A big picture of Ebola Transmission during 2013-2016 outbreak can stop future outbreaks


Days since last case of Ebola at Guinea, Sierra Leone and Liberia (Courtesy: CDC)

A globalized effort by international team of scientists, clinicians, non-governmental organizations, drug companies and many more to eradicate Ebola that shook with vast West African epidemic was brought down in 2016. A review article co-authored with Dr. Aftab Ahmad and Mr. Sagar Aryal, we tried to depict about the Ebola Outbreak situation including the controversies and solutions. What was the situation of Ebola at the end of 2016? At Biomysteries you can follow the post “Where is Ebola now? 2016 update” to find the concluding situation of Ebola.

A recent research that published in the journal Nature on 12th April 2016, international group of scientists analyzed the entire database of Ebola virus genomes for 2013 to 2016 West African Epidemic. The analysis revealed about the epidemic unfolded in small overlapping outbreaks and spread by infected travelers incite new outbreak elsewhere, this is how the transmission chain continued. But in each case it represented a missed opportunity to break that chain of transmission to make the epidemic end sooner.

In West African Ebola outbreak caused massive transmission affecting nearly 28,000 people and killing 11,000 of them. The database revealed 1,610 Ebola virus genomes have more than 5 percent of known cases – this is the largest sample analyzed for human epidemic. Pushing back the previous analysis that was focused on only single country, this research was based on three primary countries – Guinea, Sierra Leone and Liberia that were more affected by Ebola.

Another hold or importance of the paper was the united collaboration from 86 scientists from 60 different institutions from 18 different countries authored this paper. Authors’ intention was to provide a complete framework for predicting future outbreak for Ebola Virus or other similar viral spread.

[youtube https://www.youtube.com/watch?v=j4Ut4krp8GQ&w=612&h=344%5D

Please find the video above here showing three countries (Guinea in green, Sierra Leone in Blue and Liberia in red) that were mostly affected in Ebola 2013-2016 epidemic. The differential shading defines weekly incidence rates of Ebola Virus disease. In association to that the evolutionary tree on right shows the relationships between sampled Ebola lineages.

Journal Source:

Dudas G, Carvalho L, Bedford T, Tatem A, Baele G, Faria N et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017; doi:10.1038/nature22040

Further Reading:

Sarkar S. Where is Ebola now? 2016 update. Biomysteries https://biomysteries.wordpress.com/2016/07/08/where-is-ebola-now-2016-update/

Sarkar S, Aryal S, Ahmed A. The Ebola Outbreak – Controversies and Solutions 2014-15. International Journal of Microbiology and Allied Sciences. 2015; 1(4):10-17 (Link)

Posted in Bioinformatics Tools, Molecular Biology and Genetics, Uncategorized, Virology | Tagged , , , , , | Leave a comment

MiTalk Episode 4: Basics of Hepatitis C Virology

episode-4-hcvHepatitis is caused by the inflammation of the liver. The condition may also progress to cirrhosis or fibrosis and/or even liver cancer. Hepatitis is caused by an infection of virus, but apart from this causative agent toxic substances like alcohol or certain drugs and autoimmune diseases can also cause this disease.

There are five different classes of hepatitis virus – A, B, C, D and E. In this episode of Microbiology Talk (MiTalk) we discussed about Hepatitis virus C, especially covering the following topics:

  1. Classification of Hepatitis virus and Structure of Hepatitis C Virus
  • Classification or Types (A, B, C, D and E)
  • Structure and Genome of Virus
  1. Genotypes and Epidemiology statistics
  • Genotypes
  • Epidemiology
  • World, USA, South-East Asia, India, Nepal
  1. Pathogenesis and Life cycle
  • Mechanism of transmission
  • Cellular entry and replication mechanism
  • Viral evasion and restriction factors
  1. Laboratory diagnosis, prevention and treatment of Hepatitis C

So plug in your headphone and listen to Episode 4 of MiTalk. (Visit Here/Download Here)

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Mesentery – The New Organ can now change the history of Human Anatomy

Although the scientific research is advancing in recent times there are many things which still remained unexplored. In biomysteries lets me introduce you to a new organ that remained unexplored. Researchers from Ireland identified a part of our digestive tract, that was long considered to be a mere tissue is actually a full grown organ that connects abdomen to intestine. This new organ has shook the medical fields researchers to look into new understanding about bowel disease and other gut diseases.


Digital representation of peritoneum, mesentery, fascia, and intestine (Image: The Lancet, Prof. Calvin Coffey)

The new organ is named Mesentery which was long been known but never considered to be an organ. It has a complex and fragmented appearance. The anatomic description of mesocolon dates back in 1885 when Sir Frederick Treves studied human mesentery on 100cadavers. But until recently from a study carried out from University of Limeric has concluded Mesentery as a full grown organ.

