• Title/Summary/Keyword: RNA Stability

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Reference Gene Screening for Analyzing Gene Expression Across Goat Tissue

  • Zhanga, Yu;Zhang, Xiao-Dong;Liu, Xing;Li, Yun-Sheng;Ding, Jian-Ping;Zhang, Xiao-Rong;Zhang, Yun-Hai
    • Asian-Australasian Journal of Animal Sciences
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    • v.26 no.12
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    • pp.1665-1671
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    • 2013
  • Real-time quantitative PCR (qRT-PCR) is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2) in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.

Effects of Hyeolbuchukeo-tang(Xiefuzhuyu-tang) on NO Production in Aortic Vascular Smooth Muscle Cells (혈부축어탕이 대동맥 평활근 세포에서 NO 생성에 미치는 영향)

  • 허재혁;박진영;임준모;장호현;이인;문병순
    • The Journal of Korean Medicine
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    • v.24 no.2
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    • pp.166-178
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    • 2003
  • Objectives : Nitric oxide (NO) plays an important role in normal and pathophysiological cells as a messenger molecule, neurotransmitter, microbiological agent, or dilator of blood vessels and arteriosclerosis, respectively. This study was undertaken to understand the mechanism of NO production and effect of Hyeolbuchukeo-tang (Xiefuzhuyu-tang) on NO production in cultured vascular smooth muscle cell (VSMC). Methods and Results : VSMC was isolated from aorta and cultured. Cultured primary cells were identified as VSMC with anti--smooth muscle actin antibody. A large amount of NO was produced in cultured VSMC treated with $IFN-{\gamma}$ plus TNF in a time- and dose-dependent manner. $TNF-{\alpha}$ was a more efficient stimulator than $IFN-{\gamma}$ in NO production of cultured VSMC. iNOS protein wasdetected within 3 hrs and it increased up to 12 hrs in a time-dependent manner. However, accumulated NO in cytokine-treated VSMC was not detected within 3 hrs. NO production in cytokine-treated VSMC showed the dose- and time-dependent manner, and increased up to 48 hrs. The activated VSMC produced a large amount of NO (about 60 uM). Hyeolbuchukeo-tang (Xiefuzhuyu-tang) alone did not induceNO production, but it potentiated the effect of $TNF-{\alpha}$ on NO production and increased NO production by about 20%. Hyeolbuchukeo-tang (Xiefuzhuyu-tang) did not affect the transcriptional activity of iNOS gene, but increased the accumulation of iNOS. These results indicate that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) could modulate the translational level of iNOS. PKC did not modulate NO production, but calcium ionophore A23187 decreased NO production. However, Hyeolbuchukeo-tang (Xiefuzhuyu-tang) elevated the decreased NO production in A23187-treated VSMC by modulating the stability of iNOS transcripts. Half-life of the synthesized transcripts appeared to have about 6 hrs. PDTC, an $NF-{\kappa}B$ inhibitor, blocked the accumulation of iNOS mRNA, indicating that $NF-{\kappa}B$ served as an important modulator in the transcriptional regulation of iNOS. As Hyeolbuchukeo-tang (Xiefuzhuyu-tang) potentiated the effect of the $TNF-{\alpha}$ on NO production but had no additional effect on PDTC-modulated NO production, it is suggested that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) enhances the $TNF-{\alpha}-mediated$ NO production of VSMC by modulating the iNOS activity and the stability of iNOS transcripts in activated VSMC having the elevated intracellular calcium ion. Conclusions : This study suggests that Hyeolbuchukeo-tang (Xiefuzhuyu-tang) has a potential capacity for preventing and treating diseases of the circulation system, including arteriosclerosis.

