Sunday, March 20, 2016

Elizabethkingia: The Bacteria That Kicks You While You're Down

What's your biggest fear? Sharks? Heights? Cancer?

Compared to exciting threats like sharks, or falling to your death when your bungee cord snaps on your honeymoon bungee jumping excursion, infectious diseases fall pretty low on the list for most Americans. We've eradicated a number of diseases through rapid urbanization/industrialization (did you know that malaria was endemic in North America in the early decades of the union?), large-scale waste management (bye, cholera!), and widespread use of vaccinations (see: smallpox, polio, etc.).

An agar plate of bacteria and mold, from NationWell

There's a number of things to which Americans are not immune, and a large category of them is bacterial infections. I say "category", because the variety of pathogenic bacteria in the U.S. can be broken into a number of subdivisions, such as: sexually transmitted infections (those which are caused by bacteria), antibiotic/antimicrobial resistant bacteria, those spread by environmental exposure (like Borrelia spp. that causes Lyme Disease, which is transmitted by ticks), and nosocomial bacterial infections (also known as hospital-acquired infections), just to name a few.

The most well-known subdivision I mentioned above is antibiotic/antimicrobial resistant bacteria. In fact, over two million people in the U.S. are infected with antibiotic/antimicrobial resistant bacteria each year. You can dig deeper into the world of antibiotic/antimicrobial resistant bacteria on the CDC website, which rates bacterial species based on the severity of the threat they pose

Nosocomial infections, specifically, caused approximately 1.7 million infections and resulted in  99,000 deaths in 2002 (according to an estimate report from the National Nosocomial Infections Surveillance System). A similar surveillance survey by the CDC in 2011 reported over 720,000 nosocomial infections in acute care hospital facilities.

Get more information on the CDC's Hospital-Acquired Infection Data and Surveillance Report here.


I bring this up because in the span of 4 months, a bacterial infection called Elizabethkingia anophelis has killed 18 people in Wisconsin and 1 person in Michigan.


Elizabethkingia is the phylogenetic genus of 4 related species of gram negative bacteria:
  • E. anophelis, which causes respiratory infections in humans, and was originally isolated from the midgut of Anopheles mosquitoes
  • E. endophytica, which is a plant pathogen that mostly infects Zea Mays, or sweet corn
  • E. meningoseptica, which causes severe meningitis and sepsis in newborns and infants (premature newborns are particularly susceptible)
  • E. miricola, which was miraculously (pun!) isolated from condensation water on the Russian Space Station, Mir.
The genus is named after Elizabeth Osborne King, a clinical microbiologist (and a #WomanInSTEM!) who worked for the CDC in the 1940s through the 1960s, and studied meningitis in newborns. E. anophelis is common in environmental reservoirs, such as water and soil, but rarely causes infections in humans. The CDC logs only a handful of reported cases in the US each year.  

Yet, in Wisconsin, approximately 54 people have been infected since November of 2015. The outbreak is mostly affecting people who are 65 years or older, most of which had underlying health conditions. E. anophelis infects the bloodstream and occasionally the respiratory tract, causing nonspecific symptoms, including fever, chills, shortness of breath, and cellulitis. Death is usually a result of sepsis.

The current outbreak has been tracked across 12 counties, but has not specifically been labeled as a hospital-acquired infection. Infections of the current outbreak have been centered in the southeastern quarter of the state, including the Milwaukee area and surrounding suburban counties. One case in Hong Kong illustrated that the infection can be spread from mother to child. E. anophelis is an antibiotic resistant species, which is why the magnitude of the current outbreak is causing such alarm for medical professionals. Transmission from person-to-person is highly unlikely without blood-to-blood contact, meaning there must be another common source within the community. The transmission route for the most recent outbreaks that occurred prior to the current one in Wisconsin, one in Central Africa and the other in Singapore, was not determined.

So, how does this factor into our biggest fears? The infectious disease world is constantly discussing the concept of "emerging diseases", meaning rare infections that are suddenly migrating to naive populations (meaning, the population of that geographical region has never been exposed to the pathogen before) or are infecting new populations. Antibiotic resistant bacteria, like Elizabethkingia anophelis, are sometimes included in the description of emerging diseases because the acquired or developed resistance poses new problems for treatment and infection control.

