Author Archives: Sci Club

Sleep
is a necessary routine in our life, similar to food and water, to keep our body
healthy, and recharging of our brains to keep and prepared for a fresh day. Enough
sleep is essential to keep the brain active, which is critical in
concentration, learning, and memory storage. Researchers revealed that sleep
deprivation not only makes us cranky and irritable but also imparts health
burdens like blood pressure, cardiovascular disease, depression, and obesity. Evidently,
sleep follows circadian rhythms and homeostasis mechanisms. The controlled time
of sleeping and waking up without an alarm is due to circadian rhythms followed
by the synchronization of the body with the external factors such as light,
temperature and many others, and even continue in the absence of these factors.
Human body is reminded to sleep at a certain time by sleep-wake homeostasis. As
the sleep deprivation period increases, which results in a longer and deeper
sleep.  

Its interesting to have a thought about the chemistry behind sleep! Well, not everyone knows that numerous chemicals are involved throughout the sleep and wake cycle. Melatonin and adenosine, are the two most crucial molecules released in the body, which plays a pivotal role in sleep regulation. As a result of various activities, the human body burns a lot of energy, which results in the production of adenosine.  The activity of neurons is suppressed by the binding of the adenosine to the adenosine receptors embedded in neurons or nerve cells and makes us feel drowsy. The feeling of exhaustion caused by the creation of adenosine makes you sleepy as the day ends, and incomplete sleep results in tiredness. Notably, the ideal sleep burns off all the created adenosine.

The pineal gland produces melatonin when the retina is not exposed to light. The darkness inhibits the signal transfer from the suprachiasmatic nucleus (an area of the brain), which in turn causes melatonin production by the pineal gland. The melatonin is derived from tryptophan through multistep process with the aid of various enzymes. Among, one of the key enzyme is serotonin-N-acetyltransferase (SNAT), and its activity decides the melatonin production. The signal transferred by the exposure to light to the pineal gland from retina passes through the suprachiasmatic nucleus results in degradation of SNAT. Whereas, it gets phosphorylated at night and thus increases the melatonin, which is why we tend to wake up in the morning. Well, from now on, if someone stops you from sleeping, tell them you have too much adenosine left to burn off !

Written by: Supriya Jain, DST-JRF, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

Her profile: https://yenepoya.res.in/team/supriya-jain/#1561549713017-7925d3bc-4beb

Artwork: Supriya Jain

Edited by: Dr. Renjith Johnson and Saketh Kapoor

New coronavirus (CoV) is
the recent talk of the town; novel coronavirus (nCoV) is a single-stranded RNA
virus that is creating havoc in East Asian countries, especially China.
Although the new type of coronavirus virus was first isolated on January 07, 2020,
the first incidence of the disease was reported on December 31, 2019, in Wuhan
City, the capital of China's Hubei province. The patient was reported with
pneumonia with unknown etiology.

As of January 26, 2020,
over 1,975 people have fallen sick due to this virus, including 56 deaths, and
the virus is now spreading rapidly. Few cases have been reported from Thailand,
Japan, Taiwan, Hong Kong, and the Republic of Korea, where the travelers who
visited Wuhan City were detected at their respective airports by thermal
surveillance.

The virus can cause the
common cold, fever with chills, sore throat, and headache to more severe
diseases such as the Middle East respiratory syndrome (MERS) and severe acute
respiratory syndrome (SARS). The disease is zoonotic, implicating that the
virus can spread between humans and animals. Animal to human transmission
occurs through the consumption of meat or animal products. That is why it’s
first transmission has been traced back to the wet markets of Wuhan that trade
exotic wild animal food and fish which has now been shut down.

It’s nothing new or
surprising that the transmission of the virus from animals to humans exists.
Earlier, the CoV which was responsible for SARS also traveled from bats to
exotic cats, which were again sold in exotic food markets. And the aftermath of
the epidemic of SARS is a well-documented tragedy. The genome sequencing of
nCoV has identified 96% similarity with that of the bat coronavirus.

