Open Regions Research Articles

Profiling Chromatin Accessibility Responses in Goat Bronchial Epithelial Cells Infected with Pasteurella multocida.

Pasteurella multocida can cause goat hemorrhagic sepsis and endemic pneumonia. Respiratory epithelial cells are the first line of defense in the lungs during P. multocida infection. These cells act as a mechanical barrier and activate immune response to protect against invading pathogenic microorganisms. Upon infection, P. multocida adheres to the cells and causes changes in cell morphology and transcriptome. ATAC-seq was conducted to determine the changes in the chromatin open region of P. multocida-infected goat bronchial epithelial cells based on transcriptional regulation. A total of 13,079 and 28,722 peaks were identified in the control (CK) and treatment (T) groups (P. multocida infection group), respectively. The peaks significantly increased after P. multocida infection. The specific peaks for the CK and T groups were annotated to 545 and 6632 genes, respectively. KEGG pathway enrichment analysis revealed that the specific peak-related genes in the T group were enriched in immune reaction-related pathways, such as Fc gamma R-mediated phagocytosis, MAPK signaling pathway, bacterial invasion of epithelial cells, endocytosis, and autophagy pathways. Other cellular component pathways were also enriched, including the regulation of actin cytoskeleton, adherent junction, tight junction, and focal adhesion. The differential peaks between the two groups were subsequently analyzed. Compared to those in the CK group, 863 and 11 peaks were upregulated and downregulated, respectively, after the P. multocida infection. Fifty-six known transcription factor motifs were revealed in upregulated peaks in the P. multocida-infected group. By integrating ATAC-seq and RNA-seq, some candidate genes (SETBP1, RASGEF1B, CREB5, IRF5, TNF, CD70) that might be involved in the goat bronchial epithelial cell immune reaction to P. multocida infection were identified. Overall, P. multocida infection changed the structure of the cell and caused chromatin open regions to be upregulated. In addition, P. multocida infection actively mobilized the host immune response with the inflammatory phenotype. The findings provide valuable information for understanding the regulatory mechanisms of P. multocida-infected goat bronchial epithelial cells.

Abstract C054: Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines

Abstract African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remain underexplored. Using ATAC-sequencing, we characterized differences in chromatin accessibility between EA-derived versus AA-derived breast cancer cell lines across a range of breast cancer subtypes. Interestingly, our principal component analysis of the top 50,000 peaks with the most variance revealed separation of chromatin profiles by genetic ancestry specifically in TNBC cell lines (N=10). Digital footprinting analysis of differentially open chromatin regions using TOBIAS revealed significant differences in transcription factor (TF) binding by ancestry (61 TFs with a differential binding score > 0.25 or < -0.25 and FDR < 0.01). AA TNBC cell lines exhibited increased binding of transcription factors associated with epithelial-to-mesenchymal transition (ZEB1, SNAI1, GRHL2), cancer stemness and chemotherapeutic resistance (TFAP2C, NRF1), and others such as KAISO, whose aberrant expression has been previously linked to a distinct biology and poor outcomes in AA breast and prostate cancer patients. Pathway analysis of genes located within promoters of differentially open chromatin regions reveals enrichment of the following KEGG pathways in AA TNBC cells: inflammatory mediator regulation of TRP channels (p-adj = 0.009), Hippo signaling (p-adj = 0.006), Wnt signaling (p-adj = 0.031), and Rap-1 signaling (p-adj = 0.046). Together, these data reveal a differential chromatin landscape associated with the aberrant activity of critical TFs and downstream gene expression changes that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. Citation Format: Alexandra R. Harris, Vishal Koparde, Gatikrushna Panigrahi, Maeve Bailey-Whyte, Tiffany Dorsey, Stefan Ambs. Characterizing differences in the chromatin accessibility landscape by donor ancestry in human triple-negative breast cancer cell lines [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C054.

Description of the Nematode Dirofilaria repens (Nematoda, Onchocercidae) Parasitic in Dogs in Ukraine

Dirofilariasis is a zoonotic disease of domestic and wild carnivores and humans. Subcutaneous migration of the parasite Dirofilaria repens Railliet & Henry, 1911 may cause local swelling with variable localisation. In humans, this parasite can cause damage to the lungs, male genitalia and eyes. The range of D. repens is constantly expanding into new areas and, considering the zoonotic potential of this parasite, it is important to extend the existing data on the morphology of D. repens. The present study provides a morphometric description of D. repens nematodes obtained from subcutaneous tissues of dogs in Ukraine. The aim of this study was to highlight the key features for the identification of parasites of this species. For males, 27 morphometric characteristics were identified, characterising the overall size of the body and the oesophagus, the thickness of the cuticle in the region of the mouth opening, the localisation of the nerve ring and the cloaca, the morphological structure and metric parameters of the spicules, and the length of the tail. For females, 18 morphometric traits were identified that, in addition to common parameters, characterize cuticle thickness in the region of the vulva, localisation of the vulva and anus, body width in the regions of the anus and vulva, and tail length. This report adds to the existing data on the morphological and metric characteristics of D. repens nematodes.

