PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

Treading into a gray area along the spectrum of wood decay fungi

2014-06-23
(Press-News.org) One of the most basic rules for playing the game "Twenty Questions" is that all of the questions must be definitively answered by either "yes" or "no." The exchange of information allows the players to correctly guess the item in question.

Fungal researchers have been using a variation of Twenty Questions to determine if wood-decaying fungi fall under one of two general classes. If a fungus can break down all the components – cellulose, hemicellulose and lignin – of plant cell walls it is considered a white rot fungus. If a fungus can only break down cellulose and hemicellulose but not lignin, they classify it as a brown rot fungus. Known white rot fungi produce certain lignin-degrading enzymes called class II peroxidases (PODs) and a variety of enzymes that go after crystalline cellulose.

In a study published online the week of June 23, 2014 in the Proceedings of the National Academy of Sciences, a team led by U.S. Department of Energy Joint Genome Institute (DOE JGI) fungal researchers suggests that categorizing wood-decaying fungi as either white rot or brown rot may not be as clear-cut as previously thought. The discovery complicates but also broadens the range of fungal decay strategies to be explored for commercializing the process of biofuels production.

This finding emerged after researchers analyzed 33 basidiomycete fungal genomes, 22 of which are wood decayers, four of which had been recently sequenced by the DOE JGI. Based on previously sequenced genomes, the team observed that two of the new fungi, Botryobasidium botryosum and Jaapia argillacea, had the cellulose-attacking enzymes characteristic of white rot fungi, but lacked PODs, making them similar to brown rot fungi. Applying a statistical process called Principal Components Analysis (PCA) to find similarities in fungi based on their plant biomass degrading genes, they found that the two new fungi grouped close to Phanerochaete chrysosporium, the first white rot species sequenced. This was a curious finding because the new fungi were phylogenetically distant from P. chrysosporium, and, moreover, didn't have PODs.

The team then grew isolates of B. botryosum and J. argillacea on pine and aspen wood. They found that the fungi superficially degraded the wood surfaces but in localized areas, went further and broke down the cell walls and removed cellulose, hemicellulose and lignin.

"[They] show similarities to white rot fungi in … all predicted carbohydrate- and lignin-active enzymes and can degrade all components of wood, but they do so without the PODs that are a hallmark of white rot," the team reported in their paper. They also found a correlation between secondary metabolism genes, which are crucial for fungal survival, and brown rot fungi. These results, they added, suggest that the perceived dichotomy of white rot and brown rot is too simplistic and suggest that fungal wood decay capabilities be categorized instead on a continuum.

DOE JGI Fungal Genomics head Igor Grigoriev noted this wasn't the first time they'd seen a genome that appeared to blur the definitions between white rots and brown rots. "We thought we saw an anomaly with a previously sequenced white rot fungus Schizophyllum commune," he said. "Now we see a trend. This is the value of having multiple data points and so many fungal genome sequences. This is the whole point of doing fungal genomics at scale."

Dan Eastwood, a fungal researcher at Swansea University who was not involved in the study, pointed out that fungi don't have to follow rules to exhibit a decay form. "The manuscript is very timely and provides evidence for what many people in the field have suspected for some time – that simple descriptors of wood decomposition do not necessarily reflect the diversity in decay strategies exhibited by fungi," he said. "This is particularly the case when discussing the brown rot wood decay mechanism where distantly related species have evolved superficially similar decay mechanisms. This manuscript uses whole genome sequence information to outline the argument for advancing our understanding of wood decomposition away from a simplistic white versus brown rot dichotomy."

"This is the first time we see patterns of white rot without this particular enzyme," Grigoriev added. "That tells us these fungi degrade lignin using other means, which tells us POD is not the only marker for white rot. Now that it's clear that it's not the only player, we should broaden our search for enzymes that have bioenergy applications. It is important to identify a whole range of enzymes sourced from nature that can be used to develop second-generation biofuels in terms of breaking down lignin and other components in plant cell walls."

