#genomes

I know having so many base pairs makes rebasing complicated, but you're in Bilateria, so shouldn't you at LEAST be better at using git head?

Lungfish [Explained]

Transcript Under the Cut

This just in, starfish are a radially symmetrical head with a stomach.

God I love echinoderms

If you told someone that there’s an entire group of animals that develop butt first as embryos are born bilateral but then grow a radially symmetrical head like a cancer in their side that then bursts out and lives as a completely separate organism from its birth form and moves via hydraulic systems…

A small, seemingly unremarkable fern that only grows on a remote Pacific island was on Friday crowned the Guinness World Record holder for having the largest genome of any organism on Earth. The New Caledonian fern, Tmesipteris oblanceolata, has more than 50 times more DNA packed into the nucleus of its cells than humans do. If the DNA from one of the fern's cells -- which are just a fraction of a millimeter wide -- were unraveled, it would stretch out to 106 meters (350 feet), scientists said in a new study. Stood upright, the DNA would be taller than the tower that holds London's famous Big Ben bell. The fern's genome weighed in at a whopping 160 gigabase pairs (Gbp), the measurement for DNA length. That is seven percent larger than the previous record holder, the Japanese flowering plant Paris japonica.

Excerpt from this story from The Revelator:

As the environment shifts — due to climate change, habitat destruction, or other threats — we can often observe some of the ways that wildlife responds. Populations may decline. Individual animals may move. Some species may alter their behavior.

But at the same time, scientists warn, wild plants or animals may experience harder-to-detect changes — for example, alterations to their genomes, the very DNA that defines them.

It requires a sophisticated genetics laboratory to see these otherwise invisible changes at first, but they may have important implications for populations’ futures.

How exactly can threats such as climate change and habitat loss have hidden effects on a species’ genetic code? Two studies on California birds, both published in the past year, illustrate the potential — both beneficial and problematic.

The endangered southwestern willow flycatcher (Empidonax traillii extimus), ranging from California east to New Mexico and Colorado, depends on rapidly disappearing riparian habitats. As those riverbanks dry up, scientists began to wonder how the birds have adapted. They found the answers by looking to the past.

As the environment shifts — due to climate change, habitat destruction, or other threats — we can often observe some of the ways that wildlife responds. Populations may decline. Individual animals may move. Some species may alter their behavior.

But at the same time, scientists warn, wild plants or animals may experience harder-to-detect changes — for example, alterations to their genomes, the very DNA that defines them.

It requires a sophisticated genetics laboratory to see these otherwise invisible changes at first, but they may have important implications for populations’ futures.

How exactly can threats such as climate change and habitat loss have hidden effects on a species’ genetic code? Two studies on California birds, both published in the past year, illustrate the potential — both beneficial and problematic.

In summer 2023 a group of scientists published a study comparing the genomes of flycatcher specimens collected in the San Diego around the turn of the 20th century — taxidermied birds preserved in museums — with those of contemporary birds, using blood samples collected from individuals captured across willow flycatchers’ breeding range today.

The study was only possible due to rapid advances in technology.

“Until recently, it was very difficult to sequence historical specimens across their entire genome,” says Sheela Turbek, a postdoctoral fellow at Colorado State University who led the project. “DNA tends to degrade over time, and older specimens can have really low DNA concentrations.”

The results surprised Turbek and her colleagues: San Diego flycatchers’ genetic diversity has increased over time.

Most notably, this increased diversity included areas of the genome linked with climate adaptation.

Generally thought of as fierce horse warriors, the Scythians were a multitude of Iron Age cultures who ruled the Eurasian steppe, playing a major role in Eurasian history. A new study published in Science Advances analyzes genome-wide data for 111 ancient individuals spanning the Central Asian Steppe from the first millennia BCE and CE. The results reveal new insights into the genetic events associated with the origins, development and decline of the steppe's legendary Scythians.

By Arjuwan Lakkdawala

Ink in the Internet

Antibiotic-resistant bacteria are expected to claim more human lives than cancer by 2050.

Situation is only short of being declared a health emergency.

