Category Archives: synthetic biology

Grow inorganic functional nanomaterials—quantum dots—in the nucleus of live cells

I’m not sure that “transform[ing] cells into super cells, enabling them to do unimaginable thing,” as research Pang Dai-Wen says, is something that is necessary but he and at least one of his colleagues seem quite enthused by the prospect (you’ll find Pang’s quote in the press release which follows the news item).

An April 3, 2024 news item on phys.org announces the work, Note: Links have been removed,

National Science Review recently published research on the synthesis of quantum dots (QDs) in the nucleus of live cells by Dr. Hu Yusi, Associate Professor Wang Zhi-Gang, and Professor Pang Dai-Wen from Nankai University.

During the study of QDs synthesis in mammalian cells, it was found that the treatment with glutathione (GSH) enhanced the cell’s reducing capacity. The generated QDs were not uniformly distributed within the cell but concentrated in a specific area.

Through a series of experiments, it was confirmed that this area is indeed the cell nucleus. Dr. Hu said, “This is truly amazing, almost unbelievable.”

An April 3, 2024 Science China Press press release on EurekAlert, which originated the news item, fills in a few details,

Dr. Hu and his mentor Professor Pang attempted to elucidate the molecular mechanism of quantum dot synthesis in the cell nucleus. It was found that GSH plays a significant role. There is a GSH transport protein, Bcl-2, on the nucleus, which transports GSH into the nucleus in large quantities, enhancing the reducing ability within the nucleus, promoting the generation of Se precursors. At the same time, GSH can also expose thiol groups on proteins, creating conditions for the generation of Cd precursors. The combination of these factors ultimately enables the abundant synthesis of quantum dots in the cell nucleus.

Professor Pang stated, “This is an exciting result; this work achieves the precise synthesis of QDs in live cells at the subcellular level.” He continued, “Research in the field of synthetic biology mostly focuses on live cell synthesis of organic molecules through reverse genetics. Rarely do we see the live cell synthesis of inorganic functional materials. Our study doesn’t involve complex genetic modifications; it achieves the target synthesis of inorganic fluorescent nanomaterials in cellular organelles simply by regulating the content and distribution of GSH within the cell. This addresses the deficiency in synthetic biology for the synthesis of inorganic materials.”

While the synthesis of organic materials in cells remains predominant in the field of biosynthesis, this research undoubtedly paves the way for the synthesis of inorganic materials in synthetic biology. Professor Pang expressed, “Each of our advancements is a new starting point. We firmly believe that in the near future, we can use cell synthesis to produce nanodrugs, or even nanorobots in specified organelles. Moreover, we can transform cells into super cells, enabling them to do unimaginable things.” [emphasis mine]

Here’s a link to and a citation for the paper,

In-situ synthesis of quantum dots in the nucleus of live cells by Yusi Hu, Zhi-Gang Wang, Haohao Fu, Chuanzheng Zhou, Wensheng Cai, Xueguang Shao, Shu-Lin Liu , Dai-Wen Pang. National Science Review, Volume 11, Issue 3, March 2024, nwae021, DOI: https://doi.org/10.1093/nsr/nwae021 Published:: 12 January 2024

This paper appears to be open access.

Grown from bacteria: plastic-free vegan leather that dyes itself

Interesting rather than aesthetiically pleasing,

Caption: Bacteria grown and dyed shoe. Credit; Tom Ellis/Marcus Walker/Imperial College London

An April 3, 2024 news item on phys.org announces this latest example of bacterial footwear,

Researchers at Imperial College London have genetically engineered bacteria to grow animal- and plastic-free leather that dyes itself.

In recent years, scientists and companies have started using microbes to grow sustainable textiles or to make dyes for industry—but this is the first time bacteria have been engineered to produce a material and its own pigment simultaneously.

An April 3, 2024 Imperial College London (ICL) press release (also on EurekAlert) by Caroline Brogan, which originated the news item, delves further into the research, Note: Links have been removed,

Synthetic chemical dyeing is one of the most environmentally toxic processes in fashion, and black dyes – especially those used in colouring leather – are particularly harmful. The researchers at Imperial set out to use biology to solve this.

In tackling the problem, the researchers say their self-dyeing vegan, plastic-free leather, which has been fashioned into shoe and wallet prototypes, represents a step forward in the quest for more sustainable fashion.

Their new process, which has been published in the journal Nature Biotechnology, could also theoretically be adapted to have bacteria grow materials with various vibrant colours and patterns, and to make more sustainable alternatives to other textiles such as cotton and cashmere.

Lead author Professor Tom Ellis, from Imperial College London’s Department of Bioengineering, said: “Inventing a new, faster way to produce sustainable, self-dyed leather alternatives is a major achievement for synthetic biology and sustainable fashion.

“Bacterial cellulose is inherently vegan, and its growth requires a tiny fraction of the carbon emissions, water, land use and time of farming cows for leather.

“Unlike plastic-based leather alternatives, bacterial cellulose can also be made without petrochemicals, and will biodegrade safely and non-toxically in the environment.”

Designer collaboration

The researchers created the self-dyeing leather alternative by modifying the genes of a bacteria species that produces sheets of microbial cellulose – a strong, flexible and malleable material that is already commonly used in food, cosmetics and textiles. The genetic modifications ‘instructed’ the same microbes that were growing the material to also produce the dark black pigment, eumelanin.

They worked with designers to grow the upper part of a shoe (without the sole) by growing a sheet of bacterial cellulose in a bespoke, shoe-shaped vessel. After 14 days of growth wherein the cellulose took on the correct shape, they subjected the shoe to two days of gentle shaking at 30°C to activate the production of black pigment from the bacteria so that it dyed the material from the inside.

They also made a black wallet by growing two separate cellulose sheets, cutting them to size, and sewing them together.

As well as the prototypes, the researchers demonstrated that the bacteria can be engineered using genes from other microbes to produce colours in response to blue light. By projecting a pattern, or logo, onto the sheets using blue light, the bacteria respond by producing coloured proteins which then glow.

This allows them to project patterns and logos onto the bacterial cultures as the material grows, resulting in patterns and logos forming from within the material. 

Co-author Dr Kenneth Walker, who conducted the work at Imperial College London’s Department of Bioengineering and now works in industry, said: “Our technique works at large enough scales to create real-life products, as shown by our prototypes. From here, we can consider aesthetics as well as alternative shapes, patterns, textiles, and colours.

“The work also shows the impact that can happen when scientists and designers work together. As current and future users of new bacteria-grown textiles, designers have a key role in championing exciting new materials and giving expert feedback to improve form, function, and the switch to sustainable fashion.”

Greener clothes

The research team are now experimenting with a variety of coloured pigments to use those that can also be produced by the material-growing microbes.

The researchers and collaborators have also just won £2 million in funding from Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI), to use engineering biology and bacterial cellulose to solve more of fashion’s problems, such as the use of toxic chromium in leather’s production lines.

Professor Ellis said: “Microbes are already directly addressing many of the problems of animal and plastic-based leather, and we plan to get them ready to expand into new colours, materials and maybe patterns too.

“We look forward to working with the fashion industry to make the clothes we wear greener throughout the whole production line.”

The authors worked closely with Modern Synthesis, a London-based biodesign and materials company, who specialise in innovative microbial cellulose products.

This work was funded by Engineering and Physical Sciences Research Council and BBSRC, both part of UKRI.

Here’s a link to and a citation for the paper,

Self-pigmenting textiles grown from cellulose-producing bacteria with engineered tyrosinase expression by Kenneth T. Walker, Ivy S. Li, Jennifer Keane, Vivianne J. Goosens, Wenzhe Song, Koon-Yang Lee & Tom Ellis. Nature Biotechnology (2024) DOI: https://doi.org/10.1038/s41587-024-02194-3 Published: 02 April 2024

This paper is open access.

Modern Synthesis, the company with which the researchers collaborated, can be found here.

