dna

A Crash Course in CRISPR

Posted on by Darcia Schweitzer

CRISPR is a hot topic right now, and rightly so—it is revolutionizing research that relies on editing genes. But what exactly is CRISPR? How does it work? Why is everyone so interested in using it? Today’s blog is a beginner’s guide on how CRISPR works with an overview of some new applications of this technology for those familiar with CRISPR.

Introduction to CRISPR/Cas9

27850283-June-13-CRISPR-image-WEB

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) were discovered in 1987, but it took 30 years before scientists identified their function. CRISPRs are a special kind of repeating DNA sequence that bacteria have as part of their “immune” system against invading nucleic acids from viruses and other bacteria. Over time, the genetic material from these invaders can be incorporated into the bacterial genome as a CRISPR and used to target specific sequences found in foreign genomes.

CRISPRs are part of a system within a bacterium that requires a nuclease (e.g. Cas9), a single guide RNA (sgRNA) and a tracrRNA. The tracrRNA recruits Cas9, while sgRNA binds to Cas9 and guides it to the corresponding DNA sequence of the invading genome. Cas9 then cuts the DNA, creating a double-stranded break that disables its function. Bacteria use a Protospacer Adjacent Motif, or PAM, sequence near the target sequence to distinguish between self and non-self and protect their own DNA.

While this system is an effective method of protection for bacteria, CRISPR/Cas9 has been manipulated in order to perform gene editing in a lab (click here for a video about CRISPR). First, the tracrRNA and sgRNA are combined into a single molecule. Then the sequence of the guide portion of this RNA is changed to match the target sequence. Using this engineered sgRNA along with Cas9 will result in a double-stranded break (DSB) in the target DNA sequence, provided the target sequence is adjacent to a compatible PAM sequence.

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Forensic Science in Search of the ‘Disappeared’

Posted on by Terri Sundquist

By Fredy Peccerelli

Guatemala’s method of uncovering human rights violations can help other post-conflict areas, says Fredy Peccerelli.

Skeleton Teeth

During Guatemala’s internal armed conflict (1960–1996) almost 200,000 people are thought to have been killed or ‘disappeared’ at the hands of repressive and violent regimes. Those lives matter. Their families’ demands are clear: they want to know what happened to their loved ones and they want their remains returned. They need truth and justice.

Using forensic sciences, the Forensic Anthropology Foundation of Guatemala (FAFG) is assisting families by returning their loved ones’ remains, promoting justice, and setting the historical record straight.

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DNA Reveals the Identity of Jack the Ripper?

Posted on by Terri Sundquist

A wanted poster for Jack the Ripper, who was also known as Leather Apron. Image courtesy of the British Museum
A wanted poster for Jack the Ripper, who was also known as Leather Apron.
Image courtesy of the British Museum

In the late 1800s, Victorian England was mesmerized and horrified by a series of brutal killings in the crowded and impoverished Whitechapel district. The serial killer, who became known as “Jack the Ripper”, had murdered and mutilated at least five women, many of whom worked as prostitutes in the slums around London. None of these murders were ever solved, and Jack the Ripper was never identified, although investigators interviewed more than 2,000 people and named more than 100 suspects. Now, 126 years after the murders, a British author, who coincidentally has just published a book on the subject, is claiming that DNA analysis has revealed the identity of the notorious killer. DNA is often thought to be the “gold standard” of human identification techniques, so why is there so much skepticism surrounding this identification?
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Ancient Origins of a Human Gene Associated with Diabetes

Posted on by Terri Sundquist

Ancient peopleRecently, researchers of the SIGMA Type 2 Diabetes Consortium published a paper in Nature identifying a new locus associated with a higher risk of type 2 diabetes (1). Considering the increasing prevalence of this metabolic disease in today’s sugar-filled world, any discovery that helps us understand diabetes is exciting news. However, the most interesting discovery published in this paper might not be this new gene variant but rather the origin of this variant in modern human populations: Neandertals.

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ProK: An Old ‘Pro’ That is Still In The Game

Posted on by Nives Kovacevic
Proteinase K Ribbon Structure ImageSource=RCSB PDB; StructureID=4b5l; DOI=http://dx.doi.org/10.2210/pdb4b5l/pdb;
Proteinase K Ribbon Structure ImageSource=RCSB PDB; StructureID=4b5l; DOI=http://dx.doi.org/10.2210/pdb4b5l/pdb;

If you enter any molecular lab asking to borrow some Proteinase K, lab members are likely to answer: “I know we have it. Let me see where it is”. Sometimes the enzyme will be found to have expired. The lab may also have struggled with power outages or freezer malfunctions in the past. But the lab still decides to keep the enzyme. One may rightly ask – why do labs hang on to Proteinase K even when it has been stored under sub-standard conditions?

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Sonnets in DNA

Posted on by Isobel Maciver

William ShakespeareFor sixty years now, scientists have studied the role of DNA as a vehicle for the storage and transmission of genetic information from generation to generation. We have marveled at the capacity of DNA to store all the information required to describe a human being using only a 4-letter code, and to pack that information into a space the size of the nucleus of a single cell. A letter published last week in Nature exploits this phenomenal storage capacity of DNA to archive a quite different kind of information. Forget CDs, hard drives and chips, the sum of human knowledge can now be stored in synthetic DNA strands. The Nature letter, authored by scientists from the European Bioinformatics Institute in Cambridge, UK, and Agilent Technologies in California, describes a proof-of-concept experiment where synthetic DNA was used to encode Shakespeare’s Sonnets, Martin Luther King’s “I Have a Dream” speech, a picture of the Bioinformatics Institute, and the original Crick and Watson paper on the double-helical nature of DNA. Continue reading “Sonnets in DNA”

Identifying the Victims of John Wayne Gacy

Posted on by Terri Sundquist

John Wayne Gacy was a notorious serial killer who sexually assaulted and murdered 33 boys and young men in the 1970s in Chicago, Illinois. The killing spree stopped only when he was arrested in 1978 after the parents of his last victim contacted police with critical information that implicated Gacy in the boy’s disappearance. He was tried, convicted and in 1994 executed for his crimes. Of the 33 victims that police found buried in and around his home, only 25 could be identified, leaving eight victims nameless and eight families to wonder if their missing loved one died at the hands of this evil man. When all available means of identification were exhausted, these eight sets of remains were buried but not forgotten.

In 2011, these remains were exhumed and the victim’s DNA analyzed to try to provide clues as to their identity.

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How Identical are Identical Twins?

Posted on by Terri Sundquist

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?”

Analyzing DNA to Determine a Person’s Age

Posted on by Terri Sundquist

Birthday cakePeople have employed many methods to disguise their age: eating a healthy diet rich in antioxidants, exercising regularly, protecting their skin from the sun and, if all else fails, undergoing plastic surgery. However, a recent Current Biology paper may make it harder for us to hide our true age. The authors describe a real-time PCR assay that can provide an estimate of a person’s age based on a tiny blood sample (1). Continue reading “Analyzing DNA to Determine a Person’s Age”