1.Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration
Database name
|
Full name and/or description
|
URL
|
DDBJ-DNA Data Bank of Japan
|
All known nucleotide and protein sequences
|
|
EMBL-Nucleotide Sequence Database
|
All known nucleotide and protein sequences
|
|
GenBank
|
All known nucleotide and protein sequences
|
|
1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
Database name
|
Full name and/or description
|
URL
|
ACLAME
|
A classification of genetic mobile elements
|
|
CUTG
|
Codon usage tabulated from GenBank
|
|
Genetic Codes
|
Genetic codes in various organisms and organelles
|
|
Entrez Gene
|
Gene-centered information at NCBI
|
|
HERVd
|
Human endogenous retrovirus database
|
|
Hoppsigen
|
Human and mouse homologous processed pseudogenes
|
|
Imprinted Gene Catalogue
|
Imprinted genes and parent-of-origin effects in animals
|
|
Islander
|
Pathogenicity islands and prophages in bacterial genomes
|
|
MICdb
|
Prokaryotic microsatellites
|
|
NPRD
|
Nucleosome positioning region database
|
|
STRBase
|
Short tandem DNA repeats database
|
|
TIGR Gene Indices
|
Organism-specific databases of EST and gene sequences
|
|
Transterm
|
Codon usage, start and stop signals
|
|
UniGene
|
Non-redundant set of eukaryotic gene-oriented clusters
|
|
UniVec
|
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
|
|
VectorDB
|
Characterization and classification of nucleic acid vectors
|
|
Xpro
|
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes
|
|
1.2.2. Gene structure, introns and exons, splice sites
Database name
|
Full name and/or description
|
URL
|
ASAP
|
Alternative spliced isoforms
|
|
ASD
|
Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb
|
|
ASDB
|
Alternative splicing database: protein products and expression patterns of alternatively spliced genes
|
|
ASHESdb
|
Alternatively spliced human genes by exon skipping database
|
|
EASED
|
Extended alternatively spliced EST database
|
|
ECgene
|
Genome annotation for alternative splicing
|
|
EDAS
|
EST-derived alternative splicing database
|
|
ExInt
|
Exon intron structure of eukaryotic genes
|
|
HS3D
|
Homo sapiens splice sites dataset
|
|
Intronerator
|
Alternative splicing in C.elegans and C.briggsae
|
|
SpliceDB
|
Canonical and non-canonical mammalian splice sites
|
|
SpliceInfo
|
Modes of alternative splicing in human genome
|
|
SpliceNest
|
A tool for visualizing splicing of genes from EST data
|
|
1.2.3. Transcriptional regulator sites and transcription factors
Ronald L. Crawford, Don L. Crawford, quot;Bioremediation: Principles and Applicationsquot;
Cambridge University Press | 1997 | ISBN: 0521470412, 052101915X | 412 pages | File type: PDF | 10,4 mb
Industrial and agricultural activity throughout this century has led to considerable contamination of soil and groundwater resources by hazardous chemicals. The technique of bioremediation uses living organismsusually bacteria and fungito remove pollutants from soil and water with minimal disturbance to these environments. This approach, which is potentially more cost-effective than traditional techniques such as incineration of soils and carbon filtration of water, requires an understanding of how organisms transform chemicals, how they survive in polluted environments, and how they can be used in the field. This book examines these issues for many of the most serious and common environmental contaminants, presenting the most recent position on the application of bioremediation to polluted soil and water.
? Comprehensive - all important classes of organic pollutant covered in a single volume ? Practical emphasis - illustrates how to clean up various pollutants by biological means ? Authoritative - contributions from all the leading experts in this area combine to make a unique, multidisciplinary information resource ? For academics in microbiology and environmental science, also industrial and government scientists in pollution control
Contents
Preface D. Crawford; 1. Introduction R. Crawford; 2. Engineering of bioremediation processes W. Admassu and R. A. Korus; 3. Bioremediation in soil: influence of soil properties on organic contaminants and bacteria M. J. Morra; 4. Biodegradation of 'BTEX' hydrocarbons under anaerobic conditions L. Crumholtz, M. E. Caldwell and J. M. Suflita; 5. Bioremediation of petroleum contamination E. Rosenberg and E. Zon; 6. Bioremediation of environments contaminated by polycyclic aromatic hydrocarbons J. Mueller, C. Cerniglia and P. Pritchard; 7. Bioremediation of nitroaromatic compounds S. B. Funk, D. Crawford and R. Crawford; 8. A history of PCB biodegradation R. Unterman; 9. Bioremediation of chlorinated phenols J. Puhakka and E. Melin; 10. Biodegradation of chlorinated aliphatic compounds L. Wackett; 11. Microbial remediation of metals T. Roane, I. Pepper, R. Miller; 12. Molecular techniques in bioremediation M. Shields and S. Francesconi; Index.
