Origins of animals, plants, fungi, new research


This 18 June 2018 video says about itself:

Phylogenomic-wide studies of evolutionarily conserved structures of protein domains suggest Archaea is the first domain of life to diversify from a stem line of descent and co-evolve with ancestors of Bacteria and Eukarya. The proposed co-evolutionary scenario by J. T. Staley and G. Caetano-Anollés challenges popular cell fusion and two-domain of life scenarios derived from sequence analysis.

For more, read the full article here.

From Molecular Biology and Evolution (Oxford University Press):

Scientists identify rare evolutionary intermediates to understand the origin of eukaryotes

September 11, 2019

Summary: A new study provides a key insight into a milestone event in the early evolution of life on Earth — the origin of the cell nucleus and complex cells. Scientists peered deep inside current living cells, known as Archaea – the organisms that are believed to most closely resemble the ancient intermediates between bacteria and the more complex cells that we now know as eukaryotic cells.

A new study by Yale scientists provides a key insight into a milestone event in the early evolution of life on Earth — the origin of the cell nucleus and complex cells called eukaryotes.

While simple prokaryotic bacteria formed within the first billion years of the Earth, the origin of eurkaryotes, the first cells with nuclei, took much longer. Dating back to between 1.7 and 2.7 billion years ago, an ancient prokaryote was first transformed with a compartment, the nucleus, designed to keep their DNA material more protected from the environment (such as harmful UV damage). From this ancient event, relatively simple organisms, such as bacteria were transformed into more sophisticated ones that ultimately gave rise to all modern animals, plants and fungi.

The details of this key event have remained elusive for many years because not a single transitional fossil has been found to date.

Now, in a study led by Dr. Sergey Melnikov, from the Dieter Söll Laboratory in the Department of Molecular Biophysics and Biochemistry at Yale University, has finally found these missing fossils. To do so, they relied not on unearthing clay or rocks but peering deep inside current living cells, known as Archaea — the organisms that are believed to most closely resemble the ancient intermediates between bacteria and the more complex cells that we now know as eukaryotic cells.

These transitional forms are nothing like the traditional fossils we think of, such as dinosaur bones deposited in the ground or insects trapped in amber. Known as ribosomal proteins, these particular transitional forms are about 100-million times smaller than our bodies. Melnikov and his colleagues discovered that ribosomal proteins can be used as living “molecular fossils”, whose ancient origin and structure may hold the key to understanding the origin of the cell nucleus.

“Simple lifeforms, such as bacteria, are analogous to a studio apartment: they have a single interior space which is not subdivided into separate rooms or compartments. By contrast, more complex organisms, such as fungi, animals, and plants, are made up of cells that are separated into multiple compartments,” explained Melnikov. “These microscopic compartments are connected to one another via ‘doors’ and ‘gates’. To pass through these doors and gates, the molecules that inhabit living cells must carry special ID badges, some of which are called nuclear localization signals, or NLSs.”

Seeking to better understand when NLS-motifs might have emerged in ribosomal proteins, the Yale team assessed their conservation among ribosomal proteins from the three domains of life.

To date, NLS-motifs have been characterized in ten ribosomal proteins from several eukaryotic species. They compared all of the NLS-motifs found in eukaryotic ribosomal proteins (from 482 species) and tried to find a match in bacteria (2,951 species) and Archaea (402 species).

Suprisingly, they found four proteins — uL3, uL15, uL18, and uS12 — to have NLS-type motifs not only in the Eukarya but also in the Archaea. “Contrary to our expectations, we found that NLS-type motifs are conserved across all the archaeal branches, including the most ancient superphylum, called DPANN,” said Melnikov.

But since Archaea don’t have nuclei, the logical question which then arose was, why do they have these IDs? And what was the original biological function of these IDs in non-compartmentalized cells?”

“If you think about an equivalent to our discovery in the macroscopic world, it is similar to discoveries made during the last century of bird-like dinosaurs such as Caudipteryx zoui,” said Melnikov. “These ancient flightless birds have illustrated that it took multiple millions of years for dinosaurs to develop wings. Yet, strikingly, for the first few million years their wings were not good enough to support flight.”

Similarly, the study by Melnikov and colleagues suggests that, even though NLSs may not initially have emerged to allow cellular molecules to pass through microscopic doors and gates between cellular compartments, they could have emerged to fulfill a similar biological function — to help molecules get to their proper biological partners.

