| | October - December 2022 | Vol 13 | Issue 4 |
| | | | | | |
|
|
|---|
|
| Dear Members,
Bioclues is a non-profit virtual organization for, by, and of the Indian Bioinformaticians. One of the fastest growing bioinformatics societies in India. Bioclues was built on the foundation of connecting people. Bioclues aims to bring together the Indian bioinformaticians, foster a strong working mentor-mentee relationship, provide access to bioinformatics resources, organize conferences and workshops besides imparting information about research, training, education, employment, and current events and news from bioinformatics, genomics, and related fields.
Read on to know more about our latest events and members
Stay Safe | Be healthy
Editors: Team Bioclues |
| | |
|
|
|---|
|
| Introducing new executive committee of Bioclues |
| Welcome address by Dr. Gyaneshwar Chaubey,
President of Bioclues
Namaskar to all the respected members of the Bioclues family! First, I am grateful to all of you for integrating into this incredible family. I am honored to join. It has been only a short time since I formally joined this family. Nevertheless, during this time, I have come to understand that this organization is standing on a solid well-woven foundation. There is a saying that a strong foundation enables transformation, which is well reflected in every action of the organization. Every family member stands in its construction with complete devotion and strength. That's why more and more academic and social activities of this organization will strengthen not only this family but also the country socially and scientifically.
Technological advancements have enabled us to generate high-resolution data, which was impossible just ten years back. With these, we can resolve long-standing problems that were not possible earlier due to low data resolution. Data analysis, more specifically genomic data analysis, is increasingly becoming a trending practice that many budding researchers are adopting to extract valuable information to resolve the myriads of various biological processes. The magnitude of data generated and shared by scientific research has increased immeasurably. However, the number of researchers on it has not increased accordingly. This is more alarming for a country like India, which is a 'living lab' to study genetic diseases because of strict endogamy practices. Family Bioclues is needed to understand this scenario. Given the critical nature of this discipline, we need to present a state-of-the-art review that may offer a holistic view of the challenges of Bioinformatics and the methods used by researchers to help understand this landscape objectively. This gap is widening day by day, and I strongly think that the Bioclues family can take this challenge effectively to fill the gap by training young Indian minds.
The year is coming to an end. In this, we fulfilled many resolutions, and it is human nature to achieve those which could not be fulfilled with new resolutions in the next year. Bioclues will continue to serve humanity and improve the outreach activities of science. This year we will ensure our participation in many activities, including teaching science to school children. May your constant cooperation continue in all these. With these good wishes, many happy new years to the lovely Bioclues family.
Jai Hind Jai Bharat! Brief Bio-data of Dr. Gyaneshwar Chaubey, President of Bioclues Presently, He is full time Professor at Dept of Zoology, Banaras Hindu University, Varanasi, India 221005.
Career Highlights - Known for in-depth work on several ethnic groups of South Asia, including Himalayan, Andaman, Austroasiatic, Dravidian, Indian Jews, Siddi, Roma, and Parsis.
- Biological identification of ‘Ajnala skeleton’ by latest DNA analyses: 2022.
- Among the top 2% highly cited Scientists (Stanford University).
- Nation Builder Award 2021, Rotary club, Varanasi, India.
- Mainly based on our genetic research done in 2014, the Indian Government handed over the relics of Queen Ketevan to the Govt of Georgia: 2021.
- 'Most productive researcher award' 2020 in 40-55 years category at Institute of Science, BHU.
- Writing regular editorial columns ('Mudda') in India's largest Hindi daily 'Dainik Jagran' on COVID-19 and India.
- Oct 2019 felicitated by Honourable Home Minister Govt of India for outstanding work on Indian prehistory.
- Among '10 Indians To Watch Out For In 2019' by Swarajya Magazine (https://swarajyamag.com/magazine/10-indians-to-watch-out-for-in-2019).
- Was invited by National Geographic USA for presentations and panel discussion (Who we are?) in National Geographic Symposium- June 2018.
