geeklog- ultimate geek knowledge: July 2006

Every Biotechnology - All in One

All the info in this article collected by Ekendra Lamsal, please credit him not this blog while quoting.

Biotechnology Engineering

This sunrise stream of engineering has come to forefront in the recent times, thanks to pathbreaking research that is taking place in the fields of pharmaceutical, agriculture, horticulture, immunology, genetic engineering, etc. Realising the immense need for structured study in the area of biotechnology and to prepare a strong talent pool, this study has been introduced that will cover vital areas of biotechnology. As one aims towards making the world a healthier, greener, disease free place to live, in the future, all activities will doubtlessly, hover around the biotechnology as the information revolution revolved around computer science.

Biotech can be defined as any technique, product or process which uses or is derived by using any living system (plant, animal or micro-organism), to make or modify a product, to improve plants or animals, or to develop microorganisms for specific use.

After establishing itself as a IT and BPO hub, Karnataka has successfully attracted the BioTech industry. As of Q1 2004 Bangalore currently houses 92 of India's 180 biotech companies, with total actual investments of over Rs 1,000 crore, of which Rs 140 crore has been venture capital funding. The companies are encouraged to invest thanks to the presence of large R&D institutions like Indian Institute of Science and the National Centre for Biological Resources. However, it is sure to face a lot of competition from media savvy Hyderabad.

Course Objective

The objective of MDBT program is to provide intensive and up-to- date learning in the fast moving area of biotechnology to students with background in basic and applied sciences - Biology, Chemistry, Physics, Agriculture, veterinary science. The basis of structure-function interaction of biological molecules, enzymes, microbes, immune systems, gene expression, fermentation, computational techniques, cell-tissue cultures, etc. are covered (in the courses) with a view of their application for use in agriculture, food processing & drinks, pharmaceutical, computer aided designing, vaccines, and production of useful chemical products..

The course will provide in-depth knowledge of the structure and function of DNA, RNA, chromosomes, and genes.
The course will offer a definition of biotechnology, including examples of real-world applications.
The course will provide opportunities to learn laboratory techniques with the appropriate business usage.
The course offers opportunities to discuss and debate selected bio-ethical issues.

COURSE CONTENT

Course components are offered arising from the following core fields:

Biotechnology and Microbiology
Biochemistry and Cell Biology
Genetics and IPR, ethics & law, Bioengineering

Specific topics covered include:

Animal and plant tissue culture
DNA manipulation in prokaryotes and eukaryotes
Purification and analysis of recombinant proteins
Protein engineering
Directed mutagenesis
Drug design & Patenting
Principals and practice of bacterial genomic library construction using plasmid vectors
Plant in vitro micropropagation and genetic engineering
Fermentation technology
Heterologous gene expression in mammalian cells
Transgenics by microinjection

Regulation and use of Biotechnology

RESEARCH REPORT

Experimental design, execution, data analysis and write up is integrated with the coursework over 1 year full time, from January through to February.
Research projects are encouraged in the following fields:

Malaria – vaccine/drug design and testing, drug therapy immuno-modulation
Plant micro-propagation and somatic embryogenesis
Plant transformation using Agrobacterium tumefaciens
In vitro storage of plant tissues, with particular emphasis on cryo-preservation
Nocardioform bacteria and mycobacterium - cloning genes of medical and environmental importance
Plant and insect virology and breeding
Detection, molecular characterization, phylogeny and evolution of new plant viruses
Viral disease resistance and gene expression
Protein biotechnology
Oncogenic viruses and cancer
Cancer cell adhesion, invasion and metastasis
Food microbiology and bacteriocins
Molecular and cellular analysis of embryonic development
The biological basis of Metastasis and applications

--------------------------------------------------------------------------------------------------------------------

"Ethics in Modern Biology"

University of Wisconsin, Madison

Robert Streiffer, Ph. D.
Assistant Professor
University of Wisconsin-Madison
http://philosophy.wisc.edu/streiffer/

Weeks 1-2.

Course Overview; History of Biotechnology and its Regulation; Recombinant DNA Techniques
I will go over administrative details, provide a quick overview of the content and requirements of the course, and provide a brief history of biotechnology. I will also provide a lay-introduction to background biology, the basics of recombinant DNA technology, and an introduction to the regulatory framework governing biotechnology. To get started on the ethics side, we will read an early article by Stephen Stitch, a philosopher who analyzes and critiques the main moral arguments which were being made towards the beginning of the rDNA debate.

