It’s just take take take with these GAS: Bacterial modulation of host cell metabolism

Infections generally follow a similar path with some consistent steps. The microbe gains entry to the host, replicates in the host and is shed, in order to spread to a new host. Commonly this has the unfortunate side effect of making the host a bit ill.

For bacteria, replication within a host relies upon, among other things (such as avoiding the murderous cells of the host immune system), the ability of the microbe to obtain essential nutrients from the environment it finds itself in. A study published in Cell now shows that the pathogenic bacterium, group A Streptococcus (GAS), uses a mechanism that directly modulates the metabolism of the host cells in order to stimulate its own replication and proliferation.

GAS causes a variety of human infections and in fact only infects humans. Causing the well-known “strep throat” the majority of illnesses involving this bacterium are relatively mild. This is because the bacterium is commonly only found on the skin or in the throat. If this changes and the bacterium finds its way into more internal tissues, the blood or lungs for example, severe disease such as necrotising fasciitis and streptococcal toxic shock syndrome can result. Worldwide there are 700 million cases of mild GAS infection with about 650,000 cases becoming severe invasive infections. These 650,000 cases are associated with a mortality rate of around 25%.

Upon entering the host it is important for the bacteria to quickly gather nutrients in order to proliferate and truly establish itself at the site of infection. GAS attaches to host cells and releases the toxins streptolysin O (SLO) and streptolysin S (SLS) into the host cell. These toxins stimulate endoplasmic reticulum (ER) stress within the host cell. ER stress causes an increased unfolded protein response, ER-associated protein degradation (ERAD) and eventually cell death through a variety of pathways. It is associated with a medley of diseases such as diabetes and Alzheimer’s disease. In this case the change we are interested in is the increase in production of the enzyme asparagine synthetase that catalyses the production of asparagine (ASN). The researchers found that the host cell secretes increased levels of ASN which are detected by the bacterium, causing a sweeping change in gene expression that affects nearly 17% of the bacterium’s genes. These changes in gene expression include the up-regulation of genes involved in proliferation. In the absence of ASN these genes were down-regulated and the production of SLS/SLO was increased.

Graphical representation of the described pathway Image credit: Cell

Graphical representation of the described pathway
Image credit: Cell

This mechanism was only active locally and temporarily upon initial attachment, implying that this is a mechanism used by GAS to establish infection early on. Interestingly the detection of the increased ASN uses the two component system TrxSR, which is heavily involved in regulation of the bacterium’s virulence and metabolic genes. The researchers claim that this demonstrates that this pathway is an “important attribute to GAS pathogenesis” and helps the bacterium to cause severe disease. Other bacterial pathogens have been reported to benefit from host cell metabolism modulation, such as Agrobacterium tumefaciens, which makes plant cells produce opines required by the bacterium. The scientists point out that there are other pathogenic bacteria that use SLS/SLO-like toxins such as S.aureus and L.monocytogenes (both known for their ability to ruin a good takeaway or cream cake) and that it would be interesting to see if they use similar pathways. 

flu shot

Universal Flu Shot in Sight?

Influenza virus places a large burden on our society. It is estimated that the costs of everything related to influenza virus infection comes to about $87.1 billion US dollars in the United States. With the existing vaccination program against influenza virus, you may ask why there isn’t a “one size fits all” that can make us completely immune from influenza virus infection with a single vaccine. My parents have asked me that question a few weeks ago. The way how I explain it is through the use of umbrellas. Let’s say the virus carries a bright red umbrella. The immune system recognizes the red cloth on the umbrella and then mount an immune response against the red cloth. But next year, the virus mutates due to selective pressure. The virus now carries a blue umbrella. The immune system now has to go through all the processes from sensing the infection to getting rid of the infection, instead of recognizing the virus at the beginning of the infection. The current strategy that the scientists are trying to develop is the use of broadly neutralizing antibody. The broadly neutralizing antibody recognizes not the cloth of the umbrella, but the stalk of the umbrella which is common among all subtypes of influenza.

A  recent review article by Dr. Krammer and Dr. Palese from Mount Sinai has covered the challenge of this antibody in an elegant way. The real challenge behind the application of a broadly neutralizing antibody against influenza virus is that different age groups tend to have totally different exposure history to the subtypes of influenza virus. Children tend to be naive for influenza virus infection when adult are exposed to it multiple times. Furthermore, the elderly appears to mount a less effective response after a flu shot. Thus, the application of the broadly neutralizing antibody needs to be tested extensively in different age groups before rolling out.

“The initial cost of conducting these trials might seem high, but investment in universal influenza virus vaccine approaches might make it possible to overcome the threat of seasonal and pandemic influenza.”


Book Review: George W. Bush’s Decision Points

Three questions people kept asking me when I told them I was reading George W. Bush’s Decision Points:

- “Why?” My answer: I was eleven years old when Bush was elected, and he was our president through most of my teen years. I barely remember Clinton. Bush’s presidency ultimately shaped my political views, and it resulted in my fascination with learning more about the American political system.

