abroad-phd- scholorships-countries-positions-area of research-bioguide-lifescienceguider

1) chemistry scholorship info canada

2) computational materail scinece…australia

3) autoimmune-vaccine-research…taiwan

4) Mechanical design and characterisation…italy

5) cell research..belgium

6) cancer biology…denmark

spontaneous generation- needham- history of microbiology

Spontaneous generation is the hypothesis that some vital force contained in or given to

organic matter can create living organisms from inanimate objects. Spontaneous generation was

a widely held belief throughout the middle ages and into the latter half of the 19th century.

In fact, some people still believe in it today. The idea was attractive because it meshed

nicely with the prevailing religious views of how God created the universe. There was a

strong bias to legitimize the idea because this vital force was considered a strong proof of

God’s presence in the world. Many recipes and experiments were offered in proof. To create

mice, a recipe called for dirty underwear and wheat grain to be mixed in a bucket and left

open outside. In 21 days or less, you would have mice. The real cause may seem obvious from a

modern perspective, but to the proponents of this idea, the mice spontaneously arose from the

wheat kernels.
Another often-used example was the generation of maggots from meat that was left in the open.

The failing here was revealed by Francesco Redi in 1668 with a classic experiment. Redi

suspected that flies landing on the meat laid eggs that eventually grew into maggots. To test

this idea he devised the experiment shown in Figure 1-20. Here he used three pieces of meat.

One piece of meat was placed under a piece of paper. The flies could not lay eggs onto the

meat and no maggots developed. The second piece was left in the open air, resulting in

maggots. In the final test, a third piece of meat was overlaid with cheesecloth. The flies

were able to lay the eggs into the cheesecloth and when this was removed no maggots

developed. However, if the cheesecloth containing the eggs was placed on a fresh piece of

meat, maggots developed, showing it was the eggs that “caused” flies and not spontaneous

generation. This helped to end the debate about spontaneous generation for large organisms.

However, spontaneous generation was so seductive a concept that even Redi believed it was

possible in other circumstances.
Figure 1-20 The Redi experiment

Using several pieces of meat, paper and cheesecloth, Francesco Redi produced compelling

evidence against the theory of spontaneous generation. One of the strong points of this

experiment was its simplicity, which allowed others to easily reproduce it for themselves.

See the text for details of the experiment.
The concept and the debate were revived in 1745 by the experiments of John Needham. It was

known at the time that heat was lethal to living organisms. Needham theorized that if he took

chicken broth and heated it, all living things in it would die. After heating some broth, he

let a flask cool and sit at a constant temperature. The development of a thick turbid

solution of microorganisms in the flask was strong proof to Needham of the existence of

spontaneous generation. Lazzaro Spallanzani later repeated the experiments of Needham, but

removed air from the flask, suspecting that the air was providing a source of contamination.

No growth occurred in Spallanzani’s flasks and he took this as evidence that Needham was

wrong. Proponents of spontaneous generation discounted the experiment by asserting that air

was required for the vital force to work.
It was not until almost 100 years later that the great French chemist Louis Pasteur, pictured

in Figure 1-5, put the debate to rest. He first showed that the air is full of microorganisms

by passing air through gun cotton filters. The filter trapped tiny particles floating in the

air. By dissolving the cotton with a mixture of ether and alcohol, the particles were

released and then settled to the bottom of the liquid. Inspection of this material revealed

numerous microbes that resembled the types of bacteria often found in putrefying media.

Pasteur realized that if these bacteria were present in the air then they would likely land

on and contaminate any material exposed to it.
Figure 1-5 Louis Pasteur

The French microbiologist Louis Pasteur. Drawing by Tammi Henke
Pasteur then entered a contest sponsored by The French Academy of Sciences to disprove the

theory of spontaneous generation. Similar to Spallanzani’s experiments, Pasteur experiment,

pictured in Figure 1-6, used heat to kill the microbes, but left the end of the flask open to

the air. In a simple, but brilliant modification, the neck of the flask was heated to melting

and drawn out into a long S-shaped curve, preventing the dust particles and their load of

microbes from ever reaching the flask. After prolonged incubation the flasks remained free of

life and ended the debate for most scientists.
Figure 1-6 The swan neck flask experiment

Pasteur filled a flask with medium, heated it to kill all life, and then drew out the neck of

the flask into a long S shape. This prevented microorganisms in the air from easily entering

the flask, yet allowed some air interchange. If the swan neck was broken, microbes readily

entered the flask and grew.
A final footnote on the topic was added when John Tyndall showed the existence of

heat-resistant spores in many materials. Boiling does not kill these spores and their

presence in chicken broth, as well as many other materials, explains the results of Needham’s

experiments.
While this debate may seem silly from a modern perspective, remember that the scientists of

the time had little knowledge of microorganisms. Koch would not isolate microbes until 1881.

The proponents of spontaneous generation were neither sloppy experimenters nor stupid. They

did careful experiments and interpreted them with their own biases. Detractors of the theory

of spontaneous generation were just as guilty of bias, but in the opposite direction. In

fact, it is somewhat surprising that Pasteur and Spallanzoni did not get growth in their

cultures, since the sterilization conditions they used would often not kill endospores. Luck

certainly played a role. It is important keep in mind that the discipline of science is

performed by humans with all the fallibility and bias inherent in the species. Only the

self-correcting nature of the practice reduces the impact of these biases on generally held

theories. Spontaneous generation was a severe test of scientific experimentation, because it

was such a seductive and widely held belief. Yet, even spontaneous generation was overthrown

when the weight of careful experimentation argued against it. Figure 1-21 lists important

events in the spontaneous generation debate.