- Awarded by Gencove USA for sequencing 300 Zoroastrian samples:2018.
- Among 2.5% Scientists of the World (Source: ResearchGate Germany).
- Among top 1% highly cited scientists in Heredity and Genetics (Web of Science, USA).
- Featured Associate Editor at 10th Anniversary of the journal PLOS ONE.
- Based on our research on Roma (European Gypsy), Late Smt. Sushma Swaraj (Minister of External Affairs) called them the 'Children of India' in 2016.
- A column with Dr. K Thangaraj on the issue of 'Aryan Invasion' in a leading newspaper 'The Hindu'. 2017.
- Was selected as a top young researcher to meet the Nobel Laureates in 61st Lindau Nobel Laureates Meeting 2011, Germany.
Brief Bio-data of Dr. K. Sri Manjari, Secretary of Bioclues K. Sri Manjari, Ph.D. (Genetics) is a Scientific Writer at a Personalized Health Clinic, Hyderabad.
Her research is focused on Personalized Medicine, Precision Oncology, and Pharmacogenomics. Dr. Manjari was involved with the work on the genetics of chronic pancreatitis focusing on biomarker research associated with the disease.
Previously, she was a Lecturer at University College for Women, Osmania University (now Telangana Mahila Vishwavidyalayam) teaching Genetics and Biotechnology to undergraduates and postgraduates.
She has a Ph.D. in Genetics from Osmania University, with a Senior Research Fellowship from UGC on the thesis titled “Elucidation of cytokine and matrix metalloproteinase gene polymorphisms in the pathogenesis of chronic pancreatitis”
She is a Life member of the Indian Society of Human Genetics and Bioclues -BIOinformatics CLUb for Experimenting Scientists, India. She has published over 20 peer-reviewed manuscripts, reviews, and book chapters
|
|
|
|
|---|
|
| History of Bioinformatics |
| | | | | We exist in a cosmos of unparalleled amounts of biological data conceived through research, and it is the evolution of bioinformatics that has enabled its interpretation, analysis, and management. Margaret Belle (Oakley) Dayhoff, who is regarded as the "mother" of bioinformatics, was a leading proponent in the discipline.
The Atlas of Protein Sequence and Structure, published in 1965, is regarded as the foundational literature for bioinformatics. She included all 65 known protein sequences, sorted by gene family, in her paper. Following which, Emile Zuckerkandl and Linus Pauling in 1962 and 1965 published papers codifying the idea that this type of molecular analysis may aid researchers in deciphering evolutionary patterns in organisms. This eventually led to the establishment of the Protein Information Resource database of protein sequences, the first publicly accessible database system, in 1971. This was empowered by the work of Walter Goad to lay the primary framework of the GenBank database (for nucleic acid sequences).
The one-letter codes for amino-acids that we use today was pioneered by her in an effort to decrease the number of data-files utilized in the sequencing of amino acids; moreover, she has been credited for the application of computation and mathematics in the field of biochemistry. In an era where women in sciences were unheard of, she headed the Biophysical Society as the Secretary as well as the President, making her the first person to achieve such a feat.
In her graduate thesis, as a part of her PhD (under George Kimball) in Columbia University’s Department of Chemistry, she developed a method that laid the foundation for the determination of resonance energies of many polycyclic organic compounds - using punched-card business machines to apply computer capabilities, such as mass-data processing, to theoretical chemistry. She was awarded access to "cutting-edge IBM electronic data processing equipment" at the lab through Watson Computing Laboratory Fellowship for her Research Data Management Skills.
From 1948 until 1951, after receiving her PhD, Dayhoff studied electrochemistry at the Rockefeller Institute under Duncan A. MacInnes. After moving to Maryland in 1952, she received various fellowships for her model of chemical bonding with Ellis Lippincott, and was exposed to the IBM 7094. Following which, in 1960 she worked as an Associate Director in the National Biomedical Research Foundation for the next 21 years. She co-authored "COMPROTEIN: A computer program to aid primary protein structure determination" with Robert Ledley, which presented a finished computer programme for the IBM 7090 that sought to convert peptide digests to protein chain data.