Synthetic human embryos—what now? (2 of 2)

The term they’re using in the Weizmann Institute of Science’s (Israel) announcement is “a generally accurate human embryo model.” This is in contrast to previous announcements including the one from the University of Cambridge team highlighted in Part 1.

From a September 6, 2023 news item on phys.org, Note: A link has been removed,

A research team headed by Prof. Jacob Hanna at the Weizmann Institute of Science has created complete models of human embryos from stem cells cultured in the lab—and managed to grow them outside the womb up to day 14. As reported today [September 6, 2023] in Nature, these synthetic embryo models had all the structures and compartments characteristic of this stage, including the placenta, yolk sac, chorionic sac and other external tissues that ensure the models’ dynamic and adequate growth.

Cellular aggregates derived from human stem cells in previous studies could not be considered genuinely accurate human embryo models, because they lacked nearly all the defining hallmarks of a post-implantation embryo. In particular, they failed to contain several cell types that are essential to the embryo’s development, such as those that form the placenta and the chorionic sac. In addition, they did not have the structural organization characteristic of the embryo and revealed no dynamic ability to progress to the next developmental stage.

Given their authentic complexity, the human embryo models obtained by Hanna’s group may provide an unprecedented opportunity to shed new light on the embryo’s mysterious beginnings. Little is known about the early embryo because it is so difficult to study, for both ethical and technical reasons, yet its initial stages are crucial to its future development. During these stages, the clump of cells that implants itself in the womb on the seventh day of its existence becomes, within three to four weeks, a well-structured embryo that already contains all the body organs.

“The drama is in the first month, the remaining eight months of pregnancy are mainly lots of growth,” Hanna says. “But that first month is still largely a black box. Our stem cell–derived human embryo model offers an ethical and accessible way of peering into this box. It closely mimics the development of a real human embryo, particularly the emergence of its exquisitely fine architecture.”

A stem cell–derived human embryo model at a developmental stage equivalent to that of a day 14 embryo. The model has all the compartments that define this stage: the yolk sac (yellow) and the part that will become the embryo itself, topped by the amnion (blue) – all enveloped by cells that will become the placenta (pink) Courtesy: Weizmann Institute of Science

A September 6, 2023 Weizmann Institute of Science press release, which originated the news item, offers a wealth of detail, Note: Links have been removed,

Letting the embryo model say “Go!”

Hanna’s team built on their previous experience in creating synthetic stem cell–based models of mouse embryos. As in that research, the scientists made no use of fertilized eggs or a womb. Rather, they started out with human cells known as pluripotent stem cells, which have the potential to differentiate into many, though not all, cell types. Some were derived from adult skin cells that had been reverted to “stemness.” Others were the progeny of human stem cell lines that had been cultured for years in the lab.

The researchers then used Hanna’s recently developed method to reprogram pluripotent stem cells so as to turn the clock further back: to revert these cells to an even earlier state – known as the naïve state – in which they are capable of becoming anything, that is, specializing into any type of cell. This stage corresponds to day 7 of the natural human embryo, around the time it implants itself in the womb. Hanna’s team had in fact been the first to start describing methods to generate human naïve stem cells, back in 2013; they continued to improve these methods, which stand at the heart of the current project, over the years.

The scientists divided the cells into three groups. The cells intended to develop into the embryo were left as is. The cells in each of the other groups were treated only with chemicals, without any need for genetic modification, so as to turn on certain genes, which was intended to cause these cells to differentiate toward one of three tissue types needed to sustain the embryo: placenta, yolk sac or the extraembryonic mesoderm membrane that ultimately creates the chorionic sac.

Soon after being mixed together under optimized, specifically developed conditions, the cells formed clumps, about 1 percent of which self-organized into complete embryo-like structures. “An embryo is self-driven by definition; we don’t need to tell it what to do – we must only unleash its internally encoded potential,” Hanna says. “It’s critical to mix in the right kinds of cells at the beginning, which can only be derived from naïve stem cells that have no developmental restrictions. Once you do that, the embryo-like model itself says, ‘Go!’”

The stem cell–based embryo-like structures (termed SEMs) developed normally outside the womb for 8 days, reaching a developmental stage equivalent to day 14 in human embryonic development. That’s the point at which natural embryos acquire the internal structures that enable them to proceed to the next stage: developing the progenitors of body organs.

Complete human embryo models match classic diagrams in terms of structure and cell identity

When the researchers compared the inner organization of their stem cell–derived embryo models with illustrations and microscopic anatomy sections in classical embryology atlases from the 1960s, they found an uncanny structural resemblance between the models and the natural human embryos at the corresponding stage. Every compartment and supporting structure was not only there, but in the right place, size and shape. Even the cells that make the hormone used in pregnancy testing were there and active: When the scientists applied secretions from these cells to a commercial pregnancy test, it came out positive.

In fact, the study has already produced a finding that may open a new direction of research into early pregnancy failure. The researchers discovered that if the embryo is not enveloped by placenta-forming cells in the right manner at day 3 of the protocol (corresponding to day 10 in natural embryonic development), its internal structures, such as the yolk sac, fail to properly develop.

“An embryo is not static. It must have the right cells in the right organization, and it must be able to progress – it’s about being and becoming,” Hanna says. “Our complete embryo models will help researchers address the most basic questions about what determines its proper growth.”

This ethical approach to unlocking the mysteries of the very first stages of embryonic development could open numerous research paths. It might help reveal the causes of many birth defects and types of infertility. It could also lead to new technologies for growing transplant tissues and organs. And it could offer a way around experiments that cannot be performed on live embryos – for example, determining the effects of exposure to drugs or other substances on fetal development.

For people who are visually inclined, there are two videos embedded in the September 6, 2023 Weizmann Institute of Science press release.

Here’s a link to and a citation for the paper,

Complete human day 14 post-implantation embryo models from naïve ES cells by Bernardo Oldak, Emilie Wildschutz, Vladyslav Bondarenko, Mehmet-Yunus Comar, Cheng Zhao, Alejandro Aguilera-Castrejon, Shadi Tarazi, Sergey Viukov, Thi Xuan Ai Pham, Shahd Ashouokhi, Dmitry Lokshtanov, Francesco Roncato, Eitan Ariel, Max Rose, Nir Livnat, Tom Shani, Carine Joubran, Roni Cohen, Yoseph Addadi, Muriel Chemla, Merav Kedmi, Hadas Keren-Shaul, Vincent Pasque, Sophie Petropoulos, Fredrik Lanner, Noa Novershtern & Jacob H. Hanna. Nature (2023) DOI: https://doi.org/10.1038/s41586-023-06604-5 Published: 06 September 2023

This paper is behind a paywall.

As for the question I asked in the head “what now?” I have absolutely no idea.

Synthetic human embryos—what now? (1 of 2)

Usually, there’s a rough chronological order to how I introduce the research, but this time I’m looking at the term used to describe it, following up with the various news releases and commentaries about the research, and finishing with a Canadian perspective.

After writing this post (but before it was published), the Weizmann Institute of Science (Israel) made their September 6, 2023 announcement and things changed a bit. That’s in Part two.

Say what you really mean (a terminology issue)

First, it might be useful to investigate the term, ‘synthetic human embryos’ as Julian Hitchcock does in his June 29, 2023 article on Bristows website (h/t Mondaq’s July 5, 2023 news item), Note: Links have been removed,

Synthetic Embryos” are neither Synthetic nor Embryos. So why are editors giving that name to stem cell-based models of human development?

One of the less convincing aspects of the last fortnight’s flurry of announcements about advances in simulating early human development (see here) concerned their name. Headlines galore (in newspapers and scientific journals) referred to “synthetic embryos“.

