• Journal of Life Science
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• v.27 no.3
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• pp.370-381
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• 2017

Protein dephosphorylation is important for cellular regulation, which is catalyzed by protein phosphatases. Among protein phosphatases, carboxy-terminal domain (CTD) phosphatases are recently emerging and new functional roles of them have been revealed. There are 7 CTD phosphatases in human genome, which are composed of CTD phosphatase 1 (CTDP1), CTD small phosphatase 1 (CTDSP1), CTD small phosphatase 2 (CTDSP2), CTD small phosphatase-like (CTDSPL), CTD small phosphatase-like 2 (CTDSPL2), CTD nuclear envelope phosphatase (CTDNEP1), and ubiquitin-like domain containing CTD phosphatase 1 (UBLCP1). CTDP1 dephosphorylates the second phosphor-serine of CTD of RNA polymerase II (RNAPII), while CTDSP1, STDSP2, and CTDSPL dephosphorylate the fifth phosphor-serine of CTD of RNAPII. In addition, CTDSP1 dephosphorylates new substrates such as mothers against decapentaplegic homologs (SMADs), cell division cycle-associated protein 3 (CDCA3), Twist1, tumor-suppressor protein promyelocytic leukemia (PML), and c-Myc. CTDP1 is related to RNA polymerase II complex recycling, mitosis regulation and cancer cell growth. CTDSP1, CTDSP2 and CTDSPL are related to transcription factor recruitment, tumor suppressor function and stem cell differentiation. CTDNEP1 dephosphorylates LIPIN1 and is related to neural tube formation and nuclear envelope formation. CTDSPL2 is related to hematopoietic stem cell differentiation. UBLCP1 dephosphorylates 26S proteasome and is related to nuclear proteasome regulation. In conclusion, noble roles of CTD phosphatases are emerging through recent researches and this review is intended to summarize emerging roles of CTD phosphatases.

• Journal of Life Science
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• v.30 no.6
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• pp.570-579
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• 2020

Pre-mRNA splicing is a crucial step for the expression of information encoded in eukaryotic genomes. Alternative splicing occurs when splice sites are differentially recognized and more than one transcript and potentially multiple proteins are generated from the same pre-mRNA. The decision on which splice sites are selected under particular cellular conditions is determined by the interaction of proteins, globally designated as splicing factors, that guide spliceosomal components, and thereby the spliceosome, to their respective splice sites. Abiotic stresses such as heat, cold, salt, drought, and hypoxia markedly alter alternative splicing patterns in plants, and these splicing events implement changes in gene expression for adaptive responses to adverse environments. Alteration of the expression or activity of splicing factors results in alternative splicing under cold, heat, salt, or drought conditions, and alternatively spliced isoforms respond distinctly in several aspects such as expression in different tissues or degradation via nonsense-mediated decay. Spliced isoforms may vary in their subcellular localization or have different biological functions under stress conditions. Despite numerous studies, functional analyses of alternative splicing have been limited to particular abiotic stresses; the molecular mechanism of alternative splicing in abiotic stress response remains uncovered which suggests that further studies are needed in this area.

• Journal of Preventive Medicine and Public Health
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• v.49 no.6
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• pp.394-405
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• 2016

Objectives: The survival outcomes of antiretroviral treatment (ART) programs have not been systematically evaluated at the state level in India. This retrospective study assessed the survival rates and factors associated with survival among adult human immunodeficiency virus (HIV)-infected patients in Andhra Pradesh, India. Methods: The present study used data from 139 679 HIV patients aged ${\geq}15$ years on ART who were registered from 2007 to 2011 and were followed up through December 2013. The primary end point was death of the patient. Mortality densities (per 1000 person-years) were calculated. Kaplan-Meier and Cox-regression models were used to estimate survival and explore the factors associated with survival. Results: The overall median follow-up time was 16.0 months (2.0 months for the deceased and 14.0 months for those lost to follow-up). Approximately 13.2% of those newly initiated on ART died during follow-up. Of those deaths, 56% occurred in the first three months. The crude mortality rate was 80.9 per 1000 person-years at risk. The CD4 count (adjusted hazard ratio [aHR],4.88; 95% confidence interval [CI], 4.36 to 5.46 for < $100cells/mm^3$ vs. > $350cells/mm^3$), functional status (aHR, 3.05; 95% CI, 2.82 to 3.30 for bedridden vs. normal), and body weight (aHR, 3.69; 95% CI, 3.42 to 3.97 for <45 kg vs. >60 kg) were strongly associated with the survival of HIV patients. Conclusions: The study findings revealed that high mortality was observed within the first three months of ART initiation. Patients with poor baseline clinical characteristics had a higher risk of mortality. Expanded testing and counseling should be encouraged, with the goal of ensuring early enrollment into the program followed by the initiation of ART in HIV-infected patients.

