• Molecules and Cells
• /
• v.45 no.5
• /
• pp.343-352
• /
• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• ALGAE
• /
• v.37 no.3
• /
• pp.185-204
• /
• 2022

The genus Coolia A. Meunier 1919 has a global distribution and is a common member of epiphytic dinoflagellate assemblages in neritic ecosystems. Coolia monotis is the type species of the genus and was the only known species for 76 years. Over the past few decades, molecular characterization has unveiled two species complexes that group morphologically very similar species, so their limits are often unclear. To provide new knowledge on the biogeography and species composition of the genus Coolia, 16 strains were isolated from Bahía de La Paz, Gulf of California. The species were identified by applying morphological and molecular approaches. The morphometric characteristics of all isolated Coolia species were consistent with the original taxa descriptions. Phylogenetic analyses (large subunit [LSU] rDNA D1 / D2 and internal transcribed spacer [ITS] 1 / 5.8S / ITS2) revealed a species assemblage comprising Coolia malayensis, C. palmyrensis, C. tropicalis, and the C. cf. canariensis lineage. This is the first report of Coolia palmyrensis and C. cf. canariensis in Mexico and C. tropicalis in the Gulf of California. Our results strengthen the biogeographical understanding of these potentially harmful epiphytic dinoflagellate species.

• Molecules and Cells
• /
• v.45 no.2
• /
• pp.84-92
• /
• 2022

To understand the microcircuitry of the brain, the anatomical and functional connectivity among neurons must be resolved. One of the technical hurdles to achieving this goal is that the anatomical connections, or synapses, are often smaller than the diffraction limit of light and thus are difficult to resolve by conventional microscopy, while the microcircuitry of the brain is on the scale of 1 mm or larger. To date, the gold standard method for microcircuit reconstruction has been electron microscopy (EM). However, despite its rapid development, EM has clear shortcomings as a method for microcircuit reconstruction. The greatest weakness of this method is arguably its incompatibility with functional and molecular analysis. Fluorescence microscopy, on the other hand, is readily compatible with numerous physiological and molecular analyses. We believe that recent advances in various fluorescence microscopy techniques offer a new possibility for reliable synapse detection in large volumes of neural circuits. In this minireview, we summarize recent advances in fluorescence-based microcircuit reconstruction. In the same vein as these studies, we introduce our recent efforts to analyze the long-range connectivity among brain areas and the subcellular distribution of synapses of interest in relatively large volumes of cortical tissue with array tomography and superresolution microscopy.

• Nuclear Engineering and Technology
• /
• v.55 no.4
• /
• pp.1324-1331
• /
• 2023

In the present work, we carried out a molecular dynamics study of the kinetic properties of the FLiNaK molten salt, as well as a detailed study of the structure of this salt melt. The high value of the self-diffusion coefficient of fluorine ions is due to the large number of Coulomb repulsions between the most numerous negative ions. The calculated values of shear viscosity are in good agreement with the experimental data, as well as with the reference data obtained on the basis of finding the most reliable data. The total and partial functions of the radial distribution are calculated. According to the statistical analysis, fluorine ions have the greatest numerical diversity in the environment of similar ions, and sodium ions with the lowest representation in FLiNaK, have the least such diversity. For the subsystem of fluorine ions, the rotational symmetry of the fifth order is the most pronounced. Some of the fluorine ions form linear chains consisting of three atoms, which are not formed for positive ions. The results of the work give an understanding of the behavior molten FLiNaK under operating conditions in a molten salt reactor and will find application in future studies of this molten salt.

• The Bulletin of The Korean Astronomical Society
• /
• v.45 no.1
• /
• pp.64.1-64.1
• /
• 2020

Galaxy groups are the place where many galaxies feel the impact of the surroundings (e.g., merging, tidal interaction, ram pressure stripping) before joining bigger structures like (sub)clusters. A significant fraction of galaxies is quenched in the group environment. Such "pre-processing" of galaxies in groups is likely to affect galaxy evolution tremendously. To better understand how environmental processes in galaxy groups affect molecular gas, star formation activity, and galaxy evolution, we carried out CO imaging observations of group galaxies, using the Atacama Compact Array (ALMA/ACA). We selected all the targets that have been detected in the GEMS-HI survey for two groups, making the sample of 40 galaxies (18 galaxies in IC 1459 group and 22 galaxies in NGC 4636 group). Our ALMA/ACA observation is the first CO imaging survey for two groups. In this work, we present CO images of group galaxies, together with their star formation maps and HI images. Our ACA CO data show the asymmetric distribution of molecular gas in some of our samples. We discuss the impact of the group environment on molecular gas and star formation activity.