- “I didn’t know he could write. Can he?” My answer: Well, technically, he can. He wrote a book. His technique is limited and it’s not profound by any measure, but it’s a book. I’d like to say, “It’s not like he was Harvard educated!” But he was. Not as a writer, though!

- “Is it any good?”  My answer: I didn’t hate it.

Bush’s Decision Points offsets much of the vitriol directed at him during his eight-year presidency. Rather than filling the 477 pages of his memoir with disparaging remarks about his critics in the media or the Democratic Party, he explains, sometimes humorously, the triumphs and failures of his decisions. He reflects upon his judgments, the media’s portrayal of him, and controversial topics. Though there are portions of the book that are defensive, he is highly self-critical and explains where he could have made better choices. Decision Points is, for the most part, chronological, but the focus of this memoir is chronicling how he dealt with expected and unanticipated events. He does this in fourteen chapters: Quitting; Running; Personnel; Stem Cells; Day of Fire; War Footing; Afghanistan; Iraq; Leading; Katrina; Lazarus Effect; Surge; Freedom Agenda; Financial Crisis.

For Bush critics, many of the chapters should be of interest. His chapters “Stem Cells”, “Katrina”, and “Financial Crisis” were particularly interesting. After reading such chapters, it is clear the president is held accountable for events out of his control. For example, in “Katrina” Bush explains that the 1988 Stafford Act places direct responsibility of natural disasters at the local and state levels. This requires the governor of any given state to request aid from the federal government, and in the case of Louisiana, the local officials did not make any request. With the inefficiency of the local government, Bush wanted to send federal troops to Louisiana, but another law, the 1878 Posse Comitatus Act, prevented him. Ultimately, Bush deployed federal troops without law enforcement authority, but the delay in his action was greatly criticized.

Bush’s memoir does not serve as an apology for those seeking it. He does write, however, “I believe I got some of those decisions right, and I got some wrong” (476). For a presidency that some view as a “failure”, Bush tries to clarify his decisions surrounding the circumstances of events such as 9/11, Iraq, Afghanistan, Katrina, and the financial meltdown.


Book Review: Robert Rand’s Tamerlane’s Children



“No, Uzbekistan. It doesn’t even border Pakistan.”

This interchange about Uzbekistan is not farfetched for people beyond Uzbekistan’s borders.  For the average Westerner, the “-stans” (Afghanistan, Kazakhstan, Kyrgyzstan, Pakistan, Tajikistan, Turkmenistan, and Uzbekistan) of the world are a complete mystery. After September 11, 2001, Americans were quite aware of Afghanistan, and to a lesser extent, Pakistan (because of its shared southern border), but most of the former Soviet countries are still unknown to Americans. There are, after all, countries that exist between Russia, China, India, and Europe! One such country is Uzbekistan. Home to Central Eurasia’s largest population (around 30 million), Uzbekistan has played a major role in the Global War on Terror. For that reason, among many others, it’s time to start picking up books on Uzbekistan, like Robert Rand’s Tamerlane’s Children: Dispatches from Contemporary Uzbekistan.

I was quite pleased to find Rand’s book immediately before taking off for my second trip to Uzbekistan. Tamerlane’s Children proves an entertaining read, especially during the two-day trek from Atlanta to Tashkent (via Amsterdam and Istanbul, thanks to Delta, KLM, and Turkish Airlines). Rand lived and worked in Uzbekistan for three years (2001-2004) as a freelance journalist. His text is divided into two parts: first, seven chapters about various subjects, which include 9/11, Amir Timur, love, and cotton; part two has “dispatches” (diary-like entries) and a chapter on Andijon. Each part of this book serves as an illustration of contemporary life in Uzbekistan. He concedes in the introduction that the book is not a comprehensive description of Uzbekistan, but aspects of daily life he found most interesting. For anyone who hasn’t traveled to Uzbekistan, Rand’s accounts make the country seem like an extremely frustrating and sometimes backward place, which is why it may be off-putting to some. His accounts are, however comical, sometimes harsh. That isn’t to say, though, that these maddening aspects of Uzbekistan are all encompassing. The country is fascinating, beautiful, and enchanting. After all, that’s why I keep returning!

There are a few shortcomings in Rand’s book. All of his personal accounts are from Tashkent, Uzbekistan’s capital. There is virtually no information about other major cities, like Samarkand, Bukhara, Khiva, or even Timur’s birthplace, Shahrisabz.  Contemporary life in Uzbekistan is not simply life in Tashkent! Additionally, Amir Timur (Tamerlane, or Timur the Lame), the “father” of Uzbekistan, is the namesake of this book. Rand mentions that he has taken poetic license in naming the book “Tamerlane’s Children”, since modern Uzbeks don’t descend from Amir Timur. Rand includes an insightful chapter on Islam Karimov’s decision to have Amir Timur as the national hero, but the overwhelming response from people Rand interviews is that they feel no connection to Amir Timur as a “father”.  Amir Timur, portrayed as a feudal villain in Soviet historiography, has replaced Soviet heroes, like Lenin and Marx.

