Biosolutions

Neighbor-Joining Tree in phylogenetic analysis

2013-05-06T22:41:00.002+05:30

In bioinformatics, neighbor joining is a bottom-up clustering method for the creation of phenetic trees (phenograms), created by Naruya Saitou and Masatoshi Nei. Usually used for trees based on DNA or protein sequence data, the algorithm requires knowledge of the distance between each pair of taxa (e.g., species or sequences) to form the tree Neighbor joining takes as input a distance matrix specifying the distance between each pair of taxa. The algorithm starts with a completely unresolved tree, whose topology corresponds to that of a star network, and iterates over the following steps until the tree is completely resolved and all branch lengths are known: Based on the current distance matrix calculate the matrix Find the pair of taxa for which has its lowest value. Add a new node to the tree, joining these taxa to the rest of the tree. In the figure at right, f and g are joined to the tree by the new node u. Calculate the distance from each of the taxa in the pair to this new node. Calculate the distance from each of the taxa outside of this pair to the new node. Start the algorithm again, replacing the pair of joined neighbors with the new node and using the distances calculated in the previous step.

Chromatin

2013-04-17T03:03:00.003+05:30

Dotplot plotting

2013-04-17T02:59:00.002+05:30

Dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them.

Introduction One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix. Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. Identical proteins will obviously have a diagonal line in the center of the matrix. Insertions and deletions between sequences give rise to disruptions in this diagonal. Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. Because of the limited protein alphabet, many matching sequence segments may simply have arisen by chance. One way of reducing this noise is to only shade runs or 'tuples' of residues, e.g. a tuple of 3 corresponds to three residues in a row. This is effective because the probability of matching three residues in a row by chance is much lower than single-residue matches. It can be seen from Figures 3.3h,c that the number of diagonal runs in the matrix has been considerably reduced by looking for 2-tuples or 3-tuples.

Python for bioinformatics

2013-04-17T02:57:00.001+05:30

Breakthrough cancer research studies DNA

2013-04-17T02:48:00.002+05:30

Scientists say they have found dozens of DNA markers that could help predict a person's risk of developing certain types of cancer. It means tests could be used to find people at greatest risk and help them take preventative action.

Introduction to Bioinformatics

2013-04-17T02:43:00.000+05:30

Biochemistry Lecture (Protein Purification)

2013-04-16T01:12:00.001+05:30

Adrenogenital Syndrome

2013-04-16T01:08:00.000+05:30

This condition is also more properly known as congenital adrenal hyperplasia. This is a group of conditions of similar source: a family of autosomal recessive disorders of steroid hormone production in the adrenal glands leading to a deficiency of cortisol, the stress fighting hormone. The master hormonal regulatory gland, the pituitary, sensing the deficiency, secretes massive amounts of the stimulating hormone corticotropin to bring the cortisol levels up to normal. This hormone in turn causes the adrenal glands to overproduce certain intermediary hormones which have testosterone-like effects on the fetus and child, leading to so-called "virilization."

Induction Apoptosis

2013-04-14T00:09:00.004+05:30

Wildtype MEFs response to Nocodazole Video

2013-04-13T02:48:00.000+05:30

New Cancer Drug Shrinks All Tumors

2013-04-10T04:06:00.004+05:30

Calcium Signalling

2013-04-10T02:20:00.000+05:30

Calcium is a common signaling mechanism, as once it enters the cytoplasm it exerts allosteric regulatory effect on many enzymes and proteins. Calcium can act in signal transduction after influx resulting from activation of ion channels or as a second messenger caused by indirect signal transduction pathways such as G protein-coupled receptors.

Ligand gated ion channels structure and function

2013-04-10T02:16:00.000+05:30

Ligand-gated ion channels (LGICs) are a group of transmembrane ion channel proteins which open to allow ions such as Na+, K+, Ca2+, or Cl- to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand),such as a neurotransmitter.

