• Molecules and Cells
• /
• 제42권5호
• /
• pp.426-439
• /
• 2019

Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in $hfq^+$ and $Hfq^-$ backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.

• Journal of Microbiology and Biotechnology
• /
• 제32권2호
• /
• pp.149-159
• /
• 2022

Cancers of the lung and liver are the top 10 leading causes of cancer death worldwide. Thus, it is essential to identify the genes specifically expressed in these two cancer types to develop new therapeutics. Although many messenger RNA (mRNA) sequencing data related to these cancer cells are available due to the advancement of next-generation sequencing (NGS) technologies, optimized data processing methods need to be developed to identify the novel cancer-specific genes. Here, we conducted an analytical comparison between Bowtie2, a Burrows-Wheeler transform-based alignment tool, and Kallisto, which adopts pseudo alignment based on a transcriptome de Bruijn graph using mRNA sequencing data on normal cells and lung/liver cancer tissues. Before using cancer data, simulated mRNA sequencing reads were generated, and the high Transcripts Per Million (TPM) values were compared. mRNA sequencing reads data on lung/liver cancer cells were also extracted and quantified. While Kallisto could directly give the output in TPM values, Bowtie2 provided the counts. Thus, TPM values were calculated by processing the Sequence Alignment Map (SAM) file in R using package Rsubread and subsequently in python. The analysis of the simulated sequencing data revealed that Kallisto could detect more transcripts and had a higher overlap over Bowtie2. The evaluation of these two data processing methods using the known lung cancer biomarkers concludes that in standard settings without any dedicated quality control, Kallisto is more effective at producing faster and more accurate results than Bowtie2. Such conclusions were also drawn and confirmed with the known biomarkers specific to liver cancer.

• Molecules and Cells
• /
• 제45권10호
• /
• pp.738-748
• /
• 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed a serious threat to global public health. A novel vaccine made from messenger RNA (mRNA) has been developed and approved for use at an unprecedented pace. However, an increased risk of myocarditis has been reported after BNT162b2 mRNA vaccination due to unknown causes. In this study, we used single-cell RNA sequencing and single-cell T cell receptor sequencing analyses of peripheral blood mononuclear cells (PBMCs) to describe, for the first time, changes in the peripheral immune landscape of a patient who underwent myocarditis after BNT162b2 vaccination. The greatest changes were observed in the transcriptomic profile of monocytes in terms of the number of differentially expressed genes. When compared to the transcriptome of PBMCs from vaccinated individuals without complications, increased expression levels of IL7R were detected in multiple cell clusters. Overall, results from this study can help advance research into the pathogenesis of BNT162b2-induced myocarditis.

• 치위생과학회지
• /
• 제13권3호
• /
• pp.321-329
• /
• 2013

과산화수소는 치아미백에 널리 사용되는 물질로 과다 사용시 치수세포에 손상을 일으킬 수 있다. 본 연구의 목적은 활성산소인 과산화수소에 의해 유도되는 상아모세포의 단계별 분화와 LOX isoforms과의 관계를 밝히고자 하였다. 치수세포에 분화유도 배지와 과산화수소를 시간과 농도별로 처리한 후 LOX 유전자 발현은 RT-PCR로 측정하였고, LOX enzyme activity는 고감도 형광분석으로 확인하였다. 또한 가장 많은 발현억제를 보인 LOX와 LOXL을 선택하여 siRNA 처리 후 분화표지자의 발현변화와 LOX enzyme activity를 확인하였다. 1. 과산화수소 처리에 따라 LOX, LOXL, LOXL3 mRNA 발현은 농도와 시간 의존적으로 감소하였으나 LOXL2와 LOXL4 mRNA는 변화가 없었다. 2. 과산화수소 처리된 LOX enzyme activity는 0.3 mM과 24시간에서 가장 많은 증가를 보였다. 3. ALP, OPN, OCN의 mRNA 발현은 LOX와 LOXL siRNAs 모두에서 억제되었고, DMP1과 DSPP는 LOX siRNA에서 더 많은 억제 효과를 보였다. 하지만, 분화단계별(초기, 중기, 말기) 차이는 보이지 않았다. 4. LOX와 LOXL siRNAs를 처리하여 LOX enzyme activity를 측정한 결과 LOX siRNA를 처리한 실험군에서 더 많은 억제효과를 보였다. 이러한 결과는 상아모세포 성장과 분화과정에 낮은 농도의 과산화수소가 분화를 유도하고 여기에 LOX가 관련됨을 알 수 있었다. 결론적으로, 과산화수소는 LOX 유전자 발현조절을 통해 치수세포의 성장과 분화에서 중추적인 역할을 할 것이라고 생각된다.

