• BMB Reports
• /
• v.56 no.12
• /
• pp.633-644
• /
• 2023

Epigenetic mechanisms, primarily mediated through histone and DNA modifications, play a pivotal role in orchestrating the functional identity of a cell and its response to environmental cues. Similarly, the spatial arrangement of chromatin within the three-dimensional (3D) nucleus has been recognized as a significant factor influencing genomic function. Investigating the relationship between epigenetic regulation and 3D chromatin structure has revealed correlation and causality between these processes, from the global alignment of average chromatin structure with chromatin marks to the nuanced correlations at smaller scales. This review aims to dissect the biological significance and the interplay between the epigenome and 3D chromatin structure, while also exploring the underlying molecular mechanisms. By synthesizing insights from both experimental and modeling perspectives, we seek to provide a comprehensive understanding of cellular functions.

• The Bulletin of The Korean Astronomical Society
• /
• v.39 no.2
• /
• pp.55.2-55.2
• /
• 2014

Role of environments is one of today's most widely discussed and debated topic in the field of extra-galactic astronomy. Extreme morphology-density relations found in low-mass galaxies are considered to be the result of an effective role played by environment in the evolution of these galaxies. I will present the results from our dedicated study of early-type dwarf galaxies (dEs) in different environments using imaging and spectroscopic data. We find that Virgo cluster dEs have a variety of structural and kinematic properties. A significant fraction of dEs possesses disk features, such as spiral arm and bar, while a central nucleus seems to be universal in these low mass galaxies. We also find that a majority of dEs are fast rotator and their rotation curves are much steeper than that of spiral galaxies of similar mass. Finally I will discuss how the different environmental mechanisms, i.e., gas-stripping or tidal interaction, can contribute to form heterogeneous dEs in Virgo cluster.

• Applied Microscopy
• /
• v.15 no.1
• /
• pp.31-58
• /
• 1985

The morphological study on different types of cells of reproductive organ including spermatogenesis in the adult planaria was performed to observe their cytochemical and ultrastructural characteristics. 1. Spermatogenesis The circular luminated material appears immediately inside the nuclear envelope of early spermatid and is found also in the nucleus of sperm, but typical acrosomal structures cannot be observed. Approximately ten of small-sized mitochondria occur around the nucleus in the transitional phase from primary spermatocyte to secondary spermatocyte, but in sperm a long mitochondrion is closely associated with nucleus, parellel to long axis of it. The sperm has a relatively long head connected with two tails via hollow neck. 2. Reproductive organ The penis bulb and the bursa stalk were observed. (1) Penis bulb The cells constituted penis bulb are classified into six types on the basis of ultrastructure of the cells and cytochemistry of the cytoplasmic granules. 1) A-type cells: These cells exhibiting low electron density are mainly occupied by large nucleus. These cells possess two different types of granules: highly electron-dense round granules with an average size of $0.9{\mu}m$, and electron-dense granules exhibit PAS-positive reaction. 2) B-type cells contain PAS-positive granules with the size of about $0.4{\mu}m$. They are rich in free ribosomes and mitochondria. 3) C-type cells are found to be dark cells due to high electron-density. These cells are largely occupied by large nucleus. 4) D-type cells: These cells are seen as light cells which have poorly developed cell organelles. 5) E-type tells: These cells contain a large number of glycogen granules which occupy most of cell. 6) F-type cells: These arc parietal epidermal cells surrounding the genital antrum. These cells are characterized by their finger-like shapes and the presence of a number of electron-dense, irregularly-shaped structures inside cells. The relatively large electron-lucent granules can be also found. The F-type cells possess numerous microvilli on their free surfaces. (2) Bursa stalk The cells constituted bursa stalk are classified into 3 types on the basis of cell shapes and presences of electron-dense or electron-lucent granules. 7) G-type cells with a long cytoplasmic process. They have large nuclei and poorly developed cell organelles. 8) H-type cells: These cells are characterized by the presence of a long cytoplasmic process and relatively highly electron-dense cytoplasmic profile. They have poorly developed cell organelles. 9) I-type cells contain large electron-lucent granules which exhibit negative reactions with three kinds of cytochemical staining methods used in this experiment. The fine electron-dense structures can be found inside these granules.

