Lighting the Way

Author: Savannah Sadaiappen

The information used in this post can be found in the article, “Development of a low-cost and portable smart fluorometer for detecting breast cancer cells” by Mohammad Wajih Alam, Khan A. Wahid, Raghuveera Kumar Goel, and Kiven Erique Lukong, published in January 2019.

I’m sure we have all heard of the fascinating green fluorescent protein, commonly known as GFP, at least once and thought the idea of it was the coolest thing ever right? It’s basically like making the cells you’re researching glow and who doesn’t love that? It’s essentially a party…under a microscope #lit. However, the use of GFP and detecting it via fluorescence microscopy can cost scientists a lot of dolla dolla bills y’all (it’s expensive).

             https://giphy.com/gifs/migos-james-corden-carpool-karaoke-1hMhl5fpuLldDqj0Ey

Not all scientists have as much money as Takeoff (member of Migos) and unfortunately aren’t able to utilize fluorescence imaging instruments. Scientists at the University of Saskatchewan researched the development of a low-cost and portable smart fluorometer to combat this issue.

Fluorescence microscopy is based on the principle of fluorescence imaging which serves as a powerful tool in the fields of biology and chemistry to monitor cell dynamics and molecules. Commercial fluorescent microscopes have numerous advantages: live cell imaging, wide field-of-view, and sensitive sophisticated cameras for high resolution images to name a few. By fluorescently labelling proteins of interest scientists can observe/investigate any cellular process and use this to aid in the extraction of meaningful information.

 

                                      https://www.bioimager.com/microscope-fun/

Fluorescence microscopy has major applications in cancer biology where cancer cells are chemically labeled for detection. As breast cancer is the most common form of cancer affecting women with 1 in 8 women expected to be diagnosed with the diseases during her lifetime the development of a low cost and portable detection instrument offers numerous advantages to breast cancer research. The research described in the article was used to design a low-cost and portable fluorometer that can be used to detect fluorescence signals emitted from a model breast cancer cell line which have been engineered to express the green fluorescent protein (GFP). The device used utilizes a flashlight that works in the visible range which serves as an excitation source and a photodiode as a detector. It also uses an emission filter which mainly allows the fluorescence signal to reach the detector while eliminating the use of an excitation filter and dichroic mirror. The emission filter was selected so that it matches the emission wavelength if GFP which ensured that the GFP wavelength is the main wavelength allowed to pass through. The elimination of these two complicated devices is what makes the newly developed instrument compact, low-cost, portable, and lightweight. The set up of the device can be seen below in Figure 1.

 

                Fig 1. A graphical illustration and working principle of the developed device.

The device developed consists of a flashlight which works in visible range, a photodiode to detect the fluorescent signal, a microcontroller to read and transmit the data, and an LCD screen to display messages as a major component. Immortalized human breast cancer cells were used to test the fluorometer prototype. The gene encoding the Green Fluorescent Protein (GFP) was stably introduced into these cells via retroviral transduction. GFP expression of these live cells was confirmed via fluorescence microscopy which served as a control. These same samples were used to measure the intensity of the fluorescence signal using the developed fluorometer. A schematic of how the device works can be seen in figure 2.

                                             Fig 2. Operating procedure of the system

Detection of GFP in the cancer cells was successful and confirmed the development of the prototype fluorometer was successful after scientists analyzed statistics and accuracy of the device. The development of this low cost fluorometer which can measure a signal emitted by breast cancer cells expressing GFP promotes the access of fluorometers to medical and research laboratories where resources are limited. This fluorometer has broad applications in the fluorescence-based detection of multiple cancer types and can greatly impact research done by the clinical and biomedical community.

                     https://giphy.com/gifs/nickcannon-nick-cannon-MSCzxrLEF25feISTIz

 

Article can be found at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377908/ (figures also sourced from this article)

Lactose, How do you get into the cell?

By: Jordan Bourg

I bet you’ve always wondered about the mechanical properties of the insertases and translocases that move proteins around the biological membranes of all life. Well, look no further than the bacterial translocase SecYEG and the bacterial insertase YidC. These model proteins will serve as the workhorses to insert Lactose Permease (LacY) into cellular membranes. This enzyme helps lactose pass through the cell membranes to supply energy to the cell. But why just stop at the function of these membrane proteins when we can delve into the qualities that each of these possess individually and as cooperative proteins. Unfortunately, the pathways that these enzymes take to fold other proteins are largely unknown. Up until this study, many of the Insertase and Translocase mechanisms were hiding in the shadows. Fortunately, this study found a way to uncover these hidden mechanisms and bring us a little closer to understanding the cells that compose us.