Eastwood added that the work allows researchers to start to understand decay strategies in complex habitats. "Wood is a complex substrate in a complex environment," he said. "Evolution of decay mechanisms will be complex also, and the diversity in gene compliment will reflect the polyphyletic nature of superficially similar decay strategies. The future challenges are to better define the chemical environment during wood decomposition in conjunction with enzyme activity of different species that appropriately reflect their specific ecology."

INFORMATION: For more information about the DOE JGI Fungal Program, view the short video here: http://bit.ly/JGI-Fungal-vid.

The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter.

DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.


ELSE PRESS RELEASES FROM THIS DATE:

Emergence of bacterial vortex explained

Emergence of bacterial vortex explained
2014-06-23
VIDEO: When confined in a water droplet, B. subtilis bacteria collectively and spontaneously form a swirling vortex, with some bacteria moving in one direction and others moving the opposite way. Researchers... Click here for more information. PROVIDENCE, R.I. [Brown University] — When a bunch of B. subtilis bacteria are confined within a droplet of water, a very strange thing happens. The chaotic motion of all those individual swimmers spontaneously organizes into a swirling ...

Straw albedo mitigates extreme heat

2014-06-23
Wheat fields are often tilled immediately after the crop is harvested, removing the light-coloured stubble and crop residues from the soil surface and bringing dark bare earth to the top. Post-harvest tilling is a widely practised and common management technique in Europe. However, ploughed fields can have a negative effect on the local climate during a heat wave. This effect was addressed in a recent study conducted by researchers at ETH Zurich led by Edouard Davin, senior lecturer at the Institute for Atmospheric and Climate Science, and Sonia Seneviratne, professor of ...

Vaccine made from complex of two malaria proteins protects mice from lethal infection

2014-06-23
WHAT: An experimental vaccine designed to spur production of antibodies against a key malaria parasite protein, AMA1, was developed more than decade ago by scientists from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. It showed promise in test-tube and animal experiments and in early-stage clinical trials, but returned disappointing results in recent human trials conducted in malaria-endemic countries. Now, the NIAID scientists have improved on their original vaccine with a new candidate that delivers AMA1 ...

Rett syndrome drug shows promise in clinical trial

2014-06-23
CAMBRIDGE, MA -- Rett syndrome, a rare genetic disorder that causes mental retardation, autism, and physical deformities, has no cure. However, a small clinical trial has found that a growth factor known as IGF1 can help treat some symptoms of the disease. Children who received the drug for four weeks showed improvements in mood and anxiety, as well as easier breathing, in a trial led by researchers at Boston Children's Hospital. MIT scientists first identified IGF1 as a possible treatment for Rett syndrome in 2009. "This trial shows that IGF1 is safe in the cohort ...

New analysis reveals previously 'hidden diversity' of mouth bacteria

2014-06-23
MBL, WOODS HOLE, MA—A new computational method for analyzing bacterial communities has uncovered closely related, previously indistinguishable bacteria living in different parts of the human mouth. The technique, developed by Marine Biological Laboratory (MBL) scientists, provides high taxonomic resolution of bacterial communities and has the capacity to improve the understanding of microbial communities in health and disease. The study will be published in PNAS Online Early Edition the week of June 23-27, 2014. An important step in understanding the role of oral bacteria ...

Computational technique provides new insight into oral microbiome

2014-06-23
CAMBRIDGE, Mass., June 23, 2014—Scientists have applied a new technique to comprehensively analyze the human oral microbiome—providing greater knowledge of the diversity of the bacteria in the mouth. For the first-time, scientists can provide high-resolution bacterial classification at the sub-species level. This work will enable researchers to more closely examine the role of bacterial communities in health and disease. The study, "Oligotyping analysis of the human oral microbiome," will be published in the Proceedings of the National Academy of Sciences and available ...

Delivering drugs on cue

Delivering drugs on cue
2014-06-23
June 23, Boston -- Current drug-delivery systems used to administer chemotherapy to cancer patients typically release a constant dose of the drug over time - but a new study challenges this "slow and steady" approach and offers a novel way to locally deliver the drugs "on demand," as reported in the Proceedings of the National Academy of Sciences (PNAS). Led by David J. Mooney, Ph.D., a Core Faculty member at Harvard's Wyss Institute for Biologically Inspired Engineering and the Robert P. Pinkas Family Professor of Bioengineering at the Harvard School of Engineering ...