Telnet- bioinformatics- elementary commands- protocols- useful commands in computer languages- useful protocols for bioinformatics

Telnet is a user command and an underlying TCP/IP protocol for accessing remote computers. Through Telnet, an administrator or another user can access someone else’s computer remotely. On the Web, HTTP and FTP protocols allow you to request specific files from remote computers, but not to actually be logged on as a user of that computer. With Telnet, you log on as a regular user with whatever privileges you may have been granted to the specific application and data on that computer. A Telnet command request looks like this (the computer name is made-up): telnet the.libraryat.whatis.edu The result of this request would be an invitation to log on with a userid and a prompt for a password. If accepted, you would be logged on like any user who used this computer every day. Telnet is most likely to be used by program developers and anyone who has a need to use specific applications or data located at a particular host computer.Telnet was developed in 1969 beginning with RFC 15, extended in RFC 854, and standardized as Internet Engineering Task Force (IETF) Internet Standard STD 8, one of the first Internet standards. The term telnet may also refer to the software that implements the client part of the protocol. Telnet client applications are available for virtually all computer platforms. Most network equipment and operating system with a TCP/IP stack support a Telnet service for remote configuration (including systems based on Windows NT). Because of security issues with Telnet, its use has waned in favor of SSH for remote access. The Telnet program runs on your computer and connects your PC to a server on the network. You can then enter commands through the Telnet program and they will be executed as if you were entering them directly on the server console. This enables you to control the server and communicate with other servers on the network. To start a Telnet session, you must log in to a server by entering a valid username and password. Telnet is a common way to remotely control Web servers TELNET PROTOCOL SPECIFICATION The purpose of the TELNET Protocol is to provide a fairly general, bi-directional, eight-bit byte oriented communications facility. Its primary goal is to allow a standard method of interfacing terminal devices and terminal-oriented processes to each other. It is envisioned that the protocol may also be used for terminal-terminal communication (“linking”) and process-process communication (distributed computation). Telnet 5250 IBM 5250 or 3270 workstation emulation is supported via custom telnet clients, TN5250/TN3270, and IBM servers. Clients and servers designed to pass IBM 5250 data streams over Telnet generally do support SSL encryption, as SSH does not include 5250 emulation. Under OS/400, port 992 is the default port for secured telnet.

Scope of bioinformatics- jntu biotechnology bioinformatics syllabus- bioinformatics guide- unit-1

Bioinformatics is the application of computer technology to the management of biological information. It combines computer science with biology and genetics with a good-sized dollop of mathematics, statistics and other medical specialties thrown into the mix. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. Bioinformatics is not just a useful tool in biological research or drug development. It is an indispensable ally of researchers. The technology is versatile and can be applied whenever gene, protein and cell research are used for the discovery of a new drug or a new herbicide/herbicide-resistant crop combination. Drug toxicology, pharmacogenetics and clinical trial studies can also benefit from this technology which can even be used to genetically engineer crops and livestock that have enhanced nutritional qualities and the ability to produce pharmaceuticals. Recent years have seen an explosive growth in biological data. It should be managed and stored for various purposes. Also the managed data should be in tune with the current times. Here comes the relevance of bioinformatics. Bioinformatics combines the tools and techniques of mathematics, computer science and biology in order to understand the biological significance of a variety of data. So if you like to get into this new scientific field you should be fond of these ‘classic’ disciplines. Because the field is so new, almost everyone in it did something else before. Some biologist went into bioinformatics by picking up programming but others entered via the reverse route. specific areas that fall within the scope of Bioinformatics: Here are some specific areas that fall within the scope of Bioinformatics: Sequence assembly : The genome of an organism is assembled from thousands of fragments which must be correctly �stitched� together. This process, which requires the use of sophisticated computer-based methods, is carried out by a specialist in Bioinformatics. Database design and maintenance: Many pharmaceutical companies maintain private data banks of gene sequences and other biological and chemical information. These repositories must be continually updated with data generated internally and from outside sources. This is a challenging task, and the design and maintenance of these complex databases has become an important part of Bioinformatics. Sequence (gene) analysis: Once the DNA sequence of a fragment of the genome has been determined, the work has just begun; one must next understand what the function of the gene is. This involves locating regions of the gene that code for a protein product that are involved in regulation and control and also finding those sections of the gene (introns) that are clipped out and discarded. The gene may be compared against databases of known genes with well-understood function, to find clues to its role in health or disease. All of these analyses are carried out using powerful computers and specialized software, and many would consider this activity the most important area of focus within Bioinformatics. Proteomics: A relatively new area, proteomics studies not the entire genome, but rather the portion of the genome that is expressed in particular cells. This often involves cutting-edge technology, such as the use of micro arrays (�DNA-on-a-chip�) which allows the expression level of thousands of genes in a cell sample to be quickly determined. Drug discovery: It’s not easy to design drugs that choose their targets this efficiently. In fact, it’s so difficult that drug companies have hardly ever tried. They have relied instead on trial and error, testing hundreds of potential drugs in animals to find a few that actually cure without killing. But these molecular crapshoots are terribly wasteful, which is why drug designers are today turning to a fast-growing new area of computer science known as bioinformatics to fuel their endless quest for newer drugs and better targets. They are found in academic, overnment and industrial research labs. Scope of bioinformatics in India Bioinformatics career in is increasingly attracting the youngsters in India today. The scope of bioinformatics is in areas like database design and maintenance, sequence assembly, proteomics, clinical pharmacologist, sequence analysis, informatics developer and bio-analytics. Excellent job opportunities are available in Biotech and Pharmaceutical companies in India. Indian companies like Wipro, Reliance, Satyam, TCS and companies like Accelrys and IBM Life Sciences Pubgene, Silicon Genetics and Tessella offer good employments to the bioinformatics candidates. Due to increasing demand of bioinformatics candidates, a career in bioinformatics offer good prospects.

