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science-sculpt · 1 month
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Exploring RNA Interference
Imagine a molecular switch within your cells, one that can selectively turn off the production of specific proteins. This isn't science fiction; it's the power of RNA interference (RNAi), a groundbreaking biological process that has revolutionized our understanding of gene expression and holds immense potential for medicine and beyond.
The discovery of RNAi, like many scientific breakthroughs, was serendipitous. In the 1990s, Andrew Fire and Craig Mello were studying gene expression in the humble roundworm, Caenorhabditis elegans (a tiny worm). While injecting worms with DNA to study a specific gene, they observed an unexpected silencing effect - not just in the injected cells, but throughout the organism. This puzzling phenomenon, initially named "co-suppression," was later recognized as a universal mechanism: RNAi.
Their groundbreaking work, awarded the Nobel Prize in 2006, sparked a scientific revolution. Researchers delved deeper, unveiling the intricate choreography of RNAi. Double-stranded RNA molecules, the key players, bind to a protein complex called RISC (RNA-induced silencing complex). RISC, equipped with an "Argonaut" enzyme, acts as a molecular matchmaker, pairing the incoming RNA with its target messenger RNA (mRNA) - the blueprint for protein production. This recognition triggers the cleavage of the target mRNA, effectively silencing the corresponding gene.
So, how exactly does RNAi silence genes? Imagine a bustling factory where DNA blueprints are used to build protein machines. RNAi acts like a tiny conductor, wielding double-stranded RNA molecules as batons. These batons bind to specific messenger RNA (mRNA) molecules, the blueprints for proteins. Now comes the clever part: with the mRNA "marked," special molecular machines chop it up, effectively preventing protein production. This targeted silencing allows scientists to turn down the volume of specific genes, observing the resulting effects and understanding their roles in health and disease.
The intricate dance of RNAi involves several key players:dsRNA: The conductor, a long molecule with two complementary strands. