Tuesday, July 31, 2012

A Dermatophytic Divergence

ResearchBlogging.orgYour skin is a vast and complex habitat. There are all kinds of bacteria and fungi competing for every inch of real estate. But like all homesteads, resources are limited. Bacteria lower surface area pH rendering it inhospitable for others, and secrete chemical compounds to kill invaders. Fungi have found ways to more efficiently mine the "land" for minerals such as iron, as well as producing antibiotics that are specifically active against skin bacteria.

One of the families of fungi capable of infecting skin (Dermatophytes) is Arthrodermataceae, A family that includes the genera Microsporum and Trichophyton. These two fungi groups colonize keratinized areas and together are the most common cause of superficial fungal skin infections.

 A study in the July 30, 2012 edition of PLoS One takes a look at some of the closely related genes, gene clusters, that allow the species from Microsporum and Trichophyton to take such good advantage of the terrain that is your skin.

Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

In essence gene clusters are several genes that are physically linked or clustered together that share a common effect, such as production of antibiotics, or metabolically important compounds. Gene clusters can allow for quicker adaptation to new sources of sustenance as well as large scale genome remodeling. Due to the closely knit nature of gene clusters they also open the possibility of acquiring new functions by gain and loss of entire gene pathways through horizontal transfer.

Arthrodermataceae have a lot of gene clusters that many think are involved in host specificity and pathogenicity, especially when compared to other dermatophytes. Focusing on variable loci nestled inside a stable portion of the genome of Microsporum canis, Microsporum gypseum, and Trichophyton spp.; the researchers discovered three distinct conformation forms.

This variable locus(VL) has a difference of both length and functions across the three species. M. canis VL (VLA) consists of 539 base pairs that lack any protein sequencing sequences, M. gypseum (VLB) only has 35.89 bp but codes 12 different proteins, and Trichophyton spp.'s VL (VLC) is 26.78 bp long coding for 10 proteins.

When looking at the evolutionary past of the gene region it becomes apparent that the studied clusters have a very different history than the areas surrounding them. Those flanking regions have a largely vertical inheritance while the VL genes have been shaped by several different processes, including gene duplications and gene transfers.

The VL's of M. gypseum and Trichophyton spp. contain genes to produce compounds that appear to target glycine, which is the largest amino acid in human skin. This means the VL may be involved in skin colonization and thus infection. The effects of this area along with the evidence of gene duplications and losses led the team conclude that the common ancestor of these dermatophytes shared either a polymorphic version of VLB and VLC or both of them separately.

If the first scenario is correct, the common ancestor originally contained a version of the VL that alternated between the VLB and VLC form. During the evolution following that point the entire area was deleted from M. canis and the alleles were separated into the stable forms in M. gypseum and Trichophyton spp.

If the secondary version is true than at different times the main lineages came into their current genomic distributions by separate deletions in and of the VL.

It would take additional genome sequencing of closely related species in Arthrodermataceae, to determine the more likely of these two scenarios.

In the end, the mere existence of variable loci, like those in this study, could help explain how closely related species could show a dramatic difference in ability to establish an epidermal foothold.

Awesome Researchers:
Han Zhang, Antonis Rokas, & Jason C. Slot (2012). Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae PLoS One DOI: 10.1371/journal.pone.0041903

Photo creds: 
Robert J. Galindo & the CDC via Wikimedia

Monday, July 30, 2012

Inkfish: Enjoy Wine? Thank a Wasp

A much cooler contributer to Research Blogging has totally beat me to this Study. And She has done a much better job bloggin about it than I could have.

Inkfish: Enjoy Wine? Thank a Wasp: Where would we be without yeast? Sober, for one thing. And stuck assembling our sandwiches between two crackers. Humans have relied on th...

Foreign Spore Germination : Teen Skepchick

First, Teen Skepchick is cool. Second, Cordyceps are cool. Third, combining them gets a link on this blog.

Teen Skepchick Science Sunday : Zombie (Ant) Apocalypse

This is a good post about one of the most popular fungal interactions. Cordyceps enslaving the minds of carpenter ants. Plus it includes an Attenborough video, so score.

Sunday, July 29, 2012

Beetles Bring Yeast to Bamboo for Babies

ResearchBlogging.org Humans are not alone when it comes to farming. We are not even alone when it comes to growing fungi. There is a long history of fungal agriculture in social insects. Ant and termites often even go so far as to have what could basically be considered proper gardens of fungal blooms; getting them into the right growth medium, tending to their needs, even defending them from invaders. It is all quite industrial, but that is the kind of thing we come to expect from ants.

Now a Japanese study is demonstrating that at least one less industrialized, even non-social, beetle has tapped into the joys of harvesting fungi.

Fungal Farming in a Non-Social Beetle

This study focuses on a species of lizard beetle, Doubledaya bucculenta, that lives in Japan and lays eggs in dead bamboo. Collecting specimens of D. bucculenta at Kawaminami, Miyazaki Prefecture, Japan The team found that there was a white coating in internode cavities that were used to contain larvae, as well as on the larvae themselves.