Professor J. Calvin Coffey who is the professor of Surgery explained how 100years of anatomical understanding was incorrect. Some of the recent text books now need to be updated as the number of organs in our body has officially changed into 79. Although re-classification would not affect directly but will provide a clear picture of many unknown facts of bowel diseases.

Journal Source:

Coffey JC, O’Leary DP. The Mesentery: structure, function and role in disease. The Lancet (2016) 1(3):238-247. DOI: http://dx.doi.org/10.1016/S2468-1253(16)30026-7%20

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Older than “Oldest Water Found” in Canada – Unfolds mystery about Life on Earth

“Where there is life there is hope” – it has been an important quote we use to deliver anything significant about “hope”. Similarly a biological mystery was brought near at Canada where scientists had came for the oldest water, has given much more insights about even older deposits.

Back in 2013, a research team which was led by scientists from University of Toronto found water that was about a billion years of old from depth of 2.4 Km at Timmins mine. But the research findings from much beyond 2.4 Kms have insights of water which is about 2billion years older.


Dr. Barbara Sherwood Lollar (Image: Sherwood Lollar Research Group)

In an interview with BBC News Dr. Barbara Sherwood Lollar who led this investigation said, “When people think about this water they assume it must be some tiny amount of water trapped within the rock. But in fact it’s very much bubbling right up out at you. These things are flowing at rates of litres per minute – the volume of the water is much larger than anyone anticipated.”


This new investigation was carried out at a depth of about 3Km.

The research holds its importance to unfold the unique insight about the history of Earth and the origin of life. The chemical traces left behind by microbes that once lived in historic era can also unveil many mysteries.

“By looking at the sulphate in the water, we were able to see a fingerprint that’s indicative of the presence of life,” said Prof Lollar.

Apart from this amazing discovery, such important findings of watery sites on Earth can provide clues about life which might present elsewhere within the Solar System.

Read More:

World’s oldest water gets even older. BBC News. http://www.bbc.com/news/science-environment-38311781

Two-billion-year-old water found in Canada. The Weather Network. https://www.theweathernetwork.com/news/articles/two-billion-year-old-water-found-in-canada/77056/


Posted in Marine Microbiology, Molecular Biology and Genetics, Space Microbes | Tagged , | Leave a comment

Wondered why some pink stuff growing in bathroom?


You probably have freaked out sometimes by seeing the mysterious pink streaks on toilet walls or bathtubs. But have you wondered what these are? In Biological Mysteries this is also a big question but with simple answer.

The answer is obviously a tiny microbe that loves to grow on wet surfaces. The bacterial biofilm is harmless unless you are immunocompromised (poor health). They dwell mostly in the presence of phosphorous or fatty acid like toilet soaps. If you inspect they do not grow well in summer season or during hot weather.

About the tiny stuff

The bacterium is Serratia marcescens and can grow between 5 to 40ºC which is quite wide. This is the same reason that they can grow everywhere. It prefers pH between 5 to 9, which is much significant as they prefer soapy waters. If you quickly wiki about this gram negative bacterium that will more freak you out as they are one of the known contenders for Hospital Acquired Infections. But in true sense that can only happen if you are immunocompromised and have increased risk if it reaches sterile parts of the body like lungs, brain or blood.

Behind these bacteria there lies a surprising story of its identification. Sometime in 1819, one Italian resident was frightened about the bloody pollen in humid summer. The family refused to stay at home as they were feared if it was caused by some evil spirits. Later several investigations have proved this to be bacteria that are enjoying their slimy bath.

Apart from the threat of nosocomial infection, it has proved to have anti-cancer property in the red pigment (called prodigiosin) but lots more still to be investigated.

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Yoshinori Ohsumi wins Nobel Prize 2016 in medicine for his work on Autophagy

Video Courtesy: DW News

Today is the day to draw red ring in the calendar. The Nobel Prize for 2016 in Medicine has been announced and has been awarded to 71years old, Dr. Yoshinori Ohsumi for his discoveries on how cells detoxify and can repair themselves. Flipping back sometime in June this year the Japanese scientist has also been awarded with 2016 Paul Janssen Award.

The Japanese Cell Biologist received prestigious 8m Swedish Kronor (61,000,000 INR approximately) for unveiling the mechanism of autophagy.

yoshinori-ohsumi-credit-titech-30w1t2nsey2wrdrqcgoxkwAutophagy is a recycling programme of cells where scrap cells are targeted down and the useful parts are taken out to be used for new cellular components. This is a general process that occurs regularly to maintain a healthy metabolism and preventing from conditions like cancer and diabetes. Apart from that dysfunction of Autophagy has also been reported in Parkinson’s disease and other age related disorders. Several researches are still underway to find potential drug targets in various autophagy related disorders.