Let us begin with how they analyze the protein properties. In this study, they use atomic force spectroscopy to analyze the folding proteins. It does this by first unfolding the protein, and then allowing it to refold while measuring the pressure placed on the stylus. The stylus is the part that makes physical contact with the protein throughout the process. To sum things up, they take LacY that’s already imbedded in a membrane and pull it out, unfolding it in the process. They then reintroduce it into another membrane by putting it in close proximity to it (refolding it). This process can be seen in figure 1 below. This wouldn’t work unless the receiving membrane has the translocase/insertase proteins imbedded in it because the LacY can’t insert itself into the membrane. This was proven in the study by introducing the LacY to a regular membrane and receiving no insertion. The first trial they ran involved using just the insertase YidC to insert the LacY. They found that the YidC inserted the LacY at a diminished rate as more peptides were added into the membrane. They also found that the LacY segments were inserted in randomly using this insertase.  This lead to the next trial, which involved replacing YidC with the translocase SecYEG. When LacY was brought into close proximity with the membrane bound SecYEG, the segments were inserted into the membrane in sequential order. The next trial would use both the translocase and the insertase together to insert the LacY. This trial inserted the LacY sequentially showing that the SecYEG showed dominance to the YidC. They also used multiple test such as SDS-PAGE and western blot, to verify their enzyme structures were correct.

Figure 1: This figure shows the stylus extracting and unfolding the protein from the membrane. It then moves it to another area and reinserts it, allowing it to refold.

In conclusion, it was found that both the translocase and the insertase initiate the insertion with just one structural segment. They also found that the SecYEG showed dominance over YidC with respect to insertion kinetics. In addition to that, since YidC inserts randomly, it can fold the protein through 10! (3,628,800) different pathways. The SecYEG can only fold the protein in about 10 different ways due to its sequential folding. With this inmind, it has been shown that YidC usually inserts shorter peptides, while SecYEG handle longer ones. It can then be speculated that this random insertion sequence is more favorable when dealing with shorter peptides. They have proposed that both of these substantially different pathways mechanisms must be essential to protein biogenesis. As if this study wasn’t already successful enough, there “bottom-up assay” can now be used to analyze the folding of countless other membrane proteins.

Read this article: http://advances.sciencemag.org/content/5/1/eaau6824

1^st image: https://me.me/i/this-isnt-justdarkness-its-advanced-darkness-quick-meme-com-when-7063591

Figure 1: Obtained from article – http://advances.sciencemag.org/content/5/1/eaau6824

3^rd image: https://memegenerator.net/instance/73533716/me-to-me-me-but-im-lactose-intolerant-me-to-me-eat-the-cheese

Transporting Cholesterol

By Drew Norgress

This article researched the two mechanisms on how cholesterol is transported from recycling endosomes to the trans-Golgi network and which mechanism is more efficient in the distribution of cholesterol. Transportation works through a system using binding proteins called Rab11.  The two mechanisms that mediate intracellular cholesterol transport are vesicular and nonvesicular transport.  After treating cells with a metabolite of cholesterol to induce OSBP (oxysterol-binding protein) from the cytoplasm to the TGN (trans-golgi protein), cholesterol in the TGN was decreased in Rab11, RELCH, and OSBP depleted cells, but increased in the lysosome.

In this experiment, it suggested that RELCH promotes nonvesicular cholesterol transport, which are key regulators, and they transport from recycling endosomes to the TGN through membrane tethering. Using artificial liposomes indicated that the tethering mediated by these proteins is crucial for efficient cholesterol transfer between the membranes.

Read this article: http://jcb.rupress.org/content/217/5/1777 

Reference: https://phys.org/news/2018-04-key-tethering-protein-cellular-cholesterol.html

Healthy Fat, Healthy Heart?

Author: Blaire Laiche

The information used in this blog post can be found in the article, “Cholesterol Uptake Capacity: A New Measure of HDL Functionality for Coronary Risk Assessment” by Amane Harada, Ryuji Toh, Katsuhiro Murakami, Maria Kiriyama, Keiko Yoshikawa, Keiko Miwa, Takuya Kubo, Yasuhiro Irino, Kenta Mori, Nobuaki Tanaka, Kunihiro Nishimura, Tatsuro Ishida, and Ken-ichi Hirata, published September 2017.

