Srijan Haldar, Author at Adamas University

Career in Biochemistry: as an Enzymologist

One of the most efficient catalysts researched for industrial-scale catalysis are enzyme because of their multiple advantages lies in their controlling process to specificity along with their less eco-friendly nature. Due to the presence of all these characteristics in the industry, the handling cost reduces when they are used as biocatalysts in different biochemical processes.

The advantages of enzymes have been partially realized by pharmaceutical, fabrication, food, and beverage, industries. In other industries like natural gas conversion and biofuel production also It was proven the potential of enzymes. However, some disadvantages are also lines with enzymes in industries like the application of them at high-temperature processes or turbulent flow regimes due to their stability issues, use in toxic solvents. That is why concentrated techniques across different sectors are concentrating on identification and generation of robust, thermostable, biocatalysts appropriate for use in a wider range of industries. The under the mentioned table we have mention use of some enzyme in the industry:

Pharmaceuticals	Nitrile hydratase, monoamine oxidase, lipase, penicillin acylase, transaminase	To generate active pharmaceutical ingredients intermediates
Food Processing	Pectinase, amylase, isomerase, Trypsin, glucose papain.	starch to glucose production, generation of high fructose corn syrup, generation of prebiotics, debittering of fruit juice
Detergent	amylase, cellulase, Protease, lipase	removal of Stains, oils and fats removal, retention of color
Biofuels	Lipase, xylanase, cellulase	generation of fatty acid methyl esters, degradation of lignocellulosic material to produce bioethanol
Paper and Pulp	Lipase, xylanase, cellulase	Lignin Removal for better bleaching efficiency.

Application of enzymes in Industrial Catalysis

Pharmaceuticals Industry: For quite a long time, pharmaceutically active chemical productions are facilitated by the enzyme catalysis technique successfully at the industrial scale. Due to the presence of high regional, chemical, and stereo selectivities of the substrate to product conversion the enzyme catalysis became most appropriate in this sector. Product specificity is essential in a pharmaceutical method due to the streamlining of product synthesis ways followed by economic process improvement. Use of enzyme not only required here but also provide a higher production rate.

Fuel industry: Biofuel like bioalcohols, biosynthetic oils, biodiesel, and biogas considered as the supplement for fossil fuel and these have already proved its potentials. Thus to meet the global need demands are sky rocked throughout the world. Not only that production of economically feasible biofuel has double benefits it is better sustainable than the fossil one and better eco-friendly concerning the emission of carbon monoxide, nitrogen oxides, sulfur oxides, and particulate matter, etc. this production rises every year. Thus usage of enzymes also increases with that.

Bakery industry: Major of the application of enzymes found in the food industry since the mid 20^th century. Earlier, the enzyme used in these industries was mainly generated from animal and plant resources. Currently, they are derived from microbial fermentation. For example use of glucoamylase to produce better yields of glucose from starch. The process replaces the old acid hydrolysis method by reducing production cost. One enzyme used in food processing industries are protease, lipase, esterase, oxidoreductase, and isomerize, etc.

Dairy processing industry: Two major enzymes used in the dairy industry are catalase and lactase. Catalase used to remove excess H₂O₂which is due to kill pathogens in milk. Use of Lactase reduces the lactose content to prepare low lactose milk where milk flavor, sweetness and nutritional value all are increased.

Meat product processing: To improve the product quality in terms of taste, color, smell, etc, and increase the added value through by-products enzyme is used in the meat industry.

The industrial usage of enzyme accelerates due to the immobilized enzyme:

Advancement in enzyme immobilization, i.e., the add-on of the biocatalyst with a material having required chemical, physical, electrical, or mechanical properties, has shown that improvement in their activity and stability for a wide range of industrial conditions. In this field of application immobilized enzymes are quite novel and the process includes fewer processing steps.

Sometime, the benefits of immobilized enzymes must be huge to find betterment over the economics of free enzyme-catalyzed techniques which comes with a high capacity of reusability. Moreover, those must be associated with the proper function of an enzyme in the presence of an appropriate substrate.

