济南市1例输入性奥密克戎毒株刺突糖蛋白结构和功能的生物信息学分析

目的分析新冠病毒奥密克戎变异株刺突糖蛋白的结构和功能,为疫苗研发提供数据。方法对济南市1例输入性新冠病毒奥密克戎毒株,采用二代测序技术进行全基因组测序,分析刺突糖蛋白基因序列;用生物信息学方法分析刺突糖蛋白氨基酸组成、理化性质、跨膜结构、磷酸化修饰、糖基化修饰、结构域和B细胞抗原表位等生物学特性。结果测序获得1株输入性新冠病毒全基因组序列,基因组全长29847 nt,毒株基因型为XBB.1.16.1;其刺突糖蛋白由1269个氨基酸组成,存在1个跨膜螺旋区,主要分布于宿主细胞的内质网和细胞质膜中;有134个磷酸化位点、23个糖基化位点,3个蛋白结构域和11个可能的B细胞抗原表位,蛋白二级结构主要由无规则卷曲组成。结论采用生物信息学方法分析奥密克戎变异株刺突糖蛋白结构与功能,为了解刺突糖蛋白生物学信息提供数据。

Cloning and Bioinformatics Analysis of Lfcin Gene of Datong Yak

[Objective] This study was to clone Lfcin gene from Datong yak, so as to provide reference for applying this gene in feed industry and breeding industry. [Method] Using PCR technology, the lactoferricin(Lfcin)-encoding gene was obtained from genome of Datong yak; then it was cloned into pGEM-T easy vector, and then sequenced; the sequencing results were subsequently aligned with the sequences of dairy cow accessed in GenBank. Moreover, amino acid sequences of Lfcin gene from various species including yak, dairy cow, human and mouse were used for sequence alignment and phylogenesis analysis. [Result] The second exon of lactoferrin(LF) from Datong yak, which is 778 bp in length, was obtained, within which the coding region of Lfcin gene is 75 bp (25 amino acid residues); sequence analysis showed that there is discrepancy of eleven bases between Datong yak and dairy cow; Lfcin proteins from various species shared high homeology, of which that from Datong yak and dairy cow were completely identical; phylogenesis analysis showed that cladogram based on Lfcin was consistent with species evolutionary law. [Conclusion] This study laid a foundation for the prokaryotic or eukaryotic expression of Lfcin gene and further understanding the activity of Lfcin protein.

Computational analysis of genetic loci required for amphid structure and functions and their possibly corresponding microRNAs in C. elegans

Objective To examine the important roles of microRNAs （miRNAs） in regulating amphid structure and function, we performed a computational analysis for the genetic loci required for the sensory perception and their possibly corresponding miRNAs in C. elegans. Methods Total 55 genetic loci required for the amphid structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 30 genes among the 55 genetic loci selected have their possible corresponding regulatory miRNA（s）, and identified genes participate in the regulation of almost all aspects of amphid structure and function. In addition, our data suggest that both the amphid structure and the amphid functions might be regulated by a series of network signaling pathways. Moreover, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 30 genes exhibits different patterns. Conclusion We present the possible miRNA-mediated signaling pathways involved in the regulation of chemosensation and thermosensation by controlling the corresponding sensory neuron and interneuron functions. Our work will be useful for better understanding of the miRNA-mediated control of the chemotaxis and thermotaxis in C. elegans.

Bioinformatical Analysis on Sequences and Functions of Peroxidase in Arabidopsis

Plant peroxidase （POD） belongs to multigene family, which not is only one of the important enzymes responsible for the removal of active oxygen radicals, but also participates in a variety of physiological and biochemical processes and plays a crucial role in the maintenance of plant growth and development. In this study, the structures and functions of proteins encoded by 73 gene of POD family in Arabidopsis were analyzed with bioinformatics method, including the number of amino acids, isoelectric point, transmemberane domains, signal peptides, secondary structures and phosphorylation sites, and the phylogenic trees with and without signal peptides were constructed by using Mega4.0 software, to investigate the structural characteristics. In addition, the structures of AtPER members were analyzed, to reveal the relationship between the structures and functions, thereby providing theoretical basis for the research of plant oxidative stress resistance.