Week 3-4.

Technology Studies, Risk Assessment, and Pesticide Producing Crops
In addition to readings which provide a relatively neutral framework for assessing technology, we will also look at both pro- and anti-technology views. Technology studies emphasize, among other things, unintended consequences of adopting technology that tend to be overlooked, and consequences of adopting technology that have so-called revenge effects, effects which undermine the original purpose for which the technology was adopted. As an aid to understanding these views on technology, we will look at the impact of Bt-producing crops on the monarch butterfly as an example of an unintended consequence, and we will look at the argument that the use of pesticide producing crops will result in pesticide resistant pests as an example of a revenge effect.

Weeks 5-6.

Contractualism and the Imposition of Risk
We will look at an ethical theory known as contractualism, and use it to explore the question of what the moral principles are for determining how large a benefit must be in order to justify a given level of risk when utilizing biotechnology. According to contractualism, morality requires each of us to be able to justify our actions to others on principles that it would be unreasonable for them to reject. Obviously, it would not be unreasonable for someone to reject a principle which allowed me to impose any kind of risk upon them that I wanted, and so contractualism does not allow me to do so. But it would be unreasonable for someone to reject a principle which never allowed me to impose any kind of risk upon them whatsoever, and so contractualism permits me to impose some risks on others. After looking at some of the risks various kind of biotechnology impose, we will try to see what we can do by way of coming up with a reasonable middle ground.

Week 7. Patenting Life
The standard consequentialist justification for the patent system is that allowing patents on any patentable subject matter that is useful, novel, and nonobvious promotes technological innovation by increasing expected profits and thereby attracting funding for useful research and development. In this section, we will look at the kind of ethical theory known as consequentialism, of which utilitarianism is a prominent example, and analyze the consequentialist justification for patenting biotechnology. Many people also object to patenting kinds of living organisms on non-consequentialist grounds, and we will analyze the main non-consequentialist objections as well.

Week 8.

Methods and Uses of Animal Biotechnology
As a prerequisite to focusing on ethical issues arising from the application of biotechnology to animals, we will survey the methods and uses of animal biotechnology.

Week 9.

Consequentialist Considerations regarding Animal Biotechnology
In this section, we examine the main consequentialist considerations regarding animal biotechnology, including issues of human safety, animal welfare, and sociological effects.

Week 10.

Non-Consequentialist Considerations regarding Animal Biotechnology
Many people believe that even if certain kinds of animal biotechnology would be beneficial, they are nonetheless morally unacceptable. In this section, we will analyze the main non-consequentialist objections to certain kinds of animal biotechnology.

Week 11.

Alleged Regulatory Failures
The public has a profound distrust of many of the biotechnology companies and, to a certain extent, this has spilled over onto the regulatory agencies as well. As a prelude to looking at procedural and democratic considerations, we will look at some of the allegations of misconduct or neglect that have been made against the biotech companies and regulatory agencies, and some of the ethical arguments which might be deployed in the hopes of justifying conduct which at least appears to be suspect.

Week 12-15.

Procedural and Democratic Considerations
Some of the objections voiced by the public are not so much about the particular governmental decisions that have been made regarding biotechnology as they are about the political process by which those decisions, right or wrong, were made. In this section, we look at different conceptions of democracy with an aim to exploring the question of how such decisions should be made. We will explore the extent to which representatives must defer to the public's preferences, the role that public deliberation plays in a democracy, and the role that experts should play in a democracy.

What is Genetic Modification?

The techniques of modern genetics have made possible the direct manipulation of the genetic makeup of organisms.In agriculture, genetic engineering allows simple genetic traits to be transferred to crop plants from wild relatives, other distantly related plants, or virtually any other organism.

Recombinant DNA technology thus has brought a new precision to the process of crop development, which traditionally selects desired traits through crosses between crops and their wild relatives (a laborious and relatively imprecise method).

Genetic modification can be used in many ways to control a variety of traits of plants, and the consequences of one manipulation may be completely different from another based on the traits modified.

