Showing posts with label synthbio. Show all posts
Showing posts with label synthbio. Show all posts

Friday, April 4, 2025

Making Materials Progress


Make it stop: 

'Living' ceramics utilize bacteria for gas sensing and carbon capture
Dec 2024, phys.org

The work involved first 3D printing stacked, ceramic, spiral structures that could stand on their own. The structures were printed with pits on their outer surfaces to give bacteria a place to live. The larger pits were used as a way to channel nutrients to the bacteria.

To further ensure the bacteria could feed for an extended period of time, they set the structures in shallow pools of nutrient solutions. As the water in the solutions evaporated, the nutrients were pulled up to the pits containing the nutrients via capillary action. The bacteria were then allowed to multiply, filling the pores that had been designed for them. Testing showed they could survive without further nutrients for up to two weeks.

The research team used different types of bacteria for different purposes—with photosynthetic cyanobacteria, for example, the structure could serve as a CO2 extraction device, pulling the gas from the air. They also tried Escherichia coli and found that they made the structure a formaldehyde detector.

via ETH Zurich: Alessandro Dutto et al, Living Porous Ceramics for Bacteria‐Regulated Gas Sensing and Carbon Capture, Advanced Materials (2024). DOI: 10.1002/adma.202412555


Self-adjusting shading system mimics pine cones for energy-autonomous weather response
Jan 2025, phys.org

"We are achieving a shading system that opens and closes autonomously in response to changes in the weather, without the need for operational energy or any mechatronic elements. The bio-material structure itself is the machine."

It's based on pine cones. In high humidity, the cellulosic materials absorb moisture and expand, causing the printed elements to curl and open. Conversely, in low humidity, the cellulosic materials release moisture and contract, causing the printed elements to flatten and close.

via University of Stuttgart Institute for Computational Design and Construction: Tiffany Cheng et al, Weather-responsive adaptive shading through biobased and bioinspired hygromorphic 4D-printing, Nature Communications (2024). DOI: 10.1038/s41467-024-54808-8


Unoccupied housing in China's urban areas emitting massive amounts of carbon, study finds
Mar 2025, phys.org

Prior research has shown that by 2021, approximately 17% of homes built in cities in China were unoccupied. Some in the field have suggested that the number has only grown since then, to between 20 and 65 million unoccupied units. This new research found that approximately 17.4% of all new residential units built between 2001 and 2018 have never been occupied

The total the team came up with was 55.81 million tons of carbon emissions solely due to the unoccupied housing units, which they note represent approximately 6.9% of China's total residential emissions. (One source of emissions is the footprint of the materials, and the second comes from heating and cooling, because most of the units are apartment buildings with central heating and cooling.)

via Tsinghua University: Hefan Zheng et al, Unused housing in urban China and its carbon emission impact, Nature Communications (2025). DOI: 10.1038/s41467-025-57217-7

Friday, January 24, 2025

Give Me Some Skin


Nope nope nope.

Faces made of living skin make robots smile
Jun 2024, BBC News

Tokyo University makes Face on a Chip (see the above image) - The trick the team employed was to use a special collagen gel for adhesion, which is naturally viscous so difficult to feed into the minuscule perforations. But using a common technique for plastic adhesion called plasma treatment, they managed to coax the collagen into the fine structures of the perforations while also holding the skin close to the surface in question.

Something like a face-on-a-chip could be useful in research into skin aging, cosmetics, surgical procedures, plastic surgery and more. (Follow the link and watch it move.)

via Tokyo Universty: M. Kawai, M. Nie, H. Oda, S. Takeuchi. Perforation-type anchors inspired by skin ligament for robotic face covered with living skin, Cell Reports Physical Science (2024). DOI: 10.1016/j.xcrp.2024.102066. 


Scientists create 'living bioelectronics' that can sense and heal skin
May 2024, phys.org

They made a new kind of bioelectronics that uses not just the electronics and a soft layer to make them less irritating to the body, but now a layer of living cells made of a gel from tapioca starch and gelatin, with S. epidermidis microbes tucked in. S. epidermidis microbes secrete compounds that reduce inflammation. 

via University of Chicago: iuyun Shi et al, Active biointegrated living electronics for managing inflammation, Science (2024). DOI: 10.1126/science.adl1102


Rewritable, recyclable 'smart skin' monitors biological signals on demand
May 2024, phys.org

The researchers made an adhesive composite with molecules called polyimide powders that add strength and heat resistance and amine-based ethoxylated polyethylenimine - a type of polymer that can modify conductive materials - dispersed in a silicone elastomer (rubber) to monitor the pH value, glucose and lactate concentrations in sweat as well as detecting via finger prick blood draws. It can also be reprogrammed to monitor heart rate, nerve performance and sweat glucose concentrations in real time.

via Pennsylvania State University College of Engineering: Jia Zhu et al, Direct Laser Processing and Functionalizing PI/PDMS Composites for an On‐Demand, Programmable, Recyclable Device Platform, Advanced Materials (2024). DOI: 10.1002/adma.202400236


New electronic skin mimics human touch with 3D architecture
Jun 2024, phys.org

3DAE-Skin

via Tsinghua University: Zhi Liu et al, A three-dimensionally architected electronic skin mimicking human mechanosensation, Science (2024). DOI: 10.1126/science.adk5556

Friday, January 10, 2025

Everything is Everywhere All of the Sudden


I usually don't post artist renderings like this, but this is what I see when imagining everything made of computers, using ambient energy like light to control different particles each designed to take it and do different things with it but all in one jumble of matter, like an intelligent matter: Above image: An artistic depiction of a wavelength-multiplexed diffractive optical processor for 3D quantitative phase imaging. Credit: UCLA Engineering Institute for Technology Advancement [link]

On what could be called "ubiquitous computing", a legend of artificial intelligence (Hinton) describes it really well:
(What's next in computing?) My last years at Google I was thinking about analog computing ... run these big language models in analog hardware ... if you're gonna use that low power analog computation, every piece of hardware is gonna be a bit different. And the idea is that the learning is gonna make use of the specific properties of that hardware.
--Geoffrey Hinton interview, "On Working w Ilya, Choosing Problems, and the Power of Intuition", July 2024 30min?

Researchers use 'smart' rubber structures to carry out computational tasks
May 2024, phys.org

"We now know how to design simple materials so they can process information."

The research team created a rubber computer that can act as a two-bit binary counter using slender rubber elements as mechanical bits, and assembling multiple bits together in a metamaterial.

Note: The title of their demonstration video is "Can Rubber Compute?" and I now see it all as a series of experiments like the Will It Blend series, where they just do it to everything - can crystals compute? (Yes, we already know that) Can light compute? (Yes we already know that too) Can slime mold compute? But can salt compute? (Actually yes, like in a gradient of fresh water and salt water, but I was talking about a pile of table salt.) Can my sneakers compute? (I mean obviously) Can my front door compute? (Also obvious, its whole thing is to open and close like 1/0) I'm not talking about a computer screwed on top of my doorknob, I mean the door itself, the whole thing, is a computer, just by the way its materials are put together.  The garbage can? Definitely garbage cans will compute. 

via Leiden University and AMOLF: Jingran Liu et al, Controlled pathways and sequential information processing in serially coupled mechanical hysterons, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2308414121


Using DNA origami, researchers create diamond lattice for future semiconductors of visible light
May 2024, phys.org

With headlines like that, there is no further explanation. 

via Ludwig Maximilian University of Munich: Gregor Posnjak et al, Diamond-lattice photonic crystals assembled from DNA origami, Science (2024). DOI: 10.1126/science.adl2733

Also: Hao Liu et al, Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments, Science (2024). DOI: 10.1126/science.adl5549


Mechanical computer relies on kirigami cubes, not electronics
Jun 2024, phys.org

It's a mechanical computer, one that doesn't use electronics. Is that all we need to call it? A mechanical computer?

Historically, these mechanical components have been things like levers or gears. But cubes can have five or more different states. Theoretically, that means a given cube can convey not only a 1 or a 0, but also a 2, 3 or 4.

When any of the cubes are pushed up or down, this changes the geometry—or architecture—of all of the connected cubes. This can be done by pushing up or down on one of the cubes with a magnetic field. These 64-cube functional units can be grouped together into increasingly complex metastructures that allow for storing more data or for conducting more complex computations.

The cubes are connected by thin strips of elastic tape. To edit data, you have to change the configuration of functional units. That requires users to pull on the edges of the metastructure, which stretches the elastic tape and allows you to push cubes up or down. When you release the metastructure, the tape contracts, locking the cubes—and the data—in place.

"One potential application for this is that it allows for users to create three-dimensional, mechanical encryption or decryption"

via North Carolina State University: Yanbin Li et al, Reprogrammable and reconfigurable mechanical computing metastructures with stable and high-density memory, Science Advances (2024). DOI: 10.1126/sciadv.ado6476 , www.science.org/doi/10.1126/sciadv.ado6476


New material paves the way to on-chip energy harvesting
Jul 2024, phys.org

They utilize the waste heat generated during operation and convert it back into electrical energy, called "on-chip energy harvesting", and it works because they put tin in the germanium (Ge+Sn). 

via Forschungszentrum Jülich and IHP—Leibniz Institute for High Performance Microelectronics in Germany, University of Pisa, University of Bologna, University of Leeds: Omar Concepción et al, Room Temperature Lattice Thermal Conductivity of GeSn Alloys, ACS Applied Energy Materials (2024). DOI: 10.1021/acsaem.4c00275


A first physical system to learn nonlinear tasks without a traditional computer processor
Jul 2024, phys.org

They made a contrastive local learning network where components evolve on their own based on local rules without knowledge of the larger structure, similar to how neurons in the human brain don't know what other neurons are doing and yet learning emerges.