• Journal of Ginseng Research
• /
• 제40권2호
• /
• pp.160-168
• /
• 2016

Background: Ginseng (Panax ginseng Meyer) is a well-characterized medicinal herb listed in the classic oriental herbal dictionary as "Shin-nong-bon-cho-kyung." Ginseng has diverse pharmacologic and therapeutic properties. Black ginseng (BG, Ginseng Radix nigra) is produced by repeatedly steaming fresh ginseng nine times. Studies of BG have shown that prolonged heat treatment enhances the antioxidant activity with increased radical scavenging activity. Several recent studies have showed the effects of BG on increased lipid profiles in mice. In this study report the effects of water and ethanol extracts of BG on hypercholesterolemia in rats. To our knowledge, this is the first time such an effect has been reported. Methods: Experiments were conducted on male Sprague Dawley rats fed with a high-cholesterol diet supplemented with the water and ethanol extracts of BG (200 mg/kg). Their blood cholesterol levels, serum white blood cell levels, and cholesterol-metabolizing marker genes messenger RNA (mRNA) expression were determined. Liver and adipose tissues were histologically analyzed. Results: We found that BG extracts efficiently reduced the total serum cholesterol levels, low-density lipoprotein (LDL) levels with increased food efficiency ratio and increased number of neutrophil cells. It also attenuated the key genes responsible for lipogenesis, that is, acetyl-coenzyme A (CoA) acetyltransferase 2, 3-hydroxy-3-methyl-glutaryl-CoA reductase, and sterol regulatory element-binding protein 2, at the mRNA level inside liver cells. Furthermore, the BG extract also reduced the accumulation of fat in adipose tissues, and inhibited the neutral fat content in liver cells stained with hematoxylin and eosin and oil red O. Conclusion: Administration of BG extracts to Sprague Dawley rats fed with high-cholesterol diet ameliorated hypercholesterolemia, which was mediated via modulation of cholesterol-metabolizing marker genes. This data throw a light on BG's cardioprotective effects.

• Clinical and Experimental Reproductive Medicine
• /
• 제26권2호
• /
• pp.149-156
• /
• 1999

포유류의 자궁조직은 발정주기를 통하여 역동적으로 변화하고 있으며 이러한 자궁조직의 분화는 시상하부-뇌하수체-생식소를 잇는 축에 의해 조절되는 스테로이드 호르몬에 의해 이루어진다. 그러나 에스트로겐 (E)이 어떤 유전자를 발현하여 자궁 내의 변화를 일으키는지는 아직 자세히 알려지지 않고 있다. 본 연구는 난소를 절제한 성숙한 흰쥐에 E을 처리한 후 자궁조직 내에서 c-fos, c-jun 및 hsp25 mRNA의 발현 변화를 Northern blot analysis방법을 사용하여 연구한 것이다. c-fos및 c-jun 암원유전자의 mRNA발현은 E처리 후 1시간 이전부터 증가하기 시작하며, 3시간 이내에 최고치에 도달한 후 급격히 감소하여 기저수준으로 되돌아갔다. 반면에 hsp25 mRNA수준은 E처리 후 3시간 대에서 최고치를 나타내나 증가된 발현량이 서서히 감소하며 12시간이 지난 후 까지도 정상대조군에 비해 높은 수준으로 유지되었다. 이러한 E의 영향이 선별적인지를 검증하기 위하여 E의 길항제인 tamoxifen을 사전처리하고 E을 추가로 처리하여 c-fos, c-jun및 hsp25 mRNA의 발현이 최고치에 이르렀던 3시간대에 자궁조직을 얻어 각각의 유전자 발현량을 조사한 결과 E에 의해 증가되었던 c-fos, c-jun 및 hsp25 mRNA의 수준이 억제됨을 확인하였다. 이러한 결과는 E이 자궁조직에 영향을 미치는데 초기의 일시적인 변화를 보이는 암원유전자인 c-fos 및 c-jun이 중요한 역할을 하리라는 것을 시사하며 hsp25의 경우는 좀더 늦은 반응에 관여하거나 c-fos및 c-jun에 의하여 간접적으로 조절을 받을 수도 있음을 보여 주는 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
• /
• 제17권7호
• /
• pp.3437-3445
• /
• 2016