Say you go to the hospital because your appendix has ruptured. This is a routine surgery that shouldn't take much time or effort. But being in the hospital puts you at risk for infection, especially when you are in the process of recovering from a routine, but intensive, procedure. If the infection is rare, it will take your doctor a longer time to identify the culprit. If the infection is resistant to common treatments, you will have to endure more extensive treatment programs. If you are recovering from a surgical procedure, or have other open and exposed wounds, you're immune system may be otherwise preoccupied. So, a short hospital stay that should have been routine, might end up being more extensive, or putting you at a higher risk for death.

If you would like to follow the outbreak in Wisconsin, the Department of Health Services website is updated every Wednesday regarding developments in the investigation.

Wednesday, February 17, 2016

On to the Next One

Jay Z, image from Newsweek




Isn't it phenomenal that there's always a newer, more pressing issue on the horizon? In the words of Jay Z:

"Ya'll should be afraid of what I'm gonna do next"

Now that the WHO has declared the ebola outbreak completely over (with a new case reported the very next day, whoops!)...

This is the first thing I thought of when I saw the declaration of the end of the ebola outbreak.

The new focus is on the Zika virus (ZIKV) outbreak in South and Central America. I've been waiting to write this post for weeks because the news coverage is so heavy, and I didn't feel like being redundant. Everyone has heard about this "new" virus, the "new" link to microcephaly, and most recently, the anti-GMO tie to Monsanto. But, what do we really know about ZIKV? Let's break it down:

ZIKV is not a new virus.
ZIKV is a single-stranded RNA virus of the Flaviviridae family. It is related to dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), and Japanese encephalitis (JE) virus.

ZIKV structure, thanks to St. George's University in Grenada
While newly introduced to South and Central America, ZIKV has been endemic in specific regions of Africa and Asia for quite some time. ZIKV was first discovered in Uganda in 1947, yet phylogenetic analysis of the viral genome estimate that ZIKV originated sometime between 1892 and 1947 (most likely in the 1920s). Early reports stem back to the 1950s, but with evolution of arthropod-borne viruses (arboviruses), the general and non-specific symptoms reported may have been caused by a similar virus (more on that later). Both urban and sylvatic, or rural/forest-based, transmission has been reported, and ZIKV is also seen in monkeys.


Yet, the recent and substantial outbreak in South and Central America (most notably in Brazil, which reported more than 14,000 cases in a matter of months) is new and a big deal. Prior to outbreak in 2015, ZIKV was wreaking havoc on islands like French Polynesia (2013-2014) and Easter Island (2014-2015). In fact, the outbreak in French Polynesia illustrated the link between ZIKV infection and chronic neurological conditions, specifically Guillain-Barré Syndrome

Pregnant women are always seen as an "at risk" or "high risk" group.
The human body goes through a plethora of changes and adaptations when pregnant, mostly because survival of the mother is imperative for survival of the fetus. Development of the fetus is directly dependent on the numerous resources that the mother's developed body provides. The most relevant to this blog is "immunological priming", that continues after birth through contact with the mother's microbiome during the birthing process and during breast feeding.  
Given the sensitivity of this relationship, pregnant individuals are always seen as a high risk group, as some pathogens can travel across the placenta, exposing the fetus during development and before birth. Trans-placental transmission/exposure to ZIKV is currently being investigated by a number of different institutions. With the increase in microcephaly cases during the ongoing ZIKV outbreak in South and Central America, it is understandable why a potential link would cause alarm. 

One important thing to note is that Brazil is one of the few places that already had baseline incidence and prevalence data for microcephaly, making the increase in cases easier to identify. That type of data hasn't been readily available during previous outbreaks in other regions, which makes it difficult to determine whether or not ZIKV is the immediate cause. 

A mosquito bite does not guarantee disease.
Unlike it's relative, dengue virus, it is estimated that only 20% of people infected with ZIKV will become ill and experience symptoms. That means 80% of people infected are asymptomatic (meaning, they do not have any symptoms and often do not know they are infected). Symptom of ZIKV are, much like the symptoms of other arboviruses, general and non-specific. This means you experience fever, headache, rash, and joint or muscle pain. ZIKV also commonly causes conjunctivitis, or redness and swelling of the eye and skin around the eye. 
Arboviruses have been threatening to spread to North America with increasing persistence for years.
Graphic from the Institute of Medicine's presentation on Zika by Dr. Victor Dzau (2/15/2016)
North America is an anomaly in the infectious disease world. Since clearing most of the natural forests to favor rapid urbanization and industrial usage of land and resources, most hosts and vectors for many infectious diseases just won't survive in these areas. Part of that is because a majority of infectious diseases are perpetuated by tropical climates that are hospitable to the hosts and vectors (think jungles and warm/wet environments). But, some of the hosts and vectors are durable, and have taken advantage of changes in climate and global travel. 