"It can learn, in a machine learning sense, to perform useful tasks, similar to a computational neural network, but it is a physical object."

(Physical object, that's the key)

"Because the way that it both calculates and learns is based on physics, it's way more interpretable. You can actually figure out what it's trying to do because you have a good handle on the underlying mechanism. That's kind of unique because a lot of other learning systems are black boxes where it's much harder to know why the network did what it did.

via University of Pennsylvania: Sam Dillavou et al, Machine learning without a processor: Emergent learning in a nonlinear analog network, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2319718121

The optical era of science reporting where every picture has rainbows in it: Artistic depiction of diffractive information processing - Ozcan Lab at UCLA - Jul 2024

Scientists demonstrate chemical reservoir computation using the formose reaction
Jul 2024, phys.org

Good explanation by the writeup author here, Tejasri Gururaj: The field of molecular computing interests researchers who wish to harness the computational power of chemical and biological systems. In these systems, the chemical reactions or molecular processes act as the reservoir computer, transforming inputs into high-dimensional outputs. ...

The formose reaction is the only example of a self-organizing reaction network with a highly non-linear topology, containing numerous positive and negative feedback loops.

The researchers used a continuous stirred tank reactor (CSTR) to implement the formose reaction. The input concentrations of four reactants—formaldehyde, dihydroxyacetone, sodium hydroxide, and calcium chloride—are controlled to modulate the reaction network's behavior.

The output molecule is identified using a mass spectrometer, which allows them to track up to 106 molecules. 

This setup can be used to do calculations, with the reactant concentrations being the input value to any function that needs to be computed.

The team showed that it could predict the behavior of a complex metabolic network model of E. coli, accurately capturing both linear and nonlinear responses to fluctuating inputs across various concentration ranges.

Furthermore, the system demonstrated the ability to forecast future states of a chaotic system (the Lorenz attractor), accurately predicting two out of three input dimensions several hours into the future.

via Institute for Molecules and Materials at Radboud University: Mathieu G. Baltussen et al, Chemical reservoir computation in a self-organizing reaction network, Nature (2024). DOI: 10.1038/s41586-024-07567-x

Wednesday, January 10, 2024

Biocomputers and Engineered Living Material


Using mycelium to create a self-healing wearable leather-like material
Apr 2023, phys.org

Mushroom leather made of mycelium mats

via Newcastle and Northumbria Universities: Elise Elsacker et al, Fungal Engineered Living Materials: The Viability of Pure Mycelium Materials with Self‐Healing Functionalities, Advanced Functional Materials (2023). DOI: 10.1002/adfm.202301875



New biocomputing method uses enzymes as catalysts for DNA-based molecular computing
May 2023, phys.org

Traditional computer hardware is limited in its ability to interface with living organs, which has constrained the development of medical devices. Through the use of biological molecules such as DNA or proteins, biocomputing has the potential to overcome these limitations.

Biocomputing is typically done either with live cells or with non-living, enzyme-free molecules. This team has developed a platform for a third method of biocomputing: Trumpet, or Transcriptional RNA Universal Multi-Purpose GatE PlaTform.

"Trumpet is a non-living molecular platform, so we don't have most of the problems of live cell engineering. We don't have to overcome evolutionary limitations against forcing cells to do things they don't want to do."

via University of Minnesota: Judee A. Sharon et al, Trumpet is an operating system for simple and robust cell-free biocomputing, Nature Communications (2023). DOI: 10.1038/s41467-023-37752-x


Scientists make common pain killers from pine trees instead of crude oil
Jul 2023, phys.org

Using the "biorefinery" approach, the precursors for paracetamol and ibuprofen, as well as beta-blockers and an asthma inhaler drug, as well as other chemicals for perfumes and cleaning products have all been made from biorenewable β-pinene, a component of turpentine and by-product from the paper industry. (Because using oil to make pharmaceuticals is unsustainable.)

via University of Bath: Joshua Dale Tibbetts et al, Sustainable Syntheses of Paracetamol and Ibuprofen from Biorenewable β‐pinene, ChemSusChem (2023). DOI: 10.1002/cssc.202300670

AI Art - Bioalchemy Neural Net 2 - 2023

3D-printed 'living material' could clean up contaminated water
Sep 2023, phys.org

