Tapan Kumar Mohanta, Yugal Kishore Mohanta, Ahmed Al-Harrasi
{"title":"Decoding the Virtual 2D Map of the Chloroplast Proteomes.","authors":"Tapan Kumar Mohanta, Yugal Kishore Mohanta, Ahmed Al-Harrasi","doi":"10.1186/s12575-022-00186-8","DOIUrl":"https://doi.org/10.1186/s12575-022-00186-8","url":null,"abstract":"<p><strong>Background: </strong>The chloroplast is a semi-autonomous organelle having its own genome and corresponding proteome. Although chloroplast genomes have been reported, no reports exist on their corresponding proteomes. Therefore, a proteome-wide analysis of the chloroplast proteomes of 2893 species was conducted, and a virtual 2D map was constructed.</p><p><strong>Results: </strong>The resulting virtual 2D map of the chloroplast proteome exhibited a bimodal distribution. The molecular mass of the chloroplast proteome ranged from 0.448 to 616.334 kDa, and the isoelectric point (pI) ranged from 2.854 to 12.954. Chloroplast proteomes were dominated by basic pI proteins with an average pI of 7.852. The molecular weight and isoelectric point of chloroplast proteome were found to show bimodal distribution. Leu was the most abundant and Cys the least abundant amino acid in the chloroplast proteome. Notably, Trp amino acid was absent in the chloroplast protein sequences of Pilostyles aethiopica. In addition, Selenocysteine (Sec) and Pyrrolysine (Pyl) amino acids were also found to be lacking in the chloroplast proteomes.</p><p><strong>Conclusion: </strong>The virtual 2D map and amino acid composition of chloroplast proteome will enable the researchers to understand the biochemistry of chloroplast protein in detail. Further, the amino acid composition of the chloroplast proteome will also allow us to understand the codon usage bias. The codon usage bias and amino acid usage bias of chloroplast will be crucial to understanding their relationship.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"23"},"PeriodicalIF":6.4,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9749319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10366754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiangyu Li, Kai Zhao, Yun Lu, Jianming Wang, Wei Yao
{"title":"Genetic Analysis of Platelet-Related Genes in Hepatocellular Carcinoma Reveals a Novel Prognostic Signature and Determines PRKCD as the Potential Molecular Bridge.","authors":"Xiangyu Li, Kai Zhao, Yun Lu, Jianming Wang, Wei Yao","doi":"10.1186/s12575-022-00185-9","DOIUrl":"10.1186/s12575-022-00185-9","url":null,"abstract":"<p><strong>Background: </strong>Hepatocellular carcinoma (HCC) belongs to a representative lethality gastrointestinal malignancy, and comprehensive management of HCC remains intractable at present on account of its invasive biological feature that is easy to relapse and early metastasis. The intimate connection between platelets and tumor progression has been widely reported, and platelet-related indicators are also used in the clinical practice of carcinoma. This work is designed to investigate the significance of platelet-related genes in the prognostic prediction of patients with HCC and their potential role in the cross-talk between HCC cells and platelets in the tumor microenvironment.</p><p><strong>Methods: </strong>By integrating the RNA-seq data and clinicopathological information of HCC patients, we extracted prognosis-associated platelet-related genes based on the univariate cox analysis and further established a relevant prognostic signature via the lasso cox regression analysis, and two independent HCC cohorts were used as external validation. Multiple bioinformatics methods were utilized to explore the underlying functional discrepancy between different risk groups classified by the risk model. And in vitro proliferation, invasion, and migration assays were conducted to investigate the effect of platelet stimulation on HCC cells' viability and motility, and flow cytometric analysis was exerted to demonstrate the influence of HCC cells on platelet activation.</p><p><strong>Results: </strong>A novel platelet-related risk model was developed and patients both in the training and testing cohorts were divided into distinct risk subgroups according to the median risk score. It was observed that the high-risk status was closely associated with poor prognosis and worse clinicopathological parameters. Meanwhile, an obvious discrepancy in the constitution of the immune microenvironment also indicated that distinct immune status might be a potential determinant affecting prognosis as well as immunotherapy reactiveness. Moreover, in vitro experiments demonstrated that PRKCD could act as a molecular bridge between tumor cells and platelets, which could either participate in regulating tumor malignant phenotype or mediating platelet activation.</p><p><strong>Conclusions: </strong>In brief, this work reveals a novel platelet-related risk signature for prognostic evaluation of HCC patients and confirms that PRKCD is a key messenger in HCC cell-platelet interaction and plays a crucial role in mediating platelet-induced tumor progression.