BioQuakes

AP Biology class blog for discussing current research in Biology

Author: sabraina

The New and Improved CRISPR-Cas9

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On April 13, 2016

In Student Post

The CRISPR-Cas9 genome editing system has transformed into an even better version of itself. A new, elegant technique, coined by researches at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, has resolved one of the most reoccurring technical issues in genome editing.

https://commons.wikimedia.org/wiki/File:Crystal_Structure_of_Cas9_in_Complex_with_Guide_RNA_and_Target_DNA.jpg

Primarily, the CRISPR-Cas9 system works to specifically modify a cell’s DNA. CRISPR is dependent on protein Cas9, as it is specialized for cutting DNA. The DNA, at a location identified by a RNA’s sequence matching the target site, is altered by Cas9. Though it very efficient at cutting its target sites, there is a large complication in the process. Once the Cas9 is inside the cell, it can also bind and cut additional sites that are not targeted. Because of this, undesired edits are produced which can alter gene expression or kill off a gene completely. These setbacks can lead to cancer or other problems. Feng Zhang, along with his colleagues at MIT, reported that by just changing 3 out of the approximately 1,400 amino acids composing the Cas9 enzyme from S. pyogenes, a considerable reduction of “off-target editing” to undetectable levels are observed.

This newfound information was derived from studying the structure of the Cas9 protein. Since DNA is negatively charged, it binds to a positively charged groove in the Cas9 protein. The scientists predicted that by replacing some of the positively charged amino acids with a neutral charge, there would be a decrease in binding to “off target” sequences than to “on target” sequences. By mutating three amino acids, their technique proved to be successful.

The team is calling this newly-engineered enzyme “enhanced S. pyogenes Cas9” or “eSpCas9.” It’ll be particularly useful for genome editing that requires precise specificity and it is said to be available for researches worldwide.

I believe that this newfound resolution for the CRISPR-Cas9 genome editing hurtle is a huge game changer. This charge-changing approach might also be able to be used for other experiments involving RNA-guided DNA targeting enzymes. Ethical and societal concerns have also risen due to the idea of rapid and efficient genome editing. The eSpCas9 is highly beneficial in the scientific community, however there is a lot more research needed to be done in order to be used clinically.

 

Original article can be found here.

The Relationship Between Girls and Their “Skinny Jeans”

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On March 1, 2016

In Student Post

New findings suggest that the dynamic between a girl’s gene and her early socio-economic environment can dictate if they have a larger fat intake or healthier consumption in relation to others within the same class background. The gene variant is called the DRD4 repeat 7 (7 repeats). According to the McGill Centre for the Convergence of Health and Economics, girls from poorer families with DRD4 repeat 7 have an increased fat intake than other girls from the same socio-economic environment. However, girls with the gene variant from wealthier families and backgrounds have a lower fat intake. These studies portray how it isn’t solely the gene that determines an individual but how the gene influences an individuals sensitivity to environmental factors that contribute to a child’s preference to fat.

This research was done by collecting diaries by parents of 200 Canadian children (about 4 years old). Their fat, protein, and carbohydrate percentages were all measured along with their BMI and also saliva tests to see who are carries of the DRD4 repeat 7 gene. To categorize the children in their socio-economic environment, the family income was used while acknowledging the food environment (what type of foods are available in that neighborhood).

“Plasticity genes,” where carriers of gene variants might be more “open” to their environment rather than those who are not carries of gene variants, is a term used to describe the DRD4 repeat 7 gene. Researchers realized that the fat intake has a direct correlation with any modification of the girls social environment and how they are raised. Therefore, the gene itself is not to blame for a high fat intake.

The data had only shown to be consistent with girls, not boys. From an evolutionary perspective, in order to sustain hard conditions and be able to reproduce, girls had to have more weight on them. Another reason may be because the age four is not old enough to measure the gene’s activity in boys because boys can gain weight at different stages than girls.

Furthermore, this research contributes to the idea that preventing childhood obesity cannot have a general and “one size fits all” type of approach. Instead, specific approaches for certain populations is what’s needed. Especially populations that are vulnerable in adverse conditions because they are more likely to respond better if their conditions improve.

 

Original article can be found here.

Sewage Does More than Just Gross You Out… It Carries a Signal For the Microbiomes of Humans

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On December 2, 2015

In Student Post

Who knew that sewage would ever be useful. Well, it is a successful way to collect fecal bacteria from people. It can monitor, through gut microbes, the public health of a population without invading people’s privacy. The human gut microbiome consists of huge amounts of bacteria in the gastrointestinal tract. This gut bacteria has important functions in a healthy human. Recently, there has been much attention to the human microbiome, and more specifically, finding a “healthy microbiome” by identifying which bacterial communities are associated with healthy individuals. What has been hindering this experiment are financial concerns but also privacy concerns in terms of the individuals that can be screened.