"Engineered living material" - 3D-printed structure made of a seaweed-based polymer called alginate and bacteria that have been genetically engineered to produce an enzyme that transforms various organic pollutants into benign molecules. The bacteria were also engineered to self-destruct in the presence of a molecule called theophylline, which is often found in tea and chocolate. "What's innovative is the pairing of a polymer material with a biological system to create a living material."

via University of California San Diego Materials Research Science and Engineering Center: Debika Datta et al, Phenotypically complex living materials containing engineered cyanobacteria, Nature Communications (2023). DOI: 10.1038/s41467-023-40265-2


Metal-loving microbes offer a green way to refine rare earth elements
Oct 2023, phys.org

Cornell scientists have characterized the genome of Shewanella oneidensis - a metal-loving bacteria with an affinity for rare earth elements - to replace the harsh chemical processing with a benign practice called biosorption.

via Cornell: Sean Medin et al, Genomic characterization of rare earth binding by Shewanella oneidensis, Scientific Reports (2023). DOI: 10.1038/s41598-023-42742-6


New pipeline makes valuable organic acid from plants—saving money and emissions
Oct 2023, phys.org

They're making succinic acid from sugarcane using Issatchenkia orientalis, a yeast like Saccharomyces cerevisiae or the bacteria Escherichia coli, but one that thrives in pH 3-4 acidic conditions. This means it doesn't produce unwanted by-products that need to be separated-out at high cost. 

The researchers did extensive metabolic engineering to rewire I. orientalis to produce robust levels of succinic acid, which is widely used additive for food and beverages.

via University of Illinois at Urbana-Champaign Center for Advanced Bioenergy and Bioproducts Innovation, and Princeton: Vinh G. Tran et al, An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis, Nature Communications (2023). DOI: 10.1038/s41467-023-41616-9

AI Art - Bioalchemy Neural Net 3 - 2023

Scientists report completion of chromosome XI, a major step towards creating the world's first synthetic yeast
Nov 2023, phys.org

World's first synthetic yeast genome -- The synthetic chromosome has replaced one of the natural chromosomes of a yeast cell and, after a painstaking debugging process, now allows the cell to grow with the same fitness level as a natural cell. The synthetic genome will not only help scientists to understand how genomes function, but it will have many applications. 
 
via University of Nottingham and Imperial College London: Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics, Cell Genomics (2023). DOI: 10.1016/j.xgen.2023.100418.


Charged 'molecular beasts' as the foundation for new chemical compounds
Nov 2023, phys.org

They are modifying mass spectrometers to synthesize new molecules.

Note that a mass spectrometer is supposed to break things apart so you can look at them one by one, but this is now making entirely new chemicals with parts of the broken molecules. 

The basic strategy of controlling reactive chemicals in mass spectrometers is not new, but the  substances are only produced in tiny quantities and cannot be extracted. They are destroyed when the signal used for analyses is generated. 

They're doing "preparative mass spectrometry" and making new molecules. 

via Physical and Theoretical Chemistry at Leipzig University: Markus Rohdenburg et al, Chemical Synthesis with Gaseous Molecular Ions: Harvesting [B12Br11N2]− from a Mass Spectrometer, Angewandte Chemie International Edition (2023). DOI: 10.1002/anie.202308600


New antibiotic approach proves promising against Lyme bacterium
Nov 2023, phys.org

Change some of the words, or not even, and it sounds like the most diabolical scifi weapon scenario:

"This transport mechanism gets internalized in the bacterium and brings in a molecule that causes what we've described as a berserker reaction - a programmed death response," said lead author Timothy Haystead, Ph.D., professor in Duke's Department of Pharmacology and Cancer Biology. "It wipes out the bacteria - sterilizes the culture with a single dose of light. And then when you look at what occurs with electron microscopy, you see the collapse of the chromosome."

via Duke University Medical Center: Dave L. Carlson et al, Targeting Borrelia burgdorferi HtpG with a berserker molecule, a strategy for anti-microbial development, Cell Chemical Biology (2023). DOI: 10.1016/j.chembiol.2023.10.004

Tuesday, May 2, 2023

Engineering Everything

 

Engineered nanoparticles could help store excess carbon dioxide in the ocean
Nov 2022, phys.org

Hochella and his colleagues examined the scientific evidence for seeding the oceans with iron-rich engineered fertilizer particles near ocean plankton, encouraging phytoplankton to act as a carbon sink.

Researchers' analysis of 123 published studies showed that numerous non-toxic metal-oxygen materials could safely enhance plankton growth.

via Department of Energy's Pacific Northwest National Laboratory: Peyman Babakhani et al, Potential use of engineered nanoparticles in ocean fertilization for large-scale atmospheric carbon dioxide removal, Nature Nanotechnology (2022). DOI: 10.1038/s41565-022-01226-w


Cocaine synthesized in a tobacco plant
Nov 2022, phys.org

Cocaine that winds up in its leaves is not produced by elements in the plant converting 4-(1-methyl-2-pyrrolidinyl)-3-oxobutanoic acid to hyoscyamine, as has been thought. They found that it is instead produced by the two enzymes, EnMT4 and EnCYP81AN15.

