The antibody validation nightmare

Ever wondered if that antibody you used throughout your whole PhD was actually also binding to something else than its supposed target protein?

Antibody validation in tissue staining is a very difficult task!

Here is a great step-by-step validation protocol published by EuroMabNet, a network of scientists who try to improve antibody validation.

And this paper gives a useful flow chart for antibody validation.

And here is the 5 pillars of antibody validation paper which explains what can be done to validate antibodies.

 

Know your RRid!

Imagine starting a study about some cool protein.

You find some useful articles on Google Scholar. In one paper, an antibody is mentioned. The name of the company that sold it to the authors is mentioned in the Material and Method but unfortunately that company has closed down or has been swallowed by one of the Pharma giants so you cannot order. Then you realize that the company was not producing any antibodies anyway, they were buying it from another company so there is no way to trace and buy the same antibody. Nightmare…

Then imagine that instead, the paper mentions the RRid number for that antibody. You do not know about what that is but you check and find this paper that explains it all.

Now suddenly, not only you can find on the Scicrunch website which company produces this antibody and which resells it so you can buy it, but you can also search pubmed for the RRid and find all the articles that mention it, opening your eyes to lots of results about your protein that have been published specifically with using that antibody. Now you can also check if the antibody gives consistent results!

And imagine being to do this for your favorite mouse model as well. See all publications that have mentioned your mouse RRId!

But it relies on you writing the RRid of your antibody or mouse in your next publication so think about it! 😀

Transfecting hard-to-transfect cells

Here you can see a nice film of a beating cardiomyocyte.

It was transfected using Fuse-it vesicles full of the mRNA of LifeAct-tagGFP2. According to Ibidi, it also work well with primary cells which are typically difficult to transfect.

RNA-based transfection seems to be gaining speed compared to classical transfections using DNA.

If you try it, leave some comments here to tell us how it worked for you! 🙂

Great video Microcourses about microscopy

Jennifer Watson’s Microcourses channel on You Tube is really recommended to anyone who uses a microscope.

Short targetted videos that will boil down the principles of light microscopy for biologist and help you understand what you are doing.

There are a few series, each of them with a few videos and the collection is constantly growing. Remember to subscribe so you get to know when they post a new one.

Microscopy job in Manchester

Senior Experimental Officer (Bioimaging / Image Analysis) The University of Manchester, UK

The University of Manchester Bioimaging Core Facility is recruiting an image processing/analysis Senior Experimental Officer. This position is initially for 2 years, but with a view to becoming a permanent position. Manchester is a great place to live and work and you’ll be part of a team supporting over 20 microscope systems and 200 PIs. We run a mix of commercial, open source and bespoke software and the successful candidate would be responsible for developing, applying and teaching these tools to the Facility users. You don’t need to be from an academic background, we’d be very keen to recruit someone currently working within the commercial side of image analysis and a PhD is not essential – we’re looking for the right person not the right qualifications.

Due to the demand for advanced image processing and data analysis, a new position has been created to support the users of the Bioimaging Facility in the Faculty of Biology, Medicine and Health.

You will work as part of the Bioimaging team, led by Dr Peter March, but you will be responsible for developing the image processing capabilities of the Facility. Combining both commercial packages and your own bespoke scripted solutions you will provide analysis pipelines to support users who have acquired large multi-dimensional datasets using the Bioimaging Facility microscopes. You will have multiple projects to manage simultaneously and so excellent project management skills are also required.

You will have completed a PhD in science, mathematics, computer science or a relevant discipline, or equivalent experience. A knowledge of cell biology is not essential, but you must have proven experience in developing analysis pipelines and the ability to write custom scripts. Excellent communication and interpersonal skills are also required.

As an equal opportunities employer we welcome applicants from all sections of the community regardless of gender, ethnicity, disability, sexual orientation and transgender status.  All appointments are made on merit.

Please note that we are unable to respond to enquiries, accept CVs or applications from Recruitment Agencies.

Enquiries about the vacancy, shortlisting and interviews:

Name: Dr Peter March

Email: P.March@amcnhester.ac.uk Tel: 0044 161 275 1571 or 0044 7747 118 447

General enquiries:

Email: hrservices@manchester.ac.uk Tel: 0161 275 4499

Technical support:

Email: universityofmanchester@helpmeapply.co.uk Tel: 0161 850 2004

This vacancy will close for applications at midnight on the closing date.

Closing date: 30/01/2020

Salary: £41,526 to £51,034 per annum according to relevant experience.