• Journal of Life Science
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• v.14 no.5
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• pp.770-777
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• 2004

It has been previously reported that unacetylated a-tropomyosin(TM) produced in E. coli failed to bind to actin while acetylated muscle TM and Ala-Ser dipeptide fusion TM (AS-TM) bound well to actin. In order to determine the structural requirement of the amino terminus for high actin affinity, a recombinant tropomyosin (Ala-TM) that a single Ala residue was added to the amino terminus of Ala-TM was constructed, overexpressed, and purified from E. coli. Actin affinity of Ala-TM was 2.3$\times$$10^{6}$$M^{-1}$, whereas that of unacetylated TM was considerably lower than 0.1$\times$$10^{-6}$$M^{-1}$ indicating that addition of a single Ala residue to the amino terminus drastically increased, at least twenty times, actin affinity of TM. Ala-TM, however, bound to actin about three times weaker than acetylated TM and AS- TM, implying that the addition of an Ala residue was insufficient for complete restoration of high actin affinity. While Ala-TM, AS-TM, and muscle TM showed inhibition and activation of actomyosin Sl ATPase activity depending on myosin Sl concentration, the degree of inhibition and activation was different from each other. AS-TM exhibited the greatest inhibition of the ATPase at low Sl concentration, whereas the greatest activation of the ATPase was observed with muscle TM. These results, together with previous findings, strongly suggested that local structure of the amino terminus is the crucial functional determinant of TM.

• Journal of Life Science
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• v.22 no.5
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• pp.587-594
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• 2012

TMR (total mixed ration) feed was developed by adding mugwort and was fed to Korean black cattle. The effects on the physicochemical properties of the Korean black cattle, when fed mugwort, were investigated, as was the feasibility of producing beef with high quality and functionality. Korean black cattle were reared by using basal TMR (control) and basal TMR supplemented with mugwort of middle fattening 4.6% and late fattening 6.5% (treatment). The content of total catechin in Korean black cattle fed with the control and treatment was 0.262 and 0.379 mg/kg, respectively, while the content of epicatechin was 0.042 and 0.059 mg/kg, respectively, both of which were a significant increase from feeding the cattle TMR with mugwort ($p$ <0.05). There was no significant difference between the control and treatment in terms of $L^*$ (lightness), $b^*$ (yellowness), pH, VBN (volatile basic nitrogen) content, bacterial counts, water-holding capacity, freezing loss, thawing loss, cooking loss, cohesiveness, chewiness, shear force, and sensory score. TBARS (2-thiobarbituric acid reactive substances) and springiness for the control were significantly higher than the treatment ($p$ <0.05). The $a^*$ (redness), EDA (electron donating ability), hardness, and gumminess for the treatment were significantly higher than for the control ($p$ <0.05). These results suggest that the feed containing mugwort can be used to improve color and increase antioxidant ability as functional feed.

• Korean Journal of Environment and Ecology
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• v.26 no.6
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• pp.941-951
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• 2012

The changes of forest habitats and maeulsoops(village forests) in Jinan-gun, Jeollabuk-do, South Korea are examined using landscape indices and morphological pattern analysis, and their landscape-ecological implications on conserving biological diversity are presented. We used FRAGSTATS and GUIDOS software, as well as land cover maps(of 1989 and 2006) to analyze the spatial and temporal patterns of habitat composition and configuration in surrounding landscapes of 34 representative maeulsoops and Jinan-gun. The results showed decreases in the amount of core habitats and corridors and habitat connectivity at a regional scale since 1989. In addition, multi-scale habitat analysis at a focal scale revealed that the structural and functional connectivity between forest habitats surrounding maeulsoops of the year 2006 was lower than that of the year 1989. In order to reduce forest fragmentation and to enhance the connectivity among habitats, it is necessary to provide the additional habitat corridors as well as preserving existing corridors and surrounding landscapes of maeulsoops. We also suggest that a combination of landscape indices and morphological spatial pattern analysis can provide an effective tool to assess the habitat functions and configuration in a rapidly changing landscape.