We’ve all heard of them, and usually, we all shudder at the thought of them—fats. I can’t say that I have ever heard someone say that they like fat, but I do know that many of us love foods that lead to the accumulation of the pesky stuff in our body. Many would agree that eating healthy can be miserable.

Not to fear, you don’t have to look like Kevin Malone, because not all fats are bad! In fact, High-density lipoproteins (HDL) are known as the “good” fats in our body. Studies have shown that there is an inverse relationship between HDL concentration and coronary heart disease, but studies have found that HDL concentration trends alone are not enough for assessing cardiovascular risk. Thought to be a key function of HDL, is the efflux of cholesterol from macrophages into the arterial wall. Why is cholesterol uptake important? Cholesterol uptake capacity has been found to be associated with CAD (coronary artery disease) recurrence. This pathway is said to be a better indicator of cardiovascular pathology, but conventional methods are not effective, requiring radio-active labeled cholesterols.

In a recent study, it was suggested that the efficiency of HDL-induced cholesterol efflux from macrophages depends mainly on the capacity of HDL to uptake cholesterol. To test this, scientists constructed a cell-free assay system to evaluate cholesterol uptake using the fluorescently labeled reagent boron dipyrromethene difluoride (BODIPY) linked to cholesterol (14) and a specific antibody against apolipoprotein A1 (apoA1), which is the most abundant protein component of HDL. The serum HDL was taken from patients who had previously undergone successful percutaneous coronary intervention or coronary artery bypass grafting and who had been hospitalized for the purpose of CAG from April 2011 to July 2015 because of follow-up or stable angina or inducible ischemia.

Figure from: Cholesterol Uptake Capacity: A New Measure of HDL Functionality for Coronary Risk Assessment, by Herada et al., 2017

The figure above shows how the assay was performed:
(i) HDL was incubated with fluorescently labeled cholesterol
(ii) HDL with fluorescent cholesterol was captured by antibody
(iii) Fluorescence intensity that was captured in HDL not destroyed by antibody

Using the sample serum, the assay showed cholesterol uptake capacity was inversely associated with the recurrence rate of coronary lesion after re-vascularization in patients with optimal control of LDL concentration. Scientists concluded that the measurement of the cholesterol uptake capacity of HDL in the circulation may provide a means of assessing the anti-atherosclerotic functions of HDL and that the uptake-assay may provide a new diagnostic tool to prediction risk associated with CAD.

We can now rest easy knowing that science is well on its way to being able to let us eat as we please and test our serum HDL efflux of cholesterol efficiently to assess our future risk for heart disease.

Read the original article here:

Click to access jalm.2016.022913.full.pdf

References:

Click to access jalm.2016.022913.full.pdf

Gifs found on apple images

 

HDL: The Good Fat

By Mallory Robichaux

With spring break rapidly approaching, the words ‘good’ and ‘fat’ together may seem like somewhat of an oxymoron to some people. However, I’d like to introduce you the benevolent hero of the lipoprotein world, HDL, which stands for High Density Lipoprotein. HDL- cholesterol is known as the ‘good cholesterol’ because it circulates throughout your body and picks up the excess cholesterol molecules in your bloodstream and returns them to your liver, where they hide away unable to cause plaque buildup in your arteries. Plaque buildup in arteries, known as atherosclerosis, leads to blood clots and the eventual obstruction of blood flow. For this reason, higher HDL levels have long been attributed to decreased risk of coronary artery disease (CAD). High HDL levels in blood have also been attributed to suppression of prolonged inflammatory responses, which can lead to sepsis organ failure. So basically, HDL is just running around our blood doing the most for us and we have the audacity to think that all fat is bad? How rude.

We know that HDLs are small lipoproteins. They are made up of phospholipids, cholesterol and cholesteryl esters (the lipo- part of the word) and contain more than 80 associated proteins (the –protein part). Yet HDLs display a high degree of variation and intercorrelation, making it difficult to discern which parts of the lipoprotein exactly contribute to the do-gooder function of the molecule. Therefore, it is beneficial to analyze the genetic factors that contribute to the HDL proteome in order to have a better understanding of how HDL is regulated, so that we can potentially mimic those elements to synthesize treatments that could impart similar beneficial effects.