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Characterization of Homocysteine ${\gamma}$-Lyase from Submerged and Solid Cultures of Aspergillus fumigatus ASH (JX006238)

  • El-Sayed, Ashraf S.;Khalaf, Salwa A.;Aziz, Hani A.
    • Journal of Microbiology and Biotechnology
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    • v.23 no.4
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    • pp.499-510
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    • 2013
  • Among 25 isolates, Aspergillus fumigatus ASH (JX006238) was identified as a potent producer of homocysteine ${\gamma}$-lyase. The nutritional requirements to maximize the enzyme yield were optimized under submerged (SF) and solid-state fermentation (SSF) conditions, resulting in a 5.2- and 2.3-fold increase, respectively, after the last purification step. The enzyme exhibited a single homogenous band of 50 kDa on SDS-PAGE, along with an optimum pH of 7.8 and pH stability range of 6.5 to 7.8. It also showed a pI of 5.0, as detected by pH precipitation with no glycosyl residues. The highest enzyme activity was obtained at $37-40^{\circ}C$, with a $T_m$ value of $70.1^{\circ}C$. The enzyme showed clear catalytic and thermal stability below $40^{\circ}C$, with $T_{1/2}$ values of 18.1, 9.9, 5.9, 3.3, and 1.9 h at $30^{\circ}C$, $35^{\circ}C$, $40^{\circ}C$, $50^{\circ}C$, and $60^{\circ}C$, respectively. Additionally, the enzyme $K_r$ values were 0.002, 0.054, 0.097, 0.184, and 0.341 $S^{-1}$ at $30^{\circ}C$, $35^{\circ}C$, $40^{\circ}C$, $50^{\circ}C$, and $60^{\circ}C$, respectively. The enzyme displayed a strong affinity to homocysteine, followed by methionine and cysteine when compared with non-S amino acids, confirming its potency against homocysteinuria-related diseases, and as an anti-cardiovascular agent and a specific biosensor for homocysteinuria. The enzyme showed its maximum affinity for homocysteine ($K_m$ 2.46 mM, $K_{cat}\;1.39{\times}10^{-3}\;s^{-1}$), methionine ($K_m$ 4.1 mM, $K_{cat}\;0.97{\times}10^{-3}\;s^{-1}$), and cysteine ($K_m$ 4.9 m M, $K_{cat}\;0.77{\times}10^{-3}\;s^{-1}$). The enzyme was also strongly inhibited by hydroxylamine and DDT, confirming its pyridoxal 5'-phosphate (PLP) identity, yet not inhibited by EDTA. In vivo, using Swiss Albino mice, the enzyme showed no detectable negative effects on platelet aggregation, the RBC number, aspartate aminotransferase, alanine aminotransferase, or creatinine titer when compared with negative controls.

Photo-controlled gene expression by fluorescein-labeled antisense oligonucleotides in combination with visible light irradiation

  • Ito, Atsushi;Kaneko, Tadashi;Miyamoto, Yuka;Ishii, Keiichiro;Fujita, Hitoshi;Hayashi, Tomonori;Sasaki, Masako
    • Journal of Photoscience
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    • v.9 no.2
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    • pp.451-453
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    • 2002
  • A new concept of "photo" -antisense method has been evaluated, where the inhibition of gene expression by the conventional antisense method is enhanced by photochemical binding between antisense oligonucleotides conjugated with photo-reactive compound and target mRNA or DNA. Fluorescein labeled oligodeoxyribonucleotides (F-DNA) was delivered to cell nuclei in the encapsulated form in multilamellar lecithin liposomes with neutral charge. F-DNA was previously shown to photo-bind to the complementary stranded DNA, and the delivery system using neutral liposome to be effective in normal human keratinocytes. In the present study, we used human kidney cancer G401.2/6TG.1 cell line to be advantageous in reproducible experiments. p53 was adopted as a target gene since antisense sequence information has been accumulated. The nuclear localization ofF-DNA was identified by comparing the fluorescence ofF-DNA with that of Hoechst 33258 under fluorescence microscope. After 7hr incubation to accumulate p53 protein induced by UV -B, p53 protein was quantified by Western blot. After 2hrs from F-DNA application, about 30% of cell population incorporated F-DNA in their nuclei with some morphological change possibly due to liposomal toxicity. Irradiation of visible light longer than 400nm from solar simulator at this time enhanced the inhibitory action of antisense F-DNA. The present results suggest that photo-antisense method is promising to control gene expression in time and space dependent manner. Further improvement of F-DNA delivery to cancer cells in the stability and toxicity is in progress. progress.