• BMB Reports
• /
• v.57 no.6
• /
• pp.263-272
• /
• 2024

Amyloid-β (Aβ) is one of the amyloidogenic intrinsically disordered proteins (IDPs) that self-assemble to protein aggregates, incurring cell malfunction and cytotoxicity. While Aβ has been known to regulate multiple physiological functions, such as enhancing synaptic functions, aiding in the recovery of the blood-brain barrier/brain injury, and exhibiting tumor suppression/antimicrobial activities, the hydrophobicity of the primary structure promotes pathological aggregations that are closely associated with the onset of Alzheimer's disease (AD). Aβ proteins consist of multiple isoforms with 37-43 amino acid residues that are produced by the cleavage of amyloid-β precursor protein (APP). The hydrolytic products of APP are secreted to the extracellular regions of neuronal cells. Aβ 1-42 (Aβ42) and Aβ 1-40 (Aβ40) are dominant isoforms whose significance in AD pathogenesis has been highlighted in numerous studies to understand the molecular mechanism and develop AD diagnosis and therapeutic strategies. In this review, we focus on the differences between Aβ42 and Aβ40 in the molecular mechanism of amyloid aggregations mediated by the two additional residues (Ile41 and Ala42) of Aβ42. The current comprehension of Aβ42 and Aβ40 in AD progression is outlined, together with the structural features of Aβ42/Aβ40 amyloid fibrils, and the aggregation mechanisms of Aβ42/Aβ40. Furthermore, the impact of the heterogeneous distribution of Aβ isoforms during amyloid aggregations is discussed in the system mimicking the coexistence of Aβ42 and Aβ40 in human cerebrospinal fluid (CSF) and plasma.

• International Journal of Stem Cells
• /
• v.16 no.4
• /
• pp.363-375
• /
• 2023

Stem cells are the foundational cells for every organ and tissue in our body. Cell-based therapeutics using stem cells in regenerative medicine have received attracting attention as a possible treatment for various diseases caused by congenital defects. Stem cells such as induced pluripotent stem cells (iPSCs) as well as embryonic stem cells (ESCs), mesenchymal stem cells (MSCs), and neuroprogenitors stem cells (NSCs) have recently been studied in various ways as a cell-based therapeutic agent. When various stem cells are transplanted into a living body, they can differentiate and perform complex functions. For stem cell transplantation, it is essential to determine the suitability of the stem cell-based treatment by evaluating the origin of stem, the route of administration, in vivo bio-distribution, transplanted cell survival, function, and mobility. Currently, these various stem cells are being imaged in vivo through various molecular imaging methods. Various imaging modalities such as optical imaging, magnetic resonance imaging (MRI), ultrasound (US), positron emission tomography (PET), and single-photon emission computed tomography (SPECT) have been introduced for the application of various stem cell imaging. In this review, we discuss the principles and recent advances of in vivo molecular imaging for application of stem cell research.

• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.7
• /
• pp.942-948
• /
• 2005

New polymorphism of major histocompatibility complex B-G genes was investigated by amplification and digestion of a 401bp fragment including intron 1 and exon 2 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique with two restriction enzymes of Msp I and Tas I in eight breeds of Chinese indigenous chickens and one exotic breed. In the fragment region of the gene, three novel single nucleotide polymorphisms (SNPs) were detected at the two restriction sites. We found the transition of two nucleotides of A294G and T295C occurred at Tas I restriction site, and consequently led to a non-synonymous substitution of asparagine into serine at position 54 within the deduced amino acid sequence of immunoglobulin variable-region-like domain encoded by the exon 2 of B-G gene. It was observed at rare frequency that a single mutation of A294G occurring at the site, also caused an identical substitution of amino acid, asparagine 54-to-serine, to that we described previously. And the transversion of G319C at Msp I site led to a non-synonymous substitution, glutamine 62-to-histidine. The new alleles and allele frequencies identified by the PCR-RFLP method with the two enzymes were characterized, of which the allele A and B frequencies at Msp I and Tas I loci were given disequilibrium distribution either in the eight Chinese local breeds or in the exotic breed. By comparison, allele A at Msp I locus tended to be dominant, while, the allele B at Tas I locus tended to be dominant in all of the breeds analyzed. In Tibetan chickens, the preliminary association analysis revealed that no significant difference was observed between the different genotypes identified at the Msp I and Tas I loci and the laying performance traits, respectively.

• Computers and Concrete
• /
• v.8 no.2
• /
• pp.163-176
• /
• 2011

By virtue of chord-length density function from the field of statistical physics, this paper introduced a quantitative approach to estimate the distribution of cement paste thickness between aggregates in concrete. Dynamics mixing method based on molecular dynamics was employed to generate one model structure, then image analysis algorithm was used to obtain the distribution of thickness of cement paste in model structure for the purpose of verification. By comparison of probability density curves and cumulative probability curves of the cement paste thickness among neighboring aggregates, it is found that the theoretical results are consistent with the simulation. Furthermore, for the model mortar and concrete mixtures with practical volume fraction of Fuller-type aggregate, this analytical formula was employed to predict the influence of aggregate volume fraction and aggregate fineness. And evolution of its mean values were also investigated with the variation of volume fraction of aggregate as well as the fineness of aggregates in model mortars and concretes.

• Macromolecular Research
• /
• v.17 no.5
• /
• pp.296-300
• /
• 2009

Ethylene-1-butene copolymers were prepared with $SiO_2$-supported $TiCl_4$ catalyst by changing of 1-butene/ethylene molar ratio in feed, and the resulting copolymers were analyzed using temperature rising elution fractionation (TREF) and crystallization fractionation (Crystaf) methods to investigated the influence of $C_4/C_2$ molar ratio in feed on chemical compositional distribution and other parameters such as molecular weight and its distribution. TREF analysis showed that the copolymers had a broad and bimodal chemical compositional distribution (CCD) regardless of the content of 1-butene in the copolymer. The chemical composition was in the range of 5 to 55 branches per 1,000 carbons for all copolymers prepared in the study. Furthermore, the broader CCD was revealed for the copolymers having the higher content of 1-butene. Crystaf analysis did not showed a bimodal CCD for the copolymers having the 1-butene content of less than 5.1 wt%. The lower crytalline part having 1-butene content in Crystaf analysis was less than of TREF analysis.