To prove their discovery, the group genetically engineered a tobacco plant to produce the two enzymes in its leaves, which resulted in the production of small amounts of cocaine 

The team also notes that the amount of cocaine produced by the tobacco plant was far too low for use on an industrial scale; thus, their work will continue. Not mentioned in the paper is the possibility of synthesizing the two enzymes produced by both the coca and engineered tobacco plant as a more direct way to synthesize cocaine.

via Chinese Academy of Sciences: Yong-Jiang Wang et al, Discovery and Engineering of the Cocaine Biosynthetic Pathway, Journal of the American Chemical Society (2022). DOI: 10.1021/jacs.2c09091


Wednesday, October 26, 2022

Things Come To Life


Surely we won't see it until it's already infiltrating every kingdom and phylum -- what once was just a dumb robot, or a box of rocks, or a pile of dust, will soon be alive and trying to make its way in the world, commanding the same respect as the river in Ecuador that has rights, or the endangered animals in the Galapagos that have rights, or the dematerialized algorithms that exist as a dimensionally camouflaged meta-entity powered by economic incentive and psychological manipulation, which doesn't even need rights because it's the lifeline of global commerce. 

One day we'll all be held ethically liable for treating our stuff like inert, soul-less matter.



Starfish embryos swim in formation like a 'living crystal,' could inform the design of self assembling 
Jul 2022, phys.org

Fakhri says the team's observations of starfish crystals was a "serendipitous discovery." 

She and her colleagues fertilized thousands of starfish embryos, then watched as they swam to the surface of shallow dishes. "There are thousands of embryos in a dish, and they start forming this crystal structure that can grow very large," Fakhri says. "We call it a crystal because each embryo is surrounded by six neighboring embryos in a hexagon that is repeated across the entire structure, very similar to the crystal structure in graphene."

via MIT: Nikta Fakhri, Odd dynamics of living chiral crystals, Nature (2022). DOI: 10.1038/s41586-022-04889-6.


A step toward the creation of materials controlled by artificial genes
Aug 2022, phys.org

"New types of soft material robots that are controlled by chemistry instead of electronics."

Say you're making artificial humans without saying you're making artificial humans.

"Engineering synthetic chemical systems that can emulate the complex behaviors of natural gene networks that operate inside diagnostic, self-healing materials rather than organisms."

via Johns Hopkins University: Samuel W. Schaffter et al, Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks, Nature Chemistry (2022). DOI: 10.1038/s41557-022-01001-3


Synthetic mouse embryo develops beating heart
Aug 2022, BBC News

Scientists in Cambridge have created synthetic mouse embryos in a lab, without using eggs or sperm, which show evidence of a brain and beating heart.

At present, UK law permits human embryos to be studied in the laboratory only up to the fourteenth day of development, but there are no rules around synthetic embryos.

via University of Cambridge and the California Institute of Technology: Synthetic embryos complete gastrulation to neurulation and organogenesis. Gianluca Amadei et al. Nature. 2022. https://doi.org/10.1038/s41586-022-05246-3


Robo-bug: A rechargeable, remote-controllable cyborg cockroach
Sep 2022, phys.org

Powered by a solar cell which is funny because roaches hang out in the dark mostly.

RIKEN: Yujiro Kakei et al, Integration of body-mounted ultrasoft organic solar cell on cyborg insects with intact mobility, npj Flexible Electronics (2022). DOI: 10.1038/s41528-022-00207-2


Nanotubes illuminate the way to living photovoltaics
Sep 2022, phys.org

"We put nanotubes inside of bacteria" 

via Ecole Polytechnique Federale de Lausanne:  Ardemis Boghossian et al, Carbon nanotube uptake in cyanobacteria for near-infrared imaging and enhanced bioelectricity generation in living photovoltaics, Nature Nanotechnology (2022). DOI: 10.1038/s41565-022-01198-x


Post Script:
GlyNAC supplementation reverses aging hallmarks in aging humans
Aug 2022, phys.org

A randomized, double blind human clinical trial conducted by researchers at Baylor College of Medicine reveals that supplementation with GlyNAC—a combination of glycine and N-acetylcysteine—improves many age-associated defects in older humans and powerfully promotes healthy aging. 

via Baylor College of Medicine:  Premranjan Kumar et al, Supplementing Glycine and N-Acetylcysteine (GlyNAC) in Older Adults Improves Glutathione Deficiency, Oxidative Stress, Mitochondrial Dysfunction, Inflammation, Physical Function, and Aging Hallmarks: A Randomized Clinical Trial, The Journals of Gerontology: Series A (2022). DOI: 10.1093/gerona/glac135


Wednesday, October 5, 2022

Wood 2.0


Toward customizable timber, grown in a lab
May 2022, phys.org

Tunable technique to generate wood-like plant material in a lab, which could enable someone to "grow" a wooden product like a table without needing to cut down trees, process lumber, etc.