It was much difficult for Dr. Ohsumi to understand this phenomenon with lack of sophisticated techniques that are now available. In his study in yeast cells, he identified the genes involved in such process and also shown how these genes code for proteins that come together to form autophagosome membrane. He later also proved the similar phenomenon in human cells and our cell could not survive without this autophagy.

In an interview in Tokyo with reporters Ohsumi said, “As a boy, the Nobel Prize was a dream, but after starting my research, it was out of my picture.” (Courtesy: Guardian)

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Pathogenetics behind RASopathies

RASopathies are group of genetic syndromes cased due to mutation in genes (somatic) in RAS/MAPK pathway. The possible syndromes include Neurofibromatosis type 1 (NF1), Legius syndrome, Noonan syndrome (NS), Costello syndrome, autosomal dominant intellectual disability type five and many others. Commonly the RASopathoes represent developmental malformation syndrome. This article represents the short note about RASopathies and the pathogenetics behind.

RAS/MAPK Pathway


RAS/MAPK pathway plays a pivotal role in cancer as well as in development. Genetic mutation in any of the pathway molecule may lead to different RASopathies as discussed above. Ras proteins are guanosine nucleotide-bound GTPases which is activated through multiple mechanisms including growth factors binding to receptor tyrosine kinases (RTK). This binding promotes RTK to auto-phosphorylation and interaction with growth factor receptor-bound protein 2 (GRB2). GRB2 then binds to son of sevenless (SOS) that is recruited to plasma membrane.

SOS is a guanosine nucleotide exchange factors (GEFs) that increase Ras’s GDP exchange rate for GTP. The activated Ras then lead to the activation of Raf (ARAF, BRAF and CRAF). Then a serious of phosphorylated events takes place for MEK and ERK. Finally the ERK1 and ERK2 are the ultimate effectors which functions to modulate downstream molecules.

Pathogenetics in Rasopathies

Ras signals to multiple intracellular pathways and the central pathogenetic denominator for Rasopathies is RAS/MAPK pathway activation. As mentioned before each mutations within this pathay leads to different Rasopathies as the distinct mutations affect the fundamental molecular mechanism of the pathway.

Table: Functional Characterization of genes associated with RASopathies (Follow Reference)


Ras effecter pathways are down regulated or up regulated or sudden aberration due to different mutations generated within the pathway. Functional studies have generated enhanced pathway signalling due to the majority of mutations. Each Rasopathy is unrelated or unique. Upstream of Ras mutation causes aberrant Ras activation like mutation in PTPN11 and RasGAP; whereas downstream mutation of Ras may reflect intolerance for such mutations in development. It is important to decipher the function or aberration caused by the mutations to understand pathogenetic etiology.


Tidylman WE, Rauen KA (2016) Pathogenetics of the RASopathies. Human Molecular Genetics. July 12, 2016.

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Ancient Civilization of Microbes who built ‘Lost City’, Not Greeks


The formations resembling Greek ruins

Zykanthos is a Greek island in Ionian Sea and there are many stories about this lost city. It is the time when snorkelers discovered the ancient stonework and excavations in the bay off to this Greek island and government archaeologist began to investigate. The debris found might be the ruins of the city and a rare discovery in the shallow waters.

Now plucking the odd things out, archaeologists did not found shards of pottery or other valuable remnants for everyday’s existence. This would suggest that people might once have lived here and perhaps need to move away to survive, fleeing from rising water levels of sea.

After such long thoughts about the habitat, scientists finally navigated the clue. The columns and other objects found are not at all stonework but rather are the natural byproduct of breakdown methane gas. So those are ancient microbes who made it not people.

The research was published in the journal Marine and Petroleum Geology which led by the lead author Julian Andrews from University of East Anglia, England mentioned it as “cold seep” where methane in deep formations moved upward and then added sediments over sea bed. Those sediments are used by bacteria that use methane as their source of energy.

All the consumption of methane changed the chemistry of the water that lead to the saturation of sediments. The minerals precipitated and formed as rock dolomite. These dolomites cemented the sedimented particles at places forming concretions.

These concretions might have formed millions of years ago as the researchers suggested. The wonderful mystery lead by microbes are now solved which was previously misleaded.

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Say hello to Microbes! MiTalk the Radio Show

Now it is from reading to listening. A leap ahead in science communication from writing about Microbiology and now speaking about Microbiology too. It was already under future objectives of We The Microbiologist forum. Our group was under discussion about how to team up and go ahead with such an oriented Radio Show about Microbes. But finally it hit the success. The show is named MiTalk or Microbiology Talk and can be reached at www.microbiologytalk.com


It was Mr. Varun Chakrakodi who is an active science blogger from Medical Microbiology looked at the objectives listed at WTM and contacted me. I was glad to know that I was not the only person who was thinking to launch such Podcast. Soon then we team up with Dr. Sridhar Rao, Assistant Professor in Microbiology from JJM Medical College, Karnataka, India and Mr. Sagar Aryal from Kathmandu Nepal.

