Archive for December, 2009

Antibody Detection On Western Blot Membranes

Monday, December 28th, 2009

Western blotting combines gel electrophoresis with use of a membrane to separate and identify target proteins using antibodies. Proteins are separated into bands using electrophoresis, and are then transferred to a membrane using filter-paper capillary action or an electroblotting technique. The effectiveness of the transfer can be checked by means of a stain – typically Ponceau S.

The membrane is then blocked from further protein interaction with diluted bovine serum albumin or non-fat milk solution. This ensures the antibodies bind only to the proteins, and not to the membrane substrate. False positives and fuzzy results are thus minimized, giving coherent and repeatable results.

The next stage is to incubate the membrane with a diluted primary antibody solution – typically 0.5 to 5.0 mcg/mL. The membrane is rinsed to remove any unbound protein, and exposed to a secondary antibody. Primary immunoglobulins are species derived, and secondary antibodies target to a species-specific portion of the primary agent. An anti-murine (mouse) secondary, for example, will bind to all mouse-sourced primaries.

This enables labs to share primary proteins in mass quantities, producing consistency between results and reducing costs.

Secondary antibodies are linked to a biotin or reporter enzyme, such as horseradish peroxidase. When the enzyme interacts with the relevant substrate, a color-reaction agent is activated which visualizes the protein on the membrane. Other detection methods include chemoluminescence, where an agent luminesces in proportion to the amount of protein present and fluorescent dyes activated by near infra-red bandwidths of light. The latter is considered the most precise method.

We at Novus Biologicals have a huge antibody database, including the latest fluorescent products.

An Overview Of The Western Blot Immunoassay

Friday, December 25th, 2009

Western blot is a widely used immunoassay technique, used to identify proteins. Many people enter Western blot research without having a clear idea of how the technique relates to antibody usage, so we at Novus Biologicals thought it would be interesting to give a general review of this subject.

Western blotting, also called protein immunoblotting, uses gel electrophoresis to separate proteins of tissue extracts and homogenates. Native and denatured proteins are identified by their isoelectric point, electric charge, molecular weight or molecular structure (often, a combination of these).

Tissue for Western Blot analysis is blended or homogenized to break down cells and release the proteins. Bacterial and viral proteins are also identified using Western blot, and samples are not restricted to cellular tissues. Various agents, such as buffers and inhibitors, are used to encourage cell lysis, solubilize proteins and inhibit their digestion by the sample’s own enzymes. Centrifugation and filtration is used to separate the cellular components.

Polypeptides are denatured with strong reducing agents to enable proteins to be separated by molecular weight. The most common type of gel electrophoresis used is SDS-PAGE. This uses Sodium Dodecyl Sulphate (SDS) to hold the proteins in their denatured state. The negatively charged SDS coats the proteins, which then move to a positively charged electrode through an acrylamide gel.

Once identified, individual proteins are transferred to a nitrocellulose or PVDF membrane, where they are detected using specific antibodies targeted to specific globulins. Antibody suppliers, such as Novus Biologicals, specialize in supplying monoclonal and polyclonal antibodies for a wide range of antigens, most of which are suitable for Western blot analysis.

Embryonic Stem Cells No Longer The Only Option In Antibody Research

Wednesday, December 23rd, 2009

Human stem cell research has proved a controversial topic, but the latest developments could alter the debate significantly.

Among the products in our antibody database at Novus Biologicals, we have a range of stem cell marker immunoglobulins. PODXL antibodies, also known as TRA-1-60 and TRA-1-81, which fall under this category of stem cells, are widely used in cancer research. PODXL is known to be involved in the development of several aggressive cancers, among them pancreatic, breast and prostate cancer. It was first identified on the cell surfaces of epithelial cell lines.

PODXL antibodies, such as our TRA-1-81 and TRA-1-60 antibodies, are specific to human cell lines, with no immunoreactivity to murine cells being seen. Typically, this means using human embryonic stem cells (hESCs) – an area of some controversy. In January 2010, however, the University of Amsterdam published some findings suggesting an alternative source – that of human adult testes cells. These were derived from castrated adult patients undergoing prostate cancer treatment.

