DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.

BackgroundIn eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. However, the relation between nucleosome positioning and transcriptional activity has thus far not been explored in detail in the parasite.ResultsHere, we analyzed nucleosome positioning in the asexual and sexual stages of the parasite's erythrocytic cycle using chromatin immunoprecipitation of MNase-digested chromatin, followed by next-generation sequencing. We observed a relatively open chromatin structure at the trophozoite and gametocyte stages, consistent with high levels of transcriptional activity in these stages. Nucleosome occupancy of genes and promoter regions were subsequently compared to steady-state mRNA expression levels. Transcript abundance showed a strong inverse correlation with nucleosome occupancy levels in promoter regions. In addition, AT-repeat sequences were strongly unfavorable for nucleosome binding in P. falciparum, and were overrepresented in promoters of highly expressed genes.ConclusionsThe connection between chromatin structure and gene expression in P. falciparum shares similarities with other eukaryotes. However, the remarkable nucleosome dynamics during the erythrocytic stages and the absence of a large variety of transcription factors may indicate that nucleosome binding and remodeling are critical regulators of transcript levels. Moreover, the strong dependency between chromatin structure and DNA sequence suggests that the P. falciparum genome may have been shaped by nucleosome binding preferences. Nucleosome remodeling mechanisms in this deadly parasite could thus provide potent novel anti-malarial targets

Non-linear spectroscopy of rubidium: An undergraduate experiment

In this paper, we describe two complementary non-linear spectroscopy methods which both allow to achieve Doppler-free spectra of atomic gases. First, saturated absorption spectroscopy is used to investigate the structure of the $5{\rm S}_{1/2}\to 5{\rm P}_{3/2}$ transition in rubidium. Using a slightly modified experimental setup, Doppler-free two-photon absorption spectroscopy is then performed on the $5{\rm S}_{1/2}\to 5{\rm D}_{5/2}$ transition in rubidium, leading to accurate measurements of the hyperfine structure of the $5{\rm D}_{5/2}$ energy level. In addition, electric dipole selection rules of the two-photon transition are investigated, first by modifying the polarization of the excitation laser, and then by measuring two-photon absorption spectra when a magnetic field is applied close to the rubidium vapor. All experiments are performed with the same grating-feedback laser diode, providing an opportunity to compare different high resolution spectroscopy methods using a single experimental setup. Such experiments may acquaint students with quantum mechanics selection rules, atomic spectra and Zeeman effect.Comment: 16 pages, 8 figure

Nanoscale magnetic field mapping with a single spin scanning probe magnetometer

We demonstrate quantitative magnetic field mapping with nanoscale resolution, by applying a lock-in technique on the electron spin resonance frequency of a single nitrogen-vacancy defect placed at the apex of an atomic force microscope tip. In addition, we report an all-optical magnetic imaging technique which is sensitive to large off-axis magnetic fields, thus extending the operation range of diamond-based magnetometry. Both techniques are illustrated by using a magnetic hard disk as a test sample. Owing to the non-perturbing and quantitative nature of the magnetic probe, this work should open up numerous perspectives in nanomagnetism and spintronics

Transient growth in Taylor-Couette flow

Transient growth due to non-normality is investigated for the Taylor-Couette problem with counter-rotating cylinders as a function of aspect ratio eta and Reynolds number Re. For all Re < 500, transient growth is enhanced by curvature, i.e. is greater for eta < 1 than for eta = 1, the plane Couette limit. For fixed Re < 130 it is found that the greatest transient growth is achieved for eta between the Taylor-Couette linear stability boundary, if it exists, and one, while for Re > 130 the greatest transient growth is achieved for eta on the linear stability boundary. Transient growth is shown to be approximately 20% higher near the linear stability boundary at Re = 310, eta = 0.986 than at Re = 310, eta = 1, near the threshold observed for transition in plane Couette flow. The energy in the optimal inputs is primarily meridional; that in the optimal outputs is primarily azimuthal. Pseudospectra are calculated for two contrasting cases. For large curvature, eta = 0.5, the pseudospectra adhere more closely to the spectrum than in a narrow gap case, eta = 0.99

