25, ξ = 2.20 km s[superscript −1], and [Fe/H] = −2.24. Radial velocity measurements covering se....

By Julie K. Hollek,Vinicius M. Placco,Amanda I. Karakas,Matthew Shetrone,Christopher Sneden--IOP Publishing--2016-01-04
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Sequential equivalent-time sampling allows a system to acquire repetitious waveforms with frequencies beyond the Nyquist rate. This thesis documents the prototype of a digital ARM-based sequential sampling oscilloscope with peripheral hardware and software. Discussed are the designs and obstacles of various analog circuits and signal processing methods. By means of sequ....

By Qiaodan (Qiaodan Jordan) Jin Stone--Massachusetts Institute of Technology--2016-01-04
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This thesis documents the design and implementation of a new anonymous communications protocol, and an analysis of an existing protocol. NCGAB, proposed by Sergeev in 2013, eciently implements broadcast over unicast and requires no pre-existing infrastructure. We propose a second protocol, CHAP, which extends NCGAB and is designed to use wireless broadcast capabilities ....

By Colleen A Josephson--Massachusetts Institute of Technology--2016-01-04
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