bio optics and synthetic bio

Utrecht, 27 May 2016

e-super-coli

The antibiotic resistance factor MCR, which protects bacteria against the final remaining drugs of last resort, has been found in the United States for the first time—in a person, and separately, in a stored sample taken from a slaughtered pig.

Department of Defense researchers disclosed Thursday in a report placed online by the journal Antimicrobial Agents and Chemotherapy that a 49-year-old woman who sought medical care at a military-associated clinic in Pennsylvania last month, with what seemed to be a urinary tract infection, was carrying a strain of E. coli resistant to a wide range of drugs. That turned out to be because the organism carried 15 different genes conferring antibiotic resistance, clustered on two “mobile elements” that can move easily among bacteria. One element included the new, dreaded gene mcr-1.

more:

http://phenomena.nationalgeographic.com/2016/05/26/colistin-r-9/

Basic skills in the lab - the fine art of pipetting

Those of us doing molecular biology wetwork in the lab are as much connected to pipettes as most of the general public are to mobile phones.

As any precision instrument, pipettors and tips must be handled gently and with care, of course paying attention to sterility.  Experienced biohackers who should know better often use improper techniques that cause one to cringe.  

There are basic pipette skills which are essential to learn, but it doesn't end there, it is really an art.

So in this post I'm putting in a few links to learning the fine art of pipetting, from the basics to more advanced techniques.  Please add any links or pipetting stories you may have to share.  

First, there is an advanced level webinar on May 31, 2016 

Protect your Cells with Proper Pipetting - How liquid handling influences your cell culture work

also an archived webinar:

The Tip of the Iceberg – How Pipette Tips Influence Assay Results

For the basics, there are a number of good videos

We get a lot of used pipettors, What needs to be done to make sure that they are accurate?  Calibration.

serial dilution - multi-channel

Happy pipetting, brothers and sisters!

Improving HIS tagged protein purification results

For those who missed this informative webinar by Marianne Carlsson:

Tips for successful purification of his-tagged proteins, it is temporarily archived here

If you have any other tips from your own experience with purification of HIS tagged protein, please share them here.

can the entire human genome be synthesized?

...and inserted into a cell?

http://singularityhub.com/2016/05/22/is-the-world-ready-for-synthetic-life-scientists-plan-to-create-whole-genomes/

Free equipment today for biology teachers in SF Bay Area

Yesterday found a group of volunteers and myself setting up for today's event at the Bio-Link Depot in San Francisco, California.
There are tons of donated equipment and supplies available to educational institutions and science teachers.  The event runs from 10AM to 2PM.
http://us8.campaign-archive2.com/?u=78845e8a22189da7ed05a14f0&id=92335dfee8
I learned about a new group, the Chemical Exchange Network, The purpose of the Chemical Exchange Network is to facilitate the informal exchange of laboratory chemicals and information used in teaching biotechnology, biochemistry, chemistry, physics, and general science.

There is a link to it on the Bio-Link Page:
http://us8.campaign-archive2.com/?u=78845e8a22189da7ed05a14f0&id=92335dfee8

languages for bioinformatics

So my bioinformatician friends tell me that the two main computer languages they learn are Python and R.  If you are doing bioinformatics, which language do you use most and why?  For those of you who wish to learn, here are links for courses on  

1. Python
2. R





(The missing link for Learn the R statistical programming language has been fixed now)

Zika Virus - $10,000 challenge grant on experiment.com

Experiment.com is a crowdsourcing website.  12 research projects are competing to get the most backers for Zika Virus research.  The one that wins gets an additional 10k USD.  This was to be awarded April 27, does anyone know which project won? 

https://experiment.com/grants/zika-virus

Nenufar Molecules for Life is now submitting a project to experiment.com.  It is our project to express a peptide from a synthetic gene that we think may show anti-viral properties.  We don't know if it will be effective against Zika virus (or any virus).  Our experiment is to see if we can express the peptide and purify it,  if we can do that consistently, then it can be evaluated - but that is a separate set of experiments. 

We shall have some news on this project soon and will be looking for backers.

Tips for successful purification of his-tagged proteins

Tips for successful purification of his-tagged proteins webinar May 18th.

Update: archived here

PDF (presentation graphics)

If anyone is working with IMAC and would like to share a few tips or experiences of their own (what worked and what didn't) here on the blog, please fee free to share.

Animal model of in utero transmission of Zika virus

Two mouse models of Zika virus infection in pregnancy have been developed by a team of researchers at Washington University School of Medicine in St. Louis. In them, the virus migrated from the pregnant mouse’s bloodstream into the placenta, where it multiplied, then spread into the fetal circulation and infected the brains of the developing pups.

The models provide a basis to develop vaccines and treatments, and to study the biology of Zika virus infection in pregnancy.

more here:

http://www.laboratoryequipment.com/news/2016/05/mouse-models-show-how-fetuses-become-infected-zika

New Study Shows HIV Structure in Unprecedented Detail

http://www.dddmag.com/news/2016/03/new-study-shows-hiv-structure-unprecedented-detail
http://www.infectioncontroltoday.com/news/2016/05/nihled-team-discovers-new-hiv-vaccine-target.aspx

Research on antibodies for vaccine 

genetics and genomics virtual conference

May 11-12, 2016 

http://labroots.com/virtual-event/genetics-genomics-2016

healing with light part 02

This is basic information on optogenetics with animation:

2008 lecture by one of the pioneers in the field, Professor Karl Deisseroth:

Professor Deisseroth goes a little deeper into it in 2015 with recent research:

and a paper:

Targeting Neural Circuits

A course on the Ebola Virus

Here's an Emory University online course: 

Ebola Virus Disease: An Evolving Epidemic