Molecular diagnostics

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Bioinformatics

1. Molecular diagnostics:

Detection of infectious pathogens at genomic level increases the accuracy of diagnosis. Utilization of available genomic data for identifying pathogens will reduce the cost involved in the development of the diagnostic kits and increases the accuracy .We are expertise in using the genomic data to develop molecular diagnostic kits for the pathogen of interest.
These are the steps that we follow

  1. Collect the genomic data for organism of interest
  2. Identify organism specific regions in the genome against all other organisms.
  3. Identification of common specific regions across multiple strains.
  4. Development of primers
  5. Evaluation of the primer sets (based upon the geographical interest of the client)
Advantages of our support:
  1. Reduces your time, rather than experimenting over a wide range of primers
  2. Increase kit development speed and accuracy
  3. Reduces your investment
  4. Will be geographic specific.

 

2. Computational B cells epitope mapping :

Computational analysis processes reduces the amount of work done in identification of epitopes for diagnostics purpose. Identification of B cell recognizable epitopes for viral, bacterial and parasite infections driven by both locations, structure of target of interest. Many epitopes are generally common across the species and few are specific to the species. We will provide those set of epitopes common, species specific for the diagnostics purpose. B cells are going to recognize antigens, cell membrane proteins, transmembrane proteins for the case of bacteria. For the case of viruses they recognize the envelope protein.

Two types of information is available for these proteins.

  1. Primary sequence information of the protein
  2. 3D structure information of the protein.

Proteins for which 3D structure is available we can identify the surface epitopes , along with location of the epitope.
For those which don't have any 3D structure, we proceed with two approaches

  1. Model the sequence with the nearest possible 3D structure to find out possible positions of epitopes.
  2. Construction of Hydrophobicity / Hydrophilicity plots to recognize the stretch of amino acids involved in the epitope formation.

These suggested epitopes as we said will be organism specific or species specific.

 

3.Pathway mapping:

ESTs and transcriptomes are getting sequenced at a very faster rate for many organisms. Now it is time to functionally annotate the upcoming ESTs /Transcriptomes/Proteomes so that we can develop pathway models for the organisms and understand the underlying functionalities carried out by the organisms. Our pathway mapping helps in understanding

  1. Bacteria:
    1. Identification of alternative strains for production of proteins
    2. Identification of pathways active during the infection state.
    3. Identification of critical pathways for the production of metabolites.
  2. Plants:
    1. To identify disease profile of the plants , pathways active drugging the infection state
    2. Alternative sources for development of primary or secondary metabolites
    3. Development of candidate, recombinant cell lines
  3. Animals:
    1. Pathways active/regulated during the disease state.
    2. Pathways down regulated during the infection process.
    3. Development of recombinant cells

Our mapping procedure will take the Set of ESTs/Transcriptomes/Proteomes from the user and will map to the respective pathways. This will help in construction of pathway models and identification of pathways of an organism at a faster, accurate rate based.


Our pathway mapping procedure is designed for Bacterial, plants and animal models. So if you have any dataset or ESTs to get mapped we will provide you with the respective information.

 

4. Drug target identification:

In years to come the drug development procedure will be specific to the organism of interest rather than one drug which could cure many infections. Drug abuse the biggest problem that has to be solved which is resulted due to over and improper usage of drug molecules and their leak into the environment. common drug targets are effecting the entire life cycle of the patient administered with drugs. As we know that many bacteria live in symbiosis with human .If drugs start targeting common targets across the species this will harm the balance of the host. They will bleach the entire gastro intestinal system leaving few bacteria to survive. If any pathogenic or any strain gains resistance they host body is becoming breading grounds for them. No competitive bacterial growth occurs (no fight for survival). Surviving once grows whose implications are going to be immediate or later stage of the life. Some of these are getting transferred to the progenies also.


So we identify those targets that are specific to the organism, along with its drugaability information .We classify the organisms into pathogenic and nonpathogenic once. Based upon the interests we will suggest the pathogenic organism's specific target, or set of pathogenic organisms specific targets. The genomic and proteomic information will be used for the identification purpose .Along with the literature survey.

 

5. Fermentation process:

The critical steps of the fermentation processes include development of the clone, down stream process for the extraction of the protein of interest. We will assist in development of clones for the protein of interest. This includes

  1. Use of the right set of restriction enzymes to cut the genomic DNA
  2. Amplification of the gene of interest.
  3. Insertion into a vector
  4. Development of recombinant organism.(clones for the protein of intrest)
There are lacks of proteins with there own functionality, which can be commercialized .If you have any commercially important protein we will guide u for development of the protein.

 

6. Probes development for Genechip:

In the development of Gene chip probe identification is a critical step .We give the specificity to the identification by designing specific probes. Set of probes specific to bacterial/fungal or set of genes of interest will be provided by us so that your gene chip can be accurate enough to find out the pathogens such as food born pathogens, infectious pathogens or even for development of cancer markers.

 

7. Application programs development:

The base for Bioinformatics to accelerate the research helps in quick analysis of the results, data storage and retrieval is programming. We provide case specific applications to our clients interested in their data analysis. These include stand alone programs, application development or development of an online system/web interfaces Areas of interest can be data analysis, data management or algorithmic implementation.

 

8. Identification of common primers for amplification of gene of interest across set of organisms.

 

9. Identification of SSRs/VNTRs or candidate markers of interest across whole sequenced genome. Suggesting primers for the amplification of specific type of marker.