Scientists Simplifying Science

Monthly archive

January 2018

Envisagenics: Splicing with a twist!

in Entrepreneurship/Face à Face/Medness by

Innovation is a necessity for us scientists. We are encouraged to discover, invent, identify a plethora of things. Whether we hunt antibacterial compounds or work on technologies that will revolutionize gene synthesis our product is eventually innovation. We thrive on it. It is what unites us, and makes each one of us unique at the same time. Some of us take our innovation to the next level and transform it into medicine, platform, or service. Here is a two-part series discussing one scientist’s maiden venture and his journey from being a trained biologist to a bioinformatician to an entrepreneur.

In conversation with Dr. Martin Akerman

Would you like to briefly introduce yourself to our readers?

I am the co-founder and CTO of Envisagenics, originally from Argentina. During my Masters, I studied a parasitic protozoan, Leishmania, after which I got my doctorate in Bioinformatics at Technion, Israel. Then I moved to Cold Spring Harbor Laboratory (CSHL) to do my postdoc on splicing under the mentorship of Dr. Adrian R. Krainer and Dr. Michael Q. Zhang.

Tell us about your journey from being a graduate student in Israel to being a postdoc at CSHL.

As a Masters student, I was studying Kala Azar, a type of Leishmaniasis. Something happened, and I moved from being a bench scientist to computational biology. This was 2002, and there wasn’t a lot of Bioinformatics around. Hence, catching up was doable. There weren’t 100 different programming languages like today. It was mostly PERL, C++. I liked this work so much that I chose to do my Ph.D. in Bioinformatics.

When I chose my Ph.D. topic, I was very fascinated with the human genome because it was brand new. During my undergraduate days, I was taught that the human genome had 150,000 genes, and this justified the complexity of humans. However, it turned out that there are ‘only’ 20,000 genes. This revelation shocked the whole field and raised new questions, tickling my fascination like many others. I soon wanted to investigate how is it possible to have such a small number of genes and still be a complex and functional organism. Splicing seemed to be a probable answer. That’s when I made a software to study splicing regulation.

If you don’t know what splicing is, here is video for you

 

[Sorry to interrupt, but did you know programming at the time?]

No, I did not know programming; I’m self-taught. It took me a little over 2 years to learn. I mean, you never stop learning! It is impossible to score with a moving post you know. Programming is a huge part of learning bioinformatics. So I did it, and I loved it.

That is very impressive. Please continue….

So, making the SF map (Splicing Factor Motif Analysis and Prediction, published in Akerman M., 2009) software only made me more interested in splicing. I came to CSHL to continue working on splicing with two eminent scientists who were leaders in this field, Dr. Adrian R. Krainer, and Dr. Michael Q. Zhang. While the Kranier lab was primarily a biochemistry lab, the Zhang lab focused on splicing using genomic data.

What inspired you to start Envisagenics from being a postdoc?

There was something special about the Kranier lab! I was the primary bioinformatician in a lab of 20 experimental biologists. What does it imply?  Well, anything I predicted was validated experimentally. While this created a lot of pressure, it was an incredible opportunity to collaborate  and stay connected to biology.

People sought my expertise to analyze their data in various ways. I analyzed RNA-seq data, protein-protein interactions, and RNA-protein interactions in the spliceosome. I soon became addicted to the feeling of having your predictions validated in the lab. At some point, I realized that solving other’s problems was more exciting than answering questions that I came up with. I also realized that the only way to address this addiction of mine was to make a software that works and solves ‘real’ problems. The answer was in starting a company.

Did you ever want a career in academia?

Of course, I did! As a postdoc, I wanted to become a professor until I realized that I don’t. In academia I would have to move from developing one algorithm at a time, which did not allow time to focus on creating a robust piece of software available for a larger audience.

What was the turning point for your transition?

When I wanted to start a company,  I had no idea what it meant. I met some investors at the “Elevator Pitch Day” organized by the Bioenterprise Club at Cold Spring Harbor. The Bioenterprise club focuses on careers outside academia. The investors I met that day were part of the panel that listened to my first ever elevator pitch. I met my co-founder, Maria Luisa Pineda  on the same day. She was in the room working with the investors, and her job was to evaluate me. Long story short, as a result of that meeting, we started the company. She is also a trained biologist from CSHL who after graduating acquired investment experience in technology and life-sciences startup companies.

