The summer is a great time to learn some new skills and really hone data analysis techniques. I think it’s best to learn some topics — bioinformatic tools and data analysis scripting in particular — as intense multi-day workshops or a week- or two-week long short courses. Here’s a few courses that are being held this summer that may be of interest to you. I’ll be sure to post more as I hear about them.
Programming for Evolutionary Biology, Leipzig, Germany, April 3rd to April 19th, 2013
Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013
Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013
Tuber melanosporum is an important ectomycorrhizal fungus that can be cultivated with crop trees such as Hazelnut, and other truffles can be cultivated with other nut trees such as Pecan. Despite a concerted effort to understand the biology of T. melanosporum, both through a genome sequence and other molecular tools to understand population biology – as well as government efforts to promote cultivation with nut trees – harvests of the Périgord Black Truffle have been declining since the 1970s. There has been no agreement in what has been causing this decline from a community of researchers.
In a brief report entitled “Drought-Induced Decline in Mediterranean Truffle Harvest” in the journal Nature Climate Change, Büntgen et al. recently described how climate change may be affecting truffle production, either directly, or by affecting the biology of the truffle’s host trees. Such measurements are challenging in numerous regards; inspecting climate data is difficult enough, but reports of truffle harvesting are scarce for many reasons, one of which is the fact that many successful truffle collectors are reluctant to give information about their productive grounds.
The authors correlated climate details from 12 climate models with truffle harvests from various parts of Europe (namely Aragón in Spain, Périgord in southern France, and Piedmont and Umbria in Northern Italy). They observed that tree ring growth in Oak trees and truffle production were correlated and showed that increased measurements of summer evapotranspiration could explain both the reduction in plant growth and truffle production.
The authors hypothesize that tree and fungus competition for summer soil moisture may be reducing the production on truffle sporocarps. Unless the present course of climate change is reversed, it is expected that truffle harvests in Europe will continue to decline. This is bad news not just for the truffles and trees, but the people who enjoy both.
The Cucurbitaceae is an agriculturally important family of plants (think melons, pumpkins, cucumbers, squashes, etc.) and one of the most popular species in this family is Watermelon. Watermelon has been cultivated for more than 4,000 years and was most probably spread by nomadic people as a portable source of both water and pre-packaged nutrients. The estimated center of diversity of the Cucurbits is in Southern Africa. Watermelon has many cultivars – more than 200 in production worldwide – with a wide range of phenotypic diversity and a wide area of production that accounts for 7% of land grown for vegetables.
Unfortunately, Curcubits are generally susceptible to pathogens – most typically in the form of bacterial and fungal pathogens. The genomes in this group are starting to pile up which makes the family an interesting group for comparative genomics studies –particularly in the development of model species for plant pathogen studies.
Almost 47 Gb of sequence data was generated using Illumina’s sequencing platforms to give 108X coverage on the relatively small estimation of 426 Mb C. lanatus genome, while the draft is approximately 353 Mb or 83.2% of the estimated genome size. Unmapped reads, totaling almost 20% of the sequencing data, could not accurately be constructed into contigs because of explicit regions of genome duplication.
The authors estimated 23,440 genes in the watermelon genome – very close to both the cucumber genome (no surprise) and the human genome (surprise). About 85% of the genes from watermelon could be predicted on the basis of homology to other plant genes. The authors did a throughout assessment of transposable elements, various repeats, and classified functional RNAs from ribosomal RNA subunits to microRNAs. Like other plants, watermelon shows gene enrichment in subtelomeric regions. On the basis of comparison to other genome sequences, watermelon possesses the seven paleotriplications shared with the eudicots.
The authors assessed genetic diversity across varieties of C. lanatus by sequencing 20 representative accessions anywhere between 5X and 16X coverage. The estimated diversity of these accessions was considerably lower than similar arrays of accessions in maize, soybean, and rice. One explanation of the disease susceptibility of the Cucurbitaceae is this low level of genetic diversity. As a result, one objective of breeding programs for watermelon is to introduce more diversity from wild accessions.
