Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.

NucleoMap: a computational tool for identifying nucleosomes in ultra-high resolution contact maps

Although poorly positioned nucleosomes are ubiquitous in the prokaryote genome, they are difficult to identify with existing nucleosome identification methods. Recently available enhanced high-throughput chromatin conformation capture techniques such as Micro-C, DNase Hi-C, and Hi-CO characterize nucleosome-level chromatin proximity, probing the positions of mono-nucleosomes and the spacing between nucleosome pairs at the same time, enabling profiling of nucleosomes in poorly positioned regions. Here we develop a novel computational approach, NucleoMap, to identify nucleosome positioning from ultra-high resolution chromatin contact maps. By integrating nucleosome binding preferences, read density, and pairing information, NucleoMap precisely locates nucleosomes in both eukaryotic and prokaryotic genomes and outperforms existing nucleosome identification methods in sensitivity and specificity. We rigorously characterize genome-wide association in eukaryotes between the spatial organization of mono-nucleosomes and their corresponding histone modifications, protein binding activities, and higher-order chromatin functions. We also predict two tetra-nucleosome folding structures in human embryonic stem cells using machine learning methods and analysis their distribution at different structural and functional regions. Based on the identified nucleosomes, nucleosome contact maps are constructed, reflecting the inter-nucleosome distances and preserving the original data's contact distance profile.

Green Chemistry and Process Intensification: Milestones on a Sustainable Development

As a philosophical support, green chemistry (GC) becomes at present well-combined into the scientific system to assist scientists and engineers consider how to decrease or remove waste and avert the employment and formation of hazardous substances in the design phase of chemicals. Such design attempts in turn affect the full life-cycle of the chemical, from getting the starting materials until the end-use product is recycled or disposed of. There is a considerable advance noted in such direction during the last three decades, this review focuses on GC research. As a comparatively fresh technique, revision in process intensification (PI) is fast and investigation could rapidly lead to outstanding outcomes. However, numerous features of PI could take more time to be fact. Much of the study stays in academic and industrial laboratories, even if large-scale implementations of micro-reactors are actuality. Fields of PI enterprise that have progressed quickly are the expansion of carbon capture techniques, an increasing interest in GC, and the beginning of momentous study into connecting solar energy to intensified methods like chemical reactions. Electric fields (e.g., microwaves and ultrasound) are observed in larger usages, and the application of electrokinetic forces at the micro- and nanoscale persist to fascinate. Huge investigations are working for the sake of ideas like the perfect reactor. PI remains a motif leading to attain a sustainable society. This work may be an orientation in the investigation of product development and design, production and application, in a constructive and stimulating way.

Kreasi Seni Sebagai Daya Tarik Wisata Budaya di Padepokan Bagong Kussudiarja Yogyakarta

Yogyakarta is a city of education and cultural city, as well as tourist areas, are still waking life order of the society and various art and cultural activities are still maintained their authenticity. Art creations that there in hermitage is one of the cultural heritage, both in the form of classical dance, dance creations, Ballet, theatre, art and others which are the legacy of the Bagong Kussudiardja. The research method used is descriptive qualitative research with data collection techniques derived from primary data is information obtained from primary sources and secondary data is data capture techniques through observation, interview, documentation and literature. Some of the art creations in Bagong Kussudiardja is one of the artists to create and store a variety of works that made some of the Bagong Kussudiardja one of the Cultural Attractions in Yogyakarta. Art creations are in hermitage : jagongan wagen, estuary, angjasana, edukreasi, fine art, among the classical dance, sedulur Ballet, dance, dances and other activities is a form of art and cultural works with the aim that the some of the Bagong Kussudiadrja is one of the cultural heritage in Yogyakarta and Indonesia

Mosquitoes Know No Borders: Surveillance of Potential Introduction of Aedes Species in Southern Québec, Canada

Current climatic conditions limit the distribution of Aedes (Stegomyia) albopictus (Skuse, Diptera: Culicidae) in the north, but predictive climate models suggest this species could establish itself in southern Canada by 2040. A vector of chikungunya, dengue, yellow fever, Zika and West Nile viruses, the Ae. Albopictus has been detected in Windsor, Ontario since 2016. Given the potential public health implications, and knowing that Aedes spp. can easily be introduced by ground transportation, this study aimed to determine if specimens could be detected, using an adequate methodology, in southern Québec. Mosquitoes were sampled in 2016 and 2017 along the main roads connecting Canada and the U.S., using Biogent traps (Sentinel-2, Gravide Aedes traps) and ovitraps. Overall, 24 mosquito spp. were captured, excluding Ae. Albopictus, but detecting one Aedes (Stegomyia) aegypti (Skuse) specimen (laid eggs). The most frequent species among captured adults were Ochlerotatus triseriatus, Culex pipiens complex, and Ochlerotatus japonicus (31.0%, 26.0%, and 17.3%, respectively). The present study adds to the increasing number of studies reporting on the range expansions of these mosquito species, and suggests that ongoing monitoring, using multiple capture techniques targeting a wide range of species, may provide useful information to public health with respect to the growing risk of emerging mosquito-borne diseases in southern Canada.

Towards estimation of CO2 adsorption on highly porous MOF-based adsorbents using gaussian process regression approach

In recent years, new developments in controlling greenhouse gas emissions have been implemented to address the global climate conservation concern. Indeed, the earth's average temperature is being increased mainly due to burning fossil fuels, explicitly releasing high amounts of CO2 into the atmosphere. Therefore, effective capture techniques are needed to reduce the concentration of CO2. In this regard, metal organic frameworks (MOFs) have been known as the promising materials for CO2 adsorption. Hence, study on the impact of the adsorption conditions along with the MOFs structural properties on their ability in the CO2 adsorption will open new doors for their further application in CO2 separation technologies as well. However, the high cost of the corresponding experimental study together with the instrument's error, render the use of computational methods quite beneficial. Therefore, the present study proposes a Gaussian process regression model with four kernel functions to estimate the CO2 adsorption in terms of pressure, temperature, pore volume, and surface area of MOFs. In doing so, 506 CO2 uptake values in the literature have been collected and assessed. The proposed GPR models performed very well in which the exponential kernel function, was shown as the best predictive tool with R2 value of 1. Also, the sensitivity analysis was employed to investigate the effectiveness of input variables on the CO2 adsorption, through which it was determined that pressure is the most determining parameter. As the main result, the accurate estimate of CO2 adsorption by different MOFs is obtained by briefly employing the artificial intelligence concept tools.