These proteins are typically composed of at least two different domains: a transmembrane domain which includes the ion pore, and an extracellular domain which includes the ligand binding location (an allosteric binding site). This modularity has enabled a 'divide and conquer' approach to finding the structure of the proteins (crystallising each domain separately). The function of such receptors located at synapses is to convert the chemical signal of presynaptically released neurotransmitter directly and very quickly into a postsynaptic electrical signal. Many LGICs are additionally modulated by allosteric ligands, by channel blockers, ions, or the membrane potential. LGICs are classified into three superfamilies which lack evolutionary relationship: Cys-loop receptors, Ionotropic glutamate receptors and ATP-gated channels. LGICs can be contrasted with metabotropic receptors (which use second messengers), voltage-gated ion channels (which open and close depending on membrane potential), and stretch-activated ion channels (which open and close depending on mechanical deformation of the cell membrane)

Lecture on HDAC Inhibitors

2012-12-16T01:22:00.000+05:30

James Rusche, PhD, Sr. Vice President, Research and Development, Repligen Corporation, discusses the work his company has done to identify development candidate for Friedreich's Ataxia.

Ubiquitin signalling.

2012-12-10T12:50:00.002+05:30

Proteins are targeted for degradation by the proteasome with covalent modification of a lysine residue that requires the coordinated reactions of three enzymes. In the first step, a ubiquitin-activating enzyme (known as E1) hydrolyzes ATP and adenylylates a ubiquitin molecule. This is then transferred to E1's active-site cysteine residue in concert with the adenylylation of a second ubiquitin. This adenylylated ubiquitin is then transferred to a cysteine of a second enzyme, ubiquitin-conjugating enzyme (E2). In the last step, a member of a highly diverse class of enzymes known as ubiquitin ligases (E3) recognizes the specific protein to be ubiquitinated and catalyzes the transfer of ubiquitin from E2 to this target protein. A target protein must be labeled with at least four ubiquitin monomers (in the form of a polyubiquitin chain) before it is recognized by the proteasome lid.[32] It is therefore the E3 that confers substrate specificity to this system.[33] The number of E1, E2, and E3 proteins expressed depends on the organism and cell type, but there are many different E3 enzymes present in humans, indicating that there is a huge number of targets for the ubiquitin proteasome system. The mechanism by which a polyubiquitinated protein is targeted to the proteasome is not fully understood. Ubiquitin-receptor proteins have an N-terminal ubiquitin-like (UBL) domain and one or more ubiquitin-associated (UBA) domains. The UBL domains are recognized by the 19S proteasome caps and the UBA domains bind ubiquitin via three-helix bundles. These receptor proteins may escort polyubiquitinated proteins to the proteasome, though the specifics of this interaction and its regulation are unclear.[34] The ubiquitin protein itself is 76 amino acids long and was named due to its ubiquitous nature, as it has a highly conserved sequence and is found in all known eukaryotic organisms. The genes encoding ubiquitin in eukaryotes are arranged in tandem repeats, possibly due to the heavy transcription demands on these genes to produce enough ubiquitin for the cell. It has been proposed that ubiquitin is the slowest-evolving protein identified to date.

SMRT DNA Sequencing

2012-12-10T12:14:00.000+05:30

Pacific biosciences is developing a transformed DNA sequencing technology, which will revolutionize the field of genetic analysis by enabling researchers to answer questions important to human healthcare, It is called SMRT (Single Molecule Real-Time DNA Sequencing). A breakthrough technology based on the natural process that occurs every time living cells divides.

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Prior to division DNA is replicated by enzymes called DNA polymerase is which efficiently duplicating entire genomes in minutes, by reading the DNA and sequentially building a complementary strand with matching building blocks called nucleotides. Pacific biosciences SMRT sequencing harnesses the power of the polymerase as sequencing engine by eavesdropping on what works to replicate DNA, this approach is enabled by two proprietary technologies the first Phospholinked nucleotides. To visualize polymerase activity a different colored fluorescent label is attached to each of the four nucleotides ACG and T. In contrast to other sequencing approaches R phosholinked nucleotides carry their fluorescent label on the terminal phosphate rather than the base. Through this innovation enzyme cleaves away the fluorescent label as part of the incorporation process leaving behind a completely natural strand of DNA.This enables us to exploit the inherent properties of the DNA polymerase including high-speed long read length and high fidelity. The second key technology is a nano photonic visualization chamber called the Zero Mode Wave-guide or ZMW, It enables observation of the individual molecules against a required background of labeled nucleotides while maintaining a high signal-to-noise. This ZNW is a cylindrical metallic chamber approximately 70 nm wide it is illuminated/support creating an extremely small detection volume just 20 cL. Nucleotides defused in and out of the ZNW in microsecond. When the polymerase encounters the correct nucleotide it takes several milliseconds to incorporated during which time its florescent label is excited emitting light is captured by a sensitive detector. After incorporation the label is clipped off and diffuses away, The whole process repeats creating sequential bursts of light corresponding to the different nucleotides these are recorded thus building the DNA sequence.

