A novel Rhabdovirus (the same family as rabies) has been discovered in the Democratic Republic of Congo. This new virus is associated with acute hemorrhagic fever. Three cases were identified, but only one has been confirmed. The first two cases died within 2-3 days of presenting with symptoms. The third case was a nurse that had cared for the other two. The nurse survived, and the novel virus was identified in their blood. No other potential cases were found at the time. The source (hemorrhagic fever is generally a zoonotic infection) and mode of transmission have not been determined.
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002924
Monday, 1 October 2012
Thursday, 13 September 2012
Should people be paid for research tissue donations?
A piece in Science on July 6 discussed the case of Henrietta Lacks (the patient HeLa cells are derived from) and whether people who donate tissue for research purposes should receive compensation.
http://www.sciencemag.org/content/337/6090/37
This week, several letters were also published in Science that argue for or against a compensation scheme. The main issues are should compensation be given? how much? would royalties be included? would type of tissue matter? would the number of donors decrease? would compensation induce more people to consent?
Human tissue is an invaluable part of research. Those tissues that are collected are "waste" or dangerous (ex tumours). As someone that will soon rely on human tissue samples, I am in favour of whatever will send tissue my way. However, I don't feel comfortable if people aren't really ok with their tissue being used in research but are donating because they are in need of the money.
http://www.sciencemag.org/content/337/6090/37
This week, several letters were also published in Science that argue for or against a compensation scheme. The main issues are should compensation be given? how much? would royalties be included? would type of tissue matter? would the number of donors decrease? would compensation induce more people to consent?
Human tissue is an invaluable part of research. Those tissues that are collected are "waste" or dangerous (ex tumours). As someone that will soon rely on human tissue samples, I am in favour of whatever will send tissue my way. However, I don't feel comfortable if people aren't really ok with their tissue being used in research but are donating because they are in need of the money.
Fewer women enrol in HIV vaccine trials
More than half of the new HIV infections occur in women in developing countries, but only about 20% of the participants in phase I and II HIV vaccine trials are women. This makes it difficult for researchers to determine if the virus is actually effective in women. It's thought that this may be due to a couple factors - the first that women can not become pregnant during the trial, but most eligible women are usually within the reproductive age; second, women may need to seek consent from their parents or partners to participate in the trial and this may influence their willingness to participate.
http://www.nature.com/news/hiv-vaccine-trials-struggle-to-enrol-women-1.11415
Same article also on SciDev.Net (I'm not sure if access to the articles is different)
http://www.scidev.net/en/health/hiv-aids/news/hiv-vaccine-trials-struggle-to-enrol-women.html
http://www.nature.com/news/hiv-vaccine-trials-struggle-to-enrol-women-1.11415
Same article also on SciDev.Net (I'm not sure if access to the articles is different)
http://www.scidev.net/en/health/hiv-aids/news/hiv-vaccine-trials-struggle-to-enrol-women.html
Monday, 10 September 2012
Vaccine trail identifies targets for immune response that could improve future vaccines
Saw this on Twitter today and thought it was really interesting. Will post the link to the full article later.
http://www.nature.com/news/vaccine-trial-reveals-chinks-in-hiv-s-armour-1.11380
http://www.nature.com/news/vaccine-trial-reveals-chinks-in-hiv-s-armour-1.11380
Thursday, 16 August 2012
New Male Contraceptive?
There was an article published in Cell today about a potential new male contraceptive option, that would be equivalent to the pill. Matzuk et al describe a small molecule inhibitor that can inhibit the production of spermatozoa to the point of infertility in mice. When they stopped giving the mice the compound, fertility returned and the mice and their offspring appeared normal. The offspring were able to breed, and litter size, pup weight and behaviour were similar to pups sired by mice that hadn't been given the compound. The compound had no effect on hormone levels, which means the mice could engage in normal mating behaviours.
This small molecule inhibitor is very promising, and it may provide a more effective means of contraception for couples that can not use some of the current options.
A preview of the article:
http://www.cell.com/abstract/S0092-8674%2812%2900934-8?utm_source=ECE001&utm_campaign=&utm_content=&utm_medium=email&bid=38A4R3F:SKPGM2F
The article:
http://www.cell.com/abstract/S0092-8674%2812%2900929-4?utm_source=ECE001&utm_campaign=&utm_content=&utm_medium=email&bid=38A4R3F:SKPGM2F
Today's Scrabble word: Jeon for 22 points
This small molecule inhibitor is very promising, and it may provide a more effective means of contraception for couples that can not use some of the current options.
A preview of the article:
http://www.cell.com/abstract/S0092-8674%2812%2900934-8?utm_source=ECE001&utm_campaign=&utm_content=&utm_medium=email&bid=38A4R3F:SKPGM2F
The article:
http://www.cell.com/abstract/S0092-8674%2812%2900929-4?utm_source=ECE001&utm_campaign=&utm_content=&utm_medium=email&bid=38A4R3F:SKPGM2F
Today's Scrabble word: Jeon for 22 points
Monday, 13 August 2012
Zucchini Brownies
I finally had some time to do some baking, and I decided to try a recipe for Zucchini Brownies that I found on Pinterest. I was looking for a healthier option for a dessert, and zucchini is in season now, so this looked promising. The recipe is available here: TheYummyLife.com/Zucchini_Brownies.
Today's Scrabble word: CIG for 18 points
Immunology and Obesity
http://www.nature.com/ni/journal/v13/n8/full/ni.2343.html?WT.ec_id=NI-201208
Article from Nature Immunology discussing the effects of obesity on the immune system. Some facts from the article: Obesity induced inflammation contributes to the development of type 2 diabetes, atherosclerosis, liver disease and some forms of cancer. Diet induced obesity in mice impairs T cell response and causes greater severity of disease and death after infection with influenza. Obesity is associated with aberrant population expansion of cells of the immune system in adipose (fat) tissue. This produces chronic inflammation which can lead to neurodegeneration and type 2 diabetes. Obesity can compromise the efficacy of vaccination against influenza, hepatitis B and tetanus.