Cloning and Sequence Analysis of Sheeppox Virus RPO30 Gene

[Objective] The study aimed to clone RPO30 gene from Sheeppox virus （SPPV） and predict the structure and function of the sequence. [Method] RPO30 gene of SPPV was cloned with PCR, linked into pMD18-T simple vector and then transformed into E. coli DH5a. In blue-white screen, the white colonies were selected to prepare plasmids. The positive plasmids were selected by double digestion and PCR, and then sequenced. Finally, the structure and function of the sequence obtained were predicted by bioinformatics methods. [Results] The RPO30 gene was successfully obtained; its ORF was 585 bp, encoding 193 amino acids and containing a recognition site for Hind III. Moreover, the SPPV RPO30 gene shared different homologies with the RPO30 gene sequences of other pox virus strains from GenBank database. Further analysis by biological software showed that in RPO30 protein, amino acids 4-12, 18-26, 50- 61, 68- 92 and 176-190 had a high possibility to form the active center, and acting to these regions was likely to inactivate the enzyme encoded by the sequence, thus to inhibit viral replication efficiently. [Conclusion] This study will lay foundation for further study on the structure and function of RPO30.

Cloning and Identification of A New Na^+/H^+ Antiporter Gene ZmSOS1 in Maize(Zea mays L.)

[ Objective] The study aimed to clone and identify Na^＋/H^＋ antiporter genes in maize, and provided the information for characterizing the function of such genes in abiotic stress tolerance of maize. Method The in silico cloning, RT-PCR, and bioinformatics analysis were used in this study. Result By in sifico cloning, a plasma membrane Na^＋/H^＋ antiporter gene, named as ZmSOS1 （EMBL accession No. BN001309）, was cloned from maize （ Zea mays L. ）. ZmSOS1 has an open reading frame （ORF） of 3 411 bp which encoded a protein of 1 136 amino acids. By multiple sequence alignment analysis, it showed the predicated peptide of ZmSOS1 were 61% and 82% identities in amino acids to the plasma membrane Na^＋/H^＋ antiporter AtSOS1 and OsSOS1, respectively. The RT-PCR analysis revealed that ZmSOS1 could be significantly up-regulated by salt stress, which indicated ZmSOS1 might play a role in salt tolerance of maize. Conclusion ZmSOS1 is a putative plasma membrane Na^＋/H^＋ antiporter gene and may play a role in abiotic stress tolerance of maize.

Molecular Detection of Healthiness of Bombyx mori

[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screened by bioinfor- matic analysis method, and carried out real-time PCR expression analysis. [Result] The target gene Bmhsp24.3 expressed in different B. mori materials, but the expres- sion level in different materials significantly varied. The relative expression level of the gene had different degrees of changes under different rearing conditions. With the increase of rearing temperature, the gene expression was upregulated. The ma- terials with better healthiness had remarkable increase in expression of target gene, while the materials with poorer healthiness had less increase in expression of target gene. The expression difference of target gene Bmhsp24.3 was exactly consistent with the healthiness of breeds. [Conclusion] The healthiness of materials had rela- tionship with expression of target gene Bmhsp24.3. the higher the expression of tar- get gene Bmhsp24.3 was, the better the healthiness of materials was; conversely, the lower the expression of target gene Bmhsp24.3 was, the poorer the healthiness of materials was.

cDNA Cloning, Bioinformatic and Tissue-specific Expression Analysis of Porcine JARID1C Gene

Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5＇ rapid amplification of cDNA ends （5＇ RACE）, the full-length cDNA of JARIDIC （GenBank accession No. EF139241） from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame （ORF） of 4,548 bp, has been cloned. The putative porcine JARID 1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains： a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that the JARIDIC gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.