In India, no case has been
reported so far as of January 26, 2020. However, as per some media reports,
around 100 people have been kept under observation. And specimen from 7 people
with mild respiratory symptoms who have traveled from China has been sent for
investigations to the National Institute of Virology, Pune.

No drug or vaccine has
been shown to be effective against coronavirus in humans so far. It has been
reported that the nCoV and SARS CoV binds to the same receptor on human cells.
Therefore, scientists are trying to block the receptors on human cells by which
the virus finds its way to infect the human body.

Having said all this, one must follow the basic safety practices such as washing hands with soap, especially after returning from crowded places or any fish/animal market. Avoid any kind of close contact with people suffering from respiratory infections. Do not panic by reading any social media reports and let experts do the rest.

Written by: Saketh Kapoor, Research Associate, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

Further readings:

• https://www.nature.com/articles/d41586-020-00166-6

• https://www.nature.com/articles/d41586-020-00190-6

• https://www.ndtv.com/india-news/wuhan-coronavirus-monitoring-indians-in-china-closely-says-foreign-minister-s-jaishankar-on-virus-sc-2169864

• https://www.biorxiv.org/content/10.1101/2020.01.22.914952v2

• https://media.nature.com/lw800/magazine-assets/d41586-020-00190-6/d41586-020-00190-6_17590326.jpg

Image source: https://media.nature.com/lw800/magazine-assets/d41586-020-00190-6/d41586-020-00190-6_17590326.jpg

 

“Unity and co-ordination” are the two key mantras for designing a successful system or organization. Co-ordination can be achieved by forming healthy interactions between the constituent elements of the system. Interacting elements form a network and proper interaction results in the efficient flow of information or flux to achieve a particular target. So, proper networking among the constituents plays a crucial role in the success of that organization.

The essence of networking is beautifully explained by some of the well-organized systems exists in nature. Flashing pattern of light by a group of firefly may seem meaningless to us, however, it is actually their license to find a mating partner. Female firefly responds to their conspecific male partner by the synchronous flashing. A shoal formed by a group of fish is another example of nature driven network. Movement of individual fish in such a group may look like a random one while the complete system tells us how well they are coordinating with each other. Similarly, focusing on the movement of individual ant or starling may not provide much information, however, studying the movement of a group of ants or starlings can help to discover the beautiful formation of marching ants in a straight line or a murmuration of thousands of starlings. These individual elements formed a network and practiced to co-ordinate with each other to successfully build such organizations.

The list of biological metaphors for networks is huge, be it in macroscopic (organism) level to the microscopic (genes, proteins, or metabolites) level. We live in a society and interact with each other with different kind of relationships. Some of the relationships are bi-directional such as a friend, foe or unidirectional like being a fan or follower of someone. Friendship and love are some of the positive interaction exist around us whereas foe, hatred are some of the negative interactions added to such a network. Being in a society, we all are coordinating and managing these positive and negative interactions to maintain harmony in our surrounding. In the current scenario, we can clearly see and feel the network around us, and all credit goes to the growing social networking.

Protein-protein interaction, regulation of genes by transcription factors are some of the well known microscopic network present in the body. Like that of networks at the macroscopic level, we also experience positive and negative interactions at the microscopic level. Considering an instance of Gene Regulatory Network (GRN), where genes and the regulatory factors are the elements of the network, enhancing the gene expression can be considered as positive interaction whereas inhibition of gene expression is a negative interaction.

To understand the function of a system, it is important to understand the structure of the system. “System biology” is an emerging area where it entertains the systems level understanding of any functional organization. A system can be modeled into a network using the concepts of graph theory. Nodes represent the elements of the system while edges denote the interaction exists between the two nodes or elements. Studying various properties of the network helps in better understanding of the system and its behavior in various conditions. Studies have shown the existence of well co-ordination between the elements of the successful system.

