Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

BACKGROUND: Although genes on the chromosome are organized in a fixed order, the spatial correlations in transcription have not been systematically evaluated. We used a combination of genomic and signal processing techniques to investigate the properties of transcription in the genome of Escherichia coli K12 as a function of the position of genes on the chromosome. RESULTS: Spectral analysis of transcriptional series revealed the existence of statistically significant patterns in the spatial series of transcriptional activity. These patterns could be classified into three categories: short-range, of up to 16 kilobases (kb); medium-range, over 100-125 kb; and long-range, over 600-800 kb. We show that the significant similarities in gene activities extend beyond the length of an operon and that local patterns of coexpression are dependent on DNA supercoiling. Unlike short-range patterns, the formation of medium and long-range transcriptional patterns does not strictly depend on the level of DNA supercoiling. The long-range patterns appear to correlate with the patterns of distribution of DNA gyrase on the bacterial chromosome. CONCLUSIONS: Localization of structural components in the transcriptional signal revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome. The demonstration that spatial patterns of transcription could be modulated pharmacologically and genetically, along with the identification of molecular correlates of transcriptional patterns, offer for the first time strong evidence of physiologically determined higher-order organization of transcription in the bacterial chromosome

Rydberg Quantum Wires for Maximum Independent Set Problems with Nonplanar and High-Degree Graphs

One prominent application of near-term quantum computing devices is to solve combinatorial optimization such as non-deterministic polynomial-time hard (NP-hard) problems. Here we present experiments with Rydberg atoms to solve one of the NP-hard problems, the maximum independent set (MIS) of graphs. We introduce the Rydberg quantum wire scheme with auxiliary atoms to engineer long-ranged networks of qubit atoms. Three-dimensional (3D) Rydberg-atom arrays are constructed, overcoming the intrinsic limitations of two-dimensional arrays. We demonstrate Kuratowski subgraphs and a six-degree graph, which are the essentials of non-planar and high-degree graphs. Their MIS solutions are obtained by realizing a programmable quantum simulator with the quantum-wired 3D arrays. Our construction provides a way to engineer many-body entanglement, taking a step toward quantum advantages in combinatorial optimization.Comment: 8 pages, 4 figure

Simultaneous fabrication of line and dot dual nanopatterns using miktoarm block copolymer with photocleavable linker

Block copolymers with various nanodomains, such as spheres, cylinders, and lamellae, have received attention for their applicability to nanolithography. However, those microdomains are determined by the volume fraction of one block. Meanwhile, nanopatterns with multiple shapes are required for the next-generation nanolithography. Although various methods have been reported to achieve dual nanopatterns, all the methods need sophisticated processes using E-beam. Here, we synthesized a miktoarm block copolymer capable of cleavage of one block by ultraviolet. Original cylindrical nanodomains of synthesized block copolymer were successfully transformed to lamellar nanodomains due to the change of molecular architecture by ultraviolet. We fabricated dual nanopatterns consisting of dots and lines at desired regions on a single substrate. We also prepared dual nanopatterns utilizing another phase transformation from spheres to cylinders in a block copolymer with higher interaction parameter. Since our concept has versatility to any block copolymer, it could be employed as next-generation nanolithography.112Ysciescopu

Chiral self-sorted multifunctional supramolecular biocoordination polymers and their applications in sensors

Chiral supramolecules have great potential for use in chiral recognition, sensing, and catalysis. Particularly, chiral supramolecular biocoordination polymers (SBCPs) provide a versatile platform for characterizing biorelated processes such as chirality transcription. Here, we selectively synthesize homochiral and heterochiral SBCPs, composed of chiral naphthalene diimide ligands and Zn ions, from enantiomeric and mixed R-ligands and S-ligands, respectively. Notably, we find that the chiral self-sorted SBCPs exhibit multifunctional properties, including photochromic, photoluminescent, photoconductive, and chemiresistive characteristics, thus can be used for various sensors. Specifically, these materials can be used for detecting hazardous amine materials due to the electron transfer from the amine to the SBCP surface and for enantioselectively sensing a chiral species naproxen due to the different binding energies with regard to their chirality. These results provide guidelines for the synthesis of chiral SBCPs and demonstrate their versatility and feasibility for use in various sensors covering photoactive, chemiresistive, and chiral sensors

Film cooling effectiveness measurements on rotating and non-rotating turbine components