Through her expertise, she contributed to the development of thermodynamic models of cosmo-chemical systems, with Ellis Lippincott and Carl Sagan. Her computer program facilitated the study of atmospheres of Venus, Jupiter, and Mars, through the calculation of concentrations of the gasses in a planetary atmosphere.
Her contribution to sciences is not limited to research, she spent 13 years of her life guiding students in physiology and biophysics at Georgetown University Medical Center and was a part of the editorial boards for eminent scientific literature distributors such as DNA, Journal of Molecular Evolution and Computers in Biology and Medicine.
Apart from serving as a Fellow of the American Association for the Advancement of Science, she also represented the International Society for the Study of the Origins of Life as its councilor.
The research on the comparison of protein sequences and the reconstruction of evolutionary histories from sequence alignments via computers, co-authored by Richard Eck and Dayhoff, was the first to utilize computers to infer phylogenies from molecular sequences. It was the first time that computers employed the maximum parsimony technique to build an evolutionary tree using molecular sequences. She later applied similar strategies to study numerous molecular interactions - as the bovine cyclic AMP-dependent protein kinase; antithrombin-III, ovalbumin, epidermal growth factor etc.
By Ananya Verma |
|
|
|
|---|
|
| Artificial Intelligence: The Rising Star |
| | | The untold story of Artificial Intelligence (AI) converging with biological science has taken over an exciting turnover since a decade. Even though the human race has got the resources and efforts, nevertheless, the complexities faced across in each and every concern, has necessitated the need to converge the intelligent systems manifested by computer programming language as well as other tools, that collectively form artificial intelligence. AI has taken over the lead in every aspect of science especially in medical and health sciences. To diagnose, monitor, and treat genetic diseases, researchers need ever-sophisticated technology as they work to solve the many mysteries of genomics. These challenging activities are highly suited for the use of artificial intelligence systems, which simulate human intelligence in problem solving. Some of the applications are discussed below.
Given over, two major components of AI- machine learning (ML) and deep neural networks (DNN), dictates diagnosis, prognosis and treatment patterns. While the ML can be categorized broadly as supervised and unsupervised, it has various elementary tools such as support vector machines (SVM), random forest (RF), NaiveBayes (NB) etc. For example, in the field of radiology, AI has facilitated an advanced prognosis of diseases especially in tumor biology or malignancies, as in distinguishing stages of metastasis. As an illustration, ML is already making it easier to diagnose relatively common diseases like breast cancer through mammography. On the other hand, AI has already been applied to discover disease-causing genomic variations, predict the course of a certain form of cancer, and detect genetic abnormalities by studying the faces of individuals. Genetic abnormalities are frequently uncommon and famously challenging to identify. The time it takes to identify the precise genetic origin of a rare ailment ranges from five to ten years on average from the time symptoms first appear. Treatment is frequently delayed by the protracted and difficult diagnosis process, which is usually expensive and isolating.
Medical science is vision off without the implementation of pharmaceutical sciences. Over a century, various drug design platforms have effectively produced potent bioactive agents. With the concomitant emergence of AI, stringent conditions of acquiring efficient compounds has declined, since preliminary screening of compounds is virtually met. This finding made a turnover in the field of potent pharmacological agents against most of the dreadful diseases. The AI abridges prediction of 3D structure of target protein, protein-drug interaction, determining drug activity and de novo drug design. To add on, AI enables even designing multi-target and bio-specific drug molecules. The AI further facilitates prediction of existing therapeutic drug targets, which is known as AI-assisted drug repositioning or drug repurposing even as it empowers prediction of physicochemical properties as part of Quantitative-structure-activity relationship (QSAR) studies. However, proper preclinical validation of those compounds to successfully translate from bench to bedside.
