Dipolaritons in quantum dots

Abstract. Dipolaritons are quasiparticles that arise in coupled quantum wells embedded in a microcavity, they are a superposition of a photon, a direct exciton and an indirect exciton. An interesting feature of dipolaritons is that their excitons can carry an electric dipole moment. Previous works have found this kind of system suitable for terahertz lasing (Phys. Rev. A 89, 023836) and Bose-Einstein condensation (Phys. Rev. B 90, 125314). In this thesis we study a system that consists of two interacting quantum dots embedded in a microcavity, from the point of view of dipolaritons in direct analogy with the quantum well case. A constant magnetic field is also taken into account. First, the zero temperature case is studied with an exact diagonalization of a finite system hamiltonian in order to find the effects of the magnetic field on the properties of direct and indirect excitons, including their statistics. Then we include light and investigate the properties of a single dipolariton. Next, a variational approach is used to study the many-body problem and we find the effects of the magnetic field on the ground state energy and number of photons. Finally, we consider the problem at finite temperatures and use a self-consistent procedure in a Hartree-Fock-Bogoliubov approximation to find the effect of the magnetic field on the critical temperature for Bose-Einstein condensation.Los dipolaritones son cuasipartículas que surgen en pozos cuánticos acoplados embebidos en una microcavidad; son una superposición de un fotón, un excitón directo y un excitón indirecto. Una característica interesante de los dipolaritones es que sus excitones pueden tener un momento de dipolo eléctrico. Trabajos anteriores han encontrado este tipo de sistemas como candidatos para emisión en terahertz (Phys. Rev. A 89, 023836) y condensación de Bose-Einstein (Phys. Rev. B 90, 125314). En esta tesis se estudia un sistema compuesto de dos puntos cuánticos interactuantes embebidos en una microcavidad, desde el punto de vista de los dipolaritones en analogía directa con el caso de pozos cuánticos. Se incluye, además, un campo magnético constante. Primero, el caso a temperatura cero se estudia con la diagonalización exacta de un hamiltoniano de sistemas finitos, con el objetivo de encontrar los efectos del campo magnético en las propiedades de excitones directos e indirectos, incluyendo su estadística. Luego se incluye la luz y se investigan las propiedades individuales de un dipolaritón. Posteriormente, un tratamiento variacional se desarrolla para estudiar el problema de muchos cuerpos y encontrar los efectos del campo magnético en la energía del estado base y el número de fotones. Finalmente, se considera el problema a temperatura finita y se utiliza un procedimiento autoconsistente en la aproximación de Hartree-Fock-Bogoliubov para encontrar el efecto del campo magnético en la temperatura crítica para la condensación de Bose-Einstein.Maestrí

YukE is the only protein dependent upon YukBA for secretion.

<p>(A). and (B). The relative abundance of proteins detected in the culture supernatant of the wild-type strain (PY79) versus the Δ<i>yukBA</i> strain (A) or the complemented Δ<i>yukBA</i>; <i>yukBA-myc</i> strain (B). Cells were grown in nutrient-limiting 1XMC medium to mid-exponential phase, and the supernatant fractions were filtered through a 0.2 micron filter and TCA precipitated. The proteins in the culture supernatant were analyzed by mass spectrometry. Protein abundance was determined by spectral count analysis; spectral count data are combined totals from three biologically independent samples for each strain. Where no spectra were identified, an arbitrary value of 1 was assigned. The data point for YukE is circled in each graph. The point for YukE is at (95,1) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone-0096267-g002" target="_blank">Figure 2A</a> and at (95, 116) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone-0096267-g002" target="_blank">Figure 2B</a>. The complementation strain was constructed with the ectopically expressed <i>yukBA</i> gene disrupting the native <i>amyE</i> locus. Thus, as expected, AmyE peptides are underrepresented in the complementation strain as compared to both wild-type and Δ<i>yukBA</i> strains; the point located at (77, 1) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone-0096267-g002" target="_blank">Figure 2B</a> corresponds to the peptides assigned to AmyE. High levels of YueB peptides in the Δ<i>yukBA</i> and complement strains is a consequence of strain design; the <i>yuk</i> promoter was reinserted after the <i>yukBA</i> deletion to drive expression of the downstream genes.</p

YukE is secreted, and secretion of YukE depends on other proteins encoded by the <i>yuk</i>/<i>yue</i> locus.

