bioinformatics

Content related to the tag: bioinformatics

New Activity for Investigating Anti-SARS Antibodies

Blog

By: 
Sandra Porter
ACE2 bound to the SARS-CoV-2 spike protein

The Antibody Engineers NSF ATE project has published its first research project from the January 2022 Hackathon in QUBES. The project guides students through the process of investigating whether different commercial antibodies are likely to work against SARS-CoV-2 variants.

In the main research component, students use NextStrain.org and GenBank to find protein sequences from new variants and align those sequences to a spike protein complexed with an antibody. Mutations in the antibody binding site are modeled to understand how an amino acid substitution may change the chemical bonds between an antibody and... Read more

The ACE2 receptor, SARS-CoV-2, and the Antibodies that may save us

We discuss four kinds of projects that students can do to learn about molecular interactions between the novel SARS coronavirus and the cells it infects.

1. We use iCn3D to look at the SARS-CoV-2 spike protein in closed and open conformations.
2. We search for the human ACE2 gene ... View video

Filed under: iCn3DbioinformaticsCOVID-19NCBIClinVarGene databaseACE2SARS-CoV-2High school biotech

Webinar: Teaching Biotech from a Distance - Vaccine basics

Fri, Jun 5 2020
An antigen presenting cell presents a peptide antigen to a T cell

This Friday, we will have a guest speaker from the University of Washington, Center for Innate Immunity and Immune Disease, share basic concepts around vaccines. This lecture will help us prepare for a later discussion when we dive into vaccines against COVID-19 in greater detail.

Speaker : Dr. David Koelle , Center for Innate Immunity and Immune Disease, University of Washington.
Dr. Koelle studies virology and immunology, along with viral oncogenesis, tumor immunotherapy, practical vaccinology issues such as adjuvants and delivery systems ... Read more

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Webinar 9: Teaching Biotech from a Distance - DNA barcoding in a regulated environment

DNA barcoding is a popular technique for undergraduate research projects.  In this webinar, Dr. Linnea Fletcher describes how this technique can be adapted for use in biotechnology education programs by incorporating principles of working in a regulated environment such as GMPs (Good ... View video

Filed under: IAB webinarbioinformaticsbiotechnology skillsemployability skills

Webinar 8: Teaching Biotech from a Distance - Exploring immunity to COVID-19 with IEDB.org

Dr. Sandra Porter demonstrates how the Immune Epitope Database (IEDB.org) can be used for online research projects and provides an example of using this resource to investigate immunity to SARS-CoV-2 and SARS.

Speakers

Filed under: COVID-19IAB webinarantibodiesbioinformaticsimmunologyIEDB

Webinar 6: Teaching Biotech from a Distance - Quantitative RT-PCR assays and SARS-CoV-2

What's it like to scale your testing capacity from 30 tests a week to 3000 a day?  Dr. Meei-Li Huang from the Virology division at the University of Washington tells us what it was it like to work on the front line of the COVID-19 pandemic, evaluating quantitative RT-PCR assays and testing  ... View video

Filed under: online researchbioinformaticsCOVID-19IAB webinarmolecular diagnosticsquantitative RT-PCR

Webinar: Teaching Biotech from a Distance - DNA barcoding in a regulated environment

Fri, May 29 2020
A trace file from Sanger sequencing presented in FinchTV, a free program from Digital World Biology

DNA barcoding is a popular technique for undergraduate research projects. In this webinar, Dr. Linnea Fletcher will describe how this technique can be adapted for use in biotechnology education programs by incorporating principles of working in a regulated environment such as GMPs (Good Manufacturing Practices).

The Austin Community College (ACC) Biotechnology program introduces students to the 5 P’s of GMP [people, premises, processes, products and procedures (paperwork)] while they're using DNA barcoding to identify samples. Combining GMPs with DNA barcoding makes learning cGMPs ... Read more

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Webinar: Teaching Biotech from a Distance - Developing Antibodies and Vaccines to COVID-19

Fri, May 22 2020

In this webinar, we will introduce basic concepts in immunology and demonstrate how to use the Immune Epitope Database to investigate immunity to COVID-19 and gain insights into key requirements for developing antibodies and vaccines to COVID-19. We will also present an activity that students can use for a research project and investigate immunity to whatever they choose.

Speaker : Dr. Sandra Porter, Shoreline Community College, Digital World Biology, and InnovATE BIO .

Read more about ... Read more

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Detecting SARS-CoV-2 with Quantitative RT PCR - Evaluating primers

Blog

By: 
Sandra Porter
We got this mural

Evaluate primer sequences from the UW publication - this is similar to an activity in Dr. Porter's bioinformatics course ( Bioinformatics for Biology and Biotech : Learning guide 10. PCR and primer BLAST)

Before you begin : Go to the bottom of this page and download the worksheet. top

1. Pick a pair of primers and their corresponding probe to investigate from Table 1 below. There are 14 sets of primers (forward and reverse) and probe sets.

A. Only use the negative controls if you... Read more

Webinar 5: Teaching Biotech from a Distance - Examples and Sharing

Dr. Daiyuan ("Daisy") Zhang from Del Mar College described how she adapted to her college's shut down by having her students do online research related to SARS-CoV-2.  Students used nucleotide BLAST to investigate where the virus came from and look at mutations.  They used primer-blast to design ... View video

Filed under: online researchbioinformaticsCOVID-19IAB webinar

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