Apart from the medical and health science field, education patterns can be improvised which facilitates students’ ability to enhance their problem solving skills, along with student-teacher interaction through AI platforms. Although AI systems have been praised for increasing communication volume and quality, for giving huge groups of students just-in-time, individualized support, and for enhancing the sense of connection, there have been some concerns regarding accountability, agency, and surveillance issues. In reality, many of the beneficial aspects of AI systems that students and teachers find objectionable originate from them. For instance, while professors and students valued AI's speedy communication, they were also concerned about AI-based misunderstandings or deception. Although teachers and students appreciated the individualized, just-in-time support provided by AI, they were concerned that it might restrict their capacity to learn on their own. Students and teachers appreciated the social cues that AI gave, but they were uneasy with the privacy invasion brought on by AI's extensive data collection. Nonetheless, there are some atrocities associated like regulatory affairs concerning proper implantation of AI in our day-to-day life.
Whether AI is a boon or bane, that depends on how we perceive it. Let AI continuously be the rising star !! By Indrani Biswas (Ph.D.) |
|
|
|
|---|
|
| Covid Corner:
Organoid-based model to reveal the neuromolecular pathogenesis of SARSCoV-2 |
| Covid-19 is not less than a mystery for scientists across the world. Initially, the major affected organ is lungs and its respiratory functions. By using drug repurposing and vaccination methods, governments have controlled the pandemic from becoming the mass death events across the globe. However, this tiny virus is still showing its effect on other parts of the body. One of the most intriguing observations was the presence of neurological symptoms. In the last article, we have described the study that revealed the new route, TUNNEL FORMATION BETWEEN Normal and infected neurons, of infection by SARSCOV-2. In this issue of the newsletter, we come up with another study that probes how this virus disrupts neuron functioning. Alysson R. Muotri, PhD, Professor in the Departments of Pediatrics and Cellular and Molecular Medicine at the UC San Diego School of Medicine, the principal research author used the brain organoid model to understand its molecular disruptions of neurons.
The researchers infected brain organoids with SARS-CoV-2, monitored viral infection and replication, and discovered that the virus quickly reduced the number of excitatory synapses in neurons seven days post-infection. Excitatory synapses raise a neuron's firing action potential, whereas inhibitory synapses lower it.
On treatment with sofosbuvir, the infected organoids showed viral replication was inhibited and subsequently restoring of lost neurological impairments. These findings are similar to research carried out by Muotri and his team. Bioinformatics analysis predicted the safety and efficiency of sofosbuvir in the protection against Zika virus-infected neural cells
By Ananya Verma |
|
|
|
|---|
|
| | | Scientific interactions were curtailed due to COVID-19 pandemic across the world. However, we, as part of India’s largest bioinformatics society, Bioclues, have adapted to this using a virtual mode of interactions. Bioclues conducted its last two international conferences virtually (Inbix 2020 and Inbix 2021) to connect and engage different bioinformaticians and scientists to share their ideas and promote innovation in the various areas of biology.
Unfortunately, scientific interactions quality was reduced due to various reasons: technical and non-technical issues. With the end of the pandemic, the Bioclues conducted this year's international conference Indian Conference on Bioinformatics 2022 (Inbix’22) with a focal theme on Frontiers in Nutrition, Medical Genomics and Drug Discovery, in hybrid mode at Vignan (Deemed-to-be University).
The responsibility for this conference was taken by Dr. Anil Kumar, Assistant Professor and his teams from Vignan (Deemed-to-be University) and Bioclues. His hardwork and dedication resulted in the enormous enrollment for this offline conference from and India as well as outside side, thus making it an Excellent International Conference since the pandemic with vibrant interactions among entrepreneurs, scientists, eminent speakers, panel discussions by experts on Next generation sequencing, and last but not least by students who asked critical question to eminent speakers.
