THE HUMAN PROTEIN ATLAS BLOG
We would like to thank all participants of the CYTO2017 Image analysis challenge co-organized by the Cell Atlas team. And congratulate the winner, Dr. Peng Qiu from Georgia Tech, who at the time of the challenge closing had the top solution for both Challenge 2 and Challenge 3.
Though submissions this year were high-quality, and showcased the multitude of approaches to such a challenge, there is still large room for improvements in the results and some sub-challenges remain entirely unsolved. Therefore, we have decided to keep the challenge open for another year! Improvements in downloads and scoring schemes will be made.
So stay tuned for updates...Read more
Emma Lundberg Director of the Human Cell Atlas, will present a keynote lecture on June 14th, entitled ”The Cell Atlas: A subcellular map of the human proteome” on the 32ndCongress of the International Society for Advancement of Cytometry in Boston, USA.
On this occassion, the CYTO Congress together with the Human Protein Atlas have organized a challenge for analysis of the images from the Cell Atlas, culminating in presentation of results in the final conference session, where participants will present their analytical methods and findings...Read more
The Cell Atlas database was just recently released with data on more than 12.000 proteins and mapping to 30 organelles. Today, the scientific findings are published in Science in "A subcellular map of the humanproteome".
The cell is a complex entity that carries out multiple functions. In order to do this, the different parts of the cells are organized in structures, called organelles. By investigating the organelles and its proteome, and to understand how the proteins vary over time and space we can truly begin to understand human biology on a detailed level...Read more
Today we highlight another part of Swedish or Scandinavian (food) culture - "Taco Fredag" or "Taco Friday". Doesn't sound Swedish to you? But staying in on a Friday night and having tacos with your family and/or friends is a thing here, and a big thing as it happens, with supermarkets having entire sections dedicated to this tradition.
So what other image to look at in this week's edition of the Human Protein Atlas blog than the one representing TACO1. TACO1 acts as a translational activator for the mitochondrial encoded cytochrome c oxidase 1, which is a component of complex IV of the mitochondrial respiratory complex...Read more
In 2017, February 28th will be the day that in Sweden is known as "Fettisdagen", (lit. "Fat Tuesday"), in other countries known as "Mardi Gras", "Faschingsdienstag" or "Shrove Tuesday". This day was originally celebrated in the Christian tradition as the last day of a three day feast to prepare for the forty day long fasting period before Easter. Today it has been popularized and in many places around the world this day is now known for its carnivals.
In Sweden together with some other northern European countries we like to eat "semlor" on Fat Tuesday...Read more
Over the last couple of months, you have hade the pleasure to see Image of the week here on the blog, where an image we find particularly interesting has been shown and discussed. Now that our Cell Atlas is out, you can browse images of your favorite protein directly in our database! In addition to all the images we have added, there are also new "Human Cell" chapters, which provide a knowledge-based analysis of the human cellular proteomes and an entry into the Human Protein Atlas from different perspectives...Read more
Yesterday our new Cell Atlas was released, at the American Society of Cell Biology Meeting. The Cell Atlas is an open-access interactive database with unparalleled high-resolution images. It visualizes for the first time the location of over 12,000 proteins in cells – opening the way to spatial proteomics, an exciting new discipline predicted to lead to a fundamental increase in our understanding of human health and disease.
Prof Mathias Uhlen, Director of the Human Protein Atlas explains:
– After the genome projects that has characterized the number of human protein-coding genes, the next step is to elucidate the function of these proteins...Read more
Over the last couple of weeks, readers of this blog have learnt about how we culture cells, and how we prepare them for microscopy. This week, the time has come to look into the actual imaging.
Martin Hjelmare is lab manager in the Cell Profiling group, and has worked within the Human Protein Atlas since 2007, the first couple of years in the protein factory, and since 2008 in the Cell Profiling group.
– In the protein factory I learnt a lot about basic lab routines; up scaling of protein expression, coupling columns, running gels, etc. This was very useful when I started working in the group of Emma Lundberg...Read more
To prepare all the images for the Cell Atlas, released on December 4, the cells used are primed for staining and microscopy. Sample preparation is an important step when performing immunofluorescence studies. If wrongly applied it can not only cause unsuccessful detection but also generate misleading information.