"The idea is that you can grow these plant materials in exactly the shape that you need, so you don't need to do any subtractive manufacturing."

Researchers first isolate cells from the leaves of young Zinnia elegans plants, culture them in liquid medium for two days, then transfer them to a gel-based medium of nutrients and hormones. Adjusting the hormones enables researchers to tune the physical and mechanical properties of the plant cells that grow in that nutrient-rich broth. Then a 3D printer extrudes the gel into a structure in a petri dish, it incubates for three months (two orders of magnitude faster than it takes to grow a mature tree).

"In the human body, you have hormones that determine how your cells develop and how certain traits emerge. In the same way, by changing the hormone concentrations in the nutrient broth, the plant cells respond differently. Just by manipulating these tiny chemical quantities, we can elicit pretty dramatic changes in terms of the physical outcomes," Beckwith says.

via MIT: Ashley L. Beckwith et al, Physical, mechanical, and microstructural characterization of novel, 3D-printed, tunable, lab-grown plant materials generated from Zinnia elegans cell cultures, Materials Today (2022). DOI: 10.1016/j.mattod.2022.02.012

Image credit: AI Art - Wooden Futures: a complex building, large wood joinery, dowels and pegs, people walking, architectural photography. https://lexica.art/prompt/a0440fb8-21cb-4fd8-87e9-59a727ab7511


New artificial enzyme breaks down tough, woody lignin: Study shows promise for developing a new renewable energy source
Jun 2022, phys.org

"This is the first nature-mimetic enzyme which we know can efficiently digest lignin to produce compounds that can be used as biofuels and for chemical production," added Chun-Long Chen.

(Why not "biomimetic" though?)

via Pacific Northwest National Laboratory: Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities, Nature Communications (2022). DOI: 10.1038/s41467-022-30285-9


Researchers envision wood-derived, self-powered biosensors for wireless devices
Jun 2022, phys.org

Lignocellulosic nanofibrils derived from tree bark are used in a self-powered device for sending  wireless signals to a smartphone via bluetooth. Leaving about 30 percent lignin in the nanofibrils improved their performance as tribonegative materials. The principle behind the innovation is the trioboelectric effect, a form of static electricity. 

Simply by tapping the device on an acrylic plate during testing, the prototype was able to generate enough power to send out a radio-frequency ping every three minutes that was picked up by a nearby smartphone.

In theory, such a device could be inserted into the sole of a shoe to power a biosensor that sends data wirelessly.

And PFAS Free FYI:
Most current designs incorporate synthetic materials such as polytetrafluoroethylene (PTFE), also known under the brand name Teflon. However, this material persists for long periods of time in the environment and concerns have been raised about its potential health effects.

Yan and her team wanted to see if it was possible to create a natural, biodegradable substitute.

This device was able to generate 160 percent more voltage and 140 percent more current when compared with a similar device that used PTFE as the tribonegative layer.

via University of Toronto: Nicolas R. Tanguy et al, Natural lignocellulosic nanofibrils as tribonegative materials for self-powered wireless electronics, Nano Energy (2022). DOI: 10.1016/j.nanoen.2022.107337



Monday, March 28, 2022

Out To Lunch


Synthetic biology moves into the realm of the unnatural
Oct 2021, phys.org

Keeping up with the synthetic biobots.

"It's a completely new way of doing chemical synthesis. The idea of creating an organism [it's E. coli btw] that makes such an unnatural product [cyclopropanated chemicals in this case], that combines laboratory synthesis with synthetic biology within a living organism — it is just a futuristic way to make organic molecules from two separate fields of science in a way nobody's done before," said John Hartwig, UC Berkeley professor of chemistry and one of four senior authors of the study.

via University of California Berkeley: ing Huang et al, Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme, Nature Chemistry (2021). DOI: 10.1038/s41557-021-00801-3

Designing microbe factories for sustainable chemicals
Nov 2021, phys.org

The guide for how synthbio takes over the world.

In this case, it's only for one thing, called itaconic acid, which is considered one of the "top value added chemicals from biomass" in a 2004 report by the Department of Energy.

They're using what's called the Design-Build-Test-Learn strategy, where they first use AI to assist in identifying genes that can be either removed or added from the yeast Yarrowia lipolytica. Once the genes of interest are identified, the yeast is modified, "designed" if you will. Then they run it and see what kinds of products it generates via its metabolism. Eventually there will be all kinds of chemicals, from toxic dyes for clothing, to toxic catalysts for rubberized flooring, to rare chemicals, to chemicals that destroy the planet in their creation process, that will be created instead by re-engineered bacteria.

