Sangwook Park

Applying Machine Learning Techniques to Analysis of Gene Expression Data: Cancer Diagnosis

Classification of patient samples is a crucial aspect of cancer diagnosis. DNA hybridization arrays simultaneously measure the expression levels of thousands of genes and it has been suggested that gene expression may provide the additional information needed to improve cancer classification and diagnosis. This paper presents methods for analyzing gene expression data to classify cancer types. Machine learning techniques, such as Bayesian networks, neural trees, and radial basis function (RBF) networks, are used for the analysis of the CAMDA Data Set 2. These techniques have their own properties including the ability of finding important genes for cancer classification, revealing relationships among genes, and classifying cancer. This paper reports on comparative evaluation of the experimental results of these methods.

Glial expression of the 90-kDa heat shock protein (HSP90) and the 94-kDa glucose-regulated protein (GRP94) following an excitotoxic lesion in the mouse hippocampus

Heat shock proteins (HSPs) are immediately expressed in neuronal and glial cells under various stressful conditions and play a protective role through molecular chaperones. Although several studies have been focused on the expression of HSPs, little is known about HSP90s expression in glial cells under neuropathological conditions. In this study, we evaluated the expression pattern of the glial cell‐related HSP90 and GRP94 proteins, following the induction of an excitotoxic lesion in the mouse brain. Adult mice received an intracerebroventricular injection of kainic acid; the brain tissue was then analyzed immunohistochemically for HSPs and double labeling using glial markers. HSPs expression was quantified by Western blot analysis. Excitotoxic damage was found to cause pyramidal cell degeneration in the CA3 region of the hippocampus. In the injured hippocampus, reactive microglia/macrophages expressed HSP90 from 12 h until 7 days postlesion (PL), showing maximal levels at day 1. In parallel, hippocampal reactive astrocytes showed the expression of GRP94 from 12 h until 7 days PL. In general, HSPs expression was transient, peaked at 1–3 days PL and reached basal levels by day 7. For the first time, our data demonstrate the injury‐induced expression of HSP90 and GRP94 in glial cells, which may contribute to the mechanism of glial cell protection and adaptation in response to damage, thereby playing an important role in the evolution of the glial response and the excitotoxic lesion outcome. HSP90 may provide antioxidant protective mechanisms against microglia/macrophages, whereas GRP94 may stabilize the astroglial cytoskeleton and participate in astroglial antioxidant mechanisms.

Glial expression of interleukin-18 and its receptor after excitotoxic damage in the mouse hippocampus.

Interleukin (IL)-18, a member of the IL-1 cytokine family, is an important mediator of peripheral inflammation and host defence responses. However, although IL-1 is a key proinflammatory cytokine in the brain, little is known about IL-18 changes in glial cells under excitotoxic neurodegeneration. In this study, we characterized the expressions of IL-18 and IL-18 receptor (IL-18R) in kainic acid (KA)-induced excitotoxicity in mouse hippocampus by immunohistochemistry and Western blotting. IL-18 immunoreactivity was found in microglia whereas IL-18R immunoreactivity was observed in astrocytes. Levels of IL-18 and IL-18R in hippocampus homogenates increased progressively from day 1 post-KA and peaked at 3xa0days. This study demonstrates the cellular sources of IL-18 and IL-18R, and their temporal correlations after KA-insult, and suggests roles for IL-18 and IL-18R in glial cells in response to excitotoxic damage in the hippocampus.

Oligodendroglia in the avian retina: immunocytochemical demonstration in the adult bird.

