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Founding editor of JVI, Lloyd Kozloff, dies

The Journal of Virology was founded in 1967 by three scientists, including Lloyd Kozloff, who passed away this week.

Sarah Kozloff, Lloyd’s daughter, is a professor in the Film Department at Vassar College.  She told me of her scientist father about a year ago and I did a little digging to find out more about him and his career.   Kozloff began his career as a scientist in a very exciting time.  He was a part of a group of bacteriophage biologists at Cold Spring Harbor in the late 1940s and early 1950s.  Members of this group revolutionized biology by ushering in a new discipline called molecular biology.  Very little was known about viruses or the molecular mechanisms that make cells work.  Other members of this group would go on to demonstrate that DNA was the genetic material (A.D. hershey) and discover the structure of DNA (James Watson).  Sarah mentioned to me that she remembered the party that the Kozloff’s threw to celebrate Watson’s Nobel prize.  The names of scientists that are legendary to most of us were, to the Kozloffs,  part of everyday dinner table conversation about friends and colleages.

Lloyd Kozloff made some important contributions to phage biology and basic understanding of viruses.  He was one of few people using a new technique in biology: radioisotope labeling.  In a 1948 paper he used phosporus isotopes to determine that phages obtain their phosphorus primarily from the media, though he presumed it must be vis a cellular metabolic pathway.  That paper in Science, has a single table, the result of what appears to be a single experiment.  The phosphorus was all in the DNA component of the phage, something that would be important later when Hershey and Chase showed in 1952 that DNA was the genetic material.   In fact, the authors are careful to define the acronymn DNA, the macromolecule perhaps being something not too familiar to many at the time.    In a later 1956 paper, Kozloff demonstrated that the bacteriophage does something to the bacterial cell wall to allow the genetic amterial to enter, and that activity was conferred by some kind of protein.  We now know that what he was seeing was the action of lysozyme, an enzyme at the base of the bacteiophage tail that degrades the bacterial peptidoglycan wall to allow the DNA to enter the cell.

I rarely go so far back in the literature, although it is always interesting to see the foundational papers upon which our current knowledge is based, and to see the style of experiments, the difference in the style of scientific writing and presentation, and to imagine what it was like to explore virology without really understanding yet what viruses really are or how they work.

The journal of virology will be publishing an obituary and I will add a link once it is available.

The university of San francisco, where Kozloff spent the last part of his career, has a brief biography.

A scholarship fund to support graduate students has been created, to which donations can be made in his name.  (The family has specifically requested donations to this fund in lieu of flowers.  A card will be sent to the family.)


I’ll take my milk pasteurized, thanks

A recent article in Vassar’s newspaper, The Miscellany News, discussed the Vassar Raw Milk Co-op, which brings unpasteurized milk to Vassar College (Co-op offers raw milk delivery service, Nov 10,2011). The article raises several important questions about raw milk, pasteurization, and sustainable agriculture, but some of the information presented is incorrect. Importantly, Vassar’s Raw Milk Co-op website, to which readers are directed, has a great deal of misleading, incorrect or unsubstantiated information.

In the production and packaging of milk, it can become contaminated at virtually any stage of the process. That contamination, when it is by organisms like E. coli or Listeria, is what causes milkborne illness. Pasteurization, a process of heating milk to reduce the levels of microorganisms present, will kill those contaminating bacteria if they are present. The risk in drinking raw milk is due to the fact that if it does become contaminated, you will be consuming those pathogens. In a farm environment, it is safe to assume that contamination will, at some point, happen. Pasteurization is one check that we have to protect us from that.

The majority of cases of milkborne illness result in diarrhea and/or vomiting. Occasionally the symptoms can be more severe, such as in last week’s outbreak in California, in which five children have become sick. Three have been sent to the hospital with hemolytic uremic syndrome, which can lead to kidney failure. These cases have led to the recall of the organic raw milk, contaminated with E. coil 0157:H7, which has been linked to the outbreak. There are outbreaks associated with pasteurized milk as well, usually due to post-pasteurization contamination, such as at the packaging stage. However, it is estimated that only 1% of people consume raw milk, but from 2000-2007, 75% of outbreaks were associated with contaminated raw milk.

