Posts Tagged ‘genomics’

New strategies for decoding genomes

 :: Posted by American Biotechnologist on 03-29-2012

Following up on yesterday’s post “New Layer of Genetic Information Discovered,” here is a talk by Professor Jonathan Weissman on applications of the ribosome profiling approach. The talk covers:

  1. Development of ribosome profiling protocols for a wide variety of eukaryotic and prokaryotic organisms.
  2. Uses of ribosome profiling to globally monitor when chaperones, targeting factors or processing enzymes engage nascent chains.
  3. Deciphering the driving force and biological consequences underlying the choice of synonymous codons.

Spliceman to the rescue

 :: Posted by American Biotechnologist on 03-12-2012

In a brief paper in the journal Bioinformatics, Brown University researchers describe a new, freely available Web-based program called Spliceman for predicting whether genetic mutations are likely to disrupt the splicing of messenger RNA, potentially leading to disease.

“Spliceman takes a set of DNA sequences with point mutations and computes how likely these single nucleotide variants alter splicing phenotypes,” write co-authors Kian Huat Lim, a graduate student, and William Fairbrother, assistant professor of biology, in an “application note” published in advance online Feb. 10. It will appear in print in April.

Spliceman can be found at

Read more…

Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques

 :: Posted by American Biotechnologist on 02-27-2012

Richard Cronn and colleagues (from the USDA Forest Service, Oregon State University, Brigham Young University, and Linfield College) have published an overview of newly developed, up-and-coming DNA sequencing techniques as one of a series of articles in a Special Issue on Methods and Applications of Next-Generation Sequencing in Botany in the American Journal of Botany. In their article, Cronn and co-authors summarize “targeted enrichment” strategies that can be used to obtain specific DNA sequences from complex plant genomes. Articles in the Special Issue provide a detailed snapshot of how “next-generation” sequencing is transforming plant biology.

“Plant genomes range from simple to exceptionally complex,” noted Cronn. “Combining next-generation sequencing with targeted enrichment allows plant scientists to reduce the complexity of plant genomes and focus on specific genes or unique regions that are easy to analyze.”

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The special issue also includes a comprehensive review article on NGS technologies. Click here to read the review.

Grass to gas: genome map speeds biofuel development

 :: Posted by American Biotechnologist on 02-14-2012

Researchers at the University of Georgia have taken a major step in the ongoing effort to find sources of cleaner, renewable energy by mapping the genomes of two originator cells of Miscanthus x giganteus, a large perennial grass with promise as a source of ethanol and bioenergy.

Changsoo Kim, a postdoctoral research associate in the UGA Plant Genome Mapping Laboratory, identified a set of approximately 600 bits of Miscanthus DNA that can serve as diagnostic tools. The next step is to determine which pieces of DNA are diagnostic of genes that can make the plant an even better biofuel crop.

Read more…

Test your knowledge with the Personal Genome Project practice test

 :: Posted by American Biotechnologist on 01-26-2012

Anyone familiar with scientific advances in the last few years should be well acquainted with the Personal Genome Project (PGP) launched by Dr. George Church in this 2005 Nature editorial. For those of you who have been living in a secluded cave somewhere for the past 6 years, the Personal Genome Project hopes to enroll 100,000 participants from the general public who are willing to have their genomes sequenced and allow the results to be published in a massive database along with extensive information about their traits and medical history. It is hoped that the information provided will help scientists test hypotheses about the relationships among genes, traits, and environment.

Perhaps less well known is what it takes to become a volunteer for this project. In order to enroll as a volunteer, potential participants must take an entrance exam that tests basic genetics literacy, informed consent expertise, and knowledge about the rights and responsibilities of human research subjects. That’s right…you must take a test and score 100% in order to qualify for participation in the study!

In order to help volunteers study for this exam, the Alan and Priscilla Oppenheimer Foundation have created a Personal Genome Project Study Guide which has information on:

  • genetic material
  • gene transmission
  • gene expression
  • gene regulation
  • genetics and society
  • project literacy

We thought that it would be fun for readers of this blog, who should be more familiar with the above topics than the average PGP volunteer, to take the practice tests associated with the study guide to see how much they actually remember from their first year courses! The tests are multiple choice so that should help prevent total embarrassment, but my guess is that most of us would not score 100% without preparing in advance. I took the gene transmission test and scored 9/10. Not enough to qualify as a volunteer!

Try your hand a the tests below and let us know how well you performed. Good Luck!

  1. Introduction to Cells, DNA, and Genes
  2. The Structure of DNA
  3. DNA’s Role in Determining Your Traits
  4. Gene Expression and Personal Traits
  5. Meiosis
  6. Heredity
  7. Coding for Proteins
  8. Controlling Protein-Coding Genes
  9. The Benefits of Applying Genetic Technology to Health Care
  10. The Risks of Applying Genetic Technology to Health Care
  11. Participating in the Personal Genome Project
  12. Human Research Subjects

For related posts see:
A story of genomic proportion
George Church: The father of personalized genomics
Genomes, Phenomes and Personalized Medicine