Article from Nature Immunology discussing the effects of obesity on the immune system. Some facts from the article: Obesity induced inflammation contributes to the development of type 2 diabetes, atherosclerosis, liver disease and some forms of cancer. Diet induced obesity in mice impairs T cell response and causes greater severity of disease and death after infection with influenza. Obesity is associated with aberrant population expansion of cells of the immune system in adipose (fat) tissue. This produces chronic inflammation which can lead to neurodegeneration and type 2 diabetes. Obesity can compromise the efficacy of vaccination against influenza, hepatitis B and tetanus.
Friday, 10 August 2012
Arsenic Life
There's been several articles about this recently, and I've been remiss in not actually writing about them. Last year an article (http://www.sciencemag.org/content/332/6034/1163.long) was published that described a bacterium that broke the basic rules of biology and was able to grow in the presence of arsenic, with no phosphorous present. Phosphorous is one of the basic building blocks of life and is required for DNA synthesis (among other things). The authors reported that the bacteria GFAJ-1 substituted arsenic for phosphorous to sustain growth. This article sparked a lot of controversy and several labs tried to independently verify the original study. None were able to do so.
http://www.jbc.org/content/early/2012/07/13/jbc.C112.394403.full.pdf+html
This article describes the arsenic causing ribosome breakdown, that released phosphorous that the bacteria was able to use to survive. They show the same phenomena occurs with E. coli.
http://www.sciencemag.org/content/337/6093/470.abstract
In this paper they state that they were unable to detect arsenic from the DNA of cells grown in the presence of arsenic, refuting the original paper.
http://www.sciencemag.org/content/337/6093/467.abstract
A paper published at the same time as the above also refutes the original paper. The authors found that the bacteria was able to grow in low phosphorous, high arsenic environments, but that phosphorous was necessary for growth. They conclude that GFAJ-1 is an arsenic resistant, phosphorous dependent bacteria.
I've started playing Scrabble online, so I will now include a Scrabble Word of the Day and points it earned with each post. Today's Scrabble Word of the Day "zeroth" for 76 points.
Christina
http://www.jbc.org/content/early/2012/07/13/jbc.C112.394403.full.pdf+html
This article describes the arsenic causing ribosome breakdown, that released phosphorous that the bacteria was able to use to survive. They show the same phenomena occurs with E. coli.
http://www.sciencemag.org/content/337/6093/470.abstract
In this paper they state that they were unable to detect arsenic from the DNA of cells grown in the presence of arsenic, refuting the original paper.
http://www.sciencemag.org/content/337/6093/467.abstract
A paper published at the same time as the above also refutes the original paper. The authors found that the bacteria was able to grow in low phosphorous, high arsenic environments, but that phosphorous was necessary for growth. They conclude that GFAJ-1 is an arsenic resistant, phosphorous dependent bacteria.
I've started playing Scrabble online, so I will now include a Scrabble Word of the Day and points it earned with each post. Today's Scrabble Word of the Day "zeroth" for 76 points.
Christina
Thursday, 9 August 2012
The Science of Garbology
Science has a special feature this week called "Working With Waste". There are many articles that discuss ways to reduce the production of waste, or to use the waste in new ways (so it isn't wasted!). There are articles on garbology (it is a real thing), new toilets, waste water, and 0 waste challenges. All the articles can be linked to from here: http://www.sciencemag.org/site/special/waste/index.xhtml
Friday, 3 August 2012
History repeats itself?
I was away for 2 days and am just catching up on all the science reading today . . . hence a bunch of posts about cool articles. This article is particularly awesome. The scientists use "cliodynamics" or scientific methods to illuminate the past (and predict future events). They found that the USA has 50 cycles of violence. The motivating issues vary, but the violent political upheaval is surprisingly regular. The next one is expected to peak in 2020. THey also found that "empires" have cycles that extends over 2-3 centuries, which fits the patterns of instability that occurred across Europe and Asai from the fifth century BC onwards. Last year's Egyptian uprising fits right in with this.
Check out the article at Nature:
http://www.nature.com/news/human-cycles-history-as-science-1.11078
What should we learn in genetics class?
Dr. Rosemary Redfield (UBC) just published a perspective in PLoS Biology discussing how to adapt genetics teaching to be more relevant to the "real world", and to help aid student understanding and retention of the concepts. An interesting read, and (for educators) brings up some questions about if basic science courses need overhauls to better represent the scientific knowledge and applications of today.
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001356
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001356
HIV Treatment as Prevention Feature
PLoS Medicine Volume 9(7) July 2012 has a feature on the use of antiretrovirals as HIV prevention. There are a bunch of articles and different perspectives and aspects are given. I would highly recommend checking it out.
www.plosmedicine.org
www.plosmedicine.org
Tuesday, 31 July 2012
Info on the MMR scare
I'm not sure why there were some tweets about this today, since the article is over a year old, but this article explains how Dr. Andrew Wakefield "found" the "link" between MMR vaccine and autism, sparking the vaccination scare, and how Brian Deer, a journalist, exposed the fraudulent data behind the claims. Very good and interesting article. Apparently part of a series that I now must read!
bmj.com/content/342/bmj.c5347
bmj.com/content/342/bmj.c5347
Monday, 30 July 2012
Carrot (cup)Cake
For the candy carrots, I use orange Starbursts and a green gel icing pen. Unwrap the Starbursts and place on a plate. Microwave them for about 3 seconds at a time until you can mould them, but they aren't melting. Cut each candy in half along the diagonal and mould them into a cone or carrot shape. Place on the top of the frosted cake and use the icing pen to add a stem to the carrot.
This recipe also works as cupcakes. It makes about 2 dozen (24) cupcakes.
Friday, 27 July 2012
GB Virus C – potential as an HIV therapeutic?