In NY consumers can choose to buy raw milk from a farm if they determine that they are comfortable with the level of risk. But it is also important that they know the facts behind the reported benefits to balance their decision. Many proponents of raw milk claim that industrially raised, antibiotic laden cattle given GMO corn feed produce milk that needs to be pasteurized because it is inherently of poor quality and unsafe, but that organically raised pasture fed cows produce milk that is safe. That is simply untrue. Pasteurization was developed in the mid 1800s to eliminate pathogenic and spoilage microorganisms, not to fix the problems of industrialized agriculture. There is no credible scientific evidence to support the suggestion that organic pasture-fed cows generate safer milk than cows from industrial farms. Contamination by pathogenic organisms comes from fecal matter, the environment, the handlers, packaging, storage, and undetected infections in the animals, and is unrelated to diet and housing conditions.

Additional claims such as that pasteurized milk causes allergies, asthma or other conditions are not supported by the scientific literature. The claim that raw milk is better for individuals who are lactose intolerant is not supported by scientific data either, and represents a clear misinterpretation or misunderstanding of available information. The level of nutrients in raw compared to pasteurized milk is not significantly different, invalidating yet another central claim in support of raw milk.

There is an abundance of misinformation on the topic of raw milk. Unfortunately, groups like Vassar’s Raw Milk Co-op perpetuate this misinformation. At Vassar, we often say “go to the source.” This is an opportunity to practice that principle. Rather than seeking confirmation of one’s beliefs in the websites of others, we must check the original research. What is actually supported by credible scientific investigations? Is the information you are reading being correctly interpreted? Are you getting the whole story or just fragments?

There are many good things about the locavore and Slow Food movements. Supporting small local farms and sustainable agriculture, humane treatment of animals and having the sense of community achieved from getting to know the farmer who raises your food, are important to me and many people. But you don’t need to consume raw milk to do that. These issues are distinct from the question of pasteurization. If you want, you can even get the raw milk and pasteurize it yourself. Just heat your milk on the stove to 63C for 30min before drinking it.

Thanks to the students in STS/Biol 172 for discussion and research on this topic

A few links:
FDA Milk Safety

CDC Milk Safety

Review on Milk Safety and Pasteurization

A recent review of the scientific literature. Note that they included many studies of poor design, which should have been ignored.

Slightly updated and edited on December 1, 2011


I Don’t Want Dengue Fever

When a student is absent from class, they usually send me an email to explain why. Occasionally I get emails from students in my microbiology or virology classes explaining their absence from class as a result of some infectious disease and they actually seem excited about the fact that they are hosting a virus. Perhaps they feel that they are participating in the class on a whole new level or are appreciating and understanding what is going on in their body, despite feeling awful. However, I was surprised recently when I mentioned Dengue Fever and a student piped up and said “I’ve had that!” I asked Caitlyn to write about her experience, and she kindly agreed. While she is interested in learning more about the virus, I suspect she would have preferred to learn about it without first hand experience. Here is her story.

Contributed by Caitlyn Anderson ’13

Photos of Angkor Wat in Siem Reap, Cambodia. Taken by Caitlyn Anderson.