What does a typical day look like for you at work?

Well, every day is different. I coordinate with the engineering team about the technical work. We work on pilot projects and milestones with scientists in pharma company. Right now we are also spending time on how to use our latest funds; this includes planning with the Business Development team. Some grant writing is pending regarding a phase II SBIR grant. I also do coding- this is my quality time.

In short, I am involved in almost everything, which is great as I enjoy working a lot with my team.

What are the skills that help you run Envisagenics?

My knack for collaboration that I developed from my postdoc days at CSHL helps me a lot. Understanding other’s problems and using our platform in solving them is beneficial to us. Both of these support our partnerships at Pharmaceuticals.

The ability to be a team player is a considerable skill. As a leader one should also know how to distribute and delegate work, be humble, and have the ability to take and give advice from/ to your team.

Being open to taking advice from advisors and investors is a must. You are toned to listen and learn. The most essential skill is, however, to resist, be positive, and never give up.

Speaking of being a leader, do you micromanage?

No, I don’t like that. If you have to micromanage, it is not a good sign. I want people to bloom and use their creativity to see what they can do. At Envisagenics, there’s a time when we meet, and everybody brings ideas. Next, we execute the plan. You cannot deviate from the plan, because we are all connected. Everyone has ONE goal, not separate projects. So it is crucial that we plan together and stick to it. That’s what makes us a great team. However, as a leader, YOU have to make informed decisions.

Coincidence brought Martin Akerman and Maria Luisa Pineda together, and as they say, the rest is history! Keep watching this space for part 2 in this series that will discuss the challenges faced by Dr. Akerman in his transition and his visions for Envisagenics.

 

Author: Dolonchapa Chakraborty

 

Dolon is a Molecular Biologist and currently wears many hats. She freelances as a Consultant for a Toronto-based start-up, helping them with brand management, marketing, and product development. She is also an Adjunct Faculty at Mercy College in the Biology department. She blogs about various topics pertaining to Biotech and PhD in Biotech.

 

 

 

Editors: Rituparna Chakrabarti and Sayantan Chakraborty

 

 

 

 

 

 

Blog design: Rituparna Chakrabarti

Cover image: Kindly provided by ENVISAGENICS, used with permision from Dr. Martin Akerman


The contents of Club SciWri are the copyright of PhD Career Support Group for STEM PhDs (A US Non-Profit 501(c)3, PhDCSG is an initiative of the alumni of the Indian Institute of Science, Bangalore. The primary aim of this group is to build a NETWORK among scientists, engineers and entrepreneurs).

This work by Club SciWri is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License


Dealing with an epidemic

in Reporting from the Lab by

The year 2017 challenged the society with a ‘national emergency’ that led to over 60,000 deaths. Some called it an epidemic – a public health crisis – a war against drugs.  As the struggle to deal with the overwhelming opioid crisis continues, many significant steps are being taken by scientists and healthcare professionals to develop a robust arsenal to help tackle this crisis.

A recent article published in the Journal of Medicinal Chemistry describes the development of an opioid vaccine that produces antibodies against heroin, its metabolites and other commonly misused narcotics such as hydrocodone, codeine, oxymorphone, hydromorphone and oxycodone. The vaccine consists of an opioid conjugated to a larger protein carrier delivered in a liposome-based adjuvant. The antibodies produced in response to immunization with the vaccine successfully sequestered opioids in the blood preventing their penetration across the blood-brain barrier and their subsequent binding to the brain opioid receptors. More importantly, the antibodies did not interfere with current opioid management therapy including methodone, buprenorphine and naloxone.

The vaccine was tested in mice and rats for titers, potency and efficacy. Different doses of heroin ranging from 0.5mg/kg to 50mg/kg body weight were tested via either subcutaneous or intravenous routes, which mimic modes of administration for drug abuse in humans. Based on these analyses, the vaccine generated antibodies that were durable and effective in mitigating the biological effects of opioids even at lethal doses.

