对生物学课程信息化问题的思考

生物学课程信息化是信息技术与学科课程整合实践深入发展的必然结果。实现生物学课程信息化,一要还原学科课程的主体地位,实现生物学课程信息化的最优化;二要努力提升教师和学生的信息技术素养;三要研究合理利用信息资源的课程内容体系。

生物信息化实践课程教育教学改革研究

信息化实践作为生物信息学课程教育教学过程当中必不可少的重要环节,具有非常重要的作用,同时也是进一步提升学生参与性、探索性、创新思维等能力的重要表现手段。而进一步提升学生创新能力和实践能力,作为大学生培养过程当中的重要目标。在本文当中,主要是对信息化内容、教育教学方法、成绩综合评价体系等进行优化,不断促进生物信息化实践课程教学的改革,为进一步提升学生创新能力具有非常重要的作用。

试论信息化视野下的高中生物智慧课堂教学策略研究

随着时代发展,当今已经是信息化时代,教育也随着时代发展进行了变革,融入互联网技术使传统教育走向信息化教育。各国在教育方面也都投入了大量精力,教育信息化是教育的明确走向,我国在此方面经过了十几年的建设,也有了不小的成绩,同时有改变就会有问题,在教育信息化的过程中,也出现了不少问题,本文从信息化视野下高中生物智慧课堂教学的角度出发,深入分析了当前高中生物教学中存在的问题,并在信息化的视野下提出了建设智慧课堂的教学策略,努力为学生的学习营造一个良好学习氛围,促进学生在高中生物学习中不断的完善自身。

云南省生物医药产业信息化发展研究

信息化建设已成为推动生物医药行业深化改革、强化管理和内涵发展的重要保障,对加强医药行业的管理和提高效率具有十分重要的意义。云南省生物医药产业正处于机遇与挑战并存的新时期,信息化建设是推动云南医药产业蓬勃发展的必由之路。首先从云南省生物医药所处地位、企业情况、产品情况方面介绍云南省生物医药产业的基本情况;然后阐述生物医药信息化的意义和必要性;分析云南省生物医药信息化的现状,指出其存在的问题;最后提出建设云南省生物医药信息化的对策。

动物微生物及检验课程信息化“理实一体”教学模式的构建

对中职动物微生物及检验课程信息化＂理实一体＂教学模式的构建进行探讨,提出中职动物微生物及检验课程构建信息化＂理实一体＂教学模式的具体的教学措施,并进行反思。

信息化集成化信号系统在机能教学中的应用

信息化教学是时代发展的要求,实现信息化和网络化的生物信号采集处理系统的更新换代迫在眉睫。信息化集成化生物信号采集系统采用一体化设计原则,集成多种实验设备,操作简便,数据采集和处理结果准确、可靠,正逐步应用于医学机能学实验教学,改善医学院校教学环境,提高了教学质量。学校在2019年9月对四个机能学实验室进行全面升级改造,购置成都泰盟生产的BL-420I信息化集成化信号系统24套。文章对信息化集成化生物信号采集系统在医学机能学实验教学中的应用与体会进行总结,为今后机能学实验室设备更新和基础建设,提高实验教学质量提供参考。

BL-420F生物机能实验系统在动物生理实验教学中应用分析

从实验动物的正确选取、动物标本的制作、BL-420F生物机能实验系统测试方面分析蛙骨骼肌的单收缩和强直收缩、蛙坐骨神经干复合动作电位传导速度的测定、蛙心的期前收缩和代偿间歇三个经典生理实验特点以探讨BL-420F生物机能实验系统的使用体会。

Bioinformatics Analysis of IPIs in Five Northern Medicinal Plants

This study analyzed and predicted following aspects of isopentenyl py- rophosphate isomerases （IPIs） of five north medicinal plants using bioinformatics methods and tools： physical and chemical properties, hydrophobicity/hydrophilicity, trans-membrane domain, secondary structure, subcellular localization and so on. The results showed that： there was no notable difference among the physical and chem- ical properties of IPIs of the five north medicinal plants; the IPIs were mainly hy- drophilic; the IPIs were mainly located in chloroplasts by subcellular localization; serine phosphorylation sites were the most; the secondary structures mainly consist- ed of c^-helixes and random coils; no signal peptide existed, indicating that the pro- tein IPI was non-secreted protein; no trans-membrane domain existed; and one functional domain was shown, Le., Nudix Hydrolase Superfamily. This study is of great significance to research on IPI gene functions, deep research on north medic- inal plants, improvement of efficacy of north medicinal plants and rational develop- ment and utilization of medicinal plant resources.

Isolation and analysis of pepper ACC oxidase gene partial sequence

Ethylene plays an extensive role in plant growth and development.. 1-aminocyclopropane-1-carboxylate （ACC） oxidase （ACO） is the key enzyme in ethylene biosynthesis. In this study, a 354 g DNA and a 213 bp cDNA base pair （bp） candidate fragment was amplified from pepper with primers derived from the ACO sequence （AJ011109） reported by Ernesto. The putative new gene was analyzed by bioinformatics tools.