Application

The Single Molecule Real Time sequencing will be applicable for a broad range of genomics research, namely:

De novo genome sequencing: The read length from the Single Molecule Real Time sequencing is currently comparable to that from the Sanger sequencing method based on dideoxynucleotide chain termination. The longer read length allows de novo genome sequencing and easier genome assemblies.
Individual whole genome sequencing: Individual genome sequencing may utilize the Single Molecule Real Time sequencing method for the personalized medicine.
Resequencing: A same DNA molecule can be resequenced independently by creating the circular DNA template and utilizing a strand displacing enzyme that separates the newly synthesized DNA strand from the template.

Activated T Cells attacking on cancer cells

2012-12-10T00:23:00.001+05:30

Effux pumps

2012-12-10T00:20:00.000+05:30

Active efflux is a mechanism responsible for extrusion of toxic substances and antibiotics outside the cell; this is considered to be a vital part of xenobiotic metabolism. This mechanism is important in medicine as it can contribute to bacterial antibiotic resistance.

Efflux systems function via an energy-dependent mechanism (Active transport) to pump out unwanted toxic substances through specific efflux pumps. Some efflux systems are drug-specific, whereas others may accommodate multiple drugs, and thus contribute to bacterial multidrug resistance (MDR).

Bacterial efflux pumps

Efflux pumps are proteinaceous transporters localized in the cytoplasmic membrane of all kinds of cells. They are active transporters, meaning that they require a source of chemical energy to perform their function. Some are primary active transporters utilizing Adenosine triphosphate hydrolysis as a source of energy, whereas others are secondary active transporters (uniporters, symporters, or antiporters) in which transport is coupled to an electrochemical potential difference created by pumping out hydrogen or sodium ions outside the cell.

Bacterial efflux transporters are classified into five major superfamilies, based on the amino acid sequence and the energy source used to export their substrates:

1. The major facilitator superfamily (MFS)
2. The ATP-binding cassette superfamily (ABC)
3. The small multidrug resistance family (SMR)
4. The resistance-nodulation-cell division superfamily (RND)
5. The Multi antimicrobial extrusion protein family (MATE).

Of these, only the ABC superfamily are primary transporters, the rest being secondary transporters utilizing proton or sodium gradient as a source of energy. Whereas MFS dominates in Gram positive bacteria , the RND family is unique to Gram-negatives.

Function

Although antibiotics are the most clinically important substrates of efflux systems, it is probable that most efflux pumps have other natural physiological functions. Examples include:

* The E. coli AcrAB efflux system, which has a physiologic role of pumping out bile acids and fatty acids to lower their toxicity.
* The MFS family Ptr pump in Streptomyces pristinaespiralis appears to be an autoimmunity pump for this organism when it turns on production of pristinamycins I and II.
* The AcrAB–TolC system in E.coli is suspected to have a role in the transport of the calcium-channel components in the E. coli membrane.
* The MtrCDE system plays a protective role by providing resistance to faecal lipids in rectal isolates of Neisseria gonorrhoeae.
* The AcrAB efflux system of Erwinia amylovora is important for this organism's virulence, plant (host) colonization, and resistance to plant toxins.
* The MexXY component of the MexXY-OprM multidrug efflux system of P. aeruginosa is inducible by antibiotics that target ribosomes via the PA5471 gene product[1].

