BIOINFORMATICS

Defintion:Ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)

Official Symbol:RNASEL

Chromosome:1

Location : 1q25

Gene Size: 13337 BP complement(155654005..155667341)

No Exons: 6

Description:

This gene encodes a component of the interferon-regulated 2-5A system that functions in the antiviral and antiproliferative roles of interferons. Mutations in this gene have been associated with predisposition to prostate cancer and this gene is a candidate for the hereditary prostate cancer 1 (HPC1) allele. [provided by RefSeq]

Disease :

RNase L is part of the body's innate immune defense, namely the antiviral state of the cell. When a cell is in the antiviral state, it is highly resistant to viral attacks and is also ready to undergo apoptosis upon successful viral infection. Degradation of all RNA within the cell (which usually occurs with cessation of translation activity caused by protein kinase R is the cell's last stand against a virus before it attempts apoptosis.

Prostate Cancer - Radical Prostatectomy

KIF1B Gene

Definition:Kinesin family member 1B

Official Symbol:KIF1B

Chromosome:1

Location : 1p36.2

Gene Size: 170825 bp (REGION: 10193418..10364242)

No Exons:47

Description:

This gene encodes a motor protein that transports mitochondria and synaptic vesicle precursors.These proteins are essential for the transport of materials within cells. Kinesin proteins function like freight trains that transport cargo, and their structure is suited for this cargo-carrying function. One part of the protein, called the motor domain, powers the protein and its cargo along a track-like system made from structures called microtubules. Another part of the kinesin protein, which varies among family members, binds to specific materials for transport.

Kinesin Transport Protein

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Disease :
Mutations in this gene cause a, type 2A1.One KIF1B gene mutation has been detected in some patients with a form of Charcot-Marie-Tooth disease known as type 2A. The mutation changes one of the protein building blocks (amino acids) in the motor domain of kinesin family member 1B. Specifically, the amino acid glutamine is replaced by the amino acid leucine at protein position 98 (written as Gln98Leu). Although the effect of this mutation is not fully understood, the motor function of the protein and the transport of synaptic vesicles are probably disrupted. Lowered levels of synaptic vesicles at nerve endings could impair the transmission of nerve impulses, causing the symptoms of type 2A Charcot-Marie-Tooth disease.

ASPM Gene
Definition:
ASPM is a human gene whose defective forms are associated with autosomal recessive primary microcephaly."ASPM" is an acronym for "Abnormal Spindle-like, Microcephaly-associated", which reflects its being an ortholog to the Drosophila melanogaster "abnormal spindle" (asp) gene.

Chromsome: Chromosome 1

Location :1q31

Size of gene:62291bp (195319997 to195382287 complementary)

No Exons :28

No Introns:27

Description:The ASPM gene is the human ortholog of the Drosophila melanogaster 'abnormal spindle' gene (asp), which is essential for normal mitotic spindle function in embryonic neuroblasts.

Evolutionary significance:
A new allele (version) of ASPM appeared sometime between 14,100 and 500 years ago with a mean estimate of 5,800 years ago. The new allele has a frequency of about 50 percent in populations of the Middle East and Europe, it is less frequent in East Asia, and has low frequencies among Sub-Saharan African populations.

The mean estimated age of the ASPM allele of 5,800 years ago, roughly correlates with the development of written language, spread of agriculture and development of cities. Currently, two alleles of this gene exist: the older (pre-5,800 years ago) and the newer (post-5,800 years ago). About 10% of humans have two copies of the new ASPM allele, while about 50% have two copies of the old allele. The other 40% of humans have one copy of each. Of those with an instance of the new allele, 50% of them are an identical copy suggesting a highly rapid spread from the original mutation. According to a hypothesis called a "selective sweep", the rapid spread of a mutation (such as the new ASPM) through the population indicates that the mutation is somehow advantageous to the individual. As of today, there is no evidence to support the notion that the new ASPM allele increases intelligence, and some researchers dispute whether the spread of the allele even demonstrates selection. They suggest that the current distribution of the alleles could be explained by a founder effect, following an out of Africa dispersal. However, statistical analysis has shown that the older forms of the gene are found more heavily in populations that speak tonal languages like Chinese.

