Frog-Killing Chytrid Fungus Progress: Origin Found

South Korean Oriental fire-bellied toad 

Courtesy of: Frank Pasmans

Amphibians have fallen victim to a deadly skin infection, Chytridiomycosis, that can cause osmotic imbalance, organ failure, and even death since 1998. This infection has been the root cause of die-offs and extinctions of a variety of amphibian species. The origin of the fungus has been unknown, as is the cause of the fungus becoming such a threat to amphibian species. The fungus causing Chytridiomycosis is called Batrachochytrium dendronatidis. Researchers analyzed hundreds of B. dendronatidis samples from all over the world and concluded that the fungus most likely came from East Asia, originating in the beginning of the 20th century. 

Discovering the origin of  B. dendronatidis is particularly interesting, and hopefully will allow researchers to learn more about what triggers these math die-off and extinction events. Learning more about the favorable growth conditions could prevent the fungi from overtaking and claiming more amphibian lives. 

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Marijuana Traffickers: They're People Too

On September 25, it was reported by Myles Karp for the New York Times that cacao beans are in the midst of another fungal epidemic.  As a result of selective selection by humans, the fungus is able to kill a majority of the commercialized cacao strains.  Sometime around the 1940s, cacao markets were regulated to only contain a few strains of cacao.  Because of this, variation had declined greatly, causing the majority of cacao beans to be unable to adapt to new situations, such as a fungus.  This is also not the first time cacao beans had to face such an epidemic.  In the early 2000s, the world saw another cacao blight in which cacao production dropped 94%.  Not only is this bad for the chocolate market, along with the major chocolate companies, it is also detrimental to the cacao bean farmers.  Most farmers are fairly poor, and with a steep decline of cacao cultivation, their standard of living declines with it.
Marijuana traffickers is one possible origin of the current fungal epidemic.  While going in between countries, marijuana traffickers could have possibly grabbed some cacao beans from plants along the shore that were infected.  Because they were carrying these beans to their next destination, they unintentionally spread the fungus across the water to a new continent.  This, in turn, would start the spread of the fungus across the entire continent, waiting for more people or animals to spread the fungus farther until all continents are infected with the same fungal disease.
But worry not! Scientists are frantically working to make sure chocolate does not die with the millennials.  A popular company known as CATIE (The Tropical Agricultural Research and Higher Education Center) has set out to create new strains of cacao beans that is adaptable to the current environment, as well as future environments.  Even better, the new strains are being produced specifically for adaptability and flavor.  Flavor is so much a priority that any bean that tastes less than amazing is thrown out.  I think I can speak for all of us in this world when I say that they should definitely be the one holding the Nobel Prize at the end of this year.  For genetics? Maybe.  For peace? Maybe.  For the legacy of the human taste buds? Definitely.  If this doesn't give you a little more faith in humanity, try eating a fungus ridden cacao bean and reevaluate.  Overall, it is safe to say that this is the type of precaution we should take for every product that is used on a worldwide scale, including cotton, wheat, corn, even animals.  In a fight against natural selection and artificial selection, nature will always win.

The Resistance: English Ash trees fight back

    

     The Ash trees of Europe are facing the continued spread of a fungal disease that has killed a vast majority of the common tree. Ash dieback disease is caused by the fungus Hymenoscyphus fraxineus. Denmark has lost nearly all of their native ash trees to the disease and it has only recently been introduced to England where it is spreading just as rapidly. But new research reveals that English ash trees have a resistance to the disease that other European ash trees do not.
     The Guardian reports that these more resistant trees could potentially be used to breed down ash trees that could be used to repopulate the forests that have lost large portions of their native trees. There are drawbacks to this plan however. Although these English trees are more resistant to the fungus they are more susceptible to the emerald ash borer. Those working on slowing and controlling the spread of the fungal infection warn that care must be taken when selectively breeding tougher trees.