Cloning, Analysis and Prokaryotic Expression of DsSP Gene from Dunaliella salina

[Objective] The purpose of this study was to clone a starch phosphorylase gene from Dunaliella salina and to preliminarily analyze its basic properties and protein expression. [Method] RT-PCR and RACE （rapid amplification of cDNA ends） method was used for gene cloning; basic properties of the gene were analyzed using bioinformatics method; prokaryotic expression vector PGS21a-DsSP was constructed and transformed into E. coil BL21; the fusion protein was purified and detected by GST-SefinoseTM Kit and Western Blot, respectively. [Result] A starch phos-phorylase gene （GenBank accession No. KF061044） named DsSP was successfully isolated from D. salina. Basic properties, subcellular localization, secondary structure and tertiary structure of the protein were analyzed and predicted. The fusion protein was found in the supernatant and inclusion bodies. The supernatant protein was successfully purified. Western Blot analysis showed that the fusion protein was successfully expressed in E. coil BL21. [Conclusion] This study laid experimental foun- dation for further clarifying the function and mechanism of DsSP.

SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK are prognosis-related in colorectal cancer

AIM: To investigate the expression of markers that are correlated with the prognosis of colorectal cancer (CRC) patients. METHODS: One hundred and fifty-six CRC patientswere followed up for more than 3 years after radical surgery. Immunohistochemical (IHC) analysis was performed to detect the expression of 14 pathway-related markers (p53, APC, p21ras, E-cadherin, endothelin-B receptor, Shp2, ADCY-2, SPARCL1, neuroligin1, hsp27, mmp-9, MAPK, MSH2 and rho) in specimens from these patients. Bioinformatics analysis involving a Support Vector Machine (SVM) was used to determine the best prognostic model from combinations of these markers. RESULTS: Seven markers (SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK) were significantly related to the prognosis and clinical pathological features of the CRC patients (P < 0.05). Prognostic models were established through SVM from combinations of these 7 markers and proved able to differentiate patients with dissimilar survival, especially in stage Ⅱ/Ⅲ patients. According to the best prognostic model, the p53/SPARCL1 model, patients having high p53 and low SPARCL1 expression had about 50% lower 3-year survival than others (P < 0.001). CONCLUSION: SPARCL1, Shp2, MSH2, E-cadherin, p53, ADCY-2 and MAPK are potential prognostic markers in CRC. A p53/SPARCL1 bioinformatics model may be used as a supplement to tumor-nodes-metastasis staging.

Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer

AIM:To isolate and analyze the DNA sequences which are methylated differentially between gastric cancer and normal gastric mucosa. METHODS: The differentially methylated DNA sequences between gastric cancer and normal gastric mucosa were isolated by methylation-sensitive representational difference analysis (MS-RDA). Similarities between the separated fragments and the human genomic DNA were analyzed with Basic Local Alignment Search Tool (BLAST). RESULTS: Three differentially methylated DNA sequences were obtained, two of which have been accepted by GenBank. The accession numbers are AY887106 and AY887107. AY887107 was highly similar to the 11th exon of LOC440683 (98%), 3' end of LOC440887 (99%), and promoter and exon regions of DRD5 (94%). AY887106 was consistent (98%) with a CpG island in ribosomal RNA isolated from colorectal cancer by Minoru Toyota in 1999. CONCLUSION: The methylation degree is different between gastric cancer and normal gastric mucosa. The differentially methylated DNA sequences can be isolated effectively by MS-RDA.

Methylation Characteristics of Perivisceral Fat Gene in Obese Rats with Phlegm-dampness Syndrome and the Effect of Wen Dan Decoction

Objective To observe the characteristics of gene methylation in obese rats with phlegm-dampness syndrome induced by the high-fat diet, and to study the effect of Wen Dan Decoction on gene methylation after the intervention. Methods Methylation sites of genes were detected by the MeDIP-seq method. Bioinformatics method was used to analyze the gene methylation characteristics of obesity with phlegmdampness syndrome and the effect of Wen Dan Decoction. Results (1) There were 3 242 methylation differential loci in dietinduced obesity with phlegm-dampness syndrome, of which 1 243 were down-regulated and 1 999 were up-regulated, involving 1 579 differential genes. GO analysis showed that "offactory receptor activity" and others were enriched. The possible signal pathways involved were "Olfactory transduction""Tuberculosis""Systemic lupus erythematosus" and "Ribosome".(2) After the intervention of Wen Dan Decoction in obesity with phlegmdampness syndrome, 4 046 different methylation loci were obtained, including 1 067 down-regulated loci and 2 979 up-regulated loci, involving 2 068 genes. GO analysis showed that "offactory receptor activity" and others were enriched. These genes involved seven signaling pathways, such as "Metabolic pathways".(3) Between diet-induced obesity with phlegm-dampness syndrome and Wen Dan Decoction intervening obesity with the phlegm-dampness syndrome, 582 common genes of methylation differential genes were obtained. After the intervention of Wen Dan Decoction, the number of GO enrichment items was more than that of obesity with phlegm-dampness syndrome, and even the same GO enrichment items involved more genes. Conclusions The phlegm-dampness syndrome of obesityinduced by diet had the characteristics of gene methylation changes, and the intervention of Wen Dan Decoction could also affect the status of gene methylation. The genes affected by Wen Dan Decoction were closely related to the methylation gene of phlegm-dampness syndrome of obesity-induced by diet but covered a wider range.