HMGCL Gene
Defintion:3-hydroxymethyl-3-methylglutaryl-Coenzyme

Official Symbol:HMGCL

Chromosome:1

Location : 1p36.1-p35

Gene Size: 23583 bp complement(24000954..24024536)

No Exons: 9

Description:
The HMGCL gene provides instructions for making an enzyme that is found in mitochondria (the energy-producing centers inside cells). This enzyme, called 3-hydroxymethyl-3-methylglutaryl-coenzyme A (CoA) lyase, plays an essential role in breaking down proteins and fats from the diet. Specifically, 3-hydroxymethyl-3-methylglutaryl-CoA lyase is needed to process leucine, an amino acid used as a building block in many enzymes and other proteins. This enzyme is also involved in making ketones when fat is broken down by the body. These reactions produce molecules that are later used for energy.

Disease :
Many of the identified HMGCL mutations change the amino acids used as building blocks in the enzyme 3-hydroxymethyl-3-methylglutaryl-CoA lyase. Other mutations cause the production of an abnormally shortened enzyme that is missing critical components. All of these mutations disrupt the normal function of 3-hydroxymethyl-3-methylglutaryl-CoA lyase. As a result, leucine cannot be processed and ketones cannot be made properly. Because of incomplete processing, certain chemical byproducts (organic acids) can build up and cause the blood to become too acidic (metabolic acidosis). In addition, a lack of ketones causes blood sugar to become dangerously low (hypoglycemia). The effects of metabolic acidosis and hypoglycemia can damage the brain and nervous system.

MYOC Gene
Defintion:Myocilin, trabecular meshwork inducible glucocorticoid response

Official Symbol:MYOC

Chromosome:1

Location : 1q23-q24

Gene Size:17216 Bp (169,871,179 to 169,888,395) Complement

No Exons:3

Description:
The MYOC gene provides instructions for producing a protein called myocilin. Myocilin is found in certain structures of the eye, called the trabecular meshwork and the ciliary body, that regulate the pressure within the eye (intraocular pressure). It is also found in various types of muscle. Myocilin's function is not well understood, but it may help to control the intraocular pressure through its action in the muscle tissue of the ciliary body.

Disease :
Early-onset glaucoma - caused by mutations in the MYOC gene
Approximately 10 percent to 33 percent of people with juvenile open-angle glaucoma have mutations in the MYOC gene. MYOC mutations have also been detected in some people with primary congenital glaucoma.
Mutations in the MYOC gene may alter the myocilin protein so that its interactions with other proteins are impeded. Defective myocilin that is not incorporated into functional complexes may accumulate in the trabecular meshwork and ciliary body. The excess protein may prevent sufficient flow of fluid from the eye, resulting in increased intraocular pressure and causing the signs and symptoms of early-onset glaucoma.
Individuals with mutations in both the MYOC and CYP1B1 genes may develop glaucoma at an earlier age than do those with mutations in only one of the genes.

The Human Genome Project

About the Lecture

Dr. Lander is a geneticist, molecular biologist and a mathematician, with research interests in human genetics, mouse genetics, population genetics and computational and mathematical methods in biology.

He and his research group have developed many of the tools of modern genome research including genomic maps of the human, mouse and rat genomes in connection with the Human Genome Project and techniques for genetic analyses of complex, multigenic traits. He has applied these techniques to the understanding of cancer, diabetes, hypertension, renal failure and dwarfism.

Recombinant DNA Lecture by Eric S.Lander

Eric Lander was a world leader of the international Human Genome Project, the effort to map the blueprint for a human being. Today, Lander is using the knowledge of the human genome to tackle the fundamental issue of medicine: to find the causes of disease.

Lander received his Ph.D. in mathematics from Oxford in 1981, as a Rhodes Scholar. He joined Whitehead Institute in 1986 and founded the Whitehead Institute/MIT Center for Genome Research in 1990. Lander became the founding director of the newly created Broad Institute in 2003.