It had already been proven that adult murine (mouse) testicular cultures produced embryonic-type cell lines. However, these were not suitable for human-specific antibody preparations. When interest switched to tissue submitted by human donors, the results were conclusive. Several hESCs derived proteins and carbohydrate antigens were located – among them TRA-1-60 and TRA-1-81. We at Novus Biologicals have human-specific PODXL antibodies to both these antigens.

Our PODXL TRA-1-60/81 stem cell marker antibodies are widely used in cancer research. Each is specific to a particular epitope on the PODXL protein. These epitopes are involved in cell formation and differentiation, and are found on the surface of both embryonic stem cells and adult tumor cells.

The recent discovery that embryonic stem cells can be harvested from adult tissue donors has exciting implications.

Using Recombinant Proteins In Antibody Research

Monday, December 21st, 2009

Recombinant proteins are those derived from recombinant DNA. Recombinant DNA is an artificial form of DNA, made by combining protein sequences which would not occur in their natural state.

Recently, we at Novus Biologicals have been developing recombinant bacterial proteins to reproduce existing products on our antibody database. Recombinant proteins are created from complementary cDNA libraries, which contain only DNA sequences that code for specific proteins. When this cDNA is expressed as a recombinant protein, it can be used in its purified form to perform studies into, for example, enzyme kinetics and NMR. The protein can also be used to create antibodies for further research – something which has been keeping our lab staff busy in recent times!

To take this further, if DNA sequences for certain genes are unavailable or not known, antibodies could be used for screening instead. However, to start, one must have an expression library – i.e. one that contains the DNA fragments of interest, and can use these fragments to create the protein those fragments encode, in a way that is recognized by the antibody. To do this, the cDNA fragment is inserted into organism-derived DNA – typically, the plasmid of a bacterium. This results in a recombinant protein.

E. coli is one of the most widely used hosts for recombinant DNA production, having been used in the landmark research studies of 1972 and continuously since then. Recently, much progress has been made in the transcription and translation of the gene sequences. We at Novus Biologicals are taking advantage of these new developments to extend our antibody database still further.

Fluorescent Dyes And Conjugated Antibodies

Friday, December 18th, 2009

Antibody conjugation involves tagging on a protein, compound or dye, in order to track its interaction with specific antigens. It is a routine procedure in immunoassays. We at Novus Biologicals have a vast number of products in our conjugated antibody catalog, to which we are constantly adding.

One of the most exciting developments of recent years has been tagging with fluorescent dyes, such as Alexa and DyLight fluor. For example, Beta-actin antibody conjugated to DyLight 549 is used in immunofluorescent assays, using a synthetic peptide conjugated to KLH (Keyhole Limpet Haemocyanin) as the immunogen.

There are several DyLight products, categorized by a number which relates to the spectrum in which they absorb and emit light. DL 549 absorbs light at 562 nm and emits it at 576 nm. Dylight 549 labeled antibodies fluoresce with a yellow color. They are brighter and more stable than those conjugated with older dyes, such as rhodamine and Cy3. In addition, they maintain intense fluorescence over a wide range of pH values (from 4 to 9). Alexa fluor 546 works in a similar way.

Antibodies tagged with fluorescent dyes are used in a wide range of immunoassay techniques. These include flow cytometry (FACS), ELISA, Western blot and fluorescence microscopy.

We at Novus Biologicals have a broad range of protocols for the conjugation of IgG proteins. These work extremely well for a variety of species and isotypes, including IgM. Some procedures work better than others. The cross-linking techniques used to conjugate the APC phycobiliprotein, for example, are resisted by some IgM antibodies. However, we are constantly striving to overcome tricky conjugates, in order to extend our comprehensive antibody database still further.

Explaining Conjugated Antibodies

Wednesday, December 16th, 2009

A conjugated antibody (also known as a tagged, loaded or labeled antibody) is one which has been attached to a substrate such as an enzyme, toxin or inorganic compound. Modern immunoassay techniques make extensive use of proteins conjugated with fluorescent dye.

