Category Archives: Science News

Black Forest Summer School on Bioinformatics for Molecular Biologists, September 2013


Here’s another course for the summer aimed at PhD students and early career molecular biologists on mastering the use of pre-existing bioinformatics tools.  The venue sounds amazing and it looks like the perfect place to learn or hone your existing bioinformatics skills.  Francis Martin will be giving the keynote lecture so there is more incentive to attend!

Summer Bioinformatics Workshop Roundup Part Two

Metagenomics: From The Bench To Data Analysis, Heidelberg, Germany, April 14th to April 20th, 2013

EMBO course header

Joint EU-US Training in Marine Bioinformatics, Newark, Delaware, USA, June 16th to June 29th, 2013

EU-US Course Header

Summer Bioinformatics Workshop Roundup Part One

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

course one

Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013

course two

Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013

course three

The Many Stages Of Manuscript Writing

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.

Fungi: Pennsylvania’s Hidden Treasures

The following short documentary film (world cat link) was produced by Pennsylvania’s Wild Resource Conservation Program and Commonwealth Media Services to highlight the role and social impacts that forest fungi have in the state of Pennsylvania.  Since I’m located here and have some friends in the video, I thought I make it available to you for your viewing pleasure.

Fungal Meningitis Outbreak

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:

CDC fungal infections page

CDC information on fungal meningitis

CDC page on the current fungal meningitis ourbreak

As of today, October 12th, the number of infections have been reported from numerous states:

Here’s a quick informational video on fungal meningitis:

Here are some links to news articles published over the few weeks:

CDC: Multistate Meningitis Outbreak Investigation

NYT: Interactive Map – Tracking an outbreak

Meningitis: Top 10 Things CDC Says You Should Know

Fungal Meningitis From Injections: Not Even Close To Over

Republicans Grill FDA Chief On Meningitis Outbreak

Despite Antifungal Treatment, More Woes For Some Meningitis Patients

Pharmacy Owners Had No Hand In Meningitis Outbreak: Lawyers

Second Illness Is Infecting Those Struck by Meningitis

Fungal Meningitis: 404 Cases, 29 Deaths

More bacteria, fungi in drugs from Mass pharmacy

Elio Schaechter’s Small Things Considered: Fungal Meningitis

‘Worried Sick’: Meningitis Risk Haunts 14,000

Documents in Meningitis Case Show Complaints in 1999

Meningitis Outbreak: FDA re-releases list of customers

Meningitis Outbreak Spurs Calls To Strengthen FDA

Meningitis spreads to 19th state, sickens 347

PDF of Food & Drug Administration Assessment of Pharmacy Sterility

FDA: Mold seen in 83 vials of the steroid linked to fungal meningitis outbreak

FDA: Meningitis-linked Pharmacy Knew of Bacteria

Records Show Problems at Steroid Pharmacy as Far Back as ’06

Investigators visit office tied to meningitis cases

Steroid shot near spine gives illness an opening

Fungal meningitis outbreak tied to steroid shots isn’t the first, reports show

NBC News – Experts: Many ways for fungi to taint drugs / Four more die in fungal meningitis outbreak

Sterility Found Lacking at Drug Site in Outbreak

FDA warns of further risk from tainted drugs

Meningitis outbreak rises to 205 cases: CDC

Meningitis: 5th case reported in Minnesota, all women

Another death reported in meningitis outbreak

Legal recriminations begin over major U.S. meningitis outbreak

Lawmakers focus on small drugmakers as meningitis death toll rises

Rare fungal meningitis outbreak spreads to six states

Seven deaths reported in growing meningitis outbreak; second fungus found

U.S. meningitis deaths rise, prompting call for tighter drug rules

Meningitis cases raise questions about steroid shots

CDC: 12 more people infected with fungal meningitis linked to Framingham pharmacy

F.D.A. says avoid drugs from company tied to meningitis

When leaf mold gets in your steroid injection

Meningitis outbreak: 13,000 got suspect steroid shots

Epidural steroid shots debated amid meningitis scare

Rare fungal meningitis outbreak rises; 7 dead, 64 sick

Meningitis outbreak kills seven; continues spreading to ninth state

Fungal meningitis: Know the subtle symptoms

More patients linked to fungal meningitis infections, CDC says

Meningitis outbreak 2012: Steroid related fungal meningitis cases rise to 47

Seven deaths reported in growing meningitis outbreak; second fungus found

U.S. fungal meningitis infections rise to 47

CDC: Death toll in rare fungal meningitis outbreak linked to steroid injections rises to 7

Boston: Former regulator calls for more oversight of compounding pharmacies

UPDATE (December 21st, 2012): CDC Recommends Assertive Clinical Evaluation of Potential Fungal Meningitis Patients

UPDATE (December 21st, 2012): Tainted steroids cause spine infections in addition to meningitis; all patients face grueling recovery

UPDATE (January 6th, 2013): Massachusetts governor offers new pharmacy rules

The Reincarnation Of A Tree

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.