DNA That Could Make Us Superheroes

So who wants to be a superhero?

Turns out, there is a specific DNA series that can protect us from debilitating diseases.  In a recent study, approximately 600,000 genomes were sampled.  Within these samples, about 13 adults were found to harbor mutations for severe diseases.  However, these adults were not sick at all and showed no traits of the disease they were supposed to have.  This diseases include: cystic fibrosis, Smith-Lemli-Opitz syndrome, familial dysautonomia, epidermolysis bullosa simplex, Pfeiffer syndrome, autoimmune polyendocrinopathy syndrome, acampomelic campomelic dysplasia and atelosteogenesis.

So how in the world are these adults protected from these diseases?

Mutations in the individual genomes from the study are likely the answer.  Although mutations can cause diseases, they have also led to some incredible results.  So in essence, the next step would be to identify the specific gene mutations within these genomes in order to determine how exactly these people are protected from serious diseases they should have.  Easy enough, right?

Except that everyone in this study signed a consent form, so that no names would be used.  Therefore, the scientists can't go out and find the 13 "superheroes" from this study.

As a result, the research group states in their paper, "In prospective searches for resilient individuals, more appropriate consenting will be needed to link participants to their medical records and to allow for appropriate recontacting that enables follow-up characterizations, validation of their resilient condition and decoding to uncover the causes of the resilience".  Unfortunately, this raises some ethical questions.  Normally, names and identities are kept in secrecy to prevent any data on these individuals getting out and causing harm in anyway to said person.  With this study, these parameters would be slightly changed.  "[the study] exemplifies the often unforeseen benefits that can be achieved from responsible sharing of anonymized genetic and clinical data," said Dr Matthew Hurles, from the Wellcome Trust Sanger Institute.  "This poses research and ethical questions. Personally, if I were that individual, I'd happily share my genome if it could help someone else who had been dealt a less favorable genetic hand."

So the prospect of being a superhero could be a possibility after all.  Unfortunately, it wouldn't come with the abilities of flying, heat vision, super strength, or wearing a cape.  But, a superhero who is protected from numerous DNA-linked diseases and could help numbers of people get cured from said diseases sounds pretty great to me.

You can read the article that summarizes the paper here:
http://www.bbc.com/news/health-36015243

You can read the published research paper here:
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3514.html

Bacteria that Grows Better in Space than on Earth

Space is devoid of air and nutrients.  It's a vacuum that allows no life to exist outside of a sealed environment.  However, one of the many ongoing research projects in space is seeing how things fair in space that normally do well on earth.  For example, the human body, materials, and even small microorganisms are studied in space to determine the effect of space on each item.  And interestingly enough, bacteria don't really have a problem growing in a controlled environment in space.

"A lot of people as us 'why' we sent microbes into space," said Dr. David Coil, who is a lead author on this study and a microbiologist at UC Davis.  "Understanding how microbes behave in microgravity is critically important for planning long-term manned spacecraft but also has the possibility of providing new insights into how these microbes behave in human constructed environments on Earth."

After completing this experiment, however, one species of bacteria tested grew even better in space than on Earth.

Bacillus safensis, the bacteria that grew better in space, is found quite commonly here on earth.  In fact, its name is derived from its discovery on the outside of spacecraft in Florida and California.  Now this bacteria wasn't discovered when the spacecraft returned from space, it was discovered after assembly here on earth.  Its an aerobic Gram (+) bacteria (this means that the bacteria contains a thicker layer of peptidoglycan) who doesn't have any abnormal traits that differentiate it from any other bacteria on earth in terms of generic characteristics.

This bacteria, along with 47 other samples of microorganisms that were swabbed from multiple public locations as part of a nationwide citizen science project called Project MERCCURI, were sent up into space to be studied.  Most of not all of the organisms that were identified were determined to be normally found on the International Space Station (ISS).  However, it is completely unknown as to why Bacillus safensis grew 60% even better in space.

Granted, this discovery doesn't pave the way to cure cancer or anything of the sort.  However, the aspect that some bacteria can grow more efficiently in microgravity is a fantastic discovery.  From this, there is a possibility that we could isolate genes or specific features from this bacteria and use genetic engineering to grow other microorganisms or even food in microgravity.  Astronauts being able to grow vegetables and other foods within their ships as they travel through space could be a possibility if specific genes are isolated from within the genome of Bacillus safensis is a very cool thought.  Again, this is all speculation, but in the future of space travel and exploration, this could be a big discovery.

