Tag: Misc.

Fermentation microbiomes part 2 from #UCDavis: American coolship ale microbiome

 From Nick Bokulich: This is an image of the “coolship” where the cooling wort
(pre-fermented beer) is left overnight and presumably where wild
microbes are introduced to kick off the fermentation. This is the
morning after, still full of wort.

Just a quick follow up to my recent post on How did I miss this? The botrytized wine microbiome … from #UCDavis colleague David Mills.  There is a similar paper from the same group also in PLoS One from about the same time: PLOS ONE: Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale.  What a job — microbes, ales and wines, and sequencing.  One of the few times when reading a paper where I have said “I wish that was me doing that work.” … must look into getting involved in such studies …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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How did I miss this? The botrytized wine microbiome … from #UCDavis colleague David Mills

From here.

Fun use of next generation sequencing in this paper: PLOS ONE: Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine.  They used sequencing to characterize the diversity of microbes associated with botrytized wine (wine produced from grapes infected with the mold Botrytis cinerea.  They focused in particular on Dolce wine (not 100% sure what this is but I think it is wine from the Dolce winery …).  And they focused in particular on the bacteria associated with this wine as it was being produced.  Anyway … I am no food/drink microbiologist .. but this seems cool.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Important & neglected aspect of lab studies of animals : effect of habitat change on microbiome

By Aaron Logan via Wikipedia 

Very very interesting paper came out recent from some colleagues at UC Davis: PLOS ONE: Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice

Abstract: The mammalian intestine harbors a vast, complex and dynamic microbial population, which has profound effects on host nutrition, intestinal function and immune response, as well as influence on physiology outside of the alimentary tract. Imbalance in the composition of the dense colonizing bacterial population can increase susceptibility to various acute and chronic diseases. Valuable insights on the association of the microbiota with disease critically depend on investigation of mouse models. Like in humans, the microbial community in the mouse intestine is relatively stable and resilient, yet can be influenced by environmental factors. An often-overlooked variable in research is basic animal husbandry, which can potentially alter mouse physiology and experimental outcomes. This study examined the effects of common husbandry practices, including food and bedding alterations, as well as facility and cage changes, on the gut microbiota over a short time course of five days using three culture-independent techniques, quantitative PCR, terminal restriction fragment length polymorphism (TRFLP) and next generation sequencing (NGS). This study detected a substantial transient alteration in microbiota after the common practice of a short cross-campus facility transfer, but found no comparable alterations in microbiota within 5 days of switches in common laboratory food or bedding, or following an isolated cage change in mice acclimated to their housing facility. Our results highlight the importance of an acclimation period following even simple transfer of mice between campus facilities, and highlights that occult changes in microbiota should be considered when imposing husbandry variables on laboratory animals.

I personally think that we as a community are going to have to come to grips with the fact that the microbial communities in / on research organisms (of all kinds) may have a profound effect on experimental results.  This may explain many of the differences seen in experiments between facilities or over time within a facility.  In general, I think either controlling the microbes more carefully in lab experiments (e.g., using defined flora) or at least monitoring them is going to be very important to best interpret studies of plants and animals in the lab (or for that matter – in the field too).  Anyway -this paper is a tiny window into one of the ways that controlling for microbiomes may be important in lab studies.

Citation: Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, et al. (2012) Routine Habitat Change: A Source of Unrecognized Transient Alteration of Intestinal Microbiota in Laboratory Mice. PLoS ONE 7(10): e47416. doi:10.1371/journal.pone.0047416

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Guest post on "CHANCE" ChIP-seq QC and validation software

Guest post by Aaron Diaz from UCSF on a software package called CHANCE which is for ChIP-seq analyses.  Aaron wrote to me telling me about the software and asking if I would consider writing about it on my blog.  Not really the normal topic of my blog but it is open source and published in an open access journal and is genomicy and bioinformaticy in nature.   So I wrote back inviting him to write about it.  Here is his post:

CHANCE: A comprehensive and easy-to-use graphical software for ChIP-seq quality control and validation



Our recent paper presents CHANCE a user-friendly software for ChIP-seq QC and protocol optimization. Our user-friendly graphical software quickly estimates the strength and quality of immunoprecipitations, identifies biases, compares the user’s data with ENCODE’s large collection of published datasets, performs multi-sample normalization, checks against qPCR-validated control regions, and produces publication ready graphical reports. CHANCE can be downloaded here.