But embryo models, however impressive, are not embryos. To claim that the fundamental stages of embryo development that we learnt at school – fertilisation, cleavage and compaction – could now be bypassed to achieve the same result would be wrong. Nor are these objects “synthesised”: indeed, their interest to us lies in the ways in which they organise themselves. The researchers merely place the stem cells in a matrix in appropriate conditions, then stand back and watch them do it. Scientists were therefore unhappy about this use of the term in news media, and relieved when the International Society for Stem Cell Research (ISSCR) stepped in with a press release:

“Unlike some recent media reports describing this research, the ISSCR advises against using the term “synthetic embryo” to describe embryo models, because it is inaccurate and can create confusion. Integrated embryo models are neither synthetic nor embryos. While these models can replicate aspects of the early-stage development of human embryos, they cannot and will not develop to the equivalent of postnatal stage humans. Further, the ISSCR Guidelines prohibit the transfer of any embryo model to the uterus of a human or an animal.”

Although this was the ISSCR’s first attempt to put that position to the public, it had already made that recommendation to the research community two years previously. Its 2021 Guidelines for Stem Cell Research and Clinical Translation had recommended researchers to “promote accurate, current, balanced, and responsive public representations of stem cell research”. In particular:

“While organoids, chimeras, embryo models, and other stem cell-based models are useful research tools offering possibilities for further scientific progress, limitations on the current state of scientific knowledge and regulatory constraints must be clearly explained in any communications with the public or media. Suggestions that any of the current in vitro models can recapitulate an intact embryo, human sentience or integrated brain function are unfounded overstatements that should be avoided and contradicted with more precise characterizations of current understanding.”

Here’s a little bit about Hitchcock from his Bristows profile page,

  • Diploma Medical School, University of Birmingham (1975-78)
  • LLB, University of Wolverhampton
  • Diploma in Intellectual Property Law & Practice, University of Bristol
  • Qualified 1998

Following an education in medicine at the University of Birmingham and a career as a BBC science producer, Julian has focused on the law and regulation of life science technologies since 1997, practising in England and Australia. He joined Bristows with Alex Denoon in 2018.

Hitchcock’s June 29, 2023 article comments on why this term is being used,

I have a lot of sympathy with the position of the science writers and editors incurring the scientists’ ire. First, why should journalists have known of the ISSCR’s recommendations on the use of the term “synthetic embryo”? A journalist who found Recommendation 4.1 of the ISSCR Guidelines would probably not have found them specific enough to address the point, and the academic introduction containing the missing detail is hard to find. …

My second reason for being sympathetic to the use of the terrible term is that no suitable alternative has been provided, other than in the Stem Cell Reports paper, which recommends the umbrella terms “embryo models” or “stem cell based embryo models”. …

When asked why she had used the term “synthetic embryo”, the journalist I contacted remarked that, “We’re still working out the right language and it’s something we’re discussing and will no doubt evolve along with the science”.

It is absolutely in the public’s interest (and in the interest of science), that scientific research is explained in terms that the public understands. There is, therefore, a need, I think, for the scientific community to supply a name to the media or endure the penalties of misinformation …

In such an intensely competitive field of research, disagreement among researchers, even as to names, is inevitable. In consequence, however, journalists and their audiences are confronted by a slew of terms which may or may not be synonymous or overlapping, with no agreed term [emphasis mine] for the overall class of stem cell based embryo models. We cannot blame them if they make up snappy titles of their own [emphasis mine]. …

The announcement

The earliest date for the announcement at the International Society for Stem Cell Researh meeting that I can find is Hannah Devlin’s June 14, 2023 article in The Guardian newspaper, Note: A link has been removed,

Scientists have created synthetic human embryos using stem cells, in a groundbreaking advance that sidesteps the need for eggs or sperm.

Scientists say these model embryos, which resemble those in the earliest stages of human development, could provide a crucial window on the impact of genetic disorders and the biological causes of recurrent miscarriage.

However, the work also raises serious ethical and legal issues as the lab-grown entities fall outside current legislation in the UK and most other countries.

The structures do not have a beating heart or the beginnings of a brain, but include cells that would typically go on to form the placenta, yolk sac and the embryo itself.

Prof Magdalena Żernicka-Goetz, of the University of Cambridge and the California Institute of Technology, described the work in a plenary address on Wednesday [June 14, 2023] at the International Society for Stem Cell Research’s annual meeting in Boston.

The (UK) Science Media Centre made expert comments available in a June 14, 2023 posting “expert reaction to Guardian reporting news of creation of synthetic embryos using stem cells.”

Two days later, this June 16, 2023 essay by Kathryn MacKay, Senior Lecturer in Bioethics, University of Sydney (Australia), appeared on The Conversation (h/t June 16, 2023 news item on phys.org), Note: Links have been removed,

Researchers have created synthetic human embryos using stem cells, according to media reports. Remarkably, these embryos have reportedly been created from embryonic stem cells, meaning they do not require sperm and ova.

This development, widely described as a breakthrough that could help scientists learn more about human development and genetic disorders, was revealed this week in Boston at the annual meeting of the International Society for Stem Cell Research.

The research, announced by Professor Magdalena Żernicka-Goetz of the University of Cambridge and the California Institute of Technology, has not yet been published in a peer-reviewed journal. But Żernicka-Goetz told the meeting these human-like embryos had been made by reprogramming human embryonic stem cells.

So what does all this mean for science, and what ethical issues does it present?

MacKay goes on to answer her own questions, from the June 16, 2023 essay, Note: A link has been removed,

One of these quandaries arises around whether their creation really gets us away from the use of human embryos.

Robin Lovell-Badge, the head of stem cell biology and developmental genetics at the Francis Crick Institute in London UK, reportedly said that if these human-like embryos can really model human development in the early stages of pregnancy, then we will not have to use human embryos for research.

At the moment, it is unclear if this is the case for two reasons.

First, the embryos were created from human embryonic stem cells, so it seems they do still need human embryos for their creation. Perhaps more light will be shed on this when Żernicka-Goetz’s research is published.

Second, there are questions about the extent to which these human-like embryos really can model human development.

Professor Magdalena Żernicka-Goetz’s research is published

Almost two weeks later the research from the Cambridge team (there are other teams and countries also racing; see Part two for the news from Sept. 6, 2023) was published, from a June 27, 2023 news item on ScienceDaily,

Cambridge scientists have created a stem cell-derived model of the human embryo in the lab by reprogramming human stem cells. The breakthrough could help research into genetic disorders and in understanding why and how pregnancies fail.

Published today [Tuesday, June 27, 2023] in the journal Nature, this embryo model is an organised three-dimensional structure derived from pluripotent stem cells that replicate some developmental processes that occur in early human embryos.

Use of such models allows experimental modelling of embryonic development during the second week of pregnancy. They can help researchers gain basic knowledge of the developmental origins of organs and specialised cells such as sperm and eggs, and facilitate understanding of early pregnancy loss.

A June 27, 2023 University of Cambridge press release (also on EurekAlert), which originated the news item, provides more detail about the work,

“Our human embryo-like model, created entirely from human stem cells, gives us access to the developing structure at a stage that is normally hidden from us due to the implantation of the tiny embryo into the mother’s womb,” said Professor Magdalena Zernicka-Goetz in the University of Cambridge’s Department of Physiology, Development and Neuroscience, who led the work.

She added: “This exciting development allows us to manipulate genes to understand their developmental roles in a model system. This will let us test the function of specific factors, which is difficult to do in the natural embryo.”

In natural human development, the second week of development is an important time when the embryo implants into the uterus. This is the time when many pregnancies are lost.

The new advance enables scientists to peer into the mysterious ‘black box’ period of human development – usually following implantation of the embryo in the uterus – to observe processes never directly observed before.

Understanding these early developmental processes holds the potential to reveal some of the causes of human birth defects and diseases, and to develop tests for these in pregnant women.

Until now, the processes could only be observed in animal models, using cells from zebrafish and mice, for example.

Legal restrictions in the UK currently prevent the culture of natural human embryos in the lab beyond day 14 of development: this time limit was set to correspond to the stage where the embryo can no longer form a twin. [emphasis mine]

Until now, scientists have only been able to study this period of human development using donated human embryos. This advance could reduce the need for donated human embryos in research.

