News Feeds

Acclaimed photographers Paul Nicklen and Cristina Mittermeier showcase a changing planet as part of the Photo London photography fair

In Rise of the Zombie Bugs, Mindy Weisberger zooms in on how parasites hijack the brains of their tiny host animals

The discovery of the cosmic acceleration problem truly inspired me as a teenage physics nerd. Recent, related revelations about dark energy will hopefully capture the interest of today’s young science geeks, says Chanda Prescod-Weinstein

As Eurovision looms, Feedback enjoys discovering more about the winners of this year's Dance Your PhD contest, who have an original take on chemesthesis, the sense that detects the heat of chillies and the coolness of menthol

There are serious issues with new proposals to use artificial intelligence to predict future crimes, says Yu Xiong, chair of the advisory board to the UK's All-Party Parliamentary Group on the Metaverse and Web 3.0

In highly politicised times, is living off-world something we should entertain, let alone do? Adriana Marais's futurist dream Out of This World and Into the Next feels tone deaf

Women were historically excluded from health studies on the grounds that hormone fluctuations introduced "noise" into the data, and this has left us with a lack of understanding about a range of conditions

I am much relieved!

A goose-stepping duckling.  A LOT more pictures soon.

Researchers propose a new theory for the origin of dark matter, the invisible substance thought to give the universe its shape and structure. Their mathematical models show that dark matter could have formed in the early universe from the collision of massless particles that lost their energy and condensed -- like steam turning into water -- into cold, heavy particles. They report that their theory can be tested using existing data -- these dark matter particles would have a unique signature on the radiation that fills all of the universe known as the Cosmic Microwave Background.

Australian researchers have flagged some promising new approaches to treat severe burns that could save lives and dramatically improve patient recovery.

Researchers have developed a digital laboratory (dLab) system that fully automates the material synthesis and structural, physical property evaluation of thin-film samples. With dLab, the team can autonomously synthesize thin-film samples and measure their material properties. The team's dLab system demonstrates advanced automatic and autonomous material synthesis for data- and robot-driven materials science.

Researchers have developed a digital laboratory (dLab) system that fully automates the material synthesis and structural, physical property evaluation of thin-film samples. With dLab, the team can autonomously synthesize thin-film samples and measure their material properties. The team's dLab system demonstrates advanced automatic and autonomous material synthesis for data- and robot-driven materials science.

Anomalies in the moon’s gravitational field suggest our satellite’s insides are warmer on one side than the other – which means that its interior is asymmetric

The footprints of a reptile-like creature appear to have been laid down around 356 million years ago, pushing back the earliest known instance of animals emerging from the water to live on land

Premenstrual dysphoric disorder can cause monthly cycles of rage, depression, anxiety and self-harm. Treatments are limited, but new ideas about the condition could change that

This post reports a new form of life that is clearly a member of the archaea, with characteristics of that group, but also lacking a vital feature of other archaea as well as other bacteria and all eukaryotes: metabolism: the pathways (mostly involving enzymatic proteins) that keep an organism going and reproducing by converting nutrients into energy. Its lack of genes for metabolism makes it resemble a virus, what hijacks its nutrients from the cells it infects. But viruses can’t completely self-replicate like this new critter, for viruses also partly hijack the DNA/RNA replication system of their hosts.

The new creature, whose appearance is unknown since it was identified from DNA alone, must get its metabolites through association with other species. Finally, the new creature does have something that viruses lack—a complete system for replicating its genome: ribosomes, DNA, genes for transfer RNAs, and so on. In other words, in important ways it’s different from viruses, but also different from other archaea as well as bacteria and eukaryotes (organisms with “true cells” that have their DNA in the nucleus and have membrane-covered organelles like mitochondria and chloroplasts).  The DNA of this creature is in a single circular chromosome like that of bacteria and archaea. Its unique features appears to make it a member of a new domain of life.

The question is this: is this new organism even alive? Viruses are regarded by many biologists as “not alive” because they can’t grow, they have no metabolism to sustain themselves, and are completely dependent for reproduction on the replication machinery of other organisms (bacteria or eukaryotes) they parasitize.

Well, read about this new organism below, discovered by sequencing DNA inside of a singe eukaryotic cell tell me if you think it’s “alive.”

But I’m getting ahead of myself. Let’s review:

There are three domains of life: the bacteria, the archaea (discovered only in 1977 by Woese and Fox), and the eukaryotes (everything else, all having membrane bound nuclei and organelles). Together, the bacteria and archaea are called “prokaryotes” (i.e., single celled microorganisms), and everything else besides viruses comprise the “eukaryotes.”

