查看更多>>摘要：Abstract Background As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive.Objective To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently.Methods A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5′-/3′-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignments identified conserved sequences and specific primer sets were designed against these regions using a conventional tool. Primer sets chosen among the candidates were evaluated by in silico PCR and RT-qPCR.Results Out of 17 conserved sequences (totaling 4.3?kb), two primer sets targeting the nsp2 and ORF3a genes were picked that exhibited?>?99.9% in silico amplification coverage against the original dataset (230,163 genomes) when a 5% mismatch between the primers and target was allowed. In addition, the primer sets successfully detected nine SARS-CoV-2 variant RNA samples (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Iota, and Kappa) in experimental RT-qPCR validations.Conclusion In addition to the RdRp, E, N, and S genes that are targeted commonly, our approach can be used to identify novel primer targets in SARS-CoV-2 and should be a priority strategy in the event of novel SARS-CoV-2 variants or other pandemic outbreaks.
查看更多>>摘要：Abstract Background Disruption of ICT1 has been known to cause a significant deficiency in the phospholipid composition which is necessary for cell stress adaptation. However, the effects of ICT1 deletion on antioxidant research are not clear.Objective Construct a knockout strain to investigate the efficacy of ICT1 on antioxidant activity.Methods The antioxidant-related genes and phospholipid-related genes were determined by RT-PCR, the cell wall shape was observed by TME, and CWI pathway phosphorylation experiments were also analyzed by HPLC.Results The expression of antioxidant related genes and phospholipid-related genes has a slight reduction compared to the wild type. The cell wall was observed impaired with apparent CWI pathway phosphorylation weakening in the mutant.Conclusion These findings indicate the role of ICT1 on antioxidant activity because it not only directly affects phospholipid composition but also further leads to the activation of CWI.
查看更多>>摘要：Abstract Background Angiogenesis play a critical role in the development and progression of tumors in solid tumors. Vascular endothelial growth factor (VEGF) is one of the most important endothelial cell mitogen which plays a critical role in normal physiological and tumor angiogenesis.Objectives The objective of this case-control study was to investigate the association of VEGF-2578C/A, -2549 I/D, and -460T/C promoter polymorphisms with esophageal cancer risk in North-West Indians.Methods In this study, 200 sporadic esophageal cancer patients and 200 healthy, unrelated, age and gender matched controls were analyzed. The genomic DNA was extracted from blood samples using phenol chloroform method. Genotyping of VEGF-?2549I/D polymorphism was carried out by direct polymerase chain reaction (PCR) whereas VEGF -2578C/A and VEGF-460T/C) polymorphisms were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.Results AA genotype (p?=?0.005) and A allele (p?=?0.005) VEGF -2578 C/A, II genotype (p?=?0.011) and I allele (p?=?0.012) of VEGF ??2549 I/D and CC genotype (p?=?0.013) and C allele of VEGF-460T/C polymorphisms were significantly associated with increased risk of esophageal cancer. Stratification of data on the basis of gender showed that VEGF -2578 AA genotype (p?=?0.001) and A allele (p?=?0.001); VEGF -2549 II genotype (p?=?0.002) and I allele (p?=?0.002) and VEGF-?460CC genotype (p?=?0.001) and C allele (p?=?0.002) was significantly associated with increased risk of esophageal cancer in female group. Haplotype analysis revealed that A-2578 I??2549 C??460 haplotype was significantly associated with increased risk for esophageal cancer in total samples (p?=?0.008) as well as in female group (p?=?0.001).Conclusions The results of present study indicate that VEGF -2578C/A, ??2549I/D and -460T/C polymorphisms were significantly associated with increased risk of esophageal cancer in North-West Indians.
