Learning Resources for the 2016 Penn State Lectures on the Frontiers of Science
Your Health Risks: Prediction and Prevention presented by Sarah Pendergrass, Assistant Professor of Biomedical and Translational Informatics at Geisinger Health System, on January 23
Definitions (adapted from http://ghr.nlm.nih.gov/handbook)
- Precision Medicine: An emerging approach for disease treatment, prevention, and medication and procedure decisions, taking into account individual variability in genes, environment, and lifestyle for each person. We can use electronic health records (EHR), genetic data, family history data, and environmental exposure data to improve individualized health care.
- What is a genome?: A genome is an organism’s complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion DNA base pairs—is contained in all cells that have a nucleus.
- Our genome: We have 22 pairs of chromosomes (autosomes), and two sex chromosomes (X and a Y), one chromosome each from our father and our mother. Each chromosome is made up of DNA (deoxyribonucleic acid). DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). The order, or sequence, of the bases of DNA determine the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences. If you stretched the DNA in one cell all the way out, it would be about 2m long! That is a ton of information in each cell nucleus! Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people.
- Our “genes”: This is usually the term used to describe the protein coding regions of our genome. Through transcription and translation, proteins are formed. Genetic variation can impact the formation of proteins, and than thus impact downstream processes within cells, and ultimately create differences in organisms. There is much more complexity to the subject of genes, transcription and translation, and how genetic variation can affect trait variability, see more via the links provided in this document.
- Phenotype: an individual's observable traits, such as height, eye color, and blood type. The genetic contribution to phenotype is called the genotype.
- Allele: an alternative base pair, or base pairs, at a single location in the genome (also can refer to differences at the locus level).
- Single Nucleotide Polymorphism (SNP), Pronounced “Snips”: We refer to a location within the genome as a base pair location, as DNA is double stranded. We can use genotyping and sequencing to identify if bases are the same, or different, in an individual compared to other individuals, at locations across the genome. And we can determine if they have one or two differing alleles at that base pair location (because they will have two chromosomes representing each base-pair location). Relatively common variation at a single base pair location on a chromosome, compared to the general population, is called a single nucleotide polymorphism. Most of the evaluation of the relationship between genetic variation and diseases and outcomes to date have been through using SNPs, comparing the presence of genetic variation to the presence or absence of disease in a population. For example, for a given SNP, is it associated with the presence or absence of Type-II diabetes?
- Single Nucleotide Variant (SNV), Pronounced “Snivs”: With sequencing of the genome, the technology allows us to capture more of the genome individuals have, including the rare variants that individuals have. A rare variant is genetic variation at a base pair location on a chromosome that is very uncommon, these are frequently referred to as SNVs.
- Sequencing: Sequencing DNA means determining the order of the four chemical building blocks - called "bases" - that make up the DNA molecule. The sequence tells scientists the kind of genetic information that is carried in a particular DNA segment. For example, scientists can use sequence information to determine which stretches of DNA contain genes and which stretches carry regulatory instructions, turning genes on or off. In addition, and importantly, sequence data can highlight changes in a gene that may cause disease. Since the completion of the Human Genome Project, technological improvements and automation have increased speed and lowered costs to the point where individual genes can be sequenced routinely, and some labs can sequence well over 100,000 billion bases per year, and an entire genome can be sequenced for just a few thousand dollars. (from https://www.genome.gov/10001177)
- Genotyping though SNP arrays: Before sequencing technology became fast and inexpensive, identification of SNPs in individuals was pursued mainly through the use of SNP arrays. This could only cover common genetic variation, and at fewer locations across the genome.
Resources on the web:
- More about sequencing
- More about genes, genetics, and genetic variation, and proteins
- MyCode® Community Health Initiative
Precision Medicine Initiative for the United States through the National Institutes of Health
- Review of genotyping through SNP arrays
- Genome wide association studies (GWAS)
New Hope for Brain Repair, presented by Gong Chen, Professor of Biology and the Verne M. Willaman Chair in Life Sciences at Penn State, on January 30
Resources on the Web:
- National Institute of Neurological Disorders and Stroke (NINDS) Stroke Information Page
- NINDS Spinal Cord Injury Information Page
- National Institute on Aging: Alzheimer's Disease Fact Sheet
- The Alzheimer's Association: What Is Alzheimer's?
How to Stop an Epidemic, presented by Matthew Ferrari, Assistant Professor of Biology and Statistics, Penn State on February 6, 2016
Papers referenced in Ferrari's talk:
- A list of all Ferrari's papers
- Free Penn State online course: Epidemics - the Dynamics of Infectious Diseases
New Antibiotics for Drug-Resistant Infections, presented by Kenneth Keiler, Professor of Biochemistry and Molecular Biology at Penn State, on February 13, 2016
- CDC public information on antibiotic resistance
- A comprehensive study by the CDC
- WHO coverage of antibiotic resistance
- IDSA 10 X ’20 (effort to get 10 new antibiotics by 2020)
- Hunting the Nightmare Bacteria (video)
- TED talk by Maryn McKenna, a public health journalist
- Mechanisms of ribosome rescue in bacteria, by Kenneth C. Keiler published in Nature Reviews Microbiology
Invented: A Better Tool Against Cancer, presented by Tony Jun Huang, Professor of Engineering Science and Mechanics and the Huck Distinguished Chair in Bioengineering Science and Mechanics and Professor of Chemistry at Penn State, on February 20, 2016
Penn State Press Releases:
- Acoustic tweezers move cells in three dimensions, build structures
- On-Chip Processor: First Step in Point-of-Care Asthma &Tuberculosis Diagnostics
- Sound separates cancer cells from blood samples
Anti-Cancer Drugs: Discovery & Development, presented by Raymond J. Hohl, Professor of Medicine and Pharmacology, Director of the Penn State Cancer Institute, on February 27, 11 a.m.
- FDA Investigates Clinical Trial After Drug Leaves 1 Dead, 4 Seriously Injured
- ClinicalTrials.gov: A service of the U.S. National Institutes of Health, ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world. Learn more About Clinical Studies and About This Site, including relevant History, Policies, and Laws.
- NIH Clinical Research Trials and You: The National Institutes of Health’s page containing information about clinical research trials, participates rights, and general information.
Use the links to the left to access more information about the Penn State Lectures on the Frontiers of Science, including archived recordings of previous lectures.
For more information or access assistance, contact the Eberly College of Science Office of Media Relations and Public Information by telephone at (814) 867-5830 or by e-mail at firstname.lastname@example.org