The last sections of Rand’s book, however, absolve him of the text’s shortcomings. His interview with Craig Murray, Britain’s former ambassador to Uzbekistan is very revealing. The last chapter on Andijon is concise, and it explains much of the controversy surrounding the 2005 events. Most of all, Rand’s text is entertaining. For example, he writes in his entry for the 7 January 2002, “The police pulled over the car I was riding in today because, they said, I was wearing a seat belt. Nobody wears seat belts in Uzbekistan. The cops thought I had buckled up as a safety precaution because the driver had been drinking. Why else would someone buckle up?” (130). For a book about a country not many Americans are familiar with, Rand’s serves as a great introduction with its brief, succinct descriptions.


Book Review: Robert Galbraith’s The Cuckoo’s Calling

The Cuckoo’s Calling by Robert Galbraith (aka J.K. Rowling) is a quick, light read for anyone bogged down with real-world problems. Rowling’s attempt at the mystery subgenre of Mayhem Parva introduces the readers to limited settings in London, eccentric yet oddly normal characters, and a “domestic mystery” in an alleged murder.

Rowling’s protagonists, Cormoran Strike and his temporary secretary, Robin Ellacott, repeat the trope of a disheveled detective and his quick-witted Girl Friday with a contemporary, fame-obsessed twist. Strike, a wounded former military officer is paired with Robin on the day a major case is brought to his private investigative office.  John Bristow approaches Strike to investigate his late sister’s murder. Bristow’s sister, Luna Landry, is a beautiful supermodel whose sudden death is believed by all to be suicide. Strike, initially convinced that Landry committed suicide, takes on the case, and thus ensues the mystery of the plot.

The novel is eerily reminiscent of stories from TMZ, the celebrity news website. Strike, whose own celebrity roots imparts the plot with the rejection of celebrity life, knows exactly the personalities of the rich, famous, and unhappy that he needs to investigate. He and Robin spend the majority of the plot interviewing Luna’s dysfunctional family members, high fashion insiders, and hip-hop royalty. For those interested, this novel lends itself quite nicely to literary analysis through gender and pop culture studies.

Though the novel’s climax is somewhat predictable, The Cuckoo’s Calling provides us with a new set of captivating characters that promise an amusing ride through the glitz and glamour of London’s upper class.

august phd

Brief Guide to PhD Applications

Applying to doctoral programs can be an extremely stressful task, especially since each university has its own guidelines and requirements. Given the wide-ranging requirements by different programs, it is impossible to provide an all-encompassing guide to applications. This short guide, however, is an attempt at providing assistance to those interested in pursuing higher education. I treated my applications as a “course”. That is, I spent an average of 10-15 hours per week working on applications, writing, re-writing, editing, and perfecting each application. My mentors were immensely helpful in paring down my work, but my friends were crucial during this process. We set up “PhD Dates”  at cafes or somebody’s apartment, ordered food, and made sure we were productive.  After all, Downton Abbey and Game of Thrones repeats were a great distraction.

I applied to nine academic programs in Fall 2012, all in the Humanities. Five programs admitted me, and I accepted the University of Chicago’s Department of Near Eastern Languages and Civilizations.

Letters of Recommendation (began process in August):

I found it appropriate to ask three individuals who could speak to and emphasize three very different but important qualities about me. It is a bit daunting (and sometimes embarrassing) to approach a professor or teacher to ask for a letter of recommendation. What exactly is the best method of asking, “Professor, can you write a letter about how awesome I am?”

First, I chose the three people I thought would provide the fullest “picture” of who I am as an individual and as an academic. The initial email, which I sent in August (about four months prior to the first deadlines), requested a meeting to discuss my future and to receive advice. I prepared packets (although incomplete) with my curriculum vitae, a copy of my writing sample, a draft of my personal (academic) statement, and a list of potential programs and application due dates. These packets were prepared in the hopes that if my professor agreed to write a letter, I could immediately provide application information.

My undergraduate professor from Cal State Northridge, my language instructor from UChicago, and my Master’s thesis advisor from UChicago were the three people I approached to write letters of recommendation. Though I did not see all of the letters, I know that each wrote about my strengths from the experience they had working with me. This was vital, since three repetitive letters would have been pointless.  Every 4-6 weeks leading up to the December and January deadlines, I would email or meet them in person to discuss the progress of each application (i.e. whether they had started their letters, how I could improve my CV or statement).

 Networking (ongoing September-November):

The most important (and difficult!) part of this process was meeting every professor I mentioned in my applications.  I made it a point to visit many campuses (yes, I traveled quite a bit), and I went to many conferences with the knowledge that the professors I wanted to work with would be at those conferences.