D. bucculenta, its host bamboo, and W. anomalus

Analyzation of this growth consistently showed the saccharomycete yeast Wickerhamommyces anomalus present in the shoots used by D. bucculenta. Looking at bamboo not used for the incubation of young this same fungus was absent. When you find a fungus repeatedly, and only, growing in the presence of developing larvae, you might want to wonder if something is up.

By gathering and dissecting both adult males and females of D. bucculenta an interesting structure was catalogued. The females all displayed a yellowish exoskeletal pocket on the eight abdominal segment, right next to the ovipositor, and guess what they found there. Correct! They found small yeast particles that when isolated and sequenced turned up with the identical DNA of W. anomalus that had already been collected.

So, is this yeast a parasite, perhaps feeding off the larvae of the beetle or the insides of the bamboo? Or, could it be that the beetle was engaging in some low level farming, putting a crop into its young's room for later. W. anomalus is known to be saprophytic so it could potentially be using the beetle as a transport to get on the inside of freshly dead bamboo, but that would hardly be cause for the storage pocket on the female beetle. If however, the beetle were harvesting the fungus and seeding the bamboo chamber with it when she deposited her egg, how would that affect the larva?

To test this, the researchers grew some beetle larvae under a variety of scenarios. When inoculated with W. anomalus the larvae grew normally into adulthood, however when grown on sterile media or in autoclaved bamboo they stopped growing at the second instar. Furthermore after this if W. anomalus was added the larvae returned to its normal growth and development.

So, it appears that D. bucculenta does indeed harvest and transplant W. anomalus into the incubation chamber of its young. This interesting mutualistic relationship has led the beetle to becoming obligately dependent on the very fungus it developed a structure to harvest.

In the end finding this fungal farming tactic in a non-social insect could help shed light on how some of the higher levels of mutualistic cultivation developed. And in the end, the researchers think this could shed light even on how agriculture developed as a whole.

Awesome researchers:
Wataru Toki, Masahiko Tanashi, Katsumi Togashi, & Takema Fukatsu (2012). Fungal Farming in a Non-Social Beetle PLoS One DOI: 10.1371/journal.pone.0041893

Friday, July 27, 2012

Fungal Word Friday

Germ Tube

A germ tube is the initial hypha produced from a spore.

Germ tubes on C. albicans

Photo cred:
Wikimedia contributor Y tambre

Thursday, July 26, 2012

Cryptococcus neoformans Stops Pumping Iron

ResearchBlogging.org Cryptococcus neoformans is a well know fungal pathogen that can cause severe infections of the pulmonary and nervous systems. Infections of people with well functioning immune systems are rare but in those with compromised systems such as those with HIV, this opportunistic yeast is responsible for encephalitis and fungal meningitis.

Cryptococcus neoformans
Of course it needs its daily recommended allowance of vitamins and minerals. A Study conducted by scientists from Konkuk University and Chung-Ang University in Republic of Korea seeks to specifically check out the effect iron regulation has on C. neoformans day to day life.

Influence of Iron Regulation on the Metabolome of Cryptoccocus neoformans.

You see, iron is important for a whole host of processes. It is used in the tricarboxylic acid cycle, amino acid creation, respiration, as well as making lipids and sterols. The thing is, too much iron is bad, if level get to high it leads to the creation of oxygen radicals. Oxegyn radicals are bad mamma jammas; they cause things like DNA breakage and protein denaturing. Yup, iron is important, but you need to keep it in check or all kinds of things are going wrong.

It has been established that Cir1 is an important regulatory protein for iron transport and homeostasis. The same study showed Cir1 to be important to melanin formation and synthesis of spore capsules, things very important to the virulence of C. neoformans. With all of the metabolic pathways influenced by deletion of this protein and its importance on the regulation of iron, the team of researchers chose see the metabolic effects the deletion of Cir1 would have in order to get a large picture on its function in C. neoformans.

To study this they utilized Gas chromatography mass spectrometry and chemometric multivariate statistics to analyze the metabolomic profiles of a wild type and a Cir1 mutant strain lacking the regulatory protein. They attempted to find the pathway(s) most affect by a lack of Cir1 and how it affects the metabolome of C. neoformans. The strains were grown on a range of media, with varying amounts of available iron.

Because of the similarity and complexity between the Cir1 mutant and the wild type, the researchers used principle component analysis on the 972 peaks shown in the data sets, comparing the variation in 18 discriminative metabolites that showed significant difference.

When compared between the high and low iron mediums the chosen metabolites of the Cir1 strain showed little changes despite a significantly increased level of iron present in the Cir1 mutant cells. That led the team to conclude that iron availability was only responsible for minor differences in C. neoformans.

However, when looking at the regulation of genes in the wild type things were a little different. 483 genes were down-regulated and 250 were up-regulated in low iron vs high iron growth medium. Most of those differently expressed genes had to do with iron transport and homeostasis, as well as DNA repair and metabolism.

The study also showed dramatic influence of Cir1 on metabolism and production of those molecules involved.