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Occurrence of Apple stem grooving virus in commercial apple seedlings and analysis of its coat protein sequence

  • Han, Jae-Yeong;Park, Chan-Hwan;Seo, Eun-Yeong;Kim, Jung-Kyu;Hammond, John;Lim, Hyoun-Sub
    • Korean Journal of Agricultural Science
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    • v.43 no.1
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    • pp.21-27
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    • 2016
  • Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV), and Apple stem pitting virus (ASPV) have been known to induce top working disease causing economical damage in apple. Occurrences of these three viruses in pome fruit trees, including apple, have been reported around the world. The transmission of the three viruses was reported by grafting, and there was no report of transmission through mechanical contact, insect vector, or seed except some herbaceous hosts of ASGV. As RNA extraction methods for fruit trees, Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and multiplex RT-PCR techniques have been improved for reliability and stability, and low titer viruses that could not be detected in the past have become detectable. We studied the seed transmission ability of three apple viruses through apple seedling diagnosis using RT-PCR. Nineteen seeds obtained from commercially grown apple were germinated and two of the resulting plants were ASGV positive. Seven clones of the amplified ASGV coat protein (CP) genes of these isolates were sequenced. Overall sequence identities were 99.84% (nucleotide) and 99.76% (amino acid). Presence of a previously unreported single nucleotide and amino acid variation conserved in all of these clones suggests a possible association with seed transmission of these 'S' isolates. A phylogenetic tree constructed using ASGV CP nucleotide sequences showed that isolate S sequences were grouped with Korean, Chinese, Indian isolates from apple and Indian isolates from kiwi.

Selection and Characterization of Staphylococcus hominis subsp. hominis WiKim0113 Isolated from Kimchi as a Starter Culture for the Production of Natural Pre-converted Nitrite

  • Hwang, Hyelyeon;Lee, Ho Jae;Lee, Mi-Ai;Sohn, Hyejin;Chang, You Hyun;Han, Sung Gu;Jeong, Jong Youn;Lee, Sung Ho;Hong, Sung Wook
    • Food Science of Animal Resources
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    • v.40 no.4
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    • pp.512-526
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    • 2020
  • Synthetic nitrite is considered an undesirable preservative for meat products; thus, controlling synthetic nitrite concentrations is important from the standpoint of food safety. We investigated 1,000 species of microorganisms from various kimchi preparations for their potential use as a starter culture for the production of nitrites. We used 16S rRNA gene sequence analysis to select a starter culture with excellent nitrite and nitric oxide productivity, which we subsequently identified as Staphylococcus hominis subspecies hominis WiKim0113. That starter culture was grown in NaCl (up to 9%; w/v) at 10℃-40℃; its optimum growth was observed at 30℃ at pH 4.0-10.0. It exhibited nonproteolytic activity and antibacterial activity against Clostridium perfringens, a bacterium that causes food poisoning symptoms. Analysis of Staphylococcus hominis subspecies hominis WiKim0113 with an API ZYM system did not reveal the presence of β-glucuronidase, and tests of the starter culture on 5% (v/v) sheep blood agar showed no hemolytic activity. Our results demonstrated the remarkable stability of coagulase-negative Staphylococcus hominis subspecies hominis WiKim0113, especially in strain negative for staphylococcal enterotoxins and sensitive to clinically relevant antibiotics. Moreover, Staphylococcus hominis subspecies hominis WiKim0113 exhibited a 45.5% conversion rate of nitrate to nitrite, with nitrate levels reduced to 25% after 36 h of culturing in the minimal medium supplemented with nitrate (200 ppm). The results clearly demonstrated the safety and utility of Staphylococcus hominis subspecies hominis WiKim0113, and therefore its suitability as a starter culture.

Experimental Infection of Different Tomato Genotypes with Tomato mosaic virus Led to a Low Viral Population Heterogeneity in the Capsid Protein Encoding Region

  • Sihelska, Nina;Vozarova, Zuzana;Predajna, Lukas;Soltys, Katarina;Hudcovicova, Martina;Mihalik, Daniel;Kraic, Jan;Mrkvova, Michaela;Kudela, Otakar;Glasa, Miroslav
    • The Plant Pathology Journal
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    • v.33 no.5
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    • pp.508-513
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    • 2017
  • The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semiquantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection.

