If you are interested to do a project in Bioinformatics and having confusion as to which topic we can choose to do . Then this article sure would help you.Just I have given the outline of all topic headings. Read it and select which suites you. The Bioinformatics project can be categorized into two.
1. Analysis
2. Programming
ANALYSIS:
In this the various types of projects can be done.
1. Cloning and restriction studies.
2. PCR and Primer Design
3. Structure Prediction or Modeling of Proteins
4. Genome analysis and annotation
5. Nucleotide sequence and analysis
6. Structural analysis
7. Phylogenetic analysis
8. SNP Analysis
9. Gene Silencing
10. Protein Sequence Analysis
11. Comparative Genomics
12. Data mining for microarrays
13. Docking and Drug Design
14. RNA Analysis
15. Drug Target Identification.
16. Vector Construction
PROGRAMMING:
we can also do programming projects like tools developing, algorithm development. But it is not necessary for Biotech students. Though can give a try!!!
If you want to learn Basic Biotechnology, then I am sure this is the right place. It will make you to think a lot while you can learn. Before looking at the answers please think well and then proceed to see the answers!!Some of them are my own answers which can be found relevant while you can cross check with theory. Then, I can say if you wanna do any project in Gene Silencing or RNAi Technology it can be useful to you.I have also given my project outlines on Gene Silencing of HIV-1 Virus through Insilico siRNA Drug Designing.
It can be like doubts in biotechnology stream like molecular biology stating facts from basics driving you with concepts and make you to think?
I have the following questions or can say (doubts!! Fun) in mind or can say I somehow got the thoughts about it. If anybody can come out with answers its welcome!!!!
Though it may be look stupid or confusing or puzzle to you, Be Patient to read it fully. It will make you to travel inside Biotechnology for sure. Rather if you want to know about basic concepts in Biotech or Molecular Biology. This will surely help you to develop sound basic knowledge in biotechnology for sure??
If anything found wrong you can answer me and correct it. Give a thought and try to give me some comments or reply!!! I would feel much happy if any one can come out with some answers while you read.
TRAVELLING TO MOLECULAR BIOLOGY:
The Molecular Biology Basics, you would have learned the Central Dogma of Molecular Biology. Check this video for good movie on central Dogma But have any one thought about why the phenomenon is like that. Anyhow that's not my question. Read the below lines and think about it.
In the central dogma, it states the phenomenon DNA to RNA to Protein, (DNA undergoes transcription to produce mRNA and mRNA undergoes translation to produce Protein) but just consider the situation in viruses. In Viruses, there are both RNA and DNA virus. (RNA virus has RNA as Genetic material where DNA will be the genetic material in all other cases.) Q1.So, in RNA virus: Is the phenomenon RNA gives to Protein directly? If yes explain? If no then what is the mechanism? A good Video on Central Dogma concepts
MY ANSWER for Q1:
Though I want you to think about it, I just thought to give you some clue regarding it. So, you can find more information from that!!! Let me tell you something about Retro Viruses to understand. "Retro Viruses are RNA Viruses. E.g. HIV" However "Not all RNA viruses are retroviruses E.g. Measles virus and flu virus are RNA viruses"
Now!! Coming back, the answer for the question is stated below. The distinguishing feature of all retroviruses is that they replicate backward using the enzyme reverse transcriptase in the first two steps.
The first two steps of this process have no error-correction mechanisms. The three enzymes found inside a retrovirion are reverse transcriptase, integrase, and protease. However, this is not a complete answer and it can again rise to ask a question Q2.what is the need for RNA to reverse to DNA and again reversing to RNA???? Well you can say Central Dogma, however my question is what is the need? Is there any important activity which occurs by reversing to DNA? Q3. What could be the phenomenon in other RNA Viruses like Measles or Flu? I just want to stop here and leave it to you to think. However I have presented the clue of answers for these below just after DNA Viruses.
Again in DNA viruses: Q4. Simple question- does DNA virus just follows Central Dogma? If you could answer this, well I think you got the logic right!!!! Otherwise, you must get your basics well and then read this passage. You will become expert in Molecular Biology.
MY ANSWERS for Q2, Q3, Q4:
I tried to explain the concept of Retro virus. I also asked you why that RNA is reversing to DNA and then again reversing back to RNA (read statements above DNA virus). The answer is: Viruses are non-living matter. They get living only after entering the living host. Living host has DNA as genetic material. Think carefully!! Viruses should integrate into DNA of the living host to replicate. So, that's where integrase comes into picture. So, RNA has to get reversed into DNA just to get integrated into DNA of Host. (I hope now you are clear????)
More clearly, Viruses are non-living. You must not confuse Central Dogma Concepts with Viruses. The Host cells just takes up a genetic material from Virus and central dogma occurs only in host(not virus) to express the protein of virus resulting in disease(viral disease). So answer for Q4 is DNA of virus just has to get integrated into host DNA (lucky viruses, easy for them. No hell like RNA viruses!! In Funny style)
Don't stop. There are lots of puzzles to make tick of brain!!! Just the Questions will follow.
TRAVELLING INTO VIRUS WORLD:
The basic about the viruses: Viruses are non-living outside the host and only when it enters inside the host it is living (Read above-Travelling into Molecular Biology). It affects the host by producing a protein which is toxic and so viral disease may occur. Q5.Simple Question- Virus becomes living only inside cell. Is this right? Of course you can say that is correct!! Also I would like you to think in this aspect and find out the answer. Virus contains the viral protein coat (Virions). Note: This viral protein coat is also present when virus is outside host, which can be produced only by translation mechanism. Now is that above question having sense?? So, is there any mechanism outside the host happening to produce that viral protein?? So, is the saying "viruses are non-living outside the cell- Wrong"? Justify your answer.