One of the most interesting differences in the mutant was a large increase in glucose production. An increase in glucose implies that deleting the Cir1 had affects on the major carbon assimilation processes because glucose is metabolized in glycolysis and important in the TCA cycle and respiration. The TCA cycle and respiration are also influenced by iron so there is potentially connection there.

Combining those observations allows for the suggestion that an increase in intracellular iron and glucose are evidence of lowered iron requiring processes like glycolysis and respiration.

Another increase was shown in ergostol and its derivatives. Ergostol is the major constituent in fungal cell walls and is the target of some antifungal drugs. This increase of production is evidence of why Cir1 mutants have been demonstrated to be more resistant to anti-fungal treatment. A change in the production of ergostol and its derivative molecule  means a remodeling of membrane biosynthesis.

The basis of many secondary messengers, inositol was also increased significantly in the Cir1 mutant. This suggested up-regulation of inositol metabolism in Cir1 deletion was further seen by an increase in virulence important genes that are derived from it.

All of this together revealed that deletion of one of the major iron regulating genes in C. neoformans also impacts several of the iron required pathways. Taking out the Cir1 protein led to a change in respiration, glycolysis, as well as synthesis of membranes and messenger pathways.

When studying the effects of a protein, gene, or any other molecule on a system, this study demonstrates that one must remember, life is complex as all get out. While not everything is truly intertwined, the impact one thing has another is often multifaceted and unpredictable.

Awesome Researchers:
Jung Nam Choi, Jeongmi Kim, Won Hee Jung, & Choong Hwan Lee (2012). Influence of Iron Regulation on the Metabolome of Cryptococcus neoformans PLoS One DOI: 10.1371/journal.pone.0041654

Photo cred:
Centers for Disease Control and Prevention's Public Health Image Library  identification number #3771

Wednesday, July 25, 2012

How's your immune system doing? Candida albicans knows.

ResearchBlogging.org Chances are it is inside you right now, waiting. The moment you let your guard down Candida albicans will be there to spring into action. This versatile fungus can grow both as a yeast and pseudohyphally and it knows how healthy you are.

White and Opaque versions of Candida albicans
Candida albicans normally colonizes our bodies without symptoms; but when your immune system becomes compromised it takes quick advantage and moves on the offensive, generally causing minor infections but capable of much deadlier ones.

But how does it know what is up? A study published in mBio looks to answer that very question.

Variation in Candida albicans EFG1 Expression Enables Host-Dependent Changes in Colonizing Fungal Populations

Growing C. albicans in mice with healthy and immunodeficient mice, the team hoped to compare growth patterns and phenotypic variants, concentrating largely on transcription factor Efg1p activity.
Efg1p is an important physiological regulator for C. albicans and earlier studies have demonstrated that it influences the harmful potential that the fungal cell has.

In this study the scientists show that it also regulates colonization dynamics, having different expression and activity in individual cells throughout. Their study also demonstrates how the host environment changes the C. albicans population composition, thus changing the colonizer's physiology.

To test the growth rates of C. albicans with different levels of Efg1p the researchers basically fed healthy and immunosensitive mice with strains of C. albicans that had both low and high expression of the transcription factor. Then they counted fecal pellets for colonization patterns.

As it turns out those mice with strong immune systems showed a higher growth of cells with a high expression of Efg1p and those with a compromised immune system showed larger growth of those with low activity. The scientists propose that in a general,  there is a heterogeneous population growth. With that expression as the C. albicans comes into contact with an immune system it can adjust its physiology to be most productive despite the varying levels of immune system health.

What this could mean is that as the host's immune system becomes less affective the larger population of low Efg1p active cells will show a spike in growth, thus setting up the colony for engaging in pathogenic actions.

So, in the end,  measuring the ratio of high and low active Efg1p cells in a system could help to us determine host immune status as well as develop new methods for detecting and fighting Candida caused infections before they become severe or deadly.

This study gives us a small insight to how we can keep an eye on one fungus that is just waiting for us to falter.

Jessica V. Pierce, & Carol A. Kumamoto (2012). Variation in Candida albicans EFG1 Expression Enables Host-Dependent Changes in Colonizing Fungal Populations mBio DOI: 10.1128/​mBio.00117-12

Photo: Rebecca E. Zordan, Mathew G. Miller, David J. Galgoczy, Brian B. Tuch, Alexander D. Johnson via http://en.wikipedia.org/wiki/File:Whiteopaquecandida.jpg

Tuesday, July 24, 2012

A Tuesday Treat.

I have a little tasty for your eyes today. Rishard Hammond talking about my favorite fungi genus. Pilobolus.


