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1.
Chinese Journal of Biotechnology ; (12): 1815-1824, 2023.
Article in Chinese | WPRIM | ID: wpr-981172

ABSTRACT

Antimicrobial peptides (AMPs) are small molecule peptides that are widely found in living organisms with broad-spectrum antibacterial activity and immunomodulatory effect. Due to slower emergence of resistance, excellent clinical potential and wide range of application, AMP is a strong alternative to conventional antibiotics. AMP recognition is a significant direction in the field of AMP research. The high cost, low efficiency and long period shortcomings of the wet experiment methods prevent it from meeting the need for the large-scale AMP recognition. Therefore, computer-aided identification methods are important supplements to AMP recognition approaches, and one of the key issues is how to improve the accuracy. Protein sequences could be approximated as a language composed of amino acids. Consequently, rich features may be extracted using natural language processing (NLP) techniques. In this paper, we combine the pre-trained model BERT and the fine-tuned structure Text-CNN in the field of NLP to model protein languages, develop an open-source available antimicrobial peptide recognition tool and conduct a comparison with other five published tools. The experimental results show that the optimization of the two-phase training approach brings an overall improvement in accuracy, sensitivity, specificity, and Matthew correlation coefficient, offering a novel approach for further research on AMP recognition.


Subject(s)
Anti-Bacterial Agents/chemistry , Amino Acid Sequence , Antimicrobial Cationic Peptides/chemistry , Antimicrobial Peptides , Natural Language Processing
2.
Chinese Journal of Biotechnology ; (12): 3772-3786, 2023.
Article in Chinese | WPRIM | ID: wpr-1007992

ABSTRACT

Dorsal root ganglia (DRG) is an essential part of the peripheral nervous system and the hub of the peripheral sensory afferent. The dynamic changes of neuronal cells and their gene expression during the development of dorsal root ganglion have been studied through single-cell RNAseq analysis, while the dynamic changes of non-neuronal cells have not been systematically studied. Using single cell RNA sequencing technology, we conducted a research on the non-neuronal cells in the dorsal root ganglia of rats at different developmental stage. In this study, primary cell suspension was obtained from using the dorsal root ganglions (DRGs, L4-L5) of ten 7-day-old rats and three 3-month-old rats. The 10×Genomics platform was used for single cell dissociation and RNA sequencing. Twenty cell subsets were acquired through cluster dimension reduction analysis, and the marker genes of different types of cells in DRG were identified according to previous researches about DRG single cell transcriptome sequencing. In order to find out the non-neuronal cell subsets with significant differences at different development stage, the cells were classified into different cell types according to markers collected from previous researches. We performed pseudotime analysis of 4 types Schwann cells. It was found that subtype Ⅱ Schwann cells emerged firstly, and then were subtype Ⅲ Schwann cells and subtype Ⅳ Schwann cells, while subtype Ⅰ Schwann cells existed during the whole development procedure. Pseudotime analysis indicated the essential genes influencing cell fate of different subtypes of Schwann cell in DRG, such as Ntrk2 and Pmp2, which affected cell fate of Schwann cells during the development period. GO analysis of differential expressed genes showed that the up-regulated genes, such as Cst3 and Spp1, were closely related to biological process of tissue homeostasis and multi-multicellular organism process. The down regulated key genes, such as Col3a1 and Col4a1, had close relationship with the progress of extracellular structure organization and negative regulation of cell adhesion. This suggested that the expression of genes enhancing cell homestasis increased, while the expression of related genes regulating ECM-receptor interaction pathway decreased during the development. The discovery provided valuable information and brand-new perspectives for the study on the physical and developmental mechanism of Schwann cell as well as the non-neuronal cell changes in DRG at different developmental stage. The differential gene expression results provided crucial references for the mechanism of somatosensory maturation during development.