Today I read a paper and an opion
piece from advance access for the journal Clinical Infectious Disease discussing
GB virus C (GBVC) and its’ role in HIV infection. The opinion piece argued that
GBVC should be used as a biovaccine in patients with HIV, because clinical data
has demonstrated that those people coinfected with GBVC and HIV have a better
prognosis than those with HIV alone.
GBVC infection is common and
occurs worldwide. It is estimated that 1-5% of healthly blood donors in
developed countries, and up to 20% in developing countries have replicating
virus at the time of donation. GBVC has not been associated with any disease.
In fact, blood donations are not screened for presence of GBVC because no known
diseases occur in those that are infected.
GBVC infection has been
associated with prolonged survival in HIV positive people, causing a 2.5 fold
reduction in mortality during later (>5 years) stages of HIV infection. In
addition, those people coinfected have higher CD4+ T cell counts, lower HIV
viral load, delayed progression to AIDS, improved response to antiretroviral
therapy, and reduced mother-to-child transmission.
The mechanism(s) used by GBVC to
modulate HIV infection haven’t been fully elucidated, but appear to be
numerous. GBVC infection alters the expression of HIV entry receptors, and
causes the secretion of the natural proteins that bind to the receptors, making
it very difficult for the virus to spread to uninfected cells. GBVC infects the
same cells that HIV infects, and some of the proteins of GBVC are able to
inhibit replication of HIV. Without replication, the virus is unable to make
copies of itself, and spread throughout the body. Another protein from GBVC
appears to directly interact with HIV, preventing the virus from entering new
cells. Most of this should occur when GBVC is actively replicating. Once GBVC
virus has been “cleared”, antibodies against the viral protein E2 appear. These
antibodies can bind to either a cellular or viral target (it’s not known which)
and prevent HIV entry into cells. GBVC is able to alter innate and adaptive
immunity, which can help aid the anti-viral immune response to HIV infection.
Combined, all of these effects of GBVC lead to improved prognosis for people
with HIV infection.
The opinion piece makes a lot of
valid points – if GBVC is harmless (and it certainly appears that way) then
studies should be undertaken to determine if infecting HIV positive people with
GBVC will be a successful therapeutic option. All the data so far points to
yes.
For more information see:
Vahidnia et al. “Acquisition of
GB Virus Type C and Lower Mortality in Patients With Advanced HIV Disease”
Clinical Infectious Diseases
David Gretch “Advocating the
Concept of GB Virus C Biotherapy Against AIDS” Clinical Infectious Disease
For lots of research and reviews,
look up Jack T Stapleton
Wednesday, 25 July 2012
An HIV cure is feasible?
Today, in Nature Reviews Immunology, The International AIDS
Society (IAS) Scientific Working Group on HIV Cure published an opinion piece
that summarizes their recommended key goals for the international community to
establish a cure for HIV (http://www.nature.com/nri/journal/v12/n8/full/nri3262.html).
Combination, compliant use of antiretroviral drugs can
improve the health and prolong life in HIV-infected individuals, and can reduce
the rates of transmission. However, antiretroviral drugs do not fully restore health
or normal immune status in patients – or eliminate the virus from their cells.
In addition, only a minority of HIV+ people worldwide have access to
antiretroviral therapy. Although the price of antiretroviral therapy has
dropped, the cost of providing drugs to all 33+ million people infected with
HIV for the rest of their lives is astronomical. But without treatment, the
virus will be spread by those that remain untreated.
The IAS identified seven key priorities that will allow us
to achieve a sterilizing (elimination of all HIV infected cells) or functional
(lifelong control by immune system in absence of therapy, virus not completely
eradicated) cure.
The key priorities are:
-
“determine the cellular and viral mechanisms
that maintain HIV persistence during prolonged antiretroviral therapy and in
rare natural controllers” – focus on establishment of latency, ongoing viral
replication, homeostatic proliferations
-
“determine the tissue and cellular sources of
persistent simian immunodeficiency virus or HIV in animal models and in
individuals on long-term antiretroviral therapy”
-
“determine origins of immune activation and
inflammation in the presence of antiretroviral therapy and their consequences
for HIV or SIV persistence”
-
“determine host mechanisms that control HIV
replication in the absence of therapy”
-
“study, compare and validate assays to measure
persistent HIV infection and to detect latently infected cells”
-
“develop and test therapeutic agents or
immunological strategies to safely eliminate latent infection in animal models
and in individuals on antiretroviral therapy” – reverse latency, clear latently
infected cells
-
“develop and test strategies to enhance the
capacity of the host immune response to control active viral replication”
While these points are important, likely necessary to
develop a cure, I wonder if we are anywhere close to answering these questions.
Although a cure is sure to have the greatest impact on eradicating HIV, other
issues also need to be addressed. Despite effective prevention options
(condoms), 2.7 million people are infected with HIV each year. Alternative
prevention strategies (Truvada, microbicides, vaccine) could lower transmission
rates. If you stop (or significantly
lower) the spread, new infections can be prevented, which lowers the number of
people that need treatment (or the cure, when developed). Preventing the spread
of the virus should also be a focus, because there is no guarantee that
everyone infected with HIV will receive the cure. This brings me to my second
point, which is that many people (both those at “high risk” and those at “low
risk”) do not know their HIV status. If a cure is developed, how do you ensure
that everyone that is HIV+ receives it? Unless mandatory and regular testing of
every single person is undertaken people that don’t want to get tested, or
people who think they are “low risk” and have no need for testing, may continue
to spread the virus. If the goal is an “AIDS free generation”, more than the
science needs to be taken into consideration.
Wednesday, 18 July 2012
Human Food Project
I recently started following PaleoDiet4Two on Twitter. They post about something called the Human Food Project, which aims to get a picture of the human microbiome. Today they have a post that is really interesting about the relationship between diet and cognitive function in the elderly. They tie this into the issue of school lunches. This is all based on a study that was published in Nature recently.