Monday, July 23, 2012

Fungal Virulence in Eggs is Scrambled

The importance of a good infection model is immeasurable. The obvious choice to run clinical studies on for potentially pathogenic fungi is a mammal system, but those are becoming decreasingly possible due largely to moralistic reasons. While insects can be used for a lot of studies, testing virulence in warm blooded animals kinda requires something, well, a little warmer. For that reason many research groups turn to chicken embryos. A new study published on the virulence of fungi from the Lichtheimia genus has now established the chicken embryo model for this potentially deadly fungus group.
Lichtheimia corymbifera
Lichtheimia Species Exhibit Differences in Virulence Potential

Three of the five species in this genus (L. corymbifera, L. ramosa, and L. ornata) are some of the most common pathogens causing mucormycosis, a potentially fatal infection of the sinuses, lungs, or brain. While the fungi that cause this disease are common it generally only manages to take hold of those with compromised immune systems. Unfortunately, for those who contract mucormycosis, the mortality rate is near to fifty percent with large amounts of tissue invasion and destruction. This is why finding any relation to the causation of virulence is important. Any link could lead us to find ways to decrease, if not infections, at least death rates.

The group of scientists in this study infected embryonic eggs with 46 strains across all five Lichtheimia species as well as species from the closely related genus Dichotomocladium at different times of development and under different stresses.

In order to test the straight virulence levels each egg was infected with 103 spores and suffered a 70-90% mortality rate, at 104 spores the rates increased to 95-100%, and at 105 and 106 spores introduced all embryos died within 2 to 5 days.

As embryos mature, the immune system begins to develop, fighting off infection. To test the effects this increasingly complete defense system has a steady rate of 103 spores were introduced at 8, 10, and 12 days of embryonic development which showed a respectively lower or delayed mortality rate.

The team also tested the growth rates by growing the 12 main representative strains of Lichtheimia as well as a member of Dichotomocladium on a simple and complex media. Of the more virulent strains of Lichteimia L. ornata showed a decrease growth rate on complex media; however L. corymbifera and L. ramosa continued rapid growth with L. ramosa being much faster. And as was expected when grown on minimal mediums there were further reduced growth rates. And when grown under exposure to a myriad of different carbon sources to test metabolic flexibility a distinct advantage of Lichteimia species over Dichotomocladium was noted.

To determine stress resistance, and thus survivability in both the environment and the host, the 12 representative strains were tested for sensitivity to osmotic, oxidative and cell wall stress. Under osmotic stress L. ramosa showed a reduced osmotolerance when compared to L. corymbifera and L. ornata. When exposed to cell wall stress and oxidative stress it mainly was again L. ramosa that showed sensitivity when compared to the other notable species.

Unfortunately in the end the combined data could not tie down an obvious virulence pattern. With some species growing slower and others showing sensitivity to different growth medium, or stresses. The group concluded that if there is a shared virulence among these pathogens it is either a complex set of physiological traits of some other feature they did not analyze in this study. However with the now established embryonic egg model, future testing will be more readily available.

While not a giant break through, studies such as this are just as important. They may not give us some amazing insight, but they build the necessary foundation for many future studies who will surely owe their results in part to this groundwork.

Study credit: Volker U. Schwartze, Kerstin Hoffmann, Ildikó Nyilasi, Tamás Papp, Csaba Vágvölgyi, Sybren de Hoog, Kerstin Voigt, Ilse D. Jacobsen
Photo source: http://www.life-worldwide.org/fungal-diseases/lichtheimia-corymbifera/

Friday, July 20, 2012

We Can Make Him Stronger, Faster, Able to Utilize Xylose.

One thing that we can all agree on about fossil fuels is that they are non-renewable. Because of that simple fact it is obvious we have to find new and efficient ways to continue meeting our fuel needs. One of the methods growing (pun intended) in popularity is the production of bioethanol via the fermentation of plant carbohydrates.

S. cerevisiae

The yeast, Saccharomyces cerevisiae is very good at fermenting the ethanol from hexose sugars. That and its high tolerance to the ethanol it produces have led it to become one of the most utilized characters in Industrial scale bioethanol production. But it could be better.

You see, there is another sugar that exists in abundance in cellulosic biomasses. That sugar, xylose, is in fact so abundant that it is second only to glucose quantity. But S. cerevisiae just can't handle xylose. This is where we turn to another yeast, Pichia stipitis. P. Stipitis excels and turning xylose into ethanol, however it has its own short comings. This apparent upstart fails miserably when it comes to ethanol tolerance, a detrimental flaw that renders it nonviable as a large scale producer. If only there was some way to bring these two together...

Enter the duo of Wei Zhang and Anli Geng from the school of life and chemical technology of Ngee Ann Polytechnic, in Singapore. These two have contrived of a way to instill the xylose eating skills of P. stipitis into the hearty bioethanol standard bearer S. cerevisiae through genomic shuffling.

Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method

The team looked at traditional way used in teasing S. cerevisiae into fermenting xylose, generally metabolic engineering, and thought there had to be a better way. Metabolic engineering requires the  expression of multiple genes through mutagenesis and then post-evolutionary engineering. The process has to be done throughout the complex genomic pathways, and as such takes a lot of work and a lot of time. Genomic shuffling on the other hand enables the team to make changes throughout the entire genome at the same time.

Now, before you ask, "Well, then why don't we always use whole genome engineering?" know that it has its downsides. Genomic shuffling depends very heavily on protoplast fusion methods, which have stability and efficiency problems. This team's goal is to modify the method and quickly produce a strain of S. cerevisiae combined with the P. stipitis genome through direct genome isolation and transformation.

