Citizen Scientists: As Good As Gold

Citizen Scientists: As Good As Gold

Citizen Scientists: As Good As Gold

 
Mycena rosea (Bull.) Gramberg
This beautiful mushroom, the rosy bonnet (Mycena rosea), collected and described by amateur mycologist Giovanni Robich, is vouchered in the herbarium of the Museum of Natural History of Venice, Italy. In fact, the entire herbarium is curated by expert volunteers. UC Berkeley, NCBI, and CBS researchers have sequenced a DNA barcode for most species in the museum and have devised an approach to test the validity of the taxonomy curated by volunteers, showing these volunteers perform as academic researchers.

Read the Full Article at Live Science Op-Ed & Insights
Main Article
Barcoding the Venice Herbarium Collection
Barcoding

SOD in the Montesclaros Declaration

SOD in the Montesclaros Declaration

SOD in the Montesclaros Declaration
SOD Section
Complete Montesclaros Declaration
Complete Montesclaros Declaration

 

Prepared by a group of more than 70 forest pathologists (representing 17 nations) that attended an international IUFRO meeting held at the Montesclaros Monastery in Cantabria, Spain during May 23th – 27th, 2011.As scientists studying diseases of forest trees, we recognize that the international trade of plant material is increasing the risks to forest health worldwide. The evidence for this view is based on the recent, unprecedented rise in numbers of alien pathogens and pests emerging in natural and planted forest ecosystems in all parts of the globe. We thus propose a phasing out of all trade in plants and plant products determined to be of high risk to forested ecosystems but low overall economic benefit.We regard all international trade in containerized ornamental plant seedlings and trees intended as plants for instant landscape planting as low benefit in terms of overall economy but high risk to forest health. For instance, production of seedlings in low cost localities for outplanting in different and distant environments provides only a marginal net economic benefit to the whole area, but provides an efficient pathway for pathogen and pest dispersal. In addition, international trade in other plant materials (e.g., wood packaging, wood chips, etc.) should be scrutinized and more strictly regulated.

Link to Website

Rainin’s Adjustable Spacer Pippette Unboxing

Ingrid the intern unboxes the EA-8 1200 XLS adjustable spacer E4 XLS multichannel pipette.

pipetstillforwp1v3

pipetstillforwp3Multichannels are a huge time saver for any plate based assay; adjustable width multichannel pipettes are a levolution up. Yes, it’s a word DICE made up for BF4, but it describes the game changeyness of this pipette so we’re all just going to have to live with it. Turning the knob on the side of the pipet head rotates an internal cylindrical gear that changes the spacing between the tips. We know because we had Ingrid take it apart.

Being able to change the distance between the tips may not seem like a thing, until you have to individually pipet from a couple of hundred 1.5ml tubes into PCR plates or go from 24 well TC plates to 96 well assays. The adjustable width multichannel knocks them out 8 at a time. Also, have you ever noticed that the spacing of the teeth in your gel combs is just a couple mm off from a standard PCR plate? Not so much of a problem anymore.

pipetstillforwp2There are a lot more adjustments on the electronic version than any one person will probably ever need: liquid volume, separate aspirate and dispense speeds, mixing cycles, multi-dispense, reverse pipetting (no one in our lab knew what that one is but it’s gotta matter to somebody), dilution, titrations, and about a hundred other things that are configurable in the settings.

The battery life is OK; you should be able to go about a 10hr working day on one charge. Also these newer gen XLS pipettes have better ergonomics, which really matters if you are using it every day. The tip eject even seems to have a lighter touch to it, compared to older multichannels. Experienced pipetmonkeys will probably lean towards the manual models but for things like QC, GMP/GLP, or production the electronic versions could be better.  Link to the operating instructions that Ingrid didn’t read and tossed on the floor (no surprise) and to the manufacturer’s website.

Nursery-Strain of Sudden Oak Death Found in Sierra Nevada.

Nursery-Strain of Sudden Oak Death Found in Sierra Nevada.

A Disease Note in the scientific journal Phytopathology records the first instance of Phytophthora ramorum, the causal agent of Sudden Oak Death, found in the Sierra Nevada foothills of California. The June 2014 article (PDF link) is the first time that the “NA2” lineage of SOD, that is usually only found in commercial nurseries, has been isolated in the wild in California. The host plant that the disease was isolated from was an ornamental rhododendron that had been planted a year earlier. Nursery plants are highly regulated and inspected for SOD in California but this discovery illustrates the need for continued efforts to prevent the spread of SOD to previously uninfected areas.

What’s a Pipetmonkey?

What’s a Pipetmonkey?

Welcome to the Pipet Monkey Blog!

What’s a Pipet Monkey? The term is both playfully derogatory and respectful all at once.

The programming equivalent, Code Monkey, is roughly similar in usage but more demeaning and trivializing, personally. If you’re a non-American English speaker, lackey or maybe dogsbody might ring true. Shoprat was what they were affectionately and divisively called in the great past of the American manufacturing sector.

Pipet Monkeys are the highly skilled workers that, day to day, push the work of laboratory research forward, and in the modern molecular or diagnostic lab they are the pointed-end-of-the-stick of scientific endeavor.

They spend most of their day using this:gilson2

To transfer microliter amounts of liquid between tiny plastic tubes in an endless all day dance.

GIF of Jakki pipetting

They are the postdocs, grad students, undergraduates, and research assistants, who work at the crucible of scientific discovery, the lab bench. They used to be almost exclusively geeky white guys but at the bottom end of the academic food chain that’s changing. It wasn’t too many years ago that the suppliers of laboratory gloves didn’t sell hardly anything but L and XL. Now S, XS, and even XXS are available since, increasingly, the cogs in the machine are young, bright, geeky women. (Most labs are still pretty hurting on diversity, sorry.)

The work is repetitive, demanding, and can be hand-crampingly long. Laboratory protocols have detailed and exacting steps and the slightest inattention to any one of them dooms the results, wastes time and money, and pisses off everybody; including especially the hapless mistake-maker who gets to start again and stay up late tonight to make it right.

Of course the bench work could be handled by pretty much any modern liquid handling robot, of which there are numerous sweet models available; including the Hamilton Vantage line, a favorite for forensics sample processing; a very cool Andrew Alliance anthropomorphic type which we’d so like to unbox and demo (hint, hint sales reps); and the fantastic Tecan Freedom EVO model that nearly maimed me once. To be fair to the Swiss designers, it was kind of my fault for taking off some of the safety guards that clearly said, “Nicht Entfernen” on them.

Some days laboratory bench work can feel like it’s the reason they invented the digital music player. Why then does anyone spend their day in such a stressful venture?

Because science works. Empirical scientific investigation drives the work of thousands and thousands of new scientific discoveries every year. Biological science, in particular, helps explain your entire existence and you get to be there as it happens every day. Without the Pipet Monkeys there would be no understanding of DNA, diagnostic medicine, or affective drug therapies.

The Pipet Monkeys may not always get their name on the publication and you might not be introduced to them as you come through the lab door but they are always there. This is our blog of all things science, large and small.

pm4

So, dance Pipet Monkey, dance. . . .