Much like I did with my recommenders, I wrote a personalized email to each professor.  Writing personalized emails proved useful in November when two professors from different universities forwarded each other the emails I had sent them. This could have proved quite embarrassing had I sent them the same email.

In each email, I outlined my academic trajectory, but mostly focused on soliciting advice on my work.  I also asked them questions regarding their published and ongoing work.  This was the most time-consuming part of the application process, since I researched each professor and made sure they would be somebody I could work with for an extended length of time.

 Curriculum Vitae:

The easiest aspect of the application was refining my curriculum vitae. I began it as an undergraduate and continued adding to it through my Master’s program. The most troubling aspect of the CV was the order (education; presentations; publications etc). Some applications only allowed a one-page CV, so I would agonize over which sections to cut. The link to my current CV is below, and this CV is (almost) the same as the one I submitted to most doctoral programs:

Writing Sample:

The first thing I noticed about each application was that the lengths of the writing sample varied (anything from 10 pages to 30 pages).  I had three substantial papers that I produced during the first year of my MA that I thought of using for my applications.  Each paper had strengths (and unfortunately weaknesses!). The first paper had little to do with my interests as an academic, but was (as I was told by a professor) very convincing and well written. The second paper was completely in accordance with what I proposed researching as a doctoral student, but it was, I felt, not as well researched nor as credible as the first.  The third paper, which I ultimately submitted, needed some work, but had aspects that exemplified what I am capable of doing as an academic. I spent the next two months refining it, but it already encompassed one critical aspect that the other two papers did not: my language capabilities.  I had produced this paper using secondary sources in multiple languages.

Personal Statement:

I found writing a personal statement to be impossible at first, but once I began approaching it as a puzzle, it turned into an entertaining experience.  My first draft was commented on by at least ten people, each with their own opinions on what should be added or omitted. With all the comments in hand, I proceeded to write more than six versions of my personal statement.  Since the information in my statement is private, I will not provide a draft here. The following outline is of the points made in each paragraph.

Paragraph 1:  describe how my family background led to inquiries of race and religion in Central Asia; what activities increased and informed my knowledge of my proposed area of research

Paragraph 2: discuss my arrival at the University of Chicago for my Master’s; explain briefly my thesis and theoretical approach for my MA thesis

Paragraph 3: explain how my travels through Russia and Central Asia have helped form my opinions on my research; my contacts have helped provide indispensable sources

Paragraph 4 and 5: what I am proposing to do as a doctoral student; my theoretical approaches; current scholarship on the subject and the gap my research will fill; why my research will be important

Paragraph 6: “history lesson” (remember, there are people on the acceptance committees who know nothing about your proposed area of research, so it is important to provide a brief “lesson”); after providing three of four concise sentences about your focus, tie it to your research; how and where will your research add to what we know

Paragraph 7:  discuss the professors you intend on working with at the institution (mention you have met them); explain that your language skills will help in working with sources; make clear that this institution is essential for you to continue your research because of the professors and the resources at the institution.


Thoughts: Is it possible to design viruses to attack other viruses?

Yes for a short period of time. Viral infection can cause unbearable symptoms and may even lead to death if your immune system is compromised. Few weeks ago, when I was infected with the stomach flu viruses, I had absolutely nothing to do other than waiting patiently for my immune system to be activated. Is there other ways to treat viral infection, other than the well-known antiviral remedy, such as vaccines, Tamiflu and HAART?

A pediatrician pointed out the possibility of deriving viruses to target virus-infected cells last week at a Christmas party. To design such virus, one must recognize the receptors required to enter the cells. To target virus-infected cells, these receptors must be the same for the designed virus to enter. The designed virus can potentially do several things: hijack the replication machinery to repress harmful virus to replicate; repress the transcription of specific cellular factors that are required for the replication of the harmful virus; induce apoptosis (programmed cell death) quickly.

Genetic Testing: What is it?

The first point that I proposed may not be the best due to the fact that harmful viruses can still be replicated but at a slower rate. In contrast, the second point that I proposed can potentially inhibit harmful replication at the maximum level but may be detrimental to uninfected cells if the cellular factors are essential. The last point may not work due to the same reason as the previous point.

Another restriction on the design is the rapid mutation of the viruses. RNA viruses depend on the error-prone RNA polymerase to reproduce its RNA genome. For instance, HIV virus is estimated to have mutation in every single basepairs in its genome in just 24 hours. Thus, restricting the expression of cellular factors may repress viral replication for only a short period of time.