Many of the mosquito species that are required to spread these viruses have already established residency in California and Florida. So, as these viruses come closer to our geographical borders, and travel to/from endemic regions becomes more frequent, we may see some locally-acquired cases. But, the spread of a virus into a new region is a complicated process and so many factors have to overlap.

Sexual Transmission can occur, but is not common.
There have been isolated cases of sexual transmission, but the uptick in news coverage is only a result of the ZIKV madness people have seen to caught, and is most likely the mass media's way of "helping" figure out whether microcephaly is linked to ZIKV infection. Despite what you've heard, having sex with someone that has ZIKV on the head of their penis will not cause microcephaly in all of your future children. Thanks, internet.
It is common sense, from an evolutionary standpoint, if you think about it. If you are in a region where mosquitoes are plentiful and looking for a bloodmeal, you are more likely to be exposed to ZIKV by a mosquito. Yet, these viruses "survive" when they are passed from one person to the next. Without transmission, our immune systems would clear the infection or we would die, and that would be the end of the story. Your mucosal membranes are a perfect environment for transport from one human to the next, especially when small tears may occur, giving access to blood. 

Just because there is a statistical possibility for sexual transmission to occur doesn't mean it can be considered a main method of transmission. There have only been 3 confirmed cases to date of male to female transmission through unprotected sexual contact. 

When babies are at risk, money is dedicated to the cause.
In hearing that there may be a link between ZIKV infection and an increased risk for microcephaly, President Obama dedicated $1.8 billion to ZIKV research. This funding will go to the development of faster, cheaper, and more specific and sensitive diagnostic tests, vaccine development, immune profiling and characterization of ZIKV disease, and studies to definitively determine whether microcephaly in newborns can result from ZIKV infection in pregnant women.
If you are traveling to an endemic or high-risk area, you can protect yourself.
Arboviruses are some of the least feared diseases, from what I can tell based on my friends' reactions when I tell them to pack DEET and other mosquito repellents when traveling. Basically, if they are not at risk of getting malaria, they aren't worried. 
If you are worried and have travel scheduled, there is a page dedicated just to the prevention of ZIKV exposure and transmission on the CDC website.
Cartoon by Rob Rogers and (c) the Pittsburgh Post-Gazette
Now, let's all hold our breaths and see what happens during the 2016 Summer Olympics, which are being hosted in Brazil. 

Thursday, December 31, 2015

End of a Year, End of Another Decade

Everyone is posting these elaborate "BEST OF 2015" lists and photos, but for me, the end of 2015 marks another big milestone: the end of my 20s. In celebration of my 30th year in existence, I thought it would be fun to look back to what was happening in science 30 years ago.

Cover page of Science vol 231, issue 4733, released on January 3rd, 1986 - one day after I was born.




The 1980s were a decade of fearlessness in science, where there were still so many unknowns, yet everyone was excited about all of the possibilities. There were two major scientific pushes in the 1980s: space travel and deciphering the AIDS epidemic, and as you may remember (or have guessed), there were many tragedies in 1986. Let's take a look:

 January 12th: STS-61-C Space Shuttle Columbia is launched. 
Among the crew was Dr. Franklin Chang Díaz, the first Latino astronaut. Dr. Franklin Chang Díaz is an engineer and physicist of Chinese and Costa Rican descent.





January 24th: The Voyager 2 space probe made its first encounter with the planet Uranus.
Launched in 1977, Voyager 2's primary mission was to study distant planets. Voyager 2 visited the Jovian system in 1979, Saturnian system in 1981, Uranus and the Uranian system in 1986, and Neptune in 1989.Now in it's 39th year since launch, Voyager 2 is on an extended mission to study the outer reaches of the Solar System. Check out some of the images taken by Voyager 1 and Voyager 2 here.

Voyager 2, photo credit: NASA

Uranus, taken by Voyager 2 in 1986. Photo credit: NASA

January 28th: Space Shuttle Challenger (STS-51-L) explodes on launch.
On its 10th flight, Challenger exploded 73 seconds into mission launch, due to an explosion. All seven crew members and the Challenger shuttle were lost as a result of the malfunction. The shuttle and the bodies of the crew members were found mostly intact on March 9th by the US Navy.



February 21st: Nintendo releases the first game in the Legend of Zelda series in Japan.
Nerds everywhere have no idea how their lives are about to change. This may not seem directly scientific, but if we think about how far computer science and gaming science has come in 3 decades, it is revolutionary.