GM Food

Controversies Surrounding the Risks and Benefits of Genetically Modified Food

Debate about GM Food

The appearance of genetically modified foods in the marketplace has resulted in a firestorm of public debate, scientific discussion, and media coverage. A variety of ecologogical and human health concerns come with the new advances made possible by genetic modification.

What Are the Benefits?
Genetically modified foods (GM foods or GMF) offer a way to quickly improve crop characteristics such as yield, pest resistance, or herbicide tolerance, often to a degree not possible with traditional methods. Further, GM crops can be manipulated to produce completely artificial substances, from the precursors to plastics to consumable vaccines.

What are the Risks?
The power of genetic modification techniques raises the possibility of human health, environmental, and economic problems, including unanticipated allergic responses to novel substances in foods, the spread of pest resistance or herbicide tolerance to wild plants, inadvertent toxicity to benign wildlife, and increasing control of agriculture by biotechnology corporations.

=====================================================================================================

Learning About Bioinformatics at the Community College

Bioinformatics requires the "wedding" of biology, mathematics, and computer science.

Bioinformatics studies must support at least three student types.

· no computer literacy; no biology (newbie)

· biology literate; does not compute

· computer literate, but no biology

The course sequences presented in this document emphasize the computing component of bioinformatics. Given the difficulty of teaching bioinformatics at community/junior colleges, the course sequences are designed such that after two-years of study a student has developed a computing foundation that offers them numerous choices.

· The student can enter a four-year bioinformatics degree program.

· The student can enter a four-year computer science degree program [and, potentially, other computer-related degree/certificate studies].

· The student can become an entry-level (newbie) computer professional.

· If the student is a computer professional, then they have updated their computing skills and have positioned themselves to stay a computer professional.

· If the student is a professional in a field other than computing, then they are positioned to re-career into the computing profession.

Course Sequences

Two-Year Pre-Bioinformatics Newbie Program [60 credits]

Semester One

biology I

math I

english I

internet I       + email, usenet, ssh, sftp, www, XHTML, CSS, SSI

unix I           + command-line, files/directories, IO, pipes, text editor

Semester Two

biology II

math II

english II       + technical writing emphasis

internet II      + websites, XML, collaboration tools (intro)

unix II          + first programming course using bash

Semester Three

biomath III      + math III/biology III

C                + C (entire language; STDC Library)

software engineering  + structured, object, generic, extreme

unix III         + make; cvs; basic SysAdmin; ApacheAdmin; sys/web programming

digital design   + hardware (devices)

Semester Four

biomath IV       + math IV/biology IV

C++              + object-oriented/templates; data structs/algorithms

Perl and Python  + object-oriented; data structs/algorithms; REs

database I       + relational (SQL) and others

assembly         + general; c/c++ executing assembly

Two-Year Pre-Bioinformatics for Biologists [60 credits]

Semester One

biomath IV       + math IV/biology IV

internet I       + email, usenet, ssh, sftp, www, XHTML, CSS, SSI

unix I           + command-line, files/directories, IO, pipes, text editor

software engineering  + structured, object, generic, extreme

database I       + relational (SQL) and others

Semester Two

internet II      + websites, XML, collaboration tools (intro)

unix II          + first programming course using bash

bioinformatics I + biotools (software); biodatabases

digital design   + hardware (devices)

C                + C (entire language; STDC Library)

Semester Three

C++              + object oriented and generic programming

Perl and Python  + object oriented; data structs/algorithms; REs

unix III         + make; cvs; basic SysAdmin; ApacheAdmin; sys/web programming

collaboration tools   + mailing lists, wikis, slashdots, sourceforge

markup languages + XML/BIOML; DTDs/Schemas; semantic web

Semester Four

software engineering II         + the practice of programming

artificial intelligence/machine learning

computer simulation/visualization/graphics

datamining

???-Year Pre-Bioinformatics for Computer Professionals [?? credits]

The course of study for these students depend upon their computing backgrounds; they take the computer classes they are deficient in. Their course of study also depends on their math and biology backgrounds. In many cases, the student should start at the beginning as if they were a newbie.

Computer professionals who start the program at the beginning do so as if they were a graduate student in an under-graduate course.

Informatics Only Component of Bioinformatics

Bioinformatics includes the professions of System and Network Administration. Bioinformatics requires secure and reliable computing systems; however, the course sequences presented in this document do not produce System Administrators.