Stealing gene from viruses to form placenta in dogs and cats

If there weren’t viruses, our cats and dogs would not develop a placenta. A group of researchers from France discovered that in cats and dogs, the gene syncytin, responsible for creating a placenta, is stolen from retroviruses. Syncytin is highly conserved within species in the carnivora. In other words, there is a little DNA variation in the syncytin sequence. By comparing syncytin in species, the gene is stolen from viruses about 70-80 million years ago. Interestingly, syncytin is identified as an envelope gene that belongs to a provirus (provirus means a virus genome integrated into cat’s or dog’s genome). An envelope gene codes for an envelope protein. Go to the figure below: envelope protein is important in binding to cells for the virus to enter the cell. Stealing env gene from viruses is, therefore, an important mechanism for mammals to evolve. Evolution is a slow process. It depends on mutations that give rise to characteristics that may convey fitness to a particular species. By stealing an entire gene from viruses, mammals essentially skip the slow process of accumulating mutations. The researcher wrote,

“Therefore, it seems that, on several occasions in the course of mammalian evolution, env genes from endogenous retroviruses have been co-opted by their host to participate in the formation of the placenta”

The researchers also asked an interesting question after correlating the syncytin gene with the envelope gene of retroviruses. Can viruses use syncytin gene from cats and dogs as their envelope (see figure to see where the envelope protein is) to enter the cell? This group of researchers made virus mutants with cats’ or dogs’ syncytin as their envelope protein (envelope protein is responsible for binding to specific receptor to enter the cells). Then, they measured the number of viruses produced to see if syncytin is functional. In Figure C, you can see that viruses with either cat’s and dog’s syncytin can replicate in cat and dog’s cell. In sum, syncytin gene is still a functional envelope gene for virus replication.

Humans also have syncytin.

What if there are no viruses on Earth? Life would probably be developed with a difference mechanism. Given the slow rate of evolution, forming a placenta is quite unlikely.

Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):E432-41. Epub 2012 Jan 17.
Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora.
Cornelis G, Heidmann O, Bernard-Stoecklin S, Reynaud K, Véron G, Mulot B, Dupressoir A, Heidmann T.

Bacteria in your intestine is linked to Type 1 diabetes

Type 1 diabetes is commonly found in young children and adults. It is an autoimmune disease, meaning that our immune system identifies and attacks our organ as a foreign infected unit. A model (shown on the left) of the disease development has been proposed. In the model, an unknown stimulant triggers the expansion of immune B-cells and T-cells which causes inflammation and destruction of cells within the pancreatic islet. The pancreatic islet contains hormone-producing endocrine cells, such as beta cells. The beta cells are responsible in producing insulin that distributes glucose from blood to tissues. As a result of the B- and T-cells expansion, destruction of beta cells disables the production of insulin. The reduction of insulin causes a high level of glucose remained in the bloodstream. This hyperglycemia state (high glucose in the bloodstream) is known as Type 1 diabetes.

Toll like receptor is a protein that sits on the surface of cell (in most cases) to detect foreign particles that come off from bacteria or viruses. When it is activated, the signal is relayed to MyD88 in the cytoplasm (shown on right), which then indirectly activates the production of inflammatory proteins. It is recently discovered that if you take out MyD88 gene from diabetic mice, mice no longer have symptoms of diabetes. This protection appears to involve in the change of bacterial composition inside the mice without MyD88 gene. Surprisingly, if you eliminate some bacteria from the intestines in the diabetic mice (without MyD88) by antibiotic treatment, 40% of the mice tested have symptoms of diabetes. And if you eliminate all bacteria from the intestines in the diabetic mice (without MyD88), about 85% of the diabetic mice have symptoms of diabetes in 30 days. So what if you expose this germ free mice (without MyD88) with bacteria? Exposing germ free mice with bacteria reduce inflammation in the pancreatic islet, indicating that intestinal commensal bacteria prevent diabetic mice from Type 1 diabetes.

Complexity of the immune system: changes soldiers to fight

So is it possible to transplant bacteria to Type 1 diabetes patients as a cure? Quite possibly. Fecal bacteriotherapy transplantation has already been used to treat c. difficile infection. This procedure transplants the bacteria in the fecal matter from a healthy individual into the sick individual. This is thought to restore the disrupted bacterial community in the sick individual. Restoring microbiota can be a cure for autoimmune diseases, but for now, this technique has yet fully incorporated into clinical practices.

Here is an idea, there is sperm bank and egg bank out there these days. Why don’t we have a bank that stores all the fecal bacteria when we are healthy? If we get sick, we can go to the bank and restore our normal bacteria.


The “Perfect Storm” for Type 1 Diabetes. The Complex Interplay Between Intestinal Microbiota, Gut Permeability, and Mucosal Immunity. doi: 10.2337/db08-0331 Diabetes October 2008 vol. 57 no. 10 2555-2562

Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV.Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature. 2008 Oct 23;455(7216):1109-13. Epub 2008 Sep 21.


Virus Causes Cancer: Papillomavirus and Cervical Cancer

Did you know some viruses induce cancer unintentionally? Have you heard of the Gardasil vaccine that prevents cervical cancer? In the 1980s, some parts of the papillomavirus genome were discovered in patients with cervical cancer. It had been hypothesized that the integration of papillomavirus DNA causes cervical cancer. However, any testing on humans would be deemed unethical. Therefore, this hypothesis was never proven, but the proof was indirectly supported by the study with the Gardasil vaccine.

