Ebola Vaccine proves effective against Zaire strain

Usually most of the daily news is bad but today we woke up to very good news.  rVSV-ZEBOV, a recombinant, replication competent vesicular stomatitis virus-based candidate vaccine expressing a surface glycoprotein of Zaire Ebolavirus has completed phase 1 human trials in Guinea, West Africa.  Vaccine efficacy was 100%  Fast track this one please (Merck has 300,000 doses ready in case of an outbreak).  We are highly impressed by this work and hope it will serve as a model for the future of rapid drug development and deployment in response to emerging epidemics.   

http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)32621-6/fulltext

blog of interest

With final exams looming large I am not updating this blog too much right now -  I recommend checking out Jean Peccoud's blog here. I'll be back😸.

Women Scientists speak out against ignorance in high places

https://500womenscientists.org/#our-pledge

It came from outer space

https://arxiv.org/pdf/1611.07516v1.pdf

CRISPR-cas9 gene editing vs metastatic non-small-cell lung cancer

Yes, in humans.  

http://www.nature.com/news/crispr-gene-editing-tested-in-a-person-for-the-first-time-1.20988

If successful, this could be a major development in a model of therapy for curing many diseases.

San Francisco Bay Area teachers - free equipment and supplies 4 U

This Saturday

http://biolinkdepot.org/index.php/get-supplies/open-house-dates/

Collaboration with Microbes

Collaboration with Microbes Nov 5, 2016 9:30 AM West Coast time.

This full-day conference will explore fermented food and drink, our microbial commons, how fermentation might heal our planet, and microbes that could heal our body.

Tickets to attend 

DG717 Coworking / Incubation Center

717 Market Street

Suite 100

San Francisco, CA 94103

Stream it here

Blurry bands in gels?

This is a brilliant and simple fix to the problem of blurry bands we generally see in electrophoresis phosphorimager cassette images. The method uses foam-core which may be purchased inexpensively at an art supply store.  It produces higher resolution bands.  

http://rnajournal.cshlp.org/content/early/2016/10/19/rna.059303.116.full.pdf+html  

Thunderous applause to the team at Penn State.

CRISPER - Cas9 handbook

Genescript recently published "CRISPR Handbook: Enabling Genome Editing and Transforming Life Science Research" and they are making it available for free here.

Biohackers take on the insulin shortage

Podcast with Anthony Di Franco 

here



Interested?  Consider joining us online or at Counter Culture Labs in Oakland, CA USA

fiat lux

Let there be light. 

It has been said various places that light is the origin of life. 

But what is the nature of this light? 

In October 2016, astronomers reported that the very basic chemical ingredients of life—the carbon-hydrogen molecule (CH, or methylidyne radical), the carbon-hydrogen positive ion (CH+) and the carbon ion (C+)—are the result, in large part, of ultraviolet light from stars, rather than in other ways, such as the result of turbulent events related to supernovae and young stars, as thought earlier. (source wikipedia)

So - let there be Black Light, sisters and brothers...

http://www.jpl.nasa.gov/news/news.php?feature=6645

Congratulations Dr. Yoshinoi Ohsumi

BABEC Kickoff 2016 on video

For those who were not able to attend BABEC Kickoff 2016, here are videos of the speakers.  Thanks to BABEC (the acronym means Bay Area Biotechnology Education Consortium) and to the videographer, Daniel Michael of Biolink Depot, a man of many talents. Daniel also conducted the interview with biohacker Mary Ward, for this blog.  

Two women, one man and a baby

Biohack the Planet

Meet Josiah Zaynor and many more biohackers right now - this weekend at Counter Culture Labs 

4799 Shattuck

                                                           Oakland CA 94114

schedule

Meanwhile in Stockholm - human gene editing progresses

Any questions?  Email Dr Lanner here

More

and more

powerful antiviral lectin meets computer game

Soooo creative....

http://www.nature.com/ncomms/2016/160916/ncomms12549/full/ncomms12549.html


http://www.nature.com/ncomms/2016/160916/ncomms12549/extref/ncomms12549-s2.mov

Biohack the Planet Conference this weekend

Three Day Biohacking event this weekend in Oakland, CA, USA.

http://biohacktheplanet.com/speakers/


tickets

Lab equipment and supplies alert for teachers in the SF Bay area

Saturday, September 17th from 10 AM to 2 PM

Free Lab equipment and supplies  for your school.   

at 

Bldg 928
Clearwater Drive
CCSF / Bio-Link Depot
San Francisco International Airport
South San Francisco, CA 94128
(650) 821-0112

Here is where you will learn how to get supplies from the Depot. Here are the steps:

Step #1: Sign-up & Register —->>> HERE

Step #2: Check our newsletter or site for Open House Dates. We have 4-6 open houses per year.