These systems-level studies reiterate the essence of the well said proverb “United we stand, divided we fall”. This holds true for every functional system, be a macroscopic or microscopic one.

Written by:  



Mr. Santosh Kumar Behera, DBT-BINC, Junior Research Fellow, Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

 

 

 

Artwork: Ms. Nupur Agarwal

Edited by: Mr. Saketh Kapoor and Mr. Jagdish k

 

Regenerative Medicine is the baby of “Stem Cells and Developmental Biology” and  Regenerative biology precedes Regenerative Medicine. The term, “Regenerative Medicine” is in high demand now to regenerate damaged or diseased parts of the human body. Well, with special emphasis to the human body, is it possible to regenerate every part or any part by hook or crook or else, spontaneously when severed?

Have you heard of any creature that can help regenerate its head along with the brain when severed?

The spontaneous answers are:

• Yes, must be some mythological character that could do so, or,


• No, organisms such as salamanders, lizards can regenerate limb bud and tail, but reviving severed head must be an impossible task

Interestingly, some creatures on the earth can regenerate their heads when severed. These are several species of marine ribbon worms.

Regeneration of posterior end such as tails when severed has been well documented in stem cells and regenerative biology research in salamanders and lizards. However, head regeneration/anterior part of the body usually are impossible because the brain is the master regulator of all the physiological, metabolical and developmental processes. Recently, 22 species in the invertebrate phylum ‘Nemertea’ have been tested for the regeneration of both heads and tails. Out of these 22 species, 5 species are even adapted to regenerate heads when decapitated. As per the evolutionary reports, the species Lineus sanguineus has evolved the ability to regenerate its head about 10-15 million years ago that might be the reason of non- extinction of this species till date. Considering the existence of Lineus sanguineus, the species Homo sapiens are much recent in the history of evolution!

Although this work was carried out by Zattara and the team at the Smithsonian Institution’s National Museum of Natural History in Washington, D.C. USA, the work focused on evolutionary biology, rather than regenerative and stem cells biology. Hence, the head regeneration in Lineus sanguineus is likely to provide definitive cues to the stem cell-developmental and regenerative biologists for deciphering novel factors involved in difficult-to-regenerate parts of the body.

Image Description: Photograph of marine ribbon worm (Lineus sanguineus) has been shown to regenerate its head. Top panel shows the photographs taken 4 days after the head was cut off and the bottom panel shows the photograph taken 15 days after decapitation. The head has grown back 15 days after decapitation. Image/Experimentation credit: Eduardo E. Zattara

Reference: Zattara, E. E., Fernandez-Alvarez, F. A., Hiebert, T. C., Bely, A. E., & Norenburg, J. L. (2018). A phylum-wide survey reveals multiple independent gains of head regeneration ability in Nemertea. bioRxiv, 439497.

Written by: 



Dr. Bipasha Bose, Associate Professor, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

Professor Bradley’s group in Wellcome Trust Sanger Institute, UK recently reported that CRISPR-Cas9 led gene editing can lead to potential DNA damage by introducing unwanted large-scale deletions and complex rearrangements. The work which was done on cell lines derived from human and mouse have shown that this technique creates extensive DNA damage. The study was published recently in the scientific journal Nature Biotechnology. So the major implications will be that the CRISPR based therapies may not be as useful to treat diseases as we may have been thought earlier.

Two other studies which were published two months ago in the scientific journal Nature Medicine, one from the Karolinska Institute Sweden and the other from the company Novartis showed concerns that CRISPR/Cas9 editing can induce cancer.  So the promise of using this technique in clinical trials for blood-related disorders such as hemophilia, sickle cell anemia, and Beta-Thalassemia, and other disorders such as Duchenne Muscular Dystrophy which are potential candidate for gene editing could be delayed because of the astonishing results reported.