Studies on nickel uptake in transgenic Arabidopsis thaliana introduced with TgMTP1 gene encoding metal tolerance protein (TgMTP1 과발현 애기장대에서 Nickel 흡수 연구)

  • Kim, Donggiun
    • Journal of Plant Biotechnology
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    • v.42 no.4
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    • pp.409-413
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    • 2015
  • To enhance phytoremediation, which removes heavy metal from soil, transgenic plants were applied to contaminated soil. We constructed a transformation vector expressing both $TgMTP_1$ (T. goesingense metal tolerance protein):HA and TgMTP:GFP genes. Transgenic plants were generated using an Agrobacterium-mediated transformation system that expressed the two vectors. Screening and analysis confirmed the incorporation of foreign genes into the Arabidopsis thaliana genome. Callus was induced in the 116 T3 line. These transgenic plants and calli were used for further analyses on the accumulation of Ni. The 116 T3-line plants and calli from selected lines were resistant to heavy metals and accumulated Ni in their leaves. The expression level of TgMTP RNA was equal in all leaves, but protein stability increased in the leaves with Ni treatment. According to these results, we suggest that $TgMTP_1$-overexpressing plants may be useful for phytoremediation of soil.

Thermostable Xylanase from Marasmius sp.: Purification and Characterization

  • Ratanachomsri, Ukrit;Sriprang, Rutchadaporn;Sornlek, Warasirin;Buaban, Benchaporn;Champreda, Verawat;Tanapongpipat, Sutipa;Eurwilaichitr, Lily
    • BMB Reports
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    • v.39 no.1
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    • pp.105-110
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    • 2006
  • We have screened 766 strains of fungi from the BIOTEC Culture Collection (BCC) for xylanases working in extreme pH and/or high temperature conditions, the so-called extreme xylanases. From a total number of 32 strains producing extreme xylanases, the strain BCC7928, identified by using the internal transcribed spacer (ITS) sequence of rRNA to be a Marasmius sp., was chosen for further characterization because of its high xylanolytic activity at temperature as high as $90^{\circ}C$. The crude enzyme possessed high thermostability and pH stability. Purification of this xylanase was carried out using an anion exchanger followed by hydrophobic interaction chromatography, yielding the enzyme with >90% homogeneity. The molecular mass of the enzyme was approximately 40 kDa. The purified enzyme retained broad working pH range of 4-8 and optimal temperature of $90^{\circ}C$. When using xylan from birchwood as substrate, it exhibits $K_m$ and $V_{max}$ values of $2.6{\pm}0.6\;mg/ml$ and $428{\pm}26\;U/mg$, respectively. The enzyme rapidly hydrolysed xylans from birchwood, beechwood, and exhibited lower activity on xylan from wheatbran, or celluloses from carboxymethylcellulose and Avicel. The purified enzyme was highly stable at temperature ranges from 50 to $70^{\circ}C$. It retained 84% of its maximal activity after incubation in standard buffer containing 1% xylan substrate at $70^{\circ}C$ for 3 h. This thermostable xylanase should therefore be useful for several industrial applications, such as agricultural, food and biofuel.

Alteration of the Metabolome Profile in Endothelial Cells by Overexpression of miR-143/145

  • Wang, Wenshuo;Yang, Ye;Wang, Yiqing;Pang, Liewen;Huang, Jiechun;Tao, Hongyue;Sun, Xiaotian;Liu, Chen
    • Journal of Microbiology and Biotechnology
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    • v.26 no.3
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    • pp.572-578
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    • 2016
  • Communication between endothelial cells (ECs) and smooth muscle cells (SMCs) via miR-143/145 clusters is vital to vascular stability. Previous research demonstrates that miR-143/145 released from ECs can regulate SMC proliferation and migration. In addition, a recent study has found that SMCs also have the capability of manipulating EC function via miR-143/145. In the present study, we artificially increased the expression of miR-143/145 in ECs, to mimic a similar change caused by miR-143/145 released by SMCs, and applied untargeted metabolomics analysis, aimed at investigating the consequential effect of miR-143/145 overexpression. Our results showed that miR-143/145 overexpression alters the levels of metabolites involved in energy production, DNA methylation, and oxidative stress. These changed metabolites indicate that metabolic pathways, such as the SAM cycle and TCA cycle, exhibit significant differences from the norm with miR-143/145 overexpression.