FTP commands- how to use FTP- bioinformatics syllabus- bioinformatics guide- biotechnology guide- biotechnology material

FTP commands Commands which begin with the letter X are generally reserved for experimental extensions, although one should use SITE subcommands instead for this purpose. RFC959 defines the following FTP commands, which were also present in RFC765: USER: supplies the username for login PASS: supplies the password for login ACCT: supplies accounting information. For example, a user may work on multiple projects; the account can be used to ensure that the charges for the data storage are billed to the correct project. (Not commonly implemented). CWD: changes the working directory to that specified REIN: removes all authentication information and parameter settings; must be followed by relogin via USER QUIT: terminates the connection PORT: host/port specification for data transfer PASV: enter passive mode TYPE: specify data type and vertical format control (see above) STRU: specify data structure (see above) MODE: specify transmission mode (see above) RETR: initiates a data transfer from server to client, specifying name of file to retrieve STOR: initiates a data transfer from client to server, specifying name file is to be stored in on server APPE: similar to STOR, except if file already exists, append received data to end of it rather than create ALLO: allocates space for a file. Optionally, specifies the maximum size of each record. REST: specifies the restart marker from which the transfer is to resume. Originally intended for use with restart markers sent by the server in B or C mode, but later extended in RFC3659 to byte offsets specified in S mode. RNFR: to rename a file, specify the file to be renamed RNTO: to rename a file, specifies the new name for the file, and performs the rename. Often also used to implement moves. DELE: deletes a file PWD: prints the current working directory LIST: opens a data connection with A or E data type, to transfer a listing of files in the current directory. The format of data is system-specific, but intended to be human readable. NLST: similar to LIST, but transfer unadorned names of files with CRLF or NL. SITE: provides subcommands to perform system specific services. The nature of these services is undefined. STAT: without arguments, current status of connection. With argument, equivalent to LIST, but the listing is transferred over the control connection encapsulated in messages. HELP: provides HELP, optionally with an argument to specify the specific command on which help is requested. NOOP: does nothing RFC959 adds the following new commands which were not present in RFC765: CDUP: changes the working directory to the parent. Present since the notation for parent directory varies from platform to platform (although most commonly .. on systems descended from Unix or MS DOS). SMNT: mount a different file system or volume. Intended for systems such as DOS or VMS where there is a distinction between volume and directory in pathnames; but commonly unimplemented even on such systems. STOU: store unique – initiates a data transfer from client to server; server shall chose a unique name for file to be received RMD: removes a directory MKD: creates a directory PWD: prints the current directory SYST: identifies the operating system of the server RFC765 described a number of commands which were removed in RFC959. These have not been part of FTP implementations since the early 1980s, since their functionality was later replaced (in part) by SMTP: MLFL: used to send email over the data connection MAIL: used to send email over the control connection MSND: like MAIL, but sends data directly to user’s terminal rather than their mailbox MSOM: behaves as either MAIL or MSND—send to terminal if allowed, otherwise to mailbox MSAM: similar to MSOM—except that MSOM only sends to mailbox if delivery to terminal not possible; but MSAM sends to mailbox irrespective of whether terminal delivery is successfully attempted MRSQ: enables transmission of a single email to multiple users at the same host MRCP: subsequent to MRSQ, identifies one such recipient; repeated for each recipient RFC2228 adds a number of commands related to encryption and message authentication: AUTH: identifies the authentication/security mechanism to be used ADAT: specifies security data specific to the chosen AUTH mechanism PBSZ: used to negotiate maximum buffer size for encrypted data PROT: specifies protection level for data channel. Following levels are defined: C (Clear) – data channel is subject neither to encryption nor integrity protection S (Safe) – integrity protection applied to data channel E (Confidential) – encryption applied to data channel P (Private) – both encryption and integrity protection applied to data channel CCC: disables integrity protection for subsequent commands on control channel MIC: sends a command with integrity protection CONF: sends a command with confidentiality protection ENC: sends a command with both integrity and confidentiality protection RFC1639 (“FOOBAR”; succeeded RFC1545) adds support for FTP over arbitrary transport protocols, such as IPX/SPX or OSI. For this, it defines two new commands: LPRT: similar to PORT, but supports arbitrary address and port formats. LPSV: similar extension to PASV RFC2389 defines two new commands used as a generic extension mechanism for FTP: FEAT: retrieves a listing of optional features supported by FTP server OPTS: a generic mechanism for the client to specify options to arbitrary FTP commands RFC2428 adds two new commands, similar in principle to RFC1639 but differing in details: EPRT: similar to PORT, but supports arbitrary address families rather than only IPv4; specifically intended for IPv6. EPSV: similar extension to PASV LPRT sends addresses as an arbitrary octet string (albeit decimal encoded), EPRT sends them as formatted strings, the format of the string being dependent upon the address format. EPRT assumes a the use of TCP-style 16-bit port numbers, whereas LPRT is more flexible and supports transport protocols with greater than 16-bit port numbers. RFC2640 adds one new command: LANG: used to choose the language for FTP messages RFC3659 defines several new commands: MDTM: retrieve file modification time SIZE: retrieve file size MLSD: retrieve listing of files in a directory. Unlike NLST, this returns not only file names but also attributes; but unlike LIST, it returns the attributes in an extensible standardised format rather than an arbitrary platform-specific one. MLST: same as MLSD, but retrieves listing for an individual file rather than a directory. For directories, retrieves their own attributes rather than a listing of their members. MLST does not require a data connection, but returns a single line containing the listing for the requested path.