They started off by extracting the whole genome of P. stipitis, and inserting it into S. cerevisiae by electroporation. They then grew the amalgam strain in conditions that S. cerevisiae would not tolerate and obtained eight hybrid strains, which they evaluatated for ethanol production in a xylose containing broth. They picked the crem de le crem strain, F1-8, for a second round of genome reshuffling.

In this second go round; F1-8 had an extracted genome of S. cerevisiae transferred into it. The new strain was then screened on YNBXE selective plates and three positive colonies were obtained, with the strain ScF2 being the most competent ethanol producer. To see how this technique worked compared to traditional protoplast fusion methods normally used they also constructed hybrid strains of F1-8 an S. cerevisiae via that technique, they all died on the YNBXE.

Then the team compared xylose fermentation of F1-8 and ScF2 with their parent strains. ScF2 showed an improved ethanol production over both F1-8 and P. stipitis. This causes the scientists to believe that their modified genomic shuffling method could help efficiently create yeast strains with enhanced ability for turning xylose into ethanol, as it did in the ScF2 strain.

While ScF2 showed a medley of skill, including the fermentation of both glucose and xylose as well tolerance to sugars and ethanol, the researchers speculate that utilizing the new method in conjunction with rational metabolic engineering and directed evolution could lead to more improvement of the strain.

Wei Zhang, & Anli Geng (2012). Improved ethanol production by a xylose-fermenting recombinant yeast strain constructed through a modified genome shuffling method Biotechnology for Biofuels DOI: 10.1186/1754-6834-5-46

Photo Credit: WikiMedia contributor Masur


Fungal Word Friday

 A single filament of a fungal mass. Plural form is hyphae.

Hyphae of Lentilnula elodes

Photo credit Keisotyo via Wiki Commons

Thursday, July 19, 2012

One Way Street to Mycorhizzal Mutualism

Perhaps the most recognizable mushroom genus in the world, Amanita, has a vast variation of special lifestyles. Some of them live free, growing wherever they can find nutrients; others live in symbiotic relationships with plants, tethered to their host.

Amanita species

A new study, published in the July 18 PLoS One Journal, demonstrates that those Amanita species that have become symbiotic with plants have truly lost their ability to exist independently.

The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis

The team looked at 100 different species in the Genus containing only around 600, and created an extensive phylogenetic tree to show their relation to one another. They focused on what happened to the genes allowing decomposition of plant materials as they constructed the tree.

A key feature of Amanita living saprotrophic lives is that they can efficiently transform cellulose in dead plant materials into simple sugars. However, ectomycorrhizal fungi get most of their carbon from the roots of their host plant, so they don't need to keep the ability to eat cellulose.  Keeping this in mind, the scientists monitored what happened to the genes associated with these skill sets as the family tree moved from those living freely, to those species that have entered into the bonds of Mycorrhizal marriage.

As it turns out, the genes required to make two out of the three enzymes needed to decompose cellulose are lost as the species become intertwined with their host. Further experimentation demonstrated that Amanita species that have developed symbiotic relationships have lost the ability to grow on complex organic matter without supplied carbon. This means they would be unable to live in forest soil without a feed from their host plant.

The possibility of fungi to move from saprophytes to mycorrhyzals and potentially return to the former is a subject that has had much debate. The team on this study believes themselves to be the first group to combine fine-scale phylogenetic, functional gene, and experimental data in regards to this question. Their determination is that even though Amanita species retained one of the enzyme production pathways for cellulose degradation, they would be unable to return to saprophytic lives due to the loss of the other two.

There are no backsies for Mycorrhizal Amanitas.

Study and Photo credit: Benjamin E. Wolfe, Rodham E. Tulloss, Anne Pringle via PLoS One

Wednesday, July 18, 2012

There's Mycelium in Them Mines. Or, There Should Be.

Fungi are regularly used in agriculture as methods of fighting crop pathogens, as well as helping improve soil conditions. They are also an increasingly important tool for bioremediation, which is basically removing pollutants from the ground by planting things to act as chemical sinks. Well, it appears that certain fungi can also help clean polluted waters.
A study published in Proceedings of the National Academy of Sciences (PNAS) has found that Stilbella aciculosa produces superoxides during asexual reproduction.

Mn(II) oxidation by an ascomycete fungus is linked to superoxide production during asexual reproduction (abstract)

What is a superoxide, you ask? Chemically it is any compound that contains the superoxide anion (O2) and biologically it a toxin that is sometimes produced as an immune response to kill pathogens. However, in S. aciculosa, superoxide appears to serve as a cellular signal to help moderate cell differentiation. Fortunately for us humans it has the coincidental side effect of rapidly and efficiently oxidizing environmental manganese.

