Tuesday, October 28, 2014

Blogger's desk #2: Guest post- Science communication


I had requested Mr. Saumyadip Sarkar, a regular contributor to a variety of science activities online to contribute a guest post on his journey as a science communicator. The following is what he sent me, and am glad to host it on my blog.

Thank you Saumyadip Sarkar

Science Communication:

Thinking leads to activity, and activity leads to discovery. The getting the unknown thing into known is how all about science communication. The discovery of any research we mean it when we read the articles of great discoveries. The words, the steps of thinking and bringing the hard work into light, are all about holding the story towards the common people. It is the cable which joins the research and the people who reads it.

I am an individual Science Communicator. It is all about, picking up great stories of research, communicating scientists from different aspect of science background, taking interviews and highlighting them before readers. Sounds easy! Quite easy when you know the importance of science and how communicators do to seed the importance of it. A small research doesn’t remain too small, a big research sounds interesting and the artefacts are designed to confront the beauty of science. This is how a science communicator believes in science.

My journey of science communication was brought forward from a social networking site. Sounds crazy though, I grabbed some cool science freak guys and then planted a small group of microbiology lovers named “We The Microbiologist” [www.wethemicrobiologist.in]. The daily questionnaire and solving the puzzles started the game. WTM became a big early platform of discussion and then we made a science website who wished to build up science research before the readers who are actually interested to read science. Starting from magazines to events has brought forward the beauty and hope it will grow further with the interests of the readers who believes in science. Now I am a science communicator at CSIR NISCAIR’s Science Reporter Indian Magazine, Microbiology World [www.microbiologyworld.com] and my own blog Biomysteries [www.biomysteries.wordpress.com].

Taking ahead of my personal walk of being a science communicator, let me highlight you why science communication is important. In the discoveries of recent research from the developing countries always remains deep just into a three to four page publication, unless people know what you are contributing for the society. Many research publications are brought into the practical field use when searched in science websites. If we think about the current youth of developing countries specifically grab their interests when they read the whole story of a research, starting from the failures to success. If you are reading this, I would request you to just have a look into the corner up or below of any science websites, you will get the name of the science communicator who brought you the story. Keep digging your thoughts into action; because you got no worries, we are watching you!

Saumyadip Sarkar
Twitter: @iamsaumyadip

Saturday, October 25, 2014

Contestant for Clostridium difficile- C scindens


    C difficile has represented important part of current clinical microbiology research. Its attachment with antibiotic induced complications has caused sufficient investment of research. The primary current goal is treatment. As discussed previously (Link), antibiotic and vaccine strategies are currently highly explored. Of everything else the most popularity is gained by a method called Fecal transplantation or Fecal microbiota transplantation (FMT). Over the last couple of years a huge amount of research is focused on improvement of the method.

   FMT works something like the following. A fresh stool sample is obtained from a healthy donor, screened for potential enteric pathogens and a serology for antibodies to hepatitis A, B, and C, HIV etc. The stool sample is homogenized and filtered for debris. The extracted material is administered rectally through a colonoscopy or nasopharyngeally through ryles tube. The basic problem with the approach is that the testing takes takes time and the transplant is best administered within 6-8 hrs. Moreover, healthy donors are not always available at disposal. This has been overcome by using synthetic pills containing frozen fecal matter. Study has shown that with administration of 30-60 capsules over a 8 week period or less most of the participants had completely recovered.

Table 1: Organisms implicated in
interference with C difficile.
   However, there are several problems with this approach. The foremost being the fact of consuming fecal sample no matter how well it is treated. The second important problem is in getting the right donors. The screening of the donor is only as good as the laboratory test and limited to number of tests that can be done. This means that though the technique is safe, it is not out of risks, though the risk is significantly low. It is arguably better to figure out what components of the flora are really important in defense. Considering the extremely huge number of colonizing bacteria in gut, it is very difficult to ascertain the right organisms. It is also very much possible that the effect is brought by combination of bacteria's. For example various Lactobacillus and Bifidobacterium strains have been shown to significantly impact C diff invasion. Table 1 is a list of proposed organisms involved in fighting C difficile infections.