CRISPR, short for Clustered Regularly Interspaced Short Palindromic Repeats system is based on the defense mechanism used by bacteria to protect themselves against the invading viruses. The Cas9 protein which acts as molecular scissors cleaves the virus genetic material and protects the bacteria. The bacteria also store the fragmented virus genetic material, which acts as a guide for the future attack by the same virus.

The system has been tweaked by scientists to be used as a gene editing tool. So in simple terms, CRISPR/Cas9 is a genome-editing technique which cuts/breaks the DNA at a specific site(s) with the help of a guide RNA which is associated with Cas9 protein. The cell repair system then adds the new DNA at the cut site thereby activating or deactivating gene(s) to treat a certain condition.

More recently, a team from the University of Illinois invented CRISPR-SKIP technique where instead of cutting the DNA, the machinery actually causes the region of DNA to be “skipped”. Since we know that DNA contains exons (the coding regions) and introns (the non-coding regions). When the cell transcribes the gene into RNA, all the exons are stitched together which is to be used for protein synthesis. The stitching of exons happens due to the presence of specific base sequence at the start and end of each exon. CRISPR-SKIP modifies these specific base sequence, leading to exon skipping and thus the exon gets ignored during protein synthesis.

Due to the stupendous scope of its application, CRISPR was eventually touted as an ultimate method for editing genes. Treating genetic disorders and cancer, improving crop yields, reviving extinct mammals and producing designer babies are only a minuscule portion of the portrayed promises made by scientists. What eventually followed was a massive patent war between two teams. Having tested the CRISPR gene editing potential in a cell-free system, Jennifer Doudna and Emmanuelle Charpentier of U.C. Berkeley and the University of Vienna, respectively filed a patent application in the year 2012. Another patent was filed by Feng Zhang from the Broad Institute (collaboration between MIT and Harvard) in 2014. This team filed for the patent in using CRISPR in editing eukaryotic genes. Having applied through a fast-track process of review, the latter team was first awarded the patent. U.C. Berkeley and the University of Vienna appealed against this decision and claimed an ‘interference proceeding’. Stating that the claims made by the Broad Institute were ‘non-obvious’ and unique in its own right, a federal appeals court upheld the judgment passed by Patent Trial and Appeal Board in favor of the Broad Institute on September 10, 2018.

Having mentioned flaws such as off-target effects and unwanted DNA damage by various studies, this technique has a lot of outstanding potential in the scientific field. Since the CRISPR/Cas9 technique has progressed very quickly over the years, it is important to understand the reliability and after-effects of this technique.

UPDATE: Here we are in 2020, the Nobel Prize in Chemistry has been jointly awarded to Jennifer Doudna and Emmanuelle Charpentier for their breakthrough discovery of genome editing tool CRISPR.

Written by: 



Saketh Kapoor, Graduate student, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

Artwork: Saketh Kapoor and Dr. Pratigya Subba

Edited by: Dr. Raghu Bhushan

 

 

Did you know? More than 5000 people in India die every year due to Leptospirosis or Rat Fever. It mainly affects people who come in contact with contaminated soil or water during floods. Leptospirosis cases have seen to be elevated during the rainy season due to exposure to contaminated water and soil.

Rat Fever is caused by a spirochete named Leptospira. Surprisingly it’s been more than 100 years since the discovery of this bacterium yet, no rapid diagnostic tools are available. This is mainly due to the slow growth rate in culture media, laborious detection and can only be performed in reference labs with all the serovars. Interestingly, this bacterium does not only infect humans but also a variety of organisms like hamsters, swine, other rodents and cattle animals which act as carriers.

Mode of infection is through the urine of infected animals, which shed the spirochete microbes into water or soil. The bacteria can enter the body through the injured skin or mucous membranes. Drinking contaminated water can also cause infection (Refer the schematic diagram).

Is it really dangerous? Typical symptomatic human Leptospirosis shows symptoms like dengue and malarial fever (so if your doctor says no Dengue or Malaria, it can be Leptospirosis!). The severity of the disease ranges from chronic fever, cough, headache, chills, and conjunctivitis to acute meningitis, extreme fatigue, respiratory distress and some severe cases like pulmonary haemorrhage, myocarditis, renal failure, uveitis and even death.