As Melnikov explains: “Our analysis shows that in complex cells the very same IDs that allow proteins to pass through the microscopic gates are also used to recognize biological partners of these proteins. In other words, in complex cells, the IDs fulfill two conceptually similar biological functions. In the Archaea, however, these IDs play just one of these functions — these IDs, or NLSs, help proteins to recognize their biological partners and distinguish them from the thousands of other molecules that float in a cell.”

But what led to the evolution of these IDs among cellular proteins in the first place?

As Melnikov explains, “When life first emerged on the face of our planet, the earliest life forms were likely made of a very limited number of molecules. Therefore, it was relatively easy for these molecules to find one specific partner among all the other molecules in a living cell. However, as cells grew in size and complexity, it is possible, even probable, that the old rules of specific interactions between cellular molecules had to be redefined, and this is how the IDs were introduced into the structure of cellular proteins — to help these proteins identify their molecular partners more easily in the complex environment of a complex cell. Coming back to the analogy with bird-like dinosaurs, our study illustrates the remarkable similarity between how evolution happens in the macroscopic world and how evolution happens in the world that Darwin never saw — the microscopic world of invisible molecules that inhabit living cells.”

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23 new plant species discovered in China


This 2008 video says about itself:

China’s Amazing Flora | National Geographic

From deserts to lush tropical forests, one of China’s richest treasures is its plant life. Join leading botanist and NG Research and Exploration chairman Peter Raven on a tour of China’s regional flora.

From ScienceDaily:

Plant diversity and endemism in China: Unreachable locations and diverse microclimates

August 29, 2019

A new issue of the scholarly, open-access and peer-reviewed journal PhytoKeys focuses on the Chinese biodiversity hotspots and their substantial role in understanding the country’s unique flora. The special issue embarks on a treasure hunt into China’s biodiversity hotspots, including the descriptions of 23 species previously unknown to science and new insights into the ecological diversity of ferns based on their DNA sequences.

In China, biodiversity-rich landscapes vary from the dry Northwest region, through the surrounded by massive mountain ranges of the Qinghai-Tibet Plateau, to the tropical and subtropical southern China. The combination of remote and hard to reach mountain areas and diverse microclimates promises high levels of endemism.

“With extended collaboration among Chinese scientists and coordination of networks on plant conservation and taxonomy across China, we synthesize a special issue entitled “Revealing the plant diversity in China’s biodiversity hotspots”, to present the latest findings by Chinese botanists, and to update knowledge of the flora for China and adjacent countries,” explained De-Zhu Li, professor of botany at Kunming Institute of Botany (KIB), Chinese Academy of Sciences (CAS), in the editorial.

Among the newly described species, four new members of the African violet family were found from a subtropical forest in Yunnan province in southern China, discovered by researchers from Xishuangbanna Tropical Botanical Garden, CAS and their collaborators. Half of them were found only from a sole population and require further botanical examinations to deploy the conservation priorities, remark the scientists.

In another paper, scientists Yun-Feng Huang and Li-Na Dong and Wei-Bin Xu, representatives of Guangxi Institute of Botany, revealed the discovery of a new species from the primrose family. Found nowhere outside the limestone areas in Liucheng county (Guangxi, China), this rare plant species is currently facing serious threats of extinction because of the fragility and sensitivity of its habitat to the environmental changes associated with the rapid economic development of China.

Another team from the Guizhou University of Traditional Chinese Medicine and KIB describes a new representative of the parachute flowers. Ceropegia jinshaensis, characterized by the shape and size of its leaves and flowers.

“More conservation efforts are needed in this region to counteract the increasing anthropogenic disturbance and destruction,” state the leading authors from KIB, who discovered a new species of orchid in the Eastern Himalaya biodiversity hotspot.

The special issue features the description of additional two orchid species, discovered in Motuo, located at the Himalayan border between China, Myanmar and India. The region is well known for its vertical vegetation system, varying from tropical forest to permanent glaciers. Ji-Dong Ya and Cheng Liu from the KIB and Xiao-Hua Jin from the Institute of Botany, CAS underline that the difficult access to the area allows the thriving and diversification of plants.

Gingko trees, scorpions help sick people


This 2011 video is called Southern Black Rock Scorpions mating (Urodacus manicatus).