Subject(s)
Rats , Animals , Ganglia, Spinal/metabolism , Rats, Sprague-Dawley , Transcriptome , Neurons/metabolism , Schwann Cells/physiology
3.
Article in Chinese | WPRIM | ID: wpr-1038383

ABSTRACT

Objective@#To explore method for isolating and culturing human epidermal stem cells ( EPSCs) in vitro and isolating and purifying epidermal stem cell exsomes ( EPSCs-Exo) by optimizing the technical process.@*Method@#Firstly,the improved separating enzyme was used to isolate the EPSCs derived from human skin tissue.Then,an improved serum-free culture medium and 10 specific factors were combined to construct optimized 2D culture medium which could stimulate the growth of EPSCs,promote the secretion of EPSCs-Exo,maintain the stemness and proliferation of EPSCs,and delay the differentiation and maturation of EPSCs. Further,the conditions of differential centrifugation was optimized,and then the human EPSCs-Exo was successfully extracted with high efficiency and high purity.@*Results@#The human skin tissue was confirmed with the expressions of markers for epidermal cells. EPSCs were verified with high expression levels of integrin-α6,integrin-β1,P63 and CK19 by immunofluorescence staining and Western blot. The nanoparticle tracking analysis results showed the particles separated for EPSCs supernatant was saucepan with the detected diameter between 30 - 150 nm. The Western blot results showed the positive expression of membrane markers Tsg101,CD9 and CD63 and the negative expression of intracellular markers Calnexin and GAPDH.@*Conclusion@#The results show that the human-derived EPSCs have been successfully isolated and cultured in vitro,and the EPSCs-Exo have been successfully isolated and identified.

4.
Chinese Journal of Biotechnology ; (12): 961-975, 2022.
Article in Chinese | WPRIM | ID: wpr-927757

ABSTRACT

Chromatography is a basic process in the current proteomics workflow, and the retention time alignment of the chromatogram is one of the important steps to effectively improve the identification and quantification accuracy. After years of development, a series of algorithms for retention time alignment have been developed. This review summarizes the advances of chromatographic retention time alignment algorithms and tools for proteomics analysis from the perspective of proteomics users, and discusses the development and future application directions.


Subject(s)
Algorithms , Proteomics/methods
5.
Chinese Journal of Biotechnology ; (12): 4111-4123, 2021.
Article in Chinese | WPRIM | ID: wpr-921492

ABSTRACT

In case/control gene expression data, differential expression (DE) represents changes in gene expression levels across various biological conditions, whereas differential co-expression (DC) represents an alteration of correlation coefficients between gene pairs. Both DC and DE genes have been studied extensively in human diseases. However, effective approaches for integrating DC-DE analyses are lacking. Here, we report a novel analytical framework named DC&DEmodule for integrating DC and DE analyses and combining information from multiple case/control expression datasets to identify disease-related gene co-expression modules. This includes activated modules (gaining co-expression and up-regulated in disease) and dysfunctional modules (losing co-expression and down-regulated in disease). By applying this framework to microarray data associated with liver, gastric and colon cancer, we identified two, five and two activated modules and five, five and one dysfunctional module(s), respectively. Compared with the other methods, pathway enrichment analysis demonstrated the superior sensitivity of our method in detecting both known cancer-related pathways and those not previously reported. Moreover, we identified 17, 69, and 11 module hub genes that were activated in three cancers, which included 53 known and three novel cancer prognostic markers. Random forest classifiers trained by the hub genes showed an average of 93% accuracy in differentiating tumor and adjacent normal samples in the TCGA and GEO database. Comparison of the three cancers provided new insights into common and tissue-specific cancer mechanisms. A series of evaluations demonstrated the framework is capable of integrating the rapidly accumulated expression data and facilitating the discovery of dysregulated processes.


Subject(s)
Humans , Gene Expression Profiling , Gene Regulatory Networks , Microarray Analysis , Neoplasms/genetics
6.
Chinese Journal of Biotechnology ; (12): 2393-2404, 2021.
Article in Chinese | WPRIM | ID: wpr-887805

ABSTRACT

Cancers have been widely recognized as highly heterogeneous diseases, and early diagnosis and prognosis of cancer types have become the focus of cancer research. In the era of big data, efficient mining of massive biomedical data has become a grand challenge for bioinformatics research. As a typical neural network model, the autoencoder is able to efficiently learn the features of input data by unsupervised training method and further help integrate and mine the biological data. In this article, the primary structure and workflow of the autoencoder model are introduced, followed by summarizing the advances of the autoencoder model in cancer informatics using various types of biomedical data. Finally, the challenges and perspectives of the autoencoder model are discussed.