Immunohistochemical techniques were used in conjunction with an avian‐specific probe for oligodendrocyte (OLG) marker, the antibody for transferrin binding protein (TfBP), to study the characteristics and distribution of OLGs in the retina of chickens and quails. For comparison, other antibodies such as myelin basic protein, Rip, and those for labeling Müller cells and microglia were used. A large population of OLGs was found to be distributed throughout the retina, with the distinct pattern of a central‐to‐peripheral gradient. It was possible to detect a spectrum of OLG morphology that bore a resemblance to the subtype of the mammalian central nervous system. In addition to these mature OLGs, limited numbers of TfBP‐positive (TfBP+) cells with the morphology of immature OLGs were found in the immediate vicinity of the optic head. The majority of OLGs appeared in the ganglion cell layer throughout the retina, whereas OLGs in the nerve fiber layer were seen mainly in the central zone of the retina, near the optic nerve head. Double‐labeling experiments showed that OLGs were associated with myelin only in the central region, where the majority of retinal OLGs occurred, but not toward the periphery of the retina. The present study is the first comprehensive analysis of the morphological features and spatial distribution of OLGs in the adult avian retina and provides in vivo evidence for the existence of a substantial population of both mature and immature OLGs in the retina of adult birds. The putative functions of TfBP+ OLGs including myelination and the tropic role of the ganglion cells are discussed in conjunction with the physical properties of TfBP and structural characteristics of the avascular retina of birds. J. Neurosci. Res. 65:173–183, 2001.

Microglial responses in the avascular quail retina following transection of the optic nerve.

This study was undertaken to investigate microglial responses in the avascular central nervous system using the quail retina that is known to be devoid of blood vessels. Following intraorbital optic nerve transection (ONT), the quail retina was examined immunohistochemically at various times up to 6 months. A few days after transection, microglia in the inner retinal layers revealed features of activation. Activated cells displayed an amoeboid shape and enhanced QH1-immunoreactivity. The numbers of these amoeboid cells were rapidly increased, first in the inner plexiform layer (IPL), and then in the ganglion cell/nerve fiber layer (GCL/NFL) of the retina where retrograde degenerating ganglion cell processes and perikarya were located. By 6 months after transection, microglia regained their resting morphology, and their cell counts returned to control levels. At early time points of microglial activation, numerous QH1+ amoeboid cells were observed along the vitreal surface of the pecten and retinal region adjacent to the insertion of the pecten, where some amoeboid cells were attached underneath the internal limiting membrane, and appeared to squeeze through the optic nerve fiber bundles. A considerable number of these amoeboid cells in the GCL/NFL and the IPL were labeled with PCNA, suggesting that active exogenous migration (from the pecten) and in situ proliferation of precursor cells contribute to the increase in microglial population of the degenerating retina. On the other hand, TUNEL-positive microglia appeared in the GCL/NFL at later time points indicate that the decrease of microglial numbers is in part due to apoptosis in these layers. Although some aspects of microglial activation in the avascular retina appear unique, their consequences were similar to those described in vascular retinae of mammals, a finding indicates that blood vessels are not a prerequisite for microglial activation, and microglial precursors could migrate long distance to reach the lesioned site, which is not accessible via blood vessels. Our data provide the first analysis of microglial activation in the avascular central nervous system (CNS), and suggest that the quail retina is a useful model for studies of microglial behavior in CNS.

Development and characterization of 15 microsatellite loci from Lycorma delicatula (Hemiptera: Fulgoridae)

Abstract Lycorma delicatula (White 1845), which has been recently introduced into Korea, is a notorious pest on grapes. This invasive insect has rapidly spread throughout central and southern Korea. To date, we have no behavioral or population genetics information, such as invasion routes and subsequent dispersal rates in Korea, to help understand and control populations of L. delicatula. Here, we have developed 15 novel microsatellite loci for L. delicatula. The isolated loci were polymorphic, with 2 to 19 alleles in 42 individuals from a single population in Korea. The analyses revealed that all 42 individuals had different multilocus genotypes with heterozygosity ranging from 0.214 to 0.866. Eleven of the 15 loci did not deviate significantly from Hardy–Weinberg equilibrium. The isolated markers will facilitate population genetic studies of L. delicatula.