Rat fever can be prevented by consuming a prophylactic antibiotic as prescribed by the Physicians. Vaccination of the farm animals is necessary as this is another source of transmission. Simple practices like practicing good self-sanitization, avoiding swimming in the infected animal urine contaminated water bodies, avoiding direct contact with the mud or fresh water during a flood can save you from getting the Rat fever.

With fallout of severe floods in the states of Kerala and Karnataka, there is an earnest appeal for all the rescue team members helping out distressed people; Kindly make sure to incorporate all the necessary precautions like wearing the gloves, boots and take prophylactic drugs to avoid the risk of contracting Leptospirosis infection as it could get more serious in flood-affected areas. For the people who are already exposed to the conditions, kindly consult medical team deployed at the relief sites to avoid further complications, and also advise for the same to the affected people.

“Stay hygienic, Stay safe”

Written by: Mr. Mohammed Tarique, Technical Research Assistant (ICMR Project), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

Artwork: Mr. Mohammed Tarique and Mr. Utsav Sen

Edited by: Mr. Jagdish k and Mrs. Saptami U. Kanekar

In our daily life, we are frequently being told that happiness is either relative or an illusion. Some of us will not agree with this statement, some of us will say yes, and we have also experienced the happiness positively. We often find ourselves oscillate between happy and unhappy moments and realize that in fact, there is no permanent state of mind. In other words, “Change is the only constant”.

It seems that happiness is the ultimate goal or achievement of our life. Our childhood was spent having lots of fun and happiness at that time meant self-gratification. As we grew, making our parents proud gave that happiness. Gradually it got extended to our boss, life partner and kids making them happy in whatever ways it demanded. . . But this pursuit of happiness has left us in an elusive approach of chasing a mirage of so-called happiness which happens to be a crucial and ever-increasing need in every moment of our lives

What is Happiness? Why is this so important in our life? Let’s understand a scientific basis of this happiness on contrary to more of philosophical views so far. While philosophically true happiness has a different definition for each of us, science can give us a clear picture of the prevailing factors that lead to the state if being happy. There are thousands of factors involved in our happiness; from the food we eat to bed, we sleep in room temperature, which plays a role to regulate our temper and in turn, the complex functionalities of our brain. . . Understanding these factors which are related to our happiness will help us to know about our temporary state of mind.

Mechanisms that are responsible for the happy mood are very interesting though. Researchers revealed human behaviors in novel ways that weren't studied earlier. With their knowledge and advanced technology at their disposition, scientists were able to discover what goes on into our body when we experience happiness. Studies were also carried out in the area of the human brain that is responsible for happiness and positive memories as well as the neurotransmitters involved like Serotonin. In the human central nervous system (CNS), this neurotransmitter connects nerve cells and is associated with a feeling of happiness or decreased anxiety. Serotonin is a significant part of many popular drug treatments for depression and anxiety. It helps to regulate essential human functions like; learning, mood, sleep, sexuality, appetite.

Another neurotransmitter is Dopamine which is both a neurotransmitter and a neurohormone that is produced in several different areas of the brain. Dopamine is mostly associated with the "pleasure system' of the brain, providing feelings of enjoyment and motivating us to do or not to do or continue doing some activities. Assuredly, this neurotransmitter is released by naturally occurring events such as food, abuse of drugs, sex and neutral stimuli that become with them. Dopamine is often touted as a ‘reward chemical’ or part of the brain’s ‘Reward center'.  Apart from this, dopamine rewards us by regulating some critical functions such as feelings after punishment, movement, motivation, and attention, emotional responses, working memory, etc.

So if you are curious about the science of happiness, Check out your status and you will discover what it is that contributes to your Happiness...... Meet Your Happy Chemicals - BE Happy & Make Others Happy!!!

