Comprehensive analysis of circular RNAs in nasopharyngeal cancer

Zhu Si-Yu,Wang Xiao-Yi,Xie Hui,Liu Li-Zhi 한국유전학회 2023 Genes & Genomics Vol.45 No.10

Background Nasopharyngeal cancer (NPC) is a type of epithelial malignancy that is positive for Epstein-Barr virus (EBV) and affects several populations worldwide. Due to the high rates of relapse and metastasis following primary treatment, there is an urgent need to identify new candidates for NPC therapy. Recently, circular RNA (circRNA) has emerged as a promising target for cancer diagnosis and prevention. Objective This study aimed to study the circRNAs enriched in NPC patients, and further analyze potential signaling pathways involved. Methods A new bioinformatic tool named psirc was used to analyze RNA-sequencing datasets from NPC patients and normal specimens to study the NPC-enriched circRNAs. Results We identified and quantified the full-length circRNA in these samples and found the top 10 enriched circRNAs in NPC patients compared to control samples. Furthermore, we selected the most enriched circRNA, circEEF1A1_E8B1, and studied its protein coding ability, microRNA and RNA-binding protein (RBP) binding capacity. We also constructed a protein-protein interaction (PPI) network for its binding proteins and extracted hub genes. Finally, we conducted survival analysis for these hub genes in head and neck cancer patients. Conclusions In summary, our study has revealed the presence of previously unidentified circRNAs that are enriched in NPC patients. Through an analysis of their molecular functions, we have advanced our understanding of the potential role of circRNAs in NPC development.

Chinese herbal medicine for myasthenia gravis: A systematic review and meta-analysis of randomized clinical trials

Zhu Si-jia,Wang Rui-ting,Yu Ze-yu,Zheng Ruo-Xiang,Liang Chang-Hao,Zheng You-you,Fang Min,Han Mei,Liu Jian-ping 한국한의학연구원 2022 Integrative Medicine Research Vol.11 No.2

Background: Myasthenia Gravis (MG) is a disorder of neuromuscular transmission bringing mild ocular weakness to severe generalized muscle weakness and disability. The conventional treatments have longterm side effects, and Chinese herbal medicines (CHM) have shown possible effect and safety for MG patients, but the existing evidence was not robust enough and the results were out of date. Methods: Searching for randomized controlled trials (RCTs) was conducted in 7 databases and clinical trial registries until July 2021. The Risk of Bias (ROB) 2 tool was used to assess the study quality and GRADE was used to assess the quality of whole evidence. Meta-analyses were conducted and the results were presented as risk ratio (RR) or mean difference (MD) with 95% confidence interval (CI). Results: Nineteen RCTs (1283 participants) testing 13 kinds of CHM with adequate randomization were included and six RCTs investigating Compound Huangqi were included in the meta-analyses. In addition to conventional treatment, nine CHMs reduced symptom scores of MG. Compound Huangqi plus conventional treatment (pyridostigmine bromide or prednisone or both) reduced the symptom scores compared with conventional treatment (MD=-3.56, 95%CI -4.86 to -2.26). Less adverse events happened in the CHM groups (3/247 in the CHM groups, 52/245 in the control groups, RR=0.13, 95%CI 0.06 to 0.30, 9RCTs, a total of 492 participants). The effect on quality of life was inconsistent. Conclusion: Nine CHMs could probably bring benefit for MG symptom improvement. Moderate to low certainty of evidence supported Compound Huangqi added-on conventional treatment probably bring extra benefit of improving MG symptoms. Adding CHMs could be safer than giving only conventional treatment. Study registration: The protocol was registered in PROSPERO (CRD42016032718).

