• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.135-135
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• 2017

The Gramene database (http://www.gramene.org) is a powerful online resource for agricultural researchers, plant breeders and educators that provides easy access to reference data, visualizations and analytical tools for conducting cross-species comparisons. Learn the benefits of using Gramene to enrich your lectures, accelerate your research goals, and respond to your organismal community needs. Gramene's genomes portal hosts browsers for 44 complete reference genomes, including crops and model organisms, each displaying functional annotations, gene-trees with orthologous and paralogous gene classification, and whole-genome alignments. SNP and structural diversity data, available for 11 species, are displayed in the context of gene annotation, protein domains and functional consequences on transcript structure (e.g., missense variant). Browsers from multiple species can be viewed simultaneously with links to community-driven organismal databases. Thus, while hosting the underlying data for comparative studies, the portal also provides unified access to diverse plant community resources, and the ability for communities to upload and display private data sets in multiple standard formats. Our BioMart data mining interface enable complex queries and bulk download of sequence, annotation, homology and variation data. Gramene's pathway portal, the Plant Reactome, hosts over 240 pathways curated in rice and inferred in 66 additional plant species by orthology projection. Users may compare pathways across species, query and visualize curated expression data from EMBL-EBI's Expression Atlas in the context of pathways, analyze genome-scale expression data, and conduct pathway enrichment analysis. Our integrated search database and modern user interface leverage these diverse annotations to facilitate finding genes through selecting auto-suggested filters with interactive views of the results.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.12
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• pp.4915-4920
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• 2015

Background: : Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease mainly caused by mutations of the adenomatous polyposis coli (APC) gene with almost complete penetrance. These colorectal polyps are precancerous lesions that will inevitable develop into colorectal cancer at the median age of 40-year old if total proctocolectomy is not performed. So identification of APC germline mutations has great implications for genetic counseling and management of FAP patients. In this study, we screened APC germline mutations in Chinese FAP patients, in order to find novel mutations and the APC gene germline mutation characteristics of Chinese FAP patients. Materials and Methods: The FAP patients were diagnosed by clinical manifestations, family histories, endoscope and biopsy. Then patients peripheral blood samples were collected, afterwards, genomic DNA was extracted. The mutation analysis of the APC gene was conducted by direct polymerase chain reaction (PCR) sequencing for micromutations and multiplex ligation-dependent probe amplification (MLPA) for large duplications and/or deletions. Results: We found 6 micromutations out of 14 FAP pedigrees, while there were no large duplications and/or deletions found. These germline mutations are c.5432C>T(p. Ser1811Leu), two c.3926_3930delAAAAG (p.Glu1309AspfsX4), c.3921_3924delAAAA (p.Ile1307MetfsX13), c3184_3187delCAAA(p.Gln1061AspfsX59) and c4127_4126delAT (p.Tyr1376LysfsX9), respectively, and all deletion mutations resulted in a premature stop codon. At the same time, we found c.3921_3924delAAAA and two c.3926_3930delAAAAG are located in AAAAG short tandem repeats, c3184_3187delCAAA is located in the CAAA interrupted direct repeats, and c4127_4128 del AT is located in the 5'-CCTGAACA-3', 3'-ACAAGTCC-5 palindromes (inverted repeats) of the APC gene. Furthermore, deletion mutations are mostly located at condon 1309. Conclusions: Though there were no novel mutations found as the pathogenic gene of FAP in this study, we found nucleotide sequence containing short tandem repeats and palindromes (inverted repeats), especially the 5 bp base deletion at codon 1309, are mutations in high incidence area in APC gene,.

