Monthly Archives: April 2010

The 400,000 Fungi of the Cornell Plant Pathology Herbarium

The stomping ground of mycologist Kathie Hodge is in the news, being featured in the article, Library of Fungus Diversity by Jing Jin, published by The Cornell Daily Sun:

The Cornell Plant Pathology Herbarium (CUP) is located on the eastern edge of campus in a newly renovated and temperature-controlled facility. In CUP, many rows of large, dark metal cabinets neatly organize 400,000 fungal specimens by species and genus.

Prof. Kathie Hodge, plant pathology and plant microbe biology, is director of the CUP.  She refers to these cabinets as “stacks” because the fungus “herbarium” functions like a library, storing dried and pickled specimens, photographs and watercolor paintings.  The CUP lends these resources to Cornell researchers and other mycologists from around the world to study fungi.

Kudos to author Jin for doing such a nice job of explaining the purpose and value of such an herbarium collection. Professor Hodge is truly a “mycological ambassador.” I hope she does not mind that moniker! The article also features CUP curator Robert Dirig.

400,000 specimens? Not bad, not bad at all.

Myco Apps for iPhone or iPad

There are some interesting reviews of iPhone and/or iPad apps planned for future posts, but in the mean time, here is a run down of some apps of interest to the mycology community in particular. Note: All descriptions are from the developers websites or from iTunes.

Some of these look good, others… not so much. Based on the limited selection, I’d say there is plenty of room for improvement and expansion of mycological apps.

There are also some apps built on the topic of mushroom recipes and yeast infections, as well as some more general microbiology and infectious disease apps, but those are not included here.

idMushroom

idMushroom

idMushroom Browser is the first professional pictorial guide to mushrooms for the Apple iPhone and iPod Touch. It combines excellent images from a team of photographers with state-of-the-art programming concepts and a beautiful graphic interface that’s smart and easy of use. You can simply enjoy viewing the photographs, or use them for visual reference when you need to identify a mushroom. A short description and key feature list for the mushroom is included for each photograph.

The user interface is simple to use yet powerful. Beginning mushroomers as well as expert mycologists can rapidly find photos of common mushrooms without special knowledge of mycology or scientific jargon. Users can quickly list mushrooms by categories such as: group, common name, scientific name, toxicity, or edibility. A general search tool is also supplied which allows one to quickly find a mushroom by entering the scientific or common name.

Each mushroom is described with a list of attributes such as group, color, size, habitat, season, and odor. A thumbnail picture of the mushroom is also displayed as well as its scientific and common names. A textual description of the mushroom written in layman’s terms is included along with an indicator for edibility.

We believe our photo collection is unsurpassed. To see a large version of a mushroom photo simply tap the “+” below the photo on the return screen. You can enlarge the full-screen photo by tapping the display to show an enlarged version. The enlarged size photo can be scrolled to see details of a mushroom.

(Disclosure: idMushroom is a MycoRant sponsor)

Fungi Kingdom

Fungi and Fungi Kingdom

“Fungi Kingdom” is the iPad adaptation of the “Fungi” mushroom identification application. Fungi Kingdom allows you to search among nearly 500 mushroom species using a dynamic description system based on hymenium type, cap shape, hymenium attachment type, stipe characters, spore print color and/or ecological type. Selecting a mushroom from the list matching your criteria gives you access to its Wikipedia page, complete with available pictures, description, scientific classification, … The complete Fungi Kingdom database is included in the downloaded application providing full functionality where no network is available.

Common Choice Edible Mushrooms

Common Choice Edible Mushrooms

Common Choice Edible Mushrooms

A quick guide to help identify the most common choice wild edible mushrooms that people hunt for such as Morels, Chanterelles, King Boletes (Porcini), Lactarius, Lobster and Oyster Mushrooms, Lion’s Mane, Shaggy Mane, Parasols, Caesar’s Mushroom, Matsutake, Black Trumpets, Helvella, Aborted Entaloma’s, Honey Mushrooms, Hedgehogs, Blewits and much more.

Morel Mushroom Hunting Secrets

Morel Mushroom Hunting Secrets

Chris Matherly, Morel Mushroom Expert, shares many of his secrets as to when and where to find Morels including specifics for each part of the country, Morel Species identification including several High-Resolution Photos of each Morel Species, False Morel information and Photos, Recipes, Mushroom Festival Information, Questions and Answers, Directly Instant Message Chris with any question and even text him a photo for identification! There are also direct web Links to many special pages found only in the member areas of the Morel Mushroom Hunting Club, such as a very detailed “Mushroom Glossary”, Over 750 mushroom species with photos and descriptions, A Morel Message Board Forum, The famous “Morel Mushroom Finds” page with photos and locations of current finds, A Time-Lapse Video of a Morel Growing over a 2 week period, The Famous “Morel Progression Map” updated daily during season, Guided Mushroom Hunts (Forays) information, and much more!

mushroooooms!

mushroooooms!