Improved Homologous Expression of the Acidic Lipase from Aspergillus niger

Si-Yuan Zhu,Yan Xu,Xiao Wei Yu 한국미생물·생명공학회 2020 Journal of microbiology and biotechnology Vol.30 No.2

In this study, the acidic lipase from Aspergillus niger (ANL) was homologously expressed in A. niger. The expression of ANL was significantly improved by the expression of the native ANL with the introns, the addition of the Kozak sequence and the optimization of the signal sequences. When the cDNA sequence of ANL fused with the glaA signal was expressed under the gpdA promoter in A. niger, no lipase activity could be detected. We then tried to improve the expression by using the full-length ANL gene containing three introns, and the lipase activity in the supernatant reached 75.80 U/ml, probably as a result of a more stable mRNA structure. The expression was further improved to 100.60 U/ml by introducing a Kozak sequence around the start codon due to a higher translation efficiency. Finally, the effects of three signal sequences including the cbhI signal, the ANL signal and the glaA signal on the lipase expression were evaluated. The transformant with the cbhI signal showed the highest lipase activity (314.67 U/ml), which was 1.90-fold and 3.13-fold higher than those with the ANL signal and the glaA signal, respectively. The acidic lipase was characterized and its highest activity was detected at pH 3.0 and a temperature of 45ºC. These results provided promising strategies for the production of the acidic lipase from A. niger.

Association of Six Susceptibility Loci with Prostate Cancer in Northern Chinese Men

Zhang, Yu-Rong,Xu, Yong,Yang, Kuo,Liu, Ming,Wei, Dong,Zhang, Yao-Guang,Shi, Xiao-Hong,Wang, Jian-Ye,Yang, Fan,Wang, Xin,Liang, Si-Ying,Zhao, Cheng-Xiao,Wang, Fei,Chen, Xin,Sun, Liang,Zhu, Xiao-Quan,Zh Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.12

Background/Aim: Six prostate cancer (PCa) susceptibility loci were identified in a genome-wide association study (GWAS) in populations of European decent. However, the associations of these 6 single-nucleotide polymorphisms (SNPs) with PCa has remained tobe clarified in men in Northern China. This study aimed to explore the loci associated with PCa risk in a Northern Chinese population. Methods: Blood samples and clinical information of 289 PCa patients and 288 controls from Beijing and Tianjin were collected. All risk SNPs were genotyped using polymerase chain reaction (PCR)-high resolution melting curve technology and gene sequencing. Associations between PCa and clinical covariates (age at diagnosis, prostate-specific antigen [PSA], Gleason score, tumor stage, and level of aggressiveness) and frequencies of alleles and genotypes of these SNPs were analyzed using genetic statistics. Results: Among the candidate SNPs, 11p15 (rs7127900, A) was associated with PCa risk (P = 0.02, odds ratio [OR] = 1.64, 95% confidence interval [CI] = 1.09-2.46). Genotypes showed differences between cases and controls on 11p15 (rs7127900, A), 11q13 (rs7931342, T), and HNF1B (rs4430796, A) (P = 0.03, P = 0.01, and P = 0.04, respectively). The genotype TG on 11q13 (rs7931342, T) was positively associated with an increased Gleason score (P = 0.04, OR = 2.15, 95% CI = 1.02-4.55). Patients carrying TG on 17q24 (rs1859962, G) were negatively associated with an increased body mass index (BMI) (P = 0.03, OR = 0.44, 95% CI = 0.21-0.92) while those with AG on HNF1B (rs4430796, A) were more likely to have PSA increase (P = 0.002). Conclusion: Our study suggests that 11p15 (rs7127900, A) could be a susceptibility locus associated with PCa in Northern Chinese. Genotype TG on 11q13 (rs7931342, T) could be related to an increased Gleason score, AG on HNF1B (rs4430796, A) could be associated with PSA increase, and TG on 17q24 (rs1859962, G) could be negatively associated with an increased BMI in Chinese men with PCa.

