From a database of more than 200,000 high-resolution, three-dimensional images of human induced pluripotent stem cells, researchers have devised a model to quantify cell shape and internal organization. Susanne Rafelski, Deputy Director of the Allen Institute for Cell Science, revealed details of their study to Drug Target Review.
A recently published study1 from a large team of cell biologists sheds new light on cellular organisation and variability. Researchers at the Allen Institute for Cell Science, a division of the Allen Institute in Seattle, US, developed a unique mathematical framework to uncover internal organisation of cellular structures in human induced pluripotent stem cells (hiPSCs) while taking account of the wide range of variation that naturally occurs in cell shapes.
The team had to first develop standardised methods to create and image fluorescently tagged hiPSC cell lines and to segment the tagged internal structures, and the cells, before they were able to map internal organisation. All of this was built for three-dimensional (3D) images, posing extra challenges to the team as most existing methods were developed for two-dimensional (2D) images.
Dr Susanne Rafelski, who led the study, spoke with Drug Target Review about how the study was conducted, how it might apply to diseases, and future directions.
Can you give a brief overview of your research methods?
This project started in the early days of the Allen Institute for Cell Science, nearly seven years ago. We first figured out how to tag structures inside stem cells with fluorescent proteins while keeping the cells as healthy as possible. The result was the Allen Cell Collection2 of gene-edited hiPSC lines, 25 of which were used in this study. Next, we needed to figure out the best way to image these cells live and in 3D so that we could view structures in high resolution without killing them. Finally, we faced the daunting task of developing computational image analysis tools to transform our 3D microscopy images into segmented images of individual cells and their structures. At that point, we had our dataset in hand and began developing the generalisable analysis framework that was the basis of our recent paper. This framework is based on two coordinate systems for understanding the variance and organisation of hiPSCs: one for cell shape and one to map the interiors of the cells.
Stylised representation of an integrated average morphed cell showing the location of 17 select cellular structures (Credit: Thao Do, Allen Institute for Cell Science)
Our study encompasses all the expertise of our diverse team at the Allen Institute for Cell Science and is truly a collaborative effort. Our 84 co-authors include molecular biologist experts in gene editing, cell biologist experts in microscopy imaging, computational scientist experts in image and data analysis, software engineer experts in database infrastructure, and visualisation experts to develop tools for us all to explore the data. All these researchers effectively combined their expertise for this seminal work.
What is the current understanding of integrated intracellular organisation in hiPSCs, and how does it differ from other cell types?
This was a big unknown when we started this project, for hiPSCs and really any kind of cell. People had studied relationships between some individual structures in cells, such as the position of the Golgi apparatus in migrating cells, but overall internal integrated cellular organisation was not known – not in the way we needed in order to measure and quantify it. When we started tagging structures and looking at them in our hiPSC lines, the images were brand new because people just weren’t doing high-resolution 3D imaging of organisation in hiPSCs.
Our study not only builds a framework for stem cell organisation for the benefit of future experiments with this particular cell type, but also provides a roadmap for researchers to do similar analyses in other kinds of cells.
Why is understanding cell organisation so important to disease research?
We know cell organisation matters — pathologists have used visual inspection of the arrangement of cell components for decades to diagnose progression and prognosis of diseases such as cancer. But we haven’t tapped into all the information that lies in cell organisation in a quantitative way. In disease, what goes wrong in cells can often be seen by eye. Cancer pathology is a clear example of that. But by the time you can spot a disease under the microscope, it’s a big sledgehammer. What we can see by numbers and distributions of populations is far more subtle. You don’t want to catch disease when it’s a sledgehammer, you want to catch it when smaller changes are happening, because disease is the additive effect of small changes until you get to big changes.
To catch small changes, you have to have rigorous, statistical means of identifying them. That’s what we’re hoping this work can lead to.
Can you tell us more about WTC-11 hiPSC Single-Cell Image Dataset v1?
This dataset3 is so exciting, because there are very few high-resolution, 3D single-cell image datasets out there that cover such a wide range of structures. That creates a resource for scientists, including data science researchers who want to apply machine learning to cell images; now they have more than 200,000 cells they can play with. It also allows scientists to explore hypotheses about the cell biology of undifferentiated stem cells. A lot of other screening datasets use 2D images and cancer cell lines, but we needed three dimensions to analyse hiPSCs. We needed a different type of imaging, a different kind of approach. We know there is a lot of interest in utilising hiPSCs for both basic and disease-focused research, and that’s why we have made them available for anyone in the community- both non-profit and commercial research- to use.