• Proceedings of the KOSOMBE Conference
• /
• v.1998 no.11
• /
• pp.57-59
• /
• 1998

For medical students and doctors, knowledge of the three-dimensional (3D) structure of brain is very important in diagnosis and treatment of brain diseases. Two-dimensional (2D) tools (ex: anatomy book) or traditional 3D tools (ex: plastic model) are not sufficient to understand the complex structures of the brain. However, it is not always guaranteed to dissect the brain of cadaver when it is necessary. To overcome this problem, the virtual dissection programs of the brain have been developed. However, most programs include only 2D images that do not permit free dissection and free rotation. Many programs are made of radiographs that are not as realistic as sectioned cadaver because radiographs do not reveal true color and have limited resolution. It is also necessary to make the virtual dissection programs of each race and ethnic group. We attempted to make a virtual dissection program using a 3D image of the brain from a Korean cadaver. The purpose of this study is to present an educational tool for those interested in the anatomy of the brain. The procedures to make this program were as follows. A brain extracted from a 58-years old male Korean cadaver was embedded with gelatin solution, and serially sectioned into 1.4 mm-thickness using a meat slicer. 130 sectioned specimens were inputted to the computer using a scanner ($420\times456$ resolution, true color), and the 2D images were aligned on the alignment program composed using IDL language. Outlines of the brain components (cerebrum, cerebellum, brain stem, lentiform nucleus, caudate nucleus, thalamus, optic nerve, fornix, cerebral artery, and ventricle) were manually drawn from the 2D images on the CorelDRAW program. Multimedia data, including text and voice comments, were inputted to help the user to learn about the brain components. 3D images of the brain were reconstructed through the volume-based rendering of the 2D images. Using the 3D image of the brain as the main feature, virtual dissection program was composed using IDL language. Various dissection functions, such as dissecting 3D image of the brain at free angle to show its plane, presenting multimedia data of brain components, and rotating 3D image of the whole brain or selected brain components at free angle were established. This virtual dissection program is expected to become more advanced, and to be used widely through Internet or CD-title as an educational tool for medical students and doctors.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.21 no.1
• /
• pp.117-125
• /
• 2010

The tropical tasar silkworms, Antheraea mylitta (D) produce famous silk 'Kosa' in central part of India. Due to outdoor rearing it became susceptible to viral infection including cytoplasmic polyhedrosis virus (CPV). The common mode of entry of cytoplasmic polyhedrosis virus is per os and cause gresserie disease to the larvae. Histopathological studies elucidated the insect CPV virus produces infective polyhedral inclusion bodies (PIBs) in the midgut cell cytoplasm of virus infected fifth instar larvae. The PIBs multiply enormously in the cytoplasm without invading the nucleus. Ultrastructural studies confirmed the pathological effects of CPV on in midgut cell cytoplasm. The multiplication of polyhedral inclusion bodies took place into the vacuoles and form virogenic stromata in the cytoplasm of cells. However, the encapsulations of polyhedral inclusion bodies into the polyhedrin protein occurred and polyhedra were released into the lumen. At the late stage of infection, cells showed the regressed cytoplasmic organelles with large vacuoles and elongated mitochondria. Hence, the horizontal transmission of CPV causing the midgut cells disintegration in the tasar silkworm, Antheraea mylitta (D) confirmed during infection.

• BMB Reports
• /
• v.54 no.5
• /
• pp.233-245
• /
• 2021

In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.