Papilloma virus infects the basal epithelial cells (the bottom of the epithelium). Its replication cycle is tailored to the stratified structure, in which it starts by establishing itself in the basal layer, and then replicates effectively when it gets closer to the top to disseminate its progeny. The major barrier for the papillomavirus is that the top layer is made of terminally differentiated cells (meaning that they can no longer divide). This poses a threat to the replication cycle, because only dividing cells can provide the machinery for the virus to make copies of its genome. Without the machinery, the virus is at a dead end. Papillomavirus only codes for 8 proteins. 2 of them are responsible to overcome this barrier (i.e. release E2F, degrades p53). They both reactivate signaling molecules to reinitiate the cell cycle.

In the figure, G0 refers to the growth arrested phrase which the terminally differentiated cells are in. The reactivation of signaling molecules leads to the re-entry into the G1 phrase. And after G1 phase, cells can then divide, giving papillomavirus the required machinery to replicate.

It is rare that the viral DNA gets integrated into the human genome. However, when the integration happens, the proteins that are responsible for reinitiating cell cycle are made. As a result, cells with integrated genomes divide uncontrollably. And that is why papillomavirus causes cancer. So why did I say “virus causes cancer unintentionally”? The goal of viruses is to replicate and disseminate. The integration leads to the end of the replication cycle, thus cancer is not intended to happen.

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Tatyana V. Golovkina  - Associate Professor in the Department of Microbiology at the University of Chicago

5: zur Hausen H, Meinhof W, Scheiber W, Bornkamm GW. Attempts to detect virus-secific DNA in human
tumors. I. Nucleic acid hybridizations with complementary RNA of human wart virus. Int J Cancer.
6: H Zur Hausen, H Schulte-Holthausen, H Wolf, K Dörries, H Egger. Attempts to detect virus-specific DNA in
human tumors. II. Nucleic acid hybridizations with complementary RNA of human herpes group viruses. Int J
Cancer. 1974, 13 (5): 657-664
7: zur Hausen H, Gissmann L, Steiner W, Dippold W, Dreger I. Human papilloma viruses and cancer. Bibl
Haematol. 1975 ;(43):569-71.

31: Dürst M, Gissmann L, Ikenberg H, zur Hausen H. A papillomavirus DNA from a cervical carcinoma and its
prevalence in cancer biopsy samples from different geographic regions. PNAS. 1983;80(12):3812-5
32: Ikenberg H, Gissmann L, Gross G, Grussendorf-Conen EI, zur Hausen H. Human papillomavirus type-16-
related DNA in genital Bowen’s disease and in Bowenoid papulosis. Int J Cancer. 1983;32(5):563-5.
33: Boshart M, Gissmann L, Ikenberg H, Kleinheinz A, Scheurlen W, zur Hausen H. A new type of
papillomavirus DNA, its presence in genital cancer biopsies and in cell lines derived from cervical cancer.
EMBO J. 1984;3(5):1151-7.


Helicobacter Pylori: causative agent of stomach ulcer

Helicobacter pylori is a gram-negative bacterium that affects the human gastric mucosa. The bacterium is a contributor to the pathogenicity of several diseases including chronic gastritis, peptic ulcers, gastric adenocarcinomas, and gastric mucosa–associated lymphoid tissue lymphomas (3, 5). Gastric cancer still remains a concern in Asian countries, yet the incidence varies greatly amongst the different regions of Asia. Japan, Korea, and China are considered as high-risk areas, whereas Vietnam and Thailand are considered as intermediate-risk and low-risk, respectively. In Asian countries, the prevalence of gastric cancer is higher amongst the elderly population (8).

While approximately 50 percent of the world’s population may be infected with H. pylori, infection rates are generally higher in developing countries, with the majority of infections occurring during childhood, the period of highest risk. There is, however, usually a long latency period with disease manifestations appearing later in adulthood. The prevalence of H. pylori infections is variable depending on age, race, geographic area, socioeconomic status and ethnicity (3).

Recent molecular epidemiologic data suggest that this variation is likely due to the genetic diversity of H. pylori. All patients that are infected with H. pylori will develop gastritis, while there is also the possibility of ulcer disease and an increased risk to gastric cancer. As there is such great variation, many studies sought to identify the different factors that determine the disease outcome of infection. Thus far, the major virulence factors that contribute to either gastritis or gastric cancer include the cagA (cytotoxin-associated gene) and vacA (vacuolating toxin) genes, which also vary between strains different regions of the world. For instance, the 3’ repeat region of the cagA gene varies between strains from Western countries and those from East Asian countries. Furthermore, there is variation in the vacA gene structure in both the signal region, designated as s1 and s2 and the middle region, designated as m1 and m2. The most virulent genotypes amongst countries with high gastric cancer incidence rates are vacA s1/m1 and the East Asian type cagA (8)