<i>Arabidopsis</i> Serine Decarboxylase Mutants Implicate the Roles of Ethanolamine in Plant Growth and Development

Kwon, Yerim,Yu, Si-in,Lee, Hyoungseok,Yim, Joung Han,Zhu, Jian-Kang,Lee, Byeong-ha Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.3

<P>Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to plants and was previously shown to have highly specific activity to <SMALL>L</SMALL>-serine. While serine decarboxylase was biochemically characterized, its functions and importance in plants were not biologically elucidated due to the lack of serine decarboxylase mutants. Here we characterized an <I>Arabidopsis</I> mutant defective in serine decarboxylase, named <I>atsdc-1</I> (<I><U>A</U>rabidopsis <U>t</U>haliana <U>s</U>erine <U>d</U>e<U>c</U>arboxylase-1</I>). The <I>atsdc-1</I> mutants showed necrotic lesions in leaves, multiple inflorescences, sterility in flower, and early flowering in short day conditions. These defects were rescued by ethanolamine application to <I>atsdc-1</I>, suggesting the roles of ethanolamine as well as serine decarboxylase in plant development. In addition, molecular analysis of serine decarboxylase suggests that <I>Arabidopsis</I> serine decarboxylase is cytosol-localized and expressed in all tissue.</P>

Effect of pH Buffer and Carbon Metabolism on the Yield and Mechanical Properties of Bacterial Cellulose Produced by Komagataeibacter hansenii ATCC 53582

( Zhaofeng Li ),( Si-qian Chen ),( Xiao Cao ),( Lin Li ),( Jie Zhu ),( Hongpeng Yu ) 한국미생물생명공학회(구 한국산업미생물학회) 2021 Journal of microbiology and biotechnology Vol.31 No.3

Bacterial cellulose (BC) is widely used in the food industry for products such as nata de coco. The mechanical properties of BC hydrogels, including stiffness and viscoelasticity, are determined by the hydrated fibril network. Generally, Komagataeibacter bacteria produce gluconic acids in a glucose medium, which may affect the pH, structure and mechanical properties of BC. In this work, the effect of pH buffer on the yields of Komagataeibacter hansenii strain ATCC 53582 was studied. The bacterium in a phosphate and phthalate buffer with low ionic strength produced a good BC yield (5.16 and 4.63 g/l respectively), but there was a substantial reduction in pH due to the accumulation of gluconic acid. However, the addition of gluconic acid enhanced the polymer density and mechanical properties of BC hydrogels. The effect was similar to that of the bacteria using glycerol in another carbon metabolism circuit, which provided good pH stability and a higher conversion rate of carbon. This study may broaden the understanding of how carbon sources affect BC biosynthesis.

eRF1aMC and Mg2+ Dependent Structure Switch of GTP Binding to eRF3 in Euplotes octocarinatus

( Song Li ),( Yu Xin Jia ),( Wen Si Zhu ),( Bao Feng Chai ),( Ai Hua Liang ) 한국미생물 · 생명공학회 2012 Journal of microbiology and biotechnology Vol.22 No.2

Eukaryotic translation termination is governed by eRF1 and eRF3. eRF1 recognizes the stop codons and then hydrolyzes peptidyl-tRNA. eRF3, which facilitates the termination process, belongs to the GTPase superfamily. In this study, the effect of the MC domain of eRF1a (eRF1aMC) on the GTPase activity of eRF3 was analyzed using fluorescence spectra and high-performance liquid chromatography. The results indicated eRF1aMC promotes the GTPase activity of eRF3, which is similar to the role of eRF1a. Furthermore, the increased affinity of eRF3 for GTP induced by eRF1aMC was dependent on the concentration of Mg2+. Changes in the secondary structure of eRF3C after binding GTP/GDP were detected by CD spectroscopy. The results revealed changes of conformation during formation of the eRF3C·GTP complex that were detected in the presence of eRF1a or eRF1aMC. The conformations of the eRF3C·eRF1a·GTP and eRF3C·eRF1aMC·GTP complexes were further altered upon the addition of Mg2+. By contrast, there was no change in the conformation of GTP bound to free eRF3C or the eRF3C·eRF1aN complex. These results suggest that alterations in the conformation of GTP bound to eRF3 is dependent on eRF1a and Mg2+, whereas the MC domain of eRF1a is responsible for the change in the conformation of GTP bound to eRF3 in Euplotes octocarinatus.