Lastly, the authors assessed a number of key features of the C. lanatus genome (along with the other Cucurbitaceae): vascular transport of water and nutrients along vine-like stems, sugar content and accumulation, and the presence of an interesting non-essential amino acid – originally described from watermelons – called Citrulline.
The watermelon genome database is located both here and here.
Again, I’ve been in the midst of writing manuscripts and doing data analysis and haven’t been able to put as much time into this blog as I usually like. I’m also having some trouble with my server, so you’ll have to excuse the slow load times from my service provider. As well as having lots of papers in the pipeline, I am finishing up a few draft posts for the blog, so stay tuned as there is more on the way.
Speaking of paper writing, the following video has made the rounds on the internet – and with the theme of this post – I’m reproducing it here. Computer Science graduate student Timothy Weninger recently submitted a paper to a conference and created a video of his writing process.
Sorry for the lack of posts as of late, I’ve been a little swamped lately with writing and researching; unfortunately this blog has to suffer sometimes.
I don’t have time to write a complete post right now – maybe soon in the future – but I’ve been closely following the cases of fungal meningitis derived from contaminated injections of the steroid methylprednisolone acetate. Looks like the main culprit is Exserohilum rostratum, although one person has been infected with a species of Aspergillus. Both of these fungi are extremely common in soils and are plant pathogens.
Here’s some links from the CDC on the current infections:
The video below is a little on the cheesy side, but it’s an interesting take on the making of a baseball bat from White Ash trees. I thought I would post it to you in honor of the professional baseball postseason in the United States right now. Ash trees across the Eastern United States, and particularly in Pennsylvania, are quickly being destroyed by the Emerald Ash Borer, an invasive beetle which spreads fungal infections from tree to tree, so many baseball bat manufacturers are moving to using Sugar Maple.
There is a difference between the wood structure (i.e. cell wall morphology) between Ash and Maple and these slight differences in the wood grain effect how the ball is hit and how far it goes or how much control a batter has over where a ball is hit; at least some players tend to prefer one type of wood over another.
Those that know me know that I’ve got a thing for orchids. From my point of view, what’s not to like: they have exceptionally diverse morphology, have complicated natural histories, have equally diverse interactions with pollinating insects, and – most important for me – are obligate mycorrhizal formers with a wide array of fungal symbionts. I’m quite surprised we don’t have more scientists studying them.
I enjoy going to academic meetings and very frequently post information about upcoming meetings and symposia. Some people have recently asked me why I put so much emphasis on meeting information on the blog and others have asked how I decide which meetings to attend, including this recent comment. I go to meetings for many reasons – some of which I will cover here – but, specifically for me, the main reason I go to meetings is to interact with other scientists in my discipline.
I believe going to scientific meetings is a vital part of mastering how to communicate your research. The types of communication you have the opportunity to master can range from giving an oral presentation to hundreds (or perhaps thousands!) of other scientists to speaking with someone for 30 seconds in an elevator. Academic meetings give you an opportunity to master your communication skills.
Meetings are also great places to learn about the cutting edge of your research area. Often scientists will present their most recent findings prior to publication. You might be able to learn about new technologies or novel ways to analyze data before you read about them in publications. Often during the question and answer portion of talks, theories and controversial topics are discussed, with a debate in real time. I tend to return from meetings mentally energized with lots of new ideas to investigate and think about.
Meetings are great places to network and meet people in your research area. It’s easier to strike up a conversation or collaboration via email if you’ve met someone in person at a meeting. Also, if you are in academia, the people you speak with at meetings will likely be the ones who are reading your grant proposals and reviewing your manuscripts. Future job contacts and impromptu pre-interviews happen at meetings. Most importantly, there’s the added bonus of developing friendships with your fellow scientists.
Lastly, I enjoy traveling, so going to academic meetings is a way for me to mix business with pleasure, so to speak. I’ve gotten to see some truly beautiful places under the auspices of attending scientific meetings.
If you are a student or a post-doc – or have been asked to present a talk – there may often be registration discounts for meetings and symposia. You may be able to get a discount if you volunteer to help out at the registration desk or other planned events. You might also be asked to provide financial need. You should check with the meeting organizers as soon after the meeting is announced for these types of discounts.
