• Journal of Plant Biotechnology
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• v.50
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• pp.127-136
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• 2023

Water scarcity decreases the rate of photosynthesis and, consequently, the yield of banana plants (Musa spp). In this study, transcriptome analysis was performed to identify photosynthesis-related genes in banana plants and determine their expression profiles under water stress conditions. Banana plantlets were in vitro cultured on Murashige and Skoog agar medium with and without 10% polyethylene glycol and marked as BP10 and BK. Chlorophyll contents in the plant shoots were determined spectrophotometrically. Two cDNA libraries generated from BK and BP10 plantlets, respectively, were used as the reference for transcriptome data. Gene ontology (GO) enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) and visualized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway prediction. Morphological observations indicated that water deficiency caused chlorosis and reduced the shoot chlorophyll content of banana plantlets. GO enrichment identified 52 photosynthesis-related genes that were affected by water stress. KEGG visualization revealed the pathways related to the 52 photosynthesisr-elated genes and their allocations in four GO terms. Four, 12, 15, and 21 genes were related to chlorophyll biosynthesis, the Calvin cycle, the photosynthetic electron transfer chain, and the light-harvesting complex, respectively. Differentially expressed gene (DEG) analysis using DESeq revealed that 45 genes were down-regulated, whereas seven genes were up-regulated. Four of the down-regulated genes were responsible for chlorophyll biosynthesis and appeared to cause the decrease in the banana leaf chlorophyll content. Among the annotated DEGs, MaPNDO, MaPSAL, and MaFEDA were selected and validated using quantitative real-time PCR.

• BMB Reports
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• v.42 no.9
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• pp.593-598
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• 2009

Cell cycle progression is regulated by both transcriptional and post-transcriptional mechanisms. MicroRNAs (miRNAs) emerge as a new class of small non-coding RNA regulators of cell cycle as recent evidence suggests. It is hypothesized that expression of specific miRNAs oscillates orderly along with cell cycle progression. However, the oscillated expression patterns of many candidate miRNAs have yet to be determined. Here, we describe miRNA expression profiling in double-thymidine synchronized HeLa cells as cell cycle progresses. Twenty-five differentially expressed miRNAs were classified into five groups based on their cell cycle-dependent expression patterns. The cyclic expression of six miRNAs (miR-221, let-7a, miR-21, miR-34a, miR-24, miR-376b) was validated by real-time quantitative RT-PCR (qRT-PCR). These results suggest that specific miRNAs, along with other key factors are required for maintaining and regulating proper cell cycle progression. The study deepens our understanding on cell cycle regulation.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.743-748
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• 2014

The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene ($VEGF{\alpha}$) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine $VEGF{\alpha}$ belonged to the same clade of the pig $VEGF{\alpha}$. Analysis for synonymous (Ks) and non-synonymous substitution ratios (Ka) revealed that the horse $VEGF{\alpha}$ underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR) and quantitative-polymerase chain reaction (qPCR) showed ubiquitous expression of $VEGF{\alpha}$ mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of $VEGF{\alpha}$ gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.7
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• pp.921-929
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• 2013

Huoyan goose is a Chinese local breed famous for its higher laying performance, but the problems of variety degeneration have emerged recently, especially a decrease in the number of eggs laid. In order to better understand the molecular mechanism that underlies egg laying in Huoyan geese, gene profiles in the pituitary gland of Huoyan geese taken during the laying period and ceased period were investigated using the suppression subtractive hybridization (SSH) method. Total RNA was extracted from pituitary glands of ceased period and laying period geese. The cDNA in the pituitary glands of ceased geese was subtracted from the cDNA in the pituitary glands of laying geese (forward subtraction); the reverse subtraction was also performed. After sequencing and annotation, a total of 30 and 24 up and down-regulated genes were obtained from the forward and reverse SSH libraries, respectively. These genes mostly related to biosynthetic process, cellular nitrogen compound metabolic process, transport, cell differentiation, cellular protein modification process, signal transduction, small molecule metabolic process. Furthermore, eleven genes were selected for further analyses by quantitative real-time PCR (qRT-PCR). The qRT-PCR results for the most part were consistent with the SSH results. Among these genes, Synaptotagmin-1 (SYT1) and Stathmin-2 (STMN2) were substantially over-expressed in laying period compared to ceased period. These results could serve as an important reference for elucidating the molecular mechanism of higher laying performance in Huoyan geese.