S. aciculosa with a close up of manganese oxides at the base of conidia.

As it turns out manganese oxides act as environmental sponges that can degrade carbon substrates, control the availability of nutrients and help clean up pollutants, like cadmium, and arsenic. This feature is especially useful in cleaning up these chemicals in the runoff from coal mines.
Now, S. aciculosa isn't the only organism that makes superoxides, and this isn't the first time that these chemicals have been employed to clean coal mine runoff.

The same method that causes manganese oxidation in S. aciculosa also exists and functions very similarly in the common marine bacterium genus Roseobacter. This study shows an interesting evolutionary homology between a prokaryotic and a eukaryotic organism mechanics, both even using the same enzymes.

Remediation of coal mine drainage has long been done by throwing a bunch of bacteria and fungi laced organics, like crop wastes, into the mine and hoping they will do their thing. The obvious problem here is that if you don't know how the microbe produces the reactive molecule (or why it does) than you can't develop a method to coerce it into producing it. And that means just dumping them in the mine and waiting is often ineffective.

This study, demonstrating superoxide production during asexual reproduction, presents us with new potential direction for a wide range of studies from environmental chemistry, to evolutionary biology.

Study credit: Colleen M. Hansel, Carolyn A. Zeiner, Cara M. Santelli, and Samuel M. Webb.
Photo by Colleen M. Hansel

Monday, July 16, 2012

Biocontrol buddies

Obviously biocontrol is super important to agriculture. There are several methods for controlling pathogens and some of them are fungi.
One such fungus is Clonostachys rosea, which is a mycoparasite of several pathogens that live in the soil. It not only directly parasitises soil pathogens, but also competes for root colonization with, thus indirectly controlling pathogen access to crops.

Clonostachys rosea colonies on plate
As mentioned in a previous post, working multiple methods synergistically is a great way to maximize the effectiveness of overall treatment. There are however, some major downsides to this. One of the biggies is finding those that work well together.
Enter into today's equation, Pseudomonas chlororaphis. P. chlororaphis does a great job protecting crops from both seed and soil-borne pathogens by increasing plant systemic resistances of the plant as well as competing for nutrients and secreting antibiotic molecules. That last one there, the antibiotic substance (in this case the polyketide 2,3-deepoxy-2,3-didehydrrhizoxin) is the problem with combining P. chlororaphis with other methods. Specifically, 2,3-deepoxy-2,3-dide... let's just call it DDR. Anyways, DDR is an essential antifungal produced by P. chlororaphis  and as such it doesn't always play nice with the fungi we actually WANT on the crop.
This brings us back to C. rosea. This fungi has previously demonstrated that it can hold its own against some antifungal treatments, as well as inhibiting crop pathogens in a different manner than P. chlororaphis (Which is important as having two control mechanisms doing the same thing would be redundant.)
Now a graduate student at the Swedish University of Agricultural Sciences has analyzed and researched the potential of hooking these two up.

Gene expression of ABC-transporters in the fungal biocontrol agent Clonostachys rosea in response to anti-fungal metabolites from Pseudomonas chlororaphis

Jinhui Wang has looked at the production ABC transporter proteins in C. rosea and how they respond in the presence of DDR. ABC transporter proteins are basically the first line of defense against anti-fungals by translocating toxins out of the cell.
So the objective of the study was to see whether C. rosea could handle the toxins made by P. chlororaphis and then check the gene expression of ABC Transporters.
This was done by measuring biomass differences and growth rates in cultures when exposed to P. chlororaphis and its metabolites, and  then use quantitative PCR to determine the expression of 13 ABC transporter genes in C. rosea.
While biomass decreased and some of the transporter genes were induced from the P. chlororaphis, the overall decrease was slight enough that it was determined that C. rosea could potentially be a tolerant roommate for P. chlororaphis. The study did conclude that understanding the ABC transporter interactions would be necessary to really see how these two crazy kids would get along.
But once again, the future of pest control relies on finding methods that work together with one another to accomplish our Agricultural goals. And once again a fungus rises up to the challenge.

Study: Wang, Jinhui, 2012.Gene expression of ABC-transporters in the fungal biocontrol agent Clonostachys rosea in response to anti-fungal metabolites from Pseudomonas chlororaphis . Second cycle, A1E. Uppsala: SLU, Dept. of Forest Mycology and Pathology 

picture: http://www.tamagawa.ac.jp/sisetu/gakujutu/alsrc/tama_kin/slide08E.htm

Friday, July 13, 2012

Fungal Word Friday


Septate refers to fungi that have hyphae with multiple sectioned compartments by cross walls called septum.

Septate Hyphae

Photo via: Mycologue publications

Wednesday, July 11, 2012

Toss in the Plasma Grenade

Humans get infected by fungi regularly, and some of the most common culprits are the Candida species. The top fungal disease is candidiasis, which is caused by these yeasts.
Candidiasis can infect a wide number of areas on the human body including skin, nails, genitalia, even the mouth where it is known as thrush. Most of the time these infections are just superficial, but some can become quite severe or even life-threatening. The more dangerous infections are known as candidemia.