Zernicka-Goetz says the while these models can mimic aspects of the development of human embryos, they cannot and will not develop to the equivalent of postnatal stage humans.

Over the past decade, Zernicka-Goetz’s group in Cambridge has been studying the earliest stages of pregnancy, in order to understand why some pregnancies fail and some succeed.

In 2021 and then in 2022 her team announced in Developmental Cell, Nature and Cell Stem Cell journals that they had finally created model embryos from mouse stem cells that can develop to form a brain-like structure, a beating heart, and the foundations of all other organs of the body.

The new models derived from human stem cells do not have a brain or beating heart, but they include cells that would typically go on to form the embryo, placenta and yolk sac, and develop to form the precursors of germ cells (that will form sperm and eggs).

Many pregnancies fail at the point when these three types of cells orchestrate implantation into the uterus begin to send mechanical and chemical signals to each other, which tell the embryo how to develop properly.

There are clear regulations governing stem cell-based models of human embryos and all researchers doing embryo modelling work must first be approved by ethics committees. Journals require proof of this ethics review before they accept scientific papers for publication. Zernicka-Goetz’s laboratory holds these approvals.

“It is against the law and FDA regulations to transfer any embryo-like models into a woman for reproductive aims. These are highly manipulated human cells and their attempted reproductive use would be extremely dangerous,” said Dr Insoo Hyun, Director of the Center for Life Sciences and Public Learning at Boston’s Museum of Science and a member of Harvard Medical School’s Center for Bioethics.

Zernicka-Goetz also holds position at the California Institute of Technology and is NOMIS Distinguished Scientist and Scholar Awardee.

The research was funded by the Wellcome Trust and Open Philanthropy.

(There’s more about legal concerns further down in this post.)

Here’s a link to and a citation for the paper,

Pluripotent stem cell-derived model of the post-implantation human embryo by Bailey A. T. Weatherbee, Carlos W. Gantner, Lisa K. Iwamoto-Stohl, Riza M. Daza, Nobuhiko Hamazaki, Jay Shendure & Magdalena Zernicka-Goetz. Nature (2023) DOI: https://doi.org/10.1038/s41586-023-06368-y Published: 27 June 2023

This paper is open access.

Published the same day (June 27, 2023) is a paper (citation and link follow) also focused on studying human embryonic development using stem cells. First, there’s this from the Abstract,

Investigating human development is a substantial scientific challenge due to the technical and ethical limitations of working with embryonic samples. In the face of these difficulties, stem cells have provided an alternative to experimentally model inaccessible stages of human development in vitro …

This time the work is from a US/German team,

Self-patterning of human stem cells into post-implantation lineages by Monique Pedroza, Seher Ipek Gassaloglu, Nicolas Dias, Liangwen Zhong, Tien-Chi Jason Hou, Helene Kretzmer, Zachary D. Smith & Berna Sozen. Nature (2023) DOI: https://doi.org/10.1038/s41586-023-06354-4 Published: 27 June 2023

The paper is open access.

Legal concerns and a Canadian focus

A July 25, 2023 essay by Françoise Baylis and Jocelyn Downie of Dalhousie University (Nova Scotia, Canada) for The Conversation (h/t July 25, 2023 article on phys.org) covers the advantages of doing this work before launching into a discussion of legislation and limits in the UK and, more extensively, in Canada, Note: Links have been removed,

This research could increase our understanding of human development and genetic disorders, help us learn how to prevent early miscarriages, lead to improvements in fertility treatment, and — perhaps — eventually allow for reproduction without using sperm and eggs.

Synthetic human embryos — also called embryoid bodies, embryo-like structures or embryo models — mimic the development of “natural human embryos,” those created by fertilization. Synthetic human embryos include the “cells that would typically go on to form the embryo, placenta and yolk sac, and develop to form the precursors of germ cells (that will form sperm and eggs).”

Though research involving natural human embryos is legal in many jurisdictions, it remains controversial. For some people, research involving synthetic human embryos is less controversial because these embryos cannot “develop to the equivalent of postnatal stage humans.” In other words, these embryos are non-viable and cannot result in live births.

Now, for a closer look at the legalities in the UK and in Canada, from the July 25, 2023 essay, Note: Links have been removed,

The research presented by Żernicka-Goetz at the ISSCR meeting took place in the United Kingdom. It was conducted in accordance with the Human Fertilization and Embryology Act, 1990, with the approval of the U.K. Stem Cell Bank Steering Committee.

U.K. law limits the research use of human embryos to 14 days of development. An embryo is defined as “a live human embryo where fertilisation is complete, and references to an embryo include an egg in the process of fertilisation.”

Synthetic embryos are not created by fertilization and therefore, by definition, the 14-day limit on human embryo research does not apply to them. This means that synthetic human embryo research beyond 14 days can proceed in the U.K.

The door to the touted potential benefits — and ethical controversies — seems wide open in the U.K.

While the law in the U.K. does not apply to synthetic human embryos, the law in Canada clearly does. This is because the legal definition of an embryo in Canada is not limited to embryos created by fertilization [emphasis mine].

The Assisted Human Reproduction Act (the AHR Act) defines an embryo as “a human organism during the first 56 days of its development following fertilization or creation, excluding any time during which its development has been suspended.”

Based on this definition, the AHR Act applies to embryos created by reprogramming human embryonic stem cells — in other words, synthetic human embryos — provided such embryos qualify as human organisms.

A synthetic human embryo is a human organism. It is of the species Homo sapiens, and is thus human. It also qualifies as an organism — a life form — alongside other organisms created by means of fertilization, asexual reproduction, parthenogenesis or cloning.

Given that the AHR Act applies to synthetic human embryos, there are legal limits on their creation and use in Canada.

First, human embryos — including synthetic human embryos – can only be created for the purposes of “creating a human being, improving or providing instruction in assisted reproduction procedures.”

Given the state of the science, it follows that synthetic human embryos could legally be created for the purpose of improving assisted reproduction procedures.

Second, “spare” or “excess” human embryos — including synthetic human embryos — originally created for one of the permitted purposes, but no longer wanted for this purpose, can be used for research. This research must be done in accordance with the consent regulations which specify that consent must be for a “specific research project.”

Finally, all research involving human embryos — including synthetic human embryos — is subject to the 14-day rule. The law stipulates that: “No person shall knowingly… maintain an embryo outside the body of a female person after the fourteenth day of its development following fertilization or creation, excluding any time during which its development has been suspended.”

Putting this all together, the creation of synthetic embryos for improving assisted human reproduction procedures is permitted, as is research using “spare” or “excess” synthetic embryos originally created for this purpose — provided there is specific consent and the research does not exceed 14 days.

This means that while synthetic human embryos may be useful for limited research on pre-implantation embryo development, they are not available in Canada for research on post-implantation embryo development beyond 14 days.

The authors close with this comment about the prospects for expanding Canada’s14-day limit, from the July 25, 2023 essay,

… any argument will have to overcome the political reality that the federal government is unlikely to open up the Pandora’s box of amending the AHR Act.

It therefore seems likely that synthetic human embryo research will remain limited in Canada for the foreseeable future.

As mentioned, in September 2023 there was a new development. See: Part two.

Biohybrid device (a new type of neural implant) could restore limb function

A March 23, 2023 news item on ScienceDaily announces a neural implant that addresses failures due to scarring issues,

Researchers have developed a new type of neural implant that could restore limb function to amputees and others who have lost the use of their arms or legs.

In a study carried out in rats, researchers from the University of Cambridge used the device to improve the connection between the brain and paralysed limbs. The device combines flexible electronics and human stem cells — the body’s ‘reprogrammable’ master cells — to better integrate with the nerve and drive limb function.

Previous attempts at using neural implants to restore limb function have mostly failed, as scar tissue tends to form around the electrodes over time, impeding the connection between the device and the nerve. By sandwiching a layer of muscle cells reprogrammed from stem cells between the electrodes and the living tissue, the researchers found that the device integrated with the host’s body and the formation of scar tissue was prevented. The cells survived on the electrode for the duration of the 28-day experiment, the first time this has been monitored over such a long period.