 

Other recent studies have suggested that raising HDL-cholesterol levels does not necessarily lead to increased protection against CAD, because the literature explains that certain species of HDL, but not others, provide protection against CAD. So, HDL- cholesterol alone is not an accurate measure of HDL’s properties, such as protection against CAD. This study used a hybrid mouse diversity panel, which is a set of 93 inbred strains of mice exhibiting common genetic variation that resembles the human population, to better define the various species of HDL at the level of protein composition and to understand their genetic regulation. The HDL proteome and HDL function for each strain were identified through genetic mapping. Additionally, single nucleotide polymorphisms (SNPs) were used to study the genetic factors contributing to HDL composition and to analyze the function of mutated HDLs. Finally, the study used protein-protein interaction cluster analyses to build an HDL molecule and examine which proteins are core proteins and which are peripheral proteins.

HDL molecule. Graphic from NIH National Library of Medicine.

The study revealed a high level of heritability in HDL proteins, which is linked to the heritability of cholesterol levels and thus the heritability of high- cholesterol related CAD. The results of the study also show the likelihood that inheritance controls the production of HDL particles of certain protein and lipid composition that have different functions. It seems that rather than HDL-cholesterol levels alone, the capacity of the HDL molecule to take up cholesterol from the bloodstream and deliver it to the liver is a more accurate indicator of CAD prevalence. Further studies that assess the protein structure of HDL are needed to elucidate the protein or genetic factors responsible for the cholesterol-carrying ability of HDL if we hope to harness the cholesterol- fighting superpowers of this lipoprotein.

Read the original article here:

https://doc-0o-5s-apps-viewer.googleusercontent.com/viewer/secure/pdf/l2d9m5nc9ngujt5jglbhrqrh8kbc4g76/b5lbvknd7lh0gvluk6o01l6mpo4fl126/1552788375000/gmail/12474323182748213285/ACFrOgDEodngr9FF9OuPxDPnSrvClfhdAaN43t4vhr0nhbMN8JvfJJHNf1fBa2-dMQz-4V6ehemK_e7LXs86bhMRPn7Uxl4u4yaHwDxRgpAKtq4i1MXx_AONBAL6vVA=?print=true&nonce=q07j5s15smbe4&user=12474323182748213285&hash=7sjke421bg0m4738aegbt6co6grjn31e

 

 

 

Crime Scene Investigation: A New Trace Evidence

By: Claire Robichaux
Have you ever wondered if there were more ways to investigate the evidence at a crime scene? If there’s no blood or any source of DNA left at the scene, where do investigators go from there? Most trace evidence, for instance, a piece of blonde hair, is mainly categorized as class evidence rather than individual evidence- and let’s face it, think of how many people you know with blonde hair…doesn’t help investigators really get to the bottom of it. Scientists from Colorado State University set out to explore if an individual’s skin microbial signature- that is, the microbes on the surface of their skin, can be matched to objects and surfaces at crime scenes. The skin microbiome is unique to each individual and consists of bacteria, fungi and viruses.
http://mysteryreadersinc.blogspot.com/2014/04/cartoon-of-day-crime-scene-1.html

There were 4 objectives for this experiment: Objective 1 was to determine whether different types of surfaces that are touched by an individual influence the detection of an identifiable skin microbe. This experiment involved 13 participants touching 5 material types: plastic, glass, wood, ceramic, and metal. Objective 2 looked at whether the number of times the individual touches a surface influences the detection of identifiable skin microbes; plastic tiles were touched either 10, 20 or 30 times. Object 3 was to determine if skin microbes are recoverable after multiple people have touched it. This experiment was conducted in pairs. The first person would touch a tile (plastic or ceramic) 30 times followed by the second person touching it 20 times. Objective 4 looked at the stability of the microbes on a surface over time; 12 participants each touched a different plastic tile 20 times.

The results from objective 1 indicated that the skin microbial signature on a surface can be accurately linked to an individual, although the results from the ceramic and plastic tiles were most significant. Objective 2 found that the ability to recover enough microbes to correctly match the individual to their tile increased with the amount of times they touched the tile. Sequence data from tiles touched only 10 times was very poor, while tiles touched 20 and 30 times were successfully sequenced. Objective 3 led to mixed results. Some individuals leave highly traceable evidence on a background of someone else’s while others do not. Objective 4 concluded that the microbes persist on the surfaces up to about one day.

https://www.mememaker.net/template/target-lady

The results from this experiment provide crucial information that can be used by crime scene laboratories and also significantly expand the power of trace evidence analysis.

