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1.
Protein & Cell ; (12): 29-38, 2021.
Article in English | WPRIM | ID: wpr-880916

ABSTRACT

Prostate cancer is the most commonly diagnosed non-cutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.


Subject(s)
Amino Acid Sequence , Epigenesis, Genetic , Epithelial-Mesenchymal Transition , Gene Expression Regulation, Neoplastic , Hepatocyte Nuclear Factor 3-alpha/metabolism , Histone Demethylases/metabolism , Histones/metabolism , Humans , Male , Mutation , Prostate/pathology , Prostatic Neoplasms/pathology , Protein Binding , Protein Processing, Post-Translational , Receptors, Androgen/metabolism , Signal Transduction , Transcription, Genetic
2.
Braz. j. biol ; 80(1): 39-46, Feb. 2020. graf
Article in English | LILACS | ID: biblio-1089293

ABSTRACT

Abstract The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics' tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.


Resumo O presente estudo objetivou avaliar se o polimorfismo causal A122V promove alterações nas propriedades funcionais e estruturais da proteína receptora de quimiocina CXC do tipo 1 (CXCR1) de bovino Bos taurus por análises in silico. Duas sequências de aminoácidos da CXCR1 bovina foram selecionadas a partir do banco de dados UniProtKB/Swiss-Prot: a) sequência não-polimórfica (A7KWG0) contendo alanina (A) na posição 122, e b) sequência polimórfica carreando o polimorfismo A122V, causando a substituição de alanina por valina (V) na mesma posição. As sequências CXCR1 foram analisadas por diferentes ferramentas de Bioinformática para examinar o efeito desse polimorfismo sobre sua estabilidade, função e estrutura, predizer eventuais alterações na sua modelagem estrutural 3-D, bem como estimar a qualidade dos modelos preditos. O polimorfismo A122V exerceu efeitos toleráveis e não-deletérios sobre a CXCR1 polimórfica, apresentando um modelo estrutural de alfa-hélice típico de uma proteína receptora transmembranar para ambas as proteínas. Embora maiores variações nas distâncias entre os pares de aminoácidos nas posições-alvo tenham sido detectadas na proteína polimórfica, mais do que 97% dos aminoácidos em ambos os modelos foram situados em regiões ditas favoráveis e permitidas nos diagramas de Ramachandran. Evidências sustentam que o polimorfismo de nucleotídeo único A122V na proteína receptora CXCR1 está associado à aumentada incidência de mastite clínica em vacas leiteiras. Assim, as descobertas descritas aqui comprovam que a substituição do aminoácido alanina por valina provoca mudanças conformacionais locais na proteína CXCR1 polimórfica, que podem estar diretamente afetando seus mecanismos de enovelamento pós-traducionais e sua função biológica.


Subject(s)
Animals , Female , Polymorphism, Single Nucleotide , Receptors, Interleukin-8A , Cattle , Amino Acid Sequence
3.
Chinese Journal of Biotechnology ; (12): 2435-2442, 2020.
Article in Chinese | WPRIM | ID: wpr-878499

ABSTRACT

In recent years, mass spectrometry has been widely used to study membrane protein structure and function. However, the application of mass spectrometry to study integral membrane protein is limited because there are many hydrophobic amino acids in the trans-membrane domain of integral membrane protein to cause low sequence coverage detected by LC-MS/MS. Therefore, we used vitamin K epoxide reductase (VKORC1), a human integral membrane protein, as a model to optimize the digestion conditions of chymotrypsin, and developed an in-gel digestion method of chymotrypsin to improve sequence coverage of membrane protein by mass spectrometry. By exploring the effects of calcium concentration, pH value and buffer system on the percentage of sequence coverage, number of total detected and types of unique peptide, and the size of unique peptide, sequence coverage and peptide diversity could be considered under condition of Tris-HCl buffer with 5-10 mmol/L calcium ion concentration and pH value 8.0-8.5. This method could make the sequence coverage of membrane protein to reach more than 80%. It could be widely used in the study of membrane protein structure and function, identification of interaction site between membrane proteins, and identification of binding site between membrane protein and small molecular drug.