Bioinformotics Analysis for Coding SNPs of the HLA-DQA1 Gene Involved in Susceptibility to Cervical Cancer

OBJECTIVE To analyze coding SNPs of the HLA-DQA1 gene involved in susceptibility for cervical cancer by a bioinformatics approach, and to choose some SNPs that may have an association with cervical cancer. METHODS By a SNPper tool we extracted SNPs from a public database (dbSNP), exporting them in FASTA formats suitable for subsequent use. Then we used PARSESNP as a tool for the analysis of the cSNPs. RESULTS In the cSNPs of the HLA-DQA1 gene, we find that rs9272693 and rs9272703, are made up of missense mutations which convert a codon for one amino acid into a codon for a different amino acid. We chose a PSSM Difference >10 as a lower level for the scores of changes predicted to be deldterious. CONCLUSION We used a bioinformatics approach for cSNPs analysis of the HLA-DQA1 gene. This method can select the variants in a conserved region, and give a PSSM Difference score. But the results need to be verified in cervical cancer patients and a control population.

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.

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine

Realizing personalized medicine requires integrating diverse data types with bioinformatics.The most vital data are genomic information for individuals that are from advanced next-generation sequencing(NGS) technologies at present.The technologies continue to advance in terms of both decreasing cost and sequencing speed with concomitant increase in the amount and complexity of the data.The prodigious data together with the requisite computational pipelines for data analysis and interpretation are stressors to IT infrastructure and the scientists conducting the work alike.Bioinformatics is increasingly becoming the rate-limiting step with numerous challenges to be overcome for translating NGS data for personalized medicine.We review some key bioinformatics tasks,issues,and challenges in contexts of IT requirements,data quality,analysis tools and pipelines,and validation of biomarkers.

Mitosis-specific acetylation tunes Ran effector binding for chromosome segregation

Stable transmission of genetic information during cell division requires faithful mitotic spindle assembly and chromosome segregation. The Ran GTPase plays a key role in mitotic spindle assembly. However, how the generation of a chemical gradient of Ran-GTP at the spindle is coupled to mitotic post-translational modifications has never been characterized. Here, we solved the complex structure of Ran with the nucleotide release factor Mogl and delineated a novel mitosis-specific acetylation-regulated Ran-Mogl interaction dur- ing chromosome segregation. Our structure-guided functional analyses revealed that Mogl compotes with RCCl for Ran binding in a GTP/GDP-dependent manner. Biochemical characterization demonstrated that Mogl-bound Ran prevents RCCl binding and subse- quent GTP loading. Surprisingly, Ran is a bono fide substrate of TIP60, and the acetylation of Lys134 by TIP60 liberates Mogl from Ran binding during mitosis. Importantly, this acetylation-elicited switch of Ran binding to RCC1 promotes high level of Ran-GTP, which is essential for chromosome alignment. These results establish a previously uncharacterized regulatory mechanism in which TIP60 pro- vides a homeostatic control of Ran-GTP level by tuning Ran effector binding for chromosome segregation in mitosis.

Chemomics and drug innovation

Chemomics is an interdisciplinary study using approaches from chemoinformatics,bioinformatics,synthetic chemistry,and other related disciplines.Biological systems make natural products from endogenous small molecules (natural product building blocks) through a sequence of enzyme catalytic reactions.For each reaction,the natural product building blocks may contribute a group of atoms to the target natural product.We describe this group of atoms as a chemoyl.A chemome is the complete set of chemoyls in an organism.Chemomics studies chemomes and the principles of natural product syntheses and evolutions.Driven by survival and reproductive demands,biological systems have developed effective protocols to synthesize natural products in order to respond to environmental changes;this results in biological and chemical diversity.In recent years,it has been realized that one of the bottlenecks in drug discovery is the lack of chemical resources for drug screening.Chemomics may solve this problem by revealing the rules governing the creation of chemical diversity in biological systems,and by developing biomimetic synthesis approaches to make quasi natural product libraries for drug screening.This treatise introduces chemomics and outlines its contents and potential applications in the fields of drug innovation.

An overview of human protein databases and their application to functional proteomics in health and disease

Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.

Rapid progress of DNA replication studies in Archaea,the third domain of life

Archaea,the third domain of life,are interesting organisms to study from the aspects of molecular and evolutionary biology.Archaeal cells have a unicellular ultrastructure without a nucleus,resembling bacterial cells,but the proteins involved in genetic information processing pathways,including DNA replication,transcription,and translation,share strong similarities with those of Eukaryota.Therefore,archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells.Moreover,the hyperthermophilic archaea provide very stable proteins,which are especially useful for the isolation of replisomal multicomplexes,to analyze their structures and functions.This review focuses on the history,current status,and future directions of archaeal DNA replication studies.