What challenges did you encounter in your research?
There were challenges in each step along the way. We first needed to figure out how to tag structures in cells while keeping them as healthy and normal as possible. Overcoming those challenges enabled us to create the Allen Cell Collection. The next challenge was to image the cells in a standardised way. We added in some automation and developed very particular ways to image these cells, the details of which were published in the Nature paper and a protocol paper we are currently working on. Once we had the images, we needed to establish how to segment them — how to define the boundaries of each structure inside the cell and how to define the cell edges. That was a big challenge that led to the development of a software toolkit, the Allen Cell & Structure Segmenter,4 which is also openly available. Finally, there was the general challenge of integrating and quantifying all our data, which is the framework we describe in the paper.
Can you discuss any notable variations in integrated intracellular organisation that you observed in iPSCs, and what implications these variations have for our understanding of cellular function?
We developed our metrics to look at the mean location and variation in individual cellular structures, and in pairs of structures in the cell. When viewing healthy hiPSCs in interphase, we found that the wiring of internal organisation is highly consistent across cells, far more so than we expected. We then looked at two different conditions: cells at the edges of colonies, and cells undergoing mitosis. In edge cells, the wiring diagram is still consistent, but the location of many key structures inside the cell changes. That’s likely due to these edge cells not being surrounded by cells on all sides. What this tells us is that the location of cellular structures can change without changing the variability in those locations or the relationships between them. We didn’t know that before. For cells in mitosis, all of our measurements of location and wiring change, but the specific types of changes and their timing during mitosis depend on the specific structure. In all of these instances, we found that changes in location of an individual structure precede changes in their wiring, and that changes in individual structure variations generally precede changes in pairwise interactions, with a few key exceptions. This hints at a possible hierarchy of dependencies as cells reorganise, which we look forward to exploring further together with the community.
How might your research on integrated intracellular organisation in iPSCs contribute to our understanding of diseases and potential treatments?
One important aspect of our paper was that we needed to build the framework to capture the full spectrum of normal cell shapes in order to map the interiors of the cells in abnormal conditions. Because hiPSCs, and generally any population of cells, have such a wide range of shape, we needed to first cluster similarly shaped cells together so that we could compare internal organisation in a controlled manner. That means that, for researchers working on a specific disease or a drug treatment, provided those perturbations don’t drastically change the shape of the cells, they could use the same framework to compare internal organisation between healthy hiPSCs and their perturbed cells, to see if internal phenotypes have changed. Our frameworks are all quantitative so we can put numbers on all these differences, both the mean and the variation for the perturbed condition.
What future directions do you see for research in this area, and what new technologies or techniques might help advance our understanding of intracellular organisation in iPSCs?
Now that the framework has been established, and in keeping with the Allen Institute’s dedication to open science, we’re hoping scientists from around the world will use our method to study their own cell lines and uncover foundational principles of cell behaviour and organisation. Uncovering the rules of a “normal cell” and learning the full variation of what “normal” looks like is key to deepening our understanding and helping us find better treatments for disease. We and others are already applying some of the concepts in this paper to analysing cell organisation in other cell types and states, including disease states, and extending the concepts to study not just the structures inside the cell but also to look for patterns in the locations of proteins making up those structures.
Uncovering the rules of a “normal cell” and learning the full variation of what “normal” looks like is key to deepening our understanding and helping us find better treatments for disease.
Any other comments?
It was truly a privilege to be a part of such a large and interdisciplinary team effort to create something that we hope will be a great resource for the community. We anticipate that it will fill in significant gaps to be able to measure, analyse and understand how cells are organised and how this impacts cell behaviour and function.
Author bios:
Dr Susanne Rafelski
Susanne is the Deputy Director of the Allen Institute for Cell Science, which aims to understand the principles by which human induced pluripotent stem cells (hiPSC) establish and maintain robust dynamic localisation of cellular structures, and how cells transition between states during differentiation and disease. Her life-long scientific goal is to decipher the patterns and rules that transform the overwhelming complexity found inside cells into functioning units of life.