Subject(s)
Amino Acid Sequence , Chromatography, Liquid , Chymotrypsin/metabolism , Digestion , Humans , Membrane Proteins , Tandem Mass Spectrometry , Trypsin , Vitamin K Epoxide Reductases
5.
Chinese Journal of Biotechnology ; (12): 1113-1125, 2020.
Article in Chinese | WPRIM | ID: wpr-826866

ABSTRACT

ORF3 protein, the single accessory protein encoded by porcine epidemic diarrhea virus (PEDV), is related to viral pathogenicity. In order to determine the cytoplasmic location signal of PEDV ORF3, we constructed a series of recombinant plasmids carrying full-length or truncated segments of PEDV DR13 ORF3 protein. When the acquired plasmids were transfected into Vero cells, expression and distribution of the EGFP-fused full-length ORF3 protein and its truncated forms in the cells were observed by laser confocal microscopy. The results showed that ORF3 protein or their truncated forms containing 40-91 aa segment including two transmembrane domains were localized in the cytoplasm, whereas ORF3 truncated peptides without the 40-91 aa segment were distributed in the whole cell (in both cytoplasm and nucleus). This suggests that the 40-91 aa is the key structural domain determining cytoplasmic location of PEDV ORF3 protein. The discovery provides reference for further clarifying intracellular transport and biological function of PEDV ORF3 protein.


Subject(s)
Amino Acid Sequence , Animals , Chlorocebus aethiops , Coronavirus Infections , Virology , Cytoplasm , Virology , Porcine epidemic diarrhea virus , Genetics , Protein Domains , Swine , Vero Cells , Viral Proteins , Chemistry , Metabolism
6.
Mem. Inst. Oswaldo Cruz ; 115: e190338, 2020. tab, graf
Article in English | LILACS | ID: biblio-1091240

ABSTRACT

Oropouche virus (OROV) is an arthropod-borne virus of the Peribunyaviridae family, transmitted to humans primarily by Culicoides paraensis. It is one of the main arboviruses infecting humans in Brazil, primarily in the Amazon Region. Here, we report the detection of OROV in the saliva and urine of a patient whose samples were collected five days after the onset of symptoms. Nucleotide sequencing and phylogenetic analysis further confirmed the results. To our knowledge, this is the first study reporting the detection of OROV in the saliva and urine of an infected patient. In addition, the results of our study expand the current knowledge pertaining to the natural history of Oropouche fever.


Subject(s)
Humans , Female , Saliva/virology , Urine/virology , Orthobunyavirus/isolation & purification , Orthobunyavirus/genetics , Bunyaviridae Infections/diagnosis , Phylogeny , RNA, Viral/genetics , Base Sequence , Amino Acid Sequence , Reverse Transcriptase Polymerase Chain Reaction , Middle Aged
7.
Rev. bras. parasitol. vet ; 28(3): 451-457, July-Sept. 2019. tab, graf
Article in English | LILACS | ID: biblio-1042527

ABSTRACT

Abstract The msp4 gene of A. marginale is unicodon, stable and mostly homogeneous, being considered as a useful marker for phylogeographic characterization of this bacterium. The objective of this work was to analyze the phylogeography of A. marginale based on the msp4 gene in beef cattle from the Brazilian Pantanal, compared to those found in other regions worldwide. The blood samples investigated were collected from 400 animals (200 cows and 200 calves) reared in five extensive breeding farms in this region. The results indicated that of the evaluated samples, 56.75% (227/400) were positive for A. marginale based on the msp1β gene by quantitatitve PCR (qPCR), while 8.37% (19/227) were positive for the msp4 gene in the conventional PCR. In the Network distance analysis, 14 sequences from the Brazilian Pantanal were grouped into a single group with those from Thailand, India, Spain, Colombia, Parana (Brazil), Mexico, Portugal, Argentina, China, Venezuela, Australia, Italy and Minas Gerais (Brazil). Among 68 sequences from Brazil and the world, 15 genotypes were present while genotype number one (#1) was the most distributed worldwide. Both Splitstree and network analyses showed that the A. marginale msp4 sequences detected in beef cattle from the Brazilian Pantanal showed low polymorphism, with the formation of one genogroup phylogenetically related to those found in ruminants from South and Central America, Europe, and Asia.