Legend of Zelda, 1986

Here's the trailer for the upcoming release in the Legend of Zelda series:


March 3rd: The first paper on Atomic Force Microscopy is published.
Atomic Force Microscopy (AFM), or Scanning-Force Microscopy, allows for very high-resolution with demonstrated resolution on the order of fractions of a nanometer, more than 1000 times better than the optical diffraction limit.
Setup of AFM, image from Wikipedia.




April 3rd: IBM releases the first laptop computer.
It weighed 13 pounds, and looked like a little robot.

IBM "PC-Convertible", photo via Wikipedia
April 13th: The first child born to a non-related surrogate mother is born.
Produced by gestational surrogacy, this revolutionary human pregnancy resulted from the transfer of an embryo created by in vitro fertilization (IVF), in a manner so the resulting child is genetically unrelated to the surrogate.

The surrogate and biological mother, Mary Beth Whitehead, refused to cede custody of Melissa (otherwise known as "Baby M", born 4/13/86) to the couple with whom she made the surrogacy agreement. The courts of New Jersey found that Whitehead was the child's legal mother and declared contracts for surrogate motherhood illegal and invalid. However, the court found it in the best interest of the infant to award custody of Melissa to the child's biological father, William Stern, and his wife Elizabeth Stern, rather than to Whitehead, the surrogate mother.



April 25th: The Chernobyl Nuclear Power Plant exploded, causing the worst nuclear power plant disaster in history.

 

May: The first method to create part-human, part-mouse monoclonal antibodies was published. 
The development of humanized monocolonal antibodies lead the way for many medical therapeutics being used today. There are currently more than 30 FDA-approved monoclonal antibody therapies available for a wide range of diseases, including (but not limited to) cancers, autoimmune disorders like rheumatoid arthritis, severe psoraisis, Crohn's disease, transplant rejection, and cardiovascular diseases.

Image from Britannica: Monoclonal Antibodies


May: HIV is named.
The International Committee on the Taxonomy of Viruses said that the virus that causes AIDS will officially be called HIV (human immunodeficiency virus) instead of HTLV-III/LAV.

Dr. Jay Levy of UCSF, who discovered the "AIDS-related virus", or ARV, which would eventually be named Human Immunodeficiency Virus (HIV). Photo via UCSF archives.

 July: FDA approves the first genetically engineered vaccine for Hepatitis B.
Prior to the development of recombinant Hepatitis B vaccines, all Hep B vaccines were plasma-derived. Now, with the synthetically prepared vaccine, it is impossible for you to get Hepatitis B from the vaccine.


November 3rd: TIME magazine releases an issue on viruses, specifically discussing new research surrounding the HIV/AIDS epidemic. 
By the end of 1986, 85 countries had reported 38,401 cases of AIDS to the World Health Organization, including Africa (2,323), Americas (31,741), Asia (84), Europe (3,858), and Oceania (395).

From TIME: " It would be another year before the first antiviral drug against HIV, AZT, is developed, but scientists are learning more about the biology of the AIDS virus, and testing new treatments, including gene therapy."

Cover Image, credit TIME Magazine.

So there you have it: 30 years ago in science history. I hadn't really thought about it before, but my scientific career has been very representative of science in 1986. I've worked for NASA, studied HIV, and, for many years as a lying, idiot teenager, told my peers that I was the first "test tube baby".

Any guesses as to what the next 30 years will hold for science?

Tuesday, December 1, 2015

World AIDS Day 2015: Did you even notice?



December 1st is World AIDS Day. It has been for decades, and will continue to be for decades to come. Yet, did you even notice?

Years ago, I was venting to my dad about how I wish people used social media for intelligent conversation and to spread important information instead of posting pictures of their outfits and arguing over inaccurate news stories. He looked at me and said "make Facebook what you want it to be", suggesting that I ignore all my boring acquaintances and follow organizations that I believe in, instead. So that's what I did. Twitter, Facebook, and eventually Instagram. I follow government organizations relating to public and global health, nonprofit organizations, scientists, museums, etc.

But, today, I found myself frustrated again. I was looking forward to seeing posts about World AIDS Day, but I saw TWO posts on facebook, and only FIVE quick tweets (80% of which were from US government organizations like Health & Human Services or the CDC).

So, why don't we care about HIV and AIDS anymore? Why has HIV and AIDS turned into a docile disease?