H. pylori can be classified into two classes, type I and type II, based on the presence or absence of the cag pathogenicity island (4). The cag pathogenicity island is a 40 kilobase segment of DNA, consisting of 31 genes, in which the majority of them encode a type IV secretion system (T4SSs). The T4SSs are found in many Gram-negative bacteria and are ancestrally related to conjugation systems. T4SSs are functionally diverse although they generally consist of 11 VirB proteins and a coupling protein, VirD4. Currently, the role of the T4SS-specific accessory factors is unknown except for CagF and Cag L. CagF is a chaperone-like protein and is crucial for translocating CagA. The H. pylori T4SSs form a pilus for the injection of virulence factors. This is mediated by CagL, a pilus-covering protein, which acts as an adhesin to connect the T4SS with the target cells (1). Following the interaction of CagL with integrin receptors, the type IV secretion system acts as a molecular syringe and is responsible for translocating the CagA protein into gastric epithelial cells to be tyrosine phosphorylated by Src kinases (6, 9).

Phosphorylated CagA will then interact with SH2 domain-containing host cell proteins such as the tyrosine phosphatase SHP-2 and the adaptor protein CRK. The interactions of CagA with signaling molecules subsequently lead to a rearrangement of the cytoskeleton and cell elongation, referred to as a “hummingbird” morphological chance. Thus, the alteration of the host cell architecture by CagA may be a potential cause of virulence (7). The hummingbird phenotype occurs due to Cag-activated SHP-2 dephosphorylation of the focal adhesion kinase, which promotes the activation of ERK MAP kinases. Activated MAP kinases are important in cell cycle progression, which is thought to contribute to gastric cancer promotion (9).

CagA is also able to perturb cell functions through tyrosine phosphorylation-independent mechanisms. Non-phosphorylated CagA interacts with host cell proteins such as the epithelial tight junction-scaffolding protein zonulin, the cell adhesion protein E-cadherin, and other adaptor proteins. This leads to the disruption of tight and adherent junctions and induces pro-inflammatory and mitogenic responses that may be important in promoting gastric cancer (9). In vivo studies have shown that H. pylori infections are related to the release of pro-inflammatory cytokines and chemokines such as IL-8. Induction of IL-8 appears to be dependent on the cag pathogenicity island. (9).

In addition to binding to SHP-2, CagA also interacts with the C terminal Src kinase (Csk), which phosphorylates src family kinases (SFKs) and inhibits their activity. Since SFKS are responsible for CagA tyrosine phosphorylation, this indicates that there is a feedback regulatory mechanism that dampens the phosphorylation-dependent activites of CagA. This also means that the presence of a negative feedback loop may ensure that there is a balance between cagA-posiive H.pylori and the human stomach without the bacterium causing acute and fatal mucosal damage to the host (2).

Another important virulent determinant of H. pylori infections is the vacuolating cytotoxin, VacA. VacA is a secreted exotoxin that inserts itself into the epithelial cell membrane and forms an anion selective, voltage-dependent channel (7). The toxin also facilitates the formation of transmembrane pores, which increases the permeability of the gastric epithelium.  Together, these mechanisms may provide nutrients for the bacterium (4).

VacA is responsible for structurally altering epithelial cells, disrupting endosomal maturation, induces mitochondrial damage, cytochrome c release and apoptosis of gastric epithelial cells. Some studies have also suggested that VacA has multiple effects on the immune system by interfering with phagocytosis and antigen presentation. Furthermore, VacA inhibits the activation of NFAT, which is required for genes that are involved in T cell activation. Because of the dampened immune response, it is believed that H. pylori is able to evade the adaptive immune response and cause a persistent infection. The majority of these effects, however, have only been observed in vitro. It remains to be established whether the same clinical effects would be observed in vivo in humans (9).

H. pylori is able to persist in the host due to a variety of mechanisms, including preventing its own toxicity through negative feedback loops or through the suppression of the immune system. While the mechanisms for cagA as a virulence factor are becoming more evident, further research will be required to define additional molecular mechanisms.


1. Backert, S., and M. Selbach. 2008. Role of type IV secretion in Helicobacter pylori pathogenesis. Cell. Microbiol. 10:1573-1581. doi: 10.1111/j.1462-5822.2008.01156.x.

2. Hatakeyama, M. 2006. The role of Helicobacter pylori CagA in gastric carcinogenesis. Int. J. Hematol. 84:301-308. doi: 10.1532/IJH97.06166.

3. Malaty, H. M. 2007. Epidemiology of Helicobacter pylori infection. Best Pract. Res. Clin. Gastroenterol. 21:205-214. doi: 10.1016/j.bpg.2006.10.005.

4. Manente, L., A. Perna, E. Buommino, L. Altucci, A. Lucariello, G. Citro, A. Baldi, G. Iaquinto, M. A. Tufano, and A. De Luca. 2008. The Helicobacter pylori’s protein VacA has direct effects on the regulation of cell cycle and apoptosis in gastric epithelial cells. J. Cell. Physiol. 214:582-587. doi: 10.1002/jcp.21242.