A March 22, 2023 University of Cambridge press release (also on EurekAlert but published March 23, 2023) by Sarah Collins, delves further into the topic,

The researchers say that by combining two advanced therapies for nerve regeneration – cell therapy and bioelectronics – into a single device, they can overcome the shortcomings of both approaches, improving functionality and sensitivity.

While extensive research and testing will be needed before it can be used in humans, the device is a promising development for amputees or those who have lost function of a limb or limbs. The results are reported in the journal Science Advances.

A huge challenge when attempting to reverse injuries that result in the loss of a limb or the loss of function of a limb is the inability of neurons to regenerate and rebuild disrupted neural circuits.

“If someone has an arm or a leg amputated, for example, all the signals in the nervous system are still there, even though the physical limb is gone,” said Dr Damiano Barone from Cambridge’s Department of Clinical Neurosciences, who co-led the research. “The challenge with integrating artificial limbs, or restoring function to arms or legs, is extracting the information from the nerve and getting it to the limb so that function is restored.”

One way of addressing this problem is implanting a nerve in the large muscles of the shoulder and attaching electrodes to it. The problem with this approach is scar tissue forms around the electrode, plus it is only possible to extract surface-level information from the electrode.

To get better resolution, any implant for restoring function would need to extract much more information from the electrodes. And to improve sensitivity, the researchers wanted to design something that could work on the scale of a single nerve fibre, or axon.

“An axon itself has a tiny voltage,” said Barone. “But once it connects with a muscle cell, which has a much higher voltage, the signal from the muscle cell is easier to extract. That’s where you can increase the sensitivity of the implant.”

The researchers designed a biocompatible flexible electronic device that is thin enough to be attached to the end of a nerve. A layer of stem cells, reprogrammed into muscle cells, was then placed on the electrode. This is the first time that this type of stem cell, called an induced pluripotent stem cell, has been used in a living organism in this way.

“These cells give us an enormous degree of control,” said Barone. “We can tell them how to behave and check on them throughout the experiment. By putting cells in between the electronics and the living body, the body doesn’t see the electrodes, it just sees the cells, so scar tissue isn’t generated.”

The Cambridge biohybrid device was implanted into the paralysed forearm of the rats. The stem cells, which had been transformed into muscle cells prior to implantation, integrated with the nerves in the rat’s forearm. While the rats did not have movement restored to their forearms, the device was able to pick up the signals from the brain that control movement. If connected to the rest of the nerve or a prosthetic limb, the device could help restore movement.

The cell layer also improved the function of the device, by improving resolution and allowing long-term monitoring inside a living organism. The cells survived through the 28-day experiment: the first time that cells have been shown to survive an extended experiment of this kind.

The researchers say that their approach has multiple advantages over other attempts to restore function in amputees. In addition to its easier integration and long-term stability, the device is small enough that its implantation would only require keyhole surgery. Other neural interfacing technologies for the restoration of function in amputees require complex patient-specific interpretations of cortical activity to be associated with muscle movements, while the Cambridge-developed device is a highly scalable solution since it uses ‘off the shelf’ cells.

In addition to its potential for the restoration of function in people who have lost the use of a limb or limbs, the researchers say their device could also be used to control prosthetic limbs by interacting with specific axons responsible for motor control.

“This interface could revolutionise the way we interact with technology,” said co-first author Amy Rochford, from the Department of Engineering. “By combining living human cells with bioelectronic materials, we’ve created a system that can communicate with the brain in a more natural and intuitive way, opening up new possibilities for prosthetics, brain-machine interfaces, and even enhancing cognitive abilities.”

“This technology represents an exciting new approach to neural implants, which we hope will unlock new treatments for patients in need,” said co-first author Dr Alejandro Carnicer-Lombarte, also from the Department of Engineering.

“This was a high-risk endeavour, and I’m so pleased that it worked,” said Professor George Malliaras from Cambridge’s Department of Engineering, who co-led the research. “It’s one of those things that you don’t know whether it will take two years or ten before it works, and it ended up happening very efficiently.”

The researchers are now working to further optimise the devices and improve their scalability. The team have filed a patent application on the technology with the support of Cambridge Enterprise, the University’s technology transfer arm.

The technology relies on opti-oxTM enabled muscle cells. opti-ox is a precision cellular reprogramming technology that enables faithful execution of genetic programmes in cells allowing them to be manufactured consistently at scale. The opti-ox enabled muscle iPSC cell lines used in the experiment were supplied by the Kotter lab [Mark Kotter] from the University of Cambridge. The opti-ox reprogramming technology is owned by synthetic biology company bit.bio.

The research was supported in part by the Engineering and Physical Sciences Research Council (EPSRC), part of UK Research and Innovation (UKRI), Wellcome, and the European Union’s Horizon 2020 Research and Innovation Programme.

Caption: In a study carried out in rats, researchers from the University of Cambridge used a biohybrid device to improve the connection between the brain and paralysed limbs. The device combines flexible electronics and human stem cells – the body’s ‘reprogrammable’ master cells – to better integrate with the nerve and drive limb function. Credit: University of Cambirdge

Here’s a link to and a citation for the paper,

Functional neurological restoration of amputated peripheral nerve using biohybrid regenerative bioelectronics by Amy E. Rochford, Alejandro Carnicer-Lombarte, Malak Kawan, Amy Jin, Sam Hilton, Vincenzo F. Curto, Alexandra L. Rutz, Thomas Moreau, Mark R. N. Kotter, George G. Malliaras, and Damiano G. Barone. Science Advances 22 Mar 2023 Vol 9, Issue 12 DOI: 10.1126/sciadv.add8162

This paper is open access.

The synthetic biology company mentioned in the press release, bit.bio is here

‘Living medicine’ for lung infections

This is a fascinating approach to dealing with the problem of antibiotic resistant bacteria, from a January 19, 2023 news item on ScienceDaily,

Researchers have designed the first ‘living medicine’ to treat lung infections. The treatment targets Pseudomonas aeruginosa, a type of bacteria which is naturally resistant to many types of antibiotics and is a common source of infections in hospitals.

The treatment involves using a modified version of the bacterium Mycoplasma pneumoniae, removing its ability to cause disease and repurposing it to attack P. aeruginosa instead. The modified bacterium is used in combination with low doses of antibiotics that would otherwise not work on their own.

A January 19, 2023 Centre for Genomic Regulation press release (also on EurekAlert), which originated the news item, provides more technical detail about the work,

Researchers tested the efficacy of the treatment in mice, finding that it significantly reduced lung infections. The ‘living medicine’ doubled mouse survival rate compared to not using any treatment. Administering a single, high dose of the treatment showed no signs of toxicity in the lungs. Once the treatment had finished its course, the innate immune system cleared the modified bacteria in a period of four days. 

The findings are published in the journal Nature Biotechnology and are supported by the “la Caixa” Foundation through the CaixaResearch Health call. The study was led by researchers at the Centre for Genomic Regulation (CRG) and Pulmobiotics in collaboration with the Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clinic de Barcelona and the Institute of Agrobiotechnology (IdAB), a joint research institute of Spain’s CSIC and the government of Navarre. 

P. aeruginosa infections are difficult to treat because the bacteria lives in communities that form biofilms. Biofilms can attach themselves to various surfaces in the body, forming impenetrable structures that escape the reach of antibiotics. 

P. aeruginosa biofilms can grow on the surface of endotracheal tubes used by critically-ill patients who require mechanical ventilators to breathe. This causes ventilator-associated pneumonia (VAP), a condition which affects one in four (9-27%) patients who require intubation. The incidence exceeds 50% for patients intubated because of severe Covid-19. VAP can extend the duration in intensive care unit for up to thirteen days and kills up to one in eight patients (9-13%). 

The authors of the study engineered M. pneumoniae to dissolve biofilms by equipping it with the ability to produce various molecules including pyocins, toxins naturally produced by bacteria to kill or inhibit the growth Pseudomonas bacterial strains. To test its efficacy, they collected P. aeruginosa biofilms from the endotracheal tubes of patients in intensive care units. They found the treatment penetrated the barrier and successfully dissolved the biofilms. 

“We have developed a battering ram that lays siege to antibiotic-resistant bacteria. The treatment punches holes in their cell walls, providing crucial entry points for antibiotics to invade and clear infections at their source. We believe this is a promising new strategy to address the leading cause of mortality in hospitals,” says Dr. María Lluch, Chief Scientific Officer at Pulmobiotics, co-corresponding author of the study and principal investigator at the International University of Catalonia. 

With the aim of using the ‘living medicine’ to treat VAP, the researchers will carry out further tests before reaching the clinical trial phase. The treatment is expected to be administered using a nebulizer, a device that turns liquid medicine into a mist which is then inhaled through a mouthpiece or a mask. 

M. pneumoniae is one of the smallest known species of bacteria. Dr. Luis Serrano, Director of the CRG, first had the idea to modify the bacteria and use it as a ‘living medicine’ two decades ago. Dr. Serrano is a specialist in synthetic biology, a field that involves repurposing organisms and engineering them to have new, useful abilities. With just 684 genes and no cell wall, the relative simplicity of M. pneumoniae makes it ideal for engineering biology for specific applications. 

One of the advantages of using M. pneumoniae to treat respiratory diseases is that it is naturally adapted to lung tissue. After administering the modified bacterium, it travels straight to the source of a respiratory infection, where it sets up shop like a temporary factory and produces a variety of therapeutic molecules. 

By showing that M. pneumoniae can tackle infections in the lung, the study opens the door for researchers creating new strains of the bacteria to tackle other types of respiratory diseases such as lung cancer or asthma. “The bacterium can be modified with a variety of different payloads – whether these are cytokines, nanobodies or defensins. The aim is to diversify the modified bacterium’s arsenal and unlock its full potential in treating a variety of complex diseases,” says ICREA Research Professor Dr. Luis Serrano. 

In addition to designing the ‘living medicine’, Dr. Serrano’s research team are also using their expertise in synthetic biology to design new proteins that can be delivered by M. pneumoniae. The team are using these proteins to target inflammation caused by P. aeruginosa infections. 

Though inflammation is the body’s natural response to an infection, excessive or prolonged inflammation can damage lung tissue. The inflammatory response is orchestrated by the immune system, which release mediator proteins such as cytokines. One type of cytokine – IL-10 – has well-known anti-inflammatory properties and is of growing therapeutic interest. 

Research published in the journal Molecular Systems Biology by Dr. Serrano’s research group used protein-design softwares ModelX and FoldX to engineer new versions of IL-10 purposefully optimised to treat inflammation. The cytokines were designed to be created more efficiently and to have higher affinity, meaning less cytokines are needed to have the same effect. 

The researchers engineered strains of M. pneumoniae that expressed the new cytokines and tested its efficacy in the lungs of mice with acute P. aeruginosa infections. They found that engineered versions of IL-10 were significantly more effective at reducing inflammation compared to the wild type IL-10 cytokine. 

According to Dr. Ariadna Montero Blay, co-corresponding author of the study in Molecular Systems Biology, “live biotherapeutics such as M. pneumoniae provide ideal vehicles to help overcome the traditional limitations of cytokines and unlock their huge potential in treating a variety of human diseases. Engineering cytokines as therapeutic molecules was critical to tackle inflammation. Other lung diseases such as asthma or pulmonary fibrosis could also stand to benefit from this approach.” 

Here’s a link to and a citation for the paper,

Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms by Rocco Mazzolini, Irene Rodríguez-Arce, Laia Fernández-Barat, Carlos Piñero-Lambea, Victoria Garrido, Agustín Rebollada-Merino, Anna Motos, Antoni Torres, Maria Jesús Grilló, Luis Serrano & Maria Lluch-Senar. Nature Biotechnology (2023) DOI: https://doi.org/10.1038/s41587-022-01584-9 Published: 19 January 2023

This paper is open access.

I haven’t come across the Centre for Genomic Regulation before, so, here’s how they describe themselves from their website’s About Us, General Information page,

The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, created in July 2000. It is a non-profit foundation funded by the Catalan Government through the Department of Business & Knowledge and the Department of Health, the Spanish Ministry of Science & Innovation, the “la Caixa” Banking Foundation, and includes the participation of Pompeu Fabra University.  

The mission of the CRG is to discover and advance knowledge for the benefit of society, public health and economic prosperity.  

The CRG believes that the medicine of the future depends on the groundbreaking science of today. This requires an interdisciplinary scientific team focused on understanding the complexity of life from the genome to the cell to a whole organism and its interaction with the environment, offering an integrated view of genetic diseases.  

The CRG is a unique centre in Spain, based in an innovative organization research model. Group leaders at the CRG are recruited internationally and receive support from the centre to set up and run their groups. An external evaluation panel, made up of renowned leaders in the different areas, evaluates them. The result of evaluations conditions the future of the CRG scientists, no matter whether they have open-ended or time-limited contracts. This ensures the mobility and the renewal of the workforce.

There you have it.

Biosynthetic melanin nanoparticles enabled by genetically engineered bacterium

A January 13, 2023 news item on phys.org announces research into genetically engineering bacteria so they produce melanin nanoparticles, i.e., biosynthetic melanin nanoparticles, Note: Links have been removed,

Photothermal therapy (PTT) has attracted considerable attention for the treatment of tumors because it is minimally invasive and has spatiotemporal selectivity.

Melanin is a kind of multifunctional pigment found widely in mammals, plants and microbes, with great prospects as a PTT agent for cancer treatment. Unfortunately, commercially available melanin is mainly obtained by chemical synthesis or extraction from sepia, which hinders its large-scale production and causes some potential safety hazards.

Recently, a research team led by Prof. Yan Fei from the Shenzhen Institute of Advanced Technology (SIAT) of the Chinese Academy of Sciences, together with Prof. Lin Jing from Shenzhen University and Prof. Xu Xiaohong from Guangdong Medical University, heterologously expressed a tyrosinase gene in Escherichia coli to synthesize melanin nanoparticles under mild and environmentally friendly conditions.

Caption: Schematic illustration of biosynthetic melanin nanoparticles for photoacoustic imaging-guided photothermal therapy. Credit: SIAT [Shenzhen Institute of Advanced Technology]

A January 13, 2023 Chinese Academy of Sciences press release (also on EurekAlert but published January 12, 2023), which originated the news item, provides a little more detail about the research,

The biosynthetic melanin nanoparticles exhibited excellent biocompatibility, good stability, and negligible toxicity. “They had strong absorption in the near-infrared region and higher photothermal conversion efficiency (48.9%) than chemically synthesized melanin-like polydopamine nanoparticles under an 808-nm laser irradiation,” said Prof. YAN.

The researchers further evaluated the photoacoustic imaging performance and antitumor efficacy of biosynthetic melanin nanoparticles. The results showed that the biosynthetic melanin nanoparticles had excellent photoacoustic imaging performance and could be used for photoacoustic imaging-guided photothermal therapy in vivo

“Our study provided an alternative approach to synthesize PTT agents with broad application potential in the diagnosis and treatment of cancer,” said Prof. YAN.

Here’s a link to and a citation for the paper,

Biosynthesis of Melanin Nanoparticles for Photoacoustic Imaging Guided Photothermal Therapy by Meijun Fu, Yuping Yang, Zhaomeng Zhang, Yaling He, Yuanyuan Wang, Chenxing Liu, Xiaohong Xu, Jing Lin, Fei Yan. Small DOI: https://doi.org/10.1002/smll.202205343 First published: 29 December 2022

This paper is behind a paywall.