FTP- file transfer protocol- elementary commands- protocols of computer

File Transfer Protocol (FTP), a standard Internet protocol, is the simplest way to exchange files between computers on the Internet. Like the Hypertext Transfer Protocol (HTTPwhich transfers displayable Web pages and related files, and the Simple Mail Transfer Protocol (SMTP), which transfers e-mail, FTP is an application protocol that uses the Internet’s TCP/IP protocols. FTP is commonly used to transfer Web page files from their creator to the computer that acts as their server for everyone on the Internet. It’s also commonly used to download programs and other files to your computer from other servers. FTP runs on Transmission Control Protocol.ususally it has three basic modes which include active, passive and extended passive modes. In active mode, the FTP client opens a dynamic port, sends the FTP server the dynamic port number on which it is listening over the control stream and waits for a connection from the FTP server. When the FTP server initiates the data connection to the FTP client it binds the source port to port 20 on the FTP server. In passive mode, the FTP server opens a dynamic port, sends the FTP client the server’s IP address to connect to and the port on which it is listening (a 16-bit value broken into a high and low byte, as explained above) over the control stream and waits for a connection from the FTP client. In this case, the FTP client binds the source port of the connection to a dynamic port. In extended passive mode, the FTP server operates exactly the same as passive mode, however it only transmits the port number (not broken into high and low bytes) and the client is to assume that it connects to the same IP address that was originally connected to. The FTP protocol supports resuming of interrupted downloads using the REST command. The client passes the number of bytes it has already received as argument to the REST command and restarts the transfer. In some commandline clients for example, there is an often-ignored but valuable command, “reget” (meaning “get again”), that will cause an interrupted “get” command to be continued, hopefully to completion, after a communications interruption.The original FTP specification is an inherently unsecure method of transferring files because there is no method specified for transferring data in an encrypted fashion. This means that under most network configurations, user names, passwords, FTP commands and transferred files can be captured by anyone on the same network using a packet sniffer. This is a problem common to many Internet protocol specifications written prior to the creation of SSL, such as HTTP, SMTP and Telnet. The common solution to this problem is to use either SFTP (SSH File Transfer Protocol), or FTPS (FTP over SSL), which adds SSL or TLS encryption. Anonymous FTP A host that provides an FTP service may additionally provide anonymous FTP access. Users typically login to the service with an ‘anonymous’ account when prompted for user name. Although users are commonly asked to send their email address in lieu of a password, little to no verification is actually performed on the supplied data. As modern FTP clients typically hide the anonymous login process from the user, the ftp client will supply dummy data as the password (since the user’s email address may not be known to the application). For example, the following ftp user agents specify the listed passwords for anonymous logins.

Eleementary commands and protocols in bioinformatics- elementary commands and protocols in computer language- btech biotechnology- jntu- syllabus- bioinformatics material- concepts of bioinformatics

File eXchange Protocol (FXP) and (FXSP) is a method of data transfer which uses the FTP protocol to transfer data from one remote server to another (inter-server) without routing this data through the client’s connection. Conventional FTP involves a single server and a single client; all data transmission is done between these two. In the FXP session, a client maintains a standard FTP connection to two servers, and can direct either server to connect to the other to initiate a data transfer. The advantage of using FXP over FTP is evident when a high-bandwidth server demands resources from another high-bandwidth server, but only a low-bandwidth client, such as a network administrator working away from location, has the authority to access the resources on both servers. Transport Layer Security (TLS) and its predecessor, Secure Sockets Layer (SSL), are cryptographic protocols that provide security and data integrity for communications over networks such as the Internet. TLS and SSL encrypt the segments of network connections at the Transport Layer end-to-end. HyperText Transfer Protocol Standard application-level protocol used for exchanging files on the World Wide Web. HTTP runs on top of the TCP/IP protocol. Web browsers are HTTP clients that send file requests to Web servers, which in turn handle the requests via an HTTP service. HTTP was originally proposed in 1989 by Tim Berners-Lee, who was a coauthor of the 1.0 specification. HTTP in its 1.0 version was “stateless”: each new request from a client established a new connection instead of handling all similar requests through the same connection between a specific client and server. Version 1.1 includes persistent connections, decompression of HTML files by client browsers, and multiple domain names sharing the same IP address. Telnet (teletype network) is a network protocol used on the Internet or local area networks to provide a bidirectional interactive communications facility. Typically, telnet provides access to a command-line interface on a remote host via a virtual terminal connection which consists of an 8-bit byte oriented data connection over the Transmission Control Protocol (TCP). User data is interspersed in-band with TELNET control information. The term telnet may also refer to the software that implements the client part of the protocol. Telnet client applications are available for virtually all computer platforms. Most network equipment and operating system with a TCP/IP stack support a Telnet service for remote configuration (including systems based on Windows NT). Because of security issues with Telnet, its use has waned in favor of SSH for remote access. Secure File Transfer Protocol or SFTP) is a network protocol that provides file transfer and manipulation functionality over any reliable data stream. It is typically used with version two of the SSH protocol (TCP port 22) to provide secure file transfer, but is intended to be usable with other protocols as well.allows only file transfers, the SFTP protocol allows for a range of operations on remote files – it is more like a remote file system protocol. An SFTP client’s extra capabilities compared to an SCP client include resuming interrupted transfers, directory listings, and remote file removal. [1] For these reasons it is relatively simple to implement a GUI SFTP client compared with a GUI SCP client. SMTP Simple Mail Transfer Protocol, a protocol for sending e-mail messages between servers. Most e-mail systems that send mail over the Internet use SMTP to send messages from one server to another; the messages can then be retrieved with an e-mail client using either POP or IMAP. In addition, SMTP is generally used to send messages from a mail client to a mail server. This is why you need to specify both the POP or IMAP server and the SMTP server when you configure your e-mail application. IMAP Internet Message Access Protocol, a protocol for retrieving e-mail messages. The latest version, IMAP4, is similar to POP3 but supports some additional features. For example, with IMAP4, you can search through your e-mail messages for keywords while the messages are still on mail server. You can then choose which messages to download to your machine. Short for Post Office Protocol, a protocol used to retrieve e-mail from a mail server. Most e-mail applications (sometimes called an e-mail client) use the POP protocol, although some can use the newer IMAP (Internet Message Access Protocol).