Here is a hyperlink to the System Administration course sequences. [http://deru.com/~gdt/biotech/curriculum/sysadmin.html]

Inclusion of Assembly Language; Potential Alternate

Assembly language with C linkage added to satisfy ASU CS/CSE degrees. Non-CS students could take Software Engineering II. SEII uses The Practice of Programming which has the following table of contents: style, algorithms and data structures, design and implementation, interfaces, debugging, testing, performance, portability, notation. This follows the first software engineering course taken during the previous semester. Most source code examples are in C, which was learned last semester. Students get exposure to Java. Data structures and algorithms used in two other classes.

About Biology I and Biology II

The following is from Dr. Suzanne Kelly at SCC.

"Regarding the two biology courses, I think that the BIO 181 and a modified BIO 245/246 would fit. The modifications would mean that the course would focus on molecular and cellular biology for both lecture and labs. The existing BIO 245/246 used by MCC for its Biotechnology program is too much like BIO 181."

Computing Ethics and Computer Security

Every computer course includes a section on computing ethics and computing ethics only. Bioinformatics requires a merging of ethics from multiple disciplines.

Communication Skills

Communication skills are practiced in every course.

Bangalore Helix

Bangalore Helix is a biotech cluster being planned by the Karnataka government. Bangalore Helix would support biotech units with common infrastructure. It would comprise eight biotech incubators, covering a total area of 10,000 square feet. Excluding the cost of land (around Rs 60 crore) that has already been acquired, the cluster will involve an investment of Rs 100 crore.

The infrastructure support would be comprehensive, right from advance computing facilities to treated water necessary for biotech research. The incumbents of Bangalore Helix would pay for the infrastructure services.

Some of the well known companies are:

Accelrys Inc. - (A subsidiary of Pharmacopeia)
Advanta India Ltd.
Alltech Biotechnology Pvt. Ltd.
Amersham Pharmacia Biotec Asia Pacific Ltd.
Animal Biotech (Bangalore) Pvt. Ltd., anibio@hotmail.com
AstraZeneca R&D in Bangalore is an integral part of the global organization, with a mandate to discover new chemical entities for the treatment of infectious diseases of the developing world.
Avestha Gengraine Technologies Pvt. Ltd (Avesthagen)
Aurigene Discovery Technologies Ltd. (of Dr Reddy's Lab)
Bangalore Genei
Biocon
InfoPro Solutions - an infotech company focussing on the pharmaceutical and biotechnology drug development areas.
Prescientis
Sami Lab
Sartorius
Strand Genomics
Syngene International
Triesta LifeSciences
Xcyton

Companies that provide equipment and solutions for the biotech industry

Agilent Technologies - a subsidiary of HP, designs and manufactures test, measurement and monitoring instruments and solutions for life science research in pharmaceutical and Biotechnology industries.
Alfa Laval India Ltd.
ArisGlobal Software Pvt. Ltd.
Automed Systems Pvt. Ltd.

Related sites

Association of Biotechnology Led Enterprises (ABLE)
Currency exchange rates
Bangalore Bio 2004 - April 15-17, 2004
Institute of Bioinformatics and Applied Biotechnology (IBAB)
Karnataka Biotech Policy: BangaloreBio and ABLE
Insugen - a portal for diabetics

Laboratories

Biochemistry Lab
Momentum Transfer Lab
Unit Operations Lab
Cell & Microbiology Lab
Biokinetics Lab
Bioinformatics Lab
Immunology Lab
Bioprocess Control & Instrumentation Lab
Enzyme Technology Lab
Bioprocess & Automation Lab

The laboratories of the department are provided with the truly state of the art facilities to encourage students’ understanding of the intricacies of this new and rapidly growing applied science. Able and experienced assistants with the faculty help the students to utilize the equipment at these labs and conduct successful experiments.