The multiple dorsoventral origins and migratory pathway of tectal oligodendrocytes in the developing chick

Oligodendrocytes have been considered to originate in a restricted ventricular zone of the ventral neural tube and to migrate and mature in their final targets. However, recent studies indicate that oligodendrocytes arise from multiple distinct dorsoventral origins. In this study, we investigate oligodendrocyte lineage cells in the embryonic optic tectum of chick, which develops from the dorsal region of the neural tube and invasion of optic tract. Oligodendrocyte precursor cells (OPCs) first appeared bilaterally on either side of the floor plate at E5. With further development, OPCs increased and spread laterally and dorsally to populate the optic tectum. At E7, OPCs appeared in another site along the ventral midline of the third ventricle, just dorsal to the optic chiasm. To examine the migration routes of these ventrally derived OPCs, we used DiI tracing in the organic culture and retinal denervation. Our results reveal that OPCs dispersed bilaterally along the optic tract and then migrated to the optic tectum in the stratum opticum (SO). In addition to these extrinsic OPCs, OPCs intrinsic to the tectal ventricle zone were identified at E14 using a combination of immunohistochemistry and retroviral mediated lineage tracing studies. These data support stage-specific dorsoventral origins and distribution of oligodendrocytes populating the optic tectum.

Developmental Expression of Transferrin Binding Protein in Oligodendrocyte Lineage Cells of the Embryonic Chick Spinal Cord

Oligodendrocytes develop from precursor cells in the neuroepithelium of the ventral ventricular zone. Oligodendrocytes in the different stages of development are characterized by expression of a number of different marker molecules such as myelin genes, growth factors, and specific antigens. We have previously identified that transferrin binding protein (TfBP), a member of heat shock protein 90 families, is a novel avian ER-associated membrane protein that is specifically localized in oligodendrocytes in adult chicken CNS. In this study we describe the developmental expression of TfBP in the embryonic chick spinal cord. A few, distinct, TfBP+ cells appeared at the lateral margin of the subventricular neuroepithelium of the spinal cord at E7. Thereafter, some TfBP+ cells, exhibited a migrative form of unipolar or bipolar shape occurred around E8 in the mantle layer, midway between the neuroepithelium and the marginal layer of the primitive spinal cord. Thereafter, the TfBP+ cells rapidly increased in number as well as their staining intensity, and overall distribution of TfBP+ cells at E15 was comparable to that of a mature spinal cord. Our observations suggest that TfBP is expressed in the subpopulation of oligodednrcyte lineage in the development and a putative role of TfBP in relation to transferrin and iron trafficking is considered.

A new species, Hemicrepidius ( Miwacrepidius ) rubriventris sp. nov. (Coleoptera, Elateridae, Denticollinae) from Republic of Korea

The subgenus Miwacrepidius of the genus Hemicrepidius is represented by a monotypic species, H. (M.) subcyaneus (Motschulsky 1866) from Japan, and no other congener of the subgenus has been known until now. However, three female specimens of a novel species belonging to this subgenus were recently collected from the Republic of Korea. To delimitate the species boundary of the new species compared with the monotypic species, H. (M.) subcyaneus, we attempted an integrative taxonomy based on both morphological and DNA barcoding approaches. An examination of the results revealed ten diagnostic characteristics and large genetic distances, ranging from 8.40%, between these two species; therefore, we herein describe and illustrate the new species, Hemicrepidius (Miwacrepidius) rubriventris sp. nov., based on female types.xa0

Checklist of the Family Platypodidae (Coleoptera) in Korea

Abstract As a result of the survey of pinhole borers in Korea, one species, Treptoplatypus severini Blandford, was identified as a new addition to the Korean fauna. We observed 3 species, Platypus koryoensis, P. lewisi, and Treptoplatypus severini and could not examined Korean specimens of 3 previously recorded species, Crossotarsus simplex, Dinoplatypus calamus, Treptoplatypus solidus. We compared the external characteristics of male specimens of several species for the easy identification of the Korean Platypodidae, and updated the taxonomic position of the Korean species.