Evolutionary Biology

1. Evolutionary Biology Examples

2. Polio Virus • The vaccine now used to immunize against the disease poliomyelitis is a live poliovirus that we eat. • This live virus does not give us the disease (except to about 1-2 in a million people vaccinated) because it is genetically weakened (attenuated) so that our body can defeat it.

3. Attenuation • The attenuated vaccine strains came from wild, virulent strains of poliovirus, but they were evolved by Albert Sabin to become attenuated. Essentially, he grew the viruses outside of humans, and as the viruses became adapted to those non-human conditions, they lost their ability to cause disease in people.

4. This method of attenuation has been used to create many live vaccines. • When a person eats the attenuated virus, it infects his/her gut cells and starts doing what viruses do -- making copies of itself. • These viral progeny infect other cells in your gut, those in turn make other viral progeny, and so on, until you have a population of poliovirus growing inside your gut.

5. Evolution • Some of these viruses carry mutations, and some of those mutations (one or two in particular) restore most of the virulence to the virus. • In your gut, these restored viruses may have a selective advantage over the weakened viruses, and in the course of a week or so after eating the vaccine, you begin shedding virus with restored virulence. • In short, an evolutionary process inside your gut undoes Albert Sabin's attenuation of the virus.

6. Vaccine • These restored viruses do not hurt the person taking the vaccine because by the time restored viruses get to be abundant in the gut, the immune system has enough of a head start to keep the virus from getting into the central nervous system.

7. Vaccine • However, if we were to vaccinate just one person in a population of non-immunized people the restored viruses shed from this one person would infect other people and could start an epidemic of nasty poliovirus. • The WHO did all of China in 3 days, and vaccinated 90,000,000 people in India in one day.

8. Evolution leads to resistance • Isolates of the AIDS virus with up to 15 different drug-resistance mutations are known, and the latest drugs are becoming ineffective. • Some strains of bacteria are resistant to all available antibiotics. • For multi-drug resistant tuberculosis, surgery is the only cure because antibiotics don't work and only 50% of those infected survive. • Chemotherapy for cancer often fails because drug-resistant cells evolve during treatment.

9. HIV-the great evolver • The human immunodeficiency virus (HIV, shown here budding from a white blood cell) is one of the fastest evolving entities known.

10. What are the evolutionary origins of HIV? • HIV found that it is closely related to other viruses. Those viruses include SIVs (simian immunodeficiency viruses), which infect primates, and the more distantly related FIVs (the feline strains), which infect cats. • primates with SIV and wild cats with FIV don't seem to be harmed by the viruses they carry.

11. History of HIV

12. Blood Cells

13. Macrophages • Macrophages (Greek: "big eaters", makros = large, phagein = eat) are cells within the tissues that originate from specific white blood cells called monocytes. Monocytes and macrophages (differentiated monocytes) are phagocytes, acting in both nonspecific defence (or innate immunity) as well as specific defense (or cell-mediated immunity) of vertebrate animals. Their role is to phagocytize (engulf and then digest) cellular debris and pathogens either as stationary or mobile cells, and to stimulate lymphocytes and other immune cells to respond to the pathogen. macrophage of a mouse stretching its arms to engulf two particles, possibly pathogens

14. Making of antibodies • After digesting a pathogen, a macrophage will present the antigen (a molecule, most often a protein found on the surface of the pathogen, used by the immune system for identification) of the pathogen to a corresponding helper T cell. The presentation is done by integrating it into the cell membrane and displaying it attached to a MHC class II molecule, indicating to other white blood cells that the macrophage is not a pathogen, despite having antigens on its surface. • Eventually the antigen presentation results in the production of antibodies

15. T-cells • T cells belong to group of white blood cells known as lymphocytes and play a central role in cell-mediated immunity. They can be distinguished from other lymphocyte types, such as B cells and NK cells by the presence of a special receptor on their cell surface that is called the T cell receptor (TCR). The abbreviation "T", in T cell, stands for thymus since it is the principal organ for their development.

16. Helper T-cells • They are not cytotoxic or phagocytic; they activate or direct immune system. • The importance of helper T cells can be seen from HIV, a virus that infects cells that are CD4+ (including helper T cells). Towards the end of an HIV infection the number of functional CD4+ T cells falls, which leads to the symptomatic stage of infection known as the acquired immune deficiency syndrome (AIDS).

17. Why are some people resistant to HIV? • the human genome is littered with the remnants of our past battles with pathogens — and one of these remnants, a mutation to a gene called CCR5. • The mutant CCR5 allele probably began to spread in northern Europe during the past 700 years when the population was ravaged by a plague.

18. The mutant CCR5 is resistant to the disease, its frequency increased • In some parts of Europe today, up to 20% of the population carry at least one copy of the protective allele. • However, the populations of Asia and Africa were not exposed to the same epidemics; very few Asians and Africans now carry the allele http://evolution.berkeley.edu/evolibrary/article/0_0_0/medicine_04

19. CCR5 • Two new proteins found on immune cells, CCR5 and fusin (also known as CXCR4), play a key role in understanding how HIV infects cells. • One way HIV disables the immune system is by infecting and destroying CD4+ T-cells that manage immune responses. HIV actually attaches to the CD4+ protein on the surface of these and other cells to gain entry.

20. CCR5 • CD4+ protein alone is not enough to allow viral entry into cells. Scientists believe they have now identified a second doorway that the virus needs to open to infect a cell, and they have learned that this receptor may be different for different types of cells. One is called CC-CCR5 (CCR5 for short), and another is called CXCR4 or fusin.