References:

Click to access 251647.pdf

Dirty DNA

There is still a potential risk of DNA transfer even when wearing gloves and this can be problematic to examinations of clues found at a crime scene. Examiners DNA was found on surfaces, equipment, and tools in a forensic biology lab. If any of these objects contain DNA, it can contaminate the evidence of a crime scene. A key risk factor for contamination is gloves. The risk comes from how gloves are put on, what they touched, and when they are replaced.

In this experiment, 49 gloves were tested for possible contamination. Of the 49 gloves, 24 were tested and included the possibility of staff contamination and the remaining 25 gloves were tested using a software that eliminated staff DNA.

There were eleven total examinations done by five people. A metal pole, a section of a mattress, a pair of jeans, a jacket, and a bottle opener were examined for traces DNA. Trace DNA is also known as touch DNA because only a small sample is needed for testing such as skin cells left on an object after being touched. A jacket, hockey stick, two singlets (or men’s wrestling garments), a knife, and a t-shirt were examined for blood.

Here is a police officer kneeling on the ground of the crime scene. While it may seem harmless, he could possibly be transferring his or others DNA to the scene of the crime.

The average number of glove changes was 10 when examining blood. An average of 0.321 nanograms of DNA were found on gloves used to examine blood exhibits and 98% of these gloves were able to produce a DNA profile. The average number of contributors was found to be 2.3.

The average number of glove changes was 8 when examining trace. An average of 0.106 nanograms were found on gloves used to examine trace exhibits and 87% of these gloves were able to produce a DNA profile. The average number of contributors was found to be 1.3.

The gloves used at the beginning and end of the examination were found to have twice as much DNA and number of contributors than the other gloves. The best explanation for this is that DNA of the examiner is present on the packaging and then transferred to the gloves.

The major problem is that DNA can be transferred onto the gloves reducing the amount of available DNA for sampling. This can possibly allow for a guilty person to get away with the crime they have committed. Another problem is that DNA can be transferred to other crime scene clues. When the gloves were tested for staff contamination, it was found that 81% of the gloves had DNA from those directly involved with the case and 19% had DNA of those who were not directly involved with the case. Many forensic scientists are skilled at the task of handling evidence, however, law enforcement is not so careful. The best way to prevent contamination is to enforce better practice onto anyone who may be find themselves at a the scene of a crime.

 

References:

https://www.fsigenetics.com/article/S1872-4973(18)30428-9/pdf

https://www.crime-scene-investigator.net/crime-scene-contamination-issues.html

https://www.scientificamerican.com/article/experts-touch-dna-jonbenet-ramsey/

https://www.mansfieldtexas.gov/crime-scene-investigations

meme from: https://imgflip.com/i/yz640

 

 

Cracking the Criminal Case

Author: Marissa Duet

The information used in this blogpost can be found in the study “Characterizing Microbial Assemblages as Trace Evidence as Following Residential Burglaries” by Gilbert et al. published November 2018.

Many scientific milestones are relevant to other fields, such as DNA evidence being presented in a criminal court case for the first time in 1856. Just as the DNA of each and every individual is unique, the skin microbiome is also unique to each individual. The skin microbiome is composed of millions of bacteria, viruses, and fungi; while this may sound frightening, we have evolved to develop a mutually beneficial relationship with many of these microbes. By the age of 3, the skin microbiome establishes a core identity that will persist throughout one’s lifetime. Overtime, lifestyle changes will cause minor changes in signature to the microbiome that one possesses. For example, clues about a person’s diet, lifestyle, and occupation can be gathered from their microbiome. Important to the study of forensic methods, we leave a trace of our unique microbiome on the surfaces and objects that we come into contact with. The Department of Justice decided to fund the following study to deduce the integrity of using traces of microbiomes to identify perpetrators in crimes.