• Korean Journal of Plant Taxonomy
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• v.32 no.4
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• pp.467-480
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• 2002

The development of the female gametophyte of Corydalis albipetala, C. ambigua, C. filistipes, C. nobilis, C. solida, C. ophiocarpa have been comparatively investigated using laser scanning confocal microscope (LSCM) and light microscope. An archesporium was originated from one of the outmost parietal cells beneath the one-layered epidermis of protuberant nucellus, and acted directly as a megaspore mother cell (MMC). These species had linear tetrads after successional meiotic division during the megasprogenesis. A functional megasprore developed from one of the tetrad in the chalazal end, and the rest three being degenerated. The developmental type of the female gametophyte was monosporic in accordance with the Polygonum type. Prior to anthesis the female gametophyte was organized. So mature embryo sac was comprised a three-celled egg apparatus, three large antipodals were developed from the apex of each antipodal cell, and extended toward micropylar end to be contacted with egg apparatus. Two synergids were usually observed as degenerated condition, and in this time the apices of antipodal haustoria were connected with the degenerated synergids. The developmental characteristics of seven-nucleate female gametophytes were common in all the species investigated. But the shape of mature embryo sac was ovoidal in C. albipetala, C. filistipes, C. ophiocarpa and C. solida, reflexed in C. ambigua, and rather flattened ovoidal in C. nobilis. Also, the type of megasporangium was anatropous in all the species except C. ambigua with campylotropous ovule.

• Journal of Dairy Science and Biotechnology
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• v.31 no.2
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• pp.153-159
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• 2013

Lactic acid bacteria are microorganisms that are closely associated with human and/or animal environments, and are categorized as generally recognized as safe (GRAS) organisms due to their ubiquitous appearance in foods and their contribution to the healthy microflora of mucosal surfaces. This study was performed to isolate and identify lactic acid bacteria with antagonistic effects against food-borne pathogens. A total of 3,000 acid-producing bacteria were isolated from infant feces, cattle feces, goat feces, dog feces, pig feces, vaginal tracts, vegetables, fruits, Kimchi, Jeotgal, fermented sausages, raw milk, cheese, yogurt, Cheonggukjang, Meju, and Makgeolli cultured on MRS agar with 0.05% bromocresol purple. For the isolation of bacteriocin-producing bacteria, the diameter of the clear zone was measured on MRS agar plates. Twenty-six isolates exhibited strong antibacterial activity against indicator strains such as Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella enterica serovar Enteritidis. Lactic acid bacteria were identified as Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, Lactobacillus acidophilus, Lactobacillus amylovorus, Lactobacillus curvatus, Lactobacillus plantarum, and Pediococcus acidilactici by 16S rDNA gene sequence analysis. The results of this study suggest that the isolates could be used as potential probiotic starters for functional food applications.

• Korean Journal of Food Science and Technology
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• v.45 no.6
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• pp.727-734
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• 2013

Makgeolli mashes that were brewed using five different commercial nuruks (fermentation starters) were investigated for changes in physicochemistry, microbial diversity, and biogenic amine (BA) production. Mash A brewed with the nuruk (Gaeryang-nuruk) had the highest level of alcohol concentration and the greatest number of yeast cells, whereas mash E had the greatest number of bacterial cells. Only three biogenic amines were detected in the makgeolli mashes: tyramine, putrescine, and cadaverine. Using a PCR-DGGE technique, we observed that mash E had the highest BA production, and had the greatest number of bands on the denaturing gradient gels. We also observed that the numbers of bacterial cells correlated significantly with the putrescine and the total BA content, and that the BA content correlated significantly with the color values (L, a, b). This study shows that the quality of a makgeolli can depend on the type of nuruk. Therefore, we suggest that the quality management of makgeolli should start with the stage of nuruk manufacture.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.231-239
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• 2016

To study the transcript levels of epigenetically regulated genes in tobacco, we have developed a transgenic line OX1 overexpressing NtROS2a gene encoding cytosine DNA demethylation and a RNAi plant line RNAi13. It has been reported that salt- and $H_2O_2$-stress tolerance of these transgenic lines are enhanced with various phenotypic characters (Lee et al. 2015). In this paper, we conducted microarray analysis with Agilent Tobacco 4 x 44K oligo chip by using overexpression line OX1, RNAi plant line RNAi 13, and wild type plant WT. Differentially expressed genes (DEGs) related to metabolism, nutrient supply, and various stressed were up-regulated by approximately 1.5- to 80- fold. DEGs related to co-enzymes, metabolism, and methylation functional genes were down-regulated by approximately 0.03- to 0.7- fold. qRT-PCR analysis showed that the transcript levels of several candidate genes in OX1 and RNAi lines were significantly (p < 0.05) higher than those in WT, such as genes encoding KH domain-containing protein, MADS-box protein, and Zinc phosphodiesterase ELAC protein. On the other hand, several genes such as those encoding pentatricopeptide (PPR) repeat-containing protein, histone deacetylase HDAC3 protein, and protein kinase were decreased by approximately 0.4- to 1.0- fold. This study showed that NtROS2a gene encoding DNA glycosylase related to demethylation could regulate adaptive response of tobacco at transcriptional level.