Employment type: Fixed Term

Department: Biology, Medicine & Health

Hours per week: Full time

Contract Duration: From January 2020 until 31 December 2022 Job reference: BM&H-14959

Fluorophores that blink for STORM without any special buffer

Sounds good! No more buffer that stops working after one hour of imaging!

This company sells SaraFluor650 secondary antibodies. This fluorophore seems to be a natural blinker which does not need to reducing environment. Apparently it doesn’t need very bright lasers either!

Apparently they have also developed a green variant. So you can run 2-colour direct STORM on your favorite TIRF system! 😀

They also sell pH sensors and more so check their website and if you try, write a comment to let us know how things worked!

Microscopy facility job in Hungary

Dear Colleagues!

I would like to draw your attention to the open position at the Hungarian Center of Excellence for Molecular Medicine.

Best wishes,

Jozsef

———————————————————–

Advanced Core Facilities at HCEMM

High-quality molecular medicine-oriented research activities at the Hungarian Center of Excellence for Molecular Medicine (HCEMM) are supported by a matrix of advanced core facilities (ACFs). In the premises of the Hungarian Research Institutions, three ACFs are currently being set-up:

  • Functional Cell Biology and Immunology ACF (University of Szeged)
  • In vivo Imaging ACF (Semmelweis University, Budapest)
  • Single-Cell Omics ACF (Biological Research Center, Szeged)

The Call

The Project Steering Committee of the HCEMM project hereby announces a call for excellent, professional “Heads of Advanced Core Facilities”.

We are searching for Heads for each of the above ACFs who operate, manage, supervise, and develop the respective HCEMM AFC. We seek dynamic and interactive individuals with an excellent professional track record and demonstrated experience and interest in organizing and spearheading the ACF.

HCEMM is an inclusive, equal opportunity employer offering attractive working conditions and benefits appropriate to a molecular medicine research organization. Female candidates are strongly encouraged to apply.

An initial contract of 5 years will be offered to the successful candidates; this is foreseen to be extended to a maximum of 9 years, subject to an external, independent, international review. Successful candidates will receive an attractive remuneration package and an opportunity to recruit two technicians for each ACF. Importantly, the selected ACF Heads will be constantly helped and trained by heads and managers of the state-of-the-art system of Core Facilities at EMBL.

Technical notes

Please visit https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.hcemm.eu&data=02%7C01%7Csylvie.le.guyader%40KI.SE%7C096431407c66429c33c408d77ed8c1e5%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637117341763082188&sdata=AWRzMmDqkw%2B6Qtuctsvw1qmenkmrhiOUEoijTilFKFs%3D&reserved=0 for more details related to HCEMM (Synopsis of HCEMM), to the positions (Description of positions) and to the ACFs (Technical description of the ACFs) as well as the Evaluation process & Criteria.

Applicants should submit a cover letter, a CV, a detailed presentation of the professional experience, and a concise description of research interest and plans, all edited as a single PDF file, to career@hcemm.eu by January 17, 2020. Please also arrange for 3 letters of recommendation to be also emailed to career@hcemm.eu by the same deadline.

József Maléth M.D., Ph.D.

Principal Investigator, Research associate

MTA-SZTE Momentum Epithel Cell Signalling and Secretion Research Group University of Szeged, First Department of Medicine Koranyi alley 8-10, Szeged, H-6720, Hungary

Tel: +36-62-545-201

Cell: +36-70-4166500

E-mail: jozsefmaleth1@gmail.com;

maleth.jozsef@med.u-szeged.hu

Multiplexed immunostaining

It is not easy to find enough antibodies that work together to be able to label a sample with more than 4 antibodies at the same time. And even 4 is pushing it.

This paper describes a new immunostaining multiplexing method called 4i. The method is based on a special imaging buffer that prevents the antibody from being strongly bound to the sample due to the imaging process. This allows the authors to detach the antibody with gentle treatments, leaving the sample in a good shape and ready for another round of labeling and imaging.

Using this method they have successfully labelled the same sample with 40 different primary/secondary of the shelf antibody pairs!

New image analysis training school with Neubias

NEUBIAS, the Network of European BioImage Analysts, is delighted to announce two new Training Schools on BioImage Analysis:

TS14 for Early Career Investigators (Life Scientists: PhD candidates, Postdocs, Staff, …):

This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for “Work on Your Own Data” sessions assisted by experienced Analysts.

TS15 for BioImage Analysts (advanced level):

This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, at the same time as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.

The schools will be held in Bordeaux, Feb 29 – Mar 03 2019, hosted at the Centre Broca Nouvelle-Aquitaine by the Bordeaux Imaging Center (BIC) and the Interdisciplinary Institute for Neuroscience. The selected students will be able to attend the whole NEUBIAS conference as part of the training.

NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >20 specialists at the event) and “…a great mix of intensive learning and community networking” (former trainee testimonial). All schools include practical sessions “Work on Your Own Data”, plenary seminars and a session on ethics in image analysis.

Applications are now open (TS14 = 25 seats, TS15 = 35 seats and ~10+ trainers per school). Within the COST framework (funders of NEUBIAS), we will offer up to 7 travel grants per school to applicants who qualify.

Application deadline: December 12th 2019 Selection notification: December 20th 2019

More information about schools (programme & trainers) and venue, travel & lodge available at our website:

eubias.org/NEUBIAS/training-schools/

eubias.org/NEUBIAS/training-schools/eci/ts14-bordeaux-2020/

eubias.org/NEUBIAS/training-schools/analysts/ts15-bordeaux-2020/

We kindly ask that you help us reach out to all potential interested applicants.

on behalf of all NEUBIAS members, local organizers (Florian Levet and Fabrice Cordelières), scientific organizers (Romain Guiet, Elnaz Fazeli, Christian Tischer, Kota Miura, Marion Louveaux), and NEUBIAS Training Leaders Gabriel Martins and Fabrice Cordelières.

Loads of microscopy jobs in Europe and even one at KI! :)

Good luck everyone who applies!

1- microscopy postdoc job at KI

I want to draw your attention to a current announcement from us about microscopy oriented post-doc positions. See more details here.

We are looking for qualified post-doc/s (1 or 2) for both:

* Technically-oriented tasks. Mainly related to fast fluorescence imaging techniques for fast 3D imaging in living animals.

* Data processing tasks. Mainly related to advanced image processing of data from fast 3D imaging in living animals.

Martin Köhler, PhD

The Rolf Luft Research Center for Diabetes and Endocrinology

2- job in a company in Switzerland

We at Nanolive have a new job posting for an R&D Biologist/Image Analysis expert based out of our offices on Lake Geneva, Switzerland.   Do you enjoy creating custom macros or scripts and have experience with ImageJ and Cell Profiler?  Are you an expert in Live Cell Imaging and looking for a new challenge with a cutting edge technique?

Nanolive, a growing scale-up company situated at EPFL Innovation Park but moving soon to the Lake Geneva Park in Tolochenaz, has developed a disruptive technology that, for the first time ever, allows users to explore a living cell in 3D without damaging it. To support its growth, Nanolive is looking for strengthening its application portfolio and its microscopes usability with a highly motivated and outstanding Biologist with experience in ImageJ and CellProfiler.

What we are looking for:

This position is ideal for a self-motivated, enthusiastic, independent, result oriented individual. Enjoy the benefits of working in a fast-growing start-up company where your efforts play a key role in the quality and success of the 3D Cell Explorer (CX).

If so, please apply here.

Paul Carman, Nanolive SA

3- A rare job as the manager of the excellent Nikon Imaging Center in London

We are hiring a new manager for the Nikon Imaging Centre@King’s College London. Further information is below and application info is here.

Nikon Imaging Centre Manager

Research Platforms, within the Research Management & Innovation Directorate at King’s College London is seeking to appoint a full-time staff member to manage the Nikon Imaging Centre (NIC).

The NIC is a world-class light microscopy facility on Guy’s Hospital Campus of King’s College London. The NIC houses a large number of state-of-the-art imaging equipment including confocal, super-resolution and multiphoton microscopes. The role holder will be responsible for the management, support and future development of the NIC with ongoing training and consultation with both King’s College London and Nikon staff. This includes providing expert guidance in experimental design and implementation, training for the users of the NIC and managing other NIC staff members.

There will also be opportunities for the post holder to contribute actively to research both individually and in collaboration with academic staff. We are looking for scientists with a special interest in the field of application of microscopy to study biomedicine. A PhD in the field of cell biology and/or microscopy, and extensive experience in the use of multiple forms of imaging methods and image analysis are essential. Previous experience of working within a core microscopy facility is also highly desirable.

This post will be offered on an indefinite contract.This is a full-time post – 100% full time equivalent.The selection process will include a panel interview.

Grade and Salary :            The salary will be paid at Grade 7, £46,292 to £54,534 per annum inclusive of London Allowance.          Job ID :  023306

Post Date :          08-Nov-2019      Close Date :        01-Dec-2019

Professor Maddy Parsons: maddy.parsons@kcl.ac.uk

4- and a microscopy specialist in Berlin

Light microscopy specialist, Advanced Light Microscopy Technology Platform, MDC; Berlin, Germany