what is bioinformatics- bioinformatics – jntu btech biotechnology bioinformatics-

Bioinformatics is just application of It[information technology in MB[molecularbiology.
Application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development. The need for Bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal of this project – determination of the sequence of the entire human genome (approximately three billion base pairs) – will be reached by the year 2002. The science of Bioinformatics, which is the melding of molecular biology with computer science, is essential to the use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery. In recognition of this, many universities, government institutions and pharmaceutical firms have formed bioinformatics groups, consisting of computational biologists and bioinformatics computer scientists. Such groups will be key to unraveling the mass of information generated by large scale sequencing efforts underway in laboratories around the world.

         Bioinformatics deals with main applications involve
sequence analysis,genome annotation,computational evolutionary biology, biodiversity, analysis of gene expression, analysis of regulation, analysis of geneexpression, comparitive genomics, protien structure analysis

sequence analysis: analysisng dna sequences and finding out the genes that sequences that code  for the polypeptides which for the basic for the protien synthesis.
Genome annotation:the word annotation indicates  marking which applies to genes as marking the particular gens that code for particular protien.The first genome annotating software was found in 1995 by Dr.OwenWhite.

Biodiversity: In the great gene pool of different organisms there exists difference or diversity in genes and sequences . this may be because of climatic or genetic changes that occur which finally comes out with biodiversity..
 
Analysis of gene expresion:
The geneexpression levels can be estimates based on the mRNA levels .mRNA levels can be determines by techniques like
microarrays, Serial Analysis of Gene Expresion[SAGE],Expressed Sequence Tags[EST] Massively Parralel Signature Sequencing techniques.

Analysis of regulation:
Regulation is the process of controlling .Gene regulation is defined as the process of contolling either increaseing or decreasing the process of geneexpression with the assistance of harmones.Role of bioinformatics in generegulation is that it helps in anlysis of the motifs which enhances the process of geenregulation.

Comparitive genomics
It is the speacial part of bioinformatics where there exists the comparison of sequences of the species thus helping in understanding the similarities and disimilarities between the species,.compartitive genomics plays an important role in building up of evolutionary relationships among the species.

Prediction of protien structure:
bioinformatics plays an imporant role in the prediction of structure of protiens which involves the primary, secondary and teritiary structure analysis.
basic techniques which play an important role in the prediction of protien structure include homology based prediction,protien threading  and denova methods.

other applications involve
analysis of mutations in cancer genes:
In cancer, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing efforts are used to identify previously unknown point mutations in a variety of genes in cancer. Bioinformaticians continue to produce specialized automated systems to manage the sheer volume of sequence data produced, and they create new algorithms and software to compare the sequencing results to the growing collection of human genome sequences and germline polymorphisms. New physical detection technology are employed, such as oligonucleotide microarrays to identify chromosomal gains and losses (called comparative genomic hybridization), and single nucleotide polymorphism arrays to detect known point mutations.
modelling biological sysytems
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.
highthrough put image analysis
Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an observer’s ability to make measurements from a large or complex set of images, by improving accuracy, objectivity, or speed.
protien-protien docking
 protein three-dimensional structures have been determined by X-ray crystallography and Protein nuclear magnetic resonance spectroscopy (protein NMR). One central question for the biological scientist is whether it is practical to predict possible protein-protein interactions only based on these 3D shapes, without doing protein-protein interaction experiments. A variety of methods have been developed to tackle the Protein-protein docking problem, though it seems that there is still much work to be done in this field.

Gate2010-biotechnology – syllabus- mtech entrance -biotechnology syllabus – 2010

SECTION H: CHEMISTRY

Atomic structure and periodicity: Plancks quantum theory, wave particle duality, uncertainty principle, quantum mechanical model of hydrogen atom; electronic configuration of atoms; periodic table and periodic properties; ionization energy, election affinity, electronegativity, atomic size.
A D V E R T I S E M E N T

Structure and bonding: Ionic and covalent bonding, M.O. and V.B. approaches for diatomic molecules, VSEPR theory and shape of molecules, hybridisation, resonance, dipole moment, structure parameters such as bond length, bond angle and bond energy, hydrogen bonding, van der Waals interactions. Ionic solids, ionic radii, lattice energy (Born-Haber Cycle).

s.p. and d Block Elements: Oxides, halides and hydrides of alkali and alkaline earth metals, B, Al, Si, N, P, and S, general characteristics of 3d elements, coordination complexes: valence bond and crystal field theory, color, geometry and magnetic properties.

Chemical Equilibria: Colligative properties of solutions, ionic equilibria in solution, solubility product, common ion effect, hydrolysis of salts, pH, buffer and their applications in chemical analysis, equilibrium constants (Kc, Kp and Kx) for homogeneous reactions,

Electrochemistry: Conductance, Kohlrausch law, Half Cell potentials, emf, Nernst equation, galvanic cells, thermodynamic aspects and their applications.

Reaction Kinetics: Rate constant, order of reaction, molecularity, activation energy, zero, first and second order kinetics, catalysis and elementary enzyme reactions.

Thermodynamics: First law, reversible and irreversible processes, internal energy, enthalpy, Kirchoff?s equation, heat of reaction, Hess law, heat of formation, Second law, entropy, free energy, and work function. Gibbs-Helmholtz equation, Clausius-Clapeyron equation, free energy change and equilibrium constant, Troutons rule, Third law of thermodynamics.