Contemporary antibody sources sometimes supply a wide range of both polyclonal and monoclonal conjugated antibodies. For the benefits of those who are new to this area, we thought it would be a good idea to provide a synopsis on what these proteins actually are, how they work and how they are used.

Conjugated antisera are used in many research applications, from Western blotting to in vivo cellular analysis. Researchers are looking for two things – a strong signal and specificity to particular antigens. We at Novus Biologicals pride ourselves on having an extensive catalog of highly specific products, including antibodies tagged with the very latest and most effective fluorophores.

Today, hundreds of antiserum have been conjugated with protein markers and dyes for laboratory use. These are highly specific to both the antigens they target, and the assay protocol used. Modern conjugation procedures are relatively straightforward, although processes like gel filtration and spectrophotometry can pose problems on occasion. Some antibody labels, such as PE and APC, can be expensive in the quantities needed for conjugation.

Although antibody suppliers like us at Novus Biologicals supply our products solely for non-clinical use, conjugated monoclonals are also extensively used in cancer treatment. By locking onto specific antigens in cancer cells, they can deliver drugs, radiotherapy and toxins to those areas without damaging surrounding tissues. Such antibodies are commonly categorized into chemolabelled, radiolabelled and immunotoxin groups.

Bcl-2 Antibodies And Apoptosis Research

Monday, December 14th, 2009

Bcl-2 antibodies are used as markers for the Bcl-2 gene. Bcl-2 suppresses apoptosis (controlled cell death) by inhibiting caspase activity and controlling cell membrane permeability. It does this by forming mitochondrial pores on the outer membrane of the mitochondria. However, its exact mechanism of action is still not completely understood.

There are more than 25 Bcl-2 proteins, which are membrane bound and regulate apoptosis both positively and negatively. We at Novus Biologicals have a broad antibody database specific to the Bcl-2 gene, as well as anti-Bax antibodies. These two proteins are closely related, as Bax is a pro-apoptotic protein of the Bcl-2 family, forming channels in lipid membranes.

In planar lipid bilayer experiments, Bax formed ion-conducting channels which were both voltage and pH dependent. Further studies used Bax to trigger the release of liposome-encapsulated carboxyfluorescein at both acidic and neutral pH. This release could be blocked by Bcl-2 at neutral pH.

However, when antibody assays were repeated using Bcl-2 as the release agent, the protein was effective only in an acidic environment. Taken together, these studies indicate that Bax pro-apoptotic effects might be channeled through pore formation, which is antagonized by Bcl-2.

Recently, more studies have been performed using anti-Bcl-2 antibodies, in an effort to further understand Bcl-2 pore formation. Although its mechanism of action is well documented, it is still uncertain whether the mitochondrial pores which form are monomeric (composed of single molecules) or oligomeric (composed of 2 – 5 monomer units.) Studies indicate that Bcl-2 pores expand relative to the concentration of Bcl-2 present, indicating that oligomers are more likely. Bcl-2 pores are much smaller than Bax pores, suggesting that Bcl-2 is, in fact, a defective Bax gene.

GTPase Regulators And Their Antibodies

Friday, December 11th, 2009

Researchers routinely use GTP binding antibodies for the research of human disease. Thus it is worthwhile to provide a recap of the GTP binding process.

GTPases, a type of heterotrimeric G proteins, are essential to all metabolic functions. They act as molecular switches on the cell membrane, activating in response to various chemical signals. For example hormones, cytokines, physical stresses and cell-to-cell communications all activate downstream pathways. The interactions are complex, each requiring a different GTP protein. These function as molecular switches to activate or deactivate specific cellular responses.

G-proteins work by hydrolyzing GTP (guanosine triphosphate). They switch between active and inactive states, depending on whether they are GTP (guanosine triphosphate) or GDP (guanosine diphosphate) bound. In their active (GTP) state, they interact with effectors to initiate a downstream signal. In their GDP state this signal is non-functional.

G-protein activity is regulated by GEF (guanine-nucleotide exchange factor) activators, and GAP (GTPase-activating protein) ‘inactivators.’ We at Novus Biologicals have a full antibody database covering both activator and deactivator proteins.