This is a collection of intriguing mushrooms.

Nature Lexicon: Pilzfuhrer

Nature Lexicon - Pilzfurher

Der Pilzführer dokumentiert systematisch und leicht verständlich die wichtigsten und schönsten Pilzarten Mitteleuropas (vor allem Deutschland, Österreich und Schweiz). Die Anwendung bietet insgesamt über 1000 qualitativ hochwertige Fotos und umfangreiche Informationen zu jedem Pilz, die es dem interessierten Laien einfach machen, die Pilze zu identifizieren und über deren Nutzen für Natur und Gaumen mehr zu erfahren.

iChampi–English

iChampi

The ultimate application for confirmed & amateur mushroom pickers.

iFunch

You’re in the woods… looking for mushrooms or just on a walk. You know your porcini, chanterelle, parasol mushrooms, ok, but all the other species you may find? What are they called? What do they look like? Are they edible?

iFunch

Botanical Terms — A Comprehensive Glossary

Botanical Terms is the leading professional level Botanical glossary for iPhone and iTouch. With a database of hundreds of Plant Structure, Growth, Reproduction and Metabolism Terms along with Algae, Fungi and other Botanical Terms, it maintains the most comprehensive collection available right at your fingertips. No internet connection required!

Botanical Terms

Botanical Terms’ intuitive interface and fast search allow you to glean the information you need as easily as checking a text message. There’s no reason to make decisions without crystal clear definitions of all the terminology involved, Botanical Terms equips you with just that, anytime, anywhere.

iProto Yeast

Has the same functionality as iProto Human but with the proteomes of several different yeast and yeast strains.

Click for list of yeast and yeast strains included in this application

Saccharomyces cerevisiae ( Baker´s yeast )
Saccharomyces cerevisiae (strain YJM789)
Saccharomyces cerevisiae (strain AWRI1631)
Saccharomyces cerevisiae (strain RM11-1a)
Saccharomyces douglasii
Saccharomyces bayanus
Saccharomyces paradoxus
Saccharomyces monacensis
Saccharomyces mikatae
Saccharomyces castellii
Saccharomyces servazzii
Saccharomyces kudriavzevii

Saccharomyces pastorianus| ( Lager yeast )
Schizosaccharomyces pombe ( Fission yeast )
Schizosaccharomyces kambucha
Schizosaccharomyces octosporus
Schizosaccharomyces japonicus

iProto - Yeast

Cryptococcus gattii Infections on the Rise

Yeast cells of the related species C. neoformans visualized using a light India ink staining (CDC/Dr. Leanor Haley)

It’s not every day you get clued in on a story of possible mycological interest by visiting the Drudge Report (FYI, to balance things out, I also check The Huffington Post). But, there it was–Potentially deadly fungus spreading in US, Canada.

A potentially deadly strain of fungus is spreading among animals and people in the northwestern United States and the Canadian province of British Columbia, researchers reported on Thursday. The airborne fungus, called Cryptococcus gattii, usually only infects transplant and AIDS patients and people with otherwise compromised immune systems, but the new strain is genetically different, the researchers said.

(Note: Most folks don’t seem to know that species names should be italicized and therefore don’t do it. Even so, if I see that error in an excerpt, I add the italics. However, this blogging software doesn’t seem to allow italics in post titles.)

The Reuters article is based n a recent report in PLOS Pathogens, Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii published by researchers in the US, UK and Australia. PLOS Pathogens is open access so I am sure they won’t mind the full abstract being reposted here:

Cryptococcus gattii causes life-threatening disease in otherwise healthy hosts and to a lesser extent in immunocompromised hosts. The highest incidence for this disease is on Vancouver Island, Canada, where an outbreak is expanding into neighboring regions including mainland British Columbia and the United States. This outbreak is caused predominantly by C. gattii molecular type VGII, specifically VGIIa/major. In addition, a novel genotype, VGIIc, has emerged in Oregon and is now a major source of illness in the region. Through molecular epidemiology and population analysis of MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/IIc outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Combined MLST-VNTR analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak.

An interesting feature of these PLOS papers is a section called Author Summary, which seems to be a “take home message” sort of a thing that is written in less technical language:

Emerging and reemerging infectious diseases are increasing worldwide and represent a major public health concern. One class of emerging human and animal diseases is caused by fungi. In this study, we examine the expansion on an outbreak of a fungus, Cryptococcus gattii, in the Pacific Northwest of the United States. This fungus has been considered a tropical fungus, but emerged to cause an outbreak in the temperate climes of Vancouver Island in 1999 that is now causing disease in humans and animals in the United States. In this study we applied a method of sequence bar-coding to determine how the isolates causing disease are related to those on Vancouver Island and elsewhere globally. We also expand on the discovery of a new pathogenic strain recently identified only in Oregon and show that it is highly virulent in immune cell and whole animal virulence experiments. These studies extend our understanding of how diseases emerge in new climates and how they adapt to these regions to cause disease. Our findings suggest further expansion into neighboring regions is likely to occur and aim to increase disease awareness in the region.