      Clostridium difficile is a anaerobic spore-forming Gram-positive bacterium. the organism has been identified in normal gut of normal individuals also. Its number is however, very low. In patients receiving heavy antibiotic dose, the gut flora is wiped out in high levels, providing a chance (C diff is resistant to multiple drugs) to colonize and cause infection. The first step in this process is spore germination. The germination of spores is a specialized process based on sensing of environment. The signals that favor germination are called germinants. The germinants vary for species and can include anything from an ion gradient to a specific chemical such as sugar or amino acid. There are also negative signals which alert the bacteria to the hostility of environment and can restrict the bacteria from germination. In the context of C difficile taurocholate, glycocholate, cholate, and deoxycholate act as germinants; and chenodeoxycholate can competitively inhibit taurocholate-mediated germination.

       So it makes sense as to consider chenodeoxycholate, a modified bile acid or similar compounds to be an important player. In an experiment with rodent model, scientists were able to identify signature of organisms causing resistance to C diff infections. Though the exact composition was not identical between members, there was a single topper- C scindens. This is indeed a breakthrough, and fits really well into the current model. It is known that C scindens produce enzymes which convert primary bile acids into secondary bile acids in the large intestine through 7 alpha-dehydroxylation. Also, important as shown in paper, C scindens when given as a cocktail with other microbiome was more effective than C scindens alone.

     This has important implications. Foremost, is in considering a probiotic C scindens is an important candidate for the mix. Second, it is very likely that there are more organisms involved in this effect and hence a combination of just few microbes may not work effectively enough. However, if we could figure out the right combination of organisms, even partially, it could go way beyond having to administer fecal transplant and finding the right donor.

Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, & Hohmann EL (2014). Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection. JAMA PMID:25322359

Hickson M (2011). Probiotics in the prevention of antibiotic-associated diarrhoea and Clostridium difficile infection. Therapeutic advances in gastroenterology, 4 (3), 185-97 PMID:21694803

Sorg JA, & Sonenshein AL (2010). Inhibiting the initiation of Clostridium difficile spore germination using analogs of chenodeoxycholic acid, a bile acid. Journal of bacteriology, 192 (19), 4983-90 PMID: 20675492

Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross J, Toussaint NC, Xavier JB, & Pamer EG (2014). Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature PMID: 25337874

Saturday, October 18, 2014

Ebola- The current situation


   I have been covering the Ebola story for some months now and the posts have been well received by the audience. The current world news is focused on Ebola transmission. When I last wrote a "updates post" (Link), the total number of cases was already at a record high. With more and more papers pumping in, I felt this is the right time to get back into writing an update on EBOV 2014.

The current estimates is 4,500 cases (as of on 18 Oct 2014) of death, including 236 health workers with more than 9000 total reported cases (confirmed + probable + suspected). The estimates is a reflection of reported cases, and the actual number of cases is expected to be much higher due to under reporting. All cases has been stratified into 3 levels based on the evidence- confirmed, probable and suspected. See Table 1. WHO has acknowledged that it would take sometime, probably in months to completely stop the outbreak, In addition, WHO has identified 14 African countries where preparedness and containment of the disease is a priority to prevent its spread. Indeed this is the most devastating of all EBOV outbreaks to date.

   Senegal had reported a confirmed case of EBOV on 29 August 2014, in a young man who had direct contact with Ebola patient. As per the response plan, 74 close contacts of the patient was tightly monitored, strong surveillance system and public awareness programs was conducted. The result is no more case detection and WHO has officially announced Senegal free of EBOV (Link).  A fresh confirmed case of EBOV infection has been reported from Spain, a healthcare worker. She had been in contact with EBOV infected spanish citizen. A detailed report is given in WHO website (Link).

      One of the most common practice in ongoing outbreaks is to create mathematical models. However, the point of creating models is seldom understood by many. Mathematical models (MM), can predict the nature and dynamics of outbreak and is usually relevant in terms of predicting the future needs. However, they many a times fail to predict future completely since the parameters of the equation can change radically. In this sense it is important to understand that the models should be used with caution and not relied too much upon as an answer. One of the most important factors that determine the mathematical predictions and ability of outbreak, is based on a measure called as R0. R0, is an epidemiological parameter in infectious disease, which basically means basic reproduction number/ rate. It is the number of people who transmit the infection from one sick person, on average, in an outbreak, in other word "contagiousness". If R0<1 then there would be no epidemic since the outbreak would die easily. If the R0>1 then the spread will be much better. For the current strain the R0 value lies between 1 and 2.

There are 2 questions that I keep getting and bothers people. How fatal is Ebola and can Ebola be airborne.