Computational analysis of genetic loci required for synapse structure and function and their corresponding microRNAs in C. elegans

Objective To elucidate the important functions of microRNAs （miRNAs） in regulating synaptic assembly and function, we performed a computational analysis for the genetic loci required for the synaptic structure and function and their corresponding miRNAs in C. elegans. Methods Total 198 genetic loci required for the synaptic structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 163 genes among the 198 genetic loci selected have their possibly corresponding regulatory miRNA （s）, which covered most of the important genetic loci required for the synaptic structure and function. Moreover, only 22 genes among the analyzed 38 genetic loci encoding synaptic proteins have more possibility to under the control of non-coding RNA genes. In addition, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 22 genes exhibits different patterns. Condusion Here we provide the computational screen and analysis results for the genetic loci required for synaptic structure and function and their possible corresponding miRNAs. These data will be useful for the further attempt to systematically determine the roles of miRNAs in synaptic assembly and function regulation in worms.

Cloning and Expression Analysis of Arginine Decarboxylase Gene MiADC from Mango

Arginine decarboxylase （ADC） plays an important role in polyamine biosynthesis in plants. In order to study the structure and expression ofADC gene in mango, an arginine decarboxylase gene ADC, named as MiADC, was cloned and isolated from the tender leaves of mango using RACE technology, and the expression of MiADC was analyzed by qRT-PCR based on the cDNA sequence of MiADC gene in this study. The results showed that the full length of MiADC was 3 089 bp containing a 575 bp 5＇-UTR, a 2 178 bp ORF with file initial codon and the terminal codon, a 311 bp 3＇-UTR and a 25 bp poly （A）; and file MiADC had no intron. The homologous analysis in the NCBI demonstrated that the sequence of MiADC had the highest similarity at 78% to Poncirus trifoliata arginine decarboxylase gene （HQ008237.1）, and the prediction protein also had the highest homology at 78% level with Poncirus trifoliata arginine decarboxylase （AEE99192.1） . Phylogenetic tree analysis revealed that the MiADC in mango was clustered in the same clade as the arginine decarboxylase from Poncirus trifoliate. Expression analysis showed that the MiADC gene was expressed in roots, stems, leaves, flowers, fruitlet, ripe fruit, and the transcriptional level of the cloned gene was affected obviously by low temperature, which proved that the MiADC gene may be a low temperature stress responding gene.

Network Pharmacology-based Analysis on the Molecular Biological Mechanisms of Xin Hui Tong Formula in Coronary Heart Disease Treatment

Objective To investigate the potential molecular mechanism of Xin Hui Tong Formula (XHTF) in the treatment of coronary heart disease (CHD) by using network pharmacology and bioinformatics. Methods The targets network of CHD was constructed through Therapeutic Targets Database (TTD) and Drugbank database;The XHTF pharmacodynamic molecule-targets network and the XHTF pharmacodynamic molecule-CHD targets network were explored by the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP). And the multi-targets mechanism and molecular regulation network of XHTF in the treatment of CHD were explored from multiple perspectives by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathway enrichment analysis. Results A total of 88 CHD targets were screened out through the Therapeutic Targets and the Drugbank database. 393 compounds and corresponding 205 drug targets of XHTF were retrieved from TCMSP. A total of 13 known targets directly related to the development of CHD were retrieved from the disease-related databases: TP53, MAPK14, NFKB1, HSPA5, PLG, PTGS2, ADRB1, NOS2, CYP3A4, GRIA2, CYP2A6, GRIA1, PTGS1. XHTF also contained 118 drug targets that directly interact with CHD targets. GO enrichment analysis showed that the biological processes of 13 direct targets proteins were found to be mainly enriched in response to drug, cellular response to biotic stimulus, long-chain fatty acid metabolic process, fatty acid metabolic process and regulation of blood pressure. KEGG pathway enrichment analysis found that XHTF participated in the CHD pathological process mainly through retrograde endocannabinoid signaling, regulation of lipolysis in adipocytes, cAMP signaling pathway, chemical carcinogenesis and other pathways. Conclusions XHTF plays a role in the treatment of CHD through multiple targets and multiple pathways, and provides a scientific basis for the theory of "virtual standard" in the treatment of CHD.