An overview of ChIP-seq: cross-
linked chromatin is sheared,
enriched for a transcription factor
or epigenetic mark of interest
using an antibody, purified and
sequenced.

Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) is a powerful tool for constructing genome wide maps of epigenetic modifications and transcription factor binding sites. Although this technology enables the study of transcriptional regulation with unprecedented scale and throughput interpreting the resulting data and knowing when to trust the data can be difficult. Also, when things go wrong it is hard to know where to start when troubleshooting. CHANCE provides a variety of tests to help debug library preparation protocols.

One of the primary uses of CHANCE is to check the strength of the IP. CHANCE produces a summary statement which will give you an estimate of the percentage of the IP reads which map DNA fragments pulled down by the antibody used for the ChIP. In addition to the size of this signal component within the IP CHANCE reports the fraction of the genome these signal reads cover, as well as the statistical significance of the genome wide percentage enrichment relative to control in the form of a q-value (positive false discovery rate). CHANCE has been trained on CHIP-seq experiments from the ENCODE repository by making over 10,000 Input to IP and Input to replicate Input comparisons. The q-value reported gives then the fraction of comparisons between Input sample techinical replicates that report an enrichment for signal in one sample compared to another equal to the user provided sample or greater. CHANCE identifies insufficient sequencing depth, PCR amplification bias in library preparation, and batch effects.

CHANCE identifies biases in sequence content and quality, as well as cell-type and laboratory-dependent biases in read density. Read-density bias reduces the statistical power to distinguish subtle but real enrichment from background noise. CHANCE visualizes base-call quality and nucleotide frequency with heat maps. Furthermore, efficient techniques borrowed from signal processing uncover biases in read density caused by sonication, chemical digestion, and library preparation.

A typical IP enrichment report.

CHANCE cross-validates enrichment with previous ChIP-qPCR results. Experimentalists frequently use ChIP-qPCR to check the enrichment of positive control regions and the background level of negative control regions in their IP DNA relative to Input DNA. It is thus important to verify whether those select regions originally checked with PCR are captured correctly in the sequencing data. CHANCE’s spot-validation tool provides a fast way to perform this verification. CHANCE also compares enrichment in the user’s experiment with enrichment in a large collection of experiments from public ChIP-seq databases.

CHANCE has a user friendly graphical interface.
How CHANCE might be used to provide feedback on protocol optimization.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Gotta love those DNA extractions :)

Because I was so late to introduce myself, I can also talk about what we’ve been doing for the last few weeks. We’ve gone to the aquariums and collected samples, done some DNA extractions, and done PCR on our samples. Our samples came from salt water and fresh water tanks and include water, sediment, and gunk from the walls of the tanks. Our latest issue has come after PCR, while running the Gel. It seems like our issue might be all the way back in PCR A. I am very excited for the new aquatic systems that we will start sampling in the next couple weeks. We are hoping to start sampling the minute they load the tubs. Our hope is to sample very frequently in the first couple days because we know much of the microbial community will develop in this time. So what’s the point of that, you ask? Well we would love to study the succession of microbial communities in these new aquatic systems.  That’s all for now!

Aquarium Project

So the project is finally in full swing! After a couple of weeks of practice sampling and getting used to different protocols for extracting, purifying and amplifying the DNA, we have now moved on to working with our real samples. We have extracted DNA from 18 samples (includes replicates of 3) from the tropical tank and the cold water tank. Funnily, the hardest part of the project so far has been running gels. We initially hit a couple of problems such as thickness of the gel, a loose wire in a gel box and differences in loading buffers and dyes. However, now that Akshay is going to be coming in, hopefully he can give us a couple of hints from his experience from IGEM, cause god knows how many gels he had to make this summer 😛

Aquarium Blog Post 1 (#longoverdue)

So after a long and intense summer and first half of fall quarter, the iGEM international competition came and concluded. So now I get the chance to walk down the lab (towards the gel room!) a few more feet and start work on the aquarium project I am helping with in the Eisen Lab. I can now devote more time to the processes of the project, and not just be involved with going to retrive samples from the aquarium, and trying to figure out where we keep our Taq Polymerase. I will try and come in the lab in the next few days, and figure out the workflow and how to get this project going. I am very excited for the project as well as hoping for some actual success in our process. This is the first of many blog posts as well, so stay tuned for the next segment of our project!