查看更多>>摘要：Abstract Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began in 2019 but it remains as a serious threat today. To reduce and prevent spread of the virus, multiple vaccines have been developed. Despite the efforts in developing vaccines, Omicron strain of the virus has recently been designated as a variant of concern (VOC) by the World Health Organization (WHO).Objective To develop a vaccine candidate against Omicron strain (B.1.1.529, BA.1) of the SARS-CoV-19.Methods We applied reverse vaccinology methods for BA.1 and BA.2 as the vaccine target and a control, respectively. First, we predicted MHC I, MHC II and B cell epitopes based on their viral genome sequences. Second, after estimation of antigenicity, allergenicity and toxicity, a vaccine construct was assembled and tested for physicochemical properties and solubility. Third, AlphaFold2, RaptorX and RoseTTAfold servers were used to predict secondary structures and 3D structures of the vaccine construct. Fourth, molecular docking analysis was performed to test binding of our construct with angiotensin converting enzyme 2 (ACE2). Lastly, we compared mutation profiles on the epitopes between BA.1, BA.2, and wild type to estimate the efficacy of the vaccine.Results We collected a total of 10 MHC I, 9 MHC II and 5 B cell epitopes for the final vaccine construct for Omicron strain. All epitopes were predicted to be antigenic, non-allergenic and non-toxic. The construct was estimated to have proper stability and solubility. The best modelled tertiary structures were selected for molecular docking analysis with ACE2 receptor.Conclusions These results suggest the potential efficacy of our newly developed vaccine construct as a novel vaccine candidate against Omicron strain of the coronavirus.
Kim Keun-SikKang Dong-WonKim Keun-YongHeo Jung Soo...
12页
查看更多>>摘要：Abstract Background The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced.Objective To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea.Methods The mitogenome was characterized using the primer walking method with phylogenetic relationships.Results The complete mitogenome of G. naktongensis Geum River was 16,607?bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNAArg and tRNATrp) and the secondary structures in the TΨC-arm of tRNAHis. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China.Conclusions Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.
Bong Ivyna Pau NiNg Ching ChingOthman NorodiyahEsa Ezalia...
10页
查看更多>>摘要：Abstract Background Current advances in the molecular biology of multiple myeloma (MM) are not sufficient to fully delineate the genesis and development of this disease.Objective This study aimed to identify molecular targets underlying MM pathogenesis.Methods mRNA expression profiling for 29 samples (19 MM samples, 7 MM cell lines and 3 controls) were obtained using microarray. We evaluated the in vitro effects of RAD54L gene silencing on the proliferation, apoptosis and cell cycle distribution in KMS-28BM human MM cells using siRNA approach. Cell proliferation was determined by MTS assay while apoptosis and cell cycle distribution were analysed with flow cytometry. Gene and protein expression was evaluated using RT-qPCR and ELISA, respectively.Results Microarray results revealed a total of 5124 differentially expressed genes (DEGs), in which 2696 and 2428 genes were up-regulated and down-regulated in MM compared to the normal controls, respectively (fold change?≥?2.0; P?<?0.05). Up-regulated genes (RAD54L, DIAPH3, SHCBP1, SKA3 and ANLN) and down-regulated genes (HKDC1, RASGRF2, CYSLTR2) have never been reported in association with MM. Up-regulation of RAD54L was further verified by RT-qPCR (P?<?0.001). In vitro functional studies revealed that RAD54L gene silencing significantly induced growth inhibition, apoptosis (small changes) and cell cycle arrest in G0/G1 phase in KMS-28BM (P?<?0.05). Silencing of RAD54L also decreased its protein level (P?<?0.05).Conclusions This study has identified possible molecular targets underlying the pathogenesis of MM. For the first time, we reveal RAD54L as a potential therapeutic target in MM, possibly?functioning in the cell cycle and checkpoint control.
查看更多>>摘要：Abstract Background Colorectal cancer (CRC) is the third most common type of diagnosed cancer in the world and has the second-highest mortality rate. Meanwhile, South Korea has the second-highest incidence rate for CRC in the world.Objective To assess the possible influence of ethnicity on the molecular profile of colorectal cancer, we compared genomic and transcriptomic features of South Korean CRCs with European CRCs.Methods We assembled a genomic and transcriptomic dataset of South Korean CRC patients (KOCRC; n?=?126) from previous studies and European cases (EUCRC; n?=?245) selected from The Cancer Genome Atlas (TCGA). Then, we compared the two datasets in terms of clinical data, driver genes, mutational signature, gene sets, consensus molecular subtype, and fusion genes.Results These two cohorts showed similar profiles in driver mutations but differences in the mutation frequencies of some driver genes (including APC, TP53, PABPC1, FAT4, MUC7, HSPG2, GNAS, DENND5B, and BRAF). Analysis of hallmark pathways using genomic data sets revealed further differences between these populations in the WNT, TP53, and NOTCH signaling pathways. In consensus molecular subtype (CMS) analyses of the study cases, no BRAF mutations were found in the CMS1 subtype of KOCRC, which contrasts with previous findings. Fusion gene analysis identified oncogenic fusion of PTPRK-RSPO3 in a subset of KOCRC patients without APC mutations.Conclusions This study presents insights into the genomic landscape of KOCRCs and reveals some similarities and differences with EUCRCs at the molecular level.