                                                                       Figure 1: The microbiome on the hand of an individual

 For this study, ten houses were chosen to be the scene of a mock burglary. Before the invasion, microbial samples were taken from the occupants of the house, the two burglars, and 10 surfaces in the home. Two burglars, one with bare hands and one with nitrile gloves, entered the house and interacted with surfaces within the home for 30 minutes. After the invasion, microbial samples were taken from only the burglars and 10 surfaces within the home. DNA was extracted from each sample, amplified, and sequenced in attempts to identify which individuals were the burglars. It was found that around 75% of the time, the perpetrator could be identified by comparing the microbes present on the surfaces at the scene before and after the crime to the microbiome of the individuals who had interacted with the scene.

Figure 2: An example of microbial DNA sequencing in which the sample from a crime scene can be best matched to the sample of a suspect. In this case, there would be evidence supporting suspect B as the perpetrator.

 It is important to note that real life applications would not be as ideal and straightforward as this experiment. A direct comparison to the effectiveness of utilizing DNA samples hasn’t be done, as the data for DNA sampling widely varies. This study shows the need for extreme caution to be taken in preventing the contamination of crime scenes for investigative purposes. Although further studies must be done, such as investigating how long the microbiome from a perpetrator lasts at a scene, this provides a basis for future work to be done. Overall, this study shows that the human microbiome may be the newest upcoming forensic tool that had been at our fingertips all this time (quite literally).

 

References:

https://www.nij.gov/topics/forensics/evidence/trace/Pages/microbial-communities-on-skin-leave-unique-traces-at-crime-scene.aspx?utm_source=facebook&utm_medium=social-media&utm_campaign=articles

https://www.medicalnewstoday.com/articles/322069.php

https://www.ncjrs.gov/pdffiles1/nij/grants/252474.pdf

Images:

Figure 1: http://techgenmag.com/2015/06/microorganisms-that-live-on-your-hand/

Figure 2: https://www.proprofs.com/discuss/q/239073/using-fingerprinting-shown-below-which-suspect-most-likely-m

 

 

Get Your Shed Together

Author: Emily Venable

The information used in this blog post can be found in the article, “Shedding light on shedders” by Kanokwongnuwut, Martin, Kirkbride, and Linacre published June 5, 2018.

Suppose you shook the hand of a man whom you just met.  Flash forward to a few days later. You are notified by the police that your DNA was found on the knife used as a murder weapon.  How is this possible? You didn’t murder anyone (did you?).

A study done by Cynthia Cale studied whether secondary DNA transfer could falsely place someone at the scene of a crime. In the study, she asked participants to hold hands for two minutes then immediately handle knives. Sounds risky. Why not just use a stick? Anyway…  The results indicated that secondary DNA transfer was detected in 85% of the samples.  This leads one to assume that when you shook hands with Mr. Stabby, you accidentally incriminated yourself by spreading your DNA to the murder weapon. How can we explain or predict how likely we are to do this?

This is possible because of something called “DNA shedding.” Professor Linacre and his team at Flinders University have developed a test to determine how likely one is to “shed” DNA, which would raise his/her likeliness in contaminating a DNA sample.  Their test measures the deposition, collection, and amplification of DNA deposited by a range of donors allowing for an accurate determination of shedder status.  Eleven donors (5 males and 6 females) were asked to first wash their hands and then place their thumb onto a glass slide for 15 seconds 0, 15, 60, and 180 minutes after washing. Left and right thumbs were used and testing was performed in triplicate. Fluorescence microscopy was used to visualize the DNA on the slides as shown in Figure 1.

Figure 1. The four steps in DNA collection. A) Fingermark stained with Diamond Dye. B) Micro-swab removing cellular material. C) Sample area post swabbing. D) DNA on the surface has now been transferred to the swab and is in a PCR tube for processing.

It was found that two males were heavy shedders, four females were light shedders, and the remaining five (three males and 2 females) were intermediate shedders. This study further strengthened a previously made claim that men shed more than women because of their grimy little paws.  One possible reason is that men inherently shed more DNA. Another reason for this claim could be due to the size of the thumbprint; because the study measures the amount of DNA deposited by the participant, a larger thumbprint could lead to a higher yield in deposited DNA.

Determining your shedder status could determine how likely you are to contaminate your group’s lab experiment—or determine how likely you are to be wrongly accused of murder. Nevertheless, determining shedder status could help prevent contamination from unwanted DNA.

References:

https://www.ncbi.nlm.nih.gov/pubmed/29902671

https://onlinelibrary.wiley.com/doi/abs/10.1111/1556-4029.12894

https://www.forensicmag.com/article/2015/10/touch-dna-might-be-contaminating-crime-scene-evidence

Gifs found on tenor.com and giphy.com

The Fuel of the Future: increasing biofuel yield without increasing cost

By: Christopher Oubre

The information used in this blog post can be found in the review “A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology” by Hasunuma et al published October 23rd of 2013.