When it comes to choosing a meeting to attend, I prefer smaller more intimate meetings, with a range of participants in the hundreds, and not thousands like you have a tendency to find at large meetings. Large meetings can be valuable, but I personally find that it’s more difficult to see attend all the talks you want to and to locate the people you want to speak with. I will often speak to people who have attended specific meetings in the past and ask them about their experiences.
Before going to a conference, I usually get an idea of which talks I would like to see and who I would like to speak with at the meeting. This can happen before I leave for a meeting if the conference booklet is posted online, but it typically happens right after I arrive at the registration desk. Some people prepare by bringing business cards, and although I haven’t used business cards, this could help people remember you after the meeting. You also want to prepare your “talk” – whether it’s for a speaking presentation, a poster presentation, or just speaking in the hallways or at a dinner of the meeting – you should be able to communicate your research clearly in many different formats.
During the meeting, I have different strategies depending on the meeting size and the types of talks. I try to pick the talks that are most relevant to my interests, but sometimes this leaves me running between sessions. This can be a great time to “bump” into someone you want to speak with, but you may also miss important talks this way too. Sometimes, particularly at the end of meetings when my mind is overwhelmed, I sit through entire sessions just to see if there is something interesting in a disparate research area that can be applied to my research. I’ve gotten some great ideas listening to talks I thought would not be pertinent to my research. I take notes and make sure to write down literature to look up and read when I get home from the meeting.
After the meeting is over it’s important to follow up with those you have started collaborations with and those whose research papers you want to read. If you’ve taken notes, review them and think about posting them to a public forum, like a blog, so that others can share in on your meeting experience.
Knowing how connect Dropbox to remote machines has saved me some time transferring files and it’s been extremely helpful on many different levels. I can quickly pipe or send output text or images right to numerous shared devices. I can check on the progression of a pipeline running on a remote server with my mobile phone by looking at output images or files (or even quickly checking file sizes). Visualization at the command line is non-existant, so if I want to see an output figure, I can look at data output graphs quickly from Dropbox, and, if I choose to do so, can put images in a shared folder for a colleague to inspect in a matter of seconds. Before you use Dropbox at the command line, you’ll have to set up a Dropbox account.
To link Dropbox at the command line on your home computer or, perhaps more importantly, on a remote machine, you should start at the location where you want to put your Dropbox folder, such as your home directory on your machine.
Next, you’ll want to download Dropbox (here, for Linux-based machines):
Bryophytes represent a portion of the dominant vegetation in boreal forests, but very little is understood about the taxonomy, seasonality, or biomass of the fungi associated with them. Additionally, microbes associated with mosses may be responsible for nitrogen fixation and nutrient immobilization as epiphytes or on forest soils. A previous study from the Kauserud lab reported high levels of fungal biomass and active plant cell wall degrading enzymes identified from moss-associated fungi.
As I have mentioned here numerous times, fungi are notoriously hard to identify by cultural and morphological means and are extremely diverse. To understand this diversity, the authors performed 454 pyrosequencing of the ITS2 region of the ribosomal DNA operon for molecular taxonomic identification against a database of known fungal sequences. This sequencing was done in concert with an ergosterol HPLC assay that is used to estimate living fungal biomass.
The authors identified a large numbers of fungi, some presumably moss associated, and the total amount of fungi recognized was comparable to that found in forest soils. The majority of fungi were identified as Ascomycetes, which agrees with other studies investigating vascular plant phyllosphere communities using the primer pair ITS3 and ITS4. Additionally, this study identified a consistent taxonomic profile as a previous study from the Kauserud laboratory using a cloning strategy and Sanger sequencing approach. Not surprisingly, this study reports orders of magnitude more fungi but identified roughly the same groups of fungi (Helotiales, Chaetothyriales, Agaricales, and Tremellales).