Check out the article (and learn more about the Human Food Project) here:
http://humanfoodproject.com/what-can-a-100-year-old-irish-grandmother-teach-us-about-school-lunches/
And go here for the original article from Nature:
http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature11319.html
Check out the article (and learn more about the Human Food Project) here:
http://humanfoodproject.com/what-can-a-100-year-old-irish-grandmother-teach-us-about-school-lunches/
And go here for the original article from Nature:
http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature11319.html
Monday, 16 July 2012
HIV prevention drug approved by FDA
The FDA has approved the drug Truvada to prevent HIV infection in adults who do not have HIV. The drug would be used (along with safe sex practices) by people whose partners are HIV positive to prevent transmission.
For more information . . .
http://blogs.nature.com/news/2012/07/fda-approves-landmark-hiv-prevention-drug.html
http://thechart.blogs.cnn.com/2012/07/16/fda-approves-truvada-for-prevention-of-hivaids/
and lots of news stories on Google News
For more information . . .
http://blogs.nature.com/news/2012/07/fda-approves-landmark-hiv-prevention-drug.html
http://thechart.blogs.cnn.com/2012/07/16/fda-approves-truvada-for-prevention-of-hivaids/
and lots of news stories on Google News
Thursday, 12 July 2012
Fat and the Gut Microbiota
Our intestines contain millions of bacteria that help keep us healthy. They do a diverse range of things for us, and the gut microbiota (the total bacteria present) differs not only from person to person, but also differs based on the region that you live in . The gut microbiota of people that live here in North America will be drastically different than that of people from Asia, largely because our diets are very different. The North American diet tends to be high in fat. Little research has been done on the effects of a high fat diet on gut microbiota.
A study published last week in Nature found that dietary fat can alter the gut microbiota of mice, by changing the pool of bile acids. They compared diets high in milk fat and high in plant oils (unsaturated fat). Those mice that were fed a diet high in milk fat were still healthy, but had a change in their gut microbiota. If the mice were lacking an inflammatory signalling molecule called IL-10 they had an increased risk of developing colitis.
An introduction to the article:
http://www.nature.com/nature/journal/v487/n7405/full/487047a.html
The article:
http://www.nature.com/nature/journal/v487/n7405/full/nature11225.html
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice
A study published last week in Nature found that dietary fat can alter the gut microbiota of mice, by changing the pool of bile acids. They compared diets high in milk fat and high in plant oils (unsaturated fat). Those mice that were fed a diet high in milk fat were still healthy, but had a change in their gut microbiota. If the mice were lacking an inflammatory signalling molecule called IL-10 they had an increased risk of developing colitis.
An introduction to the article:
http://www.nature.com/nature/journal/v487/n7405/full/487047a.html
The article:
http://www.nature.com/nature/journal/v487/n7405/full/nature11225.html
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice
Paleoanthropology - What did our ancestors eat?
Pretty cool article in Nature that is investigating what australopithecines ate by using proportion of stable isotopes of carbon contained in fossilized teeth.
An overview of the article:
http://www.nature.com/nature/journal/v487/n7405/full/487042a.html
And the article:
http://www.nature.com/nature/journal/v487/n7405/full/nature11185.html
An overview of the article:
http://www.nature.com/nature/journal/v487/n7405/full/487042a.html
And the article:
http://www.nature.com/nature/journal/v487/n7405/full/nature11185.html
Wednesday, 20 June 2012
What defines cured for HIV?
This is a follow-up to my post on the man that was cured
of HIV with a bone marrow transplant. A presentation made at a scientific
meeting in early June provides data that indicates he still harbours some HIV,
which brings into question what constitutes “cured” when you’re talking about
HIV? This patient stopped taking antiretroviral drugs after he had the
transplant, the virus never returned and his doctors pronounced him cured from
HIV.
Steven Yuki (UCSF), who works in Joseph Wong’s lab made
the presentation at the meeting. They found some signals of HIV in the man’s
body, but are unsure if these are real or from contamination. Yuki used a
technique called polymerase chain reaction (PCR) to look for any signs of HIV. PCR
allows you to amplify small quantities of (specified sequences) nucleic acid to
determine if what you are looking for is present. When they performed PCR on
the man’s cells they detected bits of viral nucleic acid, but a collaborator in
a different lab didn’t detect any. This is highly suggestive that contamination
of Yuki’s sample occurred, but the possibility can’t be ruled out that the man
still harbours some HIV. Even more puzzling, another collaborator found signs
of the virus, but it was unable to make copies of itself, suggesting it is harmless
or defective genetic pieces of HIV. What makes this even more complicated is
that the bits of virus don’t match each other, or the virus that he was
infected with before the transplant. This provides stronger evidence that
contamination of the samples may have occurred. Alain Lafeuillade (General
Hospital of Toulon, France) wasn’t involved with the new study, but has issued
a press release and a blog post with his interpretation of the results. He
questions whether the man was reinfected with HIV and is still infectious to
others. This could be possible because the virus detected doesn’t match the
original virus the man had.
This new information calls into question what defines
being “cured” when you’re discussing HIV. If you can’t detect the virus using
p24 assays (the most common detection method), does that mean you’re cured?
What if the p24 assay is negative but HIV nucleic acid is present – are you
considered infected? Despite the question about whether he has been cured or
not, the man has been off antiretrovirals for 5 years and is healthy. I think
he, and others with HIV, would consider that cured . . . no matter what
scientists decide.
Follow me on Twitter @christinamfarr
Monday, 18 June 2012
A Scientists' Worst Nightmare
http://blogs.nature.com/news/2012/06/brains-thaw-at-harvard-repository.html
There are several things that can make up a scientists worst nightmare, ranging from lack of funding for your research, being “scooped” (someone else publishes the same thing you’ve been working on before you can, so your research is no longer novel), and a myriad of factors within your experiments. So far, the worst that has happened to me is an undergraduate student in the lab accidently contaminating the cancer cells I was working on – I didn’t know the contamination had happened and the cells don’t show any signs that there is a problem for several weeks, so I put the cells in some mice for a 12-20 week long experiment, then found out about the problem. There was no way to tell if the cells that went into the mice were contaminated, so I had to wait out the whole course of the experiment before finding out that it didn’t work. I then had to repeat the experiment, which took an additional 24 weeks (about 6 months!), and this was the last experiment I needed for my MSc thesis, so I finished 6 months later than I wanted, 1 week before my PhD program started across the country, and I had to give up the month-long trip to Europe I had been planning and saving up for over the previous year.
