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”

PowerQuant System: Tool for informed casework sample processing decisions

CottonSwabsIdentification of a crime perpetrator on the basis of DNA fingerprinting is not as easy as some of the CSI shows on television make it out to be. A sample such as blood stain, touch sample or body fluid retrieved at a crime scene is often a challenge for DNA analysts. In many instances, the samples are limited in quantity, found in dirty conditions, exposed to harsh environmental factors and are mixtures of more than one DNA—human and/or non-human. One of the most important aspects of the workflow to successfully obtain a DNA fingerprint profile is accurate quantification of human amplifiable DNA. The more information gleaned from the sample, the better equipped the DNA analyst is to determine the best course of action for obtaining a usable short tandem repeat (STR) profile from challenging samples. Therefore, Promega has developed the PowerQuant™ System, a probe-based 4-target, 5-dye real-time PCR method to a) determine human and male DNA concentrations in a sample, b) detect possible PCR inhibitors c) identify possible mixtures and d) measure DNA integrity. Continue reading “PowerQuant System: Tool for informed casework sample processing decisions”

Biology of Overeating and the Weight-Gain Cycle

ScaleA person needs to browse through any health related journal, magazine or website to find new and novel ways to reduce weight. While the options range from bariatric surgery to good old “eat-less-exercise-more” concepts, it is intriguing how the more weight a person gains, the harder it is to shed the extra calories. Losing weight is an uphill battle for majority of us. And that got me thinking about how much our biology cooperates while we try to lose weight. I came across these two elegant studies that explain why this is indeed an uphill battle. Continue reading “Biology of Overeating and the Weight-Gain Cycle”

Not Music to Everyone’s Ears

iStock_000016543302SmallWhen my son was about 2 years old, he commented that the jingles “Twinkle twinkle little star” and “alphabet song” had the same musical notation. While I do not think I am tone deaf and I do appreciate music, I had not made the connection in all these years.  Music appreciation is perhaps one of the most subjective and controversial topics. For some people, appreciating music involves understanding the technical nuances and critically evaluating artist’s mastery over the art, and for some of us, it is about simply enjoying the patterns and rhythms. While one might claim that they enjoy all kinds of music, for most of us, only certain kinds of music elicit a deeper appreciation, emotive experience and pleasure. Our music preferences are molded by exposure, cultural diversities and to some extent, mood. Music is extremely varied, and listing the kinds of music could fill pages. Arguing one kind of music is better than other is as like saying one color is better than the other.

So, what biological purpose does music serve? Continue reading “Not Music to Everyone’s Ears”

A Clean Brain Is a Healthy Brain

College student sleeping instead of studying
Can you sleep your way to a “cleaner” brain?
It is hard to undermine the role of cleanliness in disease prevention, both internally and externally. Within our body, the lymphatic system plays an important role in clearing the intercellular passages of large and potentially harmful toxic molecules and recirculate back into the blood stream. This enables the transport of these molecules to liver for inactivation and subsequent removal from the body. Therefore, lymphatic system prevents build-up of soluble proteins in the interstitial space. Typically, more metabolically active a cell is, more intricate is the lymphatic vasculature around it. This observation was in contrast to our scientific knowledge a few years ago, when we believed that due to the presence of the blood-brain barrier, there was no lymphatic system active in the brain. The brain, as we know, is highly active metabolically and the removal of harmful solutes and proteins from the neuronal vicinity is of utmost urgency. For a long time it was believed that cerebrospinal fluid (CSF), while coursing through the brain also removed cellular metabolite by products, apart from carrying nutrients to brain tissue, through a process known as diffusion. This is a rather slow process and it did not very well explain how large molecules such as proteins were removed from the interstitial place.

Recently, using two-photon imaging technique in live mice, scientists at Rochester discovered (1) that there is another vasculature functioning in the brain which circulates CSF to every corner of the brain much more efficiently, through bulk flow or convection. Continue reading “A Clean Brain Is a Healthy Brain”

Elevating “bliss” the natural way

Sun RunnersMarijuana is a highly controversial substance with roughly an equal number of supporters and opponents of its use for medicinal purposes. Marijuana is a dry, shredded mix of flowers, stems, seeds and leaves of the Hemp plant Cannabis sativa. New studies reporting the efficacy of medicinal marijuana in clinical conditions surface on a fairly regular basis, with the latest being a reported treatment for seizures. This constant influx of new information shows how little we know about the substance and how it works in the human body. So what do we know about this substance? While many psychoactive drugs clearly fall into the category of either stimulant, depressant or hallucinogen, Cannabis exhibits a mix of all properties, perhaps leaning the most towards hallucinogenic or psychedelic, though with other effects quite pronounced as well. Continue reading “Elevating “bliss” the natural way”