Step #3: Come to the Depot Open House and bring your school ID. (Prepare to volunteer: Setup- 30 minutes, breakdown 30 minutes). Shop for supplies, fill out a form listing your items and check out will all your free stuff!

(Extra Credit) Volunteer for accepting deliveries and Pre-Setup day.

Evotution before our eyes

http://www.bbc.com/earth/story/20160913-bacteria-evolve-resistance-to-antibiotics-in-just-11-days

Open source insulin project - come see us tonight.

The open source insulin project, ongoing at SF Bay Area biohacker spaces Counter Culture Labs and BioCurious Labs will have team members at California Academy of Sciences Nightlife 6 pm tonight 9-8-16.  I hope to meet some of you there...ask around for Eddy.

1665 - It was Yersinia pestis killed one out of every four people in London

otherwise know as bubonic plague...


http://www.bbc.com/news/science-environment-37287715

Gilson guide to pipetting

I put a few videos on pipetting technique here and today I found a nice pdf guide so sharing this as well:
http://www.gilson.com/Resources/Gilson%20Guide%20To%20Pipetting%20Third%20Edition.pdf

SF Bay Area: Jason Peters from UCSF to talk about CRISPR

Saturday, September 10, 2016 from 9:00 AM to 3:00 PM (PDT)
Skyline College - 3300 College Drive, Building 6 2nd floor, San Bruno, CA 94066
Would you like a free ticket?  
go here
Would you like to ride pool from Oakland? message me.

Meanwhile on Mars

http://www.chromatographytoday.com/news/gc-ms/46/breaking_news/if_there_is_no_life_on_mars_blame_the_meteorites._chromatography_investigates/40128/

MOF: metal-organic frameworks enable seeing molecular bonds in 3D

An interesting development at Prof. Omar M. Yaghi's lab at UCB:

http://newscenter.lbl.gov/2016/08/18/new-way-display-3-d-structure-molecules/

CRISPR cas-9 (More than 2 million people watched this)

CRSPR - Cas9 alternative Argonaute

Anyone working with Argonaute?  Results?  Pass or fail?



http://blog.addgene.org/comparing-cas9-to-ngago-can-the-argonautes-best-crispr

CRISPR Cas-9 in this month's National Geographic

Since the 1800's, National Geographic has been continually opening up the exploration of the universe to share with us. Here's a basic but interesting article on CRISPR Cas-9 and how it is changing our world.  


http://www.nationalgeographic.com/magazine/2016/08/dna-crispr-gene-editing-science-ethics/

Zika Virus vaccine

New vaccine proves effective in preventing Brazilian strain of Zika Virus in animal tests. 

http://www.nature.com/nature/journal/vaap/ncurrent/pdf/nature18952.pdf

Meet Dr. Chip, who will now run a few diagnostics

IBM Nanobiotechnology team's results show size-based separation of bioparticles down to 20 nanometers (nm) in diameter, a scale that gives access to important particles such as DNA, viruses and exosomes

read more here

What's going on at Indie Bio

IndieBio is a biotech startup accelerator.

https://www.youtube.com/channel/UC0FFccwm1wbmYtKfX6HDncw

CRISPR: An enzyme taken from Leptotrichia shahii can bind to and cut ss messenger RNA.

A new version of the gene-editing tool CRISPR can target and cut RNA

also see:

http://www.the-scientist.com/?articles.view/articleNo/46234/title/RNA-Targeting-CRISPR/

and

http://www.the-scientist.com/?articles.view/articleNo/45354/title/Dial-It-Up--Dial-It-Down/

Introduction to Biohacking series, Oakland, CA.

I recommend this to anyone in the SF Bay Area interested in learning the basics and getting hands on lab training.    

Counter Culture Labs, at the Omni Commons

4799 Shattuck Avenue, Oakland, CA 

Learn the basics of genetic engineering in this free class series! Programming and genetic engineering are coming closer together as fields. Learn enough to 'program' life itself. 

This class is designed for beginners. Within a few weeks, get into the lab, start doing science and gain all the basic terminology you need to join a community biology project.