Current opioid management involves the use of drugs such as methodone and buprenorphine that are synthetic opiate derivatives. They too, like heroin, bind to opioid receptors, and engender analgesic and euphoric effects. However, due to their longer half-lives (time taken by the body to clear 50% of drug is longer than heroin), the potential for dependency, overdose and abuse, although not exempt, is mitigated. On the other hand, Vivitrol by Alkermes pharmaceuticals is an opioid antagonist that can block opioid receptors from binding to opioids, thereby preventing relapse. Such interventions are currently being tested in combination with novel approaches such as digital therapeutics wherein reSET-O, an app developed by Pear Therapeutics has shown to improve abstinence and program compliance.

This paper provides a unique immunologic approach to combat opioid dependence. These studies overcome some of the previous challenges encountered with the development of opioid-based vaccines namely stable activity against heroin and its metabolites, and broad spectrum utility to remain effective even against other commonly used narcotics. As the vaccine is not effective against fentanyl, tramadone, sufentanil, nalbuphine and other non-narcotics such as aspirin, ibuprofen and acetaminophen, such drugs can be administered in vaccinated patients for pain management. However, investigation on the utility of the vaccine in humans and synergistic studies with other existing opioid management therapies are warranted.

Journal article:

A stable heroin analogue that can serve as a vaccine hapten to induce antibodies that block the effects of heroin and its metabolites in rodents and that cross-react immunologically with related drugs of abuse. Sulima A et al. Journal of Medicinal Chemistry, Dec 2017

Featured image source : Pixabay

About the author:

Radhika Raheja completed her PhD from Cornell University and is currently a Postdoctoral fellow at the Brigham and Women’s Hospital. Her research interests have centered around oncology and neuroimmunology. Among other things, she is striving to effectively communicate scientific discoveries to the community.

 

Edited by: Shreyas Jadhav, PhD

2018-The year of glass half full

in That Makes Sense by

I am not a TIME fan in any sense. However, the last issue of TIME caught my attention. The cover story was named “The Optimist,” edited by Warren Buffet, Bill Gates, Malala Yousafzai and other prominent leaders of the world. Their editorial discussed the positive changes the world is seeing despite all the negativity which surround us today.

The issue begins with a cover story of six children in Ethiopia who just celebrated their fifth birthday when compared to 30 years ago when 1 in 5 children did not survive to see this world. Malala Yousafzai narrated how Malala fund is helping to recruit female teachers in Afghanistan to work in rural schools. How in Nigeria, it helps run mentorship club to help girl resist family pressure to drop out from schools or early marriage. In Lebanon, they are developing e-learning programs to teach STEM skills to Syrian refugee girls. Budd Haeberlein from Biogen showed her optimism about finding a cure for Alzheimer’s in the near future. Bill Gates talked about his foundation’s effort to bring the death rate from 12 million a year in the 1990s to 5 million a year in 2017, and the goal is to bring this to half by 2030. If you want to help several such initiatives please go ahead and donate to UNICEF.

In the same issue, there is a column dedicated to Dr. Mathew Varghese of Delhi’s St. Stephens Hospital near Tis Hazari. Dr. Varghese, an orthopedic surgeon by training, has spent a significant part of his career going from house to house in Northern India trying to study the victims of the Polio in their social context. India has practically eradicated Polio with the number of cases reported being zero since 2011. An article in Guardian dedicated to Dr. Varghese describes him as “India’s polio pioneer works to put himself out of a job”. Dr. Varghese now runs an organization in nearly 29 states which teach medical students to understand the social context of the patients concerning the disease.

In CSG too, we got to know the incredible story of Govinda Upadhyay of LED Safari,
thanks to #CSGInsta, who dropped out of his Ph.D. to work on his startup to solve an unmet need in India-electricity. Washington Post revealed that 1.3 billion people in India remain without power. The government relies on fossil fuel to meet the energy demand which means a nearly three-fold increase in the greenhouse emission by 2030. What Upadhyay realized was that the problem was not with the limited resources but the knowledge or training to repair electrical equipment in this part of the world. He came up with a solar kit to teach kids how to use solar energy to create electricity using basic training modules. He has taken his ideas now to other African countries like Tanzania and Kenya where children can learn about solar energy and technology. The reason I liked Upadhyay’s story was it somehow is in tune with CSG’s core mission albeit looking at a different problem. We believe there are so many of us who have an inherent talent to make a mark in the world or contribute positively in their unique way and what prevents many from reaching that stage is “awareness and education”. It’s not the formal education it is more than that. If we empower this massive chunk of human resource who are disillusioned about how their education and training fits in the rapidly evolving job market, we can create several such leaders as Upadhyay (at least that is our hope).