• The Journal of Korean Medicine
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• v.26 no.3 s.63
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• pp.27-42
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• 2005

Objectives : Alzheimer's disease (AD) is a progressive and fatal neurodegenerative disease characterized by amyloid plaques and neurofibrillary tangles. These plaques are associated with degenerating neuronal processes and consist primarily of fibrillary aggregates of beta-amyloid$ protein, generated from amyloid precursor protein (APP). Another amyloidogenic fragment, the carboxyl terminus (CT) of APP, which is composed of 99-105 amino acid residues containing the complete $A{\beta}$ sequence, also appears to be toxic to neurones. Recent evidence suggest that CT105, carboxy terminal 105 amino acids peptide fragment of APP, may be an important factor causing neurotoxicity in AD. Methods : Although a variety of oriental prescriptions including Pinelliae rhizoma have traditionally been utilized for the treatment of AD, their pharmacological effects and action mechanisms have not yet been fully elucidated. In the present study, we investigated effects of the dichloromethane extract of Pinelliae rhizoma (PINR) on neurotoxicity and the formation of reactive oxygen species (ROS) and nitric oxide (NO) in SK-N-SH cells overexpressed with CT105. In addition, we evaluated its radical scavenging activity and effects on acetylcholinesterase (AChE) activity. Furthermore, effects on cognitive deficits induced by scopolamine treatment in rats were evaluated. Results ; We found in this study that PINR significantly inhibited apoptotic neuronal death induced by CT105 overexpression in SK-N-SH cells. Based on morphological examinations by phase-contrast microscopy, PINR reversed apoptotic changes of CT105-expressed cells. It was also found that PINR significantly promoted neurite outgrowth and inhibited formation of ROS nd NO. PINR was shown to scavenge DPPH radicals and noncompetitively inhibit AChE activity. Furthermore, it reduced scopolamine-induced memory impairment in rata, assessed by passive avoidance test. Conclusions : Taken together, these results demonstrate that PINR exhibits neuroprotective, antioxidant, and memory enhancing effects, and therefore may bs beneficial for the treatment of AD.

• Korean Journal of Soil Science and Fertilizer
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• v.7 no.3
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• pp.127-135
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• 1974

The samples were taken from the following localities previously classified as "Akiochi" area: Yangpyung, Puchun, and Pyungtaik, all of Kyonggi-do province. Five soil profiles were described in the field, and taken to the laboratory for physical and chemical analysis and mineralogical analysis by X-ray diffraction. The predominant clay minerals consist mainly of illite, vermiculite, chlorites and intergrade with vermiculite, and kaolinite. Illite or mica was found present in all samples and in all horizons. This was identified by the 9.83 to $10{\AA}$ (0.01) and $3.32{\AA}$ (003) basal reflections, Interhorizontal variations in mineral content and crystallinity are illustrated in their respective Xray diffractogram. Comparing the peak intensity, of the $14{\AA}$, $10{\AA}$ and $7{\AA}$ indicated the degree of weathering from the surface to the lower horizons. In general, the weathering of illite on the surface produced less pronounced $10{\AA}$ and $14{\AA}$ peak as compared to the lower horizons. The same may be said with kaolinite. On K-saturation, the $14{\AA}$ peak broadening on the low angle side was observed. This is interpreted to be due to chlorization. Heat treament from $100^{\circ}C$, $200^{\circ}C$, $400^{\circ}C$, $600^{\circ}C$, and $800^{\circ}C$. caused significant changes in the different diffractograms. Heating caused collasped of the $14{\AA}$ to $10{\AA}$ and the appearance of scattered peaks between $10-14{\AA}$. This is interpreted to the presence of vermiculite chlorite intergradient. The complete collapse of the $14{\AA}$ at $800^{\circ}C$ to $10{\AA}$ with increased intensity was attributed to the preservce of vermiculite. The principal difference among the clay minerals in each horizon is the concomitant increase and decrease in intensity with depth of the $14{\AA}$, $10{\AA}$ and $7{\AA}$ diffraction spacings. Apparently the weathering of illite ($10{\AA}$) is resulting in the formation of vermiculite ($14{\AA}$) and the interstratified material being an intermediate stage and the beginning of the formation of vermiculite. Some broadening- in the 17 to $18{\AA}$ was observed in Puchun-1 Pyungtaik-1 and Pyungtaik-2 specially so in the lower horizon in the Ca or Mg-saturated sample. Heated treatment tend to shift this peak to $14{\AA}$ indicating the presence of regular layering of the interstratified complex. The high amount of extractable aluminum and iron coupled with low exchange capacity indicate that iron and aluminum plays an important role in the weathering of these soils and is responsible to the low exchange capacity, high acidity and high phosphate absorptive capacity. The results presented substantiated the weathering sequence of Jackson in that mica ${\rightarrow}$ vermiculite ${\rightarrow}$ chloritezed vermiculite ${\rightarrow}$ kaolinite.