I have a few theories about this:

1. We're inundated with articles about how "A CURE IS RIGHT AROUND THE CORNER" or about "ONE MAN: CURED OF AIDS".
 Don't get me wrong, I have complete faith in the scientific research community and the medical community, but I'm tired of things being announced or declared in a way that isn't really all that true. We are already in an age where there is a huge distrust of science, so when breakthroughs are made, results are expected immediately. When we talk about "curing AIDS", I imagine the general masses imaging taking a huge red marker and checking a box. But, we've seen with every drug trial (I'm especially thinking of cancer drugs and the public outcry as a result of some of the waiting periods), results aren't immediate. We don't go from test tube to mass production of a perfectly effective drug. Even with animal trials, many times there are unforeseen side effects or changes in dosage efficacy.

Not to mention, the "curing" or "clearing"  of HIV has not had a lasting effect. The incredibly invasive, extensive, and expensive procedures that lead to the initial news stories are simply not feasible for everyone (and even most people!). But the realistic side of the story is often not included.

I don't say this in any way to minimize the great advancements we've seen with antiviral treatments. We are in an age where many people who are infected with HIV are living long, healthy lives as a result of treatment options and lifestyle changes.

2. HIV isn't as scary as other emergent diseases and infections.
How can we take HIV seriously as an ongoing threat if we hear about something new, unknown, and terrifying every week? There are many factors that go into viruses breaking out of a small region and spreading to previously unaffected areas. But, we are in an age of emergent diseases. Ebola has been around for decades, but up until last year, most people had never heard of it. Zika virus was isolated in specific regions of sub-Saharan Africa and Southeast Asia, and suddenly, this year, more than 14,000 people have been infected in Salvador, Brazil. Kissing bugs are in 26 states, and Aedes mosquitoes have been moving in to California for a few years now. Chikungunya is in the Caribbean and certain parts of Europe.

With scientific distrust, comes fear. Everyone is too busy fearing new viruses to remember that HIV is still here.

TEM micrograph of budding HIV virions

3. Young generations haven't experienced death from HIV and AIDS. Young generations haven't experienced the disease revolution.
The largest recorded ebola outbreak in human history happened (is still happening, albeit slower) happened in an area of the world with which most people are still not familiar. The cases that caught the most media attention were Americans that received experimental treatment.

Younger generations aren't familiar with the fear and death associated with HIV in the 80s and 90s. They aren't familiar with the imagery of that time. They aren't familiar with the huge and devastating number of children that have HIV.

This lack of realistic knowledge and awareness of HIV and AIDS has lead to incredibly sad facts, such as: 60% of HIV positive youths are not aware of their HIV status.


Speaking of statistics, its estimated that 34 million people worldwide are living with HIV.
I recently attended the American Society of Tropical Medicine and Hygiene (ASTMH) annual conference, and I collected some really devastating statistics. As of 2013, it was estimated that 3.2 million children were living with HIV worldwide, and less than 25% of them were receiving antiretroviral therapy (ART). That was almost 3 years ago.

With the bleak statistics of the number of people living with HIV who don't know their status and the number of children with HIV, we are not in the position to say that HIV is not a threat, or that "we can see the end of AIDS by 2030". If we aren't even acknowledging World AIDS Day anymore, then how can we see a future without HIV and AIDS?

Take this matter into your own hands. Get tested regularly.

Friday, November 20, 2015

Giving Thanks to Chimps

Something special happened this week that, I feel, isn't getting the attention it deserves. With Thanksgiving (US) next week, I felt it was fitting to highlight this event, because to me, it is representative of who and what we forget to be thankful for on a regular basis.

In 2013, the NIH announced it would start to phase out all research and trials involving chimpanzees, sparing only 50 chimps for support of research with very specific needs involving chimps as a model system. As of this week, the NIH has announced that they will no longer support biomedical research on chimpanzees. The NIH will no longer retain the 50 remaining chimpanzees, and they will be moved to a chimpanzee sanctuary.

Photo from National Geographic/Getty Images
 Part of the reason this is happening is because the U.S. Fish and Wildlife Service has designated chimpanzees, including those in captivity, as endangered species. The original placement of wild chimpanzees on the endangered species list occurred in 1990, after being on the "threatened" list since 1976. This is a tragic reason, but the response from the NIH is absolutely the right move. A small move, but a valuable one.