The researchers addressed seasonal variation by sampling every eight weeks between April and January over the course of a year. Quite interestingly, there is a strong consensus in this study with other research that provides evidence that fungi not only survive under snowpack, but also continue to grow during the winter months. While the researchers found consistent trends with regard to season, there were fluctuations in fungal biomass when considering host bryophyte. By using principle component analyses, the authors show that the fungal communities are structured mainly by host plant and secondarily by the type of bryophyte tissue that was sampled. This paper is an important contribution to the growing literature that show that plant-associated fungi are extremely diverse, dynamic, and show complex relationships with host plants.
I’m starting a new series of short tutorials. In a selfish way, these posts are for me – a vehicle for me to clarify my own comprehension of a given topic. I might also tell you about a solution to a problem I have been troubleshooting.
The first post in this series is about fosmids. There seems to be some public confusion as to what they are or what they can be used for – basically, I have been confused. Apparently I had forgotten my microbiology coursework along the way. Many genome sequencing projects – such as the human genome project – have utilized fosmids to create libraries prior to sequencing, but it wasn’t until hearing about JGI’s fungal and metagenomic sequencing initiatives did I hear the term fosmid mentioned frequently.
Fosmids are used when preparing genomic libraries for genome sequencing. Fosmids are circular DNA of bacterial origin – technically plasmids – but where typical plasmids exist in high copy number (up to 100 copies per cell) and possess small (3 to 6 kb) inserts, fosmids are present as a single copy in a cell and may possess inserts upwards of 40 kb. Fosmids are advantageous because they produce stable libraries for genome sequencing. They have a tendency to provide fairly uniform coverage, so they are optimal for closing gaps in whole genome alignments. In addition to genome sequencing, they have also been used for metagenomics and expression studies.
Fosmids are derived from the fertility plasmid (or F-plasmid) and are responsible for the formation of the sex pilus during bacterial conjugation. This plasmid contains both origin and partitioning genes derived from the F’-episome and as a result, the plasmid is kept as a single copy clone, which comes in handy during genomic DNA library construction. Fosmid vectors are derived from random shearing – which yields more uniform coverage when comparing against other library cloning methods.
Cosmids may also be useful for genome sequencing projects, but unlike fosmids, they are multi-copy vectors that are generally present at anywhere from 20-70 copies per cell and this high copy number leads to instability and lost segments of genomic DNA. This can be an issue for closing gaps in genome alignment, but if you’ve got high sequencing depth and a small genome to sequence, it may not be much of an issue. Most importantly, with high copy number plasmids, such as cosmids, the chance of recombination increases which can disrupt and rearrange genomic DNA inserts prior to sequencing.
Lastly, fosmids can be useful for chromosome specific sequencing and as cytological markers for chromosome identification. The image above – which comes from this paper – shows the identification of chloroplast genome isolation and sequencing from fosmids; a similar technique can be used to isolate and sequence specific chromosomes. Also, fosmids may be used as cytological markers with in situ hybridization on metaphase karyotypes and sorted using flow cytometric methods.
Finally, if you live in the New England area of North America (or don’t mind the travel) the first regional meeting of mycologists from the state of Massachusetts and the surround area will be held on October, 27th 2012. It will be aptly named MassMyco. The meeting will be held at Clark University and hosted by the Hibbett Lab. I love these small regional meetings, so perhaps I’ll try to make the trek for this one. Registration is not open yet, but check back soon.
The yeast-forming basidiomycete genus, Cryptococcus, has emerged as a significant model for both fungal genetics and pathogenicity. A long history of research compounded with numerous laboratory resources, as well as two sequenced genomes, have yielded a great deal of information on this enigmatic fungus. The new book Cryptococcus: From Human Pathogen To Model Yeast, edited by Heitman, Kozel, Kwon-Chung, Perfect, and Casadevall, features contributions from 123 authors and summarizes a vast amount of data as well as synthesizes disparate concepts on the biology of Cryptococcus. If you consider Casadevall & Perfect’s 1998 tome Cryptococcus neoformans as the groundwork for this book, then these 646 pages are evidence for the explosive advance of knowledge on Cryptococcus that has accrued over the last 12 years.