Review
The editors of this book and the contributing authors should be congratulated in providing an up to date review of this rapidly developing subject and it should be of use to many scientists interested in Bioremediation. The Association of Applied Biologists News
Download
http://uploading.com/files/am114998/0521470412Bioremediation.rar/
http://www.megaupload.com/?d=1509IFA3
Scientists at MIT mimic plant processes to build solar cells that renew themselves like living beings.
Living things don't have that many advantages over machines. We're not as quick, or as precise, and we don't have as good a memory. Moreover, while they are made of tough stuff, we are mostly composed of things that go squish. One of the limited advantages we have is that when we go squish, we have built-in repair shops. When they go crunch, they're crunched.
Self-renewal has been a goal of many different technology manufacturers, but especially the makers of solar cells. For years scientists have looked resentfully at their solar cells, the components of which wear out or break, and envied plants, which have a built-in systems that take apart and renew any worn-out bits.
MIT researchers have found a way to imitate this process:
Structure and Function in Cell Signalling E Book
John Nelson
Pub: Wiley Blackwell
Size :10 MB
Page:411
Sequence analysis is the application of Information Technologies to Molecular Biology. It deals with biological sequences, and processes them to extract significant information that may yield new insights and guidelines in the understanding of biological organisms
Basics for sequence analysis
Proteins
A protein is typically built of a series of basic blocks called amino acids , chained together in a linear sequence of blocks. Amino acids may come in a variety of shapes and properties: they may be small or bulky, hidrophobic or hidrophyllic, electrically charged or neutral, etc... hence allowing for very complex shapes and interactions to be produced.
Amino acids are commonly referred to by name or by an abbreviation, usually in three or one letter. This allows for more efficient descriptions of how they are chained together to build a protein:
Neutral-Nonpolar | 3-letter | 1-letter |
Glycine | Gly | G |
L-Alanine | Ala | A |
L-Valine | Val | V |
L-Isoleucine | Ile | I |
L-Leucine | Leu | L |
L-Phenylalanine | Phe | F |
L-Proline | Pro | P |
L-Methionine | Met | M |
Neutral-Polar | | |
L-Serine | Ser | S |
L-Threonine | Thr | T |
L-Tyrosine | Tyr | Y |
L-Tryptophan | Trp | W |
L-Asparagine | Asn | N |
L-Glutamine | Gln | Q |
L-Cysteine | Cys | C |
Acidic | | |
L-Aspartic | Asp | D |
L-Glutamic | Glu | E |
Basic | | |
L-Lysine | Lys | K |
L-Arginine | Arg | R |
L-Histidine | His | H |
Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine.
Roughly, bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; bioinformatics to them is a synonym for "computational molecular biology"- the use of computers to characterize the molecular components of living things.
Definition of Bioinformatics form various sources:-
- Bioinformatics is the science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research. (source: www.whatis.com)
- As a discipline that builds upon computational biology, bioinformatics encompasses the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.
Engineers have long dreamed of using DNA as the backbone for the next generation of computer circuits. New research shows just how it might be done.
Instead of conventional circuits built of silicon that use electrical current, computer engineers could take advantage of the unique properties of DNA, the double-helix molecule that carries life’s information. “Conventional technology has reached its physical limits," said Chris Dwyer, assistant professor of electrical and computer engineering at Duke University's Pratt School of Engineering.
Dwyer recently demonstrated that by simply mixing customized snippets of DNA and other molecules, he could create billions of identical, tiny, waffle-looking structures.
These nanostructures can then be used as the building blocks for a variety of circuit-based applications, ranging from the biomedical to the computational. Key to the promise of these DNA nanostructures is an ability to rapidly "switch" between zeros or ones -- the basic on/off binary action that powers computation. Light can be used to stimulate similar binary responses from DNA-based switches, though at a much faster rate than in silicon.
“When light is shined on the chromophores" -- parts of DNA responsible for its color -- "they absorb it, exciting the electrons,” Dwyer said. “The energy released passes to a different type of chromophore nearby that absorbs the energy and then emits light of a different wavelength. That difference means this output light can be easily differentiated from the input light, using a detector.”
Dwyer added: "This is the first demonstration of such an active and rapid processing and sensing capacity at the molecular level."
Building computers with life's building blocks
Now We Are going to launch a biotechnology magazine Which will surely help you guy's to go through new technology's and inventions of biotechnology.

Many of us invested in the success of sustainable agriculture have a knee-jerk response against genetically-modified foods, and for good reason — they often come with patent protection, pesticides, and other undesirable features. But a new development from the
National Institute of Plant Genome Research in New Delhi suggests that GMO crops could have at least one positive use: dramatically increasing the shelf life of fruits and vegetables.
Photo by The Ewan