Biotech Spring

• What is our epigenome and how does it relate to protein synthesis and gene expression?

  
  

  • Epigenome: is the pattern of gene expression in a cell
  • Protein synthesis - tells whether genes are turned off and on and the production of protein in cells 
  • Gene expression - indicates if the gene will be turned on or turned off
• What is the difference between our genome and our epigenome?

  • Genome - can be modified in diverse cell types at different times to produce many epigenomes
  • Epigenome - chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it
• How do methyl groups (methylation of our genes) affect gene expression? Where do they attach? If the methyl groups bind upstream of the gene at the promoter region, how does it affect transcription factors and gene expression?

  • Methyl groups attach directly to genes and turn off the gene
  • The methyl groups attach to cytosine and block transcription machinery from binding to DNA.
  • The methyl groups then recruit proteins that bind methylated DNA and further silence the gene.
• Acetyl groups


  Affect gene expression
• Acetyl groups


  Attach to histones
• How acetyl groups affect gene expression

  1. Attach to histones

  2. Unwind DNA from histones

  3. Genes become more accessible and can be turned on
• Epigenetic therapy


  Reprograms cells to a more normal state
• How epigenetic therapy works

  1. Uses medicine

  2. Changes things in the DNA that could have caused cancer
• Understand that our genome is fixed but that our epigenome is changeable.

  • Genome can be modified in diverse cell types at different times to produce many epigenomes
• Why are different types of cells in your body different when they all have the same exact DNA sequences and genes?

  • Nerve cells, muscle cell, intestinal cell
  • They synthesize and accumulate different sets of RNA and protein molecules
  •  in the way each cell deploys its genome
• What are histones? How do they relate to epigenetics?

  • Histones: A type of protein found in chromosomes.

  DNA wraps around the histones =  epigenome
• Compare and contrast the two different epigenetic tags we learned about in class, methylation and acetylation (how does each affect gene expression and how do they act on the DNA/histones to chase the change in expression)

  • When DNA is tightly bound to histones the genes in that region are off (inactive)
  • When DNA is loosely bound to histones the genes in the region are on (active)
  • TIGHT WRAP = inactive genes
  • LIGHT WRAP = active genes
• As methylation increases, how does the production of mRNA change? As acetylation increases, how does the production of mRNA change?

  • transcriptional silencing and gene inactivation,
  • partially blocks the RNA channel affecting the enzyme activity.
• Can epigenetic patterns be inherited?


  They can be passed on but there is highly any chance that it would stay the same because it changes over time
• What environmental factors affect our epigenome?

  • The environment can and does directly change your epigenome (gene expression)
  • exposure to metals, air pollution, benzene, organic pollutants, and electromagnetic radiation 
• Give examples of how our epigenome affects our behavior and how our behavior affects our epigenome

  • Psychological state, social interaction, disease exposure, drug addiction, alternative medicine
• Stem cells


  • Capable of dividing and renewing themselves for long periods
  • Unspecialized: another way of saying undifferentiated
  • Can give rise to specialized cell types
• Undifferentiated


  Describe cells or tissues that do not have specialized ("mature") structures or functions
• Pluripotent


  Cells that can form any cell type (except placenta)
• Multipotent


  More differentiated cells but can form a number of different cell types within the cell line
• Pluripotent cell types

  • Embryonic stem cells
  • Induced Pluripotent Stem Cells (iPS)
• Multipotent cell types


  • Adult stem cells
• Adult stem cells


  • Typically found among specialized or differentiated cells in a tissue or organ
  • More differentiated cells than embryonic stem cells
• Induced Pluripotent Stem Cells (iPS)


  • Cells created from an adult stem cell that are then reverted back to embryonic-like (undifferentiated)
• Embryonic

  • come from a 5 to 6 day old embryo. Have the potential to form any type of cell in body - 220 cells in body
• Where are each found/how are they created?

  • Embryonic: in body and all cells types (most)
  • Adult: fetal tissue, cord blood and among adult cells
  • iPS: artificially created in a lab from an adult cell
• What is the potential (multipotent or pluripotent) of each?

  • Embryonic: pluripotent
  • Adult: multipotent
  • iPS: pluripotent
• Embryonic

  • Advantages: facilitates in regenerating and repairing diseased organs and tissue
  • Disadvantages: ethical controversy, teratomas, differentiation before implant, cost/funding research, tissues rejection, politics, getting to clinical trials
• Adult

  • Advantages: matches patients cells, lack of controversy, more research done
  • Disadvantages: exists in small number (hard for therapeutic use), more hard to find, isolate, puffy and grow in lab, cell therapies require infinity of donor cells and adult cannot provide
• iPS

  • Advantages: does not involve creation/destruction of embryo, pluripotent so same as eSC, less tissue rejection due to cells from patients own body
  • Disadvantages: less known about them and many scientist say we need stem cell research to continue in order to better understand them
• Current level of understanding of each.

  • Embryonic: FDA halts the usage for cynical trials
  • Adult: FDA approves cell therapy with blood cancers
  • iPS: Not enough information
• What is a blastocyst? With what type of stem cell researcher is it associated?

  • Early stage embryo from which embryonic stem cells are obtained (tip of pencil)
  • Before women would be pregnant - early stage of development
• What are the myths/facts with regards to embryonic stem cell research?

  • Myths: researchers using mothers body to remove/abort embryo, embryo have recognizable body parts, illegal in US for eSC research 
  • Facts: blastocysts were made in lab and not women's body, eSC come from blastocysts with no discernable organs or body parts (not yet differentiated), no US federal against cloning or eSC research, it is not illegal
• What is the main purpose of a scientific journal article?  Why are they written?

  • A research investigation on a research that has taken place in order to find out using model organisms
  • Had background research done and cited
  • Shows the latest research and experiments in this field
• Know the formatting for how you wrote the journal article.

  • Your paper should be typed and double-spaced on standard-sized paper (8.5" x 11"), with 1" margins on all sides. 
  • Include a page header 
  • with the page number at the top right of every page.
  • and the  "TITLE OF YOUR PAPER" in the header flush left using all capital letters. 
  • The running head is a shortened version of your paper's title and cannot exceed 50 characters including spacing and punctuation.
  • Times New Roman Font, 12 point
  • Write the paper in past tense
• What are the main sections found in a journal article? What is the correct order of these sections?

  • Title page
  • Abstract
  • Introduction 
  • Methods
  • Results
  • Discussion
  • Acknowledgments
  • References
• What is the purpose of the Title? What must be included in the title?

  • The state the research, the authors and where its being conducted
  • title/authors/address
• How is the header different from the title?

  The header contains the title of the research nothing else
• Address


  Where the research is conducted
• Purpose of address


  To indicate where the research was carried out