Thank you interwebs: help proving fungi are cool

Well, am teaching three lectures this week on Fungal Diversity for BIS002C at UC Davis. And I decided tonight to ask the internet for help finding cool new stories on fungi. And boy did the internet come through in the clutch. Thanks internet. See Storification of Twitter and Facebook discussions below:

http://storify.com/phylogenomics/fungi-are-cool.js[View the story “Fungi are cool” on Storify]

Fungi are cool

Storified by Jonathan Eisen · Sun, Nov 04 2012 23:13:14

Twitter Discussion after I asked for suggestions …
Prepping 3 lectures on Fungal Diversity for Intro Bio class at #UCDavis – looking for suggestions for coolest recent fungal stories/studiesJonathan Eisen
@phylogenomics Saccharomyces eubayanus & the new world origin of lager yeast…jashapiro
@phylogenomics well, in the news, jump in fungi in metagenome studies in gulf post BP spill.Kenneth Bruno
@phylogenomics the obvious 1 is the fungal meningitis outbreakKitt Klaiss
@jashapiro reference?Jonathan Eisen
@phylogenomics This looks cool. I’m concerned that intro bio doesn’t have more micro, earlier. Is your syllabus available?Mark O. Martin
@KSBruno9 reference?Jonathan Eisen
@phylogenomics you can discuss Aspergillus around those iatrogenic fungal meningidites…Doctor_Strange
@phylogenomics And I love the whole story on fungi developing ability to degrade lignin leading to end of coal deposits.Kenneth Bruno
@phylogenomics I posted on FB, will get.Kenneth Bruno
@StrangeSource already on the listJonathan Eisen
Microbe domestication and the identification of the wild genetic stock of lager-brewing yeastAbstract Domestication of plants and animals promoted humanity’s transition from nomadic to sedentary lifestyles, demographic expansion, …
UW-Madison: University Communications: News PhotosPhotographs are available to media organizations and University of Wisconsin-Madison departments for news, editorial and public relations…
PLOS ONE: Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil SpillPLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific stud…
@phylogenomics I’m fond of Scott Strobel’s endophyte course and the discoveries they’re making w undergrads: http://news.yale.edu/2012/10/25/science-magazine-lauds-yale-science-discovery-courseJeramia Ory
Science Magazine lauds Yale science discovery courseAn innovative Yale science course that encourages undergraduates to discover and study plant-associated organisms has been recognized by …
@KSBruno9 heh – that is by @dr_bik … post doc in my lab …Jonathan Eisen
@phylogenomics @Dr_Bik cool, thought it was a great story. I’m from Louisiana so it was all close to home for me.Kenneth Bruno
@phylogenomics Hey, thank you! My students get taught (not by me) that bacteria are simple, don’t have cytoskeletons, no compartments, etc.Mark O. Martin
@phylogenomics @Dr_Bik Not to say that such a huge shift is necessarily a good thing…Kenneth Bruno
Biodiversity of FungiBiodiversity of Fungi is essential for anyone collecting and/or monitoring any fungi. Fascinating and beautiful, fungi are vital componen…
@phylogenomics Other thing that comes to mind is huge trend toward genome mining for secondary metabolites. Chemistry and genetics.Kenneth Bruno
World’s unique battle -Powerful Arthobortrys fungal adhesive employed to capture soil nematodenandkamat
World’s First video on soil nematode trapped by Drechslerella anchonia mycoadhesivenandkamat
@phylogenomics the responses u r getting is why twitter is cool now will spend part of today reading bout cool fungal researchSponch
May show this video by Louie Schwartzberg on fungi for #UCDavis class this week http://www.youtube.com/watch?v=EDkR2HIlEbc&feature=plcp (although will probably use w/o sound)Jonathan Eisen
Fantastic Fungi: The Forbidden Fruitlouieschwartzberg
@Sponch2 ain’t that the truthJonathan Eisen
@phylogenomics Here is a paleontological fungal/liverwort controversy! http://rlebling.blogspot.com/2012/06/when-funguses-ruled-earth.htmlMark O. Martin
A Strange Manuscript: When Giant Funguses Ruled the EarthAbout 400 million years ago, during the Devonian period, the world was a very strange place. Green plant life had begun to cover the land…
@phylogenomics Not totally fungal, but horizontal transfer of carotenoid production from fungi to aphids is cool. http://www.ncbi.nlm.nih.gov/pubmed/20431015jashapiro
