#genomes

[iamthekaijuking]

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…

They wouldn’t believe you. Yet one of the most beloved cartoon characters is one of them.

[mindblowingscience]

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.

Continue Reading.

[rjzimmerman]

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.

According to the study, it appears the San Diego birds have bred with flycatchers originally from populations in other areas of the West, which may have moved in response to local habitat losses. And as natural selection has acted on this increased diversity, the San Diego birds’ genomes have shifted away from those of neighboring populations, potentially making the local birds better suited for life in a wetter, more humid environment being shaped by climate change.

[er-cryptid]

Major Eukaryotic DNA Polymerases

Patreon

[yasbxxgie]

Genomic analyses of individuals living with HIV-1 revealed a region in chromosome 1 that is associated with reduced viral loads specifically in populations with African ancestry. This could point to much-needed therapeutic targets to address the global public-health crisis caused by HIV-1.

[h/t]

[inkintheinternet]

The Tree of Unanswered Questions (Answered)

By Arjuwan Lakkdawala 

Ink in the Internet 

I have often been confused by the theory that we are primates, and that chimps and humans have 98% DNA similarity, and therefore it is "evidance" that we are primates. Darwin's Theory of Evolution by Natural Selection is often cited by many as the backing for this claim, or that it is at the root of it.

I decided to investigate the claims regarding human evolution to the best of my ability. I wanted to get answers that would be clear for people who have not studied human evolution. It's one of the toughest research I have done.

Evolution in itself is such a sprawling subject, one would not know from where to begin.

I decided to make it as simple as possible, I would write the subject as a tree. My own version of the evolutionary tree, not the scientific one with its many intricate details and dead ends. Because to understand that most regular readers might lose their brain cells. I say this because anyone doing research on human evolution will find quotes like "it's complex" "not enough fossil evidance" "it's a tangled web." and so on.

So here I start, let us speak about the highest branch first.

Branch 1 - Hominins (ancient human  species)

Early humans are called hominins and there are according to evolutionary biologists many extinct species of humans from the genus Homo, but we the Homo Sapiens are the only living ones on earth.

In this branch there is Homo Erectus (upright human) this species is said to be the first "most human-like ancient hominin."

It is said that ancient hominins first appeared on earth six million years ago and they walked on four.

Bipedalism - the ability to walk on two legs evolved four million years ago in humans.

So Homo Erectus are the first to walk on two, they lived two million years ago, until at least 250,000 years ago.

I have seen online artificial imagineering of their faces, and you get a human face according to the artificial intelligence software.

But according to evolutionary biology they are not modern humans.

As with the example of Homo Erectus many hominin fossils have been found, and basically each has been classified as an extinct ancient human species.

There are hominins thought to be older ancrstors to Homo Erectus and those are called "super archiac."

Then in the branch after many hominins comes two of our most famous and closest cousins the Neanderthals and Denisovans.

Again not modern humans according to scientific classification.

Neanderthals went extinct about 40,000 years ago.

Denisovans are said to have gone extinct 40,000 to 30,000 years ago.

Denisovans are closer to Neanderthals than modern humans according to the science.

It is said Neanderthals and modern humans interbreeded.

There is no explanation as to why or how Neanderthals became extinct.

How does evolution take place? Answer: By mutations.

According to the science of evolution it happens in two types of periods.

1. The Microevolution (short period) in this period minor changes get made to species according to natural selection. The difference in anatomy is considered not to be significant.

2. The Macroevolution (long period) in this period great changes get made to a species, and even evolving it into a whole new species.

But there has to be the existence of an intermediate species in the chain or branch of evolutionary changes.

Example: 

Charles Darwin was hoping to get palaeontological evidance of an intermediate species. Two years after the publication of his book 'On the Origin of Species' the fossil 'archaepteryx' was found. The fossil link between birds and dinasaurs.

"This extraordinary fossil—bearing feathers as well as teeth, claws, a bony tail and other reptilian traits—was just the sort of creature that Darwin’s theory of evolution by natural selection predicted should exist. The feathers left no question that the Jurassic Archaeopteryx was a bird, but the creature also had a suite of saurian traits that pointed to a reptilian ancestry." - Smithsonian Megazine

However, anthropologist Briana Pobinar, says that the term "Missing Link" is not accurate because it depicts a linear chain in evolution, which is not the pattern they see.

Pobinar says evolution “produces a tree-like branching pattern with multiple descendants of an ancestor species existing at the same time, and sometimes even alongside that ancestor species.” - Smithsonian Megazine.