“I was infected with Dengue virus in Cambodia during the summer of 2007 while working as an intern for the Clinton Foundation. I knew before going that there was a Dengue epidemic across the country but was unwilling to give up the opportunity. It is likely that I was bitten by a mosquito carrying the virus while I was sight seeing in Siem Reap towards the end of my stay. The virus incubated within my body for a period of approximately 5 days. Thankfully, I was back on U.S. soil when the virus began to present itself. I remember feeling slightly odd as I worked the night shift at Starbucks. After I returned home I immediately went to bed. In the morning I had developed flu like symptoms with a fever of 100 degrees. My body began to feel achy and I remained in bed throughout the afternoon. By 3:00 pm my temperature had reached 103 degrees and by 5:00 pm, my temperature was up to 104 degrees and I could barely move. My mother immediately called my pediatrician who then instructed us to go to the Emergency Room. I had immense difficulties walking from my bed on the second floor to the car. When we got to Norwalk Hospital in Connecticut, I was unable to walk and required the assistance of a wheel chair. The initial reaction of the emergency room doctor who saw to me first was that I was presenting with Lyme like symptoms. However, the unbearable pain caused by the insertion of the IV into my arm was not indicative of Lyme disease so I was immediately admitted to the hospital for further tests and supportive care. A few hours later my fever had reached 105 degrees and was coupled with the sudden onset of rash covering my entire body. The virus began to affect my nervous system causing extreme skin tenderness. Infectious disease specialists were brought in to evaluate my case. A Haitian doctor was immediately convinced I had Dengue Fever because she had witnessed the disease many times. Unsure of which of the four strains I had been infected with, the doctors could not predict the clinical evolution of the disease.
My fever remained between 103 and 105 degrees for 3 days. I was treated with fluid intravenously and pain medication for my body aches and severe skin sensitivity. My body was packed with ice in an effort to lower my body temperature. While Dengue Fever is commonly referred to as “breakbone fever” because people often feel as if there bones are being crushed, I did not experience this sensation. My skin, rather than my bones and joints, was the greatest cause of my discomfort. On day 4 of my hospital stay, my fever began to go down to 100 degrees but I was transitioned to the telemetry unit so that my heart could be monitored more closely. I continued to receive IV fluids and pain medication. I remained in the telemetry unit until day 6 when I was moved to a general ward where I remained until my release from the hospital on day 8. My fever had completely dissipated but I was very weak and had trouble walking. When I returned home I slept for 16 hours a day for about a week and was able to return to school a few days later with a reduced academic schedule. About a month later I regained my strength was symptom-free.”


Goodbye Rinderpest, Hello Measles

Variola virus, the agent of smallpox, once held a lonely spot on the list of globally eradicated diseases. Now it is joined by rinderpest, the cattle plague. The OIE (Organization for Animal Health) declared the disease eradicated and the UN’s Food and Agriculture Organization (FAO) is expected to adopt a resolution in June declaring it eradicated. The disease affects cloven-hoofed animals and can have an extremely high mortality rate in some cattle and buffalo. It is also extremely contagious, so its rapid spread through livestock can have an obviously large impact on animal health, food production and livelihood of cattle farmers. Thanks to an intensive word-wide vaccination effort, rinderpest virus can now be added to the list of organisms we actually intended to make extinct.

Rinderpest is caused by rinderpest virus, a member of the Morbillivirus genus. Another member of that genus is measles virus. Oh, and there is a vaccine for that too. In fact North America was free of measles in 2002 and perhaps it was on track for global eradication. But not anymore.

My son recently turned one, so I took him to get his measles, mumps and rubella (MMR) vaccine, feeling confident that Im helping protect him from three pretty nasty viruses, and not giving him Autism. In fact, before he turned one, I’d been feeling a little anxious about getting him the vaccine soon enough. My email inbox keeps filling up with notices from ProMED mail (Program to Monitor Emerging Diseases) with news of various measles outbreaks across the globe.

There are outbreaks all over Europe, especially in France, the UK, Spain and Switzerland. The epidemic in France that started in 2008 has now reached over 14,000 people, with 9000 of those infections reported in the last 6 months. (France has a vaccination rate of about 60%. Vaccination rates in the UK bottomed out at 80% and are slowly on the rise again). Outbreaks in the USA and Canada have been small, the vaccination rates are higher but not high enough. Many of these can be tracked to travel of unvaccinated individuals to areas where measles is still endemic or flaring up. In Minnesota, an outbreak counting 21 people has sent 13 people to the hospital (an unusually high number). Of the 21 people, 8 were old enough to be vaccinated but weren’t, 7 were too young to be vaccinated, 1 was vaccinated and the status of the others is unknown.