• BMB Reports
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• v.43 no.2
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• pp.115-121
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• 2010

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.2101-2101
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• 2001

Near-infrared spectroscopy is now being used in clinical diagnosis as a non-invasive monitor of tissue oxygenation state. However, due to lack of the optical pathlength information within tissues, it is still difficult to quantitate the hemoglobin concentration with present CW techniques. Time-resolved spectroscopy (TRS), which measures temporal profiles of emerging light from tissues, enables to estimate the pathlength distribution within tissues by converting time to distance. Consequently, quantitative measurement of tissue oxygenation is possible by analyzing the data with optical diffusion equation 1) or our Microscopic Beer-Lambert law2). Time-Resolved Spectroscopy System : TRS-1O3) Our TRS-10 system consists of a three-wavelength (759, 797, 833 nm) PLP as pulsed light source, a high speed PMT with high sensitivity and three signal-processing circuits for time-resolved measurement (CFD/TAC, A/D converter and histogram memory). Optical pulse train consisting of 759, 797 and 833nm is generated by PLP at 5㎒ repetition rate and irradiated a sample through a single optical fiber. The diffuse-reflected light from the sample is collected by a bundle fiber and then detected by the PMT for single photon measurement. After being amplified by a following fast amplifier, the electrical signals for each wavelength are picked out by CFD/TAC module. Then, a signal processing circuit integrated the TRS data for each wavelength individually. The simultaneous TRS measurement for three wavelengths achieved without any optical or mechanical switch. Experiment and Results Input and detection fibers of TRS-10 were attached at the human forehead with a fiber separation of 3cm. TRS measurements were continuously performed for about 20 minutes including 2 minutes hyper ventilation. It was observed that the total hemoglobin concentration was decreasing during the hyper ventilation and recovered until 2 minutes after hyper ventilation. On the other hand, the deoxy-hemoglobin concentration began to increase after hyper ventilation and had its peak at around 2 minute later, showing 502 drop from 75% to 60% due to inhibition of breathing by performing hyper ventilation. The results showed that this system might be able to quantitate the concentrations of oxy- and deoxy-hemoglobin in the human brain.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.278-285
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• 2012

Poultry products are an important source of Salmonella enterica. An effective way to reduce food poisoning due to Salmonella would be to breed chickens more resistant to infection. Unfortunately host responses to Salmonella are complex with many factors involved. To learn more about responses to Salmonella in young chickens of 2 wk old, a cDNA Microarray containing 13,319 probes was performed to compare gene expression profiles between two chicken groups under control and Salmonella infected conditions. Newly hatched chickens were orally infected with S. enterica serovar Enteritidis. Since the intestine is one of the important barriers the bacteria encounter after oral inoculation, intestine gene expression was investigated at 2 wk old. There were 588 differentially expressed genes detected, of which 276 were known genes, and of the total number 266 were up-regulated and 322 were down-regulated. Differences in gene expression between the two chicken groups were found in control as well as Salmonella infected conditions indicating a difference in the intestine development between the two chicken groups which might be linked to the difference in Salmonella susceptibility. The differential expressions of 4 genes were confirmed by quantitative real-time PCR and the results indicated that the expression changes of these genes were generally consistent with the results of GeneChips. The findings in this study have lead to the identification of novel genes and possible cellular pathways, which are host dependent.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.116-116
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• 2017