Written by:

Mr. Utsav Sen, ICMR-Senior Research Fellow, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

 

 

Edited by: Mr. Jagdish k and Mr. Saketh Kapoor

We all are gifted naturally with immense potential for excellence. A conscious living leads to a conscious will, that is what we call is willpower. Conscious living releases so much of the latent energy that energizes our entire being to do so much. Then, where is the question of mediocrity or non-performance??? Intrigued, isn’t it!!!

The crux of the matter is how you spend your 6 pm to 9 am every single day decides how productive your 9 am to 6 pm will be. I am serious and not joking. I would request each of you who are reading this blog, to reflect upon yourselves and think how you have been spending your 6 pm to 9 am every day. You do not have to go much far in the past, but a week’s data should be sufficient to indicate the levels of your productivity, in other words, your commitment to excellence.

Well, I know the answer most of you will be having. Some of the typical answers are:

1. I am so very exhausted at the end of the day that, I freshen up and just couch with my cell phone at 6 pm and try to relax. Then, I realize it is dinner time. 3-4 hours fly off.


2. I am so very exhausted at the end of the day that, I freshen up and just switch on the TV at 6 pm as soon as I reach home and try unwinding. Then, I realize it is dinner time. 3-4 hours fly off.


3. I am so very exhausted at the end of the day that I need to get busy with the household chores such as homework of children. Then, I realize it is dinner time. 3-4 hours fly off.


4. Well, I just do things such as talking on the phone, having dinner and going to bed.


5. I go to eat out sometimes and come home late followed by sleep. 3-4 hours fly off.


6. I switch on my computer to study something and often get distracted and end up watching a movie or entertaining videos on YouTube. 3-4 hours fly off.

Some of the uncommon answers are:

1. I go home, freshen up and go to the gym or go for a walk without my cell phone or any distraction before taking to anyone or getting busy with routine chores.


2. I go home, freshen up, and sit alone reflecting upon how I had spent my day. I write down the accountability to myself for betterment before taking to anyone or getting busy with routine chores.


3. I go home, freshen up and remind myself that I am mortal and I need to live my every moment productively, reflect upon how I had spent my day and do better tomorrow. All of these I do before taking to anyone or getting busy with the chores.


4. I go home freshen up, do some yoga and meditation and self-reflection before taking to anyone or getting busy with the chores.

I understand that it takes a tremendous amount of willpower to practice what the uncommon answers correspond to and that too at the end of the day. However, the good news is that you do not need to spend the entire evening doing yoga, going for a walk, meditating, working out in the gym and reflecting on oneself. One can spend just an hour doing it and feel so much energized, focused with high levels of endorphins. Also, you will have an excellent sleep in the night. Very simple, isn’t it. Your commitment to yourself means to spend time for yourself, not much, just an hour every day (morning or evening) being with yourself, meditating, exercising and reflecting. Most important, make this a regular habit. You will be surprised to find the new scientific ideas flowing through your mind just after these precious moments with yourself. Pen them down immediately. This commitment to yourself will keep you energized as similar to an oasis in a desert before the entire world tears you apart with mediocrity.

The attitude should be: I promise to give quality time to myself because I am committed to excellence. Of course, I do not need to show off my superiority to the entire world around me. Instead, it becomes evident as I reflect more energy, more positivity, and more happiness. That creates an impact on the world around me. I do not compete with anyone; instead, I run my race to give more to myself. It is important to remind oneself that, “I have more energy to do what I am doing today and I am meant for doing more.” Efficiency and productivity are none other than excellence.
If we all practice this small exercise for one hour every day, we all can impact the world around us with excellence rather than being a little clod of mediocrity.

Happy reading!

With respect and love to all the readers of this blog.

Written by:

Dr. Bipasha Bose, Associate Professor, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.

 

 

 

Photo courtesy and Artwork by:

Mr. Utsav Sen, ICMR-Senior Research Fellow, Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore-575018, Karnataka, India.