I bring this up, not only because it is a personal issue for me, but because we benefit from products and technologies that have been tested on chimpanzees and many other animal species often without thinking about it. Historically, chimpanzees have been used for a wide range of biomedical research subjects and topics, including psychological research, and an endless list of health and medicine-related topics. Private institutions in the US started using chimpanzees in laboratory research in the 1920s, while the NIH waited until 1960 to establish the first government-operated non-human primate research center. If you want to learn about the first 100 chimpanzees brought from Africa specifically for research purposes, I highly encourage you to visit the First 100 Chimps website, from Lori Gruen.

Photo from Corbis Bettmann and National Geographic
 
Long before their use in biomedical and psychological research, many species of non-human primates were a source of heavy fascination during the height of colonialism in Africa. The two most popular past times were trying to capture live orangutans in the wild, and capturing smaller primate species to keep as pets.

Photo from the Expanded Environment
One of the most well known research areas was the use of chimpanzees for HIV research, starting in the mid-1980s. Chimpanzees are the most genetically-related species to humans, but that doesn't necessarily make them good models for research. It took almost a decade for the NIH to realize that chimpanzees are poor models for HIV research, which ceased breeding programs for federally-owned chimpanzees in 1995. At this time, there was a surplus of chimpanzees in research-associated captivity as a result of the rapid increase in HIV research, and the assumption that chimpanzees were the best animal model. Thus, Chimp Haven was founded to support the retirement of chimpanzees from biomedical research facilities, the entertainment industry, and pet trade.

Speaking of HIV research, I just had the opportunity to see Dr. Beatrice Hahn of the University of Pennsylvania speak about her non-invasive research that has answered many questions about the origin of HIV-1 and HIV-2. By using sequencing technologies to analyze fecal samples from wild primates in Africa (that her team literally collects from the ground in the jungle), she has been able to find the missing pieces of viral origin and evolution. You can find a summary of Dr. Hahn's work on her website (click her name above), or by reading this article from earlier this year.

In 2010, the NIH tried to transfer more than 200 government-owned chimpanzees to the National Primate Research Center in Texas for invasive research studies. Yes, 2010. This was more than a decade after many countries, such as New Zealand, Australia, Sweden, and the Netherlands, started to place strict bans on great ape research. Jane Goodall pressured the NIH to rethink their decision to make more chimpanzees available for invasive research, which lead to a year-long investigation into the necessity of  the use of chimpanzees for research purposes. In 2011, the NIH declared that chimpanzees are "largely unnecessary for biomedical research".

Photo from the Jane Goodall Institute
Yet, while legislation is in place to protect chimpanzees and other species from unnecessary use and cruel treatment during research, many private companies (note: not getting government funding) still have and maintain chimpanzee research facilities. Some companies in the US have already ceased using chimpanzees, or have declared that they will phase out their use of chimpanzees by 2020 (click for list of companies). If you'd like to follow the periodic retirement and movement of chimpanzees into sanctuary facilities, I encourage you to visit the Last 1000 website, also maintained by Lori Gruen.

Here's the important part from the NIH's statement from the director regarding the retirement of the last 50 chimps:

"These decisions are specific to chimpanzees. Research with other non-human primates will continue to be valued, supported, and conducted by the NIH."

Don't be fooled. This ends the use of chimpanzees in government facilities and government-funded research, but the use of chimpanzees has not been banned in the US. Private companies can still use chimpanzees and other non-human primates, as long as they adhere to the strict "humane usage" guidelines. Here is a website that will give you more information about animal species currently used in laboratory research.

Photo from KPBS

Chimpanzee research originated before many of us were born, and other than the amazing Jane Goodall, there are not many champions bringing this issue to light. When I decided to pursue biological sciences -- specifically infectious disease research -- as a career, I decided I would never take a job that would require me to do anything with animals directly, and I didn't want to be involved with projects that relied on animal research. In the time that I've been working as a scientist, the number of technologies and discoveries that minimize the need for animal research has exploded. In my opinion, we are moving towards a time in science where animal models wont be necessary anymore. There are many people that don't agree. I encourage you to look at the available facts, and decide for yourself.

But before you do that, think about the animals, and specifically the chimpanzees, that have been involved in research. Think about the animals that have been breed specifically for research purposes. Think about the biomedical advances we've had thanks to animal models. If you are going to spend some time next week thinking about what you are thankful for, consider being thankful for chimpanzees, and for the sanctuaries that are dedicated to caring for them.

Has this made you wonder what brands you use that currently test on animals? Here's a good, comprehensive list.

For a good visual guide of the history of the use of chimpanzees for research, check out this site.