There are several things that can make up a scientists worst nightmare, ranging from lack of funding for your research, being “scooped” (someone else publishes the same thing you’ve been working on before you can, so your research is no longer novel), and a myriad of factors within your experiments. So far, the worst that has happened to me is an undergraduate student in the lab accidently contaminating the cancer cells I was working on – I didn’t know the contamination had happened and the cells don’t show any signs that there is a problem for several weeks, so I put the cells in some mice for a 12-20 week long experiment, then found out about the problem. There was no way to tell if the cells that went into the mice were contaminated, so I had to wait out the whole course of the experiment before finding out that it didn’t work. I then had to repeat the experiment, which took an additional 24 weeks (about 6 months!), and this was the last experiment I needed for my MSc thesis, so I finished 6 months later than I wanted, 1 week before my PhD program started across the country, and I had to give up the month-long trip to Europe I had been planning and saving up for over the previous year.
All of this pales in comparison to what happened recently
at Harvard’s brain bank – 147 brains were lost when a freezer failed, and a
third of those brains were donated from deceased people that had autism. This
was one of only a few repositories in the US that distributes autism brain
tissue to researchers around the world. A significant source of brain tissue is
no longer available, which can hinder all sorts of future research into autism.
A bunch of things just seemed to happen all at once to cause this loss to
occur. Normally the brains are spread among a bunch of different freezers, but
they had been consolidated into one freezer for a visit from the Autism Tissue
Program. The freezer went down and the two sensors that monitor temperature and
send out an alarm also went down. From the sounds of it, no one knew anything
was wrong until the freezer (normal temperature -80C) was opened and it didn’t
feel cold inside. The odds of all these things failing during the time so many
brains were in one freezer seems highly unlikely, and an investigation is being
undertaken.
Something like this is always a fear for a scientist,
particularly when you have “precious” samples (especially from human donors,
more so when the samples can only be obtained after death) because it can take
a lot of time to replace what was lost. If your research relies on these
samples, months of time could be lost before enough samples are obtained to
resume experiments.
When I was working on my MSc thesis I was always worried
about my computer crashing, or losing my USB key, or something, so I had my
thesis and all my data backed-up in different locations, and I practically
slept with my laptop so I could easily grab it and run if there was a fire. I
don’t worry too much about incubators, fridges and freezers in the lab right
now, mostly because I don’t have anything that can’t be replaced if something
happened. My biggest worry in the lab is that someone will use my sterile water
and that will contaminate my experiment, which isn’t a big deal now, but will
be a huge issue if I’m working with mice. Soon I will constantly worry about
the BLT mice – they are so costly and one small thing could completely destroy
months of work.
Tuesday, 12 June 2012
HIV Prevention Using Microbicides
HIV prevention is a “hot” research area. A lot of time
and money is being spent to try to prevent HIV spread. There are several
avenues of research for HIV prevention, but 2 of the most popular are vaccines
and microbicides. A vaccine (with low production and distribution cost) for HIV
would be ideal, particularly if it offers long term protection with no need for
a booster. However, it has been very difficult to develop an efficacious
vaccine. HIV mutates rapidly, which means that immunity to one version of HIV
might not protect you from a different version of the virus (sort of like
getting the flu even though you’ve had the flu vaccine). Due to the lack of
success with vaccines, several research groups (mine included) are pursuing
alternative prevention strategies, such as microbicides.
Now, you may wonder why we are focussing on coming up
with new ways to prevent HIV infection when condoms can efficiently prevent HIV
infection. There are lots of reasons why people don’t use condoms. In the
developing world, where HIV burden is the highest, many women are not able to
insist on condom use, due to cultural or societal norms. These women represent
more than 50% of the new HIV infections that occur each year. Since the standard
prevention options are not feasible for them, an alternative needs to be
designed. This is why we are focusing on microbicides – ideally, women could
use them prior to intercourse and their partner doesn’t need to know.
Microbicides are drug products that are can be topically
applied to the vaginal or rectal tract to prevent infection with HIV. Many
microbicides have been under development for HIV, but none have been brought to
market yet. Several are undergoing clinical trials, and several have already
failed in clinical trials. Tenofovir is one microbicide that I have been
hearing a lot about recently. Tenofovir is an anti-retroviral that has been
formulated into a microbicide gel. Tenofovir was successful in its’ first
clinical trial, showing protection rates of 39%. However, the second trial was
recently stopped because no difference was observed between the drug group and
the placebo.
An emerging area of microbicide development is the use of
engineered bacteria. Several research groups have focussed on Lactobacillus which is a normal
component of the vaginal microflora. They hope that by engineering Lactobacillus to express or secrete an anti-HIV
protein they can, with one application, provide long-term protection from HIV
infection. Ideally, there would be no need to reapply the Lactobacillus microbicide, because the bacteria would be able to live
in the vaginal tract, and should (in theory) continually express the protein.
However, what do you do if some sort of side effect occurs? How do you kill the
engineered bacteria without destroying the natural vaginal microflora? How do
you know the bacteria is still expressing the protein?