Resumo O gene msp4 de A. marginale é unicodon, estável e pouco heterogêneo, sendo considerado como um marcador útil para caracterização filogeográfica desta bactéria. Este trabalho teve como objetivo analisar a filogeografia de A. marginale com base no gene msp4 em bovinos de corte do Pantanal Brasileiro, comparativamente a outra regiões do mundo. Alíquotas de sangue foram colhidas de 400 bovinos (200 vacas e 200 bezerros) em cinco propriedades de cria e recria extensiva. Como resultado, 56,75% (227/400) mostraram-se positivas para A. marginale pela qPCR para o gene msp1β e destas, 8,37% (19/227) amostras foram positivas na PCR convencional para o gene msp4. Na análise de distância Network, 14 sequências do Pantanal brasileiro foram agrupadas em um único grupo com as da Thailândia, Índia, Espanha, Colômbia, Paraná (Brasil), México, Portugal, Argentina, China, Venezuela, Austrália, Italia e Minas Gerais (Brasil). Dentre 68 sequências do Brasil e do mundo, constatou-se a presença de 15 genótipos, sendo o genótipo número um (#1) o mais distribuído. As sequências msp4 de A. marginale detectadas em bovinos de corte no Pantanal brasileiro apresentaram baixo polimorfismo com formação de dois genogrupos filogeneticamente relacionados àqueles encontrados em ruminantes de países das América do Sul e Central, Europa e Ásia.


Subject(s)
Animals , Male , Female , Bacterial Proteins/genetics , Cattle/microbiology , Anaplasma marginale/genetics , Phylogeography/methods , Membrane Proteins/genetics , Asia , Americas , Brazil , DNA, Bacterial/genetics , Molecular Sequence Data , Polymerase Chain Reaction , Amino Acid Sequence , Anaplasma marginale/isolation & purification , Europe , Genotype
8.
Article in Chinese | WPRIM | ID: wpr-777535

ABSTRACT

1-deoxy-D-xylulose-5-phosphate synthase2(DXS2) is the first key enzyme of the MEP pathway,which plays an important role in terpene biosynthesis of plants. According to the data of Swertia mussotii transcriptome, DXS2 gene(Gen Bank number MH535905) was cloned and named as Sm DXS2. The bioinformatics results showed that Sm DXS2 has no intron,with a 2 145 bp open reading frame encoding a polypeptide of 714 amino acids. They are belonging to 20 kinds of amino acids,and the most abundant amino acids include Ala,Gly and Trp. The predicted protein molecular weight was 76. 91 k Da and its theoretical isoelectric point(p I) was6. 5,which belonging to a hydrophilic protein. α-Helix and loop were the major motifs of predicted secondary structure of DXS2. The three function domains are TPP_superfamily,Transket_pyr_ superfamily and Transketolase_C superfamily,respectively. The Sm DXS2 protein shared high identity with other DXS2 proteins of plants. Phylogenetic analysis showed that Sm DXS2 protein is grouped with the gentian DXS2 protein. The recombinant protein of Sm DXS2 gene in Escherichia coli was approximately 92. 00 k Da(containing sumo-His tag protein 13 k Da),which was consistent with the anticipated size.This work will provide a foundation for further functional research of Sm DXS2 protein and increasing the product of iridoid compound by genetic engineering in S. mussotii.


Subject(s)
Amino Acid Sequence , Cloning, Molecular , DNA, Complementary , Genetics , Genes, Plant , Iridoids , Phylogeny , Plant Proteins , Genetics , Swertia , Genetics , Transcriptome , Transferases , Genetics
9.
Article in Chinese | WPRIM | ID: wpr-777441

ABSTRACT

To clone bHLH( basic helix-loop-helix) gene from Carthamus tinctorius,analyze the expression level in different plant tissues and construct the plant expression vector. The bHLH1 gene was cloned by RT-PCR techniques,and the protein characteristics were analyzed by bioinformatics,and phylogenetic tree was constructed. The expression of bHLH1 gene in different tissues and the roots after inoculated by Fusarium oxysporum were analyzed using real time-PCR,and the plant expression vector p BASTA-bHLH1 was constructed. The obtained ORF sequence of bHLH1 gene was 897 bp,encoded a protein of 298 amino acids. Sequence alignment and phylogenetic tree analyses showed that C. tinctorius bHLH1 had a certain homology with other species of amino acids,and was the most similar to the amino acid sequence of tobacco. Real-time PCR results showed significant differences,CtbHLH1 gene in red flower petals in different tissues and different flowering period had remarkable difference in expression level,its high amount expressed in petals,flowers third day after blossom expressed the highest quantity,at the end of the flowering the expression quantity is low. In addition,it is expressed in the root,and the expression in the stem and leaves is extremely low. The bHLH1 gene of C. tinctorius is successfully cloned,and the expression is analyzed. The plant expression vector p BASTA-bHLH is constructed.