Encapsulation or entrapment, carrier-bound attachment, and the formation of cross-linked enzyme aggregates these are the three main techniques currently used in the enzyme immobilization. Two main kinetic parameters need to find out for an immobilized enzyme to understand the efficiency of immobilization on the catalytic efficiency of the enzyme. They are maximal reaction velocity or Vmax and Michaelis constant or Km. the rate of enzyme –substrate-binding affinity and Vmax provides the rate of reaction at a specific moment. Low Km value suggests a better binding affinity between enzyme-substrate and higher suggests lesser binding affinity.

Assessment of environmental impact for enzyme implementation in the industry:

Environmental evaluation of immobilized enzyme is highly required while implementing them as biocatalyst as they are released into nature after a certain period in a bulk amount after usage. With is an aspect the life-cycle assessments and techno-economic analyses are highly important tools to assess these immobilized enzymes for commercial usage. life-cycle assessments or LCAs used to analyze the amount of energy and material used in the industry and the amount of waste and emission generated by the industry during the product formation. AS most of the cases use of enzyme positively related to the reduced usage of chemical inputs, energy, and waste streams. It is also noticed that the use of Immobilized enzyme-catalyzed technique decreased the environmental burden concerning the free enzyme-catalyzed processes. Techno-economic analyses or TEAs study the economic feasibility of the new process based on technology availability and process cost such as feedstocks, utilities, labor, and capital investments, etc.

This market is growing rapidly throughout the world. A biochemist is the most preferable candidate as an enzymologist in any of this industry. Thus it’s a golden opportunity to fix your target and enter into the specific path to achieve the goal.

How studying Biochemistry has brought changes in my life: in the perspective of future biochemists

To build large building high, bricks, cement, stone chips, blueprint, etc., everything is required Each of these materials will play an important role in determining the shape, size, and structure of the building. Just like that, we need biomolecules which are the building blocks of all living things. The knowledge of these building blocks is encapsulated in the subject ‘Biochemistry’. It helps us to understand the operating system of living bio-machines. Thus it has a huge impact on every sector of life such as agriculture, medicine, diagnostics, nutrition, forensic, pharmaceuticals, and many more. To many young minds who have chosen ‘Biochemistry’ to build their future career path, this is an interesting venture towards their dream. Let’s hear from the horse’s mouth about their feelings.

View of Ms. Samanwita Mondal (MSc 1^st year Student, Department of Biochemistry, School of Life Science, and Biotechnology).

“No one knows where the dream begins and where the truth ends”, the meaning of the line from Lila Majumder’s ‘Halde Pakhir Palok’ had always made me think from childhood. When I realized the meaning, I never thought that it’s going to happen in my life. I always dreamed to be a doctor. But there is something else written in my destiny. The journey faced many ups and downs in between my dream and destiny, finally, destiny wins the battle. And my destiny becomes Biochemistry. There’s always a story behind a story, mine is not exceptional. When I failed to grab my dream after trying several times, the combat of mind began. That time, I just had to pursue any course to get a minimum degree, as I lost all power of thinking. It’s something like “struggle for existence” according to Charles Darwin in the biological term.

My parents took me to Adamas University and enrolled in a Bachelor’s course in Biochemistry. That moment I didn’t know much about Biochemistry, according to me in medical studies there is a paper named Biochemistry, that’s it. I was a bit late when I joined university. After ten days of my joining, the first mid-term started and my condition was like drowning in water. The subject was entirely new to me, I didn’t even know what’s in the syllabus, what to read, and write in the exam. Another problem was my homesickness as for the first time I was staying in a hostel, far away from home. But, with all obstacles, I had managed to give the mid-term without any preparation and that only became possible due to encouragement from some of my teachers. I was scared when I got questions in my hand, but surprisingly the questions were not that much unknown to me! The medical preparation worked for me in that situation. Teachers were also surprised to see my exam copies. And from now on another story started to happen.

When I started to feel incompetent in all aspects after my failure, found little hope and confidence in the subject, ‘Biochemistry’. Later on, my path began to walk by holding the hand of Biochemistry. Biochemistry is the study of chemical processes within and relating to living organisms. Biochemical processes give rise to the complexity of life. Almost all areas of the life sciences are being uncovered and developed by biochemical methodology and research.