• Journal of Plant Biotechnology
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• v.38 no.2
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• pp.125-129
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• 2011

Environmental risk assessment (RA) is essential prior to the environmental release of GM crops. RA, however, costs at least 7 to 15 million US dollars and requires several years to complete field tests. Therefore, it is strongly suggested that developers of GM crops must consider all criteria for RA at the beginning stage of the development if it aims for commercialization. Previous review papers have pointed out that the "death valley" for the commercialization of GM crops is the screening stage of early GM events since many candidates are given up due to insufficient data on the molecular characterization of a GM event such as inserted gene's copy number, position of inserted site of a chromosome, flanking sequence of recombinant T-DNA, rearrangement of chromosome, and knock out of endogenous gene of host plant. Recently, Rural Development Administration (RDA) in South Korea has launched a Grand National Project named as "Next Generation of BioGreen 21 Project" from 2011 to 2020 and research funding for the development of global GM crops has been allocated to accelerate the commercialization of GM crops. In this regard, I strongly suggest that researchers involved in the development of GM crops for commercialization must conduct RA by themselves at the screening stage of pre-GM event based on the data for molecular characterization.

• Journal of Life Science
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• v.23 no.1
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• pp.24-30
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• 2013

The purpose of this study was to identify genetic polymorphisms of the mitochondrial cytochrome b (mtDNA cyt b) gene in Korean black (KB) cattle breed and to analyze the genetic relationship between the KB and other breeds. We determined the complete sequence of the mtDNA cyt b gene in 38 KB cattle. We also analyzed their genetic diversity, and phylogenetic analysis was performed by comparison with Korean cattle (KC, called Hanwoo) and breeds from China and Japan. A nucleotide substitution was detected in the KB cattle, and two haplotypes were defined. In the neighbor-joining (NJ) tree, the haplotypes of KB were located in Bos taurus lineage with those of KC, Japanese black (JB), Yanbian and Zaosheng breeds. However, the haplotypes of Chinese breeds, excluding Yanbian and Zaosheng, were separated into B. taurus and B. indicus lineages. In the NJ tree of breeds based on Dxy genetic distances, Chinese breeds mixed with B. taurus and B. indicus lineages were located between B. indicus and B. taurus lineages. KB was contained within B. taurus lineage and was determined to be genetically more closely related to two Chinese (Yanbian and Zaosheng) breeds than to KC and JB. The haplotype distribution and the results of the phylogenetic analysis suggest that KB and KC have genetic differences in their mtDNA cyt b gene sequences.

• Clinical and Experimental Reproductive Medicine
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• v.26 no.1
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• pp.103-109
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• 1999