21. CCR5 • CCR5 is present on a broad range of cells that can be infected by HIV, including T-cells and macrophages. Fusin on the other hand, is primarily found on CD4+ cells and only appears to serve as a doorway for certain types of HIV. CCR5 appears to be important for NSI strains of HIV (the strains most common in early disease), while CXCR4 appears to be more important for SI strains (a more aggressive strain seen in some people with more aggressive disease).

22. CCR5 • NSI (non-syncitium inducing) strains of HIV are the most common sexually transmitted form of the virus. This type of HIV preferentially infects macrophages (often found in the skin and mucous membrane) rather than T-cells. Therefore, it is macrophage-tropic, or M-tropic.

23. CCR5 • When HIV is transmitted sexually, it first establishes itself as an M-tropic virus, later developing into T-cell-tropic viruses in some people. These T-tropic strains that prefer to infect T-cells, are SI (syncitium inducing) viruses and may become more prevalent during later stages of the disease. It is unclear why the virus converts from an NSI to an SI strain in some people. About 50% of people who die of AIDS still have a predominant NSI strain of virus.

24. CCR5 • The SI strain of HIV is more aggressive and its prevalence correlates with more rapid disease progression. Additionally, anti-HIV drugs generally have less activity against SI strains of HIV. The most obvious difference between someone with an NSI versus an SI strain, however, is that people with an SI strain experience more rapid decline in CD4+ counts, as the SI virus preferentially infects and destroys these cells. Also, people with the SI strain tend to have a 3- to 5-fold increase in the rate of disease progression.

25. Syncitium Inducing • Syncitium inducing virus (SI) is virus that causes infected cells to form syncitia (connections) with other infected cells in tissue culture. • It is more virulent than non-syncitium inducing virus (NSI), which means that people with SI virus tend to progress more rapidly than those with NSI. Most people are infected with NSI but at some point experience a conversion to SI, which usually leads to a rise in viral laod and a more rapid decline in CD4 count.

26. Chemokines beta-chemokines, bind up CCR5 and CXCR4 and help block HIV from infecting cells MIP-1-alpha, MIP-1-beta and Rantes

27. Clinical Implications • When people inherited a defective version of CCR5 from both parents, they appeared to be resistant to infection with HIV. (The gene is considered defective because a portion of it is missing, and it thus cannot produce a functional CCR5 receptor.)

28. Contour Map Allele originated in Baltic Regions. Another alternative is that the allele may have arisen in central Europe and increased to a higher frequency in the north because of a geographical gradient in selection intensity [19].

29. Perspectives • A group from Texas has shown that resting CD4+ cells, despite bearing the CCR5 gene, are resistant to infection by HIV. Another group identified a type of cell, called a stem cell, which had CD4+ and both co-receptors on its surface, yet remained resistant to infection by HIV. What this implies is that there are other factors, beyond the expression of CD4+ and the newly identified co-receptors, which come into play with regard to HIV entry into cells.

30. A case study • In a highly publicized case in Lafayette, Louisiana in 1998, a woman claimed that her ex-boyfriend (a physician) deliberately injected her with HIV-tainted blood (HIV is the virus that causes AIDS). There were no records of her injection and no witnesses. So how could her story be tested? Evolutionary trees provide the best scientific evidence in a case like this.

31. HIV • HIV picks up mutations very fast -- even within a single individual. • If one person gives the virus to another, there are few differences between the virus in the donor and the virus in the recipient.

32. HIV • As the virus goes from person to person, it keeps changing and gets more and more different over time. • Thus, the HIV sequences in two individuals who got the virus from two different people will be very different. • Thus, if the woman's story were true, her virus should be very similar to the virus in the person whose blood was drawn but should be very different from viruses taken from other people in Lafayette.

33. A criminal Case

34. Abstract • A gastroenterologist was convicted of attempted second-degree murder by injecting his former girlfriend with blood or bloodproducts obtained from an HIV type 1 (HIV-1)-infected patient under his care. • Phylogenetic analyses of HIV-1 sequences were admitted and used as evidence in this case, representing the first use of phylogenetic analyses in a criminal court case in the United States.

35. Abstract • Phylogenetic analyses of HIV-1 reverse transcriptase and env DNA sequences isolated from the victim, the patient, and a local population sample of HIV-1-positive individuals showed the victim’s HIV-1 sequences to be most closely related to and nested within a lineage comprised of the patient’s HIV-1 sequences.

36. Abstract • Analysis of the victim’s viral reverse transcriptase sequences revealed genotypes consistent with known mutations that confer resistance to AZT, similar to those genotypes found in the patient.

37. Method • Genomic DNA from each individual was used to PCR-amplify a 858-bp env gene fragment and a 1,147-bp reverse transcriptase (RT) gene fragment

38. PCR • 200 ng of genomic DNA from the patient, victim, or any LA controls were handled and amplified separately by coamplifying the pol and env genes regions with PCR1/PCR2 and PCR5/PCR6 primer pairs to yield 1,231- and 1,288-bp fragments.

39. PCR • amplified separately a 1,147-bp pol fragment by using PCR3B/PCR4B primer pairs and a 858-bp env fragment by using PCR7B/PCR8B primer pairs. PCR products from the patient, victim, and the LA controls were directly sequenced.

40. Genetic Diversity • the extent of env genetic diversity of the suspected transmission pair, 50 molecular clones were isolated and sequenced at BCM from their respective PCR products. The molecular clones for the patient and victim were designated P01 through P50 and V01 through V50. • the most appropriate controlsfor the current study were HIV-1-infected individuals from theLafayette area.

41. Tree Suspect’s Patient Other HIV patients from LaFayette

42. Tree

43. Tree