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 : “Sexual” plant ——Plant genes contribute to a sexually transmitted disease. (Horizontal gene transfer) Section 2 : “natural in vivo system for tissue repair” ——Adult mesenchymal stem cells (Stem cell research) Case 6 : DNAs of our lives ——The role of pharmacogenomics in modern medicine (Clinic medicine research) Chapter 6: Water and Fish (Translational biology and molecular medicine)

3. Horizontal gene transfer

4. Chlamydia trachomatis The most frequently reported sexually transmitted disease in the US is caused by the parasitic bacterium Chlamydia trachomatis. 500,000 annual reported cases, ~4 million estimated annual cases. If left untreated, infections can develop into pelvic inflammatory disease (PID) and eye disease (trachoma). Infected human genital epithelial cells. Green or yellow spots. Chlamydial envelope material ("ENV")

5. Chlamydia trachomatis Chlamydia trachomatis, a gram-negative bacterium, appear as either coccoid or rod shape. Three human biovars: 1.serovars Ab, B, Ba, or C - cause trachoma: infection of the eyes, which can lead to blindness, and is prevalent in Africa 2.serovars D-K - cause urethritis, pelvic inflammatory disease, ectopic pregnancy, neonatal pneumonia, and neonatal conjunctivitis 3.serovars L1, L2 and L3 - lymphogranuloma venereum (LGV). Simpler than regular bacteria, smaller, have both DNA and RNA, but lack enzyme system for ATP and GTP, similar as virus, must live in cells. C. trachomatis may be treated with any of several bacteriostatic antibiotics: macrolides (azithromycin, clarithromycin, erythromycin, etc) or tetracyclines (doxycycline, tetracycline, etc).

7. Laboratory tests for Chlamydia trachomatis Nucleic acid amplification tests (NAAT). These tests find the genetic material (DNA) of Chlamydia bacteria. E.g. a polymerase chain reaction (PCR) test on a urine sample. Nucleic acid hybridization tests (DNA probe test). A probe test also finds chlamydia DNA. A probe test is very accurate but is not as sensitive as nucleic acid amplification tests. Enzyme-linked immunosorbent assay (ELISA, EIA). This quick test finds substances (Chlamydia antigens) that trigger the immune system to fight Chlamydia infection. Direct fluorescent antibody test (DFA). This quick test also finds Chlamydia antigens. Chlamydia cell culture. A test in which the suspected chlamydia sample is grown in a vial of cells. The pathogen infects the cells and after a set incubation time (48 hours) the vials are stained and viewed on a fluorescent light microscope.

8. The Chlamydia Genome Project A circular chromosome of about 1,045,000 base pairs (1/4 of Escherichia coli) Identified 888 protein-coding genes. Among these, some proteins appear to have an unconventional natural history. Using whole-genome sequencing, the researchers show that the exchange of DNA between different strains of Chlamydia to form new strains is much more common than expected. The genome appears to have undergone an unusually high number of horizontal gene transfer events, suggesting that the parasitic nature of C. trachomatis provides greater opportunity for gene transfer to occur. More bizarre, though, is that some of the C. trachomatis proteins are more related to green plants than to other bacteria or their human hosts.

10. Hypothetic stages of plastid origin and establishment. White, α-proteobacterial (mitochondrial) yellow, chlamydial green, cyanobacterial endosymbionts (a,b) first stage; (c) second stage; (d) third stage; (e) fourth stage. Dashed lines indicate directions of intracellular gene transfer Solid lines show protein targeting of the transferred genes Crosses indicate chlamydial endosymbiont and gene transfer processes that might not exist in extant photosynthetic eukaryotes.

11. Horizontal gene transfer

12. 1951, the transfer of a viral gene into Corynebacterium diphtheriae created a virulent from a non-virulent strain, Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of bacteria. In the mid-1980s, Syvanen predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth. The phenomenon appears to have had some significance for unicellular eukaryotes as well. There is some evidence that even higher plants and animals have been affected and this has raised concerns for safety. Some have argued that the process may be a hidden hazard of genetic engineering as it could allow transgenic DNA to spread from species to species.

13. Mechanism of HGT Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA), common in bacteria, but less so in eukaryotes. Bacterial conjugation, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact. Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage). Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales. A transposon (jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance.

14. Transformation and Bacterial conjugation

16. Viral Transduction

18. Gene transfer agent (GTA) A gene transfer agent or "GTA" is a bacteriophage-like element produced by several bacteria that mediates horizontal gene transfer. GTAs package random segments of DNA present in the host bacterium, which can be transduced to a recipient cell.

20. Transposable elements (TEs) Class I (retrotransposons): The copy and paste mechanism is similar as retroviruses, they are transcribed from DNA to RNA, and the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted at a new position into the genome.The reverse transcriptase is often encoded by the TE itself. 1.TEs with long terminal repeats (LTRs): encode reverse transcriptase, similar to retroviruses 2.LINEs: encode reverse transcriptase, lack LTRs, and are transcribed by RNA polymerase II 3.SINEs: do not encode reverse transcriptase and are transcribed by RNA polymerase III. Class II (DNA transposons): The cut-and-paste transposition mechanism of class II TEs does not involve an RNA intermediate. Transposase enzymes can be non-specific or specific when binding to target site in DNA

23. Transposon and gene trap Gene trapping is a high-throughput approach that is used to introduce insertional mutations across the mammalian genome. 1.a promoterless reporter gene and/or selectable genetic marker 2.When inserted into an intron of an expressed gene, the gene trap cassette is transcribed from the endogenous promoter of that gene. 3.Thus, gene traps simultaneously inactivate and report the expression of the trapped gene at the insertion site, and provide a DNA tag (gene trap sequence tag, GTST) for the rapid identification of the disrupted gene.