goldgi – BioQuakes

Author: goldgi

The Miracle of CRISPR/Cas9 in Gene Editing

On April 5, 2017

Some scientists say, “you can do anything with CRISPR” and others are absolutely astonished and amazed.

CRISPR can rapidly change any gene in any animal or plant with ease. It can fix genetic diseases, fight viruses, sterilize mosquitos and prepare organs for transplant. The possibilities are endless – and the prospect of designer babies isn’t far off.

https://en.wikipedia.org/wiki/CRISPR#/media/File:Crispr.png

Dead Cas9 can fix a single base pair typo in DNA’s genetic instructions. It can convert a C-G into a T-A pair. Also, we can attach fluorescent tags to dead Cas9 so researchers can locate and observe DNA or RNA in a living cell. Dead Cas9 can also block RNA Polymerase from turning on a gene, in CRISPRi. In CRISPRa, a protein that turns on genes is fused to dead Cas9.

CRISPR can be used for anything involving cutting DNA. It guides molecular scissors (Cas9 enzyme) to a target section of DNA & works to disable or repair a gene, or insert something new.

Many scientists have been thinking of improvements for this miracle gene editor. RNA Biologist Gene Yeo compares the original Cas9 to a Swiss army knife with only one application – a knife. He says that by bolting other proteins and chemicals to the blade, they transformed the knife into a multifunctional tools.

CRISPR/Cas9 is special because of its precision. It is much easier to manipulate and use compared to other enzymes that cut DNA. By using “guide RNA” it can home in on any place selected by the researcher by chemically pairing with DNA bases.

While Cas9 does have some problems, scientists definitely see the potential for greatness with a few tweaks. They wanted to ensure permanent single base pair changes, and they increased that from 15 to 75 percent. Liu used a hitchhiking enzyme called cytidine deaminase.

Scientists researched chemical tags on DNA called epigenetic marks. When scientists placed the epigenetic marks on some genes, activity shot up. This provided evidence that the mark boosts gene activity.

Case can also revolutionize RNA biology. The homing ability of CRISPR/Cas9 is what makes this seem possible. It was found that Cas9 could latch on to mRNA.

CRISPR/Cas9 was first found in bacteria as a basic immune system for fighting viruses. It zeroes in on and shreds the viral DNA. Half of bacteria have CRISPR immune systems, using enzymes beyond Cas9.

Overall scientists predict that in the next few years, results will be amazing. The many ways of using CRISPR will continue to multiply and we will see where science takes us.

Source: https://www.sciencenews.org/article/crispr-inspires-new-tricks-edit-genes

Other Sources: https://www.neb.com/tools-and-resources/feature-articles/crispr-cas9-and-targeted-genome-editing-a-new-era-in-molecular-biology

90 and Counting…

By goldgi

On March 1, 2017

In Student Post

https://commons.wikimedia.org/wiki/Woman#/media/File:Tribes_woman_with_ear_piercing.jpg

Life expectancy is continuously rising, and is expected to rise immensely in various countries around the world. The U.S however, is not increasing as drastically.

A recent study was done to predict the average life expectancy for 35 countries in the year 2030. The greatest increases were seen in females born in South Korea and males born in Hungary. The smallest increases were people born in Macedonia.

South Korean females are expected to live 6.6 years longer than they would have if they were born in 2010. Their life expectancy is 90.8 years old. WOW!

France had the second highest life expectancy for females, with 88.6 years.

Japan came in third with a predicted life expectancy of 88.4 years, not too far behind France.

The reason this news is so shocking is because scientists once believed that it would be impossible to have a life expectancy exceed 90 years, but South Korea has surpassed it. This barrier will be broken.

Professor Magid Ezzati said, “I don’t believe we’re anywhere near the upper limit of expectancy – if there even is one”.

For men, the greatest increase was in Hungary, with an estimated increase of 7.5 years more than 2010. The life expectancy is 78.2 years for boys born in 2030.

Like the females, South Korean males had the highest predicted life expectancy for 2030, with a whopping 84.1 years. Australia and Switzerland were not far behind with life expectancies of 84 years old.

The United States did not increase much. For women it was expected to increase by 2.1 years and for men it was expected to increase by 3 years. This would mean 83.3 years for women and 79.5 for men.

Researchers in the study noted that life expectancy at birth in the U.S. is already lower than most other high-income countries and that it is projected to fall further behind. Some reasons for this set back are that the U.S. has the highest homicide rates, highest death rates for women and children, and the highest average BMI of any high-income country. It is also the only country out of the 35 in the study that does not provide universal health care, so many people have unmet health care needs due to cost.

Source: http://www.livescience.com/57957-life-expectancy-increasing-2030.html

Additional Information:

https://www.nia.nih.gov/research/publication/global-health-and-aging/living-longer

http://www.slate.com/articles/health_and_science/medical_examiner/2016/12/life_expectancy_is_still_increasing.html

http://www.telegraph.co.uk/news/politics/11348561/Average-life-expectancy-heading-for-100.html

Gut Microbes and the Brain

By goldgi

On January 11, 2017

In Student Post

Neuroscientists are studying the idea that intestinal microbiota might influence brain development and behavior.

Neuroscientist Knickmeyer is looking to study 30 newborns and how they have grown into inquisitive, curious one-year olds through a series of behavioral and temperament tests. She is eager to see their faecal microbiota, bacteria, viruses and other microbes that live in their guts.

Studies of animals raised in sterile, germ-free conditions showed that these microbes in the gut influence behavior and can alter brain neurochemistry and physiology. Some research has drawn links with gut bacteria and their interactions with the brain.