From the University of California – San Francisco in the USA:

Scorpion toxin that targets ‘wasabi receptor‘ may help solve mystery of chronic pain

August 22, 2019

Researchers at UC San Francisco and the University of Queensland have discovered a scorpion toxin that targets the “wasabi receptor,” a chemical-sensing protein found in nerve cells that’s responsible for the sinus-jolting sting of wasabi and the flood of tears associated with chopping onions. Because the toxin triggers a pain response through a previously unknown mechanism, scientists think it can be used as a tool for studying chronic pain and inflammation, and may eventually lead to the development of new kinds of non-opioid pain relievers.

The scientists isolated the toxin, a short protein (or peptide) that they dubbed the “wasabi receptor toxin” (WaTx), from the venom of the Australian Black Rock scorpion. The discovery came as the researchers were conducting a systematic search for compounds in animal venom that could activate, and therefore be used to probe and study, the wasabi receptor — a sensory protein officially named TRPA1 (pronounced “trip A1”) that’s embedded in sensory nerve endings throughout the body. When activated, TRPA1 opens to reveal a channel that allows sodium and calcium ions to flow into the cell, which can induce pain and inflammation.

“Think of TRPA1 as the body’s ‘fire alarm’ for chemical irritants in the environment,” said John Lin King, a doctoral student in UCSF’s Neuroscience Graduate Program and lead author of a study published August 22, 2019 in Cell, which describes the toxin and its surprising mode of action. “When this receptor encounters a potentially harmful compound — specifically, a class of chemicals known as ‘reactive electrophiles,’ which can cause significant damage to cells — it is activated to let you know you’re being exposed to something dangerous that you need to remove yourself from.”

Cigarette smoke and environmental pollutants, for example, are rich in reactive electrophiles which can trigger TRPA1 in the cells that line the surface of the body’s airway, which can induce coughing fits and sustained airway inflammation. The receptor can also be activated by chemicals in pungent foods like wasabi, onions, mustard, ginger and garlic — compounds that, according to Lin King, may have evolved to discourage animals from eating these plants. WaTx appears to have evolved for the same reason.

Though many animals use venom to paralyze or kill their prey, WaTx seems to serve a purely defensive purpose. Virtually all animals, from worms to humans, have some form of TRPA1. But the researchers found that WaTx can only activate the version found in mammals, which aren’t on the menu for Black Rock scorpions, suggesting that the toxin is mainly used to ward off mammalian predators.

“Our results provide a beautiful and striking example of convergent evolution, whereby distantly related life forms — plants and animals — have developed defensive strategies that target the same mammalian receptor through completely distinct strategies,” said David Julius, PhD, professor and chair of UCSF’s Department of Physiology, and senior author of the new study.

But what the researchers found most interesting about WaTx was its mode of action. Though it triggers TRPA1, just as the compounds found in pungent plants do — and even targets the very same site on that receptor — the way it activates the receptor was novel and unexpected.

Black rock scorpion venom

First, WaTx forces its way into the cell, circumventing the standard routes that place strict limits on what’s allowed in and out. Most compounds, from tiny ions to large molecules, are either ingested by the cell through a complex process known as “endocytosis”, or they gain entry by passing through one of the many protein channels that stud the cell’s surface and act as gatekeepers.

But WaTx contains an unusual sequence of amino acids that allows it to simply penetrate the cell’s membrane and pass right through to the cell’s interior. Few other proteins are capable of the same feat. The most famous example is an HIV protein called Tat, but surprisingly, WaTx contains no sequences similar to those found in Tat or in any other protein that can pass through the cell’s membrane.

“It was surprising to find a toxin that can pass directly through membranes. This is unusual for peptide toxins,” Lin King said. “But it’s also exciting because if you understand how these peptides get across the membrane, you might be able to use them to carry things — drugs, for example — into the cell that can’t normally get across membranes.”

Once inside the cell, WaTx attaches itself to a site on TRPA1 known as the “allosteric nexus,” the very same site targeted by pungent plant compounds and environmental irritants like smoke. But that’s where the similarities end.