<p>A: Schematic depicting the <i>yuk</i>/<i>yue</i> locus and surrounding genes. Currently, there are five annotated genes in the <i>yuk</i> operon: <i>yukE, yukD, yukC, yukBA</i>, and <i>yueB </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone.0096267-Barbe1" target="_blank">[31]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone.0096267-SaoJose1" target="_blank">[32]</a>. Recent high throughput transcriptomics data implicates <i>yueC</i> and/or <i>yueD</i> as potential members of the <i>yuk</i>/<i>yue</i> locus as well <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096267#pone.0096267-Nicolas1" target="_blank">[33]</a>. The predicted promoter (<i>Pyuk</i>) is indicated with an arrow. Homology to genes of other ESX/Ess systems is indicated below the corresponding <i>yuk</i>/<i>yue</i> gene name. B: Secretion assay for YukE. Cells were grown in LB medium to OD600nm of approximately 1.0–1.3. The cell pellet (P) was separated from the culture supernatant (S) by centrifugation. The pellet fractions were prepared into whole cell lysates and the supernatant fractions were filtered through a 0.2 micron filter and TCA precipitated. Samples were analyzed by SDS-PAGE under reducing conditions and immunoblot analysis with an α-YukE antibody and an α-SigmaA antibody as a loading/lysis control. The supernatants are shown in two exposures; the overexposed α-YukE blot (OE) allows visualization of faint bands. Data are representative of at least three biologically independent experiments. Pellet samples are equivalent to 0.1 OD and twenty-fold more was loaded for supernatant samples. Equivalent loading of precipitated supernatant samples was confirmed by densitometry of the Coomassie-stained gel.</p

<i>yuk</i>/<i>yue</i> knockout strains do not have a growth or competition defect compared to the wild-type strain.

<p>A: Growth curve of the wild-type strain (PY79) and <i>yuk</i>/<i>yue</i> knockout strains grown in LB medium shaking at 37°C. The OD600nm was taken every 30 minutes for a total of 540 minutes. The following <i>yuk</i>/<i>yue</i> knockout strains were tested: Δ<i>yukE</i>, Δ<i>yukD</i>, Δ<i>yukC</i>, Δ<i>yukBA</i>, Δ<i>yueB</i>, and Δ<i>yukEDCBAyueBCD</i>. B: The results of a representative competition experiment between Δ<i>yukEDCBA</i> (light gray) versus the wild-type reporter strain (dark gray) in nutrient-rich LB medium. This competition had a starting ratio of 10% Δ<i>yukEDCBA</i> cells to 90% wild-type cells. The percentages were determined by counting the number of blue and white colonies on a single plate each day (typically 150–250 colonies per plate) and then calculating the percentage of colonies from each strain. Shown are the mean percentages averaged from triplicate platings for each day.</p

Die SAGAT-Methode: Welche Informationen muss der Towerlotse erfassen?

<div><p>DNA methylation regulates gene expression in many organisms. In eukaryotes, DNA methylation is associated with gene repression, while it exerts both activating and repressive effects in the Proteobacteria through largely locus-specific mechanisms. Here, we identify a critical DNA methyltransferase in <i>M. tuberculosis</i>, which we term MamA. MamA creates N⁶-methyladenine in a six base pair recognition sequence present in approximately 2,000 copies on each strand of the genome. Loss of MamA reduces the expression of a number of genes. Each has a MamA site located at a conserved position relative to the sigma factor −10 binding site and transcriptional start site, suggesting that MamA modulates their expression through a shared, not locus-specific, mechanism. While strains lacking MamA grow normally <i>in vitro</i>, they are attenuated in hypoxic conditions, suggesting that methylation promotes survival in discrete host microenvironments. Interestingly, we demonstrate strikingly different patterns of DNA methyltransferase activity in different lineages of <i>M. tuberculosis</i>, which have been associated with preferences for distinct host environments and different disease courses in humans. Thus, MamA is the major functional adenine methyltransferase in <i>M. tuberculosis</i> strains of the Euro-American lineage while strains of the Beijing lineage harbor a point mutation that largely inactivates MamA but possess a second functional DNA methyltransferase. Our results indicate that MamA influences gene expression in <i>M. tuberculosis</i> and plays an important but strain-specific role in fitness during hypoxia.</p></div

Several genes have lower expression levels in a <i>ΔmamA</i> strain.