This series of classes is strongly recommended for anyone who wants to learn how to work independently in the wetlab. There will be 5 lecture classes on Monday evenings, and 4 lab sessions on Sunday mornings, starting July 31.

What is Biohacking? Gain an introduction to this exciting new movement! Then learn about the molecules of life and how they are made.

$5 Suggested donation. No one turned away for lack of funds.

Transformation

Molecule controls infection by variety of RNA viruses

There are basically 2 parts to the immune system, innate immunity and  adaptive immunity (these may overlap).   Innate immunity refers to nonspecific defense mechanisms that come into play immediately or within hours of an antigen's appearance in the body. These mechanisms include physical barriers such as skin, chemicals in the blood, and immune system cells that attack foreign cells in the body. The innate immune response is activated by chemical properties of the antigen.
RIG-1 (Retinioic Acid Inducible Gene-1) is found in human cells.  It functions to recognize viral pathogens by their molecular patterns and like the legendary Paul Revere, gallops down signalling patways to alert and set in motion the expression of innate immune response genes.  When the transcription factor IRF3 is alerted it leaps into action and a coalition of molecules (i.e.type 1 interferon) are expressed to control the invading virus.  

So it is July, please excuse my red, white and blue interpretation,  but I think this is an important study in the development of the new generation of broad spectrum antiviral drugs.  In vitro experiments indicate compounds activating IRF3 showed activity against  West Nile virus, dengue virus and hepatitis C virus (Flaviviridae), Ebola virus, influenza A virus, Lassa virus, respiratory syncytial virus, Nipah virus (Filoviridae). Has anyone out there tested this with zika virus - also of the family Flaviviridae?  

Here is a link to the abstract and paper 

Excerpt from protocol/labnotes

Excerpt from the protocol:

Nenufar – antiviral research project 01 – Expression and purification of peptide LBOUNCER from the synthetic  gene VRBNCR-01 inserted into an e-coli plasmid vector, transformed and induced to grow on bacteria.  Explore how to do this in a fast and consistent way with the highest purity.

Experiment 01A:

DNA synthesis of the VRBNCR-01 gene which is inserted into a pET15 expression plasmid with a His 6 tag on the N-Terminus followed by a thrombin cleavage site.  The gene will be cloned into pET15b via NdeI and BamHI. We will use heat transform into competent cells, then plate out on Amp-agar to grow colonies.  Induce for expression.

Then on to Experiment 01B: purification using chromatography and SDS page

I contacted a lab in the San Francisco Bay Area where we can work.  All in all, we are going to do a lot of improvising so we can stretch the budget and work for at least 6 months on the experiment. Everyone is volunteering their time. We have wonderful mentors and we are learning by doing, the biohacker way.  It is always a steep learning curve as anyone who has worked in molecular biology knows.  The journey of discovery makes it worthwhile.  Thanks to all of you who are making this possible.

making drugs with bugs

x-ray crystallography

https://www.youtube.com/playlist?list=PLd1rN-a2xi4RHs3yY_XEbLpKz8JsPz-9F

CRISPR-Cas9 gets approved for human trials

NIH meetings held the last couple of days gave a go for the first human trials to learn how safe using the technology in humans will be.

http://www.scientificamerican.com/article/first-crispr-human-clinical-trial-gets-a-green-light-from-the-u-s/

Interview with a Biohacker

Daniel Michael, operations manager at Bio-Link Depot interviews Mary Ward, co-founder of Counter Culture Labs.   Watch Mary launch her mRNA assay experiment from Oakland, California together with an international biohacking team - into outer space!

Interview with a Biohacker

Synopsis of Project

more on bacteria in space

 Nenufar Molecules for Life now has only 22 more days to reach our goal of raising the funding to do our experiment.  So far we have 5% of our funding in place, thank you all who contributed! Please take a look at our experiment and support our project with a pledge for a donation of any amount. This is what crowdfunded science looks like: 

http://experiment.com/anti-viral

Free Equipment and Supplies for science teachers in SF Bay Area

Tomorrow, Saturday June 18 at Merritt College in Oakland, Biolink Depot will give away science equipment, furniture and supplies to school teachers.  To sign up for the event, go here.  Much that is strange and retro can be found here, and things to fill in the missing gaps in any school science lab.  

