Emma Lundberg (scientist)

Last updated
Emma Lundberg
Alma mater KTH Royal Institute of Technology
Scientific career
Institutions Science for Life Laboratory
KTH Royal Institute of Technology
Thesis Bioimaging for analysis of protein expression in cells and tissues using affinity reagents  (2008)

Emma Lundberg is a Swedish cell biologist who is a professor at KTH Royal Institute of Technology and Director of Cell Profiling at the Science for Life Laboratory. Her research considers spatial proteomics and cell biology, making use of an antibody-based approach to assess fundamental aspects of human biology. She looks to understand why certain variations in human proteins can cause disease.

Contents

Early life and education

Lundberg was an undergraduate and postgraduate student at the KTH Royal Institute of Technology. Her doctoral research introduced bio imaging as a means to understand expression in cells.[ citation needed ]

Research and career

Lundberg combines computational investigations with experimental analysis to identify the spatiotemporal expression of proteins at the level of single cells. Eukaryotic cells can support multiple processes in parallel due to the compartmentalisation of biological processes. Each specific compartment describes a particular cellular function and the molecular controllers required to complete a specific function. When defects occur within the compartments, they can give rise to various forms of human disease. [1]

Lundberg seeks to facilitate access to science and science communication. She created the human protein atlas the Cell Atlas, which looks to identify the sub cellular localisation of all human proteins. She was involved with the launch of “Project Discovery”, a citizen science project that uses members of the public to classify protein patterns. [2] She integrated this project with Eve Online , a gaming platform. [3] [4]

Lundberg spent over two years at the Stanford School of Medicine. [5] She has since made use of artificial intelligence to better understand microscopy images. [6] The models created by Lundberg assist with image acquisition, processing and analysis. They can be used to segment data, enabling statistical analysis. Preliminary work indicated that human cells were considerably more complex than previously thought, including proteins that form into unfamiliar structures. [7]

Awards and honours

Selected publications

Related Research Articles

<span class="mw-page-title-main">Proteome</span> Set of proteins that can be expressed by a genome, cell, tissue, or organism

The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of the proteome.

<span class="mw-page-title-main">Structural biology</span> Study of molecular structures in biology

Structural biology is a field that is many centuries old which, as defined by the Journal of Structural Biology, deals with structural analysis of living material at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.

<span class="mw-page-title-main">Proteomics</span> Large-scale study of proteins

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.

<span class="mw-page-title-main">Ruedi Aebersold</span> Swiss biologist (born 1954)

Rudolf Aebersold is a Swiss biologist, regarded as a pioneer in the fields of proteomics and systems biology. He has primarily researched techniques for measuring proteins in complex samples, in many cases via mass spectrometry. Ruedi Aebersold is a professor of Systems biology at the Institute of Molecular Systems Biology (IMSB) in ETH Zurich. He was one of the founders of the Institute for Systems Biology in Seattle, Washington, where he previously had a research group.

<span class="mw-page-title-main">Caspase 14</span> Protein-coding gene in the species Homo sapiens

Caspase 14 is an enzyme that in humans is encoded by the CASP14 gene.

<span class="mw-page-title-main">RRP12</span> Protein-coding gene in the species Homo sapiens

RRP12-like protein is a protein that in humans is encoded by the RRP12 gene. It is currently thought to be involved in ribosome assembly of the precursor particles of both subunits in eukaryotes and was identified as a RNA binding protein.

<span class="mw-page-title-main">RBM3</span> Protein-coding gene in the species Homo sapiens

Putative RNA-binding protein 3 is a protein that in humans is encoded by the RBM3 gene.

High throughput biology is the use of automation equipment with classical cell biology techniques to address biological questions that are otherwise unattainable using conventional methods. It may incorporate techniques from optics, chemistry, biology or image analysis to permit rapid, highly parallel research into how cells function, interact with each other and how pathogens exploit them in disease.

The Human Proteome Project (HPP) is a collaborative effort coordinated by the Human Proteome Organization. Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome.

The Human Protein Atlas (HPA) is a Swedish-based program started in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. In June 2023, version 23 was launched where a new Interaction section was introduced containing human protein-protein interaction networks for more than 11,000 genes that will add new aspects in terms of protein function.

<span class="mw-page-title-main">Single-cell analysis</span> Testbg biochemical processes and reactions in an individual cell

In the field of cellular biology, single-cell analysis and subcellular analysis is the study of genomics, transcriptomics, proteomics, metabolomics and cell–cell interactions at the single cell level. The concept of single-cell analysis originated in the 1970s. Before the discovery of heterogeneity, single-cell analysis mainly referred to the analysis or manipulation of an individual cell in a bulk population of cells at a particular condition using optical or electronic microscope. To date, due to the heterogeneity seen in both eukaryotic and prokaryotic cell populations, analyzing a single cell makes it possible to discover mechanisms not seen when studying a bulk population of cells. Technologies such as fluorescence-activated cell sorting (FACS) allow the precise isolation of selected single cells from complex samples, while high throughput single cell partitioning technologies, enable the simultaneous molecular analysis of hundreds or thousands of single unsorted cells; this is particularly useful for the analysis of transcriptome variation in genotypically identical cells, allowing the definition of otherwise undetectable cell subtypes. The development of new technologies is increasing our ability to analyze the genome and transcriptome of single cells, as well as to quantify their proteome and metabolome. Mass spectrometry techniques have become important analytical tools for proteomic and metabolomic analysis of single cells. Recent advances have enabled quantifying thousands of protein across hundreds of single cells, and thus make possible new types of analysis. In situ sequencing and fluorescence in situ hybridization (FISH) do not require that cells be isolated and are increasingly being used for analysis of tissues.

