My Research for Five Levels of Understanding
By Sadie Kiendzior, UVA ChemSciComm

These summaries describe a research project for five different levels of understanding, going from primary school to expert.

1. Primary School

When crimes happen, police officers will go to crime scenes to collect evidence that will hopefully give them a clue to discovering who the criminal is. That evidence is brought to a lab where tests are done with the goal of finding the criminals DNA. Our DNA is like a code we all have that makes us unique, we all have different DNA, and because of this we can use a person’s DNA code to identify them. However, some of these processes done at the lab take a very long time, and require a lot of work from people. My research works to create machines that can ‘trap’ the DNA for us. We do that using microfluidics, which combines small amounts of chemicals and tiny plastic containers that can do the process automatically. I also use acoustics, which involves using sounds too high for us to hear to catch the DNA and trap it so we can find the criminals identity.

2. High School

DNA testing and the demand for testing has increased dramatically since the first use of DNA evidence in the 1980s. This increasing demand for testing along with the high labor demands associated with the testing processes has created a backlog of samples awaiting testing. Sexual assault samples contribute to this backlog because they are very unique pieces of evidence, that require a lot of processing. Most often, this evidence is a cotton swab that is inserted in the vagina. From these samples, forensic investigators are looking for sperm cells from the perpetrator, or criminal. However, there are far more cells from the victim’s vagina, which contains the victims DNA which can make it difficult to actually ‘see’ the criminals DNA in a swamp of victim DNA. So, we need to separate these two types of cells, sperm cells and vaginal cells. How this separation is done currently necessitates a lot of manual intervention, thus increasing chances of contamination of the sample. We try to automate this process and miniaturize it using microfluidics and acoustics to alleviate the labor demands associated with sexual assault kit testing. Microfluidics describes the use of micro-volume chips as a platform to do chemistry on. At the smaller scales, forces act differently, and we can leverage this small world to do unique things, one of them being acoustics. Acoustic waves produce areas of high and low pressure, and this is how we hear. But they also produce significant forces on particles in solution, enough force to actually capture and trap sperm cells under fluid flow. I am working on making a home-built instrument in an enclosed format that can automatically isolate sperm cells from sexual assault samples for downstream DNA testing and criminal identification free from contamination.

3. College

Demand for DNA testing has skyrocketed since the first case that utilized it in the 1980s. As a result, more and more pieces of evidence sit awaiting testing, this is what has become known as the backlog. Sexual assault kits are particularly difficult pieces of evidence to test, and contribute to the backlog due to the labor- and time-intensive processes involved in their testing. Most often after a sexual assault, a specialized nurse will take several anatomical swabs, most notably vaginal swabs. These swabs hopefully contain sperm cells from the perpetrator of the crime, but also contain a large amount of biological material from the victim, female vaginal cells. These two different kinds of cells must be separated, before the genetic signature of the perpetrator can be obtained to identify him. My research works to try to automate and miniaturize this separation process using microfluidics and sound waves. Microfluidics describes the use of small channels and valves to move fluid around and do micro-scale chemistry reactions. At small scales, sound waves can create areas of high and low pressure and exert significant forces on particles in solutions. When a mock sexual assault sample is processed on the microchip, the sperm cells become selectively trapped in the low-pressure nodes of the acoustic wave as all other material passes by. This is how we are working to automate the process of sexual assault kit testing.

4. Graduate Student in the Discipline

As the field of forensics has been progressing, so has the demand for involved genetic testing of evidence. The increasing demand coupled with financial strains on forensic laboratories have created a backlog of samples awaiting testing. One of the most common kinds of these samples awaiting testing are sexual assault samples. Sexual assaults produce unique evidence, because the evidence is collected from the victim, but we are looking for the perpetrator’s cells. Differential extraction (DE) is the process used for the separation of sperm cells from vaginal epithelial cells in a sexual assault sample. I am trying to automate the process of differential extraction using microfluidics and acoustics. Microfluidics utilizes miniaturized platforms to do chemical reactions in an automated and enclosed fashion. Additionally, at the micron scale, novel physical phenomena can be utilized. One example that I use in my research is acoustic forces. At the micro-scale, acoustic waves can create significant forces on particles in solution. These forces redirect micron-sized particles to either the low-pressure, or high-pressure nodes of the acoustic standing wave depending on particle and fluid properties, and modulation of the flow rate of the system can allow for particles to become completely trapped and retained under flow. We apply this to the separation of sexual assault samples, where the female epithelial cells are first selectively lysed using a gently method that keeps the sperm intact. Sperm cells are then selectively retained under flow within the acoustic standing wave, and epithelial cell lysate flows past. After the sperm pellet is washed to remove any extraneous female DNA, it is eluted to its own on-chip reservoir using pneumatic valving and pumping to prevent contamination from sample-to-sample.

5. Expert

As the demand for DNA testing has increased, so has the backlog of cases awaiting DNA testing. One of the most common types of samples awaiting genetic analysis are sexual assault samples. This is because the process of testing sexual assault samples, known as differential extraction (DE), is labor intensive, prone to contamination, and overall success of the separation is dependent on analyst experience. This process involves gentle lysis of female vaginal epithelial cells, followed by several labor-intensive steps of centrifugation and washing, before the isolated sperm pellet can be extracted, amplified via PCR, and DNA fragments can be separated using capillary electrophoresis. My research works to automate this process using microfluidics and acoustophoresis. Standing acoustic waves generate forces on particles in solution that allow for the selective trapping of sperm cells under flow conditions. This allows us to automate and enclose the process of sperm cell isolation and washing, characterized by repeated centrifugation and washing steps in the traditional DE process, greatly reducing the sample handling times, as well as the overall time to extraction.

Schematic