Figure 1 a biorefinery

As nations across the world continue to feel the major annoyance and economic burden of being tied to shady and unreliable organizations such as OPEC (the organization of the petroleum exporting countries), realize the full implications of global warming, and seek a more sustainable fuel source, the idea of biofuel becomes more and more appealing. The idea of creating fuel using biological systems has been around even longer than fuels such as fossil fuels and wind power. The first biofuel, wood, has been used by humans for hundreds of thousands of years and continues to warm the homes of billions worldwide.

Figure 2. fire

Although biofuels like wood are perfectly suited to generate heat for homes, the sustainable energy source of the future will have to do more in terms of pumping pistons to power engines and spinning turbines to generate electricity. Although this ambition is much more encompassing and difficult to accomplish, it is not an ambition that hasn’t been explored in the past. For example, before the introduction of fossil fuels, the expectation was that automobiles would run on biofuels created from vegetable oils. This expectation never realized its full potential as it was discovered that internal combustion engines could instead run on the cheaper and more easily mass-produced fossil fuels.

Figure 3. diesel engine

So what happened to the idea of using bio-fuels? And if bio-fuels aren’t a new concept and the idea has been around for a while, why haven’t they ever picked up momentum? The answer to that question is complicated but currently lies tied up somewhere between politics and scientific shortcomings which are still being addressed. The main problem with using biofuels as a major source of fuel is the cost.

A paper published in the Bioresource Technology journal in 2013 has attempted to review some of the problems associated with biofuel and address these problems. The paper, entitled “A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology,” suggests that biorefineries should be looking into the use of lignocellulosic biomass from the byproduct of already occurring agricultural processes, and different biological systems to utilize this biomass and turn it into fuel. Lignocellulosic biomass was chosen as a candidate for biofuel production because it is easily assessible and already mass produced. Lignocellulosic biomass contains cellulose, hemicellulose, and lignin, and when refined, yields a highly energetic bio-ethanol which makes it a contender to be the next big fuel source.

Figure 4. cellulose, hemicellulose, and lignin from left to right

However, it is difficult to refine and very expensive because of problems associated with the saccharification and fermentation steps of its refinery. Saccharification of lignocellulosic biomass is used to hydrolyze the complex sugar into soluble simpler sugars that can be used in fermentation to make biofuel. Fermentation is the process by which energy is extracted from these sugars in the absence of oxygen. The problem with saccharification and fermentation being used simultaneously in the biorefinery of lignocellulosic biomass is that these processes have differing optimal temperatures at which they occur. Currently, this problem is being addressed by using saccharification enzymes from fungi and bacteria. However, the process of dumping fungi and bacterial enzymes into the batch of lignocellulosic biomass is expensive and a better biological system is needed in order to break down the biomass into bio-ethanol more efficiently and at a more reasonable cost. New research covered in the aforementioned paper has explored using differing microorganisms to ferment lignocellulosic substrate into bio-ethanol. This research has explored using cellulase enzyme mass produced by microorganisms and then isolated from these microorganisms, microbes with recombinant DNA better suited for fermentation, and microbes that naturally express the cellulase enzyme that can be put into the biomass to cause fermentation.

Figure 5. microbes

Although the ideal microbe for this process of turning lignocellulosic biomass into bio-ethanol has not been found, scientists are getting closer to the goal of creating such an organism as more data points towards what kind of an organism would be ideal for this job. This ideal organism will have to have a short reproduction time, be acquired and maintained cheaply, have a high tolerance to ethanol (the biorefineries yielded biofuel), and be able to ferment lignocellulosic biomass into bio-ethanol at a temperature compatible with the saccharification process. This ideal microbe is asked to do a lot, but with new age science such as advances in genetic recombination and artificial selection, perhaps we may one day be able to find a microbe capable of making the production and use of biofuels more economically achievable. Perhaps the fuel of the future requires the microbe of the future.

 

References:

https://www.sciencedirect.com/science/article/pii/S0960852412015490

https://www.merriam-webster.com/dictionary/saccharification

https://www.merriam-webster.com/dictionary/saccharification

https://www.dieselnet.com/tech/diesel_history.php