#5 Singing Coral Reefs, Gene Swapping and Stiff Cells Creating Faces

Singing coral reefs indicating healthy ecosystems, new gene exchanging technology and the cells creating faces in embryos.

Dec 12, 2021

Fish songs are indicators of reef restoration success…

Coral reefs are defined as large underwater structures that are composed of the skeletons of marine invertebrates called coral polyps. They are one of the most biodiverse ecosystems in the world supporting 25% of all marine life, yet are at threat, mainly as a result of climate change. Unprecedented damage to coral reefs around the planet is as a result of anthropogenic stressors. In response their has been a large increase in investment to counteract the damage caused, which includes the regeneration of these fundamental ecosystems.

Indonesia is one area where thousands of square metres of coral are being grown on previously destroyed reefs. A new study has found that a healthy and diverse soundscape has been restored to the reef area. Soundscapes and the noise of the ecosystem are a great way alongside visual observations to monitor this key ecosystem. Soundscapes represent a reefs ecological status. A healthy reef hosts a wide range of soniferous fishes and invertebrates that contribute towards a large and diverse acoustic landscape. The settlement of many reef organisms as well as breeding and feeding patterns can be indicated or hinted at by the soundscape of the reef system. One of the key reasons as to the importance of the soundscape is that audio devices show activity at both night and day and so demonstrate the relative health of nocturnal organisms which can often be missed. As a well as healthy coral reefs, negative changes to the health of the ecosystem as a result of environmental stressors can be indicated through the depth, variety and volume of the sound.

Due to the immense biodiversity of reefs and the species richness over a relatively small geographic area, a restored reef is not just restored coral. Coral is just part of the ecosystem, by listening to the reef, the full restoration and richness of the animals and habitat can be demonstrated. In Indonesia, a lot of new and bizarre sounds were recorded. Whilst this Indonesian coral reef soundscape is not identical to other recordings, it is similar suggesting a healthy reef.

This new study used recordings taken in 2018 and 2019 as part of the Mars Coral Reef Restoration Project. This project involves modular, artificial frames which are integrated with coral and laid over large expanses of desolate or damaged reefs. These reef frames not only help the seeded coral but help stabilise loose rubble and kickstart rapid coral growth. However, this isn’t an overnight success…

Restoration and monitoring reefs in Indonesia has been in the works for many years with Mochyudho Prasetya of the project, saying that “it was amazing to see more and more evidence that our work is helping the reefs come back to life”.

Whilst the return of a busy and “singing” soundscape indicating a health reef as well as a higher likelihood of self sustaining coral reefs, unless threats are tackled restoration will eventually be undone and become impossible. Addressing the wider problems is arguably more important than the localised work as without, climate change will eventually negate a lot of the good work achieved by the team. The study clearly shows that restoration can work, but it is only part of a solution that needs to tackle these worldwide threats.

More Information Full Article

🔁Gene Sized DNA “Swapping”?

New system has the capability of inserting entire genes into human cells?

An MIT and Harvard based research team of created a new method of prime editing that can install of swap out gene-sized DNA sequences. Prime editing is a highly accurate measurement method by which a wide diversity of human cell gene edits can be made. The technology essentially writes new genetic information into the targeted DNA site.

The team created the a system that makes two adjacent prime edits allowing the introduction of larger sequences of DNA at specific locations in the genome with few unwanted by products. This could be the first step in a new form of gene therapy which could insert therapeutic genes in a safe and highly targeted manner to replace mutated or missing genes. The technology has been named twinPE due to the nature of the twin prime editing.

The therapeutic potential of twinPE was demonstrated on the human gene linked to the rare genetic disorder; Hunter syndrome. Hunter disease is caused by a missing or malfunctioning enzyme (iduronate 2-sulfatase) and is extremely rare. This disease occurs due to the inversion of a specific 40,000 base pair long stretch of DNA. The US research team was able to introduce a similar length at the same site within the genome showing the method could be used to correct the mutation causing the disease.

What is key about this innovation, is that it directly addresses one of the limitations of the original prime editing system, which can edit only several dozen base pairs. This is insufficient in many practical applications such as genetic disease which mostly require larger edits. Furthermore this new method doesn’t sever the DNA helix simultaneously which can induce harmful chromosomal abnormalities. The ability to insert a gene in a patient at a site of our choosing without generating double strand breaks and negative by-products has been a long lasting issue with gene therapy.

This development along with others in recent years that enable DNA substitutions, insertions and deletions, promises to correct the majority of known disease causing variations.

So, some of the biology behind it?

A Prime editor protein and two prime editing guide RNAs guide the editing machinery and encode the edits.
Each of the two guide RNAs direct the editing protein to make a “nick” in the DNA at different targeted sites in the genome, avoiding the kind of double-strand break that can create other negative by products in other methods.
Two new complimentary DNA strands containing the desired sequence are then synthesised between the two created “nicks”.
Using this approach the team was able to insert, substitute or delete sequences up to about 800 base pairs long.

Furthermore the team is able to edit even larger sequences, should it be needed, This is done using their twin prime editing system to install “landing sites” in the genome for enzymes called site-specific recombinases, which catalyse the integration of DNA at specific sites in the genome.

More Information Full Article

👶Cell Stiffness Causes Face to Form?

Embryonic cells sense stiffness in order to form the face…

Developing embryo cells have the ability to sense the stiffness of other cells around them which is key in them moving together to form the face and skull.

In a recent UCL study in nature it was discovered the embryonic cells in frog embryos have the ability to travel from softer to harder regions. Where cells lack this ability and are unable to distinguish soft regions from hard regions, facial malformations or death can arise. This discovery with further research could help understand and prevent harmful birth defects.

The features of human and animal faces like the nose, lips and ear are formed and located as a result of complex and detailed movements of cells in the developing embryo. An error in the movement of cells can lead to alterations in eventual structure such as palate clefts of cranial malformations as well as death. These types of defects are the primary cause of infant mortality and so this research is key in potentially life saving research.

Embryonic cells that are responsible for facial feature formation are called neural crests. Scientists that study these are focusing on genes and molecules that control the movements of the cells with an ongoing line of work that also follow the mechanical cues as well as the genetic aspect. The neural crest of the frog is similar to that of humans and their movement is often used to study cancer. Another reason for frog use in this experiment is that they can be studied without inflicting harm.

The team has previously discovered that the stiffening of the cells proceeds the migration of the cells to form the face. For the first time it has been identified that cells can detect the stiffness in their environment to move along a stiffness gradient. Chemotaxis is the process by which cells move along a gradient of chemical signals, and is the main mechanism too explain directional migration. The research team identified a network of chemical and mechanical signals that interact cooperatively to control cell migration in the embryo. The neural crest cells induced the stiffness gradient by relying on a protein known to be involved in cell to cell adhesion. They sensed the gradient by interacting with the extracellular matrix. This allows the cells to make their own path toward stiffer regions of the embryo.

It is likely that this newly identified behaviour is likely to be found not only in the cells that form our face, but in fact the organs of the entire body. This research could play a central role in the battle against cancer.