As I have commented in a previous Ebola post, a lot of misunderstanding in science comes from the fiction movies. The movie outbreak features a mutated virus that is airborne. In real life situation, that is a totally improbable situation. I have seen internet materials, claiming it just takes a few mutations. The point is it would take too many mutations way to far that we could call it some other virus. to change the route of transmission means acquire new counter defense mechanisms, new receptors, new replication strategy. too much for a few mutations to come up with. Not even the 300 plus mutations that has been found in the new strain. People who are still in doubt, please listen to TWiV podcast #TWiV 304. To the best of the knowledge of science there is no such documented evidence.

The second question is a little more tricky to talk about. All the while you are told that EBOV is a severely fatal illness. But is it really so? The concept of fatality in infections are usually measured in terms of Case Fatality ratio. That means number of people who die in ratio to number of people who turn up into the hospital. In the current outbreak this ratio is about 50%.

In a recent paper published in lancet says (Quote from the paper)

"Results from one post-Ebola outbreak serosurvey showed that 71% of seropositive individuals did not have the disease; another study reported that 46% of asymptomatic close contacts of patients with Ebola were seropositive."

A quick conclusion that I can draw is that probably EBOV, isn't as fatal as it is projected to be. To give an exact estimate is difficult cause I'm not aware of any data in this regard. However, it could be confidently proposed that it is not 100%.

One of the latest interest in treatment of EBOV is the use of a candidate drug called Brincidofovir (CMX001). This is a chemically modified cidofovir with a lipid tail. Cidofovir is was developed as an injectable drug. The mechanism of action is not well known. The drug basically is converted to cidofovir diphosphate by phosphorylation which acts as a substrate for viral DNA polymerases, leading to inefficient processing by unknown mechanism. The drug is currently developed by chimerix. Despite the fat that EBOV is a RNA virus, in cell culture assays, the drug has shown significant activity and hence in under the consideration as a option. Thomas Eric Duncan also known as the Dallus patient, had contracted EBOV from liberia, was offered this drug as per the compassionate use protocol, without success. Another person, Ashoka Mukpo had also received the drug and seems to be recovering. Given the fact that at least 50% of the cases survive, it is hard to tell the actual efficacy of drug in this case.

From the current scenario a rough conclusion that probably the outbreak has now slowly begun to die out. With an international awareness and effort the number of reported cases slowly seems to come down. Though a complete shut down of the spread will take some time, This outbreak highlighted the lack of basic science research. And perhaps as Vincent says in his post, there is a huge need for improved funding and a tight slap on face people who say we don't need BSL-4 level research.

Martin I. Meltzer, Charisma Y. Atkins, Scott Santibanez, Barbara Knust, Brett W. Petersen, Elizabeth D. Ervin, Stuart T. Nichol, Inger K. Damon, Michael L. Washington. Estimating the Future Number of Cases in the Ebola Epidemic — Liberia and Sierra Leone, 2014–2015. MMWR. Supplement / Vol. 63 / No. 3. Link

WHO: Ebola Response Roadmap Situation Report. WHO; 15 October 2014. Link

Bellan, S., Pulliam, J., Dushoff, J., & Meyers, L. (2014). Ebola control: effect of asymptomatic infection and acquired immunity The Lancet DOI:10.1016/S0140-6736(14)61839-0

Friday, October 17, 2014

Y not an irresistible antibiotic!!


    As spoken several times in this post, anti microbial fight has been a loosing war (Link) with science running badly out of options. This is no less agreeable in many cases of hospital acquired infections (which I sometimes prefer to call "healthcare vectored" infections). With the WHO calling us into a possible post antibiotic era (Link) we are desperately looking for options. But a basic question remains in the minds of many people. Is it not possible for us to develop an irresistible antibiotic?

Source: Small things considered. Link
    I'm reminded of a post published in ASM blog (Link) which basically calls up a similar question. The beewolf wasps cultivate Streptomyces bacteria, which defends them from a pathogenic fungus. The question is why hasn't the fungus evolved resistance to these antibiotics. Seems like a fascination. But the simplest point is whenever the resistance has evolved, the wasp has lost the evolutionary advantage leading to selection of those bacterial strains that has protected them from the fungus. Its a simple Red queen hypothesis in action.

   That seems to be explain. But the question is why not make an antibiotic that is absolutely irresistible. To find such a target, it is obvious that the target molecule or structure has to be so conserved that even the slightest change is lethal. That essentially means the organism is trapped from evolving. On one hand evolving resistance is lethal, on the other hand not evolving becomes a target for antibiotic. Think about it for a moment. Such a chemical would be absolutely the golden goose of medicine.