The Minnesota outbreak emphasizes an important point: it is necessary to maintain a sufficiently high level of herd immunity to prevent outbreaks and protect those who can’t be vaccinated. For most diseases, vaccination rates need to be at or above 95% to prevent outbreaks, and may need to be even higher for measles. Virus transmission depends on the virus finding a susceptible host. If a population is primarily made up of immune individuals, the virus has a hard time maintaining a chain of transmission.

Vaccination is therefore not just a matter of personal health, but community health. Maintaining high herd immunity helps protect babies too young to be vaccinated by limiting the chances that they ever encounter the virus. Don’t just get your kids vaccinated to protect themselves, do it to protect us all.


Hey, I wonder what’s in bat poop?

I know you were thinking the same thing! Bats are suspected reservoirs for several zoonotic viruses that can cause significant disease in humans or other animals. These include the dreaded Ebola virus, Nipah virus (which causes outbreaks of encephalitis in South East Asia), Hendravirus (which causes disease in horses) and several others. So knowing what viruses are carried by bats will be important in understanding emerging zoonoses.

Several studies have identified a diverse array of viruses in bats, but using next-generation sequencing it is now possible to investigate the population of viruses carried in bats to a much deeper level. In a study published last summer, guano from bats in California and Texas was collected by placing plastic sheets below the bat roosts. The individual roosts were occupied by as many as four different bat species, so the guano collected was a mix from the different inhabitants. To isolate viral DNA and RNA, the samples were filtered to remove cells then treated with nucleases to destroy any free DNA or RNA, leaving only encapsidated viral genetic material.

In the sequenced “virome” or population of viruses in the samples, only 51-39% of the sequences(depending on collection site) had matches to genbank sequences. So once again, viromic sequencing shows us how little we know about the viral world. Of those sequences that matched known sequences, most were insect and plant viruses. The bats are insectivores and the insects are herbivores, so you can see the viral populations from each link in the food chain. Only a very small proportion of the virome was of bacteriophage origin, much less than other viromic studies in humans and horses, although its not clear why there would be such a difference. Among mammalian viruses, which made up less thatn 10% of the sequences, there were adenoviruses, coronaviruses, parvoviruses, circoviruses, astrovirsues, picornaviruses and even poxviruses. Most of these sequences only matched less than 60% to known mammalian viruses however, so its unlikely that they pose a zoonotic threat.

As researchers continue to sequence viral populations, we keep seeing mostly novel sequences, something that has decreased in bacterial and eukaryotic sequencing. That tells us we have a lot more sequencing to do if we want to understand global viral diversity. In bats however, the major question is not so much about the diversity but the threat of zoonoses. It will be interesting to see the guanome of bats in areas where zoonoses are a real problem, and I wonder if this will be a technique useful to monitor the threat of emergent diseases as the cost of high throughput sequencing continues to drop.


Smelly Cucumbers Anyone?

Somewhat to my surprise, I have recently found myself very interested in plant viruses. This started a few years ago when I ate a most delicious variety of hot pepper that apparently is infected with a virus that gives the peppers white stripes. I’ve never really given much thought to plants and plant viruses before but as I began to look into their biology it seems that plant viruses have some terrific tricks up their sleeves (if you will) to aid in their transmission.
Plants aren’t walking around coughing on each other, so most of them depend on insects to come and bite the infected plant and carry the virus to the next host. But a plant that is infected isn’t very attractive to insects, since unhealthy plants aren’t as likely to be a valuable source of food. But viruses are masters of host manipulation. A recent study looked at Cucumber mosaic virus, and its ability to attract aphids to infected leaves. It seems that aphids dont like to spend much time on infected leaves, and they dont have to. The virus sticks to the aphid mouthparts quickly and easily and the aphid can then bring it to the next plant. But the aphids still have to be attracted to the leaves, even if they dont stay for long. So how does the virus attract the aphid to the plant? Researchers set up a special chamber with a leaf from an infected and a leaf from an uninfected plant. The leaves were not visible, but could be smelled by the aphids through wire mesh. Aphids released into the chamber were more attracted to the uninfected leaf. Analysis of volitile organic compounds being released from leaves showed that both infected and uninfected leaves release compounds that aphids can smell but infected leaves release much more. So even though the meal may not be as good, the strong smell brings the aphids to the table.