查看更多>>摘要：Abstract Background Radiotherapy resistance affects the therapeutic effect of cervical squamous cell carcinoma (CSCC). Smoothened (Smo) is an anticancer target of the Hedgehog (Hh) pathway and its mutation is related to drug resistance.Objective To explore the roles of miR-326 and Smoothened (SMO) on radiation resistance in patients with cervical carcinoma.Methods Expression of miR-326 and SMO in cervical cancer tissue and radioresistant cell lines were analyzed. The radiation response with the expression of miR-326 was evaluated in tissue and cells. Bioinformatics analysis and literature review were performed to explore the target of miR-326. The regulation of miR-326 to SMO mRNA was verified through the dual-luciferase reporter assay.Results Patients with poor radiation response have lower miR-326 and higher SMO expression. Upregulation of miR-326 decreased SMO expression and its downstream proteins but does not affect the proliferation of CSCC cells. The upregulation of miR-326 increased radiation sensitivity of the CSCC cell through downregulating SMO and its downstream proteins in the Hedgehog (Hh) signaling pathway.Conclusions miR-326 may predict the treatment response to radiation, and upregulating miR-326 may improve the treatment response to radiation.
Jin XiningZhai HuijieWang PingxiZhang Xiaoxiang...
14页
查看更多>>摘要：Abstract Background There were significant differences in the change of moisture content and grain composition at the late stage of grain development among different maize varieties, but the regulation mechanism is not clear.Objective To explore the key genes causing the variation in physiological traits of two typical maize inbred lines in late grain development.Methods The grains at different development stages were selected as materials to determine the content of water, sucrose, starch and ABA. Transcriptomic and proteomic analysis of the materials were performed to screen relevant genes.Results The grain dehydration rate and the content of sucrose, starch and ABA were showed significant differences between two varieties in the late stage of grain development. The enrichment analysis of common differentially expressed genes (proteins) showed that most of the genes (proteins) were enriched in the extracellular region. The downregulated genes were mainly concentrated in carbohydrate metabolism and lipid metabolism, while the upregulated genes were mainly in response to stress. Furthermore, this study also identified many key candidate genes (dehydrin genes, pathogenesis-related genes, sucrose synthase and secondary metabolites related genes) related to late grain development of maize.Conclusions The suggested genes related to late grain development of maize can be candidates for further functional study.
查看更多>>摘要：Abstract Background Charcot-Marie-Tooth disease type 1C (CMT1C) is a rare subtype associated with LITAF gene mutations. Until now, only a few studies have reported the clinical features of CMT1C.Objective This study was performed to find CMT1C patients with mutation of LITAF in a Korean CMT cohort and to characterize their clinical features.Methods In total, 1,143 unrelated Korean families with CMT were enrolled in a cohort. We performed whole exome sequencing to identify LITAF mutations, and examined clinical phenotypes including electrophysiological and MRI features for the identified CMT1C patients.Results We identified 10 CMT1C patients from three unrelated families with p.G112S mutation in LITAF. The frequency of CMT1C among CMT1 patients was 0.59%, which is similar to reports from Western populations. CMT1C patients showed milder symptoms than CMT1A patients. The mean CMT neuropathy score version 2 was 7.7, and the mean functional disability scale was 1.0. Electrophysiological findings showed a conduction block in 22% of affected individuals. Lower extremity MRIs showed that the superficial posterior and anterolateral compartments of the calf were predominantly affected.Conclusions We found a conduction block in Korean CMT1C patients with p.G112S mutation and first described the characteristic MRI findings of the lower extremities in patients with LITAF mutation. These findings will be helpful for genotype–phenotype correlation and will widen understanding about the clinical spectrum of CMT1C.
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