Map points are scaled by hue (high predicted damage scores in brown, low in green) and plotted according to the geographical origin of the parent trees of the British Screening Panel (n = 130) and the Danish Test Panel (n = 58).

   
     I think this article and the research behind it highlight the benefit of the genetic diversity a single species across several geological locations can develop. Developing an ash tree with a resistance to both the fungal disease and emerald ash borer is the ultimate goal in this situation. If such a tree is created its introduction into the environment must be a careful undertaking. We could just as easily create a tree with a severe susceptibility to the next big disease or insect infestation.

Using Bats to Test A New Approach to the Fight Against Fungus

Fungal species have amounted to disastrous events for a diverse range of species throughout time. Hundreds of animal and plant species alike have went extinct due to strains of these silent killers. A focus recently has been the devastating effect that Pseudogymnoascus destructans have on bats. This fungal variety in particular infects bats during hibernation and leads to the lethal white-nose syndrome, causing a 90% population decrease in multiple bat species throughout the last decade.

Alike many fungal diseases affecting species worldwide, there is no known solution for most of these diseases. Since wiping out a fungal species could create more problems for the surrounding ecosystem, geneticists plan to genetically weaken the fungus to allow the species to eventually build an immunity to it. The easily sequenced and easy to grow Pseudogymnoascus destructans makes it a great model for this worldwide epidemic. 

Less virulent strains of the fungus can be genetically modified using RNAi or CRISPR. Another strategy is going to be creating a virus to infect the fungus, called a mycovirus, and in turn reduce its fitness. Experiments are currently underway by the scientists over at Revive & Restore to choose the most successful strain of the fungus to then be deployed at hibernation sites. The severity of the white-nose syndrome will then be monitored over time to see the conclusive effects of this strategy. 

Read the whole article here! 

This research caught my eye because not only do I really enjoy acts towards the conservation of living organisms, but for it to be done genetically in a way that conserves the organisms on both ends of this fight to create a peaceful solution is really awesome to me. The evolution of genomics is increasing at such a great slope and I'm excited to see where it will take us in the field of health and wellness for all living organisms. I also am really looking forward to hearing about what comes of the current research presented in this article.

The return of the Chestnut Tree! Maybe...

Scientists and genetic engineers are all gathering together to restore the American Chestnut tree. The chestnut tree used to be found in almost every state in America, but a couple years ago the tree has been dying out. The environmental department of State University of New York college recently had a brilliant idea of applying genetic engineering to help the tree. The death of billions of trees is due to a fungus called 'Cryphonectria parasitica'. Scientist will try to genetically alter the chestnut trees to resist the fungus. The enzyme or gene these scientist will be oxalate oxidase. This will counteract the oxalic acid that is secreted by the fungus. The biggest problem the scientist face is not the enzyme therapy, but the propagation of these plants. It is very difficult to propagate hardwood plants. Yet, the combination of charcoal and humic acid has been found to help propagation. I think this is really fascinating because they are really saving a species from extinction. Imagine what other species we can save. 

http://www.hngn.com/articles/193208/20160329/genetic-engineering-revive-american-chestnut-trees.htm

New Research into the Fungi in Our Body

Researchers at the University of Toronto began looking into a very common fungus in our bodies called, Candida albicans. This fungus is even more prevalent in mucus in the lungs of cystic fibrosis patients. (Cystic fibrosis is a genetic disease that causes infections in the lung due to mucus and can cause difficulty breathing for patients with it.)More often than not, this fungus does no harm, but it will attack those with weakened immune systems such as people with HIV, cancer, etc. It is particularly dangerous due to its ability to change shape from round, single-celled to long and stringy. Its ability to change shapes allows for survival in many different environments in the body. This process of transforming is called filamentation.

In this study, the researchers took samples from 28 cystic fibrosis patients for genetic sequencing. Because this fungus usually needs a trigger to change shape, the researchers looked into the genes of this fungus. All but one of the samples had a mutation in the NR1 gene which is supposed to stop the occurrence of filamentation. The fungi was exposed to the bacteria that is usually prevalent in the mucus as well. This bacteria usually secretes a molecule that stops the fungi from transforming, but the fungi seemed to have developed defenses to these bacteria.