There are a lot of issues that can arise from the use of Lactobacillus as a microbicide. My
research is investigating an alternative engineered bacteria based microbicide
system, using a bacteria called Caulobacter
crescentus. My lab has developed a system to express a wide variety of
different anti-HIV proteins on the surface of C. crescentus. These proteins are expressed at very high levels
(20% of total cell protein would contain the anti-HIV protein) and we have had
no issue with maintaining long term expression. My research is finding new
anti-HIV proteins to put on the C. crescentus,
and testing two of the most important factors of a microbicide, safety and
efficacy. I have to ensure that topical application of the C. crescentus to the vaginal tract will have no adverse effects. I
also have to determine how high protection from HIV infection is. My first
round of testing indicates that I can decrease HIV infection rates by 85%! This
is all done in a test tube, and I will eventually have to move on to testing
this in an animal system (see BLT mice blog post). All of this testing (and
some side projects that come up along the way) will compose my PhD thesis.
So far, the only downfall of the C. crescentus system is that the microbicide would need to be
applied regularly (I haven’t figured out how often yet). The bacteria can’t
survive in humans, so protection from infection will be transient. C. crescentus is cheap to grow, so this
shouldn’t be cost prohibitive, but the need for reapplication may be a deterrent
for clinical use. Indeed, it is believed that adherence to the dosing regime is
the reason why the second clinical trial of tenofovir showed no effect.
The development of a microbicide for HIV has the
potential to revolutionize the field of HIV prevention. However, there are
still a lot of problems in translating laboratory success to clinical success.
In the meantime, prevention strategies should focus on testing for infection,
condoms, and pre-exposure prophylaxis (when applicable).
Monday, 28 May 2012
Rubber Ducky Cupcakes
There’s been a lot of cool science news recently, so I’ve
fallen behind on posting new cupcake recipes. I thought I’d post instructions
on how to make your cupcakes look like rubber ducks. (This is based on the
design from the book Hello Cupcake, What’s New, which I love!) You get a huge
sugar high from eating one of these, and an even bigger one if you snack on the
starbursts and M&Ms that are the wrong colour, lick the frosting off your
fingers, and eat the extra Timbits, marshmallows, or starburst molding failures
J
Yellow food colouring
Mini M&M’s (brown, blue and green)
Marshmallows
Orange starbursts
Plain Timbits
Vanilla cupcakes in yellow or white liners (start with more than you want because it takes some practice to get them looking the way you want)
Prep Stuff:
Decorating Supplies:
Vanilla frosting (I use Betty Croker, do NOT use whipped)Yellow food colouring
Mini M&M’s (brown, blue and green)
Marshmallows
Orange starbursts
Plain Timbits
Vanilla cupcakes in yellow or white liners (start with more than you want because it takes some practice to get them looking the way you want)
Bake the cupcakes as described and let them cool
completely.
Cut the marshmallows in half diagonally.
Cut the starbursts in half and microwave for a few
seconds at a time until you can mold them into beaks (or feet). I found it
helpful to make a pointy end that could be stuck into the Timbit.
Assembling the Duckies
1.
Once they have cooled, ice the cupcakes and
place the marshmallow at one end and the Timbit at the other to make the head
and tail of the duck. Use the frosting like glue to help hold them in place.
2.
Put them in the freezer for about 15 minutes.
3.
Microwave the frosting until it is runny and use
the yellow food colouring to dye the frosting.
4.
Carefully dip the cupcake into the frosting and
let excess frosting drip off.
5.
Carefully add the starburst beak and M&M
eyes now OR wait until the frosting has hardened then add them at this point, whatever
works out better for you. You may need to use a dab of frosting to hold the
M&Ms in place. I stick the pointy end of the beak into the Timbit to help
it stay in place
To make upside down duckies:
Place the marshmallow in the opposite orientation from
the original ducky. Once it has been dipped, carefully place the starburst feet
on either side of the marshmallow tail. You may need a small dab of icing to
help them stick in place.
The placement of everything is really important, and it
took several tries to get it right. The cupcakes look really good when they are
done, but there were a lot of casualties in the process!
Sunday, 20 May 2012
BLT Mice
As I’ve alluded to in my recent posts, HIV is kind of difficult
to work with. Working with the virus in Petri dishes and cell culture flasks
isn’t too bad . . . except for the fact that it’s a level 3 pathogen in Canada,
which means I have to work with it in a special facility with restricted access
and tons of safety features. Not all research institutions have this type of
facility available, so I’m lucky to be able to do all the experiments at my research
institute.
Christina
Once I complete all the studies I can do with cells, I
will have to do my next group of studies using animals. This is done to test
the safety in a living organism (cells can only tell me so much) and provides a
more real world study system. With no idea on the safety of my compounds, I can’t
do any work using humans, which is kind of a problem when studying HIV. As
stated in its’ name, HIV is the HUMAN immunodeficiency virus. This means that
HIV only infects humans. There are other types of immunodeficiency viruses
(like simian immunodeficiency virus), but using SIV in primates, or a hybrid
SIV/HIV in primates has not had good translation to work with HIV in humans,
because there are a lot of differences between SIV and HIV. This has been a
challenge many researchers have tried to solve, and recently success has been
observed with humanized mouse models of HIV.
Before I go further I should warn you that these mice
involve some very controversial stuff. First off, working with mice, which is
always a touchy area. To humanize a mouse you need to perform a minor surgery
on them and carefully monitor the mice post-surgery to make sure they don’t
develop infections or are in pain. And, to humanize the mouse you use human
fetal tissue, which can only be obtained from aborted fetuses that are donated
to research. If you have any issues with any of these things, I would suggest
you stop reading now.
Each humanized mouse has to be created individually. This
is a very lengthy process. You begin with a mouse that, through a combination
of genetic defects, does not have an immune system. There are several different
types of immunodeficient mice you can use for humanization. I will be using the
NOD/SCID/IL2rgamma-/- mouse. That is a fancy name for a mouse that has a severe
immune deficiency and is unable to make any functional immune cells. You have
to be very careful with these mice, because if they get any sort of infection
their body can’t fight it so they will likely die. Their water and food is
specially sterilized, their lungs are monitored for infection every other
month, and sentinel mice are used to monitor for any other infections.