Conference participants - 3 Keynote speakers
- 23 Invited speakers
- 3 Industrial experts
- 616 registrants
- 5,302 abstracts
- 1 Preconference tutorial
- 17 international participants from 6 countries
Thanks to Organizing committee !
Bioclues would like to thank all the organizing committee members of Vignan (Deemed-to-be University). Thanks for providing travel support and accommodation, in the city, for all the delegates who traveled from different parts of the world. Technical team in the conference hall had done tremendous work for the smooth continuation of conference proceedings. We have been impressed with the amount of hardwork and dedication you used for cultural programmes as well as valedictory function. Finally, A whole hearted thanks to Prof. Kavi Kishor sir for helping us from inception of this conference to final day.
Vignan University under the aegis of Bioclues.org had organized Inbix’22 during October 31-November 2, 2022 which was well received by the scientific community. A gist of summary in the form of proceedings:
Nobel Laureate Dr. Sir Richard J Roberts was one of the keynote speakers of the conference who emphasized the need for students to take up Basic Research which will allow them to become industrialists. Taking himself as the best example, he set a tone on how his academic setup of basic research allowed him to start the New England Labs in Boston, USA which is now a billion dollar company. Padma Bhushan G. Padmanaban's much awaited talk on Contours of Biotechnology in India was the limelight of the conference. He emphasized how turmeric/curcumin research is largely taken up by China and making use of Ayurveda. He provided the gist of his 60 years of career research on curcumin and the growing need of phytochemicals based research in India. As an Adviser of BIRAC, he has been instrumental in identifying and recommending innovative products. His talk stole our hearts and we are very happy to have him here. Dr. Gitanjali Yadav, Senior Scientist at NIPGR spoke on the need for gene expression studies in plants and how to best utilize carbon source in plants for identifying the µg targets. Dr. D. N. Rao’s talk (IISc) on DNA-Protein interactions using Helicobacter pylori and the need for regulatory understanding of taking up pathogenesis. Prof. Chandrasegaran’s talk (John Hopkins) on CRISPR was the take home on how genome editing is well taken care of for theranostics. Dr. Bhanuprakash Reddy of National Institute of Nutrition, Hyderabad spoke on Diabetic retinopathy and retinitis pigmentosa and how it is affecting due to lack of vitamin deficiency. Healthy vitamin diet food is important for these diseases. The first day ended with wonderful posters and amazing performances by students which remains as the most remembered.
The second day was a scientific feast as Dr. Desh Pal Verma’s talk (Ohio State University) on biotic stress was a class of science in 45-minutes. His talk gave us impetus and inspiration on how translatable research could be carried out. Dr. Nese Sreenivasulu (IRRI) gave a wonderful talk on good nutrition for humans. Low glycemic (low sugar) Index rice varieties were developed by their group which can avoid diabetes and other diseases. These rice varieties will help future health development for the world. He also spoke about the development of rice lines that can prevent cancer, that help to improve zinc and iron in humans. Dr. Pushpendra Singh spoke on Leprosy which is still there in few places and expertise in these forgotten areas needs to be revamped so that good research can be taken up. Prof. Bipin Nair (Amrita University) spoke on antimicrobial resistance and the need for use of phage therapy which serves as alternatives to antibiotics as they are very specific. Dr. Jiban Jyoti Panda emphasized the need for Nanotechnology research and the essence of vaccine based technologies. Dr. Krishna Mohan Medicherla’s talk on understanding how Type 2 Diabetes in the endogamous population is altogether a different experience. Dr. Pragya Yadav’s talk (IIV) on Omicron as variants of concern and the pandemic