Big Viruses for Small Hosts

Its a common misconception among my students that simpler hosts like bacteria or single celled eukaryotes would host simpler (ie smaller) viruses, but that is certainly not the case.

Another giant virus that infects a protist has been identified and sequenced. Like its close relative Mimivirus, this new virus called Cafeteria roenbergensis virus (CroV) has a very large genome and has many genes not typically found in viruses. Before the discovery of Mimivirus, viruses were not known to encode proteins involved in protein translation. That was a function on which viruses were totally dependent on the host. However, these giant viruses seem to have their fingers in protein translation too, showing us yet another strategy in manipulating host processes. There is also block of genes that appear to be derived from bacteria. The host species, C. roebergensis, eats bacteria, so it would be interesting to know if the bacterial genes were the result of a horizontal gene transfer event from a preferred host food.

Before CroV, all giant viruses identified infect amoebas. CroV infects C. roenbergensis, a marine protist. So what is it about protists that makes them good hosts for such big viruses? Why haven’t we found giant viruses infecting other eukaryotes?
Could the explanation lie in the still murky evolutionary origin of viruses? Another recent paper attempts to put some viruses (nucleocytoplasmic large DNA viruses, including giant viruses, poxes and herpesviruses) into the tree of life along with bacteria, archaea and eukaryotes. Using genes common to all, they showed that these viruses have a very ancient evolutionary origin, probably right around the time of the appearance of eukaryotes. Were the ancestral viruses more cell-like and over time progressively lost genes?


Of Aliens and Arsenic

Or How to Screw up an Interesting Discovery with Mediocrity and Media Hype

NASA annonced an “astrobiology discovery”….Aliens! No, sorry, bacteria…in California! WOW! OK, this is no ordinary bacteria as it can grow in astonishing concentrations of arsenic, a highly toxic compound. It’s nothing new that bacteria can grow in all kinds of extreme environments, but this is growth in a lot more arsenic than we’ve seen before. The claim however is that this bacterium actually replaces phosphorus with arsenic. Phosphorus is used as part of the structure of DNA, as well as proteins and many important small metabolites, most notably ATP, used as an energy source. Arsenic is much like phosphorus but arsenic containing compounds are quite unstable in water (which is why arsenic is toxic). This would be novel in cellular life as we know it; DNA containing arsenic! I was initially very interested in this discovery…and then I read the paper.
When you make a claim as big as replacing one of the most import elements in a cell, it seems to me your data better be rock solid. The paper is quite underwhelming. Although it seems there might be arsenic associated with the DNA it certainly doesn’t provide good evidence that it’s a part of its structure. In fact, others have argued more convincingly that the trace amount of phosphorus contaminating the preparation is sufficient for the cells to use to make everything they would need to.
It seems to me this is a case of the researchers jumping ahead of themselves and interpreting something from the data that is just not there, a failure of the peer review system, and an overly enthusiastic media running with a thrilling but incorrect story about alternative branches of life and our need to re-write biology textbooks. Whats sad is that there actually is something interesting here that has been missed and would be a more reasonable interpretation of the data. This bacteria can grow at extreme concentrations of arsenic, in the near absence of phosphorus, but can still somehow scavenge those few available atoms of phosporus and use them, where probably all other organisms would have long since died of arsenic poisoning. How does it do that? This is still a fascinating bacterium…it just wont redefine life.
FInally, why am I writing about bacteria on a virology blog? I learned some time ago never to underestimate viruses. After being surprised about the existence of viruses infecting organisms in places like bubbling geothermal acid pools, I realized that where there are cells, there are viruses. I wonder if this arsenic loving bacteria is host to some interesting viruses? I bet Mono Lake, where this discovery was made, is full of interesting viruses.