• Molecules and Cells
• /
• v.38 no.5
• /
• pp.402-408
• /
• 2015

Protein O-GlcNAcylation, dictated by cellular UDP-N-acetylglucosamine (UDP-GlcNAc) levels, plays a crucial role in posttranslational modifications. The enzyme GlcNAc kinase (NAGK, E.C. 2.7.1.59) catalyzes the formation of GlcNAc-6-phosphate, which is a major substrate for the biosynthesis of UDP-GlcNAc. Recent studies have revealed the expression of NAGK in different types of cells especially in neuronal dendrites. Here, by immunocytochemistry (ICC) and immunonucleochemistry (INC) of cultured rat hippocampal neurons, HEK293T and GT1-7 cells, we have showed that NAGK immuno-reactive punctae being present in the nucleoplasm colocalized with small nuclear ribonucleoprotein-associated protein N (snRNPN) and p54NRB, which are speckle and paraspeckle markers, respectively. Furthermore, NAGK IR cluster was also found to be colocalized with GTF2H5 (general transcription factor IIH, polypeptide 5) immuno reactive punctae. In addition, relative localization to the ring of nuclear lamin matrix and to GlcNAc, which is highly enriched in nuclear pore complexes, showed that NAGK surrounds the nucleus at the cytoplasmic face of the nuclear outer membrane. By in situ proximity ligation assay (PLA) we confirmed the colocalization of NAGK with snRNPN in the nucleus and in dendrites, while we also verified the interactions of NAGK with p54NRB, and with GTF2H5 in the nucleus. These associations between NAGK with speckle, paraspeckle and general transcription factor suggest its regulatory roles in gene expression.

• Applied Microscopy
• /
• v.15 no.2
• /
• pp.10-18
• /
• 1985

The posterior hypothalamus of the hibernating greater horseshoe bats (Rhinolophus ferrumequinum korai Kuroda) were observed with an electron microscope. The posterior hypothalamus is known to be closely related to the reflex responses activated by cold, and the following observations were obtained in the cellular type of nerve cells: there are three types of neurons in the posterior hypothalamus. 1. The first type of neuron was the largest, ovoid or conical in shape, the nucleus was elliptic and the nuclear envelope had many deep invaginations. The cell organelles were well developed, in particular there was an abundance of variously shaped mitochondria, and the Golgi complex and the polysomes were observed in the cytoplasm. 2. The second type of neuron was moderate in size, ovoid or elliptic in shape, the nucleus was located nearer to the plasma membrane and the nuclear envelope had. a few invaginations. The cytoplasm was rich in amount compared with that of the third type of neuron, and the cell organelles, especially the rough endoplasmic reticulum were well developed. Also lipofuscin pigments were observed. 3. The third type of neuron was the smallest in size and round in shape. The nucleus and the nucleolus were observed in the central portion of the cell body and the nuclear envelope had a few invaginations. The cytoplasm was small compared with those of the first and second types, but the rough endoplasmic reticulum, the mitechondria and the polysomes were relatively well developed. The cytoplasm was characterized by the presence of membrane-bound small bodies with a single membrane containing a fine particular substance around the rough endoplasmic reticulum and the Golgi complexes.

• Journal of Biomedical Engineering Research
• /
• v.5 no.2
• /
• pp.111-120
• /
• 1984

A new restoration method of chest X-ray image (dual project filter) was proposed to improve SNR (signal to noise ratio) characteristics. In this method, a priori information of system and anatomical structure and statistics of projected object are used in the design of filter. Dual projection filter varies its parameters, adapting to the local regions of chest(lungregion, mediasternum, subdiaphragm) and the structure of chest (bone, tissue, blood vessel, bronchia). The performance of Dual Projection Filter was 0.1-0.2dB better than Dual Sensor Wiener Filter, which was used for initial estimate of Dual Porjection Filter.

• Bulletin of the Korean Chemical Society
• /
• v.17 no.1
• /
• pp.69-72
• /
• 1996

The NMR dipolar shift in tetrahedral and tetragonally-distorted tetrahedral complexes for Cu(Ⅱ) has been calculated adopting nonmultipole expansion method. The exact solution of ΔB/B(ppm) is exactly in agreement with multipolar results when R, the distance between the paramagnetic ion and the nucleus, is larger than 0.2 nm. The major contribution to the dipolar shift arises from 1/R3 term but the other terms, 1/R5 and 1/R7, contribute significantly to the pseudocontact shift when R is shorter than 0.5 nm. The shift is mainly due to the 3d orbitals and sensitive to distortion parameters at short range of R.