     Mutation as essential as it seems also has a slippery trick in its game. During the course of evolution, if there is an absolutely unchangeable component, they tend to become a conserved sequence. If such a component is of central importance they would be seen across multiple spectra of life. To make an antibiotic against that central component is lethal across the group. If you are to make a chemical that is on a conserved component but not central, a simple evolution will select for the strains without the component since they are accessories. The antibiotic needs to be selective and thus has to attack a component that is distinct enough, which by default means evolvable enough.

  Let me take the example of ATP synthase inhibitor (Link). ATP synthase is a very highly conserved central function enzyme. Mycobacterial ATP synthase can be inhibited by chemical such as bedaquiline. The structure of synthase is different enough from humans (otherwise it would inhibit our ATP synthesis). I said "component is distinct enough, which by default means evolvable enough". The mechanism of action was infact resolved by creating mutants. In other words, even for a chemical as good as attacking the core chemical, resistance was simply possible.

    So that automatically into question where are we going to look for new antibiotics. Of more than any, Penicillin and Streptomyces have probably given us more compounds than anything. Focus has also been on variety of plant extracts which has not yielded much success.

   Let us evoke back the concept of beewolf wasps cultivating Streptomyces bacteria. The core concept is you set a evolutionary race to come up with a better compound everytime resistance sets in. The best candidate that I could think of are normal flora. Normal flora form a part of protection by attacking the invading species. They have an evolutionary requirement to keep up in improved defense. As a proof of concept, I want to cite a article by Valluru etal. The study was able to demonstrate presence of compounds produced by Lactobacillus strains which were better active in acidic conditions.

    It is the view of many that probably over the long run, antibiotics is not an answer. It is also the view, if probiotics can be designed to attack the incoming pathogens it would produce a better outcome, since both have a competing interest. Perhaps in this regard, phages once again seems to be a great answer. 

Perhaps that answers some questions on "Why not a fixed chemical which is a irresistible chemical??"

Dasari, S., Shouri, R., Wudayagiri, R., & Valluru, L. (2014). Antimicrobial activity of Lactobacillus against microbial flora of cervicovaginal infections Asian Pacific Journal of Tropical Disease, 4 (1), 18-24. DOI: 10.1016/S2222-1808(14)60307-8

Thursday, October 09, 2014

Tuberculosis vaccines- Story so far


   As has been argued by me in this blog every now and then, Tuberculosis is one of the major research question of global medical concern. One one hand there is an increasing problem of increasing antibiotic resistance, necessity to come up with new antibiotics and non adherence to treatment, on the other hand there is a great deal of need to come up with a better vaccine. BCG represents one of the finest vaccine in terms of the number of people administered, but also the safety factor. As I have already discussed in one of my earlier post there is a great demand for design of new vaccine approach for TB. Read my previous post here and here. There are many different TB vaccines in literature. Many of them are currently undergoing clinical trials in various phase. It is nearly out of scope of this post to talk about every type out there in R&D. So, I will elaborate on a few that looks promising (but data is awaited).

  The most talked about candidate is modified Vaccinia Ankara virus expressing antigen 85A famously known as MVA85A. The vaccine was developed by researchers at Oxford. The idea behind the development was the understanding that TH1-type cellular immune response probably has good protection correlates. Mycobacterium tuberculosis antigen 85 occurs in different types- 85A, 85B and 85C. Their function is maintenance of cell integrity of the cell wall by catalyzing the transfer of mycolic acids to the cell wall arabinogalactan and synthesis of cord factor (Trehalose dimycolate). The initial work showed promising response in people primed with BCG. The interferon response was good. However, a placebo-controlled phase 2b trial, showed a very poor outcome, with a efficacy of 17·3% which is too less to be useful.

Table 1: Vectored vaccines for TB.
     Several vaccine preparations using the Antigen 85A has been tried without much success. The current interest is focussed on MVA85A-IMX313 (Link). This is a candidate TB vaccine MVA85A with the carrier protein IMX313. IMX313 is a small DNA sequence fused to an antigen gene. This fused antigen is can auto-assemble into a heptamer, which is more readily identified by the immune system.