The phylogeny (family tree) of these domains is shown below.  It was realized only recently that all organisms with true cells (e.g., us) descended from archaea, as shown below. That means three things. First, we are more closely related to the archaea (which often live in weird places like hot springs or hyper-salty water) than we are to bacteria. Eukaryotes did not evolve from bacteria.

Second, eukaryotes like us could be thought of as archaea, since we are nested within that group. In the same way, we could be thought of as fish, and birds as reptiles.

Finally, archaea are considered paraphyletic: the group does not contain all the descendants of its common ancestor. The eukaryotes are not considered archaea, but ARE descendants of the common ancestor of archaea; they just branched off later into a new domain of life.

Now this family tree was constucted from DNA sequence similarity, but archaea also share certain traits with eukaryotes that bacteria don’t have, including “shared metabolic pathways, similar enzymes involved in transcription and translation, and DNA replication mechanisms.” That is what a query to Google tells me. Remember, this area is far from my own biological expertise, so if you see an error, let me know!

This tree is from Sadava et al. 2020. Life. The science of biology. 12th edition. Oxford Univ. Press)

Here is a comparison of the traits of the groups (there are overlaps),from Wikipedia.

Note that all three groups have metabolism (pathways to produce energy and grow), and cell walls, but eukaryotes have a special cell wall with two layers of lipids and a layer of protein. Viruses, not shown in this comparison, have only a protein capsule around them. (Bacteria and archaea have more complicated cell walls.)

Viruses do not metabolize and are widely regarded as “nonliving particles”.  Bacteria and most archaea have metabolism.

The paper describing the new finding is apparently not yet published, but you can find it at bioRχiv by clicking the title below or downlading the pdf here.

How did they find this thing? In a weird way. The researchers took a single individual of the dinoflagellate Citharistes regius and amplified and sequenced all the DNA it contained. Besides the DNA of the dinoflagellate, it also found DNA from three other types of organisms: cyanobacteria (photosynthetic bacteria once called “blue-green algae”), two species of gamma proteobacteria (a well-known group) and then the weird species under consideration, which they call Candidatus Sukunaarchaeum mirabile. This apparently means it’s a candidate species that hasn’t been formally described.  We’ll call it CSM in this post. We don’t know what it looks like or what its ecology and behavior is, except we know it must be parasitic, commensal, or symbiotic with some other species. It cannot live on its own because it can’t metabolize.

Here is its genome shown in the paper. This is all we know of the organism’s biology:

(From the paper) Figure 1. The genome map of Sukunaarchaeum. From outermost to innermost circle, the positions of protein-coding genes and rRNA genes on the +/- strands, tRNA genes, GC content, and GC skew are shown. Color codes for the outermost and 2nd outermost circle: Blue, genes of unknown function; light blue, genes of known function; yellow, rRNA genes.

 

It is in the Archaea as the DNA certainly shows its affinity. But, as shown below, its lineage originated very soon after the archaea branched off from their common ancestor with bacteria.

It has a very small genome: 238,000 base pairs, though that is not the smallest genome known of any organism in the three domains of life (note I’m using “life” here, though this thing may be more virus-like and hence “not alive”).

The chomosome is circular, presumably because sequencing it, one arrives back at the beginning again.

It has 222 genes, most of which are devoted to the machinery for making copies of itself. These include transfer RNAs and ribosomal RNAs, which are not found in viruses, all of which hijack that stuff from the cells they infect.

It has NO genes for metabolism (no genes for it), so CSM must grow and divide using resources from cells that it hijacks. Other bacteria and archaea (and of course eukaryotes) have the genes for metabolic processes, making CSM more virus-like. But, as I said, it differs from viruses by having a complete set of “self-replication core machinery” and genes that are like those in archaea.

189 of its 222 genes make proteins. All but five of these are devoted to self-replication. Several are very large and strongly suggest that they constitute part of the cell wall (they call it “membrane”), though the researchers are not sure about this.

Here’s a summary of the organism. Note that its unique character, lacking metabolism, makes it distinct from other domains of archaean life.

 

And a figure from the paper  (just look at “a” on the left side) showing where it fits in the family tree of prokaryotes. It branches off from the rest of the archaea early, and then evolves very fast, as you can see by the long branch of its lineage, probably reflecting strong natural selection on the lineage.