The sample preparation performed by the Cell Atlas team includes cell fixation, permeabilization, and immunostaining with primary and secondary antibodies.
– The fixation is the crucial step, and different fixation protocols work better for different sets of proteins, Christian Gnann, a research engineer in the Cell Profiling group explains...Read more
The Human Cell Atlas, to be released on December 4, displays high resolution, multicolour images of immunofluorescently stained cells. This provides spatial information on protein expression patterns on a fine cellular and subcellular level. From the start three cell lines, U-2 OS, A-431 and U-251 MG, originating from different human tissues were chosen to be included in the immunofluorescent analysis...Read more
In less than one month from now, we will release a new version of our database, HPA16! The biggest news is the introduction of a brand new Cell Atlas. It will be an image-based atlas over the subcellular distribution of the human proteome.
– Cells are the machinery of life. Much of the bustling activity in the human cell results from proteins performing specific tasks in designated compartments, the organelles. The Cell Atlas that we are creating will be image-based and describe the subcellular distribution of the human proteome, says Emma Lundberg, Director of the Cell Atlas...Read more
This week we look at a very spooky protein, BAT3 which localizes to the nucleoplasm (looks like jack o'lanterns if you squint hard enough) and cytoplasm of the cell as seen in Figure 1 in A-431 cells.
In addition to having a spooky name, this protein, also known as BAG6, was first identified as being involved in programmed cell death (apoptosis). Subsequent studies have revealed that BAT3 plays a role in many important cellular processes including gene regulation, protein synthesis, protein quality control, and protein degradation (Binici J & Koch J. 2014)...Read more
It's time for another HPA image of the week! This week we would like to tease an annotation that is not yet publicly available, but is coming soon in the December 4 release of the Cell Atlas.
During the cell cycle, each chromosome containing your DNA replicates. During mitosis, each chromosome lines up with its copy in the middle of the cell. At this point, the copies of each chromosome are pulled apart from each other via a structure called the mitotic spindle. In order for this chromosomal separation to happen correctly, the two copies of each chromosome must be attached to the microtubules via the kinetochore ( DeLuca J.G. et al 2002)...Read more
This week, it is Mitochondrial Disease Awareness Week. Therefore we would like to take the opportunity to talk about the mitochondrial proteome, the work we do within this field, and you will even get to meet one of our researchers, involved in this work.
The mitochondria are distributed throughout the cytoplasm of the cell, each organelle enclosed by a double membrane, the inner one forming the characteristic folds known as cristae. Mitochondria are essential for producing the cell´s need of ATP through cellular respiration, but have also been shown to participate in many other cellular functions, including apoptosis, calcium storage and cellular signaling...Read more
Systematic antibody validation with siRNA for the Human Protein Atlas
Antibodies are among the most frequently used tools for basic research and clinical assays. For antibodies used in therapy or diagnostics, there are well-defined and strict guidelines that must be complied with before approval for clinical assays. For research antibodies, such guidelines have not yet been developed, despite the importance of demonstrating that they are specific, selective, and yield reproducible results in the immunoassay for which they are to be used...Read more
Version 14 of The Human Protein Atlas includes a new type of validation of antibodies that are used for determining the subcellular localization of a protein.
A set of antibodies have been analyzed in transgenic cell lines expressing GFP-tagged target protein at near-endogenous levels to confirm that the antibodies are capable of binding the target protein. The approved antibodies are then used to determine the subcellular localization of endogenous protein in a selection of cell lines. A high validation score is assigned to those genes where the same location(s) are observed for both tagged protein and protein detected using labelled antibody in non-transfected cells...Read more
Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells
The Human Protein Atlas applies antibodies for a variety of applications to map protein expression in different tissues and also at the subcellular level. Within the subcellular protein atlas, immunofluorescence (IF) is used to uncover the localization of proteins to different organelles. To ensure an accurate localization of each and very protein, the antibodies have to be specific to their target protein...Read more