MY ANSWER TO Q5:
Yeah, again just think over it before reading further!! There is no great logic however here. You must have learned about Life Cycle of Virus. In simple way to explain I have given life cycle for Virus: A video on Life cycle of HIV Virus
Attachment of the viral protein coat (virions) to the receptor and enters into host cell.
Reverse transcription of RNA to DNA using the enzyme reverse transcriptase
Integration into the host nucleus using the enzyme integrase.
Protein synthesis- viral toxic protein and viral coat protein (Note :Both are synthesized)
Virion reassembly- long proteins are split into small virions by enzyme protease
Release of virions- Virions then come out by bursting cell (Lytic Life cycle).
Hope you can find it easy. If not read the above another time as glance, you can understand more better for sure!!! (Another Video on HIV Life Cycle)
TRAVELLING INTO THE CELLS:
Basic Genetics-There are millions of tissues in our body. Tissues are made up of cells where each cell consists of 23 pairs of chromosomes of total 46 chromosomes. Each and every chromosome contains the same set of genes. Genes undergo translation mechanism to produce proteins. Am I correct? If you feel that the above sentences are correct. Then please try to answer my question. ??? Q6. Now!!! Why some cells alone are able to produce a particular type of protein and not other cells. For example: Islets of Langerhans cells are alone able to produce Insulin and not other cells. Justify?
MY ANSWER TO Q6:
Well!!! It may sound; that it's regarding Cell Biology concepts like particular cell can produce particular protein like!!(He he! Not so!!!!!!!!) I am trying my best to answer clearly. "Any cell can produce any protein" but what makes only one particular cell alone to produce protein is guided by cell signaling and gene expression regulations.
Q7. How cell biology have role in Gene Expression??
So let me explain with Insulin as example. What is Insulin??? A Hormone (Protein) needed for glucose metabolism. All the carbohydrates we eat get converted into glucose and it has to be stored in our body for use in our unhealthy (sick condition). So Insulin is needed for this job.
Now!!!! When the glucose levels are high, cell detects it and Ligands(Signal Molecules) pass the information to cell receptors and to express the Insulin Gene. This signaling is of Auto Signaling Type.
Types:
Auto Signaling- signal molecules signaling same cell.
Para Signaling-signal molecules signaling adjacent cell.
Endo Signaling- signal molecules signaling distant cell.
OOPS!!! I have gone deeper on cell biology concepts, think so. Hope you can understand.
Q8. What is gene expression regulation to do if cell signaling has made the gene active??
Cell Signals when to produce the gene. Gene Expression Regulation job is to make gene to start and stop. Once Sufficient Insulin have been produced, the process must Stop. Right! This is called as Gene Expression Regulation.
For Gene Expression Regulation- You need to know these gene elements (Promoters, Enhancers, Operators, repressors) which will be found in all genes. However Introns and repeated sequence may also play a role.
Important- you can also stop a gene expression apart from Gene Regulation by means of a technique called Gene Silencing (SWITCHING OFF OF THE GENE.) Best Video on Gene Silencing
TRAVELING INTO YOUR PROJECT:
Now you are set to do a project with the above gained BASICS. In case of Biotechnology, I can say Biotechnology is a small field with a large amount of applications. So, it's Big. Also please remember that IDEA is the project. You must think Creative. This is not like hell of sweat work you need to do in your project work. All you have to do is:
Know your field of interest to do project.(Analyze yourself to find your interest)
Get an IDEA of what you are doing to do in project.
Plan your project- Must know full detail about that Topic with greatest basic knowledge.
Formulate your Idea into step by step work.
Go for Work. (If you had worked out perfectly the above 4 points. Then sure you can expect the result you expected from your Idea!! regardless of work errors)
Now to make you understand more clearly, I can say few things about my project which can help understand better what I am trying to convey!!
I choose my project field in Molecular Biology using Bioinformatics tools.
IDEA- My topic is about "INSILICO siRNA DRUG DESIGN AND GENE SILENCING APPROACH FOR HIV-1 VIRUS IN AIDS"
Plan – how HIV (RNA virus) works, how virus gets integrated into host cells, how gene regulation takes place, how can we control gene expression –Gene Silencing?
Steps-
Prediction of the mRNA sequence in HIV virus responsible.
siRNA sequence prediction for the corresponding mRNA.
Testing the siRNA Efficiency
Checking the siRNA specificity
Predicting the suitable siRNA delivery option.
Work was using online tools.
Hope that you got the point what I was trying to convey. For Biotechnology we must learn the basics to greatest extent in some good books side by side and go for learning the syllabus books or prescribed books. (Not a great issue).
Must focus your Field of Interest and read on that at your own interest apart from learning the mixture of subjects in your every semester.
ADVAITHA ALUMNI ASSOCIATION An Alumni Association for the Department of Biotechnology, Rajalakshmi Engineering College.
Idea of Advaitha Alumni: Let us start how the idea of Alumni Association originated. To say only a few colleges have Alumni Association and so far Association for Biotech groups is quite low. As a new Department and most of us don’t have any awareness what are the opportunities and where are they available to us, it is necessary to start anAlumniAssociation. The idea is to make a very strong network by connecting all our Biotech students and staffs of Rajalakshmi Engineering College.
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