Transforming bacterial cells into living computers

If this were a movie instead of a press release, we’d have some ominous music playing over a scene in a pristine white lab. Instead, we have a November 13, 2022 Technion-Israel Institute of Technology press release (also on EurekAlert) where the writer tries to highlight the achievement while downplaying the sort of research (in synthetic biology) that could have people running for the exits,

Bringing together concepts from electrical engineering and bioengineering tools, Technion and MIT [Massachusetts Institute of Technology] scientists collaborated to produce cells engineered to compute sophisticated functions – “biocomputers” of sorts. Graduate students and researchers from Technion – Israel Institute of Technology Professor Ramez Daniel’s Laboratory for Synthetic Biology & Bioelectronics worked together with Professor Ron Weiss from the Massachusetts Institute of Technology to create genetic “devices” designed to perform computations like artificial neural circuits. Their results were recently published in Nature Communications.

The genetic material was inserted into the bacterial cell in the form of a plasmid: a relatively short DNA molecule that remains separate from the bacteria’s “natural” genome. Plasmids also exist in nature, and serve various functions. The research group designed the plasmid’s genetic sequence to function as a simple computer, or more specifically, a simple artificial neural network. This was done by means of several genes on the plasmid regulating each other’s activation and deactivation according to outside stimuli.

What does it mean that a cell is a circuit? How can a computer be biological?

At its most basic level, a computer consists of 0s and 1s, of switches. Operations are performed on these switches: summing them, picking the maximal or minimal value between them, etc. More advanced operations rely on the basic ones, allowing a computer to play chess or fly a rocket to the moon.

In the electronic computers we know, the 0/1 switches take the form of transistors. But our cells are also computers, of a different sort. There, the presence or absence of a molecule can act as a switch. Genes activate, trigger or suppress other genes, forming, modifying, or removing molecules. Synthetic biology aims (among other goals) to harness these processes, to synthesize the switches and program the genes that would make a bacterial cell perform complex tasks. Cells are naturally equipped to sense chemicals and to produce organic molecules. Being able to “computerize” these processes within the cell could have major implications for biomanufacturing and have multiple medical applications.

The Ph.D students (now doctors) Luna Rizik and Loai Danial, together with Dr. Mouna Habib, under the guidance of Prof. Ramez Daniel from the Faculty of Biomedical Engineering at the Technion, and in collaboration with Prof. Ron Weiss from the Synthetic Biology Center, MIT,  were inspired by how artificial neural networks function. They created synthetic computation circuits by combining existing genetic “parts,” or engineered genes, in novel ways, and implemented concepts from neuromorphic electronics into bacterial cells. The result was the creation of bacterial cells that can be trained using artificial intelligence algorithms.

The group were able to create flexible bacterial cells that can be dynamically reprogrammed to switch between reporting whether at least one of a test chemicals, or two, are present (that is, the cells were able to switch between performing the OR and the AND functions). Cells that can change their programming dynamically are capable of performing different operations under different conditions. (Indeed, our cells do this naturally.) Being able to create and control this process paves the way for more complex programming, making the engineered cells suitable for more advanced tasks. Artificial Intelligence algorithms allowed the scientists to produce the required genetic modifications to the bacterial cells at a significantly reduced time and cost.

Going further, the group made use of another natural property of living cells: they are capable of responding to gradients. Using artificial intelligence algorithms, the group succeeded in harnessing this natural ability to make an analog-to-digital converter – a cell capable of reporting whether the concentration of a particular molecule is “low”, “medium”, or “high.” Such a sensor could be used to deliver the correct dosage of medicaments, including cancer immunotherapy and diabetes drugs.

Of the researchers working on this study, Dr. Luna Rizik and Dr. Mouna Habib hail from the Department of Biomedical Engineering, while Dr. Loai Danial is from the Andrew and Erna Viterbi Faculty of Electrical Engineering. It is bringing the two fields together that allowed the group to make the progress they did in the field of synthetic biology.

This work was partially funded by the Neubauer Family Foundation, the Israel Science Foundation (ISF), European Union’s Horizon 2020 Research and Innovation Programme, the Technion’s Lorry I. Lokey interdisciplinary Center for Life Sciences and Engineering, and the [US Department of Defense] Defense Advanced Research Projects Agency [DARPA].

Here’s a link to and a citation for the paper,

Synthetic neuromorphic computing in living cells by Luna Rizik, Loai Danial, Mouna Habib, Ron Weiss & Ramez Daniel. Nature Communications volume 13, Article number: 5602 (2022) DOIL https://doi.org/10.1038/s41467-022-33288-8 Published: 24 September 2022

This paper is open access.

Coelacanth (a living fish fossil) may provide clue to making artificial organs for transplantation

An ancient fish called a ‘living fossil’ has helped researchers understand the basics of stem cells. This will further stem cell research and be a step in the direction of creating artificial organs. The coelacanth fish is 400 million years old. Photo: Canva. Courtesy: university of Copenhagen

A December 12, 2022 University of Copenhagen press release (also on EurekAlert) describes work which may have an impact on organ transplants,

A beating heart. A complicated organ that pumps blood around the body of animals and humans. Not exactly something you associate with a Petri dish in a laboratory.

But that may change in the future, and save the lives of people whose own organs fail. And the research is now one step closer to that.

To design artificial organs you first have to understand stem cells and the genetic instructions that govern their remarkable properties.

Professor Joshua Mark Brickman at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) has unearthed the evolutionary origins of a master gene that acts on a network of genes instructing stem cells.

“The first step in stem cell research is to understand the gene regulatory network that supports so-called pluripotent stem cells. Understanding how their function was perfected in evolution can help provide knowledge about how to construct better stem cells,” says Joshua Mark Brickman.

Pluripotent stem cells are stem cells that can develop into all other cells. For example, heart cells. If we understand how the pluripotent stem cells develop into a heart, then we are one step closer to replicating this process in a laboratory.

What are stem cells?

Stem cells are non-specialized cells found in all multicellular organisms. Stem cells have two properties that distinguish them from other cell types. On the one hand, stem cells can undergo an unlimited number of cell divisions (mitoses), and on the other hand, stem cells have the ability to mature (differentiate) into several cell types.

A pluripotent stem cell is a cell that can develop into any other cell, such as a heart cell, hair cell or eye cell.

A ‘living fossil’ is the key to understanding stem cells

The pluripotent property of stem cells – meaning that the cells can develop into any other cell – is something that has traditionally been associated with mammals.

Now Joshua Mark Brickman and his colleagues have found that the master gene that controls stem cells and supports pluripotency also exists in a fish called coelacanth. In humans and mice this gene is called OCT4 and they found that the coelacanth version could replace the mammalian one in mouse stem cells.

In addition to the fact that the coelacanth is in a different class from mammals, it has also been called a ‘living fossil,’ since approximately 400 million years ago it developed into the form it has today. It has fins shaped like limbs and is therefore thought to resemble the first animals to move from the sea onto land.

“By studying its cells, you can go back in evolution, so to speak,” explains Assistant Professor Molly Lowndes.

Assistant Professor Woranop Sukparangsi continues: “The central factor controlling the gene network in stem cells is found in the coelacanth. This shows that the network already existed early in evolution, potentially as far back as 400 million years ago.”

And by studying the network in other species, such as this fish, the researchers can distill what the basic concepts that support a stem cell are.

“The beauty of moving back in evolution is that the organisms become simpler. For example, they have only one copy of some essential genes instead of many versions. That way, you can start to separate what is really important for stem cells and use that to improve how you grow stem cells in a dish,” says PhD student Elena Morganti.

Sharks, mice and kangaroos

In addition to the researchers finding out that the network around stem cells is much older than previously thought, and found in ancient species, they also learned how exactly evolution has modified the network of genes to support pluripotent stem cells.

The researchers looked at the stem cell genes from over 40 animals. For example sharks, mice and kangaroos. The animals were selected to provide a good sampling of the main branch points in evolution.