With the clinical importance of this genus, it is no surprise that there are a myriad of researchers studying ways to combat infection. In fact many of today's antifungal drugs are effective against it, however the yeast form is known to grow hyphae into sheaths called biofilm.
Now a group of scientists lead out of Peking University, China is looking into a new tool for fighting Candida called non-thermal plasma. They are also trying to see if their method could improve the effectiveness of already established antifungal drugs on the more resistant biofilm growths.

Inactivation of Candida Biofilms by Non-Thermal Plasma and Its Enhancement for Fungistatic Effect of Antifungal Drugs

Basically the group grew ten Candida strains: 4 C. albicans, 3 C. glabrata, and 3 C. krusei and coaxed them to produce biofilms in microtiter plates. Then they treated the films with a series of timed exposures to a non-thermal plasma micro-jet. They used a mix of 98% He and 25 O2 to produce the plasma.

Huge success! They saw a dramatic decrease in the activation of yeast into new biofilm.

They then repeated this method, only while also utilizing common antifungal drugs: amphotericin B, fluconazole, and caspofungin. These drugs work great, but have troubles with those previously mentioned biofilms. This problem is increasingly important, as these filaments can adhere and grow on medical utensils and devices. But, luckily, the team yet again saw a dramatic decrease in biofilm activation and thus an increase of susceptability to the antifungals.

In today's world, where we can see a new fungal disease arise through hybridization(I know that was a plant disease, but it still applies) it is important to constantly find new ways to fight infections. Techniques like those lain out here appear to be very good steps to not only create new and novel methods, but combine them with those already known to produce magnified results. We need to keep these practices coming, to stay out in front of the creeping molds just waiting to crawl over our corpses.

Study Credit: Yi Sun, Shuang Yu, Peng Sun, Haiyan Wu, Weidong Zhu, Wei Liu, Jue Zhang, Jing Fang, Ruoyu Li

Photo credit: James Heilman, MD

Tuesday, July 10, 2012

Giant Puffball Puff Piece

So, try as I might today, I was unable to find any exciting Journal articles to share with you and felt it was destined to be a sad, post-less day. But then I saw a headline that made me smile:

Massive mushroom found in BC just the start of silly season stories

Isn't that promising?

And so is the story: Massive mushroom found in BC just the start of silly season stories Basically, Christian Therrien went hunting for mushrooms with his son Sebastien and found this giant puffball mushroom(Calvatia gigantea).

After a quick photo op and some local bragging Mr. Therrian decided to put the mushroom back, hoping the spores would help the field.

Christian Therrien and his giant mushroom

With how big the mushroom was, it was wise for him to return it to the pasture anyway because giant puffballs, while edible young, cause digestive problems if you eat them once they have begun generating spores.

A simple way to identify if the puffball is still edible (Assuming you have the right mushroom, but keying out is a different story.) is by cutting it open. If the inside is fleshy and white, it's alright: if not... well, then it's not.

The rest of the news article linked to is actually about exactly the same thing that this post is btw: silly little space filling news items. I hope it is as enjoyable for you as it has been for me, and hopefully I will find something more in depth for tomorrow.

 Photo and story courtesy of The Globe and Mail


Monday, July 9, 2012

CONvergence on the Brain

So, I spent this past weekend at CONvergence/SkepchiCON so my brain isn't quite recovered. However, I am not willing to let you go without anything, so I give you some David Attenborough.

Fungi- The Private Life of Plants excerpt

Friday, July 6, 2012

Fungal Word Friday


Asexual spores supported on a hypha, as opposed to being contained in a sporangium.

A chain of conidia

Photo via Wikimedia.org

Thursday, July 5, 2012

Come Together, Right Now.

Speckled leaf blotch is a detrimental crop disease in many parts of Europe and the Middle East. It is a fungal infection that can cut wheat crops in half. While doing genome alignment of a close relative, which infects mainly Iranian grasses instead of wheat, of the the blotch causing Zymoseptoria tritici, a group of scientist have uncovered a quite recent case of natural hybridization. Like just in the past few centuries type of recent.

 Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species (Abstract only)

Hybridization occurs when two different species manage to interbreed. While this generally leads to infertile, week and normally short-lived offspring in animals, it is a regular evolutionary happening in plants and fungi.

Isolates of Zymoseptoria pseudotritici

In this case, the scientists looked at variations of Zymoseptoria pseudotritici and found what they called "peculiar diversity patterns." They found that segments of the genome from regional samplings would go for large regions of matching base pairs, intermittent with equally long regions of variation.
This type of genome pattern is in line with a hybrid speciation event, and with further analysis of the variations the team concluded that Z. pseudotritici arose approximately 380 sexual generations.

This kind of study goes to show that hybridization of potentially dangerous(especially in agribusiness) fungi can happen very quickly on a evolutionary time scale. We have to make sure that in a global society, where potentially infested plants can be traded worldwide, we take into account the fact that such hybrids could quickly arise and devastate crop supplies.

For more on this study i give you the coverage from Science Daily: Two Species Fused to Give Rise to Plant Pest a Few Hundred Years Ago

Photo credit: Janine Haueisen

Wednesday, July 4, 2012

Happy Fungus of July!