Escherichia coli, a species of bacteria present in the human gut https://en.wikipedia.org/wiki/Gut_flora#/media/File:EscherichiaColi_NIAID.jpg

Gut Reactions

Prior to recent research, microbes and the brain have rarely been known to interact, with the exception of when pathogens penetrate the blood brain barrier. When they do, there can be intense effects. For example, the virus causing rabies elicits aggression, agitation and a fear of water. The idea that gut microbes could influence neurobiology was not ever thought of, but this is changing.

One research study showed that IBS lead to issues such as depression and anxiety. This lead scientists to wonder if psychiatric symptoms are driven by inflammation or a whacky microbiome caused by infection.

One 2011 study showed that germ-free mice were less-anxious than mice with indigenous microbes. These studies also showed that many of these behaviors are formed during a critical period during which microbes have their strongest effects. Another problem is that “germ-free” is an unnatural situation. However, it allows for researchers to learn which microbial functions are important for development of organs or cell types.

Chemical Exploration

Recent studies have found that gut microbes directly alter neurotransmitter levels, enabling their communication with neurons.

Scientists are also studying whether or not altered serotonin levels in the gut trigger a cascade of molecular events, therefore affecting brain activity.

In 2015 research showed that myelination can also be influenced by gut microbes, at least in a specific part of the brain. Germ-free mice are protected from some conditions, for example multiple sclerosis, because it is characterized by demyelination of nerve fibers. These scientists wish to use these studies to help humans who suffer from MS.

A Move to Therapy

Tracy Bale, a neuroscientist, sought to study how microbes of pregnant mothers affect their offspring. Maria Dominguez-Bello, microbiologist, wants to see if babies born through Caesarean sections end up with microbiota similar to babies born vaginally if they are swabbed on the mouth and skin with gauze taken from their mothers’ vaginas.

For Knickmeyer, the amygdala and prefrontal cortex are the brain areas that interest her the most in her studies with the newborn infants. This is because both of these areas have been affected by microbiota manipulations in rodent models. Something she is worried might affect the study is the confounding factors such as diet, home lives and environmental exposure.

Source: http://www.nature.com/news/the-tantalizing-links-between-gut-microbes-and-the-brain-1.18557

For more information:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228144/

https://www.sciencenews.org/article/microbes-can-play-games-mind

http://www.huffingtonpost.com/healthline-/gut-bacteria-and-the-brai_b_11898980.html

Tickle, Tickle!

By goldgi

On December 5, 2016

In Student Post

You might be wondering, why am I ticklish? Or, why do I laugh if somebody else tickles me, but not when I try to tickle myself? The mystery of ticklishness has been sought after for decades, including by Darwin and Aristotle.

A recent study tested ticklishness on rats, and the results were astonishing! The rats reacted to human tickles with ultrasonic “laughter cells” and emitted various calls. While many humans are most ticklish on their armpits and stomachs, rats were found to be most ticklish on their bellies and underneath their feet. They performed “joy jumps” after being tickled, which is a behavior associated with joyful subjects in various mammals.

Researchers continued searching for answers, and sought to discover how being ticklish relates to the brain and whether or not it is a trick of the brain that rewards interacting.

When researchers Shimpei Ishiyama and Michael Brecht investigated the response of the rat’s brain to tickling, they observed nerve cells that responded strongly to tickling and they found very similar responses during play behaviors as during tickling- even without the scientist touching the rat. These nerve cells also worked in reverse. For example, if the rats were made anxious, they were less ticklish and the activity in these cells were reduced. It was discovered that activity in the trunk somatosensory cortex is what led to ticklishness.

The discovery of the connection between brain responses to tickling and play was incredible.

The Resurrection of “Dead” Bacteria

By goldgi

On October 14, 2016

In Student Post

Many kinds of bacteria have the capacity to radically alter their metabolism in order to switch into a dormant state. This allows them to survive without any possibility of growth. One reason this might be advantageous to bacteria is if their microbes do not have a substantial amount of food. The cells’ revival process follows a strict genetic timetable. This is an important survival strategy.

One of the oldest types of bacteria are cyanobacteria – going back more than 3 billion years. Their activity released oxygen into the atmosphere, therefore enabling life on earth in its current state. When nitrogen, one of their major nutrients, is lacking, these cyanobacteria cease their growth and enter a dormant state. They dismantle their photosynthesis apparatus and lose their color. This allows them to survive long periods without requiring nutrients. If they become exposed to an accessible supply of nitrogen, they return to normal life within 48 hours. It is intriguing because the cells appear dead and then out of nowhere they return back to normal.

Diagram of Cyanobacteria

Through various experiments it was found that the cell revival process began almost immediately once nitrate was added. This is a highly organized process.

Phase One: Bacteria suppress all remaining photosynthesis activity and tap into reserves to obtain energy quickly

At First: Intake and processing of nitrogen. The production of protein synthesizing mechanisms are activated.

12-16 Hours Later: Photosynthesis begins

48 Hours Later: Full capacity reached. Cells begin to grow and divide again

There are copies of DNA that are not translated into proteins found in sections of uncoded RNA. These are important switches in the awakening process. This genetically coded program allows cyanobacteria to colonize environments where the nitrogen supply is inconstant. It also allows them to survive environmental stress and survive over three billion years of evolution. This is not the only bacteria that is capable of this phenomena. This can help scientists better control the spread of dangerous bacteria.

Source: https://www.sciencedaily.com/releases/2016/10/161006124409.htm

Other Resources (For More Information on This Topic):

http://phys.org/news/2012-02-bacteria-dead.html

Understanding how bacteria come back from the dead

BioQuakes

AP Biology class blog for discussing current research in Biology

Author: goldgi

The Miracle of CRISPR/Cas9 in Gene Editing

90 and Counting…

Gut Microbes and the Brain

Tickle, Tickle!

The Resurrection of “Dead” Bacteria

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