Table 2: Recombinant vaccines for TB
   Recombinant vaccines have also attracted wide attention. The widely talked about include rBCG DureC:Hly, rBCG30 and Aeras-422. rBCG DureC:Hly or more commonly known as VPM 1002, is a BCG Danish, subtype Praguen that expresses membrane-perforating listeriolysin (hly) of Listeria monocytogenes and is devoid of urease C (ΔureC hly+ BCG). The vaccine is thought to provide a balanced Th1-Th17 cytokine levels.

Table 3: Sub-unit vaccines
    The next group of vaccines include subunit vaccines. Several different proteins have been found to be important and attempts are made to create conjugates with carrier molecules for a potential candidate vaccine. Table 3 is a list of pursued vaccines in this category. Most of the listed vaccines are in phase 1 or 2 trial and intended to be used as booster vaccine.

     There are many other potential candidates that I could think of. Each with a slightly different combination and approach. The question that commonly arises is how about the modern technology of DNA vaccines. Of course that also has been tried. Some well known examples include- Ag85-Flt3 DNA; rBCG-Flt3, CFP-10 DNA, HSP65 and IL-12 HVJ-liposome, Six-gene cocktail and IL-12 etc.

     Another vaccine that is gaining popularity as a therapeutic vaccine is Ruti. It consists of detoxified liposomal fragments of Mycobacterium tuberculosis now being developed by the biotech company Archivel Farma. The vaccine induces long-term memory T-cell responses to multiple TB antigens with good tolerance. Currently Phase III is planned.

    So many vaccines in pipeline?? Why haven't we been able to develop a vaccine? The answer is the current vaccine design approach for TB at least, is a trial and error approach. There is virtually no data on the possible correlates of immune protection. That makes the development process still harder. Moreover, the current research is directed towards developing a booster or secondary vaccine which can support BCG, not a replacement. Oh yes, we need to know a lot more of TB biology if we want to start search all over again. So, the story so far is that, new vaccines are on scene, but none has reached the finished line yet...
McShane H, Pathan AA, Sander CR, Keating SM, Gilbert SC, Huygen K, Fletcher HA, & Hill AV (2004). Recombinant modified vaccinia virus Ankara expressing antigen 85A boosts BCG-primed and naturally acquired antimycobacterial immunity in humans. Nature medicine, 10 (11), 1240-4 PMID: 15502839

Desel C, Dorhoi A, Bandermann S, Grode L, Eisele B, & Kaufmann SH (2011). Recombinant BCG ΔureC hly+ induces superior protection over parental BCG by stimulating a balanced combination of type 1 and type 17 cytokine responses. The Journal of infectious diseases, 204 (10), 1573-84 PMID: 21933877

Hoft DF, Blazevic A, Abate G, Hanekom WA, Kaplan G, Soler JH, Weichold F, Geiter L, Sadoff JC, & Horwitz MA (2008). A new recombinant bacille Calmette-Guérin vaccine safely induces significantly enhanced tuberculosis-specific immunity in human volunteers. The Journal of infectious diseases, 198 (10), 1491-501 PMID: 18808333

Ly, L., & McMurray, D. (2008). Tuberculosis: vaccines in the pipeline Expert Review of Vaccines, 7 (5), 635-650 DOI: 10.1586/14760584.7.5.635

Nobel Awards 2014


Photo 1: Nobel medal. Wikipedia
Nobel prize is a recognition, given for excellence in a field of work. Here is a list of people who are recognized for their work in science research under different categories. The award is now almost universally accepted as a recognition of finest of work, though it is questioned and disputed by some.

     The birth story of Nobel award is based on the wish of Alfred Bernhard Nobel, a Swedish chemist, engineer, innovator, and armaments manufacturer. Perhaps his most famous invention is the dynamite. The recipients of the award is chosen by the Nobel foundation constituted by Nobel committee of Royal Swedish Academy of Sciences, Nobel committee of Karolinska Institutet and Norwegian Nobel Committee. The award consists of a citation, gold medal and money. However, the fame is considered far superior for the award.

Here is the list of recipients recognized for the award

The details can be found in the following links

1. http://www.nature.com/news/nobel-for-blue-led-that-revolutionized-lighting-1.16092
2. http://www.nature.com/news/nobel-for-microscopy-that-reveals-inner-world-of-cells-1.16097
3. http://www.nature.com/news/nobel-prize-for-decoding-brain-s-sense-of-place-1.16093
4. http://www.telegraph.co.uk/news/worldnews/11148871/Nobel-Prize-winners-in-peace-literature-physics-chemistry-economics-mapped-gender.html