Plant and environmental irritants alter the chemistry of the allosteric nexus, which causes the TRPA1 channel to rapidly flutter open and closed. This allows positively charged sodium and calcium ions to flow into the cell, triggering pain. Though both ions are able to enter when TRPA1 is activated by these irritants, the channel exhibits a strong preference for calcium and lets much more of it into the cell, which leads to inflammation. By contrast, WaTx wedges itself into the allosteric nexus and props the channel open. This abolishes its preference for calcium. As a result, overall ion levels are high enough to trigger a pain response, but calcium levels remain too low to initiate inflammation.

To demonstrate this, the researchers injected either mustard oil, a plant irritant known to activate the wasabi receptor, or WaTx into the paws of mice. With mustard oil, they observed acute pain, hypersensitivity to temperature and touch — key hallmarks of chronic pain — and inflammation, as evidenced by significant swelling. But with WaTx, they observed acute pain and pain hypersensitivities, but no swelling.

“When triggered by calcium, nerve cells can release pro-inflammatory signals that tell the immune system that something’s wrong and needs to be repaired,” Lin King said. “This ‘neurogenic inflammation’ is one of the key processes that becomes dysregulated in chronic pain. Our results suggest that you can decouple the protective acute pain response from the inflammation that establishes chronic pain. Achieving this goal, if only in principle, has been a longstanding aim in the field.”

The researchers believe their findings will lead to a better understanding of acute pain, as well as the link between chronic pain and inflammation, which were previously thought to be experimentally indistinguishable. The findings may even lay the groundwork for the development of new pain drugs.

“The discovery of this toxin provides scientists with a new tool that can be used to probe the molecular mechanisms of pain, in particular, to selectively probe the processes that lead to pain hypersensitivity,” Lin King said. “And for those interested in drug discovery, our findings underscore the promise of TRPA1 as a target for new classes of non-opioid analgesics to treat chronic pain.”

Additional authors include Joshua J. Emrick, Mark J.S. Kelly and Katalin F. Medzihradszky of UCSF; Volker Herzig and Glenn F. King of the Institute for Molecular Bioscience at the University of Queensland.

This study was supported by an NSF Graduate Research Fellowship (No. 1650113), a UCSF Chuan-Lyu Discovery Fellowship, and grants from the National Institutes of Health (R37 NS065071, R35 NS105038 and T32 GM007449).

The extract of the leaves of Ginkgo biloba, a popular dietary supplement, may offer some therapeutic benefits in fighting Type 2 diabetes, according to a study co-authored by a researcher at the University of Cincinnati (UC) College of Medicine: here.

What fossils are, video


This 22 August 2019 video says about itself:

Fossils 101 | National Geographic

Fossils are echoes of an ancient past. Find out about the two major categories of fossils, how fossilization occurs, and how fossils can help paint a picture of the planet’s history.

Dragonflies and young house martins


Naardermeer marsh plants, 19 August 2019

On 19 August 2019, we went to the Naardermeer nature reserve.

Near the entrance, barn swallows flying. A great crested grebe swimming.

We see construction activity. Wildlife corridors are built underneath the railway; to save lives of grass snakes, moor frogs, otters, pine martens, etc.

On the footpath to the Muggenbult viewpoint, a male black-tailed skimmer dragonfly.

A grey heron.

Naardermeer marsh plants, near dragonfly, 19 August 2019

Along this bit of marsh, a beautiful green and blue dragonfly flies. An emperor dragonfly?

Naardermeer, on 19 August 2019

Naardermeer, 19 August 2019

Rowan berries.

On the footpath, a smallish red dragonfly.

A great cormorant flying.

Naardermeer, Muggenbult, 19 August 2019

As we arrive at the Muggenbult viewpoint, a coot couple and their chick swimming.

A male gadwall duck.

White and yellow water-lily flowers.

Two adult mute swans swimming with one youngster.

Naardermeer mute swan, 19 August 2019

A great crested grebe with two youngsters.

We walk back. On the visitors’ centre buildings, house martin nests, both artificial and built by the birds themselves. To both, parent house martins fly to feed their chicks.

Naardermeer, sundew, 19 August 2019

Close to entrance/exit of the nature reserve is a patch with carnivorous plants: sundew.

Rare ghost orchids and their pollinators, video


This 6 August 2019 video from the USA says about itself:

Rare Ghost Orchid Has Multiple Pollinators | Short Film Showcase

Deep in remote Florida swamps, a team of researchers and photographers have made a new discovery that upends what we thought we knew about the ghost orchid, one of the world’s most iconic flowers, and how it reproduces.