Almost 10 million people die each year in the world from cancer according to www.ourworldindata.org 

The factors contributing to the rise in superbugs are many by which mutations and ARGs occur resulting in antibiotic-resistant bacteria. 

Antibiotics overuse and misuse are among the factors and so is hospital hygiene.

ARGs (antibiotic-resistant genes) through Horizontal Gene Transfer can occur in three main ways: Transformation - in which the bacteria picks up genetic material from the environment.

Transduction - in which bacteriophages transfer genes between bacteria when bacteria DNA gets incorporated in the genomes of the virus. This can happen during the Lytic or Lysogenic Cycles which are reproduction processes of bacteriophages.

Conjugation - in which genes are transfered between bacteria from a donor bacterium to a recipient bacterium on direct contact.

In laboratory tests transduction was observed more frequent to occur than in nature. This may or may not be a reassuring indication. Because of the abundance of phages and bacteria generally in hospitals. More studies and observation is required in this matter to have a better understanding or estimate.

Bacteriophages or phages for short, are viruses that have specifically evolved to attack bacteria and are harmless to humans. They were in fact used to treat bacterial infections before the discovery of antibiotics.

Microbiologist Felix d'Herelle in 1917 at the Institute Pasteur in Paris, published a paper in which the lysing of bacteria was described "by an invisible microbe he named Bacteriophage." 

The first recorded therapeutic use of phages was in 1919.

Phage Therapy is being explored by scientists again because of the superbug catastrophe. The increase in antibiotic-resistant bacteria is so severe that if no solution is found humanity will go back to the days of dying from the simplest of infections.

Phages have two studied functions of reproduction. One is highly in favour of elimination of bacteria which is used in phage therapy. It is the lytic cycle: the phage attaches to any of its specific target range of bacteriam and injects its DNA into it, eventually the phages multiply in the bacterium killing it.

To use this process as phage therapy it is required to identify the phages that can attack the specific bacterial infection. Since each type of phage can only attack a range of bacteria but not all bacteria.

The sides effects are not known of this treatment if there are any. What is known so far is that the phages used in the therapy should be eliminated from the human body when there is no bacterial infection host cells anymore. 

However, phages can also be a factor that contribute to bacteria getting ARGs by the lytic or the lysogenic cycle in which the phage injects its DNA into the bacterium but instead of multiplying immediately the phages are reproduced in the cell devision process of the bacterium. However, here too the phages eventually kill the bacteria cell and burst from it to infect more bacteria cells.

Bacteria can also become superbugs due to natural mutations during cell division.

Phages are the most abundant entities on earth, outnumbering all living organisms including bacteria. And have been actively evolving for billions of years.

It is suspected they might be the workers that drive evolution in species.

I interviewed some nurses who said another problem with the treatment of bacterial infections is the practise of prescribing strong antibiotics from the start. The problem with this is that if the bacteria becomes resistant there is no higher antibiotic to administer said the nurses.

Adam Hersh, M.D, Ph.D. an expert in infectious diseases writes in an article on the University of Utah website.

"When US doctors prescribe antibiotics, 60% of the time it is strong antibiotics (broad spectrum) which can kill multiple kinds of bacteria. According to a study by University of Utah researchers. But more than 25% in such cases it is useless because the infection is from a virus." He says the downside of this can be that the antibiotics kill the "good" bacteria in the body which can lead to more side effects and also contribute to antibiotic-resistant bacteria.

Copyright ©️ Arjuwan Lakkdawala 2022

Sources:

Websites

Kurzgesagt video link

Hashem Al Ghaili video link

embroidery: the telomeric effect

A karyotype, in this case it is that of a female’s, with the ends of the chromosomes highlighted with golden thread, to represent the telomeres. Telomeres are a bit like “the tips of shoelaces”, and are actually a series of DNA repeats. Every time a cell in our body divides, chromosomes can shorten at their ends, and then be rebuilt. Research has shown that unrepaired telomere shortening is one factor of the normal ageing process, amongst others, and can be somewhat malleable by a healthier lifestyle.