Dr Rachel Tompa
Rachel is Senior Editor at the Allen Institute. A former molecular biologist, she’s been writing about health and science for more than 15 years, covering a wide variety of topics including the microbiome, pregnancy, global health, science policy and infectious disease. She is also co-host and co-producer of the Allen Institute’s podcast, Lab Notes.
References:
Viana MP, Chen J, Knijnenburg TA, et al. Integrated intracellular organisation and its variations in human IPS cells. Nature. 2023;613(7943):345–54.
Cell line catalog [Internet]. ALLEN CELL EXPLORER. [cited 2023Apr4]. Available from: https://www.allencell.org/cell-catalog.html
Cell feature explorer [Internet]. Cell Feature Explorer. [cited 2023Apr4]. Available from: https://cfe.allencell.org/
Allen Cell & Structure segmenter [Internet]. ALLEN CELL EXPLORER. [cited 2023Apr4]. Available from: https://www.allencell.org/segmenter.html
The federal government is ordering the dissolution of TikTok’s Canadian business after a national security review of the Chinese company behind the social media platform, but stopped short of ordering people to stay off the app.
Industry Minister François-Philippe Champagne announced the government’s “wind up” demand Wednesday, saying it is meant to address “risks” related to ByteDance Ltd.’s establishment of TikTok Technology Canada Inc.
“The decision was based on the information and evidence collected over the course of the review and on the advice of Canada’s security and intelligence community and other government partners,” he said in a statement.
The announcement added that the government is not blocking Canadians’ access to the TikTok application or their ability to create content.
However, it urged people to “adopt good cybersecurity practices and assess the possible risks of using social media platforms and applications, including how their information is likely to be protected, managed, used and shared by foreign actors, as well as to be aware of which country’s laws apply.”
Champagne’s office did not immediately respond to a request for comment seeking details about what evidence led to the government’s dissolution demand, how long ByteDance has to comply and why the app is not being banned.
A TikTok spokesperson said in a statement that the shutdown of its Canadian offices will mean the loss of hundreds of well-paying local jobs.
“We will challenge this order in court,” the spokesperson said.
“The TikTok platform will remain available for creators to find an audience, explore new interests and for businesses to thrive.”
The federal Liberals ordered a national security review of TikTok in September 2023, but it was not public knowledge until The Canadian Press reported in March that it was investigating the company.
At the time, it said the review was based on the expansion of a business, which it said constituted the establishment of a new Canadian entity. It declined to provide any further details about what expansion it was reviewing.
A government database showed a notification of new business from TikTok in June 2023. It said Network Sense Ventures Ltd. in Toronto and Vancouver would engage in “marketing, advertising, and content/creator development activities in relation to the use of the TikTok app in Canada.”
Even before the review, ByteDance and TikTok were lightning rod for privacy and safety concerns because Chinese national security laws compel organizations in the country to assist with intelligence gathering.
Such concerns led the U.S. House of Representatives to pass a bill in March designed to ban TikTok unless its China-based owner sells its stake in the business.
Champagne’s office has maintained Canada’s review was not related to the U.S. bill, which has yet to pass.
Canada’s review was carried out through the Investment Canada Act, which allows the government to investigate any foreign investment with potential to might harm national security.
While cabinet can make investors sell parts of the business or shares, Champagne has said the act doesn’t allow him to disclose details of the review.
Wednesday’s dissolution order was made in accordance with the act.
The federal government banned TikTok from its mobile devices in February 2023 following the launch of an investigation into the company by federal and provincial privacy commissioners.
— With files from Anja Karadeglija in Ottawa
This report by The Canadian Press was first published Nov. 6, 2024.
LONDON (AP) — Most people have accumulated a pile of data — selfies, emails, videos and more — on their social media and digital accounts over their lifetimes. What happens to it when we die?
It’s wise to draft a will spelling out who inherits your physical assets after you’re gone, but don’t forget to take care of your digital estate too. Friends and family might treasure files and posts you’ve left behind, but they could get lost in digital purgatory after you pass away unless you take some simple steps.
Here’s how you can prepare your digital life for your survivors:
Apple
The iPhone maker lets you nominate a “ legacy contact ” who can access your Apple account’s data after you die. The company says it’s a secure way to give trusted people access to photos, files and messages. To set it up you’ll need an Apple device with a fairly recent operating system — iPhones and iPads need iOS or iPadOS 15.2 and MacBooks needs macOS Monterey 12.1.
