Jungmin Ha

Association of IL-17F Gene Polymorphisms With Renal Transplantation Outcome

OBJECTIVE Although interleukin 17 (IL-17) has some roles in renal transplantation, the influence of IL-17 gene single-nucleotide polymorphisms (SNPs) on renal transplantation has not been studied. METHODS The associations of 5 IL-17F gene SNPs (-1507G/A, 6329G/A, 7384A/G, 7470G/A, and 7489A/G) with renal transplantation outcome were analyzed. Polymerase chain reaction with sequence-specific primers (for -1507G/A and 6329G/A) and direct sequencing (for 7384A/G, 7470G/A, and 7489A/G) were performed on 282 renal transplantation recipients and 210 healthy controls. RESULTS IL-17F SNPs were not associated with acute rejection. Recipients with G allele on 7489A/G showed lower graft survival than recipients without G allele (P = .04). In multivariate analysis, G allele on 7489A/G was an independent risk factor for graft failure (odds ratio = 2.77, P = .03). CONCLUSION IL-17F gene SNP 7489A/G was associated with renal graft failure. Further studies are needed in larger number of patients.

Transcriptomic Profiling of Soybean in Response to High-Intensity UV-B Irradiation Reveals Stress Defense Signaling

The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B) intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants, including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.]) remain poorly understood. Here, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control), 0.5, and 6 h using RNA-seq analysis. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs) likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS) metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase) rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Our study provides valuable information for deep understanding of UV-B stress defense mechanisms and for the development of resistant soybean genotypes that survive under high-intensity UV-B stress.

The Effect of Recurrent Glomerulonephritis and Acute Rejection Episodes in Zero Human Leukocyte Antigen-Mismatched Kidney Transplantation

BACKGROUND Although human leukocyte antigen (HLA)-identical renal transplantation achieves superior graft outcomes, it does not uniformly allow indefinite graft survival. Recurrence of the original disease and effects of acute rejection episodes (ARE) may preclude indefinite survival. Herein, we have analyzed the factors that affect the graft outcomes among HLA zero-mismatch cases. METHODS We performed a retrospective, single-center study to evaluate the effect of recurrent glomerulonephritis (GN) and ARE on outcomes of grafts with zero HLA-mismatches (n = 122) versus three to four mismatches (n = 317), and five to six mismatches (n = 102). Forty-one percent of patients had GN as underlying disease. RESULTS Overall graft survival was 92.4% at 5 years and 79.6% at 10 years. HLA incompatibility did not affect graft survival: zero versus three to four versus five to six mismatches = 92.8% versus 90.8% versus 95.8% at 5 years and 82.5% versus 74.3% versus 85.1% at 10 years, respectively (P = .399). Subgroup analysis for subjects with GN revealed that ARE (P = .001) and recurrent GN (P = .003) were the risk factors for graft loss, whereas living donation was protective (P = .029). ARE was more prevalent with greater HLA incompatibility [0 (reference) < three to four < five to six mismatches; P = .047 and P = .014]. However, recurrent GN showed the opposite trend [0 (reference) > three to four > five to six mismatches; P = .106 and P = .022]. Furthermore, graft loss due to recurrent GN was significant among the HLA zero versus the three- to four-mismatch group (P = .047). CONCLUSIONS Graft survival was not affected by the degree of HLA incompatibility, which was mainly due to the recurrence of underlying disease. Therefore, a main focus should be the management of recurrence, especially among HLA-identical kidney transplantations.

Genome sequence of Jatropha curcas L., a non‐edible biodiesel plant, provides a resource to improve seed‐related traits

Summary Jatropha curcas (physic nut), a non‐edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up‐regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Transcriptomic Variation in Proanthocyanidin Biosynthesis Pathway Genes in Soybean (Glycine spp.)