When the mice are 8 weeks old they have a surgery to
implant human fetal liver and thymus under the kidney capsule. They also
receive an IV injection of human fetal stem cells (which can be derived from
the liver). The human stem cells will allow the development of all the human
immune cells, and the liver/thymus allows the T cells of the immune system to mature
properly. Because you use bone marrow (the stem cells), liver and thymus, these
mice are called BLT mice. Twelve weeks after the surgery you take blood samples
from the mice and check that all the immune cells are present. If so, the mice
can be used for infection with HIV.
The BLT mice have been shown to be susceptible to vaginal
infection with HIV, and the infection course is very similar to what is
observed in humans. Whenever I’ve presented my research I’ve been asked how
exactly you give a mouse HIV vaginally. The mouse is put under anesthesia, then
a small instrument is inserted into the vagina and HIV in saline is deposited.
The mouse is held in an inverted position so the saline doesn’t drip out. After
a few minutes, the mouse can be woken up from anesthesia. Blood samples can be
taken each week to determine HIV infection.
Today I am heading to a collaborators’ lab for 2 weeks to
receive the surgical training I need to be able to make BLT mice. These mice
will provide me with a lot of information about the “real world” uses of my
compounds. I have to do everything perfectly for this mouse experiment, because
it is really expensive. With the costs of my training trip, buying the mice,
housing the mice, buying reagents and materials, and equipment rental costs,
the 45-60 mouse cohort I can make from one set of donor organs will cost $20,000
or more.
Christina
Thursday, 17 May 2012
PrEP for HIV Prevention
Another blog post on HIV . . . it’s sort of my thing :p
(and the focus of my thesis!)
Christina
On May 10th the Antiviral Drugs Advisory
Committee of the US FDA debated whether an anti-HIV drug currently used as an
antiretroviral treatment should be approved as a prevention method for
uninfected people. It was recommended to the FDA that the drug, Truvada (made
by Gilead Sciences), be approved for pre-exposure prophylaxis (PrEP).
PrEP means that the drug is taken routinely by uninfected
people at high risk of becoming infected with HIV. It has been shown that
taking the drug daily can lower risk of infection by more than 90% in two
target groups – men who have sex with men; and uninfected heterosexual (men) with
a long-term, HIV positive partner. However, clinical trials of the drug in
heterosexual women have failed. (Also, in reading another article about this,
it was claimed risk was lowered only by 42% and 73% in separate trials...)
PrEP (like birth control) would need to be taken daily to
be effective. And, if adherence is low this could have disastrous consequences,
particularly if a backup method of prevention (condoms) is not used. As I
mentioned in my last HIV post, the virus replicates really quickly, and doesn’t
make perfect copies of itself, leading to mutated forms of the virus. Some of
these mutants could be resistant to Truvada. So, if you are not using PrEP as
prescribed and have a partner that is HIV positive, it is likely that you will
become infected with the virus. If you continue to take the PrEP irregularly,
you are putting yourself at risk of being infected with drug-resistant HIV,
which would likely make treatment more difficult. Of particular note is that HIV
treatment with Truvada must be undertaken in combination with other
antiretroviral drugs to prevent resistance.
During the clinical trials participants were monitored
monthly for HIV infection, using the most sensitive test to detect HIV, so that
PrEP could be stopped upon infection to prevent resistance. A few cases of
infection were seen in the trial participants, and just over half of them
developed resistance. This testing should be continued for those that are
taking Truvada for PrEP, but this testing was not included in the
recommendation to the FDA. Without regular testing, it is possible that HIV
could be transmitted to someone taking PrEP (remember, it isn’t 100% effective)
and they wouldn’t know about it, so they would keep taking the antiretroviral.
This will lead to development of a resistant virus, which will create a lot of problems
for further treatment once the virus is detected.
I did a PubMed search and wasn’t able to find any
clinical trial papers about Truvada, which I would really like to be able to
read before forming an opinion on this, particularly since Science and Nature
report two different statistics for protection levels. I think this approval of
Truvada could drastically lower HIV prevention rates, if used properly (and if
affordable!), however, it could also be disastrous if used improperly
(particularly without regular HIV screening). Condoms are more effective at
preventing HIV transmission and I highly recommend them because they also
protect against other STI’s and pregnancy. But, for those who are unable to use
condoms for various reasons (particularly women in developing countries),
Truvada represents a new hope for HIV prevention.
Christina
Wednesday, 16 May 2012
A cure for HIV?
According to the World Health Organization and UNAIDS,
over 33 million people worldwide are infected with HIV, the virus that causes
AIDS. Over 2 million people die AIDS-related deaths each year. HIV/AIDS has
enormous social and economic impact, particularly in developing countries.
Despite over 30 years of research into HIV, an effective method of prevention
(besides condoms) and a cure have not been found. Currently, once someone
become infected with HIV they can take a combination of anti-retroviral drugs
on a strict regimen, which should suppress the virus for several years. Eventually,
the patient develops AIDS which typically leads to death within 1 year. It is
thought that antiretroviral therapy can increase survival time by 4-12 years,
but the patient would still eventually develop AIDS.
Christina
It is really difficult to treat HIV for several reasons.
The virus replicates very fast (in less than 2 days) and doesn’t always make a
perfect copy when it replicates. This leads to mutations that can allow the
virus to become resistant to the antiretrovirals, or to escape the immune
system. All of these mutated virus also replicate quickly, so someone infected
with HIV will have millions of copies of different versions of HIV. In
addition, HIV infects (and kills) CD4+ T cells, which are a very important part
of the immune system. So, while your immune system is trying to fight a constantly
changing invader, the invader is also killing those cells that have a key role
in fighting it. What is really cool is that some genetic combinations provide
protection from infection or suppress HIV replication. One that is called Δ32
CCR5 deletion is present in a small percentage of Caucasians descended from
Western Europeans, and also prevents infection with bubonic plague.
I have only found 1 case where someone was cured of HIV.