Investigating cellular heterogeneity at the single-cell level by the flexible and mobile extrachromosomal circular DNA

Extrachromosomal circular DNA (eccDNA) is a special class of DNA derived from linear chromosomes. It coexists independently with linear chromosomes in the nucleus. eccDNA has been identified in multiple organisms, including Homo sapiens, and has been shown to play important roles relevant to tumor progression and drug resistance. To date, computational tools developed for eccDNA detection are only applicable to bulk tissue. Investigating eccDNA at the single-cell level using a computational approach will elucidate the heterogeneous and cell-type-specific landscape of eccDNA within cellular context. Here, we performed the first eccDNA analysis at the single-cell level using data generated by single-cell Assay for Transposase-Accessible Chromatin with sequencing (scATAC-seq) in adult and pediatric glioblastoma (GBM) samples. Glioblastoma multiforme (GBM) is an aggressive tumor of the central nervous system with a poor prognosis. Our analysis provides an overview of cellular origins, genomic distribution, as well as the differential regulations between linear and circular genome under disease- and cell-type-specific conditions across the open chromatin regions in GBM. We focused on some eccDNA elements that are potential mobile enhancers acting in a trans-regulation manner. In summary, this pilot study revealed novel eccDNA features in the cellular context of brain tumor, supporting the strong need for eccDNA investigation at the single-cell level.

Determination of the Chromatin Openness in Bacterial Genomes.

The hyperactive Tn5 transposase in the ATAC-seq method has been widely used to determine the open DNA regions and understand the overall epigenomic regulation in the chromatins of eukaryotic cells. Here, we describe POP-seq (Prokaryotic chromatin Openness Profiling sequencing), an adaptation of the ATAC-seq method, to interrogate changes in the openness of prokaryotic nucleoids.

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits.

The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.

Gene Regulatory Network Modeling Using Single-Cell Multi-Omics in Plants.

Single-cell multi-omics technology can be applied to plant cells to characterize gene expression and open chromatin regions in individual cells. In this chapter, we describe a computational pipeline for the analysis of single-cell data to construct gene regulatory networks. The major steps of this pipeline include the following: (1) normalize and integrate scRNA-seq and scATAC-seq data (2) identify cluster maker genes (3) perform motif finding for selected marker genes, and (4) identify regulatory networks with machine learning. The pipeline has been tested using data from the model species Arabidopsis and is generally applicable to other plant and animal species to characterize regulatory networks using single-cell multi-omics data.

Identification of DNA G–quadruplex Forming Sequence in Shrimp White Spot Syndrome Virus (WSSV)

White spot syndrome virus (WSSV) is considered one of the most infectious and lethal viruses that affect shrimp. Bioinformatic studies revealed several G-quadruplex forming sequences at the open reading frame region. Moreover, the sequences are widely conserved through all deposited WSSV sequences. Introductory structural studies on two sequences, namely WSSV131 and WSSV172, are proposed to form a quadruplex. While WSSV172 forms a mixture of quadruplex topologies, WSSV131 is suggested to form a parallel topology, as indicated by the NMR spectra and circular dichroism (CD) ellipticity pattern. CD spectra also suggested that the major parallel species of the WSSV131 sequence are found to be stable above 60 °C. Ultimately, these results may open a new strategy for WSSV treatment by targeting the quadruplex confirmation with a quadruplex binding ligand.

Structural Behavior of Prestressed RC Dapped Beam with Openings Strengthened Using CFRP Sheets

This research examines the strengthening efficiency of prestressed concrete dapped end beam with opening under monotonic point load. The study concerns with the position of the opening relative to the dapped end, the shape of opening, as circle or square, in addition, the effect of CFRP strengthening around the opening. The experimental program consisted of testing nine scaled down prestressed concrete dapped end beam specimens with single opening near the dapped end. Beam specimens consisted of one control beam and the remaining eight beams classified into two groups. The first group contained four unstrengthened specimens, whereas the second group included beams with opening strengthened using CFRP sheets. A full wrapping configuration for the opening region was adopted in this research. The results presented the detrimental influence of the openings on the shear strength of the dapped beam and the additional strength achieved from strengthening. This study concludes that the shear strength of the prestressed dapped beam decreased by the presence of openings in the web with maximum reduction about 20% when the opening was located close the dapped end. Based on the test results, the strengthened beams recovered significant part of their original load carrying capacity. Generally, prestressed dapped beams regain a maximum of 92% of their strength when openings with different configurations and locations were strengthened with full CFRP wrap.