Basis of Organic Reactions Mechanism: Elementary treatment of SN1, SN2, E1 and E2 reactions, Hoffmann and Saytzeff rules, Addition reactions, Markonikoff rule and Kharash effect, Diels-Alder reaction, aromatic electrophilic substitution, orientation effect as exemplified by various functional groups. Identification of functional groups by chemical tests

Structure-Reactivity Correlations: Acids and bases, electronic and steric effects, optical and geometrical isomerism, tautomerism, conformers, concept of aromaticity.

SECTION I: BIOCHEMISTRY

Organization of life. Importance of water. Cell structure and organelles. Structure and function of biomolecules: Amino acids, Carbohydrates, Lipids, Proteins and Nucleic acids. Biochemical separation techniques and characterization: ion exchange, size exclusion and affinity chromatography, electrophoresis, UV-visible, fluorescence and Mass spectrometry. Protein structure, folding and function: Myoglobin, Hemoglobin, Lysozyme, Ribonuclease A, Carboxypeptidase and Chymotrypsin. Enzyme kinetics including its regulation and inhibition, Vitamins and Coenzymes.

Metabolism and bioenergetics. Generation and utilization of ATP. Metabolic pathways and their regulation: glycolysis, TCA cycle, pentose phosphate pathway, oxidative phosphorylation, gluconeogenesis, glycogen and fatty acid metabolism. Metabolism of Nitrogen containing compounds: nitrogen fixation, amino acids and nucleotides. Photosynthesis: the Calvin cycle.

Biological membranes. Transport across membranes. Signal transduction; hormones and neurotransmitters.

DNA replication, transcription and translation. Biochemical regulation of gene expression. Recombinant DNA technology and applications: PCR, site directed mutagenesis and DNA-microarray.

Immune system. Active and passive immunity. Complement system. Antibody structure, function and diversity. Cells of the immune system: T, B and macrophages. T and B cell activation. Major histocompatibilty complex. T cell receptor. Immunological techniques: Immunodiffusion, immunoelectrophoresis, RIA and ELISA

SECTION J: BIOTECHNOLOGY

Advanced techniques in gene expression and analysis: PCR and RT-PCR, microarray technology, DNA fingerprinting and recombinant DNA technology; prokaryotic and eukaryotic expression systems; Vectors: plasmids, phages, cosmids and BAC.

Architecture of plant genome; plant tissue culture techniques; methods of gene transfer into plant cells and development of transgenic plants; manipulation of phenotypic traits in plants; plant cell fermentations and production of secondary metabolites using suspension/immobilized cell culture; expression of animal protein in plants; genetically modified crops.

Animal cell metabolism & regulation; cell cycle; primary cell culture; nutritional requirements for animal cell culture; techniques for mass culture of animal cell lines; application of animal cell culture for production of vaccines, growth hormones; interferons, cytokines & therapeutic proteins; hybridoma technology and gene knockout; stem cells, its application in organ synthesis; gene therapy; transgenic animals & molecular pharming.

Industrial bioprocesses: microbial production of organic acids, amino acids, proteins, polysaccharides, lipids, polyhydroxyalkanoates, antibiotics and pharmaceuticals; methods and applications of immobilization of cells and enzymes; kinetics of soluble and immobilized enzymes; biosensors; biofuels; biopesticides; environmental bioremediation.

Microbial growth kinetics; batch, fed-batch and continuous culture of microbial cells; media for industrial fermentations; sterilization of air and media, design and operation of stirred tank, airlift, plug flow, packed bed, fluidized bed, membrane and hollow fibre reactors; aeration and agitation in aerobic fermentations; bioprocess calculations based on material and energy balance; Down stream processing in industrial biotechnology: filtration, precipitation, centrifugation, cell disintegration, solvent extraction, and chromatographic separations, membrane filtration, aqueous two phase separation.

Bioinformatics: genomics; proteomics and computational biology.

SECTION K: BOTANY

Plant Systematics: Systems of classification (non-phylogenetic vs. phylogenetic – outline), plant groups, molecular systematics.

Plant Anatomy: Plant cell structure, organization, organelles, cytoskeleton, cell wall and membranes; anatomy of root, stem and leaves, meristems, vascular system, their ontogeny, structure and functions, secondary growth in plants and stellar organization.

Morphogenesis & Development: Cell cycle, cell division, life cycle of an angiosperm, pollination, fertilization, embryogenesis, seed formation, seed storage proteins, seed dormancy and germination.

Concept of cellular totipotency, clonal propagation; organogenesis and somatic embryogenesis, artificial seed, somaclonal variation, secondary metabolism in plant cell culture, embryo culture, in vitro fertilization.

Physiology and Biochemistry: Plant water relations, transport of minerals and solutes, stress physiology, stomatal physiology, signal transduction, N2 metabolism, photosynthesis, photorespiration; respiration, Flowering: photoperiodism and vernalization, biochemical mechanisms involved in flowering; molecular mechanism of senencensce and aging, biosynthesis, mechanism of action and physiological effects of plant growth regulators, structure and function of biomolecules, (proteins, carbohydrates, lipids, nucleic acid), enzyme kinetics.

Genetics: Principles of Mendelian inheritance, linkage, recombination, genetic mapping; extrachromosomal inheritance; prokaryotic and eukaryotic genome organization, regulation of gene expression, gene mutation and repair, chromosomal aberrations (numerical and structural), transposons.

Plant Breeding and Genetic Modification: Principles, methods ? selection, hybridization, heterosis; male sterility, genetic maps and molecular markers, sporophytic and gametophytic self incompability, haploidy, triploidy, somatic cell hybridization, marker-assisted selection, gene transfer methods viz. direct and vector-mediated, plastid transformation, transgenic plants and their application in agriculture, molecular pharming, plantibodies.