Although there is still no cure for this awful disease, this is one step in the right direction. Most people underestimate the impact that fungi have on health in the world. As of now there is not enough research being done on them to really understand how they impact us. Leah Cowen, head researcher, stated that fungi kill 1.5 million people every year. Why are they not getting more attention? Candida albicans is present in all of us and has a possibility of harm if in the right conditions. I definitely think more has to be done in researching this, especially if knowing more could help to cure this disease.

Foreign Genes

Horizontal gene transfer is the movement of genes from one living organism to another. There are three types of horizontal gene transfer (HGT), which are transduction, transformation, and conjugation. Transduction is the transfer of genes via virus, whereas transformation is when an organism picks up the genes floating in its environment. Conjugation involves one organism producing a pilus and injecting the genetic material into another organism. It is believed that HGT plays an important role in the evolution of many single celled organisms and in many simpler animals, such as nematode worms and beetles. However, the notion that HGT takes place in more complex animals, such as humans, has been debated over the years.

Scientists at the University of Cambridge have conducted a study about HGT and have ultimately showed that it occurs in animals more than was previously thought.  It was discovered that HGT has allowed hundreds of active foreign genes to arise in animals and is believed to have contributed to the evolution of a great deal of animals, maybe even all of them. With this new information the scientists have posited that evolution needs to be looked at in a new way.

The study evaluated the genomes of 12 species of the common fruit fly, 4 species of nematode worms, and 10 species of primates, including humans. In order to determine how likely it is that the genes were foreign it was calculated how well the genes matched to similar genes in other species. Making a comparison to other species allowed the researchers to determine how long ago the foreign genes were attained. The analysis of these genomes provided more evidence that the ABO blood group gene and genes related to metabolism enzymes were acquired by vertebrates through HGT. 17 other genes were also confirmed to have been attained through HGT, while 128 genes not previously noted as foreign were detected. The foreign genes discovered were involved in a range of activities from lipid metabolism to immune responses. The researchers also determined that bacteria and protists were the most probable source of the HGT in all species, though HGT from viruses and fungi was also seen. The HGT from fungi may be a reason why other studies have negated the idea of HGT in complex animals as they were only looking for HGT from bacteria.

This study has numerous implications for the future of genome sequencing. When genomes are sequenced bacterial sequences are often removed and are thought of as contamination. Although these bacterial sequences may be due to contamination they may also be part of an organism's genome as a result of HGT. The researchers warn that screening for contamination still needs to be in place, but that this new information about HGT should also be considered.

I think that this is such an interesting concept. When I learned about horizontal gene transfer I had always thought of it occurring between bacteria or some single celled organism. I had no idea that HGT could occur in multicellular organisms and never could have imagined that it could happen in humans. I think that this is positive though as it will contribute to the genetic variation of organisms and ultimately to evolution.  

Link to article: http://www.sciencedaily.com/releases/2015/03/150312123319.htm

Additional link: http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/genetic-exchange/exchange/exchange.html

  

Deadly Human Pathogen Cryptococcus Fully Sequenced

The strain H99, from the pathogenic lineage of Cryptococcus neoforms, has been genomically sequenced along with its complementary counterparts after a 10 year effort. This fungus gives rise to millions of cases of pneumonia and meningitis every year and up until now was a very dangerous, mysterious strain. With the genomic blueprint, scientists will be able to be able to test it repeatedly to find its weakness and how to fight against this deadly pathogen and its mutating strains. H99 is mutating strain that affects those with low immune systems such as individuals already infected with the HIV virus or transplant patients. Fred Dietrich and colleagues have isolated the strain and unraveled the genetic sequence in both a laboratory controlled setting as well as the host. This strain is so dangerous because it is able to produce genetic messages from both strands of DNA which enable it to constantly adapt to new environments thus making it a stronger, unbreakable virus. Dietrich and colleagues have uncoded the genome, DNA code, transcriptome, and the RNA molecules. There are approximately 20 million ACTG nucleotides each in the genetic code. The next step will be to mutate every gene to see which change will cause pathogenesis. This will give insight on this particular gene but will also be a point of reference for comparing other genomes of similar strains.