Lander is a member of the U.S. National Academy of Sciences, and U.S. Institute of Medicine. He was a MacArthur Fellow (1987-1992), and earned the Woodrow Wilson Prize from Princeton University(1998); the Baker Memorial Award for Undergraduate Teaching at MIT (1992); the City of Medicine Prize (2001); and the Gairdner International Prize (2002).

Using Dendritic Cells to Create Cancer Vaccines

Edgar Engleman, MD, medical director of the Stanford Blood Center, discusses his research involving the use of a special type of white blood cell as a treatment for cancer. Engleman, who is also a professor of pathology at the Stanford School of Medicine, and his team of researchers have been interested in dendritic cells, or DCs, which can provoke an immune response in the body.

The goal of this laboratory is to better understand dendritic cell biology with the objective of using this information to discover and develop more effective immunotherapeutic approaches to disease. We pursue this goal by performing experiments in both mice and humans. In our initial clinical studies antigen pulsed dendritic cells were administered to patients with cancer or life-threatening viral infections in order to induce specific immunity. The results of these trials have been extremely encouraging. More recently we have focused our studies on the development and life cycle of dendritic cells, including Langerhans cells, and the results have not only shed new light on dendritic cell biology but also have led to our ability to target dendritic cells in vivo without having to manipulate these cells in vitro. We believe that this new approach will eventually make it possible to downregulate as well as upregulate the immune system in an antigen specific manner.

Biotechnology - Will It Create a New Industry?

Henri Termeer discusses growth of the 25-year-old biotech industry, including international mergers, R&D challenges and "product based" companies verses "platform based" companies

About the Speaker

Henri A. Termeer,President and CEO, Genzyme Corporation

Henri A. Termeer was appointed president of the Genzyme Corporation in 1983 and became the chief executive officer in 1985 and chairman in 1988. Under his leadership, Genzyme has grown from a modest entrepreneurial venture into one of the world's top five biotechnology companies. Mr. Termeer is known worldwide for his contributions to the biotechnology industry and particularly noted for his expertise in financing new initiatives. His innovative approaches have earned Genzyme the Laguna Niguel Best of Biotech Award in 1991 and 1994, as well as the Laguna Niguel Hall of Fame Award in 1997.

An overivew of the KEGG bioinformatics website-Video Tutorial

An overivew of the KEGG bioinformatics website

An overivew of the KEGG bioinformatics website. As an example, protein and gene information is examined for the antibiotic resistance enzyme secreted by the bacterium Eschericia coli. 1280×720.

How to do NCBI BLAST Analysis? - Free Video tutorial

How to do NCBI BLAST Analysis ?

BLAST Analysis of Woolly Mammoth DNA using the NCBI Blastn tool. 940×716 resolution.

Overview of the UniProt Bioinformatics Website-Free Video Tutorial

UniProt is the universal protein resource, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR. This makes it the world’s most comprehensive resource on protein information.

UniProt provides four core database:

* The UniProt Knowledgebase (UniProtKB) is the central database of protein sequences with accurate, consistent, and rich sequence and functional annotation.

* The UniProt Reference Clusters (UniRef) databases provide non-redundant reference data collections based on the UniProt knowledgebase in order to obtain complete coverage of sequence space at several resolutions.

* The UniProt Metagenomics and Environmental Sequences database (UniMES) is a repository specifically developed for metagenomic and environmental sequence data.

* The UniProt Archive (UniParc) provides a stable, comprehensive sequence collection without redundant sequences by storing the complete body of publicly available protein sequence data.

This video tutorial gives an overview of the UniProt bioinformatics website. To show its practical application, the human protein college is researched, its amino acid sequence is discovered, and the blastp tool is used to BLAST the protein to find organisms having collagen with similarity.

Evolution of the protein kinase family

Evolution of the protein kinase family - Video Lecture A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins.

Python Programming-Video Tutorials

Python is a general-purpose high-level programming language. Its design philosophy emphasizes code readability.Python’s core syntax and semantics are minimalistic, while the standard library is large and comprehensive. Its use of indentation as block delimiters is unusual among popular programming languages.