Friday, October 2, 2015

Myth Campaign

I've been wanting to write this post all month, but every few weeks I'd see more examples I wanted to include, and my frustration increased exponentially. I should start by saying that I consider myself somewhat of a "political radical" of sorts. By that, I mean that, while I have a lot of respect for the idea of a true democracy, I have a low tolerance for the amount of actual representation of the average American citizen. I try not to talk about my political opinions on this blog, because frankly, that's not why I started this blog.

But, science and politics are very intertwined. From federal grants and funding initiatives for research, to government institutions and committees, there is no separation between "lab and state". Sometimes, that's a good thing. Some of the federal regulations that mandate safety and procedural guidelines for research ensure that working in research environments (labs, fieldwork, etc.) are safer for the people doing the work. Also, there have been a lot of scientific exploration and advancements due to federal funding.

Image courtesy of the Official White House Tumblr


While some presidents have taken a marked interest in science (some recent examples: G. H. W. Bush's "Decade of the Brain", and Obama's White House Science Faire), most of their actual involvement comes in the form of spewing talking points prior to being elected. How many US presidents have championed scientific innovation and research initiatives? Science has never really been on the forefront of any presidency since the moon landing.

"R&D as a Percent of the Total Federal Budget, 1962-2016" via the American Association for the Advancement of Science (AAAS), May 2015

Think about how political attitudes about science directly affect the public. The 10th anniversary of Hurricane Katrina was just a couple of months ago. Its estimated that the hurricane and flooding killed over 1,830 people and caused over $108 billion in damage. Scientists continually warn about the increasing severity of future storms and weather conditions, rising temperatures and pH changes in the ocean, and major reductions in natural resources. While no one could have anticipated the number of fatalities or the severity of the damages brought on by Hurricane Katrina, government initiatives to protect communities from future natural disasters (like, planning and response measures, zoning to recognize emergency response for all communities, etc.) may be more successful if scientists were acknowledged and involved. Instead, Senator Ted Cruz, the chairman of the United States Senate Commerce Subcommittee on Space, Science and Competitiveness, is a science denier.

Scientists and medical professionals have worked tirelessly to eradicate many diseases in the US and around the world, through the development of vaccinations and therapeautics with increased effectiveness, lasting power, and fewer side effects. Government agencies have been directly involved in funding and spearheading such initiatives. Unfortunately, some presidential candidates (whether we consider them serious or not), have decided that the subject of vaccinations are now appropriate debate material (I'm looking at you, Donald Trump, an idiot, and BEN CARSON, a retired neurosurgeon).

There's a clip in this article that shows the specific section of the republican debate where vaccines come up. Ben Carson and Donald Trump will actively talk about vaccines, but refuse to even acknowledge an important question from the moderator: "as president, you will be in charge of the Centers for Disease Control and the National Institutes of Health, both of which say you are wrong. How will you handle this situation as president?"

Meanwhile, polio is still an issue in some parts of the world, among other serious diseases that are preventable by vaccination. 

You'll also notice, if you watch that clip (and others featuring Trump talking about vaccines), that Trump is also great about reinforcing stigma around disease. Sometimes, he's blatant about it, like when he said this about ebola patients:


Other times, he's sneaky about it. During the debate, he said that "beautiful babies" are injected with huge amounts of vaccinations ("it's meant for a horse", he says, describing the supposedly cartoon-sized syringe that would never actually be used on children), and then goes on to say that the child eventually (1 week later) develops autism. Sure, no one wants their child to develop autism or any disorder, developmental or otherwise. But its clear from Trumps wording that he wouldn't consider a child with a disability as beautiful.

With the fiscal year ending, the House of Representatives has repeatedly voted on a measure to "defund" Planned Parenthood. Speaking of an issue that directly affects the all people in the US, women's health issues are always debated by presidential candidates. Even though federal funds totaling $528.4 million went to Planned Parenthood in the 2013-2014 fiscal year, the organization is not allowed to use federal funds to provide abortion services. So, by removing federal funding, 96% of the medical services Planned Parenthood provides, such as STD testing and treatment, contraceptive prescriptions and education, cancer screenings, routine check ups and gynecological exams, and prevention services, would be severely reduced. Yet, not eliminated entirely. In the 2013-2014 fiscal year, only 41% of Planned Parenthood's funding came from federal sources (through standard MediCal reimbursements, etc.). I wont go into how these services, regardless of how you feel about abortion (which only makes up 3% of Planned Parenthood's procedures), have an influence on the health and overall quality of life for many people -- not just women, not just low-income communities, and not just sexually active teens.