Enhancement of the behaviour of reinforced concrete dapped end beams including single-pocket loaded by a vertical concentrated force

In precast building construction, some beams are designed to support one or several concentrated loads resulting from the reactions of the attached cross beams. Consequently, the pocket beams without or with dapped ends may represent one of the innovative solutions to constitute the joints between the two attached members. In the present research work, the behaviour of dapped end beams that included rectangular opening loaded with in-plane force, have been investigated. Several detailing have been proposed, in addition the vertical stirrups, to improve the strength of the opening region including the use of steel fibre concrete (SFC),Configuration of the inclined crossed bars, jacketing with steel plates and the composite section technique with two arrangements of the reinforcement of the dapped end . Ten specimens have been tested under gradually increased vertical static loading. The tested specimens are categorized into two sets based on the configuration of dapped end reinforcement. Two variable have been considered which are the strengthening configuration of the opening region and the configuration of the dapped end reinforcement. The response has been discussed in terms several indicators including, the cracking and failure loads, maximum deflection, mode of failure, load-deflection curves, crack patterns, crack width, to recognize the optimum strengthening proposal of the opening. Results revealed that using the inclined steel bars (modified arrangement) yield better response than the conventional (standard) reinforcement (vertical stirrups) within the dapped end. For beams with pockets strengthened with crossed inclined bars, failure load enhanced in range of (8.5-11%) whereas the enhancement was in ranged in (8-10%) for the steel SFC method. Moreover, an improvement by about (11-13%) in load capacity increased when the jacketing with steel plates was applied. The maximum improvement was obtained when using the embedded rolled section within the opening with values of (21-23%).

Assessment of Urban Green Space Distribution within the Scope of European Green Deal Using NDVI Indice; Case of Nicosia/Cyprus

In this study, the urban green space distribution was determined, and the city's compliance with the European Green Deal was evaluated. Firstly, Landsat 8 satellite images were radiometrically corrected with the Quantum GIS software. Then, NDVI was produced using the Red-Green-Blue and Near-Infrared bands of the processed data obtained. Finally, the NDVI image with a value between -1 and +1 was reclassified to define urban open green spaces. The classification data showed that open green areas have a nonhomogeneous distribution throughout the city, and the amount of green space per capita is approximately 200 m². According to the classification results of Northern Nicosia, a surface area of 475 km², the amount of green space is calculated as 16m², constituting 2.97%. Thus, it has been concluded that open green regions are denser in certain parts of the city than others and do not have a homogeneous distribution that can serve the whole town.

High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome

N6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.

Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization

The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.

Shahid Javed Burki. Changing Perceptions and Altered Realities: Emerging Economies in the 1990s. World Bank, 2000. 198 pages. Paperback. Price not given.

Shahid Javed Burki’s Changing Perceptions and Altered Realities: Emerging Economies in the 1990s is a collection of his essays and speeches on a variety of economic issues relevant to developing countries. These range from the trend towards open regionalism in the Latin American and Caribbean region (LAC) to the challenges of integrating into the global economy faced by small states. Three points in particular are of great help in understanding the nature of the problems faced by emerging economies over the past decade. First, there exist great differences within the developing world and, by extension, in the ranks of the poor. Second, the complexity of the situation demands that domestic institutions in developing countries be made stronger and more efficient. And third, market-based policies, though far from perfect, represent the best available set of solutions to the many problems faced by the developing world.

Review of global trends in meeting the ecological challenges of the mining industry. Part II: Field tests and lab-scale analytical research in Russia

This article describes the applied research outcomes in the field of restoration ecology in the Russian regions which carry out open pit mining of solid minerals of all types. Russian ecologists address the issues connected with the evaluation and recovery of soil cover, improvement of the wildlife habitat quality, as well as with the air, water and vegetation ecosystem refining in open pit mining regions. The infomedia for dealing with ecological challenges have shaped in the course of the field testing and lab-scale analysis. All researchers highlight the large scale of the manmade damage caused to natural landscapes and emphasize the necessity of ecological balance acceleration and maintenance on the lands damaged by the mineral mining and processing industry.

Conductive Polyaniline-Indium Oxide Composite Films Prepared by Sequential Infiltration Synthesis for Electrochemical Energy Storage.