Lateral transfer of genes from fungi underlies carot… [Science. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
@jashapiro already on my list to cover .. I taught about this last few years …Jonathan Eisen
@phylogenomics Great story for a diversity course…jashapiro
Fermentation Guru Seeks Out New (and Old) Flavors”Oh, this is nice kimchi,” he said on a summer afternoon at Momofuku Noodle Bar, using chopsticks to pull crimson-coated knuckles of Napa…
@DrLabRatOry @phylogenomics I know the TAs of the class. Could get you in touch for skyping them in or send you pics from the field tripsDenina Hospodsky
Natural Products Version 2.0: Connecting Genes to Molecules – Journal of the American Chemical Society (ACS Publications)Abstract Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, b…
Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms : Abstract : Nature Reviews MicrobiologyOne of the most promising applications of synthetic biology is the biosynthesis of new drugs from secondary metabolites. Here, we survey …
Fasebook Discussion after I asked for suggestions …
Prepping 3 lectures… | FacebookJonathan Eisen wrote: Prepping 3 lectures on Fungal Diversity… Join Facebook to connect with Jonathan Eisen and others you may know.
I would go for toe jam–that’s always popular.Amy Propps
well, I already talked about fecal transplants a few weeks ago … I think I am going to avoid the gross/semi gross this timeJonathan Eisen
Other than the contaminated steroids?Joanne Manaster
Ooo, that’s a good one!Amy Propps
New Ancient Fungus Finding Suggests World’s Forests Were Wiped Out In Global CatastropheTiny organisms that covered the planet more than 250 million years ago appear to be a species of ancient fungus that thrived in dead wood…
Joanne – will cover the steroids w/o a doubt .. but I want MORE …Jonathan Eisen
Tut Shares Tomb with Former Fungi: Scientific American PodcastBrown stains on the walls of Tut’s tomb are fungal mats, indicating a hurried burial. Cynthia Graber reports The tomb of King Tutenkhamen…
A lot of news coming out of the UK just now about threat to ash trees from Chalara: http://www.bbc.co.uk/news/science-environment-20128172.Neil Saunders
ooh – King Tut fungus ..Jonathan Eisen
Chalara ash dieback outbreak: Q&AThe recent confirmed cases of Chalara ash dieback means it has become the latest threat to UK trees. Within the UK’s woodlands, ash is th…
That article looks like a stub, don’t know if there’s more to it.Amy Propps
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen – Olson – 2012 – New Phytologist – Wiley Online Library
It’s hard to go past the Cordyceps “zombie fungus” 🙂 Video – http://www.youtube.com/watch?v=XuKjBIBBAL8 and article – http://www.wired.com/wiredscience/2011/03/zombifying-ant-fungus/.Neil Saunders
4 New Species of Zombifying Ant Fungus Found | Wired Science | Wired.comSee Also: Citation: “Hidden diversity behind the Zombie-Ant fungus Ophiocordyceps unilateralis: Four new species described from Carpenter…
Cordyceps: attack of the killer fungi – Planet Earth Attenborough BBC wildlifebbcworldwide
Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food MicrobiologistsSummary: Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their d…
I think mimicry examples are cool – fungus making a pheremone http://www.pnas.org/content/104/20/8374; Gibberellin, a plant hormone, is also produced by fusarium http://www.plant-hormones.info/gibberellins.htm; Carrion smelling fungi attract flies to spread spores http://www.mapoflife.org/topics/topic_422_Mimicry-in-fungi/;Jason Stajich
Multitrophic interaction facilitates parasite-host relationship between an invasive beetle and the honey beeInternational Centre of Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya; ‡Institute of Food and Agricultural Sciences…
Plant Hormones GibberellinsGibberellins are diterpenes synthesized from acetyl CoA via the mevalonic acid pathway. They all have either 19 or 20 carbon units groupe…
“Mimicry in fungi” : Map of LifeMost of us are familiar with fungi in the form of mushrooms, some of which are brightly coloured and not likely to be mistaken for anythi…
Fungus + Virus = heat tolerance for thermophilic grasses http://www.ncbi.nlm.nih.gov/pubmed/12446900 and http://www.sciencemag.org/content/315/5811/513Jason Stajich
Thermotolerance generated by plant/fungal symbiosis. [Science. 2002] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal ToleranceA mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures. …