This unfolding of genomic sequencing is incredible and will be used as a point of reference and starting point for other strains similar to this. With this code, we can alter and see what can be added or deleted to fight against and make it more vulnerable to antibiotics. Millions of people every year are diagnosed with meningitis or pneumonia by inhaling airborne fungal spores. This is just the beginning of the fight against Cryptococcus neoforms. This fungus can be found in soil throughout the entire world.

Primary website: http://www.cdc.gov/fungal/diseases/cryptococcosis-neoformans/

Secondary website: http://www.cdc.gov/fungal/diseases/cryptococcosis-neoformans/

Labels: Cryptococcus neoform, fungus, genomic sequence, meningitis, pneumonia 

Gene Deficiency Makes Contracting Infection Easier

Deep dermatophytosis is the ability of a fungal bacteria to spread from the surface of the skin to underneath the skin and from there to other places and organs in the body. An article published in ScienceDaily discussed a research done by The Rockefeller University and Necker Medical School which discovered that a single gene in the human body is actually responsible for fungi's ability to spread beneath the skin in deep dermatophytosis. A study conducted by Jean- Laurent Casanova on 17 healthy, but deep dermatophytosis afflicted, people showed that each person's immune system was healthy and capable of fighting off infections. Casanova did find, however, the gene CARD9 was missing from each person's genome. According to the article, the lack of CARD9 prevents the body from reacting appropriately when the body is infected. As a result of this, any infections contracted by a CARD9 deficient person not only remains in the body, but also spreads to and infects other parts of the body.

Fungus attacking skin cells

Studies conducted on cases like this, where a single gene can produce a defect in people can be beneficial. This is so because they can help us gain a better understanding of other single genes which cause diseases, as well as help us take steps to treat and prevent these diseases in people susceptible to them.

New Biofuel from Horse Digestive Fungus

[caption id="attachment_7820" align="alignleft" width="530" caption="Horse Digestive Fungus"][/caption]

An article from Science Daily describes a new method of producing biofuel from horse feces.  Another article was published on MITnews.  Cellulose is the compound used for making biofuels from non-food plant materials but, it is difficult to extract through the lignin within the cell walls of plants.  In order to do this lignin must be removed, enzyme must be used to break down cellulose into sugars, then the sugars are digested by microbes to ferment into alcohol to produce the fuel.  This process is extensive and expensive.

A fungus found in the digestive tract of a horse lives on lignin-rich plants and converts the cellulose into sugars for the animal.  This could make the process biofuels much easier and less expensive.  Scientists are now trying to isolate the genes that produce these enzymes and genetically engineer them into yeasts.  Since yeasts are already commercially used for products such as antibiotics and foods, the production technology already exists.  So far all the genetic material of this gut fungus use to break down the cellulose has been isolated from horse feces.  These protein-encoding materials are named “transcriptome” facilitated the identification of hundreds of enzymes capable of breaking down the lignin and extracting cellulose.

Batman Be Aware of White Nose Syndrome!

Geomyces destructans is a fungus that has been associated with the epidemic among bats known as the white nose syndrome. Bats infected with this fungus, die of the combination of starvation and dehydration. Little is known about why this fungus affects bats in this way. So far approximately 8,000 to 11,000 bats have died. Sixteen US states and four Canadian provinces that bats inhabit have been affected. So far there has been 100 percent mortality rate among bats that are infected. From researching other websites about Geomyces destructans, it is safe to say that this is a fairly new fungus which is apart of the Ascomycota family. Fungal DNA analysis of the ITS and SSU regions confirmed this.

The Battle for Bats: White Nose Syndrome <--- Video link