By the way, a Planned Parenthood clinic in Thousand Oaks, CA was set on fire this week.

So, while you listen to presidential candidates ramp up their campaign circuits, and recycle talking points that don't actually address any of the serious questions asked of them, think about where science and medicine fall into play. What do these issues actually mean for the future of the American economy? How do politicians navigate these issues for the American public? Just think about it.

Sunday, August 30, 2015

Jail-house Cough

When the world of somewhat rare infectious diseases collides with prison and inmate issues, it causes an uproar of excitement in my house. Education and advocacy are large themes in my marriage. It's obvious that STEM education is my driving force, but my husband focuses his efforts on issues associated with significantly skewed stigma and underrepresented topics, such as advocacy for mental health patients and inmates. He actually teaches a class on prison issues at UC Berkeley, and leads a volunteer group that takes UC Berkeley students into San Quentin Prison to tutor inmates that are working towards obtaining a GED. Its not uncommon that he will have to cancel volunteer shifts due to prison-wide lockdowns (most often due to fog), but Thursday night's lockdown had us talking.

As I've mentioned before, prisons are an epidemiological hotbed for infectious diseases. Sticking a large number of people in small, confined communal living quarters with inadequate medical care is one of the fastest ways to allow diseases to spread. So, hearing that the lockdown on Thursday and Friday were due to the potential spread of disease, we were not alarmed. When we heard it was Legionnaires' Disease and that one case had been confirmed with 30 other inmates presenting symptoms, we were surprised.

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Image from PrimeWater Membranes


Legionnaires' Disease, or "legionellosis", is a bacterial infection caused by Legionella spp. (most commonly Legionella pneumophila) and leads to the development of atypical pneumonia. Legionnaire's disease is most well known for its debut in 1976, when a L. pneumophila epidemic was traced back to the Philadelphia Convention of the American Legion. More than 30 people died as a result. Yet, L.micdadei had already been isolated from human blood in the mid 1940s. As usual, only a handful of disease nerds care about a disease before an epidemic occurs.

These two, specifically. (Credit: Wikipedia)
 Legionnaire's Disease is spread through droplets of water containing the bacteria, especially in warm environment that cause steam and aerosolization, like showers, hot tubs, wet saunas, humidifiers, and faucets.The CDC also lists "decorative fountains" as a potential source, which, I have to admit, made me laugh. I mean, think about all the major hospitals that have massive decorative fountains in their entrance/courtyards! Double threat!

Legionella spp. have developed a somewhat symbiotic relationship with larger protozoae, such as amoebas, that create large biofilms that can protect the Legionella bacteria. Outbreaks are most common in places that house lots of people for extended periods of time, like hotels, office buildings, retirement homes and convalescent facilities, hospitals, cruise ships, and prisons. Legionella spp. also like to live in wet soils.  Despite the dependency on aerosolization for transmission, Legionnaires' Disease is not spread from person to person. A reservoir, like water or soil, is required for the transmission of the disease.

Amoeba engulfing and releasing bacteria. (Via Pall Corp.)
 If you inhale contaminated water, the bacteria travel through your respiratory tract and into your lungs. This triggers your immune system, and trolling macrophages engulf the bacteria. While engulfing the bacteria through phagocytosis is one method (of many) your immune system uses to identify and destroy invaders, many infectious agents have learned to exploit this mechanism. Once in the macrophage, the bacterium will multiply, causing tons of bacterial cells to explode out of the macrophage and continue spreading the infection throughout your tissues.

While your body is working to fight off the rapidly replicating Legionella bacteria, you'll start to experience symptoms, such as fever, chills, and a cough. Depending on the severity of your infection, you can cough up blood, sputum, or a combination of the two. Chest pains are common, and some people can also experience diarrhea and vomiting. A combination of chest x-rays and bacterial culturing will land you with a diagnosis of Legionnaires' Disease. Since this is mostly rare form of pneumonia, it is incredibly important to get an accurate diagnosis. Since Legionnaires' Disease is caused by a bacterial infection, there are specific antibiotics that can be used to treat your infection. As always, when left untreated, the disease will get significantly worse, and may be fatal. Pneumonia is a significant cause of death for those who have compromised immune systems, and for children without access to medical care.

So, San Quentin Prison has shut off their water supply (with the exclusion of toilets, that have now been deemed okay), but this still raises the question of how extensive the contamination is. If only one person was affected, it may have been an isolated incident from an isolated source. Yet, with 30 potential patients, this is a larger issue that most likely stems from the prison's water source.