GEF proteins translate signals from a variety of stimuli including G-protein-coupled receptors, receptor tyrosine kinases and adhesion molecules, to promote GTP binding and signal activation. The signals are terminated by GAP action, which promotes hydrolysis of GTP to GDP – thus returning the G-proteins to their inactive state. GDI (G-nucleotide dissociation inhibitors) regulators also exist, which are specific to the Rho/Rac and Rab sub-groups of G-proteins and also influence G-protein signaling via a GDP/GTP binding mechanism.

The use of antibodies to study G-proteins and their regulators is an important part of human disease research. We at Novus Biologicals have an enormous antibody database, to which new antibodies are constantly being added.

Use Of FANC Antibodies To Study The Fanconi Anaemia Pathway In F And D1 cells

Wednesday, December 9th, 2009

Fanconi anaemia (FA) is an autosomal-recessive disorder, characterized by skeletal abnormalities, progressive bone marrow failure and cellular hypersensitivity to DNA damaging agents such as Mitomycin C. FA also increases the likelihood of cancerous tumors and childhood leukemia.

Fanconi anaemia (FA) is a known complication of cancer therapy, and the use of FANC antibodies form a routine part of cancer research. Antibody suppliers, such as Novus Biologicals, supply anti-FANC antibodies which interact with FANC proteins in Western blot analysis and similar assays.

The FANCD2 protein is of particular importance, and is activated via the interaction of several other FANC proteins in a nuclear complex. This process (known as monoubiquitination) results in the formation of FANCD2/BRCA1 nuclear foci.

The FANCD2 protein is essential for the resistance of DNA cross-linking. It is also vital for arresting DNA synthesis following exposure to ionizing radiation, meaning it plays an important role in cell repair following cancer therapy. Several studies have concentrated on the FANCD2 pathway in patient-derived Fanconi anaemia cell lines, using anti-FANC antibodies such as those in Novus Biologicals’ antibody catalog.

We at Novus Biologicals cover the full range of FANC antibodies. Our antibody catalog includes FANCA, FANCB, FANCG, FANCE, FANCL, FANCM, FANCI, FANCC and FANCF antibodies, as well as FANCD2. These are used to study various elements of the D2 pathway. For example, FANCF antibodies have been used to track FANCF protein expression in human lymphoblasts, thus providing essential data on the role of FANCF in the formation of active FANCD2 foci.

The Role Of Antibodies In Cobalt Chloride Induced Apoptosis In PC12 Cells

Monday, December 7th, 2009

Various studies have been performed tracking the involvement of p38 mitogen-activated protein kinase (MAPK) and caspase-3 antibodies in cobalt chloride (CoCl2) induced apoptosis in PC12 cells.

Studies have proven the usefulness of CoCl2 treatment to induce apoptosis in PC12 rat tumor cells. Treating these cells with CoCl2 leads to programmed cell death (apoptosis). Such cells provide a simple and useful model for the study of hypoxia-related neuronal disorders, as hypoxia involves a lack of oxygen.

The mechanism of action is known to involve caspase cleavage. Antibody suppliers, such as Novus Biologicals, supply caspase and p38 antibody preparations, which are then used to study caspase cleavage in PC12 cells. p38 MAP Kinase (MAPK), also known as RK and CSBP, is known to be a pro-apoptotic factor, which when activated leads to the cleavage of caspase-3; thus, MAPK antibodies and caspase-3 antibodies are often used in tandem.

Much of this ground-breaking research was carried out in 2001, when researchers at the Shanghai Institute generated the viral caspase inhibitor gene p35 from PC12 cells. The effect of p35 on CoCl2 induced apoptosis was then studied. From these experiments, it was shown that caspase-3 proteases may be involved in CoCl2 induced apoptosis of PC12 tumor cells. The apoptotic marker p38 MAPK was also activated by the process. When blocked, cell death was inhibited. This study had huge implications for future research into disorders induced by hypoxia.

Recently, we at Novus Biologicals have used suspension culture techniques to produce CoCl2 treated lysates, specific for use as positive controls for the hypoxia antibodies on our antibody database. These are proving invaluable to neuronal research.