Characterization of transcription factor genes related to cold tolerance in Brassica napus

Brassica napus is the third most important oilseed crop in the world; however, in Korea, it is greatly affected by cold stress, limiting seed growth and production. Plants have developed specific stress responses that are generally divided into three categories: cold-stress signaling, transcriptional/post-transcriptional regulation, and stress-response mechanisms. Large numbers of functional and regulatory proteins are involved in these processes when triggered by cold stress. Here, our objective was to investigate the different genetic factors involved in the cold-stress responses of B. napus. Consequently, we treated the Korean B. napus cultivar Naehan at the 4-week stage in cold chambers under different conditions, and RNA and cDNA were obtained. An in silico analysis included 80 cold-responsive genes downloaded from the National Center for Biotechnology Information (NCBI) database. Expression levels were assessed by reverse transcription polymerase chain reaction, and 14 cold-triggered genes were identified under cold-stress conditions. The most significant genes encoded zinc-finger proteins (33.7%), followed by MYB transcription factors (7.5%). In the future, we will select genes appropriate for improving the cold tolerance of B. napus.

Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean)

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.

Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean)

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.

RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves, and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.

Analysis of Urolithiasis / 대한비뇨기과학회지

The problem of urolithiasis remains unsolved despite a vast amount of clinical observation and experimental research. But the accurate analysis of urinary stone is fundamental for study of the etiology of stone formation and essential for treatment of urinary stone and its prevention. A retrospective review of stone analysis was performed by special analytic facilities, Louis C. Herring and Company, which was certified by many urologists in worldwide. The stones were obtained from the patients visited our hospital during the period from September, 1987 to July, 1992. And the following results were obtained. 1. The male to female ratio was approximately 1.9:1, and 76.7% of patients of urinary calculi were distributed in 30 to 60 years old. 2. The location of urinary calculi were ureter 57.5%, kidney 35.2%, bladder 4.2% and urethra 3.1%. 3. Among the all components analyzed in this study, calcium oxalate monohydrate was the most common constituents, comprising 84.5% of the total. And the calcium oxalate dihydrate and calcium phosphate were the second common constituents, comprising 72.5 %. 4. Calculi of mixed component, comprising 86.5 %, was more common than those of single component, comprising 13.5%. Calcium oxalate monohydrate was the most common component in both pure and mixed stone. 5. Reclassifying authors' result according to the main group for comparison with previous other results, authors' result was different form those of western, but similar with middle and far eastern results.

A Case of Renal Cell Carcinoma in Children / 대한비뇨기과학회지

Renal cell carcinoma in children has been considered as a rare clinical disease entity. A case of right renal cell carcinoma in a 13-year-old boy is presented with a brief review of literature.

Detection of Mycobacterium tuberculosis in Urine by Nested Polymerase Chain Reaction / 대한비뇨기과학회지

Today, genitourinary tuberculosis as well as tuberculosis of other organs have decreased in its incidence with development of antituberculosis drugs. However, it is still very frequent in Korea. There are still great deal of difficulties in finding Mycobacterium tuberculosis from urine because of variations in method of taking urine sample and techniques of examination. For these matters, early diagnosis was difficult indeed. For this reason, we performed amplification of Mycobacterial DNA from urine by use of the Polymerase Chain Reaction, and urine AFB smear from Apr., 1993 to Feb., 1994 and achieved following results. l. In order to increase sensitivity and specificity, we performed nest PCR. and primers used each cases were a) INS1 and INS2, which amplify 245-base pair sized DNA, b) Pt3 and Pt6, which amplify 188-base pair. The sequences of primers were INS1 (5'-CGTGAGGGCATCGAGGTGGC-3'), INS2 (5'- GCGTAGGCGTCGGTGACAAA-3'), Pt3(5'-GAACGGCTGATGACCAAACT-3'), and Pt6( 5'-ACGTAGGCGAACCCTGCCCA-3') (Table l). And after 30 cycles of amplification, unique Mycobacterium tuberculosis DNA band was found ( Figure). 2. Total number of confirmed genitourinary tuberculosis were 35 cases, 19 cases were positive in both PCR and AFB smear, other 15 cases were positive only in PCR and in one case, PCR was negative but positive in AFB smear (Table 2).