Slowly, I got to understand the chemistry inside the Biochemistry. I found my success from the subject. I got my lost confidence back, day by day by involving in the subject, the help of my friend-philosopher-guide like teachers. They are like my pillars, I know because of them I will never lose my way again in the dark. And yes, now I can proudly say that I have taken the subject into the core of my heart, that’s why I have dared to dream again.

My dream changes from doctor to be a successful Biochemist. Perhaps, that is how destiny meets with reality. Now, I truly believe that no poison can kill a positive thinker, and no medicine can save a negative thinker. With this positive energy, I want to make sense of the significance of the word “Adamas” in my future.

(Writer has been selected for a short time project at National Changhua University of Education, Taiwan, 2020).

View of Ms. Manisha De ( BSc 3^rd year Student in Department of Biochemistry, School of Life Science and Biotechnology).

Hi! To all the people, who are reading this, you’ve found your way to the tiny corner of my world, where I have shared some regular basis about the things that excite and challenge me in Science, specifically in Biochemistry. There’s one important thing to know about me at the start: I am a huge nerd about the molecules and reactions. While many students break into a cold sweat at the mentioning of ‘reactions and the molecular structures’ involving them. Students generally find them to be a topic to mug-up, but it is just the reverse. The chemistry behind every molecular structure paves the way to easily make through the reactions which keep on taking place in every cell of every individual. It is highly fascinating to see the world through a lens of molecules and their interactions. I love thinking about the molecules that drive our lives and the environment around us. Starting from the necessity of the water molecule, repairing of the damaged DNA to the fighter in us to face the foreign world, every single protein involved in the above-mentioned phases has literally created a fascination towards Biochemistry. Isn’t it very interesting to know that mundane things like the smell of the air after it rains or the way a hot iron straightens hair or even the bubble formed while washing clothes also have molecular explanations! There’s a hidden richness of molecular phenomena around us. Molecules shape the world.

When we look at the fields that study molecules of life, it doesn’t help that the names of many related disciplines are so damn confusing. Chemical Biology, Biochemistry, Molecular Biology, and Biological Chemistry all mean roughly the same thing in the dictionary. However, those of us working in these fields know that they refer to different communities that have distinct organizational cultures, and that target different types of problems using different methods and technologies. To me, Biochemistry seeks to explain biology at the chemical scale. Starting with simple building blocks like carbon, oxygen, hydrogen, and nitrogen, how can complex things as a tree, cat, or human emerge from these materials? Or even a single, replicating bacterial cell? There are biochemical questions to answer at every level of complexity.

On a serious note, it has encouraged me to look through the ingredients of every other strip of a tablet and supported me in narrating the physiological action of the well-known Paracetamol. The swelling of a region on an ant bite quickly reminds me of the inflammation pathway and makes me feel relieved when I remember that my own WBCs in the blood is there to heal the inflammation. As a whole, Biochemistry has been my pupil to observe the great challenges surrounding nature and rule a confident life over it.

(Writer was awarded Best Speaker award for a project presentation on ‘Stereochemical Effects on Drugs’2019).

Student Contributors:

Samanwita Mondal (MSc 1^st year Student, Department of Biochemistry, School of Life Science and Biotechnology).
Manisha De (BSc 3^rd year Student, Department of Biochemistry, School of Life Science and Biotechnology).

Is SARS-CoV-2 more deadly than SARS-CoV?

Student Contributor: Ms. Manisha De (BSc 3^rd year Student, Department of Biochemistry, School of Life Science and Biotechnology)

Currently, Human existence is threatened by the newly emerged human coronaviruses (HCoVs) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing global pandemic disease outbreak (COVID-19). It has till now resulted in more than 1 lakh deaths worldwide and is losing its control as the number of days increases. A few years back in 2003 world was similarly threatened by a close SARS-CoV a close relative of SARS-CoV-2. That epidemic resulted in more than 8000 infections cases and 800 deaths which is much smaller in scale concerning COVID-19. Traditional public health measures used during SARS were successful and included active case detection, isolation of cases, contact tracing and quarantine of all contacts, social distancing, and community quarantine. Within 8 months these measures successfully able to eradicate SARS.

Its almost 4 months since the emergence of SARS-CoV-2, and there is hardly any remark of its stabilization. So, the question arises even there are many similarities between SARS-CoV and SARS-CoV-2 present whether the measures applicable during SARS-CoV can be effective during today’s pandemic?

Homology analysis: According to genome analyzing COVID-19(SARS-COV-2) has 89% nucleotide identity with batSARS-like-CoVZXC21 and 82% with that of human SARS-CoV. Like SARS-CoV and MERS-CoV, the SARS-COV-2 genome contains two ﬂanking untranslated regions (UTRs) and a single long open reading frame(orf) encoding a polyprotein[1]. Further on comparing protein homology using NCBI Blastp the amino acid sequences of 28 proteins in SARS-CoV-2 were found homologous to SARS-CoV with an identity value≥65%, and query coverage≥95%[2].

Phylogenetic Analysis:

With respect to evolutionary tree the distance of SARS-CoV (Accession no.- AY274119)

(Red coloured) is closer to SARS-CoV-2 (Accession no.-MN975262) strains than MERS-CoV (Accession no.- KC164505JX869059) (Blue coloured).

Genomic comparison: There are six regions of difference (RD) in the genome sequence between SARS-CoV and SARS-CoV-2; RD1, RD2, and RD3 (448nt, 55nt, and 278nt, respectively) are partial coding sequences of the orf lab gene; RD4 and RD5 (315nt and 80nt, respectively) are partial coding sequences of the S gene; RD6 is 214nt in size and is part of the coding sequence of the orf7b and orf8 genes. These RDs may help in the development of new vaccines/drugs against SARS-CoV-2.

Proteomic comparison: Although proteins from SARS and SARS-CoV-2 were treated as homologous, two proteins (orf8 and orf10) in SARS-CoV-2 are not homologous to that in SARS-CoV. They differ in the amino acid sequence of orf8 in SARS-CoV-2 [3].Orf8 protein of SARS-CoV-2 does not contain a known functional domain or motif. Therefore, it will be clinically effective to analyze the biological function of these two speciﬁc proteins (orf8 and orf10) in SARS-CoV-2. Spike protein S2 in SARS-CoV-2 is highly conserved and shares 99% identity with those of the two bats SARS-like CoVs (bat-SL-CoVZXC21 and bat-SL-CoVZC45) and human SARS-CoV [3]. Thus, the broad-spectrum antiviral peptides against S2 have the potential to be effective treatment [4].

Transmission power: On another note, the transmissibility might be higher for COVID19 than for SARS. R₀ is a central concept in infectious disease epidemiology, indicating the risk of an infectious agent for its epidemic potential. A recent review (published in February 2020) found the average R₀ of COVID19 to be 3·28 and median R₀ to be 2·79, higher than that of SARS [5]. Despite massive containment efforts—it is certainly much faster than that reported for SARS between November 2002, and March 2003.

Infectious period: In contrast to COVID-19, identification was comparatively easier, and also isolation was effective for SARS as the peak viral shedding occurred after patients were quite ill with respiratory symptoms. Although mildly symptomatic patients have been reported for SARS, no known transmission occurred from these patients. Whereas, transmission during the early phases of illness was found to contribute to COVID-19 cases. Therefore, at the time of widespread community transmission is already evident for COVID19.

CFR (Case Fatality Ratio): Even if the CFR of COVID19 (possibly <2%) is far lower than that of SARS (10%), this is not reassuring, as a highly transmissible disease with low CFR will result in many more cases, and therefore also ultimately more deaths than SARS.[4]

Therefore, as there is no effective therapeutics or vaccines, the best way to deal with severe infections of CoVs is to control the source of infection, early diagnosis, reporting, isolation, supportive treatments, and timely publishing epidemic information to avoid unnecessary panic. For individuals, good personal hygiene, fitted masks, ventilation, and avoiding crowded places will help to prevent CoVs infection.

Reference:

Chan, et al. (2020). Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerging microbes & infections, 9(1), 221-236.
Xu, J et al. (2020). Systematic comparison of two animal-to-human transmitted human coronaviruses: SARS-CoV-2 and SARS-CoV. Viruses, 12(2), 244.
Chan, J et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes. Infect. 2020, 9, 221–236.
Xia, S et al.A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike. Sci. Adv. 2019, 5, eaav4580
Wilder-Smith, A et al. (2020). Can we contain the COVID-19 outbreak with the same measures as for SARS?. The Lancet Infectious Diseases.