In an article from the recently published December issue of New Yorker, Richard Haas, an American diplomat was quoted, referring to the fact that the world is entering an era without obvious leadership. However, to me, I think the new world is exploding with leaders who have been inspired to solve some of the most challenging questions of our times, and we don’t necessarily have to wait for political leaders to take in charge of our fate. As long as there are men and women who are aware of the problems that surround us and finds out a way to solve them howsoever small the problem may be and howsoever small a community the solution helps, our future in this planet looks bright.

PS: If you know people who are making small impacts in the world, let us know their story. Write to me at ananda1979@gmail.com

References:
http://time.com/5086870/bill-gates-guest-editor-time/

https://www.theguardian.com/global-development/2013/jun/21/india-polio-pioneer

https://goo.gl/7wRDi2 (Washington Post)

Photograph Courtesy:

(Wikimedia Commons) https://goo.gl/WYWrBp

Children at a vaccinations clinic near Sululta, Ethiopia, May 2012

Edited by : Mahamaya Bhattacharyya

Attribution: Yasmin Abubeker/DFID

Obsession & Opinions Cover Image: Manasi Pethe, Ph.D.  San Diego

The contents of Club SciWri are the copyright of PhD Career Support Group for STEM PhDs (A US Non-Profit 501(c)3, PhDCSG is an initiative of the alumni of the Indian Institute of Science, Bangalore. The primary aim of this group is to build a NETWORK among scientists, engineers and entrepreneurs).

This work by Club SciWri is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

CSG’s Data Science Venture: A new beginning

in ClubSciWri/Data Science by

Data generation and analysis is not a new concept. While high throughput scientific data has been generated by the likes of genome sequencers and the Large Hadron Collider, large swathes of commercial data has been generated by Amazon, Netflix, Google and social media platforms. Thinking in a more organized manner, every aspect of life, be it mechanics, biology, social media or weather, all generate data. Analyzing this data gives rise to meaningful trends and patterns, which can be used to ask questions that would reveal logical answers to various different aspects of life. For example, can we predict the next big disease outbreak using patient data from hospitals, so healthcare organizations can be better prepared to handle the outbreak; combine domain specific knowledge from modern medicine to build models that suggest what type of treatments will work for a given disease. In other words, by analyzing data, we can make better decisions and efficiently allocate resources to tackle existing problems.

Many trillions of gigabytes of data is generated everyday. It is estimated that by 2018 we will be generating about 50,000GB/second. GIS images, preferences on shopping, movies and shows on television networks, GPS based trends, social media behavior, photos and videos acquired by smartphones all contribute to very simple forms of data that is generated and stored by companies. Another example is healthcare, where patient metrics have been collected over a century, in the form of qualitative observations, images and numbers. Meaningful trends can be identified from this data by using predictive models and visualization tools.  In order to identify trends and build these models,  appropriate questions need to be asked of a data set.

With a growing trend in data analysis, there is an increasing demand for people who can perform such analyses. Scientists, by virtue of their training, are required to frame questions as the starting point of any project. They work to find answers to their questions by designing experiments, building numerical or analytical models and sometimes combining all three methods.  Since these people know how to extract useful information from a bunch of messy, unclean data, they are fast becoming the lifeline of data science. A number of scientists are self-teaching themselves at least one relevant coding language and are playing around with open-source biological and other data sets.