challenge gave novel insights into recombination. The day ended with oral, poster and virtual presentations apart from BIRD Awards and a panel discussion giving a new time learning experience on how next generation sequencing could be the key with new developments of evolutionary biology. Dr. Rathnagiri Polavarapu gave a much needed recipe for value - added translational research and how his group and company have produced several wonderful diagnostic kits. Dr. Thangaraj’s (CDFD) spoke on Indian genetic ancestry and how the association of specific genes with diseases was uncovered using population based genetic studies. Dr. Narahari Sastry’s talk on need for computational aided drug discovery (CADD) in the realm of student centric project activities set the tone. Dr. Nirmal K Lohiya, Emeritus Professor from University of Rajasthan in his inspirational talk showed how Papaya seeds were influential in Androgen receptor mediated pathways. Dr. JSS Prakash’s talk on Cyanobacterial exosome degradome pathways was an eye opener and a complete out of box talk. Dr. Chandana Basu's talk on hair genetics set the tone of the conference on how traits adapt. Dr. Rupert Ecker (Austria), Dr. Spandan Chaudhary of Unipath Labs, Dr. Ravi Chilukoti of MGI introduced their company’s profiles besides specifying need for academia-industry collaborations. The conference ended with a culminating talk on secondary agriculture by Dr. DPS Verma. Besides this, there were cultural events and social networking which were unforgettable. Entire details of the program is available at inbix.bioclues.org |
|
|
|
|---|
|
| | | | | In ‘Sci’versation with Prash: Vinod Kumar Nigam, Ph.D. |
| Professor, BIT Mesra, India on November 10, 2022. |
| | |
|
| | |  | | |
| A teach in Webinar to crack CSIR-NET: |
| Pranita Bhatele, Ph.D & Krithika Anbazhagan Ph.D on Nov 27, 2022. |
| | |
|
|
|---|
|
| | | How to make an effective CV and Cover Letter/ Statement of Purpose |
| Prashanth N Suravajhala Ph.D, Principal Scientist, Amrita School of Biotechnology on Dec 7, 2022. |
| | |
|
| | | In ‘Sci’versation with Prash: Nidhi Gupta, Ph.D. & Surendra Nimesh, Ph.D. |
| IIS University, Jaipur & CURAJ, Kishangarh on December 14, 2022. |
| | |
|
|
|---|
|
| | | Open for Climate Change Justice - One liner and Quiz competition |
| by Ananya Verma and Somenath Dutta, Chairs of Bioclues’ Student Chapters October 24 - 30, 2022, as part of International Open Access Week |
|
|
|
|---|
|
| Introducing IN-KIND Life Memberships |
| Dear Members, Bioclues as a non-profit organization would like to introduce 100 "in-kind" Life Members (LM) of our society and accorded from all States and Union Territories of India. In the next one month, we want to have 100 "in-kind" LMs who are needy, facing financial problems, but love doing bioinformatics, and are eager to join this society. If you have any student who is deprived of taking services at the expense of not being able to pay the membership fee, please let us know! The members would be given a full fee waiver for Life Membership. We anticipate that these less-privileged members will bring one paid LM each in due course.
Contact our secretary, Dr. K. Sri Manjari, to express your interest at s...@bioclues.org |
|
|
|
|---|
|
| | | Welcome to our new Life Members! - S. Madhu Balaji
- Shiva Vasudev
- Rupasree Mukhopadhyay
- KSN Jyothi
- Md. Nazneen Bobby
- S.Krupanidhi
- M. Indira
- Naayaa Mehta
- Chandana Basu
- Ziaul Hasan
- Sheshadri S
- Vandana Devaiah
|
| | |
|
| Benefits enjoyed by a Life Member |
| | |
|
|
|---|
|
| | | | |  | | |
|
|
| | | Enabling everyone to do science that matters by always pushing the limits |
|
|
|
|---|
|
| | |  | | |
|
|
| | | A solution provider for Precision Medicine / Next-Generation Digital Pathology and provides fully integrated cutting-edge tissue cytometers |
|
|
|
|---|
|
| WOULD YOU LIKE TO CONTRIBUTE? |
| We would love to publish your research highlights, achievements, popular science articles, poems, drawing, cartoon or photographs. Write to us at sak...@bioclues.org.
Newsletter Editors: Team Bioclues |
|
|
|
|---|
|
| | | | |
|
|