Subject(s)
Amino Acid Sequence , Basic Helix-Loop-Helix Transcription Factors , Genetics , Carthamus tinctorius , Genetics , Cloning, Molecular , Flowers , Genetics , Gene Expression Regulation, Plant , Genetic Vectors , Phylogeny , Plant Proteins , Genetics
10.
Blood Research ; : 17-22, 2019.
Article in English | WPRIM | ID: wpr-739439

ABSTRACT

Genetic hemoglobin disorders are caused by mutations and/or deletions in the α-globin or β-globin genes. Thalassemia is caused by quantitative defects and hemoglobinopathies by structural defect of hemoglobin. The incidence of thalassemia and hemoglobinopathy is increased in Korea with rapid influx of people from endemic areas. Thus, the awareness of the disease is needed. α-thalassemias are caused by deletions in α-globin gene, while β-thalassemias are associated with decreased synthesis of β-globin due to β-globin gene mutations. Hemoglobinopathies involve structural defects in hemoglobin due to altered amino acid sequence in the α- or β-globin chains. When the patient is suspected with thalassemia/hemoglobinopathy from abnormal complete blood count findings and/or family history, the next step is detecting hemoglobin abnormality using electrophoresis methods including high performance liquid chromatography and mass spectrometry. The development of novel molecular genetic technologies, such as massively parallel sequencing, facilitates a more precise molecular diagnosis of thalassemia/hemoglobinopathy. Moreover, prenatal diagnosis using genetic testing enables the prevention of thalassemia birth and pregnancy complications. We aimed to review the spectrum and classification of thalassemia/hemoglobinopathy diseases and the diagnostic strategies including screening tests, molecular genetic tests, and prenatal diagnosis.


Subject(s)
Amino Acid Sequence , Anemia , Blood Cell Count , Chromatography, Liquid , Classification , Clinical Laboratory Techniques , Diagnosis , Electrophoresis , Erythrocytes , Genetic Testing , Hematology , Hemoglobinopathies , High-Throughput Nucleotide Sequencing , Humans , Incidence , Korea , Mass Screening , Mass Spectrometry , Molecular Biology , Parturition , Pregnancy Complications , Prenatal Diagnosis , Thalassemia
11.
Article in English | WPRIM | ID: wpr-761732

ABSTRACT

Both Plasmodium spp. and Toxoplasma gondii are important apicomplexan parasites, which infect humans worldwide. Genetic analyses have revealed that 33% of amino acid sequences of inner membrane complex from the malaria parasite Plasmodium berghei is similar to that of Toxoplasma gondii. Inner membrane complex is known to be involved in cell invasion and replication. In this study, we investigated the resistance against T. gondii (ME49) infection induced by previously infected P. berghei (ANKA) in mice. Levels of T. gondii-specific IgG, IgG1, IgG2a, and IgG2b antibody responses, CD4+ and CD8+ T cell populations were found higher in the mice infected with P. berghei (ANKA) and challenged with T. gondii (ME49) compared to that in control mice infected with T. gondii alone (ME49). P. berghei (ANKA) + T. gondii (ME49) group showed significantly reduced the number and size of T. gondii (ME49) cysts in the brains of mice, resulting in lower body weight loss compared to ME49 control group. These results indicate that previous exposure to P. berghei (ANKA) induce resistance to subsequent T. gondii (ME49) infection.