An HIV-positive patient with acute myeloid leukemia was given a hematopoietic
stem cell transplant (basically a bone marrow transplant). Since this patient
had both AML and HIV there wouldn’t be very many (or maybe even any) treatment
options available, so this situation provided the opportunity to try something
new. The doctors decided to give them a hematopoietic stem cell transplant
using cells from a donor that had the Δ32 CCR5 deletion. The transplanted cells
would not be infected with HIV, and should be able to destroy any remaining
HIV-infected cells in the patient. So far, HIV suppression has been observed in
this patient, and they have stopped taking antiretrovirals!
Walker et al (http://jvi.asm.org/content/86/10/5719.abstract)
were interested in creating a gene therapy vector that could provide protection
from HIV infection. They created a gene therapy vector that would induce the
Δ32 CCR5 deletion, in addition to expressing TRIM5α (shown to prevent HIV
replication) and a TAR decoy (which should prevent HIV replication).
To determine if this gene therapy vector could be
clinically relevant, it needs to be tested in an animal model, which is difficult
for HIV. HIV is the HUMAN immunodeficiency virus, which means it can only
infect humans. This has posed a huge problem for HIV researchers, but a pretty
cool solution has been found – you can create mice that have a human immune
system (there will be a blog about how to do this soon, because I’m going to
learn how to make my own franken-mice). These mice can be infected with HIV and
the infection is similar to what is observed in people.
Walker et al isolated CD34+ hematopoietic stem cells and
infected them with the gene therapy vector, then injected the cells into mice.
These stem cells developed into immune system cells, including the CD4+ T cells
that HIV can infect. The CD4+ T cells appeared functionally normal and
contained the gene therapy vector.
Once they verified everything was working as expected,
they infected the mice with HIV and monitored the mice. They found that the
mice that received the gene therapy vector had significantly enhanced survival
of CD4+ T cells after HIV infection. However, the level of HIV virus in the blood
was not changed. This suggests that the gene therapy vector was able to keep
the CD4+ T cells alive, but didn’t stop HIV from replicating.
This study is a good start for using gene therapy as HIV
prevention, but follow-up work on why the HIV levels in blood were unchanged
should be undertaken. It is also important to realize that in this study they
were sort of putting the cart before the horse – they gave the mice the gene
therapy vector before HIV infection. To build on this study they should infect
mice with HIV then give them a bone marrow transplant with hematopoietic stem
cells that contain the gene therapy vector to see if the HIV infection is cured
– it would be more clinically relevant that way. This sort of treatment would
be a long way from the clinic, particularly since you’re dealing with a
treatment option that could be highly controversial, since it involves stem
cells and gene therapy. I am definitely going to keep my eyes on this field!
Christina
Sunday, 13 May 2012
Let them eat dirt!
Many epidemiological studies have led to the hygiene
hypothesis. The hygiene hypothesis proposes that exposure to microbes in early
childhood can decrease susceptibility to allergies and diseases such as asthma,
irritable bowel disease (IBD) and autoimmune diseases. It’s believed that this
early exposure to microbes helps the immune system function properly, which
prevents the “overactivation” of an immune response that occurs in the case of
allergies, asthma, etc. When it “overactivates” the immune system sees
something that is not dangerous (ex. dust, pollen, peanuts) as harmful, and
“freaks out”, releasing all sorts of inflammatory mediators that cause symptoms
from a runny nose to full-blown anaphylactic shock. In most cases, this would be
annoying or inconvenient, but in some cases it can be deadly. Although a lot is
known about WHAT happens when the allergen or disease is triggered, it is not
known WHY. Several studies have produced observations that suggest this is all
related to hygiene, specifically that exposure to microbes in early childhood
lowers the chance someone will develop allergies, asthma, IBD, etc. It has been
suggested that this could be related to how “clean” we are now, particularly
with the use of antibacterial soaps. It has been observed that more people in
developed countries have allergies/asthma/IBD/autoimmune diseases. And, within
developed countries, children that are from rural areas have lower rates of
allergies and asthma compared to their counterparts in cities. It wasn’t really
known why this was the case, but a recent paper in Science (http://www.sciencemag.org/content/336/6080/489.full)
has provided some evidence about the immune system cells that are involved.
It has been hypothesized that invariant natural killer T
(iNKT) cells play an important role in the pathogenesis of ulcerative colitis
and asthma. These cells recognize lipid antigens and release large amounts of
proinflammatory factors (called cytokines) when they are activated. Olszak et
al investigated the age-dependent regulation of iNKT cells by use of microbes
in mouse models of IBD and asthma.
They worked with germ-free (GF) and specific-pathogen-free
(SPF) mice. GF mice are born without the bacteria that are normally present,
and are protected from any bacterial exposure over their life. SPF mice are
free of certain bacteria that would cause disease, but the normal intestinal
bacteria are present. They found that the numbers of iNKT cells were increased
in GF mice and appeared to be stable for life. When they induced colitis in the
mice they found that the GF mice were more sensitive to colitis, with more
severe weight loss, pathology, and higher mortality rates compared to SPF mice.
If they re-established the microbiota (all the bacteria that should be present)
in the GF mice, they found that the iNKT levels and severity of colitis was not
reduced. If they took pups that had a GF mother and raised them in SPF
conditions, they found a complete normalization of iNKT cells and reduced
susceptibility to colitis. This indicated that the microbiota present at birth
has life-long effects on health. They repeated these studies with a mouse model
of asthma and had very similar observations.
This study fits with the epidemiological studies that led
to the hygiene hypothesis, showing that early life exposure to microbes decreases
susceptibility to diseases such as IBD and asthma, where as absence of microbial
exposure may have the opposite effect. This is one of the first studies that
provides a mechanism to explain the epidemiological observations that compose
the hygiene hypothesis.
So, I’m not saying that you should feed your kids dirt,
or stop them from washing their hands before eating, but let them play in the
dirt and don’t freak out if they lick their shovel – it just might lower their
risk of inflammatory diseases ;p
Christina
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