Toponomics is a discipline in systems biology, molecular cell biology, and histology concerning the study of the toponome of organisms. It is the field of study that purposes to decode the complete toponome in health and disease —which is the next big challenge in human biotechnology after having decoded the human genome.

An imaging cycler microscope (ICM) is a fully automated (epi)fluorescence microscope which overcomes the spectral resolution limit resulting in parameter- and dimension-unlimited fluorescence imaging. The principle and robotic device was described by Walter Schubert in 1997 and has been further developed with his co-workers within the human toponome project. The ICM runs robotically controlled repetitive incubation-imaging-bleaching cycles with dye-conjugated probe libraries recognizing target structures in situ (biomolecules in fixed cells or tissue sections). This results in the transmission of a randomly large number of distinct biological informations by re-using the same fluorescence channel after bleaching for the transmission of another biological information using the same dye which is conjugated to another specific probe, a.s.o. Thereby noise-reduced quasi-multichannel fluorescence images with reproducible physical, geometrical, and biophysical stabilities are generated. The resulting power of combinatorial molecular discrimination (PCMD) per data point is given by 65,536k, where 65,536 is the number of grey value levels (output of a 16-bit CCD camera), and k is the number of co-mapped biomolecules and/or subdomains per biomolecule(s). High PCMD has been shown for k = 100, and in principle can be expanded for much higher numbers of k. In contrast to traditional multichannel–few-parameter fluorescence microscopy (panel a in the figure) high PCMDs in an ICM lead to high functional and spatial resolution (panel b in the figure). Systematic ICM analysis of biological systems reveals the supramolecular segregation law that describes the principle of order of large, hierarchically organized biomolecular networks in situ (toponome). The ICM is the core technology for the systematic mapping of the complete protein network code in tissues (human toponome project). The original ICM method includes any modification of the bleaching step. Corresponding modifications have been reported for antibody retrieval and chemical dye-quenching debated recently. The Toponome Imaging Systems (TIS) and multi-epitope-ligand cartographs (MELC) represent different stages of the ICM technological development. Imaging cycler microscopy received the American ISAC best paper award in 2008 for the three symbol code of organized proteomes.

<span class="mw-page-title-main">Ronald Beavis</span> Canadian protein biochemist

Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.

<span class="mw-page-title-main">KIAA0825</span> Protein-coding gene in the species Homo sapiens

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Mathias Uhlén is a Swedish scientist and Professor of Microbiology at Royal Institute of Technology (KTH), Stockholm. After a post-doc period at the EMBL in Heidelberg, Germany, he became professor in microbiology at KTH in 1988. His research is focused on protein science, antibody engineering and precision medicine and range from basic research in human and microbial biology to more applied research, including clinical applications. He is member of several academies and societies, including Royal Swedish Academy of Science (KVA), National Academy of Engineering (NAE) and the Swedish Academy of Engineering Science (IVA). Dr Uhlen was the Founding Director of the national infrastructure Science for Life Laboratory (SciLifeLab) from 2010-2015

Paola Picotti is an Italian biologist who is Professor for Molecular Systems Biology at ETH Zürich. She is Deputy Head of the Institute for Molecular Systems Biology. Her research investigates how the conformational changes of proteins impact cellular networks. She was awarded the 2020 ETH Zürich Rössler Prize and the 2019 EMBO Gold Medal.

Kathryn S Lilley is a professor of biochemistry at the University of Cambridge, director of the Cambridge Center for Proteomics, and an elected member of the European Molecular Biology Organization (EMBO).

Ilaria Testa is an Italian-born scientist who is a Fellow at the SciLifeLab in Stockholm and an Associate Professor at the Department of Applied Physics at the School of Engineering Science at the KTH Royal Institute of Technology. She has made major contributions to advanced microscopy, particularly superresolution microscopy.

References

  1. "Emma Lundberg". SciLifeLab. Retrieved 2022-03-13.
  2. "Mapping of cells and proteins improved with help of gamers and AI". KTH. Retrieved 2022-03-13.
  3. Armitage, Hanae (2018-08-22). "Massive online space game refines protein localization". Scope. Retrieved 2022-03-13.
  4. Vogt, Nina (October 2018). "Raising the game in image classification". Nature Methods. 15 (10): 759. doi:10.1038/s41592-018-0162-4. ISSN   1548-7105. PMID   30275575. S2CID   205573216.
  5. "Lundberg Lab". cellprofiling.org. Retrieved 2022-03-13.
  6. 1 2 3 Lundberg, Emma; Communications, Corporate (2022-01-10). "Applying AI and Machine Learning in Microscopy and Image Analysis".{{cite journal}}: Cite journal requires |journal= (help)
  7. "We might not know half of what's in our cells, new AI technique reveals". ScienceDaily. Retrieved 2022-03-13.
  8. Philippidis, Alex (2018-05-21). "Top 10 Under 40". GEN - Genetic Engineering and Biotechnology News. Retrieved 2022-03-13.
  9. "Latest RMS Scientific Achievement Award winners announced". Wiley Analytical Science. Retrieved 2022-03-13.