Subject(s)
Amino Acid Sequence , Animals , Antibody Formation , Body Weight , Brain , Humans , Immunoglobulin G , Malaria , Membranes , Mice , Parasites , Plasmodium berghei , Plasmodium , Toxoplasma , Toxoplasmosis
12.
Article in English | WPRIM | ID: wpr-760353

ABSTRACT

Avian malaria is one of the most important general blood parasites of poultry in Southeast Asia. Plasmodium (P.) juxtanucleare causes avian malaria in wild and domestic fowl. This study aimed to identify and characterize the Plasmodium species infecting in Thai native fowl. Blood samples were collected for microscopic examination, followed by detection of the Plasmodium cox I gene by using PCR. Five of the 10 sampled fowl had the desired 588 base pair amplicons. Sequence analysis of the five amplicons indicated that the nucleotide and amino acid sequences were homologous to each other and were closely related (100% identity) to a P. juxtanucleare strain isolated in Japan (AB250415). Furthermore, the phylogenetic tree of the cox I gene showed that the P. juxtanucleare in this study were grouped together and clustered with the Japan strain. The presence of P. juxtanucleare described in this study is the first report of P. juxtanucleare in the Thai native fowl of Thailand.


Subject(s)
Amino Acid Sequence , Animals , Asia, Southeastern , Asian Continental Ancestry Group , Base Pairing , Cytochromes c , Cytochromes , Electron Transport Complex IV , Humans , Japan , Malaria, Avian , Parasites , Plasmodium , Polymerase Chain Reaction , Poultry , Sequence Analysis , Thailand , Trees
13.
Article in Chinese | WPRIM | ID: wpr-774577

ABSTRACT

Armillaria gallica is a facultative parasitic fungus which is the only nutrient source of Gastrodia elata during its cultivation.Chitinase,as a glycosidic hydrolytic enzyme,plays an important role in the growth,development,stress tolerance and symbiotic signal transduction of A. gallica. There were 22 chitinase genes in A. gallica. Bioinformatics analysis of amino acid sequence of these chitinase genes revealed that 12 chitinase genes contained glycosidase 18 family( GH18) domain. Chitinase amino acid sequences of A. gallica,A. ostoyae,G. elata,Saccharomyces cerevisiae and Trichoderma harzianum were analyzed byclustering trees,so as to further predict the gene function of chitinase in A. gallica. Induction of A. gallica branching with strigolactone analogue GR24,high-throughput sequencing technology based on the induction of branch group( MHJ1),uninduced branch group( MHJ2) and blank control group( MHJ3) is used to detect the expression quantity,the transcription level data of 22 chitinase genes were obtained and the heat map was generated for expression pattern analysis. It was found that 8 genes may be involved in physiological processes such as A. gallica branching,cell wall degradation and remodeling. In this paper,the function of chitinase gene in A. gallica was just preliminarily analyzed and predicted.


Subject(s)
Amino Acid Sequence , Armillaria , Chitinases , Computational Biology , Trichoderma
14.
Chinese Journal of Biotechnology ; (12): 1234-1246, 2019.
Article in Chinese | WPRIM | ID: wpr-771805

ABSTRACT

1,3-1,4-β-glucanase (E.C.3.2.1.73) is an important industrial enzyme which cleave β-glucans into oligosaccharides through strictly cutting the β-1,4 glycosidic bonds in 3-O-substituted glucopyranose units. Microbial 1,3-1,4-β-glucanase belongs to retaining glycosyl hydrolases of family 16 with a jellyroll β-sandwich fold structure. The present paper reviews the industrial application and protein engineering of microbial β-glucanases in the last decades and forecasts the research prospects of microbial β-glucanases.


Subject(s)
Amino Acid Sequence , Glycoside Hydrolases , Models, Molecular , Protein Engineering , Substrate Specificity
15.
Chinese Journal of Biotechnology ; (12): 102-113, 2019.
Article in Chinese | WPRIM | ID: wpr-771396

ABSTRACT

The biogenic monoamine 5-hydroxytryptamine (5-HT) is an ancient intracellular signaling molecule widely distributed in all animals with nervous systems, and has been implicated in principal behaviors. Tryptophan hydroxylase (TRH) induces a highly specific catalytic reaction that converts L-tryptophan (tryptophan) to 5-hydroxy-L-tryptophan (5-HTP) that is subsequently used as a substrate by aromatic L-amino acid decarboxylase (DDC) to form 5-HT. Five-HT is an ancient intracellular signaling molecule that is widely distributed in the animal kingdom and has been implicated in regulating the behaviors of animals with nervous systems. However, the role of TRH in Lepidoptera is not well understood. In this study, we cloned 1 667 bp cDNAs of Bombyx mori TRH (BmTRH), which contains a 1 632 bp open reading frame (ORF). Homology analysis revealed that BmTRH shared high amino acid identity with Homo sapiens TPH and Drosophila TRH (DmTRH). The high homology (70%) of BmTRH with DmTRH suggested that BmTRH could have a function similar to DmTRH. Gene expression analysis revealed that BmTRH was mainly expressed in head and central nervous (CNS). Moreover, immunohistochemistry and Western blotting analyses showed that BmTRH was detected only in larval nervous tissues. Taken together, our results indicate that BmTRH could likely function in the regulation of neural activities in B. mori. The transcripts of B. mori decarboxylase (BmDDC) and B. mori phenylalanine hydroxylase (BmPAH) whose proteins had TRH activity, were also expressed in the CNS tissues, indicating that unlike in Drosophila, two distinct mechanisms likely regulate 5-HT synthesis in silkworm.