With good open-source research and information like this directly available, there isn’t much need for me to add anything else!

More on C. gattii

Why we should care about Cryptococcus gattii

A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada)

Cryptococcus gattii Research at the University of British Columbia

Deadly New Fungus Emerging in Oregon Expected to Spread

Cryptococcus gattii at University of Adelaide

A Podcast on C. gattii from the CDC

News From the WNS Front

It looks like things are going to get worse before they get better when it comes to bats and the fungal scourge of white nose syndrome (WNS). Over the past month there has been steady production of web updates on the spread of  the disease and recently there has been an uptick.

What Can Be Done About WNS?

What can be done about WNS? It seems that no one is sure, but monitoring of bat colonies indicates the fungal infection, that can dramatically reduce bat populations, is spreading. The recent spate of WNS news reports is truly alarming.  The following articles continue to raise awareness of this troubling problem.

Based on a flurry of recent articles out of Connecticut, the bats in this state seem to be pretty hard hit. To make matters worse, the fungal infection is turning up in ever increasing numbers of bat caves as the disease spreads further to the South and West in the United States, and even to the North into Canada.

Deadly Bat Fungus Detected in Smokey Mountains

A news release from the Great Smoky Mountains National Park said the debilitating fungus was confirmed by the U.S. Geological Survey’s National Wildlife Health Center in Madison, Wis. Besides the one confirmed case, photos of Indiana brown bats in the cave show conditions consistent with early stages of the syndrome.

DEP: Outlook for Connecticut’s Bats is Bleak

A syndrome that attacks hibernating bats continues to kill them at alarming rates both in Connecticut and in expanding areas range-wide, which will lead to a dramatic reduction in the size of the state’s bat population this summer, according to wildlife experts at the Connecticut Department of Environmental Protection (DEP).

Deadly Bat Fungus Appears to be Spreading

It’s the grim news that wildlife biologists have dreaded all winter: Officials from the state Department of Environmental Protection will confirm this morning that population counts of hibernating bats show that they continue to be decimated by the disease known as white-nose syndrome, and that some species might even be threatened with extinction. “The numbers are devastating for Connecticut bats,” said one DEP official. “The onslaught of white-nose just won’t stop.”

Bat Die-off Could Have Disastrous Effect on Ecology

“This is the worst wildlife catastrophe the country has seen since the extinction of the passenger pigeon,” said Mollie Matteson, conservation advocate with the nonprofit center. “Without aggressive efforts to secure their habitat and stem further losses from all causes, including probable human transmission of the new bat disease, these bats may soon join the sad list of American species we know only from textbooks and museums.”

Fungus Threat to bats Reaches Missouri. What’s the Weathernbird Say?

For the first time, a  fungus that’s been killing bats in the Eastern United States has been detected in a bat in Missouri’s Pike County. Conservation officials say the disease — white nose syndrome — has killed more than a million bats since it was first discovered in upstate New York in 2006.

White Nose Syndrome Spreads Among Bats in Tennessee

TWRA officials suggest cave divers to decontaminate their gear after going into a cavern. It is believed the fungus spores could be spread from cave to cave by people or other animals. “It could be spread airborne, it could be spread from a raccoon going into one cave and then going into another,“ said Wyatt. Hartley fears the situation will only grow more intense over time unless someone finds a working solution.

Fungus Strikes Bat Species in Five States

U.S. scientists say they’ve identified a deadly fungus that’s threatening nine bat species in Georgia, Kentucky, North Carolina, South Carolina, and Tennessee. Officials at the USDA’s Southern Research Station in Asheville, N.C., said the fungus — called white-nose syndrome — kills bats that hibernate in caves and mines.

Fungus Kills Off 90% of NJ Bat Population

A fungus has killed off about 90 percent of the state’s bat population, according to scientists who recently conducted a count of hibernating bats. The devastation was shocking in the largest hibernation spot for bats in New Jersey – Morris County’s Hibernia Mine. As many as 30,000 bats normally spend the winter, but a recent count found only about 1,700 alive – and many of those showed signs of infection, said Mick Valent, principal zoologist with the state’s Endangered and Non-game Species Program.

http://www2.tricities.com/tri/news/local/article/white_nose_syndrome_spreads_among_bats_in_tennessee/44865/

Mushrooms, a Most Hated Food?

A blog called The Stir recently had a short post on the most hated foods. According to 9 Foods We Love to Hate, mushrooms came it at number 5. In this admittedly unscientific poll, the only foods ranked worse than mushrooms were anchovies, onions, liver and tofu. Well!