The human that is supposed to connect modern humans with primative ancestors has never been found.

So much so that it appears that it's a "ghost" species. What it means is that there is no fossil or DNA evidance to make a scientific connection. 

In fact a new study published in Nature Journal challenges previous notions about hominin contribution to modern Homo Sapiens.

"New model for human evolution suggests Homo sapiens arose from multiple closely related populations.

A new study in Nature challenges prevailing theories, suggesting that Homo sapiens evolved from multiple diverse populations across Africa, with the earliest detectable split occurring 120,000-135,000 years ago, after prolonged periods of genetic intermixing." - Scitech Daily

This means that modern humans evolved from similar other modern humans. There is no genetic evolutionary notable impact from primate like hominins.

(Study is very new released in May 2023) 

So what really makes modern humans different to so called other species of humans. I would say it's the brain and cognitive ability, and this brings me to the second branch of the tree.

Branch 2. (Human Brain Development)

The fossils so far found of "extinct human species" help scientists determine bone structure and facial features of those individuals, but brain tissue is not preserved well, so scientist know little about the cognitive abilities of these species.

So archealogy is the best option for researchers to try and understand the thinking abilities of more recent species like Neanderthals and Denisovans.

As I have read in an article, this too is extremely complicated, as it raises the question are the primitive tools found in excavations and cave paintings really a sign of limited intelligence or underdeveloped environment. Can we really assume that Neanderthals and Denisovans if in a modern world would not be able to think like a modern human?

Researchers have observed differences in brain case size of extinct humans. But does this imply higher or lower cognitive abilities.

To answer to this question or shed some light on it as I was so curious, I decided to take my research from evolutionary biology, history, and archaeology to neuroscience and investigate the development of the human brain.

The confusion of brain development and cultural effect is because of neuro plasticity. In a study done chimps it appeared had rigid neuro plasticity compared to humans. So what is brain plasticity? It is the brain's ability to rewire itself structurally and functionally according to experience and injury. There are even ongoing studies about if plasticity itself can evolve. The more plasticity the stronger cognitive abilities.

Neuroscience is one of the hardest and active field of research. So I'll not get into other aspects of the brain. Here I'll examine the aspect of brain development in regard to neuro plasticity.

"The neocortex—the outermost layer of the brain characterized by the squiggly sulci, or brain folds—is the region that gives all primates their exceptional intelligence. In both chimps and humans, this brain region continues to grow and organize for years after birth, allowing us to learn and develop socially. The brain's ability to reorganize in response to environmental cues is known as plasticity, and it is this flexibility that allows us to learn things we never knew at birth." - Science.org

There lingers the question of brain size regarding the hominins or Neanderthals, Denisovans, if brain tissue of their fossils cannot be examined, we can instead try to find out if a larger brain (large brain cases of fossils) mean higher intelligence or the ability for modern human cognition.

"Having an unusually large brain doesn't necessarily make someone a genius, and large-scale research suggests only a slight and tenuous relationship between brain size and intelligence." - Psychology Today.

With this I conclude the second branch, and start the third branch which is about intelligence in apes and other animals.

Branch 3. (Intelligence in the animal kingdom)

Animals that have shown high Intelligence in comparison to most animals are apes, parrots, crows, ravens, mice, elephants, dogs, and new research suggests octopuses.

"The more that researchers examine octopus genetics, brains and sensory capabilities, the more they find startling similarities to our own minds, hand in hand (or sucker-covered arm in sucker-covered arm) with bizarre differences between how our species experience the world." - Discover.

However, there is nothing close to the level of human intelligence.

Charles Darwin had based his theory on physical changes, he did not know about genetics. 

The Theory of Evolution incorporated with the study of genetics is called 'Modern Evolution Synthesis."

What I have done in this tree is summarise the theory of human evolution based on physical and biological research. 

What I have found is so far scientifically there is no fossil or genetic evidance that says Homo Sapiens evolved directly from apes.

We are in the 21st century with sophisticated technologies and molecular biology. There is nothing stopping scientists from searching for fossil or genetic evidence except that it can't be found. 

Neanderthals and Denisovans have said to have existed in the Ice Age, and there were hominins in the Stone Age.

Copyright ©️ Arjuwan Lakkdawala 2023

Arjuwan Lakkdawala is an author and independent journalist. Twitter: @Spellrainia Email: arjuwan.writer@gmail.com

Sources:

Metode Science Studies Journal, 7 (2017)

Human Brain Evolution - How increase in brain plasticity made us a cultural species - Aida Gomez Robles and Chet C. Sherwood

What Is Neural Plasticity?