PHOTO CREDIT: Alex Alexiev, UC Davis (CC BY 4.0)


To read more about this experiment, check out the PeerJ article here:

http://static.peerj.com/pressReleases/2016/Press-Release-Coil.pdf

In addition, another news story about this discovery can be read here:

http://phys.org/news/2016-03-bacteria-space-earth.html

Eliminating Autoimmune Diseases

Autoimmune diseases affect numerous people throughout the world.  Rheumatoid arthritis, asthma, multiple sclerosis; they are all diseases we have heard of before.  The prospect of a treatment being possible is a tough obstacle to climb, for autoimmune diseases are incredibly hard to treat.  How soon could we expect some sort of drug that would help us combat such diseases?

Well, the wait may only be a little bit longer.

Scientists from Russia, Germany and Great Britain have recently created a prototype of a new antibody-based drug for autoimmune diseases.  This new drug, being called MYSTI (Myeloid-Specific TNF Inhibitor), focuses on the Tumer Necrosis Factors (TNF) produced by macrophages in the body.  This protein belongs to the family of cytokines, which help control inflammation, counterbalance tumor formation, and regulate the immune system against a plethora of diseases.  However, there are two sides to this small protein.  The "good" TNFs help the body by performing the actions listed above.  The "bad" TNFs are ones that do not function correctly and can promote serious diseases in the body.

In order to create a drug that would focus on the bad TNFs without harming the good TNFs, the scientists focused on bispecific antibodies.  EurekAlert gives a specific but brief description of bispecific antibodies:

Each B-lymphocyte produces against a particular antigen only one antibody type consisting of two pairs of heavy and light chains. Though scientists learned long time ago to produce artificial, 'chimeric' antibodies that are able to stick to two proteins simultaneously with various Fab-fragments. Such antibodies are called bispecific. One of its advantages - a possibility to connect different cells using such an antibody - this was already used to produce effective cure for several kinds of tumors. In antibody bioengineering field, a particular type of antibodies from camel, lama or shark, which contain only heavy chains, can be used. 

By utilizing these bispecific antibodies, the team of researchers successfully created a sample of bispecific antibodies that selectively inhibit the bad TNFs without altering the function of the good TNFs.  "This work lasted nearly ten years. The article describes only the tip of the iceberg," said Sergei Nedospasov, who was the main author of this study.  In addition, this research proves through scientific means that it is entirely possible to focus on a specific cytokine and produce it through a particular type of cell lineage.

Granted, this does not mean that the cure for cancer and all autoimmune diseases is at hand.  However, this is an incredible step into learning more about these diseases and finding a successful treatment that will help millions of people around the world.

More information on this topic can be found here:

http://www.eurekalert.org/pub_releases/2016-02/lmsu-adg022916.php

The scientific paper that was published on this topic can be found here:

http://www.pnas.org/content/early/2016/03/01/1520175113.full

Reviving an Extinct Zebra Subspecies

Just outside of Cape Town in South Africa, there is a valley that roams with zebras.  More specifically, these zebras are known as Quaggas, which are a subspecies of the plains zebra.  The main difference between the Quaggas and the zebras we all know well reside in the markings on the body.  The Quaggas have no markings near the back of their bodies and have darker brown coloration.

The second difference between the two subspecies is that the Quaggas died out in 1883 after being hunted to extinction in the 19th century.  So how did the Quaggas end up just outside of Cape Town?

A DNA project for the Quaggas was founded by the late Reinhold Rau, a German-born South African natural historian, who had DNA samples from a quagga skin at the South African Museum analysed.  The DNA was found to be very similar to the zebras we see today, so zebras with weak or nonexistent streaks near the rear were selected for this project.  These zebras, although still field zebras, contained fragments or small traits of Quagga DNA within their own DNA, thus the weak/nonexistent strips on their hinds.  To exhibit more and more of the Quagga genes, selected zebras were bred together to try and produce the coloring found on the Quagga species.  After 5 generations of selective breeding, the project is satisfied that it has recreated the Quagga.  "To all intents and purposes they are the Quagga back again.  The project has been a complete success," says Eric Harley, a retired professor of chemical pathology at the University of Cape Town.  "We don't do genetic engineering, we aren't cloning, we aren't doing any particularly clever sort of embryo transfers - it is a very simple project of selective breeding."

However, the project has faced numerous criticism from many scientists who argue that selective breeding is mainly used for profits.  In addition, they state that the process is unjustifiable and should not have occurred.  "I think there is controversy with all programs like this.  There is no way that all scientists are going to agree that this is the right way to go," said Harley.  "We are a bunch of enthusiastic people trying to do something to replace something that we messed up many years ago."  Even facing some strong criticism, this project has seemingly brought the Rau-Quagga (named after the project to create distinction from its forebears) out of extinction and back into the wild.  Unlike other hybrid animals that have received treatment, the newly bred Rau-Quagga can reproduce among themselves, ensuring that with the right care and protection, this species can survive and thrive.

For more information on this topic, check out these links:

http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html
http://www.sciencealert.com/scientists-say-they-ve-revived-an-extinct-sub-species-of-zebra

"I think there is controversy with all programmes like this. There is no way that all scientists are going to agree that this is the right way to go," he said.
"We are a bunch of enthusiastic people trying to do something to replace something that we messed up many years ago."


Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

"I think there is controversy with all programmes like this. There is no way that all scientists are going to agree that this is the right way to go," he said.
"We are a bunch of enthusiastic people trying to do something to replace something that we messed up many years ago."


Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

"We don't do genetic engineering, we aren't cloning, we aren't doing any particularly clever sort of embryo transfers—it is a very simple project of selective breeding," he said.

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

"We don't do genetic engineering, we aren't cloning, we aren't doing any particularly clever sort of embryo transfers—it is a very simple project of selective breeding," he said.

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

"To all intents and purposes they are the quagga back again. The project has been a complete success."

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

"To all intents and purposes they are the quagga back again. The project has been a complete success."

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

by the late Reinhold Rau, a German-born South African natural historian, who had DNA samples from a quagga skin at the South African Museum analysed

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

by the late Reinhold Rau, a German-born South African natural historian, who had DNA samples from a quagga skin at the South African Museum analysed

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

by the late Reinhold Rau, a German-born South African natural historian, who had DNA samples from a quagga skin at the South African Museum analysed

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#jCp

by the late Reinhold Rau, a German-born South African natural historian, who had DNA samples from a quagga skin at the South African Museum analysed

Read more at: http://phys.org/news/2016-02-south-africa-revives-extinct-zebra.html#j

The Microbial Way of Reducing CO2 Emissions in the Air

As of now, CO2 emissions have been a continuous and growing threat to our environment.  The rises in
greenhouse gasses and carbon dioxide have slowly pushed our global climate towards a catastrophic environment, one which will completely manifest in the future if we don't act soon.  Scientists, researchers, and engineers alike have been searching for a new and improved way to eliminate the rise of carbon dioxide within our air.  Now, we may actually have a plausible way to reduce emissions that is efficient, beneficial to the environment, and cost effective.

All it takes is a little help from the microbial world.

The nonphotosynthetic bacterium, Moorella thermoacetica, actually does not use photosynthesis to create energy.  In fact, it utilizes the acetyl-CoA pathway to cycle carbon in the environment.  Normally, the amount of carbon this bacterium cycles is small, leading to a small amount of acetic acid that is produced.  However, researchers Kelsey K. Sakimoto, Andrew Barnabas Wong, and Peidong Yang conducted a recent study to determine if the efficiency and amount of carbon that is cycled by M. thermoacetica could be improved.

The research team used a hybrid approach and combined Moorella thermoacetica and cadmium sulfide nanoparticles to enable an increase in photosynthesis of acetic acid from carbon dioxide.  This reaction is a two step synthesis.  To begin with, "the precipitation of CdS (cadmium sulfide nanoparticles) by Moorella thermoacetica is triggered by the addition of Cd2+ and cysteine as the sulfure source.  Moorella thermoacetica uses photogenerated electrons from illuminated CdS to carry out photosynthesis.  The absorption of a photon by CdS produces an electron and hole pair, e- and h+.  The electron generates a reducing equivalent that is passed on [...] to synthesize acetic acid from Co2."  Essentially, the addition of CdS to Moorella thermoacetica allows the bacterium a greater capacity for the photosynthesis of acetic acid from CO2.  From this, the team concluded that the amount of acetic acid that was synthesized was greater than the amount produced solely by the bacterium.