NIH announces meeting about the first-in-human use of gene editing via CRISPR/Cas9 technology

The recombinant DNA Advisory committee is holding a meeting on June 21-22 2016 on CRISPR/Cas 9 use in humans with a T cell immunotherapy protocol that involves the use of CRISPR/Cas9 to edit two genes in T cells also modified to express T cell receptors targeting myeloma, melanoma, and sarcoma tumor cells.  The meeting is open to the public or can be attended remotely by the webcast link here on the days of the meeting.  More info here  

We have less than 30 days to go to raise our goal for our proposed experiment, please support our project with a donation and/or pass the word.

http://experiment.com/anti-viral

programming language for living cells

MIT biological engineers have created a programming language that allows them to rapidly design complex, DNA-encoded circuits that give new functions to living cells.

Using this language, anyone can write a program for the function they want, such as detecting and responding to certain environmental conditions. They can then generate a DNA sequence that will achieve it.

more...

A new method for use in pathogen identification

The method uses magnetic beads coated with Fc-mannose-binding lectin to isolate pathogens from fluid or tissue samples.

news 

http://wyss.harvard.edu/viewpressrelease/267

and the paper here:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156287#abstract0

LIGO detects gravitational waves

Lab management

I found a service that looks useful for anyone running a lab, is anyone using Quartzy? 

https://www.quartzy.com/

Nenufar's founder makes shocking confession

Put “biohacking definition” into google search and what comes up?

bi·o·hack·ing

ˈbīōhakiNG/

noun

1. the activity of exploiting genetic material experimentally without regard to accepted ethical standards, or for criminal purposes.

To be clear, I’m a biohacker.  

To some scientists, biohacker is a bad word. Shoddy, dangerous experiments in makeshift labs by relatively untrained people with more enthusiasm than academic training producing unverified results, and more like accusations assail us.  According to the definition above, biohackers are suspicious characters, perhaps some shadowy gang of unethical thugs.  Is this definition actually supported by facts?   Is the world really in danger of bizarre bio-organisms being created in biohacker labs and getting loose in the world to raise havoc?

Or - is biohacking rather an entry point to science, open to anyone who has the will to learn the theory and practice of biology and to put it into practice by developing practical applications?  What role if any does biohacking play in the advancement and evolution of science and technology?  Are biohackers any more or less ethical than scientists working in corporate environments?  If you are a scientist, researcher, biohacker, or just watching from the sidelines, what is your opinion of the biohacking movement?   Are you a biohacker? 

actual photos taken in a biohacking lab

molecular biology - DNA replication and repair

One of the better things about living in the 21st century - MOOCs!

MIT MOOC starting June 7 for 8 weeks. it's an advanced level course, and it is free to take the course.  

Climb on board here

big list of Zika Virus resources

http://www.cidrap.umn.edu/infectious-disease-topics/zika#literature

molecular biology lab tutorials

Here's some nice molecular biology lab tutorials and protocols from our friends at the-odin.com

How does the immune system responds to Ebola Virus?

Four Ebola patients received care at Emory University Hospital, presenting a unique opportunity to examine the cellular immune responses during acute Ebola virus infection. We found striking activation of both B and T cells in all four patients. Plasmablast frequencies were 10–50% of B cells, compared with less than 1% in healthy individuals. Many of these proliferating plasmablasts were IgG-positive, and this finding coincided with the presence of Ebola virus-specific IgG in the serum. Activated CD4 T cells ranged from 5 to 30%, compared with 1–2% in healthy controls. The most pronounced responses were seen in CD8 T cells, with over 50% of the CD8 T cells expressing markers of activation and proliferation. Taken together, these results suggest that all four patients developed robust immune responses during the acute phase of Ebola virus infection, a finding that would not have been predicted based on our current assumptions about the highly immunosuppressive nature of Ebola virus. Also, quite surprisingly, we found sustained immune activation after the virus was cleared from the plasma, observed most strikingly in the persistence of activated CD8 T cells, even 1 mo after the patients’ discharge from the hospital. These results suggest continued antigen stimulation after resolution of the disease. From these convalescent time points, we identified CD4 and CD8 T-cell responses to several Ebola virus proteins, most notably the viral nucleoprotein. Knowledge of the viral proteins targeted by T cells during natural infection should be useful in designing vaccines against Ebola virus.

read the paper here

https://experiment.com/projects/can-we-express-a-synthetic-gene-of-interest-in-bacteria-for-study-as-an-antiviral

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