Subject(s)
Humans , Algorithms , Informatics , Neoplasms/diagnosis , Neural Networks, Computer
7.
Chinese Journal of Biotechnology ; (12): 1619-1632, 2019.
Article in Chinese | WPRIM | ID: wpr-771768

ABSTRACT

With the development of mass spectrometry technologies and bioinformatics analysis algorithms, disease research-driven human proteome project (HPP) is advancing rapidly. Protein biomarkers play critical roles in clinical applications and the biomarker discovery strategies and methods have become one of research hotspots. Feature selection and machine learning methods have good effects on solving the "dimensionality" and "sparsity" problems of proteomics data, which have been widely used in the discovery of protein biomarkers. Here, we systematically review the strategy of protein biomarker discovery and the frequently-used machine learning methods. Also, the review illustrates the prospects and limitations of deep learning in this field. It is aimed at providing a valuable reference for corresponding researchers.


Subject(s)
Humans , Algorithms , Biomarkers , Machine Learning , Mass Spectrometry , Proteomics
8.
Chinese Journal of Biotechnology ; (12): 1571-1580, 2019.
Article in Chinese | WPRIM | ID: wpr-771772

ABSTRACT

Extracellular matrix (ECM) proteins play an important role in a series of biological processes in the cell, and their abnormal regulation can lead to many diseases. The theoretical ECM reference dataset is the basis for efficient identification of extracellular matrix proteins. Researchers have developed various ECM protein prediction tools based on machine learning methods. In this review, the main strategy of development of ECM protein prediction tools that based on machine learning methods has been introduced. Then, advances and specific characters of the existing ECM protein prediction tools have been summarized. Finally, the challenges and possible improvements of ECM protein prediction tools are discussed.


Subject(s)
Extracellular Matrix , Extracellular Matrix Proteins
9.
Chinese Journal of Biotechnology ; (12): 1295-1306, 2019.
Article in Chinese | WPRIM | ID: wpr-771799

ABSTRACT

Tumor-specific gene mutations might generate suitable neoepitopes for cancer immunotherapy that are highly immunogenic and absent in normal tissues. The high heterogeneity of the tumor genome poses a big challenge for precision cancer immunotherapy. Mutations characteristic of each tumor can help to distinguish it from other tumors. Based on these mutations' characteristic, it is possible to develop immunotherapeutic strategies for specific tumors. In this study, a tumor neoantigen prediction scheme was proposed, in which both the intracellular antigen presentation process and the ability to bind with extracellular MHC molecule were taken into consideration. The overall design is meritorious and may help reduce the cost for validation experiments compared with conventional methods. This strategy was tested with several cancer genome datasets in the TCGA database, and a number of potential tumor neoantigens were predicted for each dataset. These predicted neoantigens showed tumor type specificity and were found in 20% to 70% of cancer patients. This scheme might prove useful clinically in future.


Subject(s)
Humans , Antigens, Neoplasm , Computational Biology , Genome, Human , Immunotherapy , Mutation , Neoplasms
10.
Chinese Journal of Biotechnology ; (12): 525-536, 2018.
Article in Chinese | WPRIM | ID: wpr-690151

ABSTRACT

Exponential growth of the mass spectrometry (MS) data is exhibited when the mass spectrometry-based proteomics has been developing rapidly. It is a great challenge to develop some quick, accurate and repeatable methods to identify peptides and proteins. Nowadays, the spectral library searching has become a mature strategy for tandem mass spectra based proteins identification in proteomics, which searches the experiment spectra against a collection of confidently identified MS/MS spectra that have been observed previously, and fully utilizes the abundance in the spectrum, peaks from non-canonical fragment ions, and other features. This review provides an overview of the implement of spectral library search strategy, and two key steps, spectral library construction and spectral library searching comprehensively, and discusses the progress and challenge of the library search strategy.