It is important that scientists who wish to train themselves for this relatively new profession benefit not only from a plethora of resources available online but also from appropriate interactions with the data science community. The purpose being not to feel lost in the huge online community that already exists, but to receive relevant pointers to resources and networking. The PhDCSG group has been especially instrumental in providing professional development guidance and resources to scientists especially from the STEM fields. Their recent initiative, called the Data Science Club has been created with this same objective: to train PhDs in relevant data science skills and also guide them towards career opportunities in this area. The club functions on the mentor-mentee format, with one mentor assigned to a group of 3-5 mentees. The mentees have been acquiring coding skills since the inception of the club and have an active network available to discuss projects, job openings, problem solving etc. The club will soon embark upon undertaking challenges from freely sourced data sets as well as smaller projects that are being out-sourced to the club members.

The goal of the club is two fold-  firstly by introducing people to the wonderful world of data science and machine learning, the club aims to help those who want to familiarize themselves with data science tools and apply them to various types of problems in disciplines like science, industry, education etc.  Their second goal is to keep in touch with the rapidly advancing field of data science, the academic leaps and its subsequent applications to various domains. The aim is to present articles at various levels, from building data based stories using visualizations to reviews and implementations of some of the newest techniques in machine learning.

Infographically Speaking…

Big Data, Big Returns

From Visually.

 

There are vast opportunities waiting to be harnessed in this field and scientists have a very unique opportunity on their hands: to take up the challenge of this newer profession and start making sense of the vast amounts of data that have already been generated in the world. After all, who understands data better than a scientist?!

 

If you want to learn about data science or discuss interesting ideas and projects please write to us. We would love to collaborate with data science practitioners and start ups looking to develop machine learning and data science solutions. So please feel free to connect with us at csgdatascience@gmail.com

 

 

 

About the Author:

Pawan Nandakishore  is a postdoctoral researcher at International center for theoretical sciences (ICTS). He is a PhD from the Max Planck Institute for Dynamics and Self Organization. His background is experimental physics, with a specialization in soft matter. Do feel free to write to him at pawan.nandakishore@gmail.com

 

Edited by:

Anshu Malhotra is an assistant scientist at Emory University and she is actively involved in co-ordinating the activities in CSG’s flagship mentor-mentee program (Gurukool). She is actively involved in bench-based research in pediatric oncology and is strongly interested in developing skills in data science. CSG’s current venture, the Data Science club is Anshu’s latest passion and she hopes that this platform will bring more life scientists together to train themselves and network in this budding new profession. In her spare time, she dabbles into artwork of 3D murals.

 

Cover Image: Vinita Bharat

 

The contents of Club SciWri are the copyright of PhD Career Support Group for STEM PhDs (A US Non-Profit 501(c)3, PhDCSG is an initiative of the alumni of the Indian Institute of Science, Bangalore. The primary aim of this group is to build a NETWORK among scientists, engineers and entrepreneurs).

This work by Club SciWri is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

The Year That It Was – 2017

in ClubSciWri/Newsletter by

Another year has come to an end! On this first day of a new year, new month and a new week, the Newsletter team wish you a fantastic kick-start. We have many reasons to celebrate the year 2018; one being we will soon be one year old, but the biggest joy is each day we are celebrating altruism in the Scientific Community.

The Newsletter team, together with Club SciWri and CSG, worked relentlessly to provide a collaboration platform to STEM professionals who are passionate about Science beyond the laboratory doors.

Being the first year in circulation, we have faced a few organizational hurdles. However, with each success and mistake, we learnt a lot. Through our 40 campaigns in 9 months, the team kept chasing the vision “for the scientist by the scientist.”

We ensured an amalgamation of different aspects of science. Our repository has it all!!! Whether, the articles are essential for career development/job offers, or for the stories which leave us awe inspired by the beauty of science, there is real value in the stuff.

 

 

(Topics we shared in the Club SciWri Weekly Briefings, Image courtesy Rituparna Chakrabarti)

As the New Year begins, we decided to have a recap on0 how we grew more vibrant as a team. Among the best additions to our group, the bunch of freelance writers stood out. Aditi (Chiplunkar) Khandekar, Nidhi Subhashini, Sven Truckenbrodt and Tanmoy Samaddar have been the key players in our content research, design and writing. Abhiyan Viplav, Kashyap Krishnasamy, Nisha Peter, Vignesh Narayan Hariharan and I have been the Hawk eyes for the editorial job. We are delighted that midst the organizational restructuring, the successful collaboration and extensive understanding between the writers and the editors assured campaign publication every Thursday, during 2017. Every team needs a backbone, for us Somdatta Karak took up the role gracefully. She assured initial smooth sailing and tethered the team spread across 4 different time zones.

