Rate zonal density gradient ultracentrifugation analysis of repair of radiation damage to the folded chromosome of Escherichia coli

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution April 1978The structure of the membrane-free nucleoid of Escherichia coli and of unfolded chromosomal DNA was investigated by sedimentation on neutral sucrose gradients after irradiation with 60Co gamma-rays and ultraviolet light (2S4nm). Irradiation both in vivo and in vitro was used as a molecular probe of the constraints on DNA~packaging in the bacterial chromosome. The extremely gentle lysis and unfolding procedures which were developed yielded undamaged, replicating genomes, thus permitting direct measurement of the formation and repair of DNA double-strand breaks at biologically-significant doses of ionizing radiation. In vitro UV-irradiation of nucleoids resulted in an increase in the observed rate of sedimentation due to the formation of an unknown photo-product. In contrast, UV-irradiation of wild-type cells in vivo showed evidence of the formation of incision breaks which resulted in the relaxation of supercoiling in the nucleoid. Strand breakage was also observed following in vivo UV-irradiation of a uvrB-5 strain, but at a lower rate and also accompanied by considerable unfolding of the chromosome. Such lesions may have been the result of direct photochemical reactions in the nucleoid, or enzyme activity associated with a uvr-independent mode of repair. The number of domains of supercoiling was estimated at 170 per genome equivalent of DNA based on measurements of relaxation caused by single-strand break formation in in vivo- and in vitro-gamma-irradiated folded chromosomes. Similar estimates based on the target size of RNA molecules responsible for maintaining the compact packaging of the nucleoid predicted negligible unfolding due to the formation of RNA single-strand breaks at doses up-to 10 Krad, and were born out by experimental measurements. Unfolding of the nucleoid in vitro by limit-digestion with RNase or by heating at 70° resulted in DNA complexes with sedimentation coefficients of 1030±59S and 625±15S respectively. The difference in these rates was apparently due to more complete deproteinization and thus less mass in the heated material. These structures are believed to represent intact, replicating genomes in the form of complex-theta structures containing 2-3 genome equivalents of DNA. The rate of formation of double-strand breaks was determined from molecular weight measurements of thermally unfolded chromosomal DNA gamma-irradiated in vitro. Break formation was linear with dose up to 10 Krad, resulting in 0.27 double-strand breaks per kilorad per genome equivalent of DNA and requiring 1080 eV/double-strand break. The influence of possible non-linear DNA conformations of these calculations is discussed. Repair of ionizing radiation damage to folded chromosomes was observed within 2-3 hours of post-irradiation incubation in growth medium. A model based on recombinational repair is proposed to explain the formation of 2200-2300S material during early stages of incubation and subsequent changes in the gradient profiles. Such behavior is not observed for post-irradiation incubation of wild-type cells in buffer or for a recA-13 strain incubated in growth medium. Association of unrepaired DNA with plasma membrane is proposed to explain the formation of a peak of rapidly sedimenting material (>>3100S) during the later stages of repair. Direct evidence of repair of double-strand breaks during post-irradiation incubation in growth medium was obtained from gradient profiles of DNA from RNAse-digested chromosomes. The sedimentation coefficient of broken molecules was restored to the value of unirradiated DNA after 2-3 hours of incubation, and the fraction of the DNA repaired in this fashion was equal to the fraction of cells which survived at the same dose. An average of 2.7 double-strand breaks per genome per lethal event was observed, suggesting that 1-2 double-strand breaks per genome are repairable in this strain of E. coli

Search for resonant production of strongly coupled dark matter in proton-proton collisions at 13 TeV

The first collider search for dark matter arising from a strongly coupled hidden sector is presented and uses a data sample corresponding to 138 fb&minus;1, collected with the CMS detector at the CERN LHC, at s&radic; = 13 TeV. The hidden sector is hypothesized to couple to the standard model (SM) via a heavy leptophobic Z&prime; mediator produced as a resonance in proton-proton collisions. The mediator decay results in two &ldquo;semivisible&rdquo; jets, containing both visible matter and invisible dark matter. The final state therefore includes moderate missing energy aligned with one of the jets, a signature ignored by most dark matter searches. No structure in the dijet transverse mass spectra compatible with the signal is observed. Assuming the Z&prime; boson has a universal coupling of 0.25 to the SM quarks, an inclusive search, relevant to any model that exhibits this kinematic behavior, excludes mediator masses of 1.5&ndash;4.0 TeV at 95% confidence level, depending on the other signal model parameters. To enhance the sensitivity of the search for this particular class of hidden sector models, a boosted decision tree (BDT) is trained using jet substructure variables to distinguish between semivisible jets and SM jets from background processes. When the BDT is employed to identify each jet in the dijet system as semivisible, the mediator mass exclusion increases to 5.1 TeV, for wider ranges of the other signal model parameters. These limits exclude a wide range of strongly coupled hidden sector models for the first time.</p