BACKGROUND Proanthocyanidins are oligomeric or polymeric end products of flavonoid metabolic pathways starting with the central phenylpropanoid pathway. Although soybean (Glycine spp.) seeds represent a major source of nutrients for the human diet, as well as components for the cosmetics industry as a result of their high levels of flavonoid metabolites, including isoflavonoids, anthocyanins and proanthocyanidins, the genetic regulatory mechanisms underlying proanthocyanidin biosynthesis in soybean remain unclear. RESULTS We evaluated interspecific and intraspecific variability in flavonoid components in soybean using 43 cultivars, landraces and wild soybean accessions. We performed transcriptomic profiling of genes encoding enzymes involved in flavonoid biosynthesis using three soybean genotypes, Hwangkeum (elite cultivar), IT109098 (landrace) and IT182932 (wild accession), in seeds. We identified a Glycine max landrace, IT109098, with a proanthocyanidin content as high as that of wild soybean. Different homologous genes for anthocyanidin reductase, which is involved in proanthocyanidin biosynthesis, were detected as differentially expressed genes between IT109098 and IT182932 compared to Hwangkeum. CONCLUSION We detected major differences in the transcriptional levels of genes involved in the biosynthesis of proanthocyanidin and anthocyanin among genotypes beginning at the early stage of seed development. The results of the present study provide insights into the underlying genetic variation in proanthocyanidin biosynthesis among soybean genotypes.

Transcriptomic profiling of soybean in response to UV-B and Xanthomonas axonopodis treatment reveals shared gene components in stress defense pathways

Soybean (Glycine max [L.]) has evolved to survive under abiotic and biotic stress conditions by utilizing multiple signaling pathways. Although several studies have revealed shared defense signaling pathways in plants, the majority of components at the convergence points of signaling pathways triggered by both abiotic and biotic stress remain poorly understood. Here, we profiled the overall transcriptional responses of soybean to two different types of stress using the UV-B-resistant cultivar, Buseok, and the UV-B-sensitive cultivar, Cheongja 3, as well as two near isogenic lines carrying bacterial leaf pustule (BLP) disease-resistant and -susceptible alleles. We compared transcript abundance and identified genes that commonly respond to UV-B stress and BLP disease. In addition, we surveyed the co-localization of differentially expressed genes (DEGs) and their paralogs with abiotic and biotic stress-related quantitative trait loci (QTLs) on the soybean genome. Among 14 DEGs that respond to both stresses, five DEGs are involved in the jasmonic acid (JA) metabolic pathway, encoding Jasmonate ZIM (Zinc-finger protein expressed in Inflorescence Meristem) domain-containing protein 1 (JAZ 1), a negative regulator of JA signaling. Two DEGs for JAZ 1 were co-localized with biotic stress-related QTLs. One DEG encoding the stress-induced protein starvation-associated message 22 and its two paralogs were co-localized with both abiotic and biotic stress-related QTLs. The results of this study help elucidate general responses to abiotic and biotic stress in soybean, thereby helping breeders improve stress-resistant soybean cultivars.

Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity

MADS-box genes are involved in plant reproductive development. However, the role of gene nucleotide diversity in soybean flowering and maturity remains unknown. Therefore, in this study, the distribution of DNA polymorphisms in the putative MADS-box gene located near the quantitative trait loci (QTL) for flowering time and maturity was targeted for association analysis using Glycine max (cultivated soybean) and Glycine soja (wild soybean). Sixteen single nucleotide polymorphisms identified in the upstream region of the putative MADS-box gene around QTL Pod mat 13-7 and Fflr 4-2 on chromosome 7 were found to be highly associated with maturity in soybean. The genetic diversity between cultivated soybeans and the wild relative was comparable, although the early maturity group (EMG) was less diverse than the late maturity group (LMG) of the cultivated soybean. Population size changes of the MADS-box gene in this soybean germplasm appeared to result from non-random selection. A selective pressure seemed to act on this gene in the EMG, while the LMG and G. soja were in genetic equilibrium. Neutrality tests and the constructed neighbor-joining tree indicate that the EMG of G. max has experienced strong artificial selection for its domestication and genetic improvement.