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"22"},"PeriodicalIF":3.7,"publicationDate":"2022-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9719151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10333145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Circadian gene CSNK1D promoted the progression of hepatocellular carcinoma by activating Wnt/β-catenin pathway via stabilizing Dishevelled Segment Polarity Protein 3.","authors":"Mengqi Zhu, Jianping Zhang, Saiyan Bian, Xue Zhang, Yiping Shen, Zhiyu Ni, Shiyu Xu, Chun Cheng, Wenjie Zheng","doi":"10.1186/s12575-022-00183-x","DOIUrl":"https://doi.org/10.1186/s12575-022-00183-x","url":null,"abstract":"<p><strong>Purpose: </strong>A variety of studies have connected circadian rhythm to the initiation and progression of hepatocellular carcinoma (HCC). The purpose of this study was to figure out about the circadian genes' profile characteristics, prognostic significance, and targeted values in HCC.</p><p><strong>Methods: </strong>The expression profiles and prognostic significance of circadian genes in the cancer genome atlas liver hepatocellular carcinoma (TCGA-LIHC) database were investigated using bioinformatics analysis. The expression features of Casein Kinase 1 Delta (CSNK1D), a robust signature gene, was further detected by immunohistochemistry, western blotting and Real-time quantitative PCR (RT-qPCR) in a local HCC cohort. The effect of CSNK1D on corresponding phenotypes of HCC cells was evaluated using Cell Counting Kit-8 (CCK8), flowcytometry, clone assay, Transwell assay, and xenograft assay. In addition, the underlying mechanisms of CSNK1D in the Wnt/β-catenin signaling were validated by multiple molecular experiments.</p><p><strong>Results: </strong>Abnormal expression of the Circadian genome was associated with the malignant clinicopathological characteristics of HCC patients. A 10 circadian gene-based signature with substantial prognostic significance was developed using Cox regression and least absolute shrinkage and selection operator (LASSO) analysis. Of them, CSNK1D, significantly elevated in a local HCC cohort, was chosen for further investigation. Silencing or overexpression of CSNK1D significantly reduced or increased proliferation, invasion, sorafenib resistance, xenograft development, and epithelial-mesenchymal transformation (EMT) of HCC cells, respectively. Mechanically, CSNK1D exacerbated the aggressiveness of HCC cells by activating Wnt/β-catenin signaling through interacting with Dishevelled Segment Polarity Protein 3 (DVL3).</p><p><strong>Conclusions: </strong>The Circadian gene CSNK1D was found to contribute to HCC progression by boosting the Wnt/β-catenin pathway, hinting that it could be a prospective therapeutic target for HCC.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"21"},"PeriodicalIF":6.4,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9717411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10321211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The untargeted urine volatilome for biomedical applications: methodology and volatilome database.","authors":"Maria Llambrich, Jesús Brezmes, Raquel Cumeras","doi":"10.1186/s12575-022-00184-w","DOIUrl":"10.1186/s12575-022-00184-w","url":null,"abstract":"<p><p>Chemically diverse in compounds, urine can give us an insight into metabolic breakdown products from foods, drinks, drugs, environmental contaminants, endogenous waste metabolites, and bacterial by-products. Hundreds of them are volatile compounds; however, their composition has never been provided in detail, nor has the methodology used for urine volatilome untargeted analysis. Here, we summarize key elements for the untargeted analysis of urine volatilome from a comprehensive compilation of literature, including the latest reports published. Current achievements and limitations on each process step are discussed and compared. 34 studies were found retrieving all information from the urine treatment to the final results obtained. In this report, we provide the first specific urine volatilome database, consisting of 841 compounds from 80 different chemical classes.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"20"},"PeriodicalIF":6.4,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9714113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10321195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bashar Haruna Gulumbe, Usman Abubakar Haruna, Joseph Almazan, Ibrahim Haruna Ibrahim, Abdullahi Adamu Faggo, Abbas Yusuf Bazata