Low-temperature is one of the environmental stress factors that affect plant growth and development and consequently limit crop productivity. The control of seed germination under low-temperature is organized by many genes which are called quantitative trait loci (QTLs). High germination rate for low-temperature is an important factor of growing rice. Previously, we identified a major QTL controlling low-temperature germinability in rice using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon (Rufi) and the Korean japonica cultivar, 'Hwaseongbyeo (HS)'. A $BC_3F_7$ line (TR5) showed better low-temperature germinability than its recurrent parent. TR5 was crossed with HS to develop a segregating F2:3 populations for the target QTL. Six SSR markers polymorphic between HS and Rufi were used to screen and fine map the qLTG1. The qLTG1 on chromosome 1, which accounted for 55.5% of the total phenotypic variation, confirmed that Rufi allele enhanced the low-temperature germinability. Intervals between markers CRM16 and CRM15, four candidate genes were identified. The identified candidate genes, which are encoded by a protein of unknown function, showed their direct involvement on seed germination at low-temperature. To identify genes targeted by qLTG1, we investigated the expression profiles of these candidate genes and germination behavior of qLTG1 under different stress conditions and compared to HS, Rufi, and TR5 at $13{\pm}2^{\circ}C$ for 3 days after incubation. Furthermore, transgenic rice plants will also be developed to conduct a detailed investigation on low-temperature germinability. Hence, the QTL for low-temperature germinability would be useful in rice breeding programs especially in the development of lines possessing low-temperature germinability.

• Journal of the Korean Home Economics Association
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• v.48 no.2
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• pp.121-134
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• 2010

This study was performed to develop the semi-quantitative food frequency questionnaire (SQFFQ) for assessing the usual dietary intake of Korean adolescents. For that, we used 24 hour recall data from the 2005 NHANES(the Third Korean National Health and Nutrition Examination Survey). The cumulative percent contribution and cumulative multiple regression coefficients of 17 nutrients(energy, protein, fat, carbohydrate, fiber, calcium, phosphorus, iron, sodium, potassium, vitamin A, retinol, ${\beta}$-carotene, thiamin, riboflavin, niacin, vitamin C) of each food were computed. Among 687 food items, 265 food items were selected and grouped depending on similarities in ingredients, nutrient profiles, and/or culinary usage and re-added food items which were excluded for seasonal effect. Finally, total 19 food groups, 87 food items, were included in SQFFQ. Food intake frequency was quantified using nine categories. The portion size was classified depending on the average size of each selected food item. Each portion size was then categorized as one of three amounts: small (0.5 times), medium (1 times), and large (1.5 times). The SQFFQ covered 91.9% of the intake of 17 nutrients in 2005 NHANES and 86.6% in 2001 NHANES. Therefore, by testing the validity of developed SQFFQ using nutrient intakes, this list was valid to evaluate the usual daily intake in Korean adolescents.

• Animal cells and systems
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• v.12 no.3
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• pp.165-170
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• 2008

Cuticular hydrocarbons(CHCs) of the epicuticle wax layer are so far used to differentiate the insects in species and subspecies levels. In this study, four species of malaria vectors(genus Anopheles) were collected from various localities in southern Iran. Twenty specimens of each species were randomly selected and one epicuticular extract was prepared of every five specimens. FID-GC profiles of the extracts did not show any qualitative difference. Using significant difference of CHC mass at retention time(RT) 39.6, the two species of An. sacharovi and An. fluviatilis could be distinguished. Similarly, the two species of An. superpictus & An. sacharovi and An. dthali & An. sacharovi were differentiated by their CHC level at RT 28.5. An. sacharovi was distinguished by integratable peaks at RTs 29.7, 30.6, 30.7, 31 and 32.6 while the other three species just indicated trace peaks at the same RTs. Similarly, An. dthali could be known by an integratable peak at RT 26.2 while An. fluviatilis and An. superpictus indicated trace peaks at the same RT. Integratable peaks and traces at RTs 27.4 and 28.5 were respectively used to differentiate An. superpictus from An. fluviatilis. Lastly, CHC trace amount of An. superpictus at RT 39.6 is another indicator to distinguish it from An. fluviatilis with an integratable peak at the same RT. In harmony with other studies worldwide we hereby report that quantitative analysis of CHCs was successfully applied to differentiate the four Anopheles species of southern Iran.