11.
Military Medical Sciences ; (12): 111-116, 2015.
Article in Chinese | WPRIM | ID: wpr-460247

ABSTRACT

Objective China has the biggest population of commonly encountered liver diseases , so hepatology resear-ches are of great importance to human health .In order to comprehensively collect/organize and effectively share/display liv-er physiopathology knowledge scattered around databases and literature , a Human Liver Disease Ontology ( HuLDO ) is built and applied in many ways .Methods HuLDO systematically classified and annotated various human liver diseases based on extensive cross mapping and integration of several authoritative nomenclatures of diseases and two monographs of hepatology .Results In the present version , HuLDO encompassed knowledge of 227 human liver diseases and was enriched by plenty of synonyms,definitions, descriptions, references, and logical or pathological relations between different disea-ses.Compared with other existing nomenclatures , HuLDO extended far beyond them in the scope of liver diseases .Several applications of HuLDO in database construction , knowledge collection and text mining were also described .Conclusion HuLDO offers a sound basis for knowledge mining , data integration and data analysis in the field of hepatology .HuLDO is publicly available at ftp://liveratlas.hupo.org.cn/5.liver 5.liver%20Disease%20Ontology/.

12.
Chinese Journal of Biotechnology ; (12): 1094-1104, 2014.
Article in Chinese | WPRIM | ID: wpr-279444

ABSTRACT

As a statistical method integrating multi-features and multi-data, meta-analysis was introduced to the field of life science in the 1990s. With the rapid advances in high-throughput technologies, life omics, the core of which are genomics, transcriptomics and proteomics, is becoming the new hot spot of life science. Although the fast output of massive data has promoted the development of omics study, it results in excessive data that are difficult to integrate systematically. In this case, meta-analysis is frequently applied to analyze different types of data and is improved continuously. Here, we first summarize the representative meta-analysis methods systematically, and then study the current applications of meta-analysis in various omics fields, finally we discuss the still-existing problems and the future development of meta-analysis.


Subject(s)
Genomics , Meta-Analysis as Topic , Proteomics , Statistics as Topic
13.
Chinese Journal of Biotechnology ; (12): 1026-1035, 2014.
Article in Chinese | WPRIM | ID: wpr-279449

ABSTRACT

With the rapid development of genome sequencing technologies, a large amount of prokaryote genomes have been sequenced in recent years. To further investigate the models and functions of genomes, the algorithms for genome annotations based on the sequence and homology features have been widely implemented to newly sequenced genomes. However, gene annotations only using the genomic information are prone to errors, such as the incorrect N-terminals and pseudogenes. It is even harder to provide reasonable annotating results in the case of the poor genome sequencing results. The transcriptomics based on the technologies such as microarray and RNA-seq and the proteomics based on the MS/MS have been used widely to identify the gene products with high throughput and high sensitivity, providing the powerful tools for the verification and correction of annotated genome. Compared with transcriptomics, proteomics can generate the protein list for the expressed genes in the samples or cells without any confusion of the non-coding RNA, leading the proteogenomics an important basis for the genome annotations in prokaryotes. In this paper, we first described the traditional genome annotation algorithms and pointed out the shortcomings. Then we summarized the advantages of proteomics in the genome annotations and reviewed the progress of proteogenomics in prokaryotes. Finally we discussed the challenges and strategies in the data analyses and potential solutions for the developments of proteogenomics.


Subject(s)
Genomics , Molecular Sequence Annotation , Prokaryotic Cells , Metabolism , Proteomics , Tandem Mass Spectrometry
14.
Article in Chinese | WPRIM | ID: wpr-403803

ABSTRACT

As the complexity of samples and experimental processes, the repeatability of mass spectrometry experiments is still not satisfactory, the results of peptide identification and quantification show high randomicity), the probability of peptide being detected by mass spectrometry in proteome research, especially in quantitative proteomic study, has received much attention. Therefore, a lot of experimental researches have been done, as well as a number of computational prediction methods have been developed. In this article, we summarized the important factors impacting the peptide detectability, investigated the existing prediction methods) and reviewed their applications in experimental study.

