1. Molecular Biology C SSheng Zhao ( 赵晟 ), Biochemistry and Molecular Department of Medical school in Southeast University CCouse QQ Club: 112342994 ( 分子生物学 C ) WWeb: http://teaching.ewindup.info/ EEmail: shengzhao@seu.edu.cn or windupzs@gmail.com QQQ /MSN/Skype/gChat: windupzs@gmail.com MMobile:18551669724 or 13675130010 Conception, theory, research, and application ——Logic and LIY (Learn It Yourself)

2. Section 1 : DNA barcode ——Unveiling nature's most hidden diversity (The basic use of GenBank) Section 2: From invisible to visible ——Discovery new microbe / pathogen (Traditional molecular cloning and high throughput techniques) Case 2 : Talking to your family ——Hereditary parentage (Searching on PubMed and other knowledge database) Chapter 2: Data Are Mad Too (Biological Database)

3. Unveiling nature's most hidden diversity

4. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence 2.Blast a sequence 3.Submit a sequence 4.Functional analysis of a sequence Splicing Expression Evolution Literature

5. 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence Basic use of GenBank

6. 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence

7. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence

8. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence

9. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence

10. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence

11. Basic use of GenBank 1.Searching a gene or protein Genome sequence mRNA sequence Protein sequence 2.Blast a sequence 3.Submit a sequence 4.Functional analysis of a sequence Splicing Expression Evolution Literature

12. DNA fingerprint/profile

13. Short Tandem Repeat (STR) DNA profiling of human cell lines Cross-contamination among cultured cell lines has occurred at frequencies ranging from 16 to 35%! Hypervariable regions: which consist of variable number tandem repeat (VNTR) units from minisatellite DNA

14. DNA barcode and biodiversity uses a short genetic marker in an organism's DNA to identify it as belonging to a particular species

15. DNA barcode and biodiversity

16. PopSets in GenBank Population study data sets (epidemiology) Population study data sets (epidemiology) Nucleotide sequence Nucleotide sequence Protein sequence Protein sequence A set of DNA sequences for analyzing evolutionary relatedness of a population. A set of DNA sequences for analyzing evolutionary relatedness of a population. Different members of the same species Different members of the same species Organisms from different species Organisms from different species Aligned sequences submitted as a set describing evolutionary events and population variation Aligned sequences submitted as a set describing evolutionary events and population variation population genetic population genetic Phylogenetic Phylogenetic mutation study. mutation study.

17. PopSets in GenBank

18. Snapping shrimp (a special species example)

19. Snapping shrimp Top view Side view Frontal view

20. Snapping shrimp The loudest animal in the sea. Produce a zero to peak source level up to 190 dB re 1 μPa in less 1 millisecond. The animal snaps a specialized claw shut to create a cavitation bubble that generates acoustic pressures of up to 80 kPa at a distance of 4 cm from the claw. As it extends out from the claw, the bubble reaches speeds of 60 miles per hour (97 km/h) Sonoluminescence from the collapsing cavitation bubble reaches over 4,700°C. (the surface temperature of the sun is 5,500 °C). The snapping is used for hunting (hence the alternative name "pistol shrimp"), as well as for communication.

21. Lake Victoria Lake Tanganyika Lake Malawi Cichlid: Astatotilapia burtoni Lake Tanganyika, East African Rift More than 1600 species of cichlids swim in fresh water around the world

22. Cichlid: Astatotilapia burtoni Lake Tanganyika, East African Rift Males of many sand-dwelling species of Lake Malawi cichlid build elaborate sandcastle bowers, the shape of which varies greatly among species. These bowers are a focal point for male courtship displays. Mating takes place in the bower, after which the female leaves with the fertilized eggs in her mouth. Bowers of a: Copadichromis sp, b: Tramitichromis sp, c: Lethrinops lethrinus, and d: Lethrinops auritus.

23. Cichlid: Astatotilapia burtoni Lake Tanganyika, East African Rift The thousands of closely related cichlid fishes in the lakes of East Africa are an ideal model system for understanding the genetic basis of vertebrate speciation The most spectacular radiations of vertebrates are the species flocks of cichlids in the lakes of East Africa, where in the last 10 million years almost 2,000 unique species have evolved. A few species have initiated rapid adaptive radiations, which have culminated in flocks of several hundred closely related but phenotypically diverse species. Few systems offer the opportunity to study so many recent, ongoing and replicate speciation events These radiations have occurred in such a short period of time (and in spite of significant levels of gene flow) that classic models of speciation do not easily explain cichlid evolution

24. Other Specialized Database 1.miRBase: the microRNA database http://mirbase.org/ A searchable database of published miRNA sequences and annotation. Predicted hairpin portion of a miRNA transcript The location and sequence of the mature miRNA sequence (termed miR). 2.Jackson Lab http://www.jax.org/ Mouse Genome Informatics (MGI) Search for JAX® Mice Mouse Phenome Database 3.ATCC http://www.atcc.org/ Cell biology collection ： High performance cells and culture systems Microbiology collections 4.Addgene http://www.addgene.org/ a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmid 5.BrainInfo http://braininfo.rprc.washington.edu/ Structures in the brain. Search Brain Atlases NeuroMaps lets you map and display any kind of data on standard Atlas templates and print or download figures for presentation or publication. Contains ontologies of human, macaque and rodent brain atlases.

25. Through the gut: You are what you eat! Discovered by Chen-Yu Zhang's group at Nanjing University (2012, Cell research) 1.Significantly expanded the functions of miRNAs; 2.is an extremely intriguing and novel idea that has far-ranging implications for human health and metabolism; 3.shed new light on our understanding of cross-kingdom (such as animal- plant) interactions, or perhaps even the 'co-evolution', and to open new ways of thinking about regulation of miRNAs, and about the potential roles of exogenous miRNAs such as those from food, plants and insects in prey-predator interactions; 4.provides evidence that plant miRNAs maybe the seventh "nutrient" in the food (the six others are: H 2 O, protein, FFA, carbohydrate, vitamins and real elements); 5.provides a novel mechanism of development of metabolic disorder. 6.provides evidence that plant miRNAs may represent essential functional molecules in Chinese traditional herb medicine 7.Safety of Transgenic food ——Comments from Science Magazine, 2012

26. Through the gut: You are what you eat! New foods for thought——Reviewed by Kendal D. Hirschi

27. Not only through the gut: as a more general communication Circulating microRNA Secreted microRNA Exogenous plant microRNA

28. Through the gut: You are what you eat??? The new study, published in RNA Biology, 2013, the Johns Hopkins group says: Supports conventional wisdom that genetic material from food would have little chance of surviving the digestive system, much less crossing the intestinal lining to enter the bloodstream “It’s disappointing in a sense — it would open up so many therapeutic possibilities if microRNAs from food really could get into our blood and regulate our genes…” Does see some targeted plant microRNAs in the macaques’ blood. But when they ran the experiment several times, they got highly variable results Debate is still going on. But beyond the fact that people won’t be picking up prescription lettuce at the pharmacy anytime soon, he adds, the larger lesson is that scientific research’s capacity for self-correction is alive and well.

29. Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses —— Zhen Zhou et.al.Cell Research, Oct 7 th, 2014