For iPhones, go to settings, tap Sign-in & Security and then Legacy Contact. You can name one or more people, and they don’t need an Apple ID or device.
You’ll have to share an access key with your contact. It can be a digital version sent electronically, or you can print a copy or save it as a screenshot or PDF.
Take note that there are some types of files you won’t be able to pass on — including digital rights-protected music, movies and passwords stored in Apple’s password manager. Legacy contacts can only access a deceased user’s account for three years before Apple deletes the account.
Google
Google takes a different approach with its Inactive Account Manager, which allows you to share your data with someone if it notices that you’ve stopped using your account.
When setting it up, you need to decide how long Google should wait — from three to 18 months — before considering your account inactive. Once that time is up, Google can notify up to 10 people.
You can write a message informing them you’ve stopped using the account, and, optionally, include a link to download your data. You can choose what types of data they can access — including emails, photos, calendar entries and YouTube videos.
There’s also an option to automatically delete your account after three months of inactivity, so your contacts will have to download any data before that deadline.
Facebook and Instagram
Some social media platforms can preserve accounts for people who have died so that friends and family can honor their memories.
When users of Facebook or Instagram die, parent company Meta says it can memorialize the account if it gets a “valid request” from a friend or family member. Requests can be submitted through an online form.
The social media company strongly recommends Facebook users add a legacy contact to look after their memorial accounts. Legacy contacts can do things like respond to new friend requests and update pinned posts, but they can’t read private messages or remove or alter previous posts. You can only choose one person, who also has to have a Facebook account.
You can also ask Facebook or Instagram to delete a deceased user’s account if you’re a close family member or an executor. You’ll need to send in documents like a death certificate.
TikTok
The video-sharing platform says that if a user has died, people can submit a request to memorialize the account through the settings menu. Go to the Report a Problem section, then Account and profile, then Manage account, where you can report a deceased user.
Once an account has been memorialized, it will be labeled “Remembering.” No one will be able to log into the account, which prevents anyone from editing the profile or using the account to post new content or send messages.
X
It’s not possible to nominate a legacy contact on Elon Musk’s social media site. But family members or an authorized person can submit a request to deactivate a deceased user’s account.
Passwords
Besides the major online services, you’ll probably have dozens if not hundreds of other digital accounts that your survivors might need to access. You could just write all your login credentials down in a notebook and put it somewhere safe. But making a physical copy presents its own vulnerabilities. What if you lose track of it? What if someone finds it?
Instead, consider a password manager that has an emergency access feature. Password managers are digital vaults that you can use to store all your credentials. Some, like Keeper,Bitwarden and NordPass, allow users to nominate one or more trusted contacts who can access their keys in case of an emergency such as a death.
But there are a few catches: Those contacts also need to use the same password manager and you might have to pay for the service.
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Is there a tech challenge you need help figuring out? Write to us at onetechtip@ap.org with your questions.
LONDON (AP) — Britain’s competition watchdog said Thursday it’s opening a formal investigation into Google’s partnership with artificial intelligence startup Anthropic.
The Competition and Markets Authority said it has “sufficient information” to launch an initial probe after it sought input earlier this year on whether the deal would stifle competition.
The CMA has until Dec. 19 to decide whether to approve the deal or escalate its investigation.
“Google is committed to building the most open and innovative AI ecosystem in the world,” the company said. “Anthropic is free to use multiple cloud providers and does, and we don’t demand exclusive tech rights.”
San Francisco-based Anthropic was founded in 2021 by siblings Dario and Daniela Amodei, who previously worked at ChatGPT maker OpenAI. The company has focused on increasing the safety and reliability of AI models. Google reportedly agreed last year to make a multibillion-dollar investment in Anthropic, which has a popular chatbot named Claude.
Anthropic said it’s cooperating with the regulator and will provide “the complete picture about Google’s investment and our commercial collaboration.”
“We are an independent company and none of our strategic partnerships or investor relationships diminish the independence of our corporate governance or our freedom to partner with others,” it said in a statement.
The U.K. regulator has been scrutinizing a raft of AI deals as investment money floods into the industry to capitalize on the artificial intelligence boom. Last month it cleared Anthropic’s $4 billion deal with Amazon and it has also signed off on Microsoft’s deals with two other AI startups, Inflection and Mistral.