It’s not new, but there’s a lot of good population biology/epidemiology on sudden oak death (Phytophthera ramorum)–especially the function of landscaping plants as vectors.If you want to use human health as a hook, you can’t go wrong with fungal sec…See MoreKen Callicott
Ken – phytophtera is not a fungus though …Jonathan Eisen
That’s right! I keep forgetting that work that showed them completely unrelated (well, you know what I mean) to the actual fungi–the curse of spending too much time around people who refer to them as water molds.Ken Callicott
look this video Jonathan Eisen….it’s amazing.. http://www.youtube.com/watch?v=Pq1x5V2-3w0Felipe Gainza Cortes
BBC Planet Earth Cordyceps Fungus Finding of the holy mushroom – Diknek lorrie’sdnlscratcher
The deadly chytrid fungus: a story of an emergin… [PLoS Pathog. 2010] – PubMed – NCBIPubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citation…
underwater fruiting Psathyrella in Oregon discoved 3 years ago: http://2pat.files.wordpress.com/2011/05/underwater-mushroom-oregon.jpgDamon Tighe
WordPress
From a business side of things: 1) Using Oyster mushrooms to treat terrestial oil spills 2) BTTR in Emeryville that uses the left over coffee grounds to produce oyster mushrooms from whole foods etc 3) Eben Bayer’s TED talk on using mycellium to make packaging materials 4) Staments TED talk…fungus as pesticide replacement. 5) Cordyceps sinensis – Asia’s viagra, easily one of the most expensive mushrooms in the world and the hunt for them is causing major environmental problems in India the past summers.Damon Tighe
Eben Bayer: Are mushrooms the new plastic? | Video on TED.comTED Talks Product designer Eben Bayer reveals his recipe for a new, fungus- based packaging material that protects fragile stuff like fu…
Paul Stamets: 6 ways mushrooms can save the world | Video on TED.comTED
John Taylor’s recent reverse ecology study of NeurosporaMatthew Kane
Cambridge librarian finds forgotten fungus Charles Darwin brought back on the Beagle (and it was still wrapped in his newspaper)Fungi and seaweed collected by Charles Darwin on the Beagle Voyage has been uncovered wrapped in newspaper in a Cambridge University libr…
Also James Scott’s work on the angel’s share fungus http://www.wired.com/magazine/2011/05/ff_angelsshare/ and for the future lawyers in the room, what happens when fungal growth can be attributed to the distillers and thus they can be sued for this as …See MoreJason Stajich
The Mystery of the Canadian Whiskey Fungus | Wired Magazine | Wired.comThe air outside a distillery warehouse smells like witch hazel and spices, with notes of candied fruit and vanilla-warm and tangy- mellow…
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Quick post: nice microbial genomes database: MGBD (hat tip to Google Scholar Updates)

Just discovered this paper: MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.  Seems to be a useful microbial genomes database with some nice associated tools.  Among the potentially useful features:

General Ortholog Table
Select your own organisms for a Custom Ortholog Table
Add your own genome in My MBGD Mode

And more.  Anyway – worth checking out.

I note – I found out about this via Google Scholar Updates:

For more on Scholar Updates see here.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

You win some, you lose some

Our project is starting to pick up! After our initial sampling/sequencing period, we realized that there is actual DNA we can work with from the tanks. This past week, we started our actual sample collecting from the tropical tank. We collected 3 sets of samples from the sediment, walls, and water. Throughout the week, we extracted the DNA and ran PCR on all 9 samples (plus one negative control). Today, we completed the gel electrophoresis and got some unpleasant results. Unfortunately, we couldn’t see the primer bands and the DNA bands didn’t show up like we thought they would. This means something went wrong in our PCR, but we don’t know if it was during PCR16SA or PCR16SB. Well, it’s back to the drawing board! Starting next week, we will be re-running the PCR on the 9 samples and possible collecting more samples from other tanks.

Although this week’s results were a bust, we know that there is definitely some DNA present that we can work with. I’m sure we’ll be finding some pretty cool things as we continue sampling and sequencing. 🙂