Rapid DNA Technology: Establishing your Identity in Less than Two Hours

DNA SequenceWhile the forensic and general communities continue to argue about the merits of the recent Supreme Court ruling on collection of samples from arrestees prior to conviction, I am fascinated by the technology that make this question relevant. The conventional way of generating a DNA profile from a sample by STR (short tandem repeat) analysis is a long process involving a series of steps that require sophisticated expensive equipment, trained personnel and, more importantly, time. The actual process of DNA analysis consists of a) sample collection, b) DNA extraction, c) PCR amplification using 16 or more unique fluorescently labeled primer sets d) capillary electrophoresis to size labeled DNA amplicons, e) software analysis to size DNA fragments and allele calls based on migration of allelic ladder fragments, and f) comparison to known profiles in the database. This entire workflow can typically take days or even weeks, and therefore it is not surprising that we see newspaper reports of backlogs of criminal and other property cases. With these time ranges, the sample collected at a site would be of no practical use to most ongoing investigations. Continue reading “Rapid DNA Technology: Establishing your Identity in Less than Two Hours”

“Fingerprinting” Your Cell Lines

Working in the laboratoryResearchers working with immortalized cell lines would readily agree when I state that it is almost impossible to look at cells under the microscope and identify them by name. There are phenotypic traits, however they do change with change in media composition, passage number and in response to growth factors. I remember the pretty arborizations my neuroblastoma cell line SH-SY5Y exhibited in response to nerve growth factor treatment. Thus physical appearance is not a distinguishing feature. Currently, in many labs, researchers typically use more than one cell line, and more than likely, share the same lab space to passage cells and the same incubator to grow the cells. In such scenarios, it is not difficult to imagine that cell lines might get mislabeled or cross-contaminated. For example HeLa cells, one of the fastest growing cell lines have been shown to invade and overtake other cell lines.

Misidentification of cell lines has deep and severe implications. A review of cell lines used to study esophageal adenocarcinoma found that a large number of the cell lines were actually derived from lung or gastric cancers. Unfortunately, by the time this error was discovered, data from these cell line studies were already being used for clinical trials and other advanced studies and publications. Moreover, the cell lines were being to screen and design and test specific cancer drugs which ended up in flawed clinical trials. Continue reading ““Fingerprinting” Your Cell Lines”

Chromatography and “Air Traffic Control” Interplay Direct Olfactory Function

It is not difficult to appreciate why a keen sense of smell is important to well-being and to general living. While it signals the presence of delicious (or stale) food before we can even see or taste it, it has obvious great survival value to be able to alert living beings of danger such as certain poisons, leaking gas or fire. Humans are known to identify about 10,000 different types of odors. Of course dogs have vastly improved and keener sense of smell than human beings.

When odorant molecules (molecules that we can smell) reach the nostril, they dissolve in the mucus and bind to olfactory receptors present on the cilia of each sensory neuron. This binding activates a G-protein coupled cascade involving adenylyl cyclase. This causes the release of cyclic AMP and opening of cAMP-dependent sodium channels. Influx of sodium causes the membrane to depolarize and activate an action potential for propagation of the signal to the brain where it is analyzed and decoded(1). This seems pretty straightforward until one realizes the sheer magnitude of smells we are able to identify using this mechanism. Continue reading “Chromatography and “Air Traffic Control” Interplay Direct Olfactory Function”

Dyed cells live longer?

When I first came across an article about methylene blue being protective against neuronal death, I was intrigued. I had always associated methylene blue (sometimes confused with methyl blue—an entirely different molecule) with staining nucleic acids or proteins following membrane transfer or with staining bacteria or its use as a redox indicator. It turns out that methylene blue (MB) has an extremely wide range of applications: commercial (dye in the textile / paper industry), laboratory (supravital dye, redox indicator) and an amazingly large plethora of clinical and therapeutic (early Alzheimer’s disease, mild cognitive impairment) applications(1). In fact, MB is an FDA-grandfathered antidote for the treatment of methemoglobinemia, a condition characterized by elevated levels of oxidized form of hemoglobin that interferes with its ability to release oxygen to the tissues.

What makes this compound, so rightly called “magic bullet” so unique and versatile? Continue reading “Dyed cells live longer?”