Detailed film cooling effectiveness distributions were measured on the stationary blade tip and on the leading edge region of a rotating blade using a Pressure Sensitive Paint technique. Air and nitrogen gas were used as the film cooling gases and the oxygen concentration distribution for each case was measured. The film cooling effectiveness information was obtained from the difference of the oxygen concentration between air and nitrogen gas cases by applying the mass transfer analogy. In the case of the stationary blade tip, plane tip and squealer tip blades were used while the film cooling holes were located (a) along the camber line on the tip or (b) along the span of the pressure side. The average blowing ratio of the cooling gas was controlled to be 0.5, 1.0, and 2.0. Tests were conducted in a five-bladed linear cascade with a blow down facility. The free stream Reynolds number, based on the axial chord length and the exit velocity, was 1,100,000 and the inlet and the exit Mach number were 0.25 and 0.59, respectively. Turbulence intensity level at the cascade inlet was 9.7%. All measurements were made at three different tip gap clearances of 1%, 1.5%, and 2.5% of blade span. Results show that the locations of the film cooling holes and the presence of squealer have significant effects on surface static pressure and film-cooling effectiveness. Same technique was applied to the rotating turbine blade leading edge region. Tests were conducted on the first stage rotor of a 3-stage axial turbine. The Reynolds number based on the axial chord length and the exit velocity was 200,000 and the total to exit pressure ratio was 1.12 for the first rotor. The effects of the rotational speed and the blowing ratio were studied. The rotational speed was controlled to be 2400, 2550, and 3000 rpm and the blowing ratio was 0.5, 1.0, and 2.0. Two different film cooling hole geometries were used; 2-row and 3-row film cooling holes. Results show that the rotational speed changes the directions of the coolant flows. Blowing ratio also changes the distributions of the coolant flows. The results of this study will be helpful in understanding the physical phenomena regarding the film injection and designing more efficient turbine blades

The Health Status of Informal Waste Collectors in Korea

Background: A broad, holistic approach was performed among informal waste collectors (IWCs) in Korea to understand their complex multidimensional health and safety problems. Methods: In the quantitative study, a survey of IWCs was conducted at four junk shops in Gangbuk-gu, Seoul, and survey data were used to calculate age-standardized prevalence rates based on comparisons with the general population in Korea. A qualitative study was also performed to provide more details on IWCs’ occupational and musculoskeletal injuries and depression. Results: In the quantitative study, the age-standardized prevalence rate (aSPR) of occupational injury was higher than that of the general standard population (aSPR: 10.42, 95% confidence interval (CI) 5.19–18.64) and that of blue-collar workers (aSPR: 4.65, 95% CI 2.32–8.32). Regarding musculoskeletal problems, compared to employed populations, the aSPRs of shoulder pain (aSPR: 2.63, 95% CI 1.60–4.06), wrist pain (aSPR: 3.33, 95% CI 1.33–6.86), knee pain (aSPR: 1.51, 95% CI 1.01–2.17), and ankle pain (aSPR: 3.54, 95% CI 1.14–8.26) were higher. Regarding psychological problems, depression (aSPR: 2.55, 95% CI 1.27–4.56) and suicidal or self-harm ideation (aSPR: 2.09, 95% CI 1.11–3.58) were higher compared to general populations. Through the qualitative study and case study on muscular problems, more details on the work environment problems of IWCs were obtained. Conclusions: IWCs are exposed to various occupational hazards and lack proper protection. They show a high prevalence of occupational injury, musculoskeletal disease, and depression

A Novel Interposer Channel Structure with Vertical Tabbed Vias to Reduce Far-End Crosstalk for Next-Generation High-Bandwidth Memory

In this paper, we propose and analyze a novel interposer channel structure with vertical tabbed vias to achieve high-speed signaling and low-power consumption in high-bandwidth memory (HBM). An analytical model of the self- and mutual capacitance of the proposed interposer channel is suggested and verified based on a 3D electromagnetic (EM) simulation. We thoroughly analyzed the electrical characteristics of the novel interposer channel considering various design parameters, such as the height and pitch of the vertical tabbed via and the gap of the vertical channel. Based on the frequency-dependent lumped circuit resistance, inductance, and capacitance, we analyzed the channel characteristics of the proposed interposer channel. In terms of impedance, insertion loss, and far-end crosstalk, we analyzed how much the proposed interposer channel improved the signal integrity characteristics compared to a conventional structure consisting of micro-strip and strip lines together. Compared to the conventional worst case, which is the strip line, the eye-width, the eye-height, and eye-jitter of the proposed interposer channel were improved by 17.6%, 29%, and 9.56%, respectively, at 8 Gbps. The proposed interposer channel can reduce dynamic power consumption by about 28% compared with the conventional interposer channel by minimizing the self-capacitance of the off-chip channel