Occupancy maps of 208 chromatin-associated proteins in one human cell type

Transcription factors are DNA-binding proteins that have key roles in gene regulation. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP–seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium

Overhead tank is the potential breeding habitat of Anopheles stephensi in an urban transmission setting of Chennai, India

Background: Wells and overhead tanks (OHT) are the major breeding sources of the local malaria vector, Anopheles stephensi in the Indian city of Chennai; they play a significant role in vector breeding, and transmission of urban malaria. Many other man-made breeding habitats, such as cemented cisterns/containers, barrels or drums, sumps or underground tanks, and plastic pots/containers are maintained to supplement water needs, temporarily resulting in enhanced mosquito/vector breeding. Correlating breeding habitats with immature vector abundance is important in effective planning to strengthen operational execution of vector control measures. Methods: A year-long, weekly study was conducted in Chennai to inspect available clear/clean water mosquito breeding habitats. Different breeding features, such as instar-wise, immature density and co-inhabitation with other mosquito species, were analysed. The characteristics of breeding habitats, i.e., type of habitat, water temperature and presence of aquatic organisms, organic matter and green algal remnants on the water surface at the time of inspection, were also studied. Immature density of vector was correlated with presence of other mosquito species, malaria prevalence, habitat characteristics and monthly/seasonal fluctuations. All the data collected from field observations were analysed using standard statistical tools. Results: When the immature density of breeding habitats was analysed, using one-way ANOVA, it was observed that the density did not change in a significant way either across seasons or months. OHTs contributed significantly to the immature population when compared to wells and other breeding habitats of the study site. The habitat positivity of wells and OHTs was significantly associated with the presence of aquatic organisms, organic matter and algal remnants. Significant correlations of malaria prevalence with monthly immature density, as well as number of breeding habitats with immature vector mosquitoes, were also observed. Conclusions: The findings that OHTs showed fairly high and consistent immature density of An. stephensi irrespective of seasons indicates the potentiality of the breeding habitat in contributing to vector density. The correlation between vector breeding habitats, immature density and malaria prevalence indicates the proximity of these habitats to malaria cases, proving its role in vector abundance and local malaria transmission. The preference of An. stephensi to breed in OHTs calls for intensified, appropriate and sustained intervention measures to curtail vector breeding and propagation to shrink malaria to pre-elimination level and beyond

Expanded encyclopaedias of DNA elements in the human and mouse genomes

All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442

Corrosion Behaviour of TiN/a-C Superhard Nanocomposite Coatings Prepared by a Reactive DC Magnetron Sputtering Process

Nanocomposite coatings of TiN/a-C were prepared on tool steel substrates using a multitarget reactive DC magnetron sputtering process at various TiN layer thicknesses (0.6x2013;2.8 nm). The a-C layer thickness was approximately 0.45 nm. Structural characterisation of the coatings was done by X-ray diffraction (XRD). Incorporation of an a-C phase in TiN matrix reduced crystallite size of the coatings, as13; revealed by XRD and atomic force microscopy. XRD data showed that the nanocomposite coatings exhibited {111} texture and the average crystax2013;llite size was ca. 7.5x2013;9.0 nm. Nanoindentation data showed that 1.5 xB5;m thick nanocomposite coatings exhibited a maximum hardness of 5100 kg mm-2. The potentiodynamic polarisation of 1.5 xB5;m thick coatings in 0.5 MHCl solution indicated that the nanocomposite coatings exhibited superior corrosion protection of the tool steel substrate as compared to the single layer TiN coatings of similar thicknesses. Enhancement in the corrosion behaviour of the nanocomposite coatings has been attributed to small crystallite size and dense microstructure. Potentiodynamic polarisation studies conducted on ca. 100 nm thick nanocomposite coatings revealed that for a given a-C layer thickness the corrosion current decreased with a decrease in TiN layer thickness. This was supported by scanning electron microscopy (SEM) studies on the corroded samples. The SEM micrographs showed that density and diameter of the corrosion pits were smaller for nanocomposite coatings as compared to single layer TiN coatings of similar thicknesses

Corrosion behavior of nanolayered TiN/NbN multilayer coatings prepared by reactive direct current magnetron sputtering process

TiN, NbN and TiN/NbN multilayer coatings were deposited on tool steel substrates using a reactive DC magnetron sputtering process. The coatings were characterized using X-ray diffraction, nanoindentation, atomic force microscopy, scanning electron microscopy (SEM) and energy-dispersive X-ray analysis. The corrosion behavior of TiN/NbN multilayer coatings was studied in 0.5 M HCl and 0.5 M NaCl solutions using potentiodynamic polarization and compared with single layered TiN and NbN coatings. Approximately 1.5 x3BC;m thick coatings of TiN, NbN and TiN/NbN multilayers showed good corrosion protection of the tool steel substrate and multilayer coatings performed better than single layered coatings. The corrosion behavior of the multilayers improved with total number of interfaces in the coatings. In order to conclusively demonstrate the positive effect of layering, corrosion behavior of 40-layer TiN/NbN multilayers was studied at lower coating thicknesses (32x2013;200 nm) and compared with single layer TiN coatings of similar thicknesses. The polarization data and SEM studies of these coatings indicated that the corrosion behavior improved with coating thickness and multilayers showed better corrosion resistance as compared to the single layer coatings. Other studies such as intrinsic corrosion, effects of Ti interlayer and post-deposition annealing on the corrosion behavior of the multilayer coatings are also presented in this paper. The results of this study demonstrate that nanolayered multilayers can effectively improve the corrosion behavior of transition metal nitride hard coatings. 13; 13