In tribute to Fourth of July I present to you red, white and blue in mushroom.

Witch's Hat (Hygrocybe Conica)
Slimy Beech Tuft (Oudemansiella mucida)
Steel Blue Entoloma (Entoloma hochstetteri)

Photo credits: Daniel Schwen, Walter Baxter, Ian Dodd

Tuesday, July 3, 2012

Bats that Roost Together Get White Nose Syndrome and Die Together

White Nose syndrome is a newly introduced disease caused by the fungus Geomyces destructans, which appears to have recently been introduced into North America from Europe and was first diagnosed in 2006. The disease gets its name due to the white fungal growth on the muzzle and wings seen on hibernating bats.
Little Brown Bat infected with Geomyces destructans
Once infected, the bats routinely rouse during typical times of torpor when they normally are conserving energy. This unfortunately ends with the bats going through excessive weight loss and eventual starvation in winter months, when they cannot find food to sustain this activity. The mortality rate in some colonies is as high as 95%.

Now, a study published in the July 2, 2012 edition of Ecology Letters has linked the social interactions of various bat populations to rates of infection from G. destructans.
Sociality, density-dependence and microclimates determine the persistence of populations suffering from a noval fungal disease, white-nosed syndrome

The authors of the articles examined colony sizes of 120 different populations across 6 different species of bat in the northeastern United States. They did this by utilizing colony counts issued by trained biologists in state natural resource agencies during the typical months of Hibernacula over various years from 1979 to 2010.  This allowed for population growth measurements both before and after the fungus was introduced into the population.

The team found that infection rates of WNS was not based solely on population size, but more closely related to population roosting density and socialization rates of the bats. This information can then be used to extrapolate which species are at the most risk of severe population decline and potential extinction.
All sample populations decreased in growth after WNS infection and 32 of the 120 groups actually became locally extinct. Bats that routinely roost solitarily, such as the tricoloured bats, were noted to only have severe infections during times when the bats were drawn into larger groups such as overwinter roosting. This lead the teams to conclude that while they would be a loss of population size, the overall population could stabilize once the animal population density became low enough to allow for more the bats to roost more spaced out from one another. Bats such as the little brown bat however are known to roost regularly in large close knitted colonies. These bats are not likely to stabilize in decline once hitting a lower population size, and instead continue the spiral until extinction.

With this study we can determine which species of bat populations are at the most risk of extinction once infected with g. destructans, and with that knowledge we can adjust our tactics of fighting a powerful pathogen to those groups that are in the direst situations.

Photo credit: Alan Hicks, NY Department of Environmental Conservation

Monday, July 2, 2012

Finding Fungal Infections Fast

Fungal infections are rough. Once they have infected a host, they are difficult to fully cure. Because of that tenacity it is very important to identify not only that one has a fungus, but what kind of fungus it is, quickly.
Unfortunately there are a lot of problems with the diagnostics implemented in today’s medicine.  Cultures of fungi can take a long time to bring results, and even then they can be false negatives.  Diagnosing from nucleic-acid amplification can detect a fungus, but with that there are several step techniques that must be done after the amplification to present any kind of difference in some of the major fungi. If you are rich you can always go for the DNA sequencing, but that is not something that can feasibly be done for every infection. So with all of these time consuming, expensive and/or inaccurate techniques we find ourselves without an ideal set of diagnostics tools.

But we got people on that.

A new study published July 2, 2012 in PLoS One has demonstrated a new PCR Method (Polymerase-Chain Reaction High-Resolution Melting) that shows promise at not only detecting both yeasts and filamentous fungi, but also differentiating between them, as well as between some of the more relevant yeast species.

According to the teams journal article, over the past thirty years there has been a large uptake in reported fungi infections. Yeasts have been more responsible for serious disease but with filamentous fungi showing up in conditions such as Keratitis.

Fungal Keratitis
Keratitis is a condition in which the cornea becomes inflamed. A study in the March 2000 issue of Ophthalmology found 88 cases of fungal keratitis at the L.V. Prasad Eye Institute in India.

With this increase, as well as the different therapies that are needed for treatment,  the team felt it was important to find a less labor intensive and cheaper method than DNA sequencing of quickly identifying what fungus is causing an infection.

To accomplish this, the team took a variety of samples from isolated strains as well as, suspected infections, and suspected bacterial/viral infections. They took these samples and extracted DNA, then mixed them with specific primers diluted in MeltDoctor® HRM Master Mix (CandUn, and FungUn for yeast, and FilamUn and FungUn for filamentous suspects).  They then monitored the yields of DNA extracted and what PCR inhibitors arose.

With their method the team managed to detect and differentiate between 0.1 colony forming units/µl. The new technique even detected and characterized fungi in 7 out of 10 suspect cultures that appeared negative.

It is always good to hear of new methods being developed that show promise of helping quickly and accurately diagnosing disease agents. The faster we find our culprit, the faster we can find ways to effectively fight it.

Sunday, July 1, 2012

Mycena mushroom drawing.

Nothing important today, just a drawing I did of some mushrooms from the Mycena genus.