Bioinformatic Analysis of Structural Proteins of Paramyxovirus Tianjin Strain

The amino acid sequences of the NP, P, M, F, HN and L proteins of the paramyxovirus Tianjin strain were analyzed by using the bioinformatics methods. Phylogenetic analysis based on 6 structural proteins among the Tianjin strain and 25 paramyxoviruses showed that the Tianjin strain belonged to the genus Respirovirus, in the subfamily Paramyxovirinae, and was most closely related to Sendai virus (SeV). Phylogenetic analysis with 14 known SeVs showed that Tianjin strain represented a new evolutionary lineage. Similarities comparisons indicated that Tianjin strain P protein was poorly conserved, sharing only 78.7% - 91.9% amino acid identity with the known SeVs, while the L protein was the most conserved, having 96.0% - 98.0% amino acid identity with the known SeVs. Alignments of amino acid sequences of 6 structural proteins clearly showed that Tianjin strain possessed many unique amino acid substitutions in their protein sequences, 15 in NP, 29 in P, 6 in M, 13 in F, 18 in HN, and 29 in L. These results revealed that Tianjin strain was most likely a new genotype of SeV. The presence of unique amino acid substitutions suggests that Tianjin strain maybe has a significant difference in biological, pathological, immunological, or epidemiological characteristics from the known SeVs.

Bioinformatics Analysis of Upland Cotton Gene GhCRE1

Cytokinin plays a very important role in plants growth and development,and CRE1 has been identified as a cytokinin receptor.However,the biological function of CRE1 in cotton remains unclear.In this paper,GhCRE1 gene was cloned and its sequence was analyzed by bioinformatics.The results revealed that GhCRE1 had 11 exons and 10 introns,and its molecular weight,theoretical isoelectric point(pI)and number of amino acids differed from those of the homologous gene in Theobroma cacao and Arabidopsis thaliana,with three different protein domains.15 unidentified proteins were found in potential interaction with CRE1 protein and 2 phosphorylation sites on CRE1 protein sequence were predicted by mutiple bioinformatics websites.Additionally,8 cis-acting regulatory elements were detected on CRE1 promoter sequence,and found related to light signal and hormone.These results were conducive to unfolding the function of GhCRE1 in upland cotton.

Bioinformatics Analysis of VOZ Gene Family in Populus trichocarpa

To explore the biological characteristics of Vascular plant One-Zinc finger(VOZ)gene family in Populus trichocarpa,this paper used bioinformatics to analyze the nucleotide sequences and protein sequences of four members of VOZ gene family of P.trichocarpa.The results showed that the four PtVOZ genes of P.trichocarpa were evenly distributed on four chromosomes.The length and molecular weight of the encoded protein were almost the same,and the subcellular localization was located in the nucleus,belonging to the unstable acidic hydrophilic non-aliphatic soluble protein.The gene structures were all in the patterns of 4 exons and 3 introns.The proportion order of PtVOZ transcription factor secondary structure components was random coil>αhelix>extended strand>βsheets,and the tertiary structure was very similar in spatial conformation.The phylogenetic tree analysis showed that P.trichocarpa was more closely related to VOZ transcription factors of dicotyledons.The four PtVOZ genes of P.trichocarpa were expressed in seedlings and different tissues,but there were differences in the expression intensity.This study provided a necessary theoretical basis for further exploring the molecular biological function of PtVOZ genes.

Identification of key genes and related pathways in hepatocarcinoma usingbioinformatics analysis

Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.