5. Ogura, K., S. Maeda, M. Nakao, T. Watanabe, M. Tada, T. Kyutoku, H. Yoshida, Y. Shiratori, and M. Omata. 2000. Virulence factors of Helicobacter pylori responsible for gastric diseases in Mongolian gerbil. J. Exp. Med. 192:1601-1610.

6. Ogura, K., S. Maeda, M. Nakao, T. Watanabe, M. Tada, T. Kyutoku, H. Yoshida, Y. Shiratori, and M. Omata. 2000. Virulence factors of Helicobacter pylori responsible for gastric diseases in Mongolian gerbil. J. Exp. Med. 192:1601-1610.

7. Tummala, S., S. Keates, and C. P. Kelly. 2004. Update on the immunologic basis of Helicobacter pylori gastritis. Curr. Opin. Gastroenterol. 20:592-597.

8. Uchida, T., L. T. Nguyen, A. Takayama, T. Okimoto, M. Kodama, K. Murakami, T. Matsuhisa, T. D. Trinh, L. Ta, D. Q. Ho, H. H. Hoang, T. Kishida, T. Fujioka, M. Moriyama, and Y. Yamaoka. 2009. Analysis of virulence factors of Helicobacter pylori isolated from a Vietnamese population. BMC Microbiol. 9:175. doi: 10.1186/1471-2180-9-175.

9. Wen, S., and S. F. Moss. 2009. Helicobacter pylori virulence factors in gastric carcinogenesis. Cancer Lett. 282:1-8. doi: 10.1016/j.canlet.2008.11.016.


Virus lives within a virus: Virophage

There are viruses living inside viruses. It is not an imagination of a virologist. Indeed, there are viruses living within one of the biggest viruses on the planet. We call this group of viruses,  virophage. There are also viruses that can infect bacteria, and we call them bacteriophage (see diagram on right). Here, an emerging field will be discussed: virophage.

Mimivirus was first discovered in 1992 from a cooling tower during a pneumonia outbreak in England. Due to its abnormal large size, mimivirus was first mistaken as a member of the bacteria. It was named as Bradford coccus. Through genomic sequencing and an observation of viral eclipse phrase, mimivirus was re-defined as a member of the viruses. Mimivirus replicates within the cytoplasm in free-living amoeba. The replication of mimivirus leads to lysis of amoeba. In 2008, researchers observed viral particles inside mimivirses (see figure on left). These small viruses (also called virophage) are called Sputnik virophage. Sputnik can’t replicate in amoeba alone. It requires Mimivirus to be present for growth. However, the growth of sputnik virus is not beneficial for the mimivirus. It causes abnormal assembly of the mimivirus. Interestingly, Sputnik produces three proteins that are similar to proteins found in mimivirus, suggesting genes can be transferred between the host and the symbiont.

The network of relationships between amoeba, mimivirus and sputnik virus are summarized here in the figure shown on left. Green arrow means the relationship is positive. Red means the relationship is negative. First, amoeba provides an environment for mimivirus to grow. However, the replication of mimivirus leads to the release of new mimiviruses, in which the release requires the lysis of the amoeba (shown at the bottom). Therefore, the presence of mimivirus is deleterious for amoeba. In contrast, the presence of mimivirus is favorable for the growth of sputnik. But sputnik affects the proper assembly of mimivirus while it indirectly favors the growth of amoeba by getting rid of pathogenic mimivirus.

This complex yet not so complicated network of symbiotic relationships within amoeba has conveyed an important point. Everything is dependent on each other. Without one, one may succeed or fail miserably. To sustain our current network, we must balance the act of symbionts and host. So one does not go to extinction.

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Supplement 1: Here is the replication cycle of mimivirus. Mimivirus replicates within amoeba. At the end, amoeba is lysed to release progeny viruses:

Supplement 2: Here is a comparison between several aspects of the mimivirus and the virophage sputnik:


Parasitoid viruses. by Nancy beckage and Jean-Michel Drezen

The virophage as a unique parasite of the giant mimivirus. La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D. Nature. 2008 Sep 4;455(7209):100-4.

Sputnik, a virophage infecting the viral domain of life. Desnues C, Boyer M, Raoult D. Adv Virus Res. 2012;82:63-89.

Q&A: how to set up the template you want on fast ABI 7500 real time PCR machine

After struggling for an hour on the fast real time PCR system from applied biosystem, I finally realize how to properly arrange the cells you want in the template.

First, create the template based on how many samples and duplicates you have. Ignore how they are not arranged in the way you want it first. Before proceeding to the next step where you adjust the experiment condition, make sure you have all the samples listed along with the correct targets.

Then save the template. And then you will be brought to a new page, where you can copy and paste around cells. At that point, you can adjust the template all you want, before loading your plate, and starting the protocol.