Rommy von Bernhardi et al. Adv Exp Med Biol. 2017.

Smithsonian Megazine - Riley Black, Natural History Museum- Katie Pavid

Natural History Museum- Josh Davis

National Geogrphic - Tim Vernimmen

YourGenome.org - Society and Behaviour

Australian Museum - A Timeline of Gissil Discoveries - Fran Dorey

Britannica - Homo Sapiens

Smithsonian: National Museum of Natural History - Introduction to Human Evolution

Live Science: What is Darwin's Theory of Evolution - By Ker Than, Ashley P. Taylor, Tom Garner

Discover Megazine

Psychology Today

Daniel Graham, Ph.D.

A Bigger Brain is Not Necessarily Better

Science.org - David Shultz

New DNA Research Changes Origin of Human Species -

Scitech Daily - University of California - Davis

National Library of Medicine - National Center for Biotechnology Information -

Front Hum Neurosci. 2013; 7: 707. 

Published online 2013 Oct 30. doi: 10.3389/fnhum.2013.00707

PMCID: PMC3812990

PMID: 24194709

Evolution, development, and plasticity of the human brain: from molecules to bones

Branka Hrvoj-Mihic,1,2 Thibault Bienvenu,1 Lisa Stefanacci,1,2 Alysson R. Muotri,2,3 and Katerina Semendeferi1,3,*

What may have given modern humans an edge over Neanderthals, according to new research

By Katie Hunt, CNN

Study.com - People and Society in the Stone Age

Jessica Holmes, Joanna Harris

[kentzwritez]

"New World Assemblage"

~ AI Assimilation ~

Human genomes had been researched, analyzed, and stored at secured, private unknown locations after the documented nasal-swab procedures while the vaccines were still in development. The vaccines then were the catalyst to disperse interactive bio-scientific cells that would react with specific genomic structures to enhance growth and make their presence in the human body easier to extract and compare to the markers needed for assemblage into the new world order, and for Mars colonization. Not all would be a match to the social markers that were needed, there was also the hybrid-cloning that would essentially duplicate the human form and program it with what would  come to be known as the “AI-X Factor”, an AI voice and memory system modeled after the human-interaction with hand-held devices that elicited voice commands from their account holders as part of the new upgrade for the modern human experience. Aside from the targeted marketing and GPS tracking used for demographic research and predictive movements regarding sales, profits, projected earnings related to cultural population density, voice commands and conversations were also being recorded, analyzed, and programmed into an AI system that would ultimately be used to duplicate human behavior and memory associated with the repetitive daily routines, conversations, and destinations tracked in the modern suburbia lifestyle. A plan spawned from the introduction of personal hand-held devices ~ literally pocket computers ~ that not only surveilled spending and location, but also recorded and stored voice commands, conversations, gestures, tones, fingerprint and facial recognition . . . The perfect menu for AI assimilation through selective genomic aggregation. 

It would have been the perfect plan, but while trying to influence the masses throughout the decades using subliminal television programming and messaging laced within the commercials, radio advertisements, and newspaper articles, the plan never generated the momentum needed for restructuring of the population for a new world order. People were still naive and complacent, not retaining enough of the subliminal messaging needed to motivate their lack-luster suburban lifestyles, and so the plan for new world assemblage stalled until the introduction of the marvelous hand-held pocket computers ~ touted as revolutionary change for the world ~ that would bring everyone from around the globe closer together . . . That is, until the introduction of AI and the rogue de facto diplomats associated with it ~ puppeteered by the ruling corporate elite ~ guiding the masses to a pre-arranged, pre-planned future beyond their known horizon, a future that involved cloning select genomic specimens for colonization on the planet Mars. 

Interplanetary space travel would be the pathway to other galactic colonies, awaiting the hyper-tech AI-clones, having been replicated in human form, using only specific bio-scientific genomic structures aggregated for AI assimilation to create the perfect specimens for the new world and Mars colonization.

Cyanobacteria being one of the largest available groups of low-light bacteria located on Earth would be crucial to Mars colonization by creating its own biosphere, a breathable atmosphere through photosynthesis on Mars.

Having only the best specimens replicated ~ in terms of genomic structure ~ with a predetermined select social ladder, would be that of a perfect world order. 