In order to determine that this process was successful, the team conducted another experiment where different components of the reaction were removed.  For example, the team removed the light source in one round and the CdS in another round.  As a result, the amount of acetic acid that was created in the absence of light slowly declined to 25% of the regular amount after 4 days, while the amount that was created with just Moorella thermoacetica dropped to almost 0% after only one day.  This confirms that Moorella thermoacetica and CdS hybrids exposed to light produce acetic acid from CO2.

Overall, this new discovery could pave the way for reduced carbon emissions in our air.  In addition, this hybrid organism could provide the ability to study biological systems and carbon cycling that may take place.  Granted, this would not be an overnight process, and a large amount of the bacterium would be required.  But it is an excellent first step into a budget friendly and efficient way to reduce carbon dioxide in the atmosphere.

For more information on Moorella thermoacetica, click these links (note the last one is an entire paper on the genome and properties of this bacterium):
https://microbewiki.kenyon.edu/index.php/Moorella_thermoacetica
http://research.uvu.edu/wilson/bacterium.htm
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575129/

For more information on this study, the link to the research paper is provided here:
http://science.sciencemag.org/content/351/6268/74.full

The New Ninth Planet

Could you imagine a planet that could actually be classified as the new ninth planet in our solar system beyond Pluto?  One that completes a revolution around the Sun every 20,000 or so years?  How about a planet that could possibly be 5,000 times the size of Pluto?

Or how about 10 times the size of Earth?

Researchers at Caltech have finally found substantial evidence that a planet exists within a unique orbit in the outer solar system.  Granted, this planet has not been observed directly yet (the picture above is an artist's rendering, R. Hurt at Caltech).  However, researchers Konstantin Batygin and Mike Brown used mathematical modeling and complex computer models and simulations to determine the identity of the ninth planet.  "Although we were initially quite skeptical that this planet could exist, as we continued to investigate its orbit and what it would mean for the outer solar system, we became increasingly convinced that it is out there," says Batygin. "For the first time in over 150 years, there is solid evidence that the solar system's planetary census is incomplete."

Since the beginning of the debate on whether extreme Kuiper Belt objects existed, the idea of a planet far out in the Kuiper Belt was tossed around.  However, the idea never really took root, for the observation of such a planet was never seen, and data was inconclusive.  Beginning in 2014, the idea based on a paper published by Chad Trujillo and Scott Sheppard arose from the observation on distant objects in the Kuiper Belt and their obscure orbital feature.  Brown brought is thoughts to Batygin, and the two worked for a year and a half on this problem. 

Their efforts on observing the Kuiper belt and the many objects within slowly brought forth fruit.  They initially saw that 6 objects had elliptical orbits that fell within the same direction in physical space, indicating that something was affecting the orbits.  Secondly, they disproved that the simple amount of objects would affect the orbits of the 6 objects, calculating that the Kuiper Belt would require over 100 times the amount of mass it has today.  Finally, after numerous computer simulations, they discovered that a massive planet in an anti-aligned orbit (180 degrees from all other objects and known planets in the solar system) matched the data that they had received.

"Your natural response is 'This orbital geometry can't be right.  This can't be stable over the long term because, after all, this would cause the planet and these objects to meet and eventually collide,'" said Batygin.  However, due ti a mechanism known as mean-motion resonance, the massive planet actually propels the objects away from it as the objects in the Kuiper pass by it due to its unique orbit.

So essentially, the evidence for a ninth planet in deep space in our solar system is overwhelming.  But it has not been observed just yet.  "I would love to find it," says Brown. "But I'd also be perfectly happy if someone else found it.  That is why we're publishing this paper.  We hope that other people are going to get inspired and start searching [...] All those people who are mad that Pluto is no longer a planet can be thrilled to know that there is a real planet out there still to be found.  Now we can go and find this planet and make the solar system have nine planets again."