{"title":"Combating the menace of antimicrobial resistance in Africa: a review on stewardship, surveillance and diagnostic strategies.","authors":"Bashar Haruna Gulumbe, Usman Abubakar Haruna, Joseph Almazan, Ibrahim Haruna Ibrahim, Abdullahi Adamu Faggo, Abbas Yusuf Bazata","doi":"10.1186/s12575-022-00182-y","DOIUrl":"10.1186/s12575-022-00182-y","url":null,"abstract":"<p><p>The emergence of antibiotic-resistant pathogens has threatened not only our ability to deal with common infectious diseases but also the management of life-threatening complications. Antimicrobial resistance (AMR) remains a significant threat in both industrialized and developing countries alike. In Africa, though, poor clinical care, indiscriminate antibiotic use, lack of robust AMR surveillance programs, lack of proper regulations and the burden of communicable diseases are factors aggravating the problem of AMR. In order to effectively address the challenge of AMR, antimicrobial stewardship programs, solid AMR surveillance systems to monitor the trend of resistance, as well as robust, affordable and rapid diagnostic tools which generate data that informs decision-making, have been demonstrated to be effective. However, we have identified a significant knowledge gap in the area of the application of fast and affordable diagnostic tools, surveillance, and stewardship programs in Africa. Therefore, we set out to provide up-to-date information in these areas. We discussed available hospital-based stewardship initiatives in addition to the role of governmental and non-governmental organizations. Finally, we have reviewed the application of various phenotypic and molecular AMR detection tools in both research and routine laboratory settings in Africa, deployment challenges and the efficiency of these methods.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"24 1","pages":"19"},"PeriodicalIF":3.7,"publicationDate":"2022-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9685880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10384510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giulia Santopolo, Antonio Clemente, Estrella Rojo-Molinero, Sara Fernández, María Concepción Álvarez, Antonio Oliver, Roberto de la Rica
{"title":"Improved cytometric analysis of untouched lung leukocytes by enzymatic liquefaction of sputum samples.","authors":"Giulia Santopolo, Antonio Clemente, Estrella Rojo-Molinero, Sara Fernández, María Concepción Álvarez, Antonio Oliver, Roberto de la Rica","doi":"10.1186/s12575-022-00181-z","DOIUrl":"https://doi.org/10.1186/s12575-022-00181-z","url":null,"abstract":"<p><strong>Background: </strong>Phenotyping sputum-resident leukocytes and evaluating their functional status are essential analyses for exploring the cellular basis of pathological processes in the lungs, and flow cytometry is widely recognized as the gold-standard technique to address them. However, sputum-resident leukocytes are found in respiratory samples which need to be liquefied prior to cytometric analysis. Traditional liquefying procedures involve the use of a reducing agent such as dithiothreitol (DTT) in temperature-controlled conditions, which does not homogenize respiratory samples efficiently and impairs cell viability and functionality.</p><p><strong>Methods: </strong>Here we propose an enzymatic method that rapidly liquefies samples by means of generating O<sub>2</sub> bubbles with endogenous catalase. Sputum specimens from patients with suspected pulmonary infection were treated with DTT, the enzymatic method or PBS. We used turbidimetry to compare the liquefaction degree and cell counts were determined using a hemocytometer. Finally, we conducted a comparative flow cytometry study for evaluating frequencies of sputum-resident neutrophils, eosinophils and lymphocytes and their activation status after liquefaction.</p><p><strong>Results: </strong>Enzymatically treated samples were better liquefied than those treated with DTT or PBS, which resulted in a more accurate cytometric analysis. Frequencies of all cell subsets analyzed within liquefied samples were comparable between liquefaction methods. However, the gentle cell handling rendered by the enzymatic method improves cell viability and retains in vivo functional characteristics of sputum-resident leukocytes (with regard to HLA-DR, CD63 and CD11b expression).</p><p><strong>Conclusion: </strong>In conclusion, the proposed enzymatic liquefaction method improves the cytometric analysis of respiratory samples and leaves the cells widely untouched for properly addressing functional analysis of lung leukocytes.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":" ","pages":"17"},"PeriodicalIF":6.4,"publicationDate":"2022-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9673301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40496652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hyueyun Kim, Ji Ha Choi, C. Moon, J. Kang, M. Woo, Minsuk Kim
{"title":"Shrimp miR-965 transfers tumoricidal mitochondria","authors":"Hyueyun Kim, Ji Ha Choi, C. Moon, J. Kang, M. Woo, Minsuk Kim","doi":"10.1186/s12575-022-00178-8","DOIUrl":"https://doi.org/10.1186/s12575-022-00178-8","url":null,"abstract":"","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":" ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42149571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xu Zhang, Wenwen Chen, Dan Guo, Yarui Li, Yan Zhao, Mudan Ren, Guifang Lu, Xinlan Lu, Shuixiang He