The Application of Decellularized Adipose Tissue Promotes Wound Healing

Xia Zenan,Guo Xiao,Yu Nanze,Zeng Ang,Si Loubin,Long Fei,Zhang Wenchao,Wang Xiaojun,Zhu Lin,Liu Zhifei 한국조직공학과 재생의학회 2020 조직공학과 재생의학 Vol.17 No.6

Background: Due to adipose-derived stem cells (ASCs) being easy to obtain, their rapid proliferation rate, and their multidirectional differentiation capabilities, they have been widely used in the field of regenerative medicine. With the progress of decellularized adipose tissue (DAT) and adipose tissue engineering research, the role of DAT in promoting angiogenesis has gradually been emphasized. Methods: We examined the biological characteristics and biosafety of DAT and evaluated the stem cell maintenance ability and promotion of growth factor secretion through conducting in vitro and in vivo studies. Results The tested ASCs showed high rat:es of proliferation and adhered well to DAT. The expression levels of essential genes for cell stem maintenance, including OCT4, SOX2, and Nanog were low at 2–24 h and much higher at 48 and 96 h. The Adipogenic expression level of markers for ASCs proliferation including PPARγ, C/EPBα, and LPL increased from 2 to 96 h. Co-culture of ASCs and DAT increased the secretion of local growth factors, such as VEGF, PDGF-bb, bFGF, HGF, EGF, and FDGF-bb, and secretion gradually increased from 0 to 48 h. A model of full-thickness skin defects on the back of nude mice was established, and the co-culture of ASCs and DAT showed the best in vivo treatment effect. Conclusion: The application of DAT promotes wound healing, and DAT combined with ASCs may be a promising material in adipose tissue engineering and regenerative medicine.

Effect of cation ratio and order on magnetic circular dichroism in the double perovskite Sr₂Fe₁₊ <i> _x </i>Re_1- <i> _x </i>O₆

Ho, Ping-Luen,Yu, Chu-Ping,Zhang, Qiqi,Song, Kyung,Buban, James P.,Choi, Si-Young,Dunin-Borkowski, Rafal E.,Mayer, Joachim,Tai, Nyan-Hwa,Zhu, Jing,Jin, Lei,Zhong, Xiaoyan Elsevier 2018 Ultramicroscopy Vol.193 No.-

<P><B>Abstract</B></P> <P>Superexchange-based magnetic coupling of the two <I>B</I>-site cations in rock-salt-ordered double perovskite oxides is extremely sensitive to the cation ratio and degree of order. However, as a result of the limited spatial resolution of most magnetic characterization techniques, it is challenging to establish a direct relationship between magnetic properties and structure in these materials, including the effects of elemental segregation and cation disorder. Here, we use electron energy-loss magnetic chiral dichroism together with aberration-corrected electron microscopy and spectroscopy to record magnetic circular dichroism (MCD) spectra at the nm scale, in combination with structural and chemical information at the atomic scale from the very same region. We study nanoscale phases in ordered Sr<SUB>2</SUB>[Fe][Re]O<SUB>6</SUB>, ordered Sr<SUB>2</SUB>[Fe][Fe<SUB>1/5</SUB>Re<SUB>4/5</SUB>]O<SUB>6</SUB> and disordered Sr[Fe<SUB>4/5</SUB>Re<SUB>1/5</SUB>]O<SUB>3</SUB> individually, in order to understand the role of cation ratio and order on local magnetic coupling. When compared with ordered Sr<SUB>2</SUB>[Fe][Re]O<SUB>6</SUB>, we find that antiferromagnetic Fe<SUP>3+</SUP>-O<SUP>2−</SUP>-Fe<SUP>3+</SUP>superexchange interactions arising from an excess of Fe suppress the MCD signal from Fe cations in ordered Sr<SUB>2</SUB>[Fe][Fe<SUB>1/5</SUB>Re<SUB>4/5</SUB>]O<SUB>6</SUB>, while dominant Fe<SUP>3+</SUP>-O<SUP>2−</SUP>-Fe<SUP>3+</SUP>antiferromagnetic coupling in disordered Sr[Fe<SUB>4/5</SUB>Re<SUB>1/5</SUB>]O<SUB>3</SUB> leads to a decrease in MCD signal down to the noise level. Our work demonstrates a protocol that can be used to correlate crystallographic, electronic and magnetic information in materials such as Sr<SUB>2</SUB>Fe<SUB>1+</SUB> <I> <SUB>x</SUB> </I>Re<SUB>1-</SUB> <I> <SUB>x</SUB> </I>O<SUB>6</SUB>, in order to provide insight into structure-property relationships in double perovskite oxides at the atomic scale.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Local measurements of magnetic circular dichroism, atomic arrangement, cation order, chemical state and elemental distribution from the very same region provide an improved understanding of structure-property relationships at the nm scale in double perovskites with different structural complexities. </LI> <LI> Antiferromagnetic Fe<SUP>3+</SUP>-O<SUP>2−</SUP>-Fe<SUP>3+</SUP>superexchange interactions arising from an excess of Fe suppress the magnetic circular dichroism signal from Fe cations in ordered Sr<SUB>2</SUB>[Fe][Fe<SUB>1/5</SUB>Re<SUB>4/5</SUB>]O<SUB>6</SUB>, when compared with ordered Sr<SUB>2</SUB>[Fe][Re]O<SUB>6</SUB>. </LI> <LI> Dominant Fe<SUP>3+</SUP>-O<SUP>2−</SUP>-Fe<SUP>3+</SUP>antiferromagnetic coupling in disordered Sr[Fe<SUB>4/5</SUB>Re<SUB>1/5</SUB>]O<SUB>3</SUB> leads to a decrease in magnetic circular dichroism signal down to the noise level. </LI> </UL> </P>