Economic Botany: A general account of economically and medicinally important plants- cereals, pulses, plants yielding fibers, timber, sugar, beverages, oils, rubber, pigments, dyes, gums, drugs and narcotics. Economic importance of algae, fungi, lichen and bacteria.

Plant Pathology: Nature and classification of plant diseases, diseases of important crops caused by fungi, bacteria and viruses, and their control measures, mechanism(s) of pathogenesis and resistance, molecular detection of pathogens; plant-microbe beneficial interactions.

Ecology and Environment: Ecosystems types, dynamics, degradation, ecological succession; food chains and energy flow; vegetation types of the world, pollution and global warming, speciation and extinction, conservation strategies, cryopreservation, phytoremediation.

 

SECTION L: MICROBIOLOGY

Historical Perspective: Discovery of microbial world; Landmark discoveries relevant to the field of microbiology; Controversy over spontaneous generation; Role of microorganisms in transformation of organic matter and in the causation of diseases.

Methods in Microbiology: Pure culture techniques; Theory and practice of sterilization; Principles of microbial nutrition; Enrichment culture techniques for isolation of microorganisms; Light-, phase contrast- and electron-microscopy.

Microbial Taxonomy and Diversity: Bacteria, Archea and their broad classification; Eukaryotic microbes: Yeasts, molds and protozoa; Viruses and their classification; Molecular approaches to microbial taxonomy.

Prokaryotic and Eukaryotic Cells: Structure and Function: Prokaryotic Cells: cell walls, cell membranes, mechanisms of solute transport across membranes, Flagella and Pili, C

Capsules, Cell inclusions like endospores and gas vesicles; Eukaryotic cell organelles: Endoplasmic reticulum, Golgi apparatus, mitochondria and chloroplasts.

Microbial Growth: Definition of growth; Growth curve; Mathematical expression of exponential growth phase; Measurement of growth and growth yields; Synchronous growth; Continuous culture; Effect of environmental factors on growth.

Control of Micro-organisms: Effect of physical and chemical agents; Evaluation of effectiveness of antimicrobial agents.

Microbial Metabolism: Energetics: redox reactions and electron carriers; An overview of metabolism; Glycolysis; Pentose-phosphate pathway; Entner-Doudoroff pathway; Glyoxalate pathway; The citric acid cycle; Fermentation; Aerobic and anaerobic respiration; Chemolithotrophy; Photosynthesis; Calvin cycle; Biosynthetic pathway for fatty acids synthesis; Common regulatory mechanisms in synthesis of amino acids; Regulation of major metabolic pathways.

Microbial Diseases and Host Pathogen Interaction: Normal microbiota; Classification of infectious diseases; Reservoirs of infection; Nosocomial infection; Emerging infectious diseases; Mechanism of microbial pathogenicity; Nonspecific defense of host; Antigens and antibodies; Humoral and cell mediated immunity; Vaccines; Immune deficiency; Human diseases caused by viruses, bacteria, and pathogenic fungi.

Chemotherapy/Antibiotics: General characteristics of antimicrobial drugs; Antibiotics: Classification, mode of action and resistance; Antifungal and antiviral drugs.

Microbial Genetics: Types of mutation; UV and chemical mutagens; Selection of mutants; Ames test for mutagenesis; Bacterial genetic system: transformation, conjugation, transduction, recombination, plasmids, transposons; DNA repair; Regulation of gene expression: repression and induction; Operon model; Bacterial genome with special reference to E.coli; Phage ? and its life cycle; RNA phages; RNA viruses; Retroviruses; Basic concept of microbial genomics.

Microbial Ecology: Microbial interactions; Carbon, sulphur and nitrogen cycles; Soil microorganisms associated with vascular plants.

SECTION M. ZOOLOGY

Animal world: Animal diversity, distribution, systematics and classification of animals, phylogenetic relationships.

Evolution: Origin and history of life on earth, theories of evolution, natural selection, adaptation, speciation.

Genetics: Principles of inheritance, molecular basis of heredity, mutations, cytoplasmic inheritance, linkage and mapping of genes.

Biochemistry and Molecular Biology: Nucleic acids, proteins, lipids and carbohydrates; replication, transcription and translation; regulation of gene expression, organization of genome, Kreb’s cycle, glycolysis, enzyme catalysis, hormones and their actions, vitamins.

Cell Biology: Structure of cell, cellular organelles and their structure and function, cell cycle, cell division, chromosomes and chromatin structure. Eukaryotic gene organization and expression (Basic principles of signal transduction).

Animal Anatomy and Physiology: Comparative physiology, the respiratory system, circulatory system, digestive system, the nervous system, the excretory system, the endocrine system, the reproductive system, the skeletal system, osmoregulation.

Parasitology and Immunology: Nature of parasite, host-parasite relation, protozoan and helminthic parasites, the immune response, cellular and humoral immune response, evolution of the immune system.

Development Biology: Embryonic development, cellular differentiation, organogenesis, metamorphosis, genetic basis of development, stem cells.

Ecology: The ecosystem, habitats, the food chain, population dynamics, species diversity, zoogerography, biogeochemical cycles, conservation biology.

Animal Behaviour: Types of behaviours, courtship, mating and territoriality, instinct, learning and memory, social behaviour across the animal taxa, communication, pheromones, evolution of animal behaviour.

Application of transport phenomena principles-momentum-heat transfer-mass transfer

Transport phenomenon is any of various mechanisms by which particles or quantities move from one place to another. The laws which govern transport connect a flux with a “motive force”. Three common examples of transport phenomena are diffusion, convection, and radiation. The science of transport phenomena is a great complement to rheological study of Newtonian fluids.