{"title":"Circ_0003570 Suppresses the progression of hepatocellular carcinoma through miR-182-5p/STARD13 regulatory axis.","authors":"Xu Zhang, Wenwen Chen, Dan Guo, Yarui Li, Yan Zhao, Mudan Ren, Guifang Lu, Xinlan Lu, Shuixiang He","doi":"10.1186/s12575-022-00176-w","DOIUrl":"https://doi.org/10.1186/s12575-022-00176-w","url":null,"abstract":"<p><strong>Background: </strong>Emerging evidence have revealed that circRNAs exert important biological effects in the development and progression of various diseases, including cancer. Our study aimed to elaborated the biological effects of hsa-circ_0003570 in hepatocellular carcinoma (HCC) development at the molecular level.</p><p><strong>Results: </strong>The results of functional experiments showed that knockdown of circ_0003570 induced HCC cell growth, migration and invasion, whereas overexpression of circ_0003570 presented the opposite effects. In vivo experiments, xenograft tumors grown from circ-overexpressed cells had smaller tumor volume and weight than the control group. Further investigations suggested that circ_0003570 may function as a competing endogenous RNA via competitively binding miR-182-5p and thereby regulating the repression of downstream target gene STARD13, which were demonstrated by dual luciferase reporter assay and functional rescued experiments.</p><p><strong>Conclusions: </strong>Taken together, circ_0003570 suppresses the development of HCC by modulating miR-182-5p/STARD13 axis.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":" ","pages":"14"},"PeriodicalIF":6.4,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9563790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33513219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Single-cell and WGCNA uncover a prognostic model and potential oncogenes in colorectal cancer.","authors":"Ziyang Di, Sicheng Zhou, Gaoran Xu, Lian Ren, Chengxin Li, Zheyu Ding, Kaixin Huang, Leilei Liang, Yihang Yuan","doi":"10.1186/s12575-022-00175-x","DOIUrl":"https://doi.org/10.1186/s12575-022-00175-x","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. Single-cell transcriptome sequencing (scRNA-seq) can provide accurate gene expression data for individual cells. In this study, a new prognostic model was constructed by scRNA-seq and bulk transcriptome sequencing (bulk RNA-seq) data of CRC samples to develop a new understanding of CRC.</p><p><strong>Methods: </strong>CRC scRNA-seq data were downloaded from the GSE161277 database, and CRC bulk RNA-seq data were downloaded from the TCGA and GSE17537 databases. The cells were clustered by the FindNeighbors and FindClusters functions in scRNA-seq data. CIBERSORTx was applied to detect the abundance of cell clusters in the bulk RNA-seq expression matrix. WGCNA was performed with the expression profiles to construct the gene coexpression networks of TCGA-CRC. Next, we used a tenfold cross test to construct the model and a nomogram to assess the independence of the model for clinical application. Finally, we examined the expression of the unreported model genes by qPCR and immunohistochemistry. A clone formation assay and orthotopic colorectal tumour model were applied to detect the regulatory roles of unreported model genes.</p><p><strong>Results: </strong>A total of 43,851 cells were included after quality control, and 20 cell clusters were classified by the FindCluster () function. We found that the abundances of C1, C2, C4, C5, C15, C16 and C19 were high and the abundances of C7, C10, C11, C13, C14 and C17 were low in CRC tumour tissues. Meanwhile, the results of survival analysis showed that high abundances of C4, C11 and C13 and low abundances of C5 and C14 were associated with better survival. The WGCNA results showed that the red module was most related to the tumour and the C14 cluster, which contains 615 genes. Lasso Cox regression analysis revealed 8 genes (PBXIP1, MPMZ, SCARA3, INA, ILK, MPP2, L1CAM and FLNA), which were chosen to construct a risk model. In the model, the risk score features had the greatest impact on survival prediction, indicating that the 8-gene risk model can better predict prognosis. qPCR and immunohistochemistry analysis showed that the expression levels of MPZ, SCARA3, MPP2 and PBXIP1 were high in CRC tissues. The functional experiment results indicated that MPZ, SCARA3, MPP2 and PBXIP1 could promote the colony formation ability of CRC cells in vitro and tumorigenicity in vivo.</p><p><strong>Conclusions: </strong>We constructed a risk model to predict the prognosis of CRC patients based on scRNA-seq and bulk RNA-seq data, which could be used for clinical application. We also identified 4 previously unreported model genes (MPZ, SCARA3, MPP2 and PBXIP1) as novel oncogenes in CRC. These results suggest that this model could potentially be used to evaluate the prognostic risk and provide potential therapeutic targets for CRC patients.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":" ","pages":"13"},"PeriodicalIF":6.4,"publicationDate":"2022-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9484253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40365112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}