Jeong-An Gim

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator–prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator–prey relationships in complex freshwater ecosystems.

The novel MER transposon-derived miRNAs in human genome.

MicroRNAs (miRNAs) are small RNA molecules (~20-30 nucleotides) that generally act in gene silencing and translational repression through the RNA interference pathway. They generally originate from intergenic genomic regions, but some are found in genomic regions that have been characterized such as introns, exons, and transposable elements (TE). To identify the miRNAs that are derived from palindromic MERs, we analyzed MER paralogs in human genome. The structures of the palindromic MERs were similar to the hairpin structure of miRNA in humans. Three miRNAs derived from MER96 located on chromosome 3, and MER91C paralogs located on chromosome 8 and chromosome 17 were identified in HeLa, HCT116, and HEK293 cell lines. The interactions between these MER-derived miRNAs and AGO1, AGO2, and AGO3 proteins were validated by immunoprecipitation assays. The data suggest that miRNAs derived from transposable elements could widely affect various target genes in the human genome.

Genome-Wide Identification and Classification of MicroRNAs Derived from Repetitive Elements

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

Genome-wide analysis of DNA methylation patterns in horse

BackgroundDNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.ResultsWe report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.ConclusionsWe provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

MicroRNA-124 regulates glucocorticoid sensitivity by targeting phosphodiesterase 4B in diffuse large B cell lymphoma

Glucocorticoids (GCs) are chemotherapeutic drugs commonly used to treat hematological malignancies. However, a significant fraction of patients develop resistance to GCs during treatment. A better insight into how GC resistance develops is therefore needed. It was previously shown that cyclic AMP (cAMP) induces sensitivity to GCs by inhibiting the AKT/mTOR/MCL1 signaling, while high levels of phosphodiesterase 4B (PDE4B) reverse the effect of cAMP on GC responses in B-cell lymphoma. Here, we show that miR-124 influences GC-induced apoptosis by directly targeting PDE4B. Stable expression of miR-124 in diffuse large B cell lymphoma (DLBCL) cell lines diminished PDE4B expression. This was associated with increased cAMP levels, inhibition of the AKT/mTOR/MCL1 survival pathway, upregulation of GRα expression, and improved sensitivity to GCs in the presence of forskolin, an activator of adenylyl cyclase. Interestingly, miR-124 did not affect GC sensitivity in the absence of forskolin, indicating that the effect of this miRNA is accomplished via downregulation of PDE4B expression. Further, restoration of PDE4B expression in miR-124 cells rescued the phenotypic effect of this miRNA, demonstrating the critical role of PDE4B in miR-124-mediated regulation of the GC response. Our study supports the notion that miR-124 could be an attractive therapeutic target for overcoming GC resistance in DLBCL.

Integrated late onset Alzheimer's disease (LOAD) susceptibility genes: Cholesterol metabolism and trafficking perspectives

Late onset Alzheimers disease (LOAD) is the most common type of dementia and is characterized by decreased amyloid-β (Aβ) clearance from the brain. Cholesterol regulates the production and clearance of Aβ. Genome-wide association study (GWAS) suggests that at least 20 genes are associated with LOAD. The genes APOE, CLU, SORL1, PICALM, and BIN1 have a relatively high LOAD susceptibility. Additional experimental and bioinformatic approaches to integrate data from genetics, epigenetics, and molecular networks may further increase our understanding of LOAD in relation to cholesterol metabolism and trafficking.

Genome-Wide Analysis of DNA Methylation before-and after Exercise in the Thoroughbred Horse with MeDIP-Seq

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.

Search of optimal locations for species- or group-specific primer design in DNA sequences: Non-dominated Sorting Genetic Algorithm II (NSGA-II)

Abstract In this study, we applied Non-dominated Sorting Genetic Algorithm II (NSGA-II) to the problem of identifying appropriate locations in cytochrome oxidase I (COI) gene for species- or group-specific primer design. As concerns about ecological management grow, quantification of predator-prey interaction has become a central issue in ecology. Recently, improved techniques have allowed for the extensive use of genomic DNA barcoding for qualitative analysis. However, quantification of DNA barcoding results is important and still needs to be resolved. Even though species- or group-specific primers that can be used for samples containing multiple species are difficult to design, species- or group-specific primers are a practical solution for quantification in the current era. To resolve this issue, we present here an efficient method for discovering the regions of a DNA sequence that have the highest inter-species variability by applying the NSGA-II algorithm. DNA sequence information for the COI gene region was obtained for 24 species from Jo et al. (2014). These sequences were transformed into binary data, either 0 (not different) or 1 (different), to reflect sequence conservation at each base for all combinations of two species. These data were analyzed by two objective functions, the average and standard deviation of the difference, which were used in the NSGA-II algorithm to search for appropriate DNA locations for species-specific primer design. The NSGA-II program identified four solutions (possible primer binding sites); consequently NSGA-II is believed to be a suitable algorithm for species-specific primer design, and is expected to make this difficult and time-consuming process more efficient.

Genetic structure and variability of the working dog inferred from microsatellite marker analysis

Working dogs serve as military watch dogs, search dogs, rescue dogs, and guide dogs with un-come-at-able character. They are drafted by in-training examination including concentration, capacity for locomotion, boldness and earthly desires. In this study, genetic diversity and relationships among two groups of working dogs (pass and fail group in-training examination) were assessed based on 15 microsatellite markers in 25 individuals of working dogs (military watch dogs and Korean search dogs). For the 15 microsatellite markers, the values of allelic richness (AR) ranged from 2.21 (pass group) to 1.60 (fail group) in military watch dogs, while AR ranged from 2.79 (pass group) to 2.72 (fail group) in Korean search dogs. Among 52 different alleles of military watch dogs, 22 alleles were detected in pass group only, while 8 alleles in fail group only. In case of Korean search dogs, 3 alleles were observed in pass group only, while 13 alleles in fail group only. These group-specific unique alleles reflect good biomarker for selecting working dogs (military watch dogs and Korean search dogs), indicating that those group specific microsatellite alleles could separate working dogs to be pass or fail group in out-training dog population. Taken together, this study demonstrates the feasibility of microsatellite analyses for the selection of superior working dogs objectively. Furthermore, this approach could be used for the proper selection of working dogs in combination with in-training examination.

Comparative evaluation of 16S rRNA gene in world-wide strains of Streptococcus iniae and Streptococcus parauberis for early diagnostic marker

Two bacterial etiological agents of the disease, Streptococcus iniae and Streptococcus parauberis has been associated with fish mortalities and heavy economic loss in all over the world. Bacterial identification based on 16S rRNA sequencing is very fast, accurate and reliable in comparison to other traditional phenotype methodologies. In this study, we investigate the usefulness of this method for diagnosis and identification of Streptococcus species. We have selected 61 phylogeographic strains of Streptococcus (34 strains of S. iniae and 27 strains of S. parauberis) and designed the universal primer against the identified most hypervariable region of the 16S rRNA gene. Our universal primer able to identify any geographical strains and offers a useful and fast alternative in a clinical laboratory under routine conditions. Based on our studies, we have developed an algorithm for appropriate control of S. iniae and S. parauberis disease. We suggested the phenotype observation along with universal primer combination to detect any kind of infection or carriers at early stages.