 

(In the Image: Top row (L-R) Kashyap and Somdatta; Middle row up (L-R) Rituparna, Nidhi, Abhiyan and Tanmoy; Middle row down (L-R) Sven and Aditi; Bottom row (L-R) Nisha and Vignesh)

We are extremely thankful to have our SciArties Vinita Bharat’s Fuzzy Synapse and Ipsa Jain’s IpsaWonders, their contributions added a different charm to our newsletter.

(In the Image: L-R Vinita and Ipsa)

Our Nine Best Shares

Here we recount the most read and liked issues of Club SciWri Weekly Briefings – 2017 from each month.

  1. April: published on 20th April, 2017
  2. May: published on 18th May, 2017
  3. June: published on 1st June, 2017
  4. July: published on 13th July, 2017 (Our Pick!)
  5. August: published on 3rd August, 2017
  6. September: published on 21st September, 2017
  7. October: published on 5th October, 2017
  8. November: published on 16th November, 2017
  9. December: published on 7th December, 2017

The Aftermath

Ours is a young endeavour within Club SciWri. However, we are steadily gaining our readership. This is indeed reflected in our subscription base, as we initially had only 12 subscribers and now we have reached to 530 active subscribers, spread across 3 continents.

The active members of CSG help us achieve our social media readership per campaign in the range of 120 – 2,400. We are thankful to them for keeping the platform alive with their dynamic shares, lively discussions and constant feedback. Secondly, our average campaign ;open rate is 15 %, which is higher than the industrial campaigns (13.09 %). Our 13th July, 2017, campaign witnessed so far the record-breaking 28.02 % open rate.

(The graph depicts the % of open rate, click rate and the industry average open rate of the campaigns published between April- December, 2017, generated using MailChimp)

The core team (Abhiyan, Kashyap, Nisha and I) love to experiment with new content every week and are always taking the lead on how to gain visibility for our contributors. Feel free to leave us your feedback. We hope by the end of 2018, we will reach a subscription base of 2,000 + globally, therefore looking forward to the collaboration with the CSG – University Representatives. Our current readers’ base is mostly concentrated in the USA, France, Germany, the UK and India. Hand-in-hand with Club SciWri we aim to expand our viewership in 2018 beyond these countries.

(Interactive map depicting the top locations where our newsletter is read, generated with MailChimp)

The Newsletter team take immense pride in providing a platform to those who are passionate about science communication with the perk of visibility. If you think you could be one of us in 2018, get connected with us on LinkedIn, Twitter, Facebook or just drop me an email at rituparna.chakrabarti@sciwri.club.

Our journey so far wouldn’t have been possible without your support and we look forward to many more chapters in the coming year. If you haven’t yet subscribed to our newsletter, we assure you that 2018 will be more exciting.

Happy New Year!!


Cover Image: Pixabay

Rituparna is the lead editor of the Newsletter team at Club SciWri. She pursued her Ph.D. in Neuroscience from Georg-August University (Göttingen, Germany) and is currently a post-doctoral fellow at the Center for Biostructural Imaging of Neurodegeneration (BIN), Göttingen. Over years, she has gained technical expertise in electron and high-resolution light microscopy, in order to study the nanostructures of specialized chemical synapses in the sensory systems. She likes to have a bird’s eye view of her undertakings and gets excited with analytics. Passionately believes in, correct simplification of science, therefore engages in different scientific communication and public outreach projects. To unwind herself she plays mandolin and eagerly looks for a corner at a coffee house to slide herself in with a good read or company.


The contents of Club SciWri are the copyright of PhD Career Support Group for STEM PhDs (A US Non-Profit 501(c)3, PhDCSG is an initiative of the alumni of the Indian Institute of Science, Bangalore. The primary aim of this group is to build a NETWORK among scientists, engineers and entrepreneurs).

This work by Club SciWri is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

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