Like, imagine if you wanted some adhesive to hang a sign on the door that said Out to Lunch, so you swallowed a capsule of some magic human engineering dust, and within a couple minutes, your spit is now sticky enough to tack a sign on your door. That's quite a stretch, but that's the idea. (Granted we are not as simple to re-engineer as a bacterium, but it's the analogy that counts.)

via Pacific Northwest National Laboratory: Andrew D. McNaughton et al, Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling, ACS Synthetic Biology (2021). DOI: 10.1021/acssynbio.1c00267


Novel artificial genomic DNA can replicate and evolve outside the cell
Nov 2021, phys.org

Sorry I didn't get that, could you repeat?

To date, it has been impossible to create a reaction system in which the genes necessary for DNA replication are expressed while those genes simultaneously carry out their function.

They added the genes necessary for transcription and translation to the artificial genomic DNA, which I think means that once a yeast has been re-engineered (see above), it can then reproduce itself, instead of us re-engineering it over and over?

via Japan Science and Technology Agency: Hiroki Okauchi et al, Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System, ACS Synthetic Biology (2021). DOI: 10.1021/acssynbio.1c00430


Algorithms mimic the process of biological evolution to learn efficiently
Nov 2021, phys.org

And just another synth bio advance in synthetic biology.

They're using synaptic plasticity as a model for understanding biological information processing, i.e., computers that learn. But their model uses an algorithm based on the process of biological evolution, i.e., natural selection. It's called "evolving-to-learn" (E2L).

via European Human Brain Project, Institute of Physiology, University of Bern, the RIKEN Center for Brain Science in Tokyo, and others: Jakob Jordan et al, Evolving interpretable plasticity for spiking networks, eLife (2021). DOI: 10.7554/eLife.66273


Scientists develop the 'evotype' to unlock power of evolution for better engineering biology
June 2021, phys.org

They're making sure that engineered biosystems aren't static, but evolve, like if you made a watch that kept changing itself to adapt to your lifestyle, "they design living populations that continue to mutate, grow and undergo natural selection." I think the keyword is "self-improving" biotechnologies

via University of Bristol: Simeon D. Castle et al, Towards an engineering theory of evolution, Nature Communications (2021). DOI: 10.1038/s41467-021-23573-3

Image credit: It's just a close-up of an enterococcus

Thursday, July 1, 2021

Shoots Lasers

A disposable living laser printed on chip for drug screening
Mar 2021, phys.org

Sounds to me like a 3-D printed, engineered bacteria that shoots lasers:
disposable living laser on chip by encapsulating living bacteria inside. Strong laser emissions generated from bacteria inside the droplet will be dramatically enhanced during drug interactions.

The tiny lasers serve as a highly sensitive culture-free sensor

can be directly printed from an office inkjet printer

via Nanyang Technological University: Xuerui Gong et al. Imaging-Based Optofluidic Biolaser Array Encapsulated with Dynamic Living Organisms, Analytical Chemistry (2021). DOI: 10.1021/acs.analchem.1c00020
Image credit: Quantum Causal Loop - NeoLeo

Friday, January 15, 2021

Cyborgs Among Us


Next-generation brain implants with more than a thousand electrodes can survive for more than six years
Apr 2020, phys.org

Get it straight - they're growing glass to implant into the brain.
Researchers have demonstrated the ability to implant an ultrathin, flexible neural interface with thousands of electrodes into the brain with a projected lifetime of more than six years.

25 micrometers thick with 360 electrodes.

Thermally grown layer of silicon dioxide less than a micrometer thick can ward off the hostile environment within the brain, degrading at a rate of only 0.46 nanometers per day

Because this form of glass is biocompatible, any trace amount that dissolves into the body should not create any problems of its own.

Next-gen organoids grow and function like real tissues
Sep 2020, phys.org

Read the whole article and watch the video. Jeez.

Intestinal organoids. They're bio-engineered miniature intestines using a an artificial gut-shaped microchannel. Mini-guts.

They make the substrate out of proteins already found in the gut, cross-linking them into a hydrogel and forming it from a laser printer-cutter. The substrate, or scaffold, is then seeded with intestinal stem cells, that know how to do nothing else but make an intestine. And they do.

Homeostatic mini-intestines through scaffold-guided organoid morphogenesis, Nature (2020). DOI: 10.1038/s41586-020-2724-8


A lab that reads—and writes—our dreams
Apr 2020, phys.org

Dormio is a glovelike device that allows researchers to communicate with sleeping subjects as they slip into hypnogogia - a fleeting semi-conscious state between wakefulness and sleep, by tracking heart rate, muscle tone and skin conductance, as well as playing a word or other audio sound as subjects drift into the transitional sleep stage.

