Discovering Biology in a Digital World™

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Posts from ScienceBlogs, 2006 to 2017, can be found in the archive.

A recent article from STAT news (1) relayed the story of Jaci, a young woman in Iowa dying from a rare form of ALS, and her parents heroic efforts to help her get access to an untested drug.

Interestingly, the drug is an antisense oligonucleotide. Antisense oligos are short pieces of DNA, that bind to complementary molecules of mRNA and target them for destruction. These types of drugs are interesting because they can prevent the production of toxic proteins.

In Jaci’s case, her form of ALS results from a toxic version of the FUS protein. Normally, FUS is found in the ... Read more

Immuno-biotechnology and Bioinformatics in Community Colleges

Immuno-biotechnology an important field of biotechnology. With the advent of advanced DNA sequencing, and other technologies, immuno-biotechnology has significantly increased the use of computing technologies to decipher the meaning of large datasets and predict interactions between immune receptors (antibodies / T-Cell receptors / MHC) and their targets. Progress toward developing an immuno-bioinformatics course with Shoreline Community College is summarized in the attached presentation. Read more

Immunoproteosome

In early April 2019, the Institute for Systems Biology (ISB, Settle WA) hosted its 18th annual symposium. This year's theme focused on translational biology, which is the practice of commercializing research discovery. Over the two-day symposium, the audience was informed about the latest in the research and development of new products for fighting cancer with immunotherapy and combating research to improve global health.

Meeting Highlights - Immunotherapy

One of ISB's strong values is communicating science to public. This meeting was no exception; much of it ... Read more

Shoreline Immuno-Bioininformatics Instance

It would be unfair to teach an advanced bioinformatics class without getting into the weeds of command line interfaces (CLIs), heading, tailing, greping, and wc-ing files, piping programs together, and running a bioinformatics program and working with its output. Hence, in the final component of the immuno-bioinformatics class that we [Digital World Biology] are developing for Shoreline Community College will use cloud computing in the CyVerse environment to run IgBLAST. Read more

Community colleges: the new frontier for advanced biotechnology education and laboratory services: a recap.

Back in March, we [Digital World Biology, Bio-Link.org, and the AC2 Bio-Link Regional Center] hosted a panel discussion at the ABRF annual meeting to introduce community colleges to ABRF and vise versa. I am pleased to report that the session was a great success. Read more

Growth of NAR BioDBs

I always look forward to sharing the Nucleic Acids Research (NAR) database issue . This year's blog topic is immunology. The NAR archive lists 31 immunologic databases, but only seven or so are active, and others are not listed in the NAR archive. Read the blog learn more.

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Odysseus at battle

Bioinformatics is full of unexpected adventures. Some are related to data discoveries, but many more are related to navigating the maize of software needed to implement a solution.

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Immunoprofiling sample preparation

DNA sequencing-based immunoprofiling quantitatively measures AR diversity in samples by determining the sequences of V(D)J junctions. AR receptor diversity is vast due to a combinatorial rearrangement process that inserts a variable number of random DNA bases at each junction. In the sequencing process V(D)J junctions are amplified with V and J gene specific primers and, to be quantitative, differences in amplification rates that are due to primer sequences must be factored into each assay. Read more

Immunoprofiling steps of the general workflow

Immunoprofiling is the quantitative measurement of antigen receptors (ARs; antibodies or T-cell receptors) in a sample and is a hot area in biotechnology. Immunoprofiling is used to assess the diversity of antigen receptors (ARs: antibodies and T-Cell receptors) and how this diversity changes in response to allergens, infections, or vaccines. In cancer therapy, Immunoprofiling is used to develop biomarkers and understand how an individual’s immune cells fight tumors, and predict individuals' response to immunotherapy. Read more

Timeline of the National Science Foundation's Advanced Technology Education program

Last week I attended my first NSF ATE PI meeting. As a contributing member of Digital World Biology's ATE project entitled " A Bridge to Bio-Link's Future ," I participated in the conference by preparing and staffing our booth in the first evening's showcase.

As a brief background, the NSF (National Science Foundation) ATE (Advanced Technology Eduction) program celebrated its 25 th anniversary this year. ATE's mission is to support innovations in technical education at two- ... Read more

A fun thing we can do with molecular models is to create art. In Molecule World™ , the residue coloring option applies a different color to each amino acid and nucleotide. When we're characterizing a protein and trying to understand its function, the residue coloring option helps us identify repetitive or unusual amino acid sequences, but we can also use this coloring option to have fun.

The video at the end shows all the steps put together.

1. Find and download a spherical protein structure. ... Read more

Cytochrome C oxidase is a molecule that none of us air-breathing creatures can live without. It's also really interesting. This protein complex is a dimer of two smaller complexes. Each of the smaller complexes contains 13 different proteins and two heme groups.

Oxidized Cytochrome C Oxidase. Each protein chain is colored differently.
Arrows point to the active site in subunit I.

The two heme groups are both part of the cytochrome c oxidase subunit I protein. The DNA sequence of this protein is used for many types of DNA barcoding.

The two heme groups in Cytochrome C ... Read more

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