Background: There is an increasing concern in the role of microRNA (miRNA) in the pathogenesis of bone metastasis (BM) secondary to prostate cancer (CaP). In this exploratory study, we hypothesized that the expression of vinculin (VCL) and chemokine X3C ligand 1 (CX3CL1) might be down-regulated in clinical samples, most likely due to the post-transcriptional modification by microRNAs. Targeted genes would be up-regulated upon transfection of the bone metastatic prostate cancer cell line, PC3, with specific microRNA inhibitors. Materials and Methods: MicroRNA software predicted that miR-21 targets VCL while miR-29a targets CX3CL1. Twenty benign prostatic hyperplasia (BPH) and 16 high grade CaP formalin-fixed paraffin embedded (FFPE) specimens were analysed. From the bone scan results, high grade CaP samples were further classified into CaP with no BM and CaP with BM. Transient transfection with respective microRNA inhibitors was done in both RWPE-1 (normal) and PC3 cell lines. QPCR was performed in all FFPE samples and transfected cell lines to measure VCL and CX3CL1 levels. Results: QPCR confirmed that VCL messenger RNA (mRNA) was significantly down-regulated while CX3CL1 was up-regulated in all FFPE specimens. Transient transfection with microRNA inhibitors in PC3 cells followed by qPCR of the targeted genes showed that VCL mRNA was significantly upregulated while CX3CL1 mRNA was significantly down-regulated compared to the RWPE-1 case. Conclusions: The down-regulation of VCL in FFPE specimens is most likely regulated by miR-21 based on the in vitro evidence but the exact mechanism of how miR-21 can regulate VCL is unclear. Up-regulated in CaP, CX3CL1 was found not regulated by miR-29a. More microRNA screening is required to understand the regulation of this chemokine in CaP with bone metastasis. Understanding miRNA-mRNA interactions may provide additional knowledge for individualized study of cancers.

• Tuberculosis and Respiratory Diseases
• /
• 제60권6호
• /
• pp.663-672
• /
• 2006

연구배경: 미세먼지는 여러 가지 유기물과 무기물의 복합체로 그 구성 성분이 시간과 장소에 따라 다르고 모양과 크기도 일정하지 않으며, 특히 지름 $10{\mu}m$이하의 미세먼지 (particulate matter 10; $PM_{10}$)는 흡입이 가능한 입자의 크기여서 하부기관지 및 폐의 가스-교환부분까지 침착하여 호흡기계에 손상을 일으킬 수 있다. 본 연구에서는 황사에 포함된 $PM_{10}$과 비황사 시기에 포집된 $PM_{10}$이 폐상피세포주에 작용하여 전염증성 사이토카인(proinflammatory cytokine) 및 cytokine messenger RNA(mRNA)의 발현에 어떤 영향이 있는지를 관찰하여 기관지 천식과 만성 폐쇄성 폐질환등 호흡기 질환의 증상 악화기전에 미치는 역할을 규명하고자 하였다. 연구방법: 공기 포집기(HV 500F, sibata model)를 이용하여 황사와 비황사 기간에 하루 6시간씩 실외의 장소에서 대기분진을 membrane filter에 포집한 다음, $PM_{10}$입자를 추출하고 폐암 상피세포주인 A549 cells(한국세포은행주)에 $PM_{10}$을 농도에 맞게($10{\mu}g/ml$, $100{\mu}g/ml$, $500{\mu}g/ml$) 노출시켰다. 각각의 노출된 세포로부터 interleukin(IL)-$1{\alpha}$, $IL-1{\beta}$, IL-8, granulocyte macrophage colony stimulating factor(GM-CSF)의 mRNA를 역전사중합효소연쇄반응(reverse transcriptase polymerase chain reaction; RT-PCR) 방법으로 측정하였다. 결 과: 황사 및 비황사 기간 중 포집된 $PM_{10}$을 가했을 시 가하지 않은 대조군에 비하여 $IL-1{\alpha}$, $IL-1{\beta}$, IL-8, granulocyte macrophage colony stimulating factor (GM-CSF)의 m'RNA와 cytokine의 발현이 유의하게 높았으며, 황사 기간의 고농도의 $PM_{10}$에 노출된 세포의 $IL-1{\alpha}$ mRNA는 비황사 기간의 $PM_{10}$에 노출된 세포의 mRNA보다 증가되어 있었다. 결 론: $PM_{10}$은 A549 cells에서 전염증성 사이토카인의 발현을 증가시키고 비황사 기간보다 황사 기간 중 대기 중에서 채취한 $PM_{10}$에 노출된 A549 cells에서 일부의 전염증성 사이토카인의 mRNA발현을 더욱 증가시키는 것을 알 수 있었다. 따라서 황사 기간의 $PM_{10}$에 의한 일부의 전염증성 사이토카인의 발현 증가가 만성 호흡기 질환의 증상 악화기전에 연관되어 있을 가능성을 시사하였다.

