nanobiology post genomics & bioinformatics

Wel-come TO All Of U: 

Wel-come TO All Of U By:- Pramod Rathor BSH-08-048

Title: 

Title Nano-biology, Post genomics & Bioinformatics

Nano-biology: 

Nano-biology Nano- biology is a general description of basic biological research that is either performed on the nanoscale, or that is aided by nanoscale technologies. This encompasses multiple research topics that are often hard to group within some of the more common nano biological research categories. At the molecular level, all biological systems are made up of nanoscale components. The DNA, RNA, lipids, carbohydrates and proteins that make up each of our cells are all nanoscale molecules that can be studied or manipulated using nanotechnology.

Cont….: 

Cont…. Nanobiological structures and systems research can include a wide variety of technologies and biological systems, but mainly focuses on using nanotechnology to detect, measure, or probe biological systems. The advantage of using nanotechnology for these purposes comes from the unique physical properties that can be achieved at the nanoscale. For instance, nanotechnology can be used to create nanochips or nanopatterned devices to screen large numbers of biological targets. Because of the small size of these systems, researchers can use smaller sample sizes, perform faster analyses, or use smaller amounts of expensive chemicals and reagents. In addition, unique physical phenomena at the nanoscale can be harnessed for sensing, detection, and analytical purposes. Many electrical and optical properties that occur at the nanoscale are responsive to biological molecules, yielding highly sensitive analytical techniques.

Nanomedicine : 

Nanomedicine Nanomedicine is a broad topic area that can encompass many of the other research areas within nanobiology. For our purposes, however, we can define nanomedicine as the application of nanotechnology towards the medical field. This can include the development of new types of sensors and analytical tools, as well as nanoscale methods of delivering therapeutic drugs or diagnosing disease. Many of the exciting advances within nanotechnology are beginning to be harnessed by the medical field. Nanoparticles and nano-engineered substances have been used for drug delivery and similar systems have been used to target disease-causing agents and tumor cells for therapeutics.

Cont…….: 

Cont……. A brief list of nanomedical research topics is listed below: - Nano drug delivery and therapeutics -Nanodevices for imaging, sensing, and analytical purposes -Nanoparticles and quantum dot labeling for diagnostics -Nanoparticles-based therapies for disease

Nanostructures in Biological Systems: 

Nanostructures in Biological Systems Gold Nanoparticles Inhibit Angiogenesis. Quantum Dots can be used to detect respiratory syncytial virus (RSV) infection PLGA for drug delivery system. NanoXray offres a dramatic innovation in cancer therapy, based on a technology that is designed to allow destruction of cancer cells by inert particles.

Cancer Detection and Diagnosis: 

Cancer Detection and Diagnosis Nanodevices could exam tissue or cell samples without physically altering them. Improving miniaturization will allow nanodevices to contain the tools to perform multiple tests simultaneously. Leading to faster, more efficient, and less sample consuming diagnostic tests

Cont….: 

Cont…. Nanobiological devices or nanorganisms can attach to selected tissues, provide medical images of those tissues and surrounding areas, and repair tissue damage from injury or disease without invasive surgery.

Post -genomics: 

Post -genomics Genomics encompasses everything from sequencing genomes, ascribing functions to genes, and studying the structure of genes (gene architecture). Post-genomics takes these techniques further, studying patterns in how genes are transcribed into messenger RNA, the chemical that carries the instructions for forming proteins (transcriptomics), in the way genes are expressed as proteins (proteomics), and in how they influence the chemicals that control our cellular biochemistry and metabolism (metabolomics).

Genomics: 

Genomics The term genomics was coined by Thomas Roderick in 1986. Genomics Post -genomics Pre- genomics

Post - genomics: 

Post - genomics It includes the study of following:- (1) Genome :- Bioinformatics (2) Transcriptome :- Micro arrays , SAGE. (3) Proteome :- GC-MS, LC- MS , 2D Gels. (4) Phenotype :- Comparative genomics.

Genome: 

Genome Term was 1 st coined by H. Winkler in 1920. The complete set of chromosomal & extra chromosomal gene of an organism is called as the genome. The reasons for sequencing the genome are:- (1) It provide the knowledge of total no. of all genes. (2) It shows relationship b/w genes. (3) It provide opportunities to exploit the sequence for desired experimentation. (4) It provide all genetic information about the organism. (5) Genome sequence act as an archive of all genetic informations.

Cont….: 

Cont…. Some of the complete sequenced genomes are:- (1) Human genome - 3×10 9 bp. (2) E. coli – 4.639×10 6 bp. (3) Yeast – 12.2×10 6 bp. (4) D. melanogaster- 160×10 6 bp.