Cryptococcus species, arguably the most important fungal pathogen of mammals, are common in immuno-compromised hosts; HIV-associated cryptococcosis alone infects more than 1 million people per year. For example, Cryptococcus has been laboratory confirmed in Sub-Saharan African countries to be responsible for anywhere from 10 to 70% of fatal meningitis cases over the last two decades. A well-publicized outbreak of a particularly virulent strain of C. gattii was determined to be the causative agent of more than 200 cases of human meningitis in non-immuno compromised individuals within the Pacific Northwest over the last decade. A concerted global consortium of medical mycology researchers the majority of whom are authors of chapters in this book have provided the foundation for establishing Cryptococcus as the model system for understanding fungal pathogenesis in both a medical and veterinary setting.
Species of Cryptococcus entered my personal radar when they kept turning up in plant-associated environmental samples. Wanting to get up to speed with natural history, population genetics, and methods for typing Cryptococcal diversity, this book was an obvious entry point for me. Chapters here are dedicated to identification from environmental niches – such as the description of avian- or plant-associated vectors – as well as population biology to phylogeography, and species complexes to hybridization.
Copiously illustrated throughout, notable figures include those documenting Cryptococcus morphology, cell and molecular biological networks, secondary metabolite chemistry, and gene and genome structure. Chapters devoted to phylogeography and species complexes have detailed phylogenetic trees and distribution maps. Additionally, this wouldn’t be a clinical textbook if it didn’t include a series of color and monochrome plates of human and animal infections that remind you why you have – or haven’t – studied medical mycology.
Mycologists aren’t the only ones who will find this resource useful. Geared toward a wide array of specialists, this book is equally applicable to the interests of clinicians and physicians, microbiologists and immunologists, disease ecologists and epidemiologists, and, to a lesser extent, public health and policy administrators. The book succeeds in connecting and interpreting basic research science and applying this knowledge in a clinical context.
The book consists of a whopping 44 chapters separated into seven sections. These sections are devoted to general biology; genetics and genomics; virulence; environmental interactions and population biology; immune host responses; pathogenesis; and diagnosis, treatment, and prevention. Each of the sections consist of five to eight chapters and each informative chapter stands on its own – concise enough to allow for discrete chunks of reading without overwhelming the reader. In fact, I would argue that the book’s greatest strength is cohesive breadth blended with factual depth. My only criticism and this is an extremely minor one is that the book as a whole is slightly overwhelming in scope. This by no means indicates a lack of vision from the authors or editors, but reflects their desire to take into consideration the complete state of knowledge relating to Cryptococcus and its biology. As a result, the contributors have not only provided a truly fascinating and utterly comprehensive collection of everything Cryptococcus, but have set the bar high for the best treatise on fungal biology at the genus level. I would consider this book essential for anyone working directly with Cryptococcus or wanting to get up to speed and for mycologists looking for a framework to fully grasp the biology of an important model fungus.
The Organizing Committee cordially invites you to the 7th International Conference on Mycorrhiza (ICOM7) to be held from 6th to 11th January’ 2013 in New Delhi, the capital Republic of India. Organized by TERI under the auspices of the International Mycorrhiza Society and in collaboration with the Mycorrhiza Network, this 6 day gala event would bring the ICOM legacy to Asia for the first time.
The theme of this conference, “Mycorrhiza for all – An Under Earth Revolution” is wisely chosen so that it may prove to be the epicenter of a new revolution that our planet is in dire need of. A change that would help minimise the usage of chemical fertilizer on soil and hence leave the least environmental footprint.
I'm a biologist with broad interests, focused mainly on fungal and plant genomics and understanding how these two diverse groups of organisms interact with each other.
I am mainly interested in the mycorrhizal fungal symbiosis, the meta-taxonomic and metagenomic assessment of plant-associated environments, and the dissection of interactions of fungus and plant: from cell-to-cell contact to the modification of gene expression resulting from these communications.
I typically use laboratory techniques and field studies addressing more specific questions using controlled experiments. I have increasingly turned to bioinformatic techniques to handle the analysis of genomic data so I spend a lot of time in front of a computer.
You can read more about me and my interests at my website.
Please get in touch with me by emailing me at josh...@gmail.com