New Insights Into Refractory Chronic Cough and Unexplained Chronic Cough: A 6-Year Ambispective Cohort Study

Zhang Mengru,Morice Alyn H.,Si Fengli,Zhang Li,Chen Qiang,Wang Shengyuan,Zhu Yiqing,Xu Xianghuai,Yu Li,Qiu Zhongmin 대한천식알레르기학회 2023 Allergy, Asthma & Immunology Research Vol.15 No.6

Purpose: Only limited studies have depicted the unique features and management of refractory chronic cough (RCC) and unexplained chronic cough (UCC). These led to the initiation of this study, which reported the demographic characteristics, manifestations, and long-term outcomes on a large series of consecutive RCC/UCC patients, providing a guideline-led real-world clinical experience. Methods: Retrospective baseline information was obtained from Clinical Research Database (January 2016 to May 2021). At least 6 months after the last clinic visit, included subjects were prospectively followed up. Results: Three hundred and sixty-nine RCC and UCC patients (199 females, 53.9%) were analyzed. The median cough duration was 24.0 (12.0–72.0) months. Laryngeal symptoms were reported in 95.9% of the patients. The common triggers for coughing were talking (74.9%), pungent odors (47.3%), eating (45.5%), and cold air (42.8%). RCC was considered in 38.2%, and the remainder of 228 patients had UCC, with an equal sex distribution (P = 0.66). Among the 141 RCCs, 90.8% (128) had refractory reflux cough, which was more responsive to current treatments (P < 0.01). Although most features and test results between RCC and UCC were similar, UCC was more commonly inappropriately treated (P < 0.01). Nineteen (7.7–41.1) months after the final clinic visit, 31.2% still coughed persistently, while 68.8% reported cough improvement or remission. RCC reported more favorable treatment outcomes (including cough improvement, control, and spontaneous remission) than UCC (P < 0.01). Coughs with long duration before the initial cough clinic visit (P < 0.01), frequent urinary incontinence (P < 0.01), and being sensitive to “talking” (P < 0.01) or “cold air” (P < 0.01) were less likely to be solved. Conclusions: The current treatments only improve cough symptoms in two-thirds of patients. Clinical indicators for treatment failure were those coughing for long duration and being sensitive to “talking” or “cold air.”