Molecular cloning and transcriptional analysis of a NPY receptor-like in common Chinese cuttlefish Sepiella japonica

Neuropeptide Y(NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica( SjNPYR-like) was identified and characterized. The full-length SjNPYR-like cDNA was cloned containing a 492-bp of 5′ untranslated region(UTR), 1 182 bp open reading frame(ORF) encoding a protein of 393 amino acid residues, and 228 bp of 3′ UTR. The putative protein was predicted to have a molecular weight of 45.54 kDa and an isoelectric point(pI) of 8.13. By informatic analyses, SjNPYR-like was identified as belonging to the class A G protein coupled receptor(GPCR) family(the rhodopsin-type). The amino acid sequence contained 12 potential phosphorylation sites and five predicted N-linked glycosylation sites. Multiple sequence alignment and 3D structure modeling were conducted to clarify SjNPYR bioinformatics characteristics. Phylogenetic analysis identifies it as an NPYR with identity of 33% to Lymnaea stagnalis NPFR. Transmembrane properties of SjNPYR-like were demonstrated in vitro using HEK293 cells and the p EGFP-N1 plasmid. Relative quantifi cation of SjNPYR-like mRNA level confi rmed a high level expression and broad distribution of SjNPYR-like in various tissues of female S. japonica. In addition, the transcriptional profile of SjNPYR-like in the brain, liver, and ovary during gonadal development was analyzed. The results provide basic understanding on the molecular characteristics of SjNPYR-like and its potentially physical functions.

Expression and Analysis of Microtus fortis against Schistosoma japonicum CD36 Gene

The total RNA was extracted from Microtusfortis liver tissue which before being infected and after being infected 10 d and 15 d by the Schistosoma japonicum cercariae. Using Rattus norvegicus CD36 gene probe to hybridize analysis of CD36 difference expression in the Microtus fortis liver tissues which were infected with Schistosorna japonicum before and after being infected. At the same time, the cDNA sequence and encoded amino acid sequence of the Rattus norvegicus CD36 gene and CD36 protein structural domains were analysized by using bioinformatics. The results showed that the CD36 expression levels in the liver tissue of Microtus fortis after being infected were significantly higher than before being infectied. The Rattus norvegicus CD36 cDNA sequence of a total length is 1625 bp and encoded 472 amino acid residues and Rattus norvegicus CD36 protein containing a CD36 superfamily domain.

Characterizing and annotating the genome using RNA-seq data

Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.

Overview of available methods for diverse RNA-Seq data analyses

RNA-Seq technology is becoming widely used in various transcriptomics studies;however,analyzing and interpreting the RNA-Seq data face serious challenges.With the development of high-throughput sequencing technologies,the sequencing cost is dropping dramatically with the sequencing output increasing sharply.However,the sequencing reads are still short in length and contain various sequencing errors.Moreover,the intricate transcriptome is always more complicated than we expect.These challenges proffer the urgent need of efficient bioinformatics algorithms to effectively handle the large amount of transcriptome sequencing data and carry out diverse related studies.This review summarizes a number of frequently-used applications of transcriptome sequencing and their related analyzing strategies,including short read mapping,exon-exon splice junction detection,gene or isoform expression quantification,differential expression analysis and transcriptome reconstruction.

The diagnostic and prognostic value of CCTs in human hepatocellular carcinoma: a study based on integrated bioinformatics

Chaperonin-containing tailless complex polypeptide 1(CCT) is a group of genes involved in protein folding. It has been reported to be associated with the genesis and development of multiple tumors. However, the expression levels and functions of distinct CCTs involved in carcinogenesis and progression of hepatocellular carcinoma(HCC) have not been systematically analyzed. In the present study, we aimed to investigate the expression and mutation patterns, diagnostic and prognostic value, and functional enrichment of CCTs in HCC using ONCOMINE, GEPIA, the Human Protein Atlas, cBioPortal, Kaplan-Meier Plotter, and R language. The transcriptional and translational levels of all CCT family members were remarkably higher in HCC patients and related to the tumor stage. All CCT family members, especially CCT2 and CCT8, might serve as promising diagnostic, prognostic markers as well as therapeutic targets for HCC.