Improved Hardness of Approximation for Stackelberg Shortest-Path Pricing

We consider the Stackelberg shortest-path pricing problem, which is defined as follows. Given a graph G with fixed-cost and pricable edges and two distinct vertices s and t, we may assign prices to the pricable edges. Based on the predefined fixed costs and our prices, a customer purchases a cheapest s-t-path in G and we receive payment equal to the sum of prices of pricable edges belonging to the path. Our goal is to find prices maximizing the payment received from the customer. While Stackelberg shortest-path pricing was known to be APX-hard before, we provide the first explicit approximation threshold and prove hardness of approximation within 2−o(1). We also argue that the nicely structured type of instance resulting from our reduction captures most of the challenges we face in dealing with the problem in general and, in particular, we show that the gap between the revenue of an optimal pricing and the only known general upper bound can still be logarithmically large

Essential spectra of difference operators on \sZ^n-periodic graphs

Let (\cX, \rho) be a discrete metric space. We suppose that the group \sZ^n acts freely on $X$ and that the number of orbits of $X$ with respect to this action is finite. Then we call $X$ a \sZ^n-periodic discrete metric space. We examine the Fredholm property and essential spectra of band-dominated operators on $l^p(X)$ where $X$ is a \sZ^n-periodic discrete metric space. Our approach is based on the theory of band-dominated operators on \sZ^n and their limit operators. In case $X$ is the set of vertices of a combinatorial graph, the graph structure defines a Schr\"{o}dinger operator on $l^p(X)$ in a natural way. We illustrate our approach by determining the essential spectra of Schr\"{o}dinger operators with slowly oscillating potential both on zig-zag and on hexagonal graphs, the latter being related to nano-structures

Room temperature triggered single-photon source in the near infrared

We report the realization of a solid-state triggered single-photon source with narrow emission in the near infrared at room temperature. It is based on the photoluminescence of a single nickel-nitrogen NE8 colour centre in a chemical vapour deposited diamond nanocrystal. Stable single-photon emission has been observed in the photoluminescence under both continuous-wave and pulsed excitations. The realization of this source represents a step forward in the application of diamond-based single-photon sources to Quantum Key Distribution (QKD) under practical operating conditions.Comment: 10 page

Turbulent drag on a low-frequency vibrating grid in superfluid He-4 at very low temperatures

We present measurements of the dissipative turbulent drag on a vibrating grid in superfluid He-4 over a wide range of (low) frequencies. At high velocities, the dissipative drag is independent of frequency and is approximately the same as that measured in normal liquid He-4. We present measurements on a similar grid in superfluid He-3-B at low temperatures which shows an almost identical turbulent drag coefficient at low frequencies. However, the turbulent drag in He-3-B is substantially higher at higher frequencies. We also present measurements of the inertial drag coefficient for grid turbulence in He-4. The inertial drag coefficient is significantly reduced by turbulence in both superfluid and normal liquid He-4

Surface-induced charge state conversion of nitrogen-vacancy defects in nanodiamonds

We present a study of the charge state conversion of single nitrogen-vacancy (NV) defects hosted in nanodiamonds (NDs). We first show that the proportion of negatively-charged NV$^{-}$ defects, with respect to its neutral counterpart NV$^{0}$, decreases with the size of the ND. We then propose a simple model based on a layer of electron traps located at the ND surface which is in good agreement with the recorded statistics. By using thermal oxidation to remove the shell of amorphous carbon around the NDs, we demonstrate a significant increase of the proportion of NV$^{-}$ defects in 10-nm NDs. These results are invaluable for further understanding, control and use of the unique properties of negatively-charged NV defects in diamondComment: 6 pages, 4 figure