Colleges and Universities

1. Acharya Institute of Technology http://www.acharyainstitutions.org

B.E. in Biotechnology Engineering - 8 semesters

Courses affiliated to Visveswaraiah Technological University, Belgaum.
Courses Approved by All India Council for Tec

Head of the Department :
Dr. Tarasaraswathi, Ph.D

Areas of Expertise : Cell Biology & Genetics, Microbiology, Molecular Biology,
Tissue Culture, Enzyme Technology and Immunology

Dr. Chandramati Shankar, Ph.D

Ms. Kavitha, B.E

2. http://tm.wc.ask.com/

3.http://www.fbae.org/Channels/Biotech_education/List_of_colleges_offering_BE_in_Biotechnology.htm

· 4. Acharya Institute of Technology
1st Cross
1st stage, Peenya
Bangalore - 560 058
Ph: 080-8398699, 8398711
Fax: 080-8378268
e-mail: director@acharyainstitutions.org
Url: www.acharyainstitutions.org

· B. M. S. College of Engineering
Bull Temple Road
Basavanagudi
Bangalore - 560 019 Ph: 080-6611586, 6615455
Fax: 080-661357
e-mail: bmsceppl@rediffmail.com
Url: www.bmsce.org

· Basaveshwar Engineering College Nijalingappa Nagar
Bagalkot - 587 102
Ph: 0835-420560
Fax: 0835-420504
e-mail: principal@becbgk.edu
Url: http://www.becbgk.edu/

· BVB College of Engineering
Vidyanagar
Hubli - 580 031
Ph: 0836-372076
Fax: 0836-374985
e-mail: principal@bvb.edu

· Bapuji Institute of Engineering and Techonlogy
P.B. No. 325
Shamanur Road
Davangere - 577 004
Ph: 08192-22245, 21461
Fax: 08192-23261
e-mail: principal@bietdvg.edu
Url: www.bietdvg.edu

· CMR Institute of Technology
132, Kundalahalli
I. T. Park Road
Near AECS layout
Bangalore - 560 037
Ph: 080-8524466, 8524630
Fax: 080-8524477
e-mail: cmrit@mantraonline.com

· GMIT
P. B. No. 4
Karur Division
Poona - Bangalore Road
Davangere - 577 006
Ph: 08192-33377, 33399
Fax: 08192-33344
e-mail: info@set-gmit.org
Url: www.set-gmit.org

· KLES College of Engineering and Technology
Udymabag
Belgaum - 590 008
Ph: 0831-440322
Fax: 0831-441644
e-mail: kleprinc_bgm@yahoo.com

· M. S. Ramaiah Institute of Technology
M. S. R. Nagar
Bangalore - 560 054
Ph: 080-3600822, 3606934
Fax: 080-3603124
e-mail: principal@msrit.edu
Url: www.msrit.edu

· M. V. J. College of Engineering (MVJCE)
Whitefield
Bangalore - 560 067
Ph: 080-8452324/635
Fax: 080-8451524
e-mail: principal@mvjeducation.com
Url: www.mvjeducation.com

· Nagarjuna college of Engineering and Technology
#38/1, Ramagondanahalli
Yelahanka Hobli
Bangalore - 560 064
Ph: 080-8564004/02
Fax: 080-8561885
Url: www.nagarjunaeducation.com

· New Horizon College of Engineering
Kadabhisanahalli
Varthur Hobli
Panathur Post
Bangalore - 560 087
Ph: 080-8440666/532
Fax: 080-5263042
e-mail: nhel@rediffmail.com
Url: www.newhorizonindia.edu

· NMAM Institute of Technology
Nitte
Udupi - 574 110
Ph: 08258-41264,20039
Fax: 08258-41265
e-mail: nmamit.eng.coll@hotmail.com
Url: www.nittetrust.org

· PES Institute of Technology
100 ft Ring Road
BSK III Stage
Bangalore - 560 085
Ph: 080-6721983/2108
Fax: 080-6720886
e-mail: pesit@yahoo.com
Url: www.pes.edu

· PA College of Engineering Kairangala
Mangalore
Url: www.paengg.com

· R. V. College of Engineering
R. V. Vidyaniketan Post
12th KM Mysore Road
Bangalore - 560 059
Ph: 080-8601701/0184
Fax: 080-8602914
e-mail: principal@rvce.ac.in
Url: www.rvce.ac.in

· Shreedevi Institute of Engineering, Tumkur

· Sir M. Visvewsvaraya Institute of Technology
Hunasamaranahalli
Via Yelahanka
Bangalore - 562 157
Ph: 080-8467248/77024
Fax: 080-8467081
e-mail: sirmvit@bgl.vsnl.net.in
Url: www.sirmvit.edu