Dr. Rao is the mentor of this show management and also a co-host of this show. He is well known about his medical microbiology notes he shares over his own website which is filled with wonderful knowledge database for students. Mr. Sagar Aryal was approached to be the co-host of MiTalk while we were discussing over this podcast. He has been an obvious person who can lead with the knowledge he bears about Microbiology. Mr. Aryal is well known for his notes he shares through his website and only Microbe active science communicator from Nepal.

So here is the team:

  • Mr. Varun C.N. – who is the chief-host of MiTalk and associates in recording and managing the shows with notes. He is also co-editor of the content in website.
  • Dr. Sridhar Rao – co-host and mentor of MiTalk. He guides the whole system.
  • Mr. Sagar Aryal – co-host and associates in web management. He is the chief-editor of the website and content.
  • Mr. Saumyadip Sarkar – co-host and manage the recording. I audit the recording and also communicate Scientists who can be the part of this show.

There are so much to explain about Microbiology and it can be well placed while we discuss over some mysteries which is solved, debatable or still under mystery. We try to pull those topics which is important to talk and can be communicated with general audience. It is open access and can be accessible through iTunes . So you can plug in your headphones and you can listen to MiTalk even though you are traveling.

It was published on 4th of September 2016 as the first Microbiology Radio Podcast from South-Asia. I feel many of the science lovers listen to many Microbiology Podcast but this might be little different why? Here are some reasons:

  1. General to Hard Core Science: Here we talk about general topics and even pull in research papers. So if you are a student and wish to explore more about Microbiology then you can easily understand and also make notes if needed. Researchers too can have the complete overview about the topic including research notes which are vital.
  2. Join the Show: It is much enthusiastic to know that Scientists can join for a talk in one of our show either voluntarily or even we try to contact to share his/her views over his own research field.
  3. Science apart from Microbiology: It is not just Microbiology but at the end of the show we often conclude with “Science aside Microbiology” which can be important and fun.
  4. Comments and Answers: What you suggest, comment or add is important. It is obvious you may wish to add some point about the show, add some comments, email us with possible topics, or anything about Microbiology. If it is worth sharing or could be discussed we will refer your name in the show.

You are very much welcome for Microbiology Talk. Please listen to the shows which is released twice in a month. Subscribe to get regular updates and mail us your views.


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I support open access research! But why?


It has been a long debate between open access and restricted access of research. So what is open access? Simply it is free from all restrictions of copyright and licence. We often find some of the conference papers, research articles, book chapters, etc are not freely accessible and one has to pay some amount to get the full access. On the other side there are organizations who publish research opening gates of full access of all the materials. So here are important notes about why open access research is vital.

Students prospective

Students keep on looking things and search articles over internet. It is obvious that they cannot pay such hurdles to complete their school or college assignments. Open access research can expand the information which is more relevant than in restricted access which will provide just an outlook of the content. Internet is the source of education and hence pupils use the resources to go through research papers. Even to cite them you need the full access of the paper so that you can read the content.

Scientists or Researchers’ prospective

This is under the highest category. Researchers keep on searching things that is vital for their experiments. A small hint can sculpture the whole hypothesis. So it is important to read the whole matter of the content than just the overview. No researchers wish to deduce amounts from their funds to perform study. It also pours an important effect to avoid duplication of research.

Science communicators’ acts as a bridge that communicates different readers providing the importance of research materials that is full of scientific terms into simple understandable formats. Research is useless if it is not shared. So, open access research is probable of fetching more citations than restricted access which is much overlooked.

Experimental protocols also seem to be important and for different research the protocols are modified according to the type of samples or conditions they study. It is a hurdle too if there is a barrier. Most protocols cannot be standardised and require help for such protocols. So open access breaks this barrier and also helps researchers gain citation.

Why are there restricted accesses?

erik12_1383873905Restricted access is important too. Some of the confidential datasets cannot welcome public to impose threats. It is like a home with uninvited guests. But if you provide greetings to some people whom you know is better from any threat.

On publishers point of view both for profit or non-profit, by some it is mostly observed that they shuffle between open access and restricted access. So it is a kind of strategic business to run a journal.

Many researches can also be a part of social threat. Many formulas which should be enclosed to improvement of living can be used by terrorists in the negative shades. Confidential barrier allows people to know who actually wants the access of the research.


In conclusion, it is good to add that still in my personal motif I support open access research and it is very important for development of scientific research. It fetches a lot of solutions and exposure of scientific activity required nowadays. Confidential barrier is important too, for avoiding unwanted situations. Scientific research data is an asset and hence protecting it is also a duty.

Let me know what you think about open access and restricted access in the comment box. I will try to reply most of you. Do not forget to vote 🙂

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