Composites of conductive polymers (CP) and metal oxides (MO) have attracted continued interest in the past decade for diverse application fields because the synergistic effects of CP and MO enable the realization of unusual electronic, electrochemical, catalytic, and mechanical properties of the composites. Herein, we present a novel method for the sequential infiltration synthesis of composite films of polyaniline (PANI) and indium oxide (InO x ) with high electrical conductivities (4-9 S/cm). The synthesized composite films were composed of two phases of graded concentration: InO x with oxygen vacancies and PANI with partially protonated molecular units. The PANI-InO x composite films displayed enhanced electrochemical activity with a pair of well-defined redox peaks. The open interfacial regions between the InO x and PANI phases may provide efficient pathways for ion diffusion and active sites for improved charge transfer.

Broadband Labyrinthine Acoustic Insulator

Ventilated acoustic insulation currently represents one of the most promising research directions in applied acoustics. With the ongoing development and application of acoustic metamaterials, tremendous progress has been made in this space. In this work, we propose a ventilated acoustic insulator based on a labyrinthine metamaterial, a design that consists of a peripheral, circumferential labyrinthine region and a central ventilated, open region. Herein, we demonstrate the potential for this design to yield high-performance wide-band acoustic insulation, a performance metric currently lacking in this class of acoustic silencers, in combination with ventilation. The silencing effect of the labyrinthine acoustic insulator is theoretically and experimentally verified in the frequency range from 1025 to 2000 Hz. Our reported design establishes the foundation for the development of increasingly broadband ventilated acoustic insulators.

Deeper Integration or Open Regionalism in the Indian Ocean Rim Association (IORA): A CGE Approach

The Indian Ocean Rim Association (IORA) is a regional association based on the principle of open regionalism to promote liberalization through trade and investment facilitation. This study compares two main scenarios with the ingredients of a deeper regional integration compared to the IORA's present open regionalism status. Scenario I evaluates the effects of gradual tariff cuts on IORA, while Scenario II combines the impact of tariff cuts, non-tariff measures (NTM) reduction, and trade facilitation. A recent recursive dynamic model, called Global Trade Analysis Project recursive dynamic model (GTAP-RD), was used to understand the adjustment path. The result shows welfare gain for all IORA countries when a trade liberalization involving tariff cuts is complemented with NTM reduction and trade facilitation. In addition, the "NTM spillover" effect on some non-IORA members (the rest of Gulf Cooperation Council, the rest of Greater Arab Free Trade Agreement, and the United Kingdom) was observed. The results suggest that IORA has more to gain if it involves a deeper regional integration than the present form of open regionalism.

Analysis of Chromatin Openness in Testicle Tissue of Yak and Cattle-Yak.

Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produce sperm, which adversely restricted the fixation of heterosis. Many prior attempts have been made to decipher the mechanism underlying the spermatogenesis stagnation of cattle-yak. However, the open chromatin region (OCR) map of yak and cattle-yak testes has not been generated yet. Here, we have analyzed the OCRs landscape of testicular tissues of cattle-yak and yaks by performing ATAC-seq technology. The OCRs of cattle-yak and yak testes displayed similar genome distribution and showed priority in intergenic regions, introns and promoters. The pathway enrichment analysis indicated that the differential OCRs-related genes were involved in spermatogenesis, involving the cell cycle, as well as Hippo, mTOR, MAPK, Notch, and Wnt signaling pathways. The integration of ATAC-seq and mRNA-seq indicated that the majority of the gene expression levels were positively correlated with chromatin openness. At the same time, we have identified a number of transcription factors (TFs) related to spermatogenesis and the differential expression of these TFs may contribute to the spermatogenesis stagnation of the cattle-yak. Overall, the findings of this study provide valuable information for advancing the research related to yak crossbreeding improvement and sperm production stagnation of cattle-yak.

Energetic Charged Particle Observations During Juno's Close Flyby of Ganymede

AbstractOn 7 June 2021, NASA's Juno mission obtained unique measurements of Ganymede's magnetosphere during a close flyby that brought the spacecraft within ∼1,000 km of its surface. Here Jupiter Energetic particle Detector Instrument observations are presented and analyzed. The electron pitch angle distributions reveal distinct regions of Ganymede's magnetosphere that can be characterized as inbound and outbound magnetospheric boundaries, a magnetotail/wake region, and Ganymede's open field line region. Evidence for energy dependent electron pitch angle structuring is also documented both outside and within Ganymede's magnetosphere. Electron precipitation is observed and mapped to Ganymede's surface along Juno's magnetic footpoint.