Fungus is a Food?

Now my interest in fungi is not primarily as a food, but I like a good mushroom now and then. It got me to thinking though. Occasionally I search twitter to see what people are saying about mushrooms (and other mycologically relevant topics) and there is definitely a split between those who proclaim a love of the things and those who take every opportunity to disparage the noble fruit bodies. I decided to take a look today and see what the general drift of attitudes was.

I searched Twitter for “mushrooms” and in the last 4 hours there have been over a hundred tweets that mention them. Some are weird and undecipherable, some are from restaurants simply posting their daily specials, some are from ‘shroom heads extolling the virtues of their favorite hallucinogen, and some can actually be interpreted as either being in favor of the edible mushroom and some against. I checked 100 that were related to food and cooking and found the following:

Seemingly like mushrooms — 84

Seemingly hate mushrooms — 16

So, according to this informal (and also admittedly unscientific analysis) it seems like the mushroom lovers outnumber the mushrooms haters by a healthy margin! I think I’ll take a survey at work tomorrow to see how these figures compare!

The Petri Dish Art of Klari Reis

Petri Dish by Klari Reis

It is possible that leaving an agar plate laying around the lab for a month could produce something akin to art. Or, microbes can be deliberately arranged on a nutrient surface to produce interesting images a la Nial Hamilton. Then again, when it comes to Petri dish art, there is no reason why any living organisms need be included at all, or even real Petri dishes for that matter.

Meet Artist Klari Reis

Artist Klari Reis has created a series of biology-inspired works that invoke the beauty and endless variety of microorganisms, without any naturally-occurring materials. Who is Klari Reis?

Klari Reis received her M.A. in painting from the City and Guilds of London Art School in 2004. She is currently painting in her native Northern California where the presence of many of the world’s top pharmaceutical companies and research institutions serves as her muse.

Klari Reis is an artist, not a scientist, and was trained as an architectural draftsman and designer. She has a penchant for clean forms and grids, geometric organization, the ‘containing line’ and finely-wrought surfaces. She considers it an advantage that she is not a classically trained painter who might be too invested in traditional themes or media.

A Petri Dish For Every Day of the Year

Petri Dish by Klari Reis

Klari’s latest project is a collection of 365 “Petri dishes”–one for each day of the year. All the artwork is created from an epoxy polymer; there are no actual cultures used in the art. The plastic is dyed with pure pigments and dyes and sometimes both water-based and oil based paints.

Although the series does  have a correlation with the days of the year, she did not produce one per day. “No,” she explains, “unfortunately, I worked on a few almost everyday for a year. I then picked my favorites for each day of the year.”

Some of them look like they were intentionally designed to look like fungi. Sometimes this was intentional, other times, it’s just the way it turned out. That’s how art works.

“I occasionally try to make a Petri dish painting look exactly like an image I have been inspired by.  However, I usually like to work just from memory and do my best to recall the natural formations seen and the way the shapes and reactions made me feel.”

Petri Dish by Klari Reis

Biology Inspires Art

Reis is known for her biological inspiration. She previously produced a series of one hundred images based on drugs. Microbially inspired works seem like a natural follow on to that. When asked about it, Reis seemed to agree.

“My work for the past six years has revolved around cellular imagery and natural formations. Evolving into working with Petri dishes seemed like a logical next step to emphasis the overall theme in my artwork. I have been creating groupings of small Petri dish paintings for two years now. However, I am always working on large scale paintings at the same time. I am currently manufacturing large scale Petri dishes with a 45-inch diameter to create larger scale works with the same depth as their smaller counterparts.”

Reis uses brightly colored dyes to emphasize the different elements of an actual living culture. The results can be strikingly similar to real colonies on a plate.

Petri Dish by Klari Reis

She studied organism growing in Petri dishes at Kings College in London and at St. Thomas’ Hospital, before starting the project. More recently she also did research for her art at two different South San Francisco Biotech firms. “I also own my own microscope and do my own small experiments at home,” she adds.

I asked Klari to explain a little more about her relationship with these biotech companies that  she had cooperation from. “At all locations I looked at everything I could get my hands on under the microscope. At first, focusing on cellular reactions to pharmaceuticals. These days I am inspired by naturally occurring patterns and formations in our bodies, and elsewhere.”

Petri Dish by Klari Reis

You can learn more about the inspiration for Kkari’s work at her website klariart.com. Her Petri dish installations are on display in a number of art collections around the world, including those of the Royal Family of Abu Dhabi, the Keck Graduate Institute in California, and the MEG Center in Oxford England. Three hundred Petri paintings are on public display at the Peninsula Shanghai Hotel and, if you are ever on a Royal Caribbean cruise, be sure to check out the 1,500 Petri paintings that are featured in a large installation aboard the ship Oasis of the Seas.

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