<p>Expression of each gene was determined by quantitative PCR in the indicated H37Rv-derived strains and is displayed as a relative value compared to expression of the housekeeping gene <i>sigA</i> in the same strain. Values shown are the mean of three technical replicates. Error bars denote standard deviation. (*) denotes P<0.05 compared to the wildtype and complemented strains (ANOVA with Tukey's post test). The wildtype and complemented strains were not significantly different from each other for any of the genes tested. The experiment was performed using RNA from different cultures than those used to prepare RNA for microarrays.</p

Quantitation of total N⁶-MdA content in <i>M. tuberculosis</i>.

<p>Genomic DNA from the indicated strains was digested to individual nucleosides and methylation content determined by liquid chromatography-coupled tandem mass spectrometry. Results are expressed as the amount of N⁶-MdA per nucleotide (left axis) and percentage of adenines that are methylated in each genome (right axis). Each represents at least three biological replicates. Outliers were removed using Grubbs criteria and error bars represent ± standard deviation. (A) Analysis of the contribution of wildtype and mutant forms of MamA to total adenine methylation levels in strain H37Rv. (B) Analysis of the contributions of MamA and HsdM to total adenine methylation levels in Euro-American (H37Rv) and Beijing (HN878) strain backgrounds.</p

Transcriptional start site (TSS)-mapping reveals a consistent spatial relationship between MamA sites and TSSs of methylation-affected genes.

<p>TSSs in strain H37Rv were mapped by the strategy outlined in (A). mRNA was circularized before random-primed synthesis of cDNA. Dashes indicate the variable 3′ end of an mRNA. Gene-specific primers were then used to amplify and sequence 5′-3′ junctions. Junctions appear as transitions from clean to messy sequence due to the variable 3′ ends. (B) TSS-mapping sequence traces are shown for the four genes whose expression is reproducibly affected by MamA. MamA sites, putative sigma factor −10 binding sites, TSSs and ORFs are shown as indicated in the key.</p

MamA is a DNA methyltransferase that protects <i>lppC</i> from endonucleolytic cleavage.

<p>(A) Southern blotting strategy to assess the status of a PvuII site near the 3′ end of <i>lppC</i>. Genomic DNA was digested with PvuII and analyzed by Southern blot with a probe hybridizing as shown. Fully cleaved DNA generates a 1.8 kb product, while protected DNA produces a 2.1 kb product. (B) DNA from the vaccine strain <i>M. bovis</i> BCG and from <i>M. tuberculosis</i> strains of the Euro-American lineage (Erdmann and CDC1551) is partially protected from PvuII cleavage while DNA from a Beijing lineage strain (HN878) is not. (C) Genetic deletion of <i>mamA</i> abrogates protection of <i>lppC</i>, while deletion of <i>hsdM</i> does not affect protection. (D) Protection is restored by complementation of a <i>ΔmamA</i> strain with an ectopic copy of <i>mamA</i>, but not by empty vector or <i>mamA^E270A</i>. (E) Sequence context of the assayed PvuII site. Underlined bases are predicted to block PvuII if methylated.</p

Deletion of <i>mamA</i> does not grossly affect growth rate or fitness of <i>M. tuberculosis</i> during mouse infection.

<p>(A) The indicated H37Rv-derived strains were normalized at a calculated optical density of 0.01 in Sauton's media and monitored by optical density on the days indicated. Points indicate the mean of triplicate cultures and error bars denote standard deviation. Similar results were obtained in 7H9 medium and by plating for CFU. (B) Mice were infected by the aerosol route with approximately 10,000 CFU of a mixture of unmarked wildtype H37Rv and one of three isogenic <i>mamA</i> mutants marked with kanamycin resistance. Groups of four mice per condition were sacrificed at the indicated time points and the lung burden of total and marked bacilli was determined. The mean proportion of marked bacteria is indicated. Error bars denote standard deviation.</p