Objective: Heat shock protein 70-2 (Hsp70-2) gene knockout mice are found to have premeiotic arrest at the primary spermatocyte stage with a complete absence of spermatids and spermatozoa. This observation led to the hypothesis that hspA2 may be disrupted in human testes with abnormal spermatogenesis. To test this hypothesis, we studied the mRNA expression of hspA2 in infertile men with azoospermia. Design: The mRNA expression were analyzed by competitive RT-PCR among testes with normal spermatogenesis, pachytene spermatocyte arrest, and sertoli-cell only syndrome. Materials and methods: Testicular biopsy was performed in men with azoospermia (n=15). Specimens were subdivided into three groups: (group 1) normal spermatogenesis (n=5), (group 2) spermatocyte arrest (n=5), (group 3) Sertoli-cell only syndrome (n=5). Total RNA was extracted by Trizol reagent. Total extracted RNA was reverse transcribed into cDNA and amplified by PCR using specific primers for hspA2 target cDNAs. A competitive cDNA fragment was constructed by deleting a defined fragment from the target cDNA sequence, and then coamplified with the target cDNA for competitive PCR. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as an internal control. Results: On Competitive RT-PCR analyses for hspA2 mRNA, significant amount of hspA2 expression was observed in group 1, whereas a constitutively low level of hspA2 was expressed in groups 2 and 3. Conclusion(s): The study demonstrates that the hspA2 gene expression is down-regulated in human testes with abnormal spermatogenesis, which in turn suggests that hspA2 gene may play a specific role during meiosis in human testes.

• Journal of Life Science
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• v.22 no.10
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• pp.1428-1433
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• 2012

Longevity is an exciting but difficult subject to study because it is determined by complex processes that require the coordinated action of several genetic factors as well as physiological and environmental influences. Genetic approaches have been applied to animal models to identify the molecular mechanism responsible for longevity. Several experimental model organisms obtained over the last decades suggest that the complete deletion of a single gene by gene targeting has proven to be an invaluable tool for the discovery of the mechanisms underlying longevity. The first discovery of long-lived mutants came from Caenorhabditis elegans research, which identified the insulin/IGF-1 pathway as responsible for longevity in this worm. IGF-1 is a multifunctional polypeptide that has sequence similarity to insulin and is involved in normal growth and development of cells. Several factors in the IGF-1 system have since been studied by gene targeting in the control of longevity in lower species, including nematode and fruit fly. In addition, significant progress has been made using mice models to extend the lifespan by targeted mutations that interfere with growth hormone/IGF-1 and IGF-1 signaling cascades. A recent finding that IGF-1 is involved in aging in mice was achieved by using liver-specific knockout mutant mice, and this clearly demonstrated that the IGF-1 signal pathway can extend the lifespan in both invertebrates and vertebrate models. Although the underlying molecular mechanisms for the control of longevity are not fully understood, it is widely accepted that reduced IGF-1 signaling plays an important role in the control of aging and longevity. Several genes involved in the IGF-1 signaling system are reviewed in relation to longevity in genetically modified mice models.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.536-557
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• 2020

Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.

• Korean Journal of Microbiology
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• v.41 no.4
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• pp.246-254
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• 2005

Analysis of the complete genome of Neurospora crassa reveals that at least 19 proteins contain tetratricopeptide repeat (TPR) motifs. One of them shows over $60\%$ homology to Ssn6 of Saccharomyces cerevisiae, a universal repressor that mediates repression of genes involved in various cellular processes. Mutant strains generated by RIP (repeat-induced point mutation) process showed four distinctive vegetative growth patterns and slow growth in various rates. Firstly, a mutant showed denser mycelial growth, yellow, csp, and looked like ropy mutant. Secondly, slower growth, dense mycelial, and conidial phenotype. Thirdly, extremely slower growth and aconidial. And finally, flat, tittle aerial hyphae, acon, and similar with a rco-1 RIP mutant. They are all male-fertile, yet female-sterile and produced little or no perithecium. It seems that various phenotypes were occurred depending upon mostly likely, the degree of RIP. These results indicate that this gene may be involved in several cellular possess during vegetative growth, and asexual and sexual development. Therefore it is pleiotropic. Sequence analysis of cDNA shows that it encodes a putative 102 kDa protein composed of 917 amino acids, and has six introns. It is designated rcm-1 (regulation of conidiation and morphology).