Bone loss persists 2 years after weight loss surgery

2014-06-23
CHICAGO, IL — A new study shows that for at least two years after bariatric surgery, patients continue to lose bone, even after their weight stabilizes. The results—in patients undergoing gastric bypass, the most common type of weight loss surgery—were presented Monday at the joint meeting of the International Society of Endocrinology and the Endocrine Society: ICE/ENDO 2014 in Chicago. "The long-term consequences of this substantial bone loss are unclear, but it might put them at increased risk of fracture, or breaking a bone," said Elaine Yu, MD, MSc, the study's principal ...

A disease of mistaken identity

A disease of mistaken identity
2014-06-23
The symptoms of Cushing disease are unmistakable to those who suffer from it – excessive weight gain, acne, distinct colored stretch marks on the abdomen, thighs and armpits, and a lump, or fat deposit, on the back of the neck. Yet the disorder often goes misdiagnosed. To help combat misdiagnosis, Saleh Aldasouqi, an associate professor in the College of Human Medicine at Michigan State University, is drawing more attention to the rare disease through a case study, which followed a young patient displaying classic, yet more pronounced signs of the condition. Caused ...

Date labeling confusion contributes to food waste

Date labeling confusion contributes to food waste
2014-06-23
Date labeling variations on food products contribute to confusion and misunderstanding in the marketplace regarding how the dates on labels relate to food quality and safety, according to a scientific review paper in the July issue of Comprehensive Reviews in Food Science and Food Safety. This confusion and misunderstanding along with different regulatory date labeling frameworks, may detract from limited regulatory resources, cause financial loss, and contribute to significant food waste. In the United States, the United States Department of Agriculture Economic Research ...

LAST 30 PRESS RELEASES:

Bioinformatics approach could help optimize soldiers’ training for improved readiness and recovery

Earth scientists describe a new kind of volcanic eruption

Warmer wetter climate predicted to bring societal and ecological impact to the Tibetan Plateau

Feeding infants peanut products protects against allergy into adolescence

Who will like beetle skewers? What Europeans think about alternative protein food

ETRI wins ‘iF Design Award’ for mobile collaborative robot

Combating carbon footprint: novel reactor system converts carbon dioxide into usable fuel

Investigating the origin of circatidal rhythms in freshwater snails

Altering cellular interactions around amyloid plaques may offer novel Alzheimer’s treatment strategies

Brain damage reveals part of the brain necessary for helping others

Surprising properties of elastic turbulence discovered

Study assesses cancer-related care at US hospitals predominantly serving minority populations compared with non-minority serving hospitals

First in-human investigator-initiated clinical trial to launch for refractory prostate cancer patients: Novel alpha therapy targets prostate-specific membrane antigen

Will generative AI change the way universities communicate?

Artificial Intelligence could help cure loneliness, says expert

Echidnapus identified from an ‘Age of Monotremes’

Semaglutide may protect kidney function in individuals with overweight or obesity and cardiovascular disease

New technique detects novel biomarkers for kidney diseases with nephrotic syndrome

Political elites take advantage of anti-partisan protests to disrupt politics

Tiny target discovered on RNA to short-circuit inflammation, UC Santa Cruz researchers find

Charge your laptop in a minute? Supercapacitors can help; new research offers clues

Scientists discover CO2 and CO ices in outskirts of solar system

Theory and experiment combine to shine a new light on proton spin

PKMYT1, a potential ‘Achilles heel’ of treatment resistant ER+ breast cancers with the poorest prognosis

PH-binding motifs as a platform for drug design: Lessons from protease-activated receptors (PARs)

Virginia Tech researcher creates new tool to move tiny bioparticles

On repeat: Biologists observe recurring evolutionary changes, over time, in stick insects

Understanding a broken heart

Genetic cause of rare childhood immune disorders discovered

With wobbling stars, astronomers gauge mass of 126 exoplanets and find 15 new ones

[Press-News.org] Treading into a gray area along the spectrum of wood decay fungi