Structure, hardness and thermal stability of TiAlN and nanolayered TiAlN/CrN multilayer films

TiAlN films were deposited on silicon (1 1 1) substrates from a TiAl target using a reactive DC magnetron sputtering13; process in Ar+N2 plasma. Films were prepared at various nitrogen flow rates and TiAl target compositions. Similarly, CrN films were prepared from the reactive sputtering of Cr target. Subsequently, nanolayered TiAlN/CrN multilayer films were deposited at various modulation wavelengths (L). X-ray diffraction (XRD), energy dispersive X-ray analysis, nanoindentation and atomic force microscopy were used to characterize the films. The XRD confirmed the formation of superlattice structure at low modulation wavelengths. The maximum hardness of TiAlN/CrN multilayers was 3900 kg/mm2, whereas TiAlN and CrN films exhibited maximum hardnesses of 3850 and 1000 kg/mm2 , respectively. Thermal stability of TiAlN and TiAlN/CrN multilayer films was studied by heating the films in air in the temperature range (TA) of 500x2013;900 xB0;C for 30 min. The XRD spectra revealed that TiAlN/CrN multilayers were stable up to 800 xB0;C and got oxidized substantially at 900 'C. On the other hand, the TiAlN films were stable up to 700 'C and got completely oxidized at 800 xB0;C. Nanoindentation measurements performed on the films after heat treatment showed that TiAlN retained a hardness of 2200 kg/mm2 at TA=700 xB0;C and TiAlN/CrN multilayers retained hardness as high as 2600 kg/mm2 upon annealing at 800'C

Superhard nanocomposite coatings of TiN/a-C prepared by reactive DC magnetron sputtering

Single layer TiN coatings were prepared on silicon (111) substrates using a multi-target reactive DC magnetron sputtering process at various nitrogen flow rates and substrate biases. TiN coatings prepared at a nitrogen flow rate of 0.6 sccm, a power density of 5.4 W/cm2 and a substrate bias of x2212;275 V, showed a nanoindentation hardness of 3300 kg/mm2, whereas amorphous carbon (a-C) coatings prepared under similar deposition conditions exhibited a hardness of 800 kg/mm2. Subsequently, nanocomposite coatings of TiN/a-C were prepared on silicon (111) and M3 tool steel substrates by rotating the substrate back and forth between the titanium and the graphite targets. The nanocomposite coatings were prepared at various carbon concentrations. Structural characterization of the coatings was done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The compositions of the coatings were determined using energy dispersive X-ray analysis (EDAX). The nanocomposite coatings exhibited a broad (111) reflection of cubic TiN phase in XRD data. Nanoindentation data showed that about 1.5-x3BC;m-thick TiN/a-C nanocomposite coatings exhibited a maximum hardness of 4800 kg/mm2 at a carbon concentration of approximately 17 at.%. The TEM micrographs showed that TiN nanocrystals were embedded in a-C matrix and the average crystallite size was 78 xC5;. The selected area electron diffraction of the nanocomposite coatings showed the presence of both nanocrystalline (TiN) and amorphous (a-C) phases. This was confirmed by high-resolution TEM studies

In vitro Evidence that an Aqueous Extract of Centella asiatica Modulates alpha-Synuclein Aggregation Dynamics

alpha-Synuclein aggregation is one of the major etiological factors implicated in Parkinson's disease (PD). The prevention of aggregation of alpha-synuclein is a potential therapeutic intervention for preventing PD. The discovery of natural products as alternative drugs to treat PD and related disorders is a current trend. The aqueous extract of Centella asiatica (CA) is traditionally used as a brain tonic and CA is known to improve cognition and memory. There are limited data on the role of CA in modulating amyloid-beta (A beta) levels in the brain and in A beta aggregation. Our study focuses on CA as a modulator of the alpha-synuclein aggregation pattern in vitro. Our investigation is focused on: (i) whether the CA leaf aqueous extract prevents the formation of aggregates from monomers (Phase I: alpha-synuclein + extract co-incubation); (ii) whether the CA aqueous extract prevents the formation of fibrils from oligomers (Phase II: extract added after oligomers formation); and (iii) whether the CA aqueous extract disintegrates the pre-formed fibrils (Phase III: extract added to mature fibrils and incubated for 9 days). The aggregation kinetics are studied using a thioflavin-T assay, circular dichroism, and transmission electron microscopy. The results showed that the CA aqueous extract completely inhibited the alpha-synuclein aggregation from monomers. Further, CA extract significantly inhibited the formation of oligomer to aggregates and favored the disintegration of the preformed fibrils. The study provides an insight in finding new natural products for future PD therapeutics

Effect of Plasma Treatment on Native Defects and Photocatalytic Activities of Zinc Oxide Tetrapods

ZnO tetrapods, as a ZnO nanostructure with a low defect concentration, were subjected to plasma treatments using different gases to induce different types of defects in the samples and examine their effects on sample properties. Hydrogen and argon plasmas resulted in significant oxygen deficiencies, but no defect emission appeared. Oxygen plasma had only a minor effect on the sample composition, but it resulted in the appearance of defect emission and a significant overall reduction in luminescence intensity. On the other hand, the photocatalytic activity was significantly reduced in samples exhibiting oxygen deficiencies. It can thus be concluded that oxygen vacancies do not participate in the green emission of ZnO and also that their presence at the sample surface does not enhance the photocatalytic activity.Department of Electronic and Information Engineerin