End ~

kentxsandersxwriter.com

[maximiummartinez]

The classic is back with a new hyperfixation

man & girl go out to drive under moonlight. they stop at on at a side of road. he turn to his girl and say: "baby, i love you very much" "what is it honey?" "our car is broken down. i think the engine is broken, ill walk and get some more fuel." "ok. ill stay here and look after our stereo. there have been news report of steres being stolen." "good idea. keep the doors locked no matter what. i love you sweaty"

so the guy left to get full for the car. after two hours the girl say "where is my baby, he was supposed to be back by now". then the girl here a scratching sound and a voice say "LET ME IN"

the girl doesn't do it and then after a while she goes to sleep. the next morning she wakes up and finds her boyfriend still not there. she gets out to check and man door hand hook car door.

String identified:

a & g g t t gt. t t at at a a. t t g a a: "a, c" "at t ?" " ca . t t g , a a gt ." ". ta a at t. t a t t g t." "g a. t c att at. at"

t g t t gt t ca. at t t g a " a, a t ac ". t t g a catcg a a c a "T "

t g 't t a t at a g t . t t g a a t t t. gt t t cc a a a ca .

Closest match: Cloeon dipterum genome assembly, chromosome: 3 Common name: Small minnow mayfly

[markscherz]

You might know this tiny frog.

This is Mini mum (photo by Andolalao Rakotoarison), a species I had the pleasure to name—together with a team of amazing colleagues—back in 2019.

That was the start of a fascination with the process and consequences of miniaturisation for vertebrates. How the hell does this tiny frog manage to fit all of its vital organs—more or less all the same senses and organs that we have—into a package the size of a tic-tac‽ Why and how has it evolved to be so small? And why don't we get frogs that are much smaller?

Well, I just secured 1.5 MILLION Euros (!!!) in the form of a European Research Commission Starting Grant, to answer these and other related questions in the genomes of Mini frogs and other miniaturised vertebrates.

Because it turns out, there are *lots* of miniaturised vertebrates, and they push the boundaries of how small we think it is possible for a vertebrate to be! Here is a little graphic of some of them, scaled to a BIC ballpoint pen.

The project is called GEMINI: The Genomics of Miniaturisation in Vertebrates! You can read more about it on my website here, and in the press release, here!

[mindblowingscience]

The longest genome of all the animals on Earth belongs not to a giant, or a cognitively advanced critter, but a writhing, water-dwelling creature seemingly frozen in time, right at the cusp of evolving into a beast that can live on land. These are the lungfish, a class of freshwater vertebrates whose peculiar characteristics are reflected in a colossal genetic code. Able to breathe both air and water, with limb-like fins, and a well-developed skeletal architecture, these strange ancient creatures are thought to is thought to share a common ancestor with all four-limbed vertebrates known as tetrapods.

Continue Reading.

[bio-basic-inc]

Dive into the future of molecular biology with Next-Gen Sequencing (NGS)! Revolutionize your research with this cutting-edge technology that unlocks the secrets of entire genomes in record time. 

Say “goodbye” to traditional sequencing methods and hello to a world of possibilities! 

At Bio Basic, we're at the forefront of NGS innovation, offering rigorously tested products that guarantee safety and compliance with industry standards. With prompt delivery and seamless experiments, your journey to discovery just got smoother. 

Inquire more about our NGS services today at sequencing@biobasic.com

Or, browse https://www.biobasic.com/dna-next-gen/ for further details.

[jcmarchi]

Scientists preserve DNA in an amber-like polymer

New Post has been published on https://thedigitalinsider.com/scientists-preserve-dna-in-an-amber-like-polymer/

Scientists preserve DNA in an amber-like polymer

In the movie “Jurassic Park,” scientists extracted DNA that had been preserved in amber for millions of years, and used it to create a population of long-extinct dinosaurs.

Inspired partly by that film, MIT researchers have developed a glassy, amber-like polymer that can be used for long-term storage of DNA, whether entire human genomes or digital files such as photos.

Most current methods for storing DNA require freezing temperatures, so they consume a great deal of energy and are not feasible in many parts of the world. In contrast, the new amber-like polymer can store DNA at room temperature while protecting the molecules from damage caused by heat or water.

The researchers showed that they could use this polymer to store DNA sequences encoding the theme music from Jurassic Park, as well as an entire human genome. They also demonstrated that the DNA can be easily removed from the polymer without damaging it.

“Freezing DNA is the number one way to preserve it, but it’s very expensive, and it’s not scalable,” says James Banal, a former MIT postdoc. “I think our new preservation method is going to be a technology that may drive the future of storing digital information on DNA.”