Researchers from MBL (Marine Biological Laboratory) and the UWM (University of Wisconsin-Milwaukee) School of Freshwater Sciences proposed the idea of using sewage as a population that consists of a signal for human microbiomes. The scientists used oligotyping to compare 137 healthy people’s gut bacteria (provided by the Human Microbiome Project) to the bacterial communities of more than 200 sewage samples from 71 different U.S. cities. Researchers realized that geographically distributed populations consists of a similar core set of bacteria and its members symbolize many different communities within U.S. adults. The percent of obese people in a city is used by the study as a measure of a lifestyle difference which indicates that this bacteria community structure is accurate in detecting obesity in a city. Lifestyle differences are important because they can change the human gut microbiome and an indicator of obesity is the microbial community composition. This process of working with microbiomes of individuals is similar to drawing a map of a specific geographical area and fishing out new understandings and patterns. If it weren’t for the sewage, the scientists wouldn’t have been able to differentiate the cities based on their level of obesity. This type of approach can be effective when it comes to answering concerns about public health, without undermining the privacy of individuals.

I found it interesting how this profound yet relatively small experiment is even part of a bigger plan to create better water pollution and public health assessments. Do you think it can lead a better water pollution and efficient public health assessments? Overall, it’s amazing how new technologies can aid in decrypting information from complicated environments. I’m excited to see where this experiment takes us as it leads researchers and scientists in a more knowledgeable outlook on our environment and in public health.

The original article can be found here.

Elephant Trunks: The Most Convenient Way to Reach Food

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On November 9, 2015

In Student Post

New studies have indicated that elephants are using the air that they blast through their trunks to grasp for food in hard-to-reach areas. Way back when, Charles Darwin had even suggested that elephants might manipulate their breath to reach food. Scientists from Kyoto University and SOKENDAI decided to research this behavior in elephants. They predicted that the farther away the piece of food is, the more frequently the elephants would use their breath/air through their trunks to bring it near them. To test their hypothesis, they observed two captive, female elephants, Suzuko and Mineko at the Kamine Zoo. The researchers created this virtual grid in a ditch, enclosing the elephants. They placed food in different areas of the grid. The various types of food included: apples, bamboo, fallen leaves, potatoes, and hay. After spacing out these foods, they filmed the elephants trying to reach for them. 128 trials took place over 32 days; each trial started when it was audible that the elephants began blowing and ended when they finally got the food or gave up. Many other factors played a role in this experiment such as the position and shape of the elephant trunks, the frequency and duration of blowing, and the ability to track the movement of food across the area.

The scientist’s research concluded that on average, it took 3 blasts of air for an elephant to obtain inaccessible food and was less likely to use this technique if the food was nearby. Mineko was the dominant female who was much more skilled at altering the position of her trunk to aim more specifically at the food to push it in the correct direction. This particular behavior has brought up discussion of whether an elephant’s breath can be defined as a “tool” or not; similar to how chimpanzees use sticks to catch ants. It’s been concluded that this study creates a new possibility to rethink the term “tool” and to possibly redefine it. For this behavior to be defined as a “tool,” it shouldn’t solely be debated as whether it’s a physical object or not, but more of how it is a physiological process that promotes problem-solving. I thought this new finding was very interesting because I was unaware at how proficient an elephant can be with its breath. Furthermore, I love how this study promoted discussion on a different topic: what can be defined as a “tool” for animals nowadays. Do you think an elephant’s breath can be referred to as a “tool?” Please share your thoughts! In my opinion, I think it can definitely be referred to as a tool because it aids in carrying out a particular function. If only humans had this type of tool… we wouldn’t have to awkwardly reach across the dinner table ever again!

The original article can be found here.

For more information about the study, check out this article and video: Elephants Use Their Trunks as Leaf-Blowers to Reach for Food.

Serious Monkey Business Going on with these Tanzanian Monkeys

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On October 12, 2015

In Student Post

https://commons.wikimedia.org/wiki/File:Udzungwa_Red_Colobus_Stevage.JPG

https://commons.wikimedia.org/wiki/File:Udzungwa_Red_Colobus_Stevage.JPG

A team from the University of Oregon comprised of Maria Jose Ruiz-Lopez, a postdoctoral researcher, and Nelson Ting, a corresponding author and professor of anthropology, have discovered why a specific species of endangered monkeys in Tanzania are living in various different geographical areas that are increasingly becoming isolated from one another. It has been concluded that this situation is due to the monkey’s closeness to villages and the intentional forest fires by humans in an effort to create space for crops. Lopez collected 170 fecal samples of the Udzungwa red colobus monkey, a specific monkey used as indicator species in ecological change, for DNA analysis over five distinct forests in the Eastern Afromontane Hotspot. To approach this experiment, the team used landscape-genetics, a method that merges landscape ecology and population genetics. Though odd to use in tropical settings, this technique allowed them to investigate the dissimilarities between 121 monkeys and how human activity influences ecological changes. The largest difference between monkeys were of those who were separated by villages and/or zones that had a history of the highest density fires. The researches studied multiple variables at once and the monkey’s proximity to villages and man-made fires was still the most significant. Because these fires are stopping the monkeys from migrating, smaller groups of them are becoming more isolated, resulting in a decrease of genetic diversity and yielding to extinction variables.

This experiment regarding behavioral ecology, a way in which organisms react to abiotic factors in their environment, made me contemplate the human’s role in the environment and how we are strongly affecting the possible extinction or conservation of animals. This particular ecosystem is rich in diversity and it would be a tragedy for it to fall to extinction! There is no direct solution to this problem; after all, to have the power to alter a human’s ecological footprint and their decision whether to burn a forest or not is quite hard to seize control of. Do you believe with enough awareness and education, local communities would be able to create a local solution to save the diverse genes of these monkeys?

Original article can be found here.

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