Study of quark and gluon jet substructure in Z plus jet and dijet events from pp collisions

Measurements of jet substructure describing the composition of quark- and gluon-initiated jets are presented. Proton-proton (pp) collision data at s&radic; = 13 TeV collected with the CMS detector are used, corresponding to an integrated luminosity of 35.9 fb&minus;1. Generalized angularities are measured that characterize the jet substructure and distinguish quark- and gluon-initiated jets. These observables are sensitive to the distributions of transverse momenta and angular distances within a jet. The analysis is performed using a data sample of dijet events enriched in gluon-initiated jets, and, for the first time, a Z+jet event sample enriched in quark-initiated jets. The observables are measured in bins of jet transverse momentum, and as a function of the jet radius parameter. Each measurement is repeated applying a &ldquo;soft drop&rdquo; grooming procedure that removes soft and large angle radiation from the jet. Using these measurements, the ability of various models to describe jet substructure is assessed, showing a clear need for improvements in Monte Carlo generators.</p

Search for long-lived particles produced in association with a Z boson in proton-proton collisions at root s=13 TeV

A search for long-lived particles (LLPs) produced in association with a Z boson is presented. The study is performed using data from proton-proton collisions with a center-of-mass energy of 13 TeV recorded by the CMS experiment during 2016&ndash;2018, corresponding to an integrated luminosity of 117 fb&minus;1. The LLPs are assumed to decay to a pair of standard model quarks that are identified as displaced jets within the CMS tracker system. Triggers and selections based on Z boson decays to electron or muon pairs improve the sensitivity to light LLPs (down to 15 GeV). This search provides sensitivity to beyond the standard model scenarios which predict LLPs produced in association with a Z boson. In particular, the results are interpreted in the context of exotic decays of the Higgs boson to a pair of scalar LLPs (H &rarr; SS). The Higgs boson decay branching fraction is constrained to values less than 6% for proper decay lengths of 10&ndash;100 mm and for LLP masses between 40 and 55 GeV. In the case of low-mass (&asymp; 15 GeV) scalar particles that subsequently decay to a pair of b quarks, the search is sensitive to branching fractions B(H &rarr; SS) &lt; 20% for proper decay lengths of 10&ndash;50 mm. The use of associated production with a Z boson increases the sensitivity to low-mass LLPs of this analysis with respect to gluon fusion searches. In the case of 15 GeV scalar LLPs, the improvement corresponds to a factor of 2 at a proper decay length of 30 mm.</p

Search for new physics in the lepton plus missing transverse momentum final state in proton-proton collisions at root s=13 TeV

A search for physics beyond the standard model (SM) in final states with an electron or muon and missing transverse momentum is presented. The analysis uses data from proton-proton collisions at a centre-of-mass energy of 13 TeV, collected with the CMS detector at the LHC in 2016&ndash;2018 and corresponding to an integrated luminosity of 138 fb&minus;1. No significant deviation from the SM prediction is observed. Model-independent limits are set on the production cross section of W&rsquo; bosons decaying into lepton-plus-neutrino final states. Within the framework of the sequential standard model, with the combined results from the electron and muon decay channels a W&rsquo; boson with mass less than 5.7 TeV is excluded at 95% confidence level. Results on a SM precision test, the determination of the oblique electroweak W parameter, are presented using LHC data for the first time. These results together with those from the direct W&rsquo; resonance search are used to extend existing constraints on composite Higgs scenarios. This is the first experimental exclusion on compositeness parameters using results from LHC data other than Higgs boson measurements. &nbsp;</p

Search for single production of a vector-like T quark decaying to a top quark and a Z boson in the final state with jets and missing transverse momentum at root

A search is presented for single production of a vector-like T quark with charge 2/3 e, in the decay channel featuring a top quark and a Z boson, with the top quark decaying hadronically and the Z boson decaying to neutrinos. The search uses data collected by the CMS experiment in proton-proton collisions at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 137 fb&minus;1 recorded at the CERN LHC in 2016&ndash;2018. The search is sensitive to a T quark mass between 0.6 and 1.8 TeV with decay widths ranging from negligibly small up to 30% of the T quark mass. Reconstruction strategies for the top quark are based on the degree of Lorentz boosting of its final state. At 95% confidence level, the upper limit on the product of the cross section and branching fraction for a T quark of small decay width varies between 15 and 602 fb, depending on its mass. For a T quark with decay widths between 10 and 30% of its mass, this upper limit ranges between 16 and 836 fb. For most of the studied range, the results provide the best limits to date. This is the first search for single T quark production based on the full Run 2 data set of the LHC. &nbsp;</p