15.
Article in Chinese | WPRIM | ID: wpr-399243

ABSTRACT

Objective To evaluate the effect of continuous aspiration of subglottic secretions (CASS) on the prevention of ventilator-associated pneumonia (VAP) in mechanically ventilated patients. Methods Patients ventilated mechanically at the ICU from October, 2004 to April,2006 were randomly divided into 2 groups: one group received CASS and the other did not (NASS group). CASS was performed immediately after admission for patients in the CASS group. The diagnosis d VAP was made based on clinical presentations, and the evaluation of YAP was done using simplified version of the clinical pulmonary infection score (CPIS). The general status of the patients, days of ventilated treatment, the volume of daily aspirated aubglottic secretions, the morbidity and timing of VAP, days of stay in ICU and mortality within 28 days of hospitalization were recorded. Results One hundred and one patients were included in the study. There were 48 patients in the CASS group who were treated with mechanical ventilation more than 48 hours,and 43 patients in the NASS group. There was no significant difference in the general status of the patients and days of ventilation between 2 groups with the averaged score of APACHE Ⅱ being 20.8± 6.1. The average of CPIS was of 5.6±1.0 when VAP was diagnosed. The mean volume of aspirated subglottic secretions within the first 24 hours in the CASS group (n=48) was (27.2±21.2)ml. The morbidity of VAP in the CASS and the NASS groups was 25.0% and 46. 5% respectively (P=0.032), and the length of time before the onset of VAP in these 2 groups was (7.3±4.2) days and (5.1±3.0) days respectively (P=0.100). There was a significant increase in the percentage of gram-positive cocci from the lower respiratory tracts in the NASS group compared with that in the CASS group (P=0.004). In the CASS group, the volume of the first daily aspirated subglottic secretions in patients with VAP was significantly less than that in patients without VAP(P =0.006). The morbidity of VAP in patients with failed early aspiration (the volume of first daily aspirated secretions≤20 ml) was significantly higher than that in patients in whom the aspiration was effective (P<0.01). The length of mechanical ventilation in patients with VAP was significantly longer than that in patients without VAP(P=0.000). The in-hospital mortality in patients with VAP was significantly higher than that in patients without VAP(P=0.009), and the mortality in 28 days after admission in patients with VAP was significantly higher than that in patients without VAP(P=0.035).Conclusion Effective continuous aspiration of subglottic secretions could significantly reduce the morbidity of early-onset VAP.

16.
Article in Chinese | WPRIM | ID: wpr-589695

ABSTRACT

The combination of tandem spectrometry and database searching is one of the most popular technologies for protein identification.However,only those proteins in the searching database could be identified,and current database is far from completeness.So it is necessary to mining the MS/MS data comprehensively,in which novel protein identification is the most important one.The definition of novel protein could be divided into three levels according to their annotations of sequences and functions.As a part of protein identification,the main approaches used to identify novel protein are basing on the following two different ways:de novo sequencing combined with similarity search and searching against nucleotide acid databases such as EST or genome databases.Several mature or newly developed methods and techniques were summarized,and the problems and strategies discussed here would be helpful for the related researches.

17.
Article in Chinese | WPRIM | ID: wpr-409592

ABSTRACT

Data analysis poses a significant challenge to the large-scale proteomics studies. Based on the structured and controlled vocabularies-Gene Ontology (GO), and the GO annotation from related databases, a strategy composed of several programs and local databases is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration. This strategy has been successfully used in the Human Fetal Liver (HFL) proteomic research, which is available online at http://www.hupo.org.cn/GOfact/.

18.
Article in English | WPRIM | ID: wpr-57929

ABSTRACT

PURPOSE: The purpose of this study is to investigate fundamental aspects of the dose response of fluorescent screen-based electronic portal imaging devices (EPIDs). MATERIALS AND METHODS: We acquired scanned signal across portal planes as we varied the radiation that entered the EPID by changing the thickness and anatomy of the phantom as well as the air gap between the phantom and the EPID. In addition, we simulated the relative contribution of the scintillation light signal in the EPID system RESULTS: We have shown that the dose profile across portal planes is a function of the air gap and phantom thickness. We have also found that depending on the density change within the phantom geometry, errors associated with dose response based on the EPID scan can be as high as 7%. We also found that scintillation light scattering within the EPID system is an important source of error. CONCLUSION: This study revealed and demonstrated fundamental characteristics of dose response of EPID, as relative to that of ion chambers. This study showed that EPID based on fluorescent screen cannot be an accurate dosimetry system

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