Transcriptome: 

Transcriptome When a gene is switched on , it expresses through formation of a RNA transcript. The gene transcript may be identified to determine the gene. To approach this goal, specific RNA is extracted from the cell. By using this RNA C DNA is synthesized & used as hybridization probe. The C DNA copy of the gene being studied is immobilized on the solid support. Then this DNA is hybridized with the hybridization probe synthesized from RNA transcript. A hybridization signal is observed when the gene transcripts are present in the extract of RNA. For every coding gene in the genome , this method is repeated and the whole m RNA molecule of cell is analysed , this is called as transcriptome. Thus the term transcriptome has been coined to describe the complement of m RNA transcribed from the genome of a cell.

Microarray (DNA Chips): 

Microarray (DNA Chips) DNA chips are high density miniaturized microarrays of large number of DNA sequences which are attached in a fixed positions in a systematic order on a solid support. DNA fragments from unknown gene are placed using robotic device that accurately deposits nanoliter quantity of DNA solution on a surface. The UV. Light is used to cross link the DNA to the glass slides. The DNA fragements get attached to the surface. The principle of DNA microarrays lies on the base pairing or hybridization b/w nucleotides. The DNA chips contain known oligonucleotides sequences or the c DNA of known function . Thus a single DNA chip can give the complete picture of whole genome of an organism.

Application of DNA chips: 

Application of DNA chips (1) Identification of tissue specific genes. (2) discovery of drugs. (3) proteomics. (4) functional genomics. (5) DNA sequencing. (6) Agricultural biotechnology.

Proteome : 

Proteome It is used to describe the total sets of proteins expressed from the transcriptome of a cell. Proteomics is the identification , analysis and large scale characterization of proteome expressed by any given cells, tissue , organs under the defined conditions. The major objective of proteomics are :- (1) to characterized the post transcriptional modifications in protein. (2) to prepare 3D map of a cell indicating the exact location of protein. (3) proteomics provide the information about genome function that m RNA can not.

Bioinformatics: 

Bioinformatics The genomic sequence is a highly encrypted code containing the information for building and maintaining a functional organism. The study of the information content of genomes is called bioinformatics. In brief, bioinformatics is the management and analysis of biological information stored in databases.

Database : 

Database A database is a repository of sequences (DNA or amino acids) which provide a centralised and homogeneous view of its contents. The repository is created and modified through a database management system . Every data item in the database is structured according to a scheme , defined as a set of pre- specified rules through the data definition language. The content of database can be accessed through a graphical user interface (GUI).

Cont….: 

Cont…. Classification:- Database Sequence Database Structural Database Involve the sequence of both protein & nucleic acids Involve only protein Database

Slide 23: 

Sequence database Gen Bank EMBL DDBJ Uniprot US based Collection of various biological data European resource of nucleotide sequence data DNA data Bank of Japan Universal protein resource www.ncbi.nlm.nih.gov www.ebi.ac.uk www.uniprot.org

Slide 24: 

Structural database PDB –Protein Data Bank SCOP –Structural Classification Of Protein www.pdb.org www.scop.berkeley.edu

Nomenclature: 

Nomenclature The IUPAC had made certain recommendation as follows:- (1) Alphabets - Nucleotides. (2) Words - Gene ( Prokaryotes ) Introns ( eukaryotes) (3) Sentence - operon (Prokaryotes) Gene (eukaryotes) (4) Punctuation – Regulatory gene (5) Chapter - chromosomes

Information Sources : 

Information Sources (1) Gen Bank :- Collection of various biological data. (2) EMBL ( European Molecular Biology Laboratory) :- resource of nucleotide sequence data (3) DDBJ :- The DNA Bank of Japan . (4) Uniprot :- The universal protein resource

Gene bank @ NCBI: 

Gene bank @ NCBI Hosted @ www.ncbi.nlm.nih.gov Searching protein sequences in NCBI (National Center For Biotechnology Information):- Open your net and enter www.ncbi.nlm.nih.gov in to address bar. On the top bar search option select “ protein ” from menu. Enter the Gene bank Accession number or name of protein whose sequence is to be retrived. Click begin search and all the information regarding the protein is shown in the windows.

BLAST: 

BLAST Basic Local Alignment Search Tool or BLAST:- It is an algorithm for comparing primary biological sequence information, such as amino acid sequences of different proteins or the nucleotides of DNA sequences. Use of BLAST:- It is used for identifying the species, locating domains, establishing phylogeny , DNA mapping & comparison.

BLAST Search: 

BLAST Search Open the net and enter the www.blast.ncbi.nlm.nih.gov Click on the link to the standard protein blast and look on the page and become the familiar with the data required to search.

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