• 한국환경과학회지
• /
• 제24권5호
• /
• pp.623-631
• /
• 2015

Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). This study, the mRNA expression profiles provide insight into the mechanism of action of cadmium in Fleshy shrimp (Fenneropenaeus chinensis). The ability of genomic technologies was contributed decisively to development of new molecular biomarkers and to the determination of new possible gene targets. Also, it can be approach for monitoring of trace metal using oligo-chip microarray-based in potential model marine user level organisms. 15K oligo-chip for F. chinensis that include mostly unique sets of genes from cDNA sequences was developed. A total of 13,971 spots (1,181 mRNAs up- regulated and 996 down regulated) were identified to be significantly expressed on microarray by hierarchical clustering of genes after exposure to cadmium for different conditions (Cd24-5000 and Cd48-1000). Most of the changes of mRNA expression were observed at the long time and low concentration exposure of Cd48-1000. But, gene ontology analysis (GO annotation) were no significant different between experiments groups. It was observed that mRNA expression of main genes involved in metabolism, cell component, molecular binding and catalytic function. It was suggested that cadmium inhibited metabolism and growth of F. chinensis.

• Fisheries and Aquatic Sciences
• /
• 제19권4호
• /
• pp.18.1-18.10
• /
• 2016

In this study, to clarify the function of $PoPLC-{\beta}1$, in response to stress challenge, we examined the $PoPLC-{\beta}1$ expression pattern in response to external stress (pathogen-associated molecular pathogen challenge and environmental challenge including temperature and salinity). $PoPLC-{\beta}1$ expression analysis of tissue from olive flounder showed that the messenger RNA (mRNA) was predominantly expressed in the brain, heart, eye, liver, spleen, and stomach. We also tested the mRNA expression of the $PoPLC-{\beta}1$ in the spleen and kidney of olive flounder by RT-PCR and real-time PCR following stimulation with lipopolysaccharide (LPS), concanavalin A (ConA), or polyinosinic:polycytidylic acid (PolyI:C) and compared with the inflammatory cytokines IL-1b and IL-6 in the stimulated flounder tissues. Each of the spleen and kidney and mRNA transcripts of $PoPLC-{\beta}1$ were increased 30- and 10-fold than normal tissue at 1-6 h post injection (HPI) with PolyI:C when the expression of $PoPLC-{\beta}1$ transcript was similar to LPS and ConA. We also tested the expression of $PoPLC-{\beta}1$ in response to temperature and salinity stress. The expression of $PoPLC-{\beta}1$ also was affected by temperature and salinity stress. Our results provide clear evidence that the olive flounder $PLC-{\beta}1$ signal pathways may play a critical role in immune function at the cellular level and in inflammation reactions. In addition, $PLC-{\beta}1$ appears to act as an oxidative-stress suppressor to prevent cell damage in fish.