(From paper) Figure 2. Phylogenetic placement of Sukunaarchaeum within the Archaeal domain. a, Maximum likelihood (ML) phylogenetic tree based on a concatenated alignment of 70 conserved archaeal marker proteins. The tree was inferred under the LG+C60+F+I+R10 model, based on a dataset of 150 taxa and 18,286 sites. The scale bar represents the estimated number of substitutions per site.

To summarize:

CSM is an Archaea as seen from its DNA sequence.  Of this there is no doubt.

But unlike other Archaea or even bacteria, it has NO metabolic machinery. In this way it’s similar to a virus.

But it is dissimilar to viruses because it has the complete machinery for self-replicating its genome, which viruses lack.

Ergo, it must be associated in some way with other organisms to be able to replicate.

We have no idea what it looks like, though it almost certainly is a cell rather than a virus.

Here’s how the authors highlight CSM’s uniqueness:

The discovery of Sukunaarchaeum not only expands the known boundaries of archaeal diversity but also challenges fundamental concepts of cellular life. The extreme metabolic simplification raises fundamental questions about the minimal requirements for cellular life. Sukunaarchaeum, focused almost entirely on genetic self-perpetuation, represents a compelling example of how far metabolic reduction can proceed within a cellular framework. Its minimal genome, absolute host dependence necessitated by profound metaboliceduction, rapid evolution, and significant investment in large, membrane-associated proteins potentially mediating host interaction constitute a unique combination of characteristics that are collectively reminiscent of viruses. Nonetheless, Sukunaarchaeum remains fundamentally cellular – a key distinction from viruses, which typically lack their own core replication machinery genes and rely on host systems. It possesses ribosomes and the core transcriptional and translational apparatus inherited from cellular ancestors. Thus, while clearly cellular, its extreme metabolic dependence and specialization for self-replication are virus-like in nature, suggesting that Sukunaarchaeum may represent the closest cellular entity discovered to date that approaches a viral strategy of existence.

The authors found this organism by sequencing a single eukaryotic cell; CSM was likely inside this cell, like a virus in a human cell, but we don’t know if CSM damages its host(s) in any way. It is likely that many more organisms like this exist but aren’t known because people don’t do DNA sequencing of entire single-celled eukaryotes very often. Dinoflagellates are aquatic organisms, but there may be more stuff like CSM found by sequencing DNA in the soil.

I’ll add that this organism might give us an idea of how viruses originated because, if it loses some of its core replication machinery and genes for making membranes, it would become a virus. It is unlikely to be a virus that might develop into an archaean, as it already is an archaean with a membrane, but would have to evolve a tremendous amount of new metabolic machinery to be able to fuel itself, and that metabolic machinery would have to be genetically similar to the metabolic machinery of already-existing archaea.  That would be an unheard-of event of convergent evolution, thus very unlikely.  This thing, so far, is sui generis.

Finally, IS IT ALIVE? That, as you might guess, depends on your definition of “life”.

If you count the ability to self-replicate on its own, CSM is alive. In that sense viruses are not alive, and most of us think they’re not. (Bur remember that it needs to be assocated with another species to self-replicate.)

But if you count the ability to sustain itself by metabolizing and fueling its own replication, then it is NOT alive.

You pays your money, you takes your choice.

New device can give peace of mind and reduce anxiety for breastfeeding moms. It uses bioimpedance, which is currently used to measure body fat, and streams clinical-grade data to a smartphone or tablet in real time. Developed by physicians and engineers, device was tested by new moms. Technology could particularly benefit fragile babies in the NICU, who have precise nutritional needs.

An international team of researchers has discovered saarvienin A, a new type of glycopeptide antibiotic. Their findings introduce a compound with strong activity against highly resistant bacterial strains.

In many neurodegenerative diseases, proteins misfold and clump together in brain tissue. Scientists developed a new therapy made of peptides and a sugar that naturally occurs in plants. The therapeutic molecules self-assemble into nanofibers, which bond to the neuron-killing proteins. Now trapped, the toxic proteins can no longer enter neurons and instead harmlessly degrade.

When biting into a chili pepper, you expect a fiery sensation on your tongue. This spiciness is detected because of capsaicinoid compounds. But for some peppers, despite high levels of capsaicinoids, the heat is mysteriously dull. Now, researchers have identified three compounds that lessen peppers' pungency. These results challenge the reliability of the century-old Scoville scale, which traditionally bases its rating on two capsaicinoids.