Vertical visual features have a strong influence on cuttlefish camouflage

Author Posting. © Marine Biological Laboratory, 2013. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 224 (2013): 110-118.Cuttlefish and other cephalopods use visual cues from their surroundings to adaptively change their body pattern for camouflage. Numerous previous experiments have demonstrated the influence of two-dimensional (2D) substrates (e.g., sand and gravel habitats) on camouflage, yet many marine habitats have varied three-dimensional (3D) structures among which cuttlefish camouflage from predators, including benthic predators that view cuttlefish horizontally against such 3D backgrounds. We conducted laboratory experiments, using Sepia officinalis, to test the relative influence of horizontal versus vertical visual cues on cuttlefish camouflage: 2D patterns on benthic substrates were tested versus 2D wall patterns and 3D objects with patterns. Specifically, we investigated the influence of (i) quantity and (ii) placement of high-contrast elements on a 3D object or a 2D wall, as well as (iii) the diameter and (iv) number of 3D objects with high-contrast elements on cuttlefish body pattern expression. Additionally, we tested the influence of high-contrast visual stimuli covering the entire 2D benthic substrate versus the entire 2D wall. In all experiments, visual cues presented in the vertical plane evoked the strongest body pattern response in cuttlefish. These experiments support field observations that, in some marine habitats, cuttlefish will respond to vertically oriented background features even when the preponderance of visual information in their field of view seems to be from the 2D surrounding substrate. Such choices highlight the selective decision-making that occurs in cephalopods with their adaptive camouflage capability.This work was funded by the United States Department of Defense (grant number W911- NF-07-D-0001)

Expression of squid iridescence depends on environmental luminance and peripheral ganglion control

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of Company of Biologists for personal use, not for redistribution. The definitive version was published in Journal of Experimental Biology 217 (2014):850-858, doi:10.1242/​jeb.091884.Squids display impressive changes in body coloration that are afforded by two types of dynamic skin elements: structural iridophores (which produce iridescence) and pigmented chromatophores. Both color elements are neurally controlled, but nothing is known about the iridescence circuit, or the environmental cues, that elicit iridescence expression. To tackle this knowledge gap, we performed denervation, electrical stimulation and behavioral experiments using the long-fin squid, Doryteuthis pealeii. We show that while the pigmentary and iridescence circuits originate in the brain, they are wired differently in the periphery: (i) the iridescence signals are routed through a peripheral center called the stellate ganglion and (ii) the iridescence motorneurons likely originate within this ganglion (as revealed by nerve fluorescence dye fills). Cutting the inputs to the stellate ganglion that descend from the brain shifts highly reflective iridophores into a transparent state. Taken together, these findings suggest that although brain commands are necessary for expression of iridescence, integration with peripheral information in the stellate ganglion could modulate the final output. We also demonstrate that squids change their iridescence brightness in response to environmental luminance; such changes are robust but slow (minutes to hours). The squid's ability to alter its iridescence levels may improve camouflage under different lighting intensities.This research was supported by the ONR Basic Research Challenge grant no. N00014-10-1-0989 and by the AFOSR grant FA9950090346.2015-03-1

Search for strongly interacting massive particles generating trackless jets in proton-proton collisions at root s=13 TeV

A search for dark matter in the form of strongly interacting massive particles (SIMPs) using the CMS detector at the LHC is presented. The SIMPs would be produced in pairs that manifest themselves as pairs of jets without tracks. The energy fraction of jets carried by charged particles is used as a key discriminator to suppress efficiently the large multijet background, and the remaining background is estimated directly from data. The search is performed using proton&ndash;proton collision data corresponding to an integrated luminosity of 16.1fb&minus;1, collected with the CMS detector in 2016. No significant excess of events is observed above the expected background. For the simplified dark matter model under consideration, SIMPs with masses up to 100GeV are excluded and further sensitivity is explored towards higher masses.</p

Search for supersymmetry in final states with two or three soft leptons and missing transverse momentum in proton-proton collisions at root s=13 TeV

A search for supersymmetry in events with two or three low-momentum leptons and missing transverse momentum is performed. The search uses proton-proton collisions at s&radic; = 13 TeV collected in the three-year period 2016&ndash;2018 by the CMS experiment at the LHC and corresponding to an integrated luminosity of up to 137 fb&minus;1. The data are found to be in agreement with expectations from standard model processes. The results are interpreted in terms of electroweakino and top squark pair production with a small mass difference between the produced supersymmetric particles and the lightest neutralino. For the electroweakino interpretation, two simplified models are used, a wino-bino model and a higgsino model. Exclusion limits at 95% confidence level are set on &chi;&sim;02/&chi;&sim;&plusmn;1 masses up to 275 GeV for a mass difference of 10 GeV in the wino-bino case, and up to 205(150) GeV for a mass difference of 7.5 (3) GeV in the higgsino case. The results for the higgsino are further interpreted using a phenomenological minimal supersymmetric standard model, excluding the higgsino mass parameter &mu; up to 180 GeV with the bino mass parameter M1 at 800 GeV. In the top squark interpretation, exclusion limits are set at top squark masses up to 540 GeV for four-body top squark decays and up to 480 GeV for chargino-mediated decays with a mass difference of 30 GeV.</p