More on this story can be read here:

http://www.caltech.edu/news/caltech-researchers-find-evidence-real-ninth-planet-49523

http://www.npr.org/sections/thetwo-way/2016/01/20/463087037/hints-of-a-hidden-distant-planet-in-our-solar-system

"Your natural response is 'This orbital geometry can't be right. This can't be stable over the long term because, after all, this would cause the planet and these objects to meet and eventually collide,'" says Batygin. - See more at: http://www.caltech.edu/news/caltech-researchers-find-evidence-real-ninth-planet-49523#sthash.1jpSItWM.dpuf

"Although we were initially quite skeptical that this planet could exist, as we continued to investigate its orbit and what it would mean for the outer solar system, we become increasingly convinced that it is out there," says Batygin, an assistant professor of planetary science. "For the first time in over 150 years, there is solid evidence that the solar system's planetary census is incomplete." - See more at: http://www.caltech.edu/news/caltech-researchers-find-evidence-real-ninth-planet-49523#sthash.1jpSItWM.dpuf

mathematical modeling and computer simulations

, Konstantin Batygin and Mike Brown

, Konstantin Batygin and Mike Brown

, Konstantin Batygin and Mike Brown

/R. Hurt (IPAC)

/R. Hurt (IPAC)

/R. Hurt (IPAC)

/R. Hurt (IPAC)

Re-engineering Ants By Altering Genes in the Brain

Much like humans, ants respond to certain behavioral changes or environmental aspects that they encounter.  When an ant is hungry, it acts accordingly.  When an ant is threatened, again it acts accordingly.  Even within the ant hill, the ant's behavior may be subject to change depending on situations it encounters.  Now these changes in behavior are a result of genes located in the brain, and were observed within carpenter ants that were observed in a study co-authored by NYU Langone researchers and publishers.  With this discovery, focusing on specific genes to target certain behaviors in humans may be possible in the near future.

To further dive into the specifics, the researchers focused on a compound known to block the action of a group of enzymes, histone deacetylases (HDACs), which would activate genes that would cause the carpenter ant worker to behave like another ant without altering the coding for the gene itself.  Therefore, more work is being done to discover what else can be altered without changing or rewriting the genes themselves in ants or even humans.

Furthermore, the researchers conducted a series of tests on a female carpenter ant to regulate whether she became a guard ant (major in size) or a scout ant (minor in size).  To further elaborate on what the study focused on, an excerpt from the news article on EurekaAlert! was taken that describes the components within the ant that the scientists studied:

Specifically, the study found that foraging behavior as a caste-specific trait in the ant C. floridanus is controlled by the interplay between well-known families of enzymes: histone acetyltransferases (HATs), and histone deacetylases (HDACs). As their names suggest, HAT enzymes attach acetyl groups to histones, protein spools that DNA is wrapped around, to turn on genes. HDACs remove the groups from histones to turn off gene expression.

By focusing on the HDACs, the team was able to use HDAC inhibitors to alter the behavior in the guard ants and cause them to scout for food.  Essentially, the major ants were reprogrammed to function like the minor ants.  In addition, it wasn't just one gene that was activated within the major ants.  The experiment found that hundreds of genes in the central ant brain linked to hormone signaling, the sending of signals along nerve pathways, and the building of connections between nerve cells were all altered or activated in a different way than a normal major ant without HDAC inhibitors.  

With this discovery, and the results surrounding the use of HDAC inhibitors in ants, it seems entirely possible to alter behaviors and even which genes are activated in a multitude of organisms, including humans.  Granted, humans and ants do not share the exact same genetic blueprint, but the idea and the science behind it gives us a unique opportunity to possibly alter mental diseases in the brain, behavioral issues, and other problems within humans.  As stated by Danny Reinberg, PhD, the Terry and Mel Karmazin Professor in the Department of Biochemistry and Molecular Pharmacology at NYU Langone, and a corresponding study author, "While no one is saying that ant behavior extends to humans, we believe, nonetheless, that this work promises to help guide the future use of HDAC inhibitors, which are already being studied as potential treatments for schizophrenia, depression, and neurodegenerative diseases."

More information on this topic can be found here:

http://www.eurekalert.org/pub_releases/2015-12/nyu-sb123115.php