Impact of lockdown on street animals

Student contributor: Ms. Kasturi Dan (BSc 1^ST year Student, Department of Biochemistry, School of Life Science and Biotechnology).

From the mouth of a street dog:

“Hello everyone”, I am Kalu, or Lalu or whatever name you may use to call me, I always respond to you anyway. Now you must be wondering who is this Kalu or Lalu. I am the street dog you cross every day while going to work, school, etc. We are born on the road, spend our entire life there, and eventually die there. We survive on whatever little we get.

In the morning, I just sit right in front of the corner tea-stall where many people gather and sometimes a few kind ones throw me some biscuits and that becomes my breakfast. Well, sometimes I receive none but I never complain, I still sit there every day. Getting lunch is usually easier. I just have to wait outside the roadside hotels and food stalls where so many people eat regularly and most of them keep plenty of food on their plates. Dinner might not be that plenty but it is still enough. Usually, apart from small fights with my fellow mates for food or sudden acts of cruelty like throwing of stones at us without any provocation by some silly kids and sometimes even adults, we street dogs don’t have much problem in surviving, but that was until a few days back when suddenly almost all shops closed, streets have become so empty. It feels weird. What has become to this busy city? Where has everyone gone? And the very few who still come out are wearing a strange thing covering their nose and mouth and they seem so frightened. There are no tea stalls, roadside food stalls or hotels open for me to get food, and even if I at all find some stalls open and people in them, they just chase me away if I go near them. Nobody gives me biscuits anymore. I don’t remember the last time I ate a proper meal. I am becoming weak day by day. I completed one year just yesterday and received a cruel birthday present from a very kind man who used to give me biscuits almost every day. When I saw him, I ran to him with such great expectations that I will finally get something to eat but instead of food, he suddenly picked up a brick and threw it at me. Ouch! It hurt. I don’t have much breath left in me to even scream or shout but I was shocked at his behavior. Why did he hurt me? What did I do wrong? I was just happy to see him. We just want some love, is that our fault? I don’t know what is going on but can guess that people are themselves afraid, too afraid to act sensibly. But don’t hurt us, don’t misunderstand us. We have not brought or are responsible for whatever it is you are afraid of. Then why are you being cruel to us? This is our world too. We have as much right to live like you. So please let us live too. Please…

Scientific Facts regarding the transmission of SARS-COV-2 form animal to Human and vice versa:

Although very rare it was reported previously that some of the coronavirus (Severe acute respiratory syndrome or SARS and Middle East respiratory syndrome or MERS) among large coronavirus families which infect animal can also infect human beings. COVID-19 causing virus SARS-COV-2 spreads mainly from person to person through respiratory droplets from coughing, sneezing, and talking.

Domesticated animals and birds like dogs, pig chicken cannot be infected by SARS-COV-2. It was tested on beagle dogs. Five three months old dogs were inoculated and kept along with two other uninoculated dogs. According to the swab test report among the virus inoculated five beagle dogs two were seroconverted but the other three and the two uninoculated dogs were all reported seronegative for SARS-COV-2. Moreover, when a similar kind of test was performed on pigs, chickens, and ducks none of them showed the presence of viral RNA in the swab test. These studies show that these animals might have very low or zero susceptibility to the novel coronavirus.

However, this report indicated that cats can be infected by SARS-COV-2. A study conducted by the Jianzhong Shi et al. showed five domestic cats were subjected to SARS-COV-2 in their nasal region. After a six days incubation period viral RNA, as well as infectious virus particles were detected in the upper respiratory tracts of all experimental models. They have also reported the cat to cat transmission is possible through droplets. But these cats are tested in laboratory conditions where this small batch of the animal was subjected to a very high dose of SARS-COV-2. This kind of high dose is not at all possible in a real life scenario. Moreover, there is no such report found which indicate that the infected cats can transmit the virus to a human. (These preliminary reports not gone through the peer-review process).

Reference:

1. Susceptibility of ferrets, cats, dogs, and different domestic animals to SARS-coronavirus-2. doi: https://doi.org/10.1101/2020.03.30.015347

2. https://www.nature.com/articles/d41586-020-00984-8