Meet Marty Ensenberger, Senior Research Scientist on the Spectrum CE System

29160613_lPromega will soon introduce the Spectrum CE System for forensic and paternity analysis. Building this system requires the efforts of many people from many disciplines—from our customers who have told us their needs to the engineers and scientists building the instrument and ensuring its performance. Periodically we will introduce our Promega Connections readers to a team member so that you can have a sneak peak and behind-the-scenes look at Spectrum CE System  and the people who are creating it (of course if you truly want to be the first to know, sign up at www.promega.com/spectrum to receive regular, exclusive updates about Spectrum CE).

Today we introduce Marty Ensenberger, Senior Research Scientist on the Spectrum CE System. Continue reading “Meet Marty Ensenberger, Senior Research Scientist on the Spectrum CE System”

Mitochondrial DNA Typing in Forensics

23540687_lMitochondria, often thought of as powerhouses of the cell, are fascinating eukaryotic organelles with a double-layered membrane and their own genome. Mitochondrial DNA (Mt DNA) is typically about 16570 bases, circular, highly compact, haploid and contains 37 genes, all of which are essential for normal mitochondrial function. Thirteen of these genes provide instructions for making enzymes involved in oxidative phosphorylation, a process that uses oxygen and simple sugars to create adenosine triphosphate (ATP), the cell’s main energy currency. The remaining genes code for transfer RNA (tRNA) and ribosomal RNA (rRNA) which are necessary for translating messenger RNA transcribed from nuclear DNA, into protein molecules.

One of the most important characteristics of mitochondrial genome that is relevant to field of forensics is the copy number. Continue reading “Mitochondrial DNA Typing in Forensics”

Cell Line Misidentification Rears Its Ugly Head

Cancer cell illustrationBack in 2009, we reported on the problem of cell line contamination (1). In that article we reported the statistics that an estimated 15–20% of the time, the cell lines used by researchers are misidentified or cross-contaminated with another cell line (1). This presents a huge problem for the interpretation of data and the reproducibility of experiments, a key pillar in the process of science. We have revisited this topic several times, highlighting the issues cell and tissue repositories have discovered with cell lines submitted to them (2) and discussing the new guidelines issued by ANSI (3,4) for researchers regarding when during experimental processes cell lines should be authenticated and what methods are acceptable for identifying cell lines.

Just recently two papers were voluntarily retracted by their authors because of cross contamination among cell lines used in the laboratories. The first that came to my attention represented the first retraction from Nature Methods in its nine years of publication. In this paper, cross contamination of a primary gliomasphere cell lines with HEK cells expressing GFP resulted in “unexplained autofluorescence” associated with tumorigenicity (5). The second paper, retracted from Cancer Research by the original authors, was also another cross contamination story involving HEK cells (6). In this story a gene was incorrectly described as a tumor suppressor, that when silenced led to the formation of tumors in nude mice. It turns out that the contaminating HEK cells also failed to express this same gene.

So because of cross contamination of cell lines, two groups have voluntarily retracted papers. Being open and honest about what had happened with the cell lines and reaching the decision to retract the papers could not have been an easy thing, but these decisions benefit the scientific community in many ways. Obviously they benefit the researchers doing work on the specific research questions addressed by the papers by preventing researchers from pursuing paths that lead to dead ends. But in the bigger picture these retractions reinforce the argument that cell line authentication needs to become a routine and accepted part of any experimental process that depends on cell culture if we are to have confidence in the experimental results.

References

  1. Dunham, J.H. and Guthmiller, P.  (2009) Doing good science: Authenticating cell line identity. Promega Notes 101, 15–18.
  2. Duham, J.H. and Guthmiller, P. (2012) Doing good science: Authenticating cell line identity. Promega PubHub. [Internet: Accessed September 2013]
  3. Gopal, A. (2013) Fingerprinting  your cell lines. Promega Connections blog [Internet: Accessed September 2013]
  4. Sundquist, T. (2013) Preventing the heartache of cell line contamination. Promega Connections blog [Internet: Accessed September 2013]
  5. Evanko, D. (2013) A retraction resulting from cell line contaminationMethagora blog. [Internet Accessed September 2013]
  6. Negorev, D. (2013) Retraction: Sp100 as a potent tumor suppressor: Accelerated senescence and rapid malignant transformation of human fibroblasts through modulation of an embryonic stem cell program. Can. Res. 73, 4960.

Your Day in Court: Becoming an Effective Expert Witness

TrialAs scientists, we’ve all have those moments when we are asked to explain to a nonscientist—maybe Mom or Grandpa—what it is we do all day in the lab. Or maybe someone asks us a seemingly innocent question such as “How can DNA be used to identify someone?” Do you try to teach them about polymorphic DNA sequences, population genetics, PCR, capillary electrophoresis, the necessary statistical calculations and all of the other factors involved? Even if your audience members are patient enough for that, will they understand, or will their eyes glaze over after the first 10 minutes? If you’re like me, you give your inquisitor the high-level, 30,000-foot overview of the topic and hope that that is enough to satisfy their curiosity. Answer the question, but don’t get bogged down in too much detail unless your audience really seems genuinely interested in delving further.

That’s all fine and good if you can get away with that approach, but there are situations where the high-level overview won’t suffice. Continue reading “Your Day in Court: Becoming an Effective Expert Witness”

DNA Typing: Useful Tool to Solve Crimes or Invasion of Privacy?

DNA in a test tubeThis year marks the tenth anniversary of the complete human genome sequence. The Human Genome Project revealed a surprising fact: Only 1% of our genome encodes proteins. This equates to a paltry 20,000–25,000 genes. The function of the other 99% of our DNA remained a mystery. Shortly after the sequencing was completed, the National Human Genome Research Institute (NHGRI) launched a new research project, termed the Encyclopedia Of DNA Elements (ENCODE), to identify DNA elements and try to find a purpose for the other 99% of our DNA. This project has contributed greatly to our understanding of the human genome, as documented in the 30 ENCODE-related papers published in Nature, Genome Research and Genome Biology in 2012 (see the Nature web site. However, the ENCODE project is being used in an unforeseen way: to support an appeal to the recent US Supreme Court decision about the constitutionality of collection and analysis of DNA from arrestees.

Continue reading “DNA Typing: Useful Tool to Solve Crimes or Invasion of Privacy?”

How Identical are Identical Twins?

Identical twins are derived from the same fertilized ovum and, therefore, should be…well… identical, right? They look the same and often dress the same, especially as children, and many people often have a hard time distinguishing one twin from the other. They are indistinguishable by genetic testing.

However, identical twins are not always identical, as the authors of a recent letter to the editor of Forensic Science International Genetics point out (1). Continue reading “How Identical are Identical Twins?”