Subject(s)
Amino Acid Sequence , Animals , Bombyx , Cloning, Molecular , DNA, Complementary , Insect Proteins , Phenylalanine Hydroxylase , Tryptophan Hydroxylase
16.
Chinese Journal of Biotechnology ; (12): 319-326, 2019.
Article in Chinese | WPRIM | ID: wpr-771374

ABSTRACT

This study aimed to obtain a recombinant human-source collagen for industrialization. First, based on the Gly-X-Y sequence of human type I collagen, we optimized the hydrophilic Gly-X-Y collagen peptide, designed the human collagen amino acid sequence and the corresponding nucleotide sequence. Next, the expression vector pPIC9K-COL was constructed via endonuclease digestion technology. We obtained an engineering strain of human-source collagen by electrotransforming Pichia pastoris, and then it was fermented, purified and identified. As a result, the expression level reached 4.5 g/L and the purity was over 95%. After amino acid N-terminal sequencing, molecular weight analysis, amino acid analysis and collagenase degradation test, we confirmed that the obtained collagen was consistent with designed primary structure of human-source collagen. After freeze-drying, we analyzed the collagen by scanning electron microscope and cell cytotoxicity, confirming that the collagen has porous fiber reticular structure and superior cytocompatibility. This indicates that human-source collagen has potential to be applied as biomedical material. In conclusion, we successfully obtained the expected human-source collagen and laid a foundation to its further application.


Subject(s)
Amino Acid Sequence , Biocompatible Materials , Collagen , Freeze Drying , Humans , Pichia , Recombinant Proteins
17.
Chinese Journal of Biotechnology ; (12): 435-444, 2019.
Article in Chinese | WPRIM | ID: wpr-771363

ABSTRACT

Genes belonging to the elongases of very long chain fatty acid (ELOVL) family affect many physiological functions in organism. In this paper, Bmelo424 gene, a member of the ELOVL family in silkworm, was cloned and its ORF was 558 bp. Its protein sequence was predicted to have four transmembrane domains, six serine phosphorylation sites, eight threonine phosphorylation sites and four tyrosine phosphorylation sites, and its subcellular localization was in the endoplasmic reticulum. Secondary structure analysis showed that the percentage of alpha-helix and beta-strand was 26.7% and 20% respectively. The results of fluorescence quantitative PCR showed that Bmelo424 gene was expressed in all tissues of silkworm, especially with the highest expression in head. By heterologous expression of Bmelo424 gene in Saccharomyces cerevisiae, the effect of Bmelo424 gene on fatty acid elongation was studied. GC-MS results indicated that the fatty acid content of C16:1n-7 in S. cerevisiae with pYES2-Bmelo424 recombinant plasmid increased significantly, whereas the content of C16:0, C18:0 and C18:1n-9 decreased. The results of temperature stress revealed that Bmelo424 gene could improve the low temperature adaptability of S. cerevisiae, but its high temperature adaptability decreased. This provides a reference for exploring the function of Bmelo424 gene in silkworm.


Subject(s)
Acetyltransferases , Amino Acid Sequence , Animals , Bombyx , Cloning, Molecular , Fatty Acids , Saccharomyces cerevisiae
18.
Chinese Journal of Biotechnology ; (12): 687-696, 2019.
Article in Chinese | WPRIM | ID: wpr-771341

ABSTRACT

In order to provide a theoretical basis for better understanding the function and properties of proteins, we proposed a simple and effective feature extraction method for protein sequences to determine the subcellular localization of proteins. First, we introduced sparse coding combined with the information of amino acid composition to extract the feature values of protein sequences. Then the multilayer pooling integration was performed according to different sizes of dictionaries. Finally, the extracted feature values were sent into the support vector machine to test the effectiveness of our model. The success rates in data set ZD98, CH317 and Gram1253 were 95.9%, 93.4% and 94.7%, respectively as verified by the Jackknife test. Experiments showed that our method based on multilayer sparse coding can remarkably improve the accuracy of the prediction of protein subcellular localization.