There are three main categories of transport phenomena:
Heat transfer,
Mass transfer, and
Momentum Transfer (Fluid Mechanics)

The generalized method adopted for solving transport phenomena problems start with quantity analysis for any given system as:
(Rate of quantity IN) + (Rate of Production of the quantity) = (Rate of quantity OUT) + (Rate of Accumulation of the Quantity)

Heat transfer is the transition of thermal energy from a hotter object to a cooler object (“object” in this sense designating a complex collection of particles which is capable of storing energy in many different ways)
Conduction is the transfer of heat by direct contact of particles of matter. The transfer of energy could be primarily by elastic impact as in fluids or by free electron diffusion as predominant in metals or phonon vibration as predominant in insulators
Convection is the transfer of heat energy between a solid surface and the nearby liquid or gas in motion. As fluid motion goes faster the convective heat transfer increases. The presence of bulk motion of fluid enhances the heat transfer between the solid surface and the fluid.
   Natural Convection: is when the fluid motion is caused by buoyancy forces that result from the density variations due to variations of temperature in the fluid. For example in the absence of a external source when the mass of the fluid is in contact with the hot surface its molecules separate and scatter causing the mass of fluid to become less dense. When this happens, the fluid is displaced vertically or horizontally while the cooler fluid gets denser and the fluid sinks. Thus the hotter volume transfers heat towards the cooler volume of that fluid.[3]
Forced Convection: is when the fluid is forced to flow over the surface by external source such as fans and pumps. It creates an artificially induced convection current.

 Radiation is the transfer of heat energy through empty space.

Application of heat transfer in bioprocessing:

Heat transfer is typically studied as part of a general chemical engineering or mechanical engineering curriculum. Typically, thermodynamics is a prerequisite to undertaking a course in heat transfer, as the laws of thermodynamics are essential in understanding the mechanism of heat transfer

A heat exchanger is a device built for efficient heat transfer from one fluid to another, whether the fluids are separated by a solid wall so that they never mix, or the fluids are directly contacted. Heat exchangers are widely used in refrigeration, air conditioning, space heating, power generation, and chemical processing. One common example of a heat exchanger is the radiator in a car, in which the hot radiator fluid is cooled by the flow of air over the radiator surface
Condensation heat transfer

Condensation occurs when a vapor is cooled and changes its phase to a liquid. Condensation heat transfer, like boiling, is of great significance in industry. During condensation, the latent heat of vaporization must be released. The amount of the heat is the same as that absorbed during vaporization at the same fluid pressure.
There are several modes of condensation:
Homogeneous condensation (as during a formation of fog).
Condensation in direct contact with subcooled liquid.
Condensation on direct contact with a cooling wall of a heat exchanger-this is the most common mode used in industry

Mass transfer is the transfer of mass from high concentration to low concentration. The phrase is commonly used in engineering for physical processes that involve molecular and convective transport of atoms and molecules within physical systems. Mass transfer includes both fluid flow and separation unit operations.

Some common examples of mass transfer processes are the evaporation of water from a pond to the atmosphere; the diffusion of chemical impurities in lakes, rivers, and oceans from natural or artificial point sources; mass transfer is also responsible for the separation of components in an apparatus such as a distillation column. In HVAC examples of a heat and mass exchangers are cooling towers and evaporative coolers where evaporation of water cools that portion which remains as a liquid, as well as cooling and humidifying the air passing through.
The driving force for mass transfer is a difference in concentration; the random motion of molecules causes a net transfer of mass from an area of high concentration to an area of low concentration. The amount of mass transfer can be quantified through the calculation and application of mass transfer coefficients. Mass transfer finds extensive application in chemical engineering problems, where material balance on components is performed.

A fractionating column or fractionation column is an essential item used in the distillation of liquid mixtures so as to separate the mixture into its component parts, or fractions, based on the differences in their volatilities. Fractionating columns are used in small scale laboratory distillations as well as for large-scale industrial distillations.

Vapor-liquid equilibrium, abbreviated as VLE by some, is a condition where a liquid and its vapor (gas phase) are in equilibrium with each other, a condition or state where the rate of evaporation (liquid changing to vapor) equals the rate of condensation (vapor changing to liquid) on a molecular level such that there is no net (overall) vapor-liquid interconversion.

Liquid-liquid extraction, also known as solvent extraction and partitioning, is a method to separate compounds based on their relative solubilities in two different immiscible liquids, usually water and an organic solvent. It is an extraction of a substance from one liquid phase into another liquid phase. Liquid-liquid extraction is a basic technique in chemical laboratories, where it is performed using a separatory funnel. This type of process is commonly performed after a chemical reaction as part of the work-up.

a separation process is used to transform a mixture of substances into two or more distinct products. The separated products could differ in chemical properties or some physical property, such as size, or crystal modification or other separation into different components.

 

Fick’s first law relates the diffusive flux to the concentration field, by postulating that the flux goes from regions of high concentration to regions of low concentration, with a magnitude that is proportional to the concentration gradient (spatial derivative). In one (spatial) dimension,

Momentum transfer:

 momentum (pl. momenta; SI unit kg·m/s, or, equivalently, N·s) is the product of the mass and velocity of an object (p = mv). For more accurate measures of momentum,
momentum transfer is the amount of momentum that one particle gives to another particle.
In the simplest example of scattering of two particles with momenta p1,p2 going into two particles with momenta p3,p4, the momentum transfer is given by
q = p1 – p3 = p4 – p2
where the last identity expresses momentum conservation. Momentum transfer is an important quantity because  is a better measure for the typical distance resolution of the reaction than the momenta themselves.
Application:

Fluid mechanics is the study of how fluids move and the forces on them. (Fluids include liquids and gases.) Fluid mechanics can be divided into fluid statics, the study of fluids at rest, and fluid dynamics, the study of fluids in motion. It is a branch of continuum mechanics, a subject which models matter without using the information that it is made out of atoms. Fluid mechanics, especially fluid dynamics, is an active field of research with many unsolved or partly solved problems