The ability of efflux systems to recognize a large number of compounds other than their natural substrates is probably because substrate recognition is based on physicochemical properties, such as hydrophobicity, aromaticity and ionizable character rather than on defined chemical properties, as in classical enzyme-substrate or ligand-receptor recognition. Because most antibiotics are amphiphilic molecules - possessing both hydrophilic and hydrophobic characters - they are easily recognized by many efflux pumps.

Blastocyst Formation Video

2012-12-09T13:22:00.000+05:30

The morula is a solid ball of about 16 undifferentiated, spherical cells. As cell division continues in the morula, the blastomeres change their shape and tightly align themselves against each other. This is called compaction and is likely mediated by cell surface adhesion glycoproteins.

RNAi Transfection

2012-12-09T11:15:00.000+05:30

RNA interference (RNAi) technology is revolutionizing the biological discovery process as well as target discovery and validation. Using RNAi, you can turn gene expression "off", or knock it down, to better understand its function and role in disease. High-efficiency transfection is an essential first step for achieving effective gene knockdown.

Proliferation of T cell by IL-10

2012-12-07T17:45:00.000+05:30

CTLA-4 and Mechanism of action of anti-CTLA4

2012-12-06T02:24:00.000+05:30

CTLA4 (Cytotoxic T-Lymphocyte Antigen 4) also known as CD152 (Cluster of differentiation 152) is a protein that plays an important regulatory role in the immune system. In humans, the CTLA4 protein is encoded by the CTLA4 gene.

Malaria lifecycle

2012-11-28T05:48:00.000+05:30

Leading vs. Lagging strand replication

2012-11-26T12:15:00.001+05:30

Leading strand

The leading strand is the template strand of the DNA double helix so that the replication fork moves along it in the 3' to 5' direction. This allows the newly synthesized strand complementary to the original strand to be synthesized 5' to 3' in the same direction as the movement of the replication fork. On the leading strand, a polymerase "reads" the DNA and adds nucleotides to it continuously. This polymerase is DNA polymerase III (DNA Pol III) in prokaryotes and presumably Pol ε in yeasts. In human cells the leading and lagging strands are synthesized by Pol α and Pol δ within the nucleus and Pol γ in the mitochondria. Pol ε can substitute for Pol δ in special circumstances.

Lagging strand The lagging strand is the strand of the template DNA double helix that is oriented so that the replication fork moves along it in a 5' to 3' manner. Because of its orientation, opposite to the working orientation of DNA polymerase III, which moves on a template in a 3' to 5' manner, replication of the lagging strand is more complicated than that of the leading strand. On the lagging strand, primase "reads" the DNA and adds RNA to it in short, separated segments. In eukaryotes, primase is intrinsic to Pol α. DNA polymerase III or Pol δ lengthens the primed segments, forming Okazaki fragments. Primer removal in eukaryotes is also performed by Pol δ.[18] In prokaryotes, DNA polymerase I "reads" the fragments, removes the RNA using its flap endonuclease domain (RNA primers are removed by 5'-3' exonuclease activity of polymerase I [weaver, 2005], and replaces the RNA nucleotides with DNA nucleotides (this is necessary because RNA and DNA use slightly different kinds of nucleotides). DNA ligase joins the fragments together.

Avery–MacLeod–McCarty experiment

2012-11-26T11:51:00.000+05:30

The Avery–MacLeod–McCarty experiment was an experimental demonstration, reported in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty, that DNA is the substance that causes bacterial transformation. It was the culmination of research in the 1930s and early 1940s at the Rockefeller Institute for Medical Research to purify and characterize the "transforming principle" responsible for the transformation phenomenon first described in Griffith's experiment of 1928: killed Streptococcus pneumoniae of the virulent strain type III-S, when injected along with living but non-virulent type II-R pneumococci, resulted in a deadly infection of type III-S pneumococci. In their paper "Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Deoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III", published in the February 1944 issue of the Journal of Experimental Medicine, Avery and his colleagues suggest that DNA, rather than protein as widely believed at the time, may be the hereditary material of bacteria, and could be analogous to genes and/or viruses in higher organisms.