The researchers used artificial intelligence to build three-dimensional models of the different OCT4 proteins. The researchers could see that the general structure of the protein is maintained across evolution. While the regions of these proteins known to be important for stem cells do not change, species-specific differences in apparently unrelated regions of these proteins alter their orientation, potentially affecting how well it supports pluripotency.

“This a very exciting finding about evolution that would not have been possible prior to the advent of new technologies. You can see it as evolution cleverly thinking, we don not tinker with the ‘engine in the car’, but we can move the engine around and improve the drive train to see if it makes the car go faster,” says Joshua Mark Brickman.

The study is a collaborative project spanning Australia, Japan and Europe, with vital strategic partnerships with the groups of Sylvie Mazan at the Oceanological Observatory of Banyuls-sur-Mer in France and professor Guillermo Montoya at Novo Nordisk Foundation Center for Protein Research at University of Copenhagen.

Caption: Coelacanth-fish and other animals. Credit: By Woranop Sukparangsi Courtesy: University of Copenhagen

Here’s a link to and a citation for the paper,

Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency by Woranop Sukparangsi, Elena Morganti, Molly Lowndes, Hélène Mayeur, Melanie Weisser, Fella Hammachi, Hanna Peradziryi, Fabian Roske, Jurriaan Hölzenspies, Alessandra Livigni, Benoit Gilbert Godard, Fumiaki Sugahara, Shigeru Kuratani, Guillermo Montoya, Stephen R. Frankenberg, Sylvie Mazan & Joshua M. Brickman. Nature Communications volume 13, Article number: 5537 (2022) DOI: https://doi.org/10.1038/s41467-022-32481-z Published: 21 September 2022

This paper is open access.

Living photovoltaics with carbon nanotubes (CNTs)?

A September 12, 2022 news item on phys.org has an interesting lede,

“We put nanotubes inside of bacteria,” says Professor Ardemis Boghossian at EPFL’s School of Basic Sciences. “That doesn’t sound very exciting on the surface, but it’s actually a big deal. Researchers have been putting nanotubes in mammalian cells that use mechanisms like endocytosis, that are specific to those kinds of cells. Bacteria, on the other hand, don’t have these mechanisms and face additional challenges in getting particles through their tough exterior. Despite these barriers, we’ve managed to do it, and this has very exciting implications in terms of applications.”

A September 16, 2022 Ecole Polytechnique Fédérale de Lausanne (EPFL) press release (also on EurekAlert but published September 12, 2022), which originated the news item, goes on to describe this work in the field of ‘nanobionics,

Boghossian’s research focuses on interfacing artificial nanomaterials with biological constructs, including living cells. The resulting “nanobionic” technologies combine the advantages of both the living and non-living worlds. For years, her group has worked on the nanomaterial applications of single-walled carbon nanotubes (SWCNTs), tubes of carbon atoms with fascinating mechanical and optical properties.

These properties make SWCNTs [single-walled carbon nanotubes] ideal for many novel applications in the field of nanobiotechnology. For example, SWCNTs have been placed inside mammalian cells to monitor their metabolisms using near-infrared imaging. The insertion of SWCNTs in mammalian cells has also led to new technologies for delivering therapeutic drugs to their intracellular targets, while in plant cells they have been used for genome editing. SWCNTs have also been implanted in living mice to demonstrate their ability to image biological tissue deep inside the body.

Fluorescent nanotubes in bacteria: A first

In an article published in Nature Nanotechnology, Boghossian’s group with their international colleagues were able to “convince” bacteria to spontaneously take up SWCNTs by “decorating” them with positively charged proteins that are attracted by the negative charge of the bacteria’s outer membrane. The two types of bacteria explored in the study, Synechocystis and Nostoc, belong to the Cyanobacteria phylum, an enormous group of bacteria that get their energy through photosynthesis – like plants. They are also “Gram-negative”, which means that their cell wall is thin, and they have an additional outer membrane that “Gram-positive” bacteria lack.

The researchers observed that the cyanobacteria internalized SWCNTs through a passive, length-dependent and selective process. This process allowed the SWCNTs to spontaneously penetrate the cell walls of both the unicellular Synechocystis and the long, snake-like, multicellular Nostoc.

Following this success, the team wanted to see if the nanotubes can be used to image cyanobacteria – as is the case with mammalian cells. “We built a first-of-its-kind custom setup that allowed us to image the special near-infrared fluorescence we get from our nanotubes inside the bacteria,” says Boghossian.

Alessandra Antonucci, a former PhD student at Boghossian’s lab adds: “When the nanotubes are inside the bacteria, you could very clearly see them, even though the bacteria emit their own light. This is because the wavelengths of the nanotubes are far in the red, the near-infrared. You get a very clear and stable signal from the nanotubes that you can’t get from any other nanoparticle sensor. We’re excited because we can now use the nanotubes to see what is going on inside of cells that have been difficult to image using more traditional particles or proteins. The nanotubes give off a light that no natural living material gives off, not at these wavelengths, and that makes the nanotubes really stand out in these cells.”

“Inherited nanobionics”

The scientists were able to track the growth and division of the cells by monitoring the bacteria in real-time. Their findings revealed that the SWCNTs were being shared by the daughter cells of the dividing microbe.  “When the bacteria divide, the daughter cells inherent the nanotubes along with the properties of the nanotubes,” says Boghossian. “We call this ‘inherited nanobionics.’ It’s like having an artificial limb that gives you capabilities beyond what you can achieve naturally. And now imagine that your children can inherit its properties from you when they are born. Not only did we impart the bacteria with this artificial behavior, but this behavior is also inherited by their descendants. It’s our first demonstration of inherited nanobionics.”

Living photovoltaics

“Another interesting aspect is when we put the nanotubes inside the bacteria, the bacteria show a significant enhancement in the electricity it produces when it is illuminated by light,” says Melania Reggente, a postdoc with Boghossian’s group. “And our lab is now working towards the idea of using these nanobionic bacteria in a living photovoltaic.”

“Living” photovoltaics are biological energy-producing devices that use photosynthetic microorganisms. Although still in the early stages of development, these devices represent a real solution to our ongoing energy crisis and efforts against climate change.

“There’s a dirty secret in photovoltaic community,” says Boghossian. “It is green energy, but the carbon footprint is really high; a lot of CO2 is released just to make most standard photovoltaics. But what’s nice about photosynthesis is not only does it harness solar energy, but it also has a negative carbon footprint. Instead of releasing CO2, it absorbs it. So it solves two problems at once: solar energy conversion and CO2 sequestration. And these solar cells are alive. You do not need a factory to build each individual bacterial cell; these bacteria are self-replicating. They automatically take up CO2 to produce more of themselves.  This is a material scientist’s dream.”

Boghossian envisions a living photovoltaic device based on cyanobacteria that have automated control over electricity production that does not rely on the addition of foreign particles. “In terms of implementation, the bottleneck now is the cost and environmental effects of putting nanotubes inside of cyanobacteria on a large scale.”

With an eye towards large-scale implementation, Boghossian and her team are looking to synthetic biology for answers: “Our lab is now working towards bioengineering cyanobacteria that can produce electricity without the need for nanoparticle additives. Advancements in synthetic biology allow us to reprogram these cells to behave in totally artificial ways. We can engineer them so that producing electricity is literally in their DNA.”

Other contributors

University of Freiburg
Swiss Center for Electronics and Microtechnology
University of Salento
Sapienza University of Rome

Here’s a link to and a citation for the paper,

Carbon nanotube uptake in cyanobacteria for near-infrared imaging and enhanced bioelectricity generation in living photovoltaics by Alessandra Antonucci, Melania Reggente, Charlotte Roullier, Alice J. Gillen, Nils Schuergers, Vitalijs Zubkovs, Benjamin P. Lambert, Mohammed Mouhib, Elisabetta Carata, Luciana Dini & Ardemis A. Boghossian. Nature Nanotechnology (2022) DOI: https://doi.org/10.1038/s41565-022-01198-x Published: 12 September 2022

This paper is behind a paywall.