Thursday, January 14, 2021

Eternal Life - D Melanogaster and C Elegans Live Forever


Scientists may have found one path to a longer life
Jul 2020, phys.org

I'm not interested in the article, just that these two man, they're already famous, and now they're eternal!

The above image is about allometric scaling, in this case metabolic rate vs body mass. It's not a direct connection to lifespan, but pretty close. We can now put C Elegans and D Melanogaster off the chart. 


Study finds hyperbaric oxygen treatments reverse aging process
Nov 2020, phys.org

Holy grail they say.

Friday, July 10, 2020

When Biology Takes a Back Seat


Powerful antibiotic discovered using machine learning for first time
Feb 2020, The Guardian
The drug works in a different way to existing antibacterials and is the first of its kind to be found by setting AI loose on vast digital libraries of pharmaceutical compounds.
“In terms of antibiotic discovery, this is absolutely a first,” said Regina Barzilay, a senior researcher on the project and specialist in machine learning at Massachusetts Institute of Technology (MIT). 
“I think this is one of the more powerful antibiotics that has been discovered to date,” added James Collins, a bioengineer on the team at MIT. “It has remarkable activity against a broad range of antibiotic-resistant pathogens.” 
To find new antibiotics, the researchers first trained a “deep learning” algorithm to identify the sorts of molecules that kill bacteria. To do this, they fed the program information on the atomic and molecular features of nearly 2,500 drugs and natural compounds, and how well or not the substance blocked the growth of the bug E coli.
Once the algorithm had learned what molecular features made for good antibiotics, the scientists set it working on a library of more than 6,000 compounds under investigation for treating various human diseases. Rather than looking for any potential antimicrobials, the algorithm focused on compounds that looked effective but unlike existing antibiotics. This boosted the chances that the drugs would work in radical new ways that bugs had yet to develop resistance to. 
Jonathan Stokes, the first author of the study, said it took a matter of hours for the algorithm to assess the compounds and come up with some promising antibiotics. One, which the researchers named “halicin” after Hal, the astronaut-bothering AI in the film 2001: A Space Odyssey, looked particularly potent.

Reprogramming of immune system cures child with often-fatal fungal infection
June 2020, phys.org
"Immune modulation isn't currently part of the strategy with any of these severe infections," said Dr. Manish Butte, the report's senior author, who holds the E. Richard Stiehm Endowed Chair in Pediatric Allergy, Immunology and Rheumatology at the David Geffen School of Medicine at UCLA. "Our case suggests that rather than hoping to get the upper hand with more and more antibiotics or antifungals, we can have some success by combining these established approaches with the new idea of programming the patient's immune response to better fight the infection."
Synthetic red blood cells mimic natural ones, and have new abilities
June 2020, phys.org

Bioengineers have made synthetic red blood cells that have all the same abilities of natural blood cells, and even a few more.

On a sidenote, I'm also thinking about the Impossible burger that uses synthetically produced hemoglobin. And on a supersidenote, that had me wondering what's worse, humans eating animals, or humans trying to avoid eating animals so they re-engineer a bacteria's genetic code so that it can make blood, and then take that blood and add it to a plant, so that we can eat plants that taste like meat. Like, bacteria didn't even bleed before we got involved, and now that they do, doesn't that mean we should stop eating them too?

Post Script on Biomimicry

A self-cleaning surface that repels even the deadliest superbugs
Dec 2019, phys.org

Researchers develop new method to remove dust on solar panels
Dec 2019, phys.org
Taking a cue from the self-cleaning properties of the lotus leaf, researchers at Ben-Gurion University of the Negev have shed new light on microscopic forces and mechanisms that can be optimized to remove dust from solar panels to maintain efficiency and light absorption. The new technique removed 98 percent of dust particles.
In a new study published in Langmuir, the researchers confirmed that modifying the surface properties of solar panels may greatly reduce the amount of dust remaining on the surface, and significantly increase the potential of solar energy harvesting applications in the desert.
Particle removal increased from 41 percent on hydrophilic smooth Si wafers to 98 percent on superhydrophobic Si-based nanotextured surfaces.
"We determined that the reason for the increased particle removal is not low friction between the droplets and the superhydrophobic surfaces," Heckenthaler says. "Rather, it is the increase in the forces that can detach particles from the surfaces. The experimental methods we used and the criterion for particle removal we derived can be implemented to engineer self-cleaning surfaces exhibiting different chemistries and/or textures."
-image source: I really hate it when websites don't credit their artwork (almost as much as I hate the threeway image clusterfu**ing olympics performed by Google-Getty-Pinterest triangle). This image came from the site at this link, but they list no artist credits.