Subject(s)
Algorithms , Amino Acid Sequence , Computational Biology , Protein Transport , Proteins , Subcellular Fractions , Support Vector Machine
19.
Chinese Journal of Biotechnology ; (12): 697-706, 2019.
Article in Chinese | WPRIM | ID: wpr-771340

ABSTRACT

Endogenous peptides, in the form of cytokines, growth hormones and hormone peptides, play an important role in human hormones, nerves, cell growth and reproduction. Neuropeptide is a kind of endogenous peptide, which is related to the physiological activities of pain, sleep, emotion, learning and memory. Neuropeptides exist not only in the nerve cells of the brain, but also in other body fluids and organs. At present, there is still a lack of research on endogenous peptides, especially on neuropeptides. In this study, high-throughput liquid chromatography tandem mass spectrometry was used to identify the distribution of endogenous peptides in the pancreas, heart, liver and kidney as well as the types of neuropeptides. The results showed that the number of endogenous peptides and neuropeptides in the liver was the highest while that of the pancreas was the lowest. The identified endogenous peptides were organ-specific and presented different dynamic distribution in four kinds of organs. The number of LPV (Longest peptide variant) of neuropeptide in the four organs varies greatly, and the distribution of gene family is also different. For example, neuropeptide in pancreas belongs to Glucagon family, while neuropeptide in heart belongs to ACBD7, Granins, PEBP and other families. The identification results will provide reference value for the mechanism study of diseases and the research and development of therapeutic drugs.


Subject(s)
Amino Acid Sequence , Animals , Carrier Proteins , Chromatography, Liquid , Humans , Mass Spectrometry , Mice , Peptides
20.
Article in Chinese | WPRIM | ID: wpr-772336

ABSTRACT

BACKGROUND@#Non-small cell lung cancer (NSCLC) have the highest incidence of lung cancer which treatment principles are diagnosis and treatment as early as possible. Because of its insidious onset and lack of specific markers for early screening, most patients are at an advanced stage when diagnosed which results in a low 5-year survival rate and poor prognosis. Therefore Exploring a sensitive biomarker is the focus of current diagnosis and treatment of lung cancer. The aim of this study is to investigate the biological markers in serum of patients with I-IIb stage NSCLC by differential peptidomics analysis.@*METHODS@#The serum peptidome was compared and analyzed among the groups of normal health controls, benign lung diseases and early stage NSCLC patients using a nano ultra-performance liquid chromatography combined with a quadrupole-orbitrap mass spectrometer. The differentially expressed polypeptides were identified and analyzed quantitatively to screen the tumor biomarkers for the early diagnosis of NSCLC patients.@*RESULTS@#According to the Swiss-Prot database, a total of 545 polypeptides originated from 118 proteins were identified. The spectral numbers of serum polypeptides in each group were compared and a total of 201 polypeptides differentially expressed were found. Following a quantitative analysis of the above peptides, we found that there were 7 peptides with the coefficient of variation (CV) less than 30% and among them the peptide of QGAKIPKPEASFSPR from ITIH4 was down-regulated and the peptide of CDDYRLC from MGP was up-regulated in NSCLC group.@*CONCLUSIONS@#The tumor biomarkers obtained by serum peptidome technology can provide a new clue for early diagnosis of NSCLC and the specific peptides hydrolyzed from ITIH4 and MGP may be the serum biological markers for early NSCLC patients.


Subject(s)
Adult , Aged , Amino Acid Sequence , Biomarkers, Tumor , Blood , Chemistry , Carcinoma, Non-Small-Cell Lung , Blood , Diagnosis , Early Detection of Cancer , Female , Humans , Lung , Pathology , Lung Neoplasms , Blood , Diagnosis , Male , Middle Aged , Neoplasm Staging , Peptides , Blood , Chemistry , Proteomics , Methods , Sensitivity and Specificity , Young Adult
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