Frank Fenner 1914-2010

It is with great sadness that I report the death of one of my science heroes, Frank Fenner. One of the key people involved in the eradication of smallpox, he was also a prolific researcher in poxvivrology, and discoverer of the virus I study, ectromelia virus. Although I never met him, I have read many of his papers and they have influenced my own research and interests.

Here is the text of the email I received this morning, from Julio Lincio:

“Frank John Fenner AC, CMG, MBE, FRS, FAA (born 21 December 1914,died 22 November 2010) was an Australian scientist with a distinguished career in the field of virology. His two greatest achievements are cited as overseeing the eradication of smallpox during his term as Chairman of the Global Commission for the Certification of Smallpox Eradication, and the control of Australia’s rabbit plague through the introduction of myxoma virus.

Professor Fenner was Director of the John Curtin School from 1967 to 1973. During this time he was also Chairman of the Global Commission for the Certification of Smallpox Eradication. In 1973 Professor Fenner was appointed to set up the new Centre for Resource and Environmental Studies at the Australian National University (ANU). He held the position of Director until 1979.

Professor Fenner has been elected a fellow of numerous faculties and academies, including Foundation Fellow of the Australian Academy of Science (1954), Fellow of the Royal Society (1958), and Foreign Associate of the United States National Academy of Sciences (1977).

During his career Professor Fenner received many awards. Among these are the Britannica Australia Award for Medicine (1967), the Australia and New Zealand Association for the Advancement of Science Medal (1980), the World Health Organization Medal (1988), the Japan Prize (1988), the Senior Australian Achiever of the Year (1999), the Albert Einstein World Award for Science (2000), and the Prime Minister’s Science Prize (2002).

A man of decisive scientific action and strong opinions, Professor
Fenner’s last interview with The Australian is extremely thought provoking and can be found here

A summary of Frank’s remarkable career can be found here


A Universal Flu Vaccine?

The flu comes back year after year, and every season we get vaccinated (well, some of us anyway).  Why do we need to keep getting a new shot for the flu while for others, like measles, we got way back in childhood and are done with it for the rest of our lives?

Our immune response to influenza involves production of antibodies, large proteins that specifically bind to the virus and help clear it out or neutralize it.  It seems like the key to influenza immunity is neutralizing antibodies, antibodies that bind to the virion and prevent it from attaching to the host cell.  You can imagine this large protein just being physically in the way, preventing the virus from binding the host receptor.  The immune response that develops from natural exposure or vaccination generates neutralizing antibodies to HA, a viral envelope protein that is necessary for attachment to the host.  I’ve mentioned HA in a previous post about influenza.  The problem is that last season’s neutralizing antibodies dont bind to this season’s virus.  Although it may be nearly identical to the virus from a past season, the new strain’s HA is slightly different, and those differences are enough to evade existing neutralizing antibodies.

Now a new approach to vaccination has shown that it may be possible to develop a vaccine that illicits broadly neutralizing antibodies, that is, antibodies that will protect against  influenza strains with slightly different HAs.  They used a prime/boost approach, in which a DNA vaccine was used to induce an initial response against HA, and then boosted with a regular seasonal flu vaccine.  The only difference between this and what is currently done is the addition of the DNA vaccine.  However the response seems quite different.  Neutralizing antibodies were generated that can neutralize a variety of different influenza viruses.  It seems the vaccine induced antibodies to a different part of HA.  Antibodies are so specific, the dont recognize the whole HA, but rather discrete parts of it.  The part recognized by these antibodies, called the stem, is highly conserved, meaning it doesnt change season to season.

This raises many interesting questions and possibilities.  Could we soon have a universal vaccine that will protect us for life or at least for many years?  Why did the change in vaccine regimen induce antibodies to a different part of HA?  Why does the current vaccine or natural exposure fail to develop antibidies to the conserved portion of HA? Will the conserved portion of HA eventually change too, if sufficient selective pressure is applied through mass vaccination?