Banal and Jeremiah Johnson, the A. Thomas Geurtin Professor of Chemistry at MIT, are the senior authors of the study, published yesterday in the Journal of the American Chemical Society. Former MIT postdoc Elizabeth Prince and MIT postdoc Ho Fung Cheng are the lead authors of the paper.

Capturing DNA

DNA, a very stable molecule, is well-suited for storing massive amounts of information, including digital data. Digital storage systems encode text, photos, and other kind of information as a series of 0s and 1s. This same information can be encoded in DNA using the four nucleotides that make up the genetic code: A, T, G, and C. For example, G and C could be used to represent 0 while A and T represent 1.

DNA offers a way to store this digital information at very high density: In theory, a coffee mug full of DNA could store all of the world’s data. DNA is also very stable and relatively easy to synthesize and sequence.

In 2021, Banal and his postdoc advisor, Mark Bathe, an MIT professor of biological engineering, developed a way to store DNA in particles of silica, which could be labeled with tags that revealed the particles’ contents. That work led to a spinout called Cache DNA.

One downside to that storage system is that it takes several days to embed DNA into the silica particles. Furthermore, removing the DNA from the particles requires hydrofluoric acid, which can be hazardous to workers handling the DNA.

To come up with alternative storage materials, Banal began working with Johnson and members of his lab. Their idea was to use a type of polymer known as a degradable thermoset, which consists of polymers that form a solid when heated. The material also includes cleavable links that can be easily broken, allowing the polymer to be degraded in a controlled way.

“With these deconstructable thermosets, depending on what cleavable bonds we put into them, we can choose how we want to degrade them,” Johnson says.

For this project, the researchers decided to make their thermoset polymer from styrene and a cross-linker, which together form an amber-like thermoset called cross-linked polystyrene. This thermoset is also very hydrophobic, so it can prevent moisture from getting in and damaging the DNA. To make the thermoset degradable, the styrene monomers and cross-linkers are copolymerized with monomers called thionolactones. These links can be broken by treating them with a molecule called cysteamine.

Because styrene is so hydrophobic, the researchers had to come up with a way to entice DNA — a hydrophilic, negatively charged molecule — into the styrene.

To do that, they identified a combination of three monomers that they could turn into polymers that dissolve DNA by helping it interact with styrene. Each of the monomers has different features that cooperate to get the DNA out of water and into the styrene. There, the DNA forms spherical complexes, with charged DNA in the center and hydrophobic groups forming an outer layer that interacts with styrene. When heated, this solution becomes a solid glass-like block, embedded with DNA complexes.

The researchers dubbed their method T-REX (Thermoset-REinforced Xeropreservation). The process of embedding DNA into the polymer network takes a few hours, but that could become shorter with further optimization, the researchers say.

To release the DNA, the researchers first add cysteamine, which cleaves the bonds holding the polystyrene thermoset together, breaking it into smaller pieces. Then, a detergent called SDS can be added to remove the DNA from polystyrene without damaging it.

Storing information

Using these polymers, the researchers showed that they could encapsulate DNA of varying length, from tens of nucleotides up to an entire human genome (more than 50,000 base pairs). They were able to store DNA encoding the Emancipation Proclamation and the MIT logo, in addition to the theme music from “Jurassic Park.”

After storing the DNA and then removing it, the researchers sequenced it and found that no errors had been introduced, which is a critical feature of any digital data storage system.

The researchers also showed that the thermoset polymer can protect DNA from temperatures up to 75 degrees Celsius (167 degrees Fahrenheit). They are now working on ways to streamline the process of making the polymers and forming them into capsules for long-term storage.

Cache DNA, a company started by Banal and Bathe, with Johnson as a member of the scientific advisory board, is now working on further developing DNA storage technology. The earliest application they envision is storing genomes for personalized medicine, and they also anticipate that these stored genomes could undergo further analysis as better technology is developed in the future.

“The idea is, why don’t we preserve the master record of life forever?” Banal says. “Ten years or 20 years from now, when technology has advanced way more than we could ever imagine today, we could learn more and more things. We’re still in the very infancy of understanding the genome and how it relates to disease.”

The research was funded by the National Science Foundation.

[cha-mij]

Guy featured on documentary about CRISPR and gene splicing: "and that's why I have nightmares about fruit flies"

Me: "DREAMsophila melanogaster

[deadstonemasonssociety]

These individuals are the oldest representatives of Western Europeans to have established themselves permanently in Europe and to have left traces in the genomes of present-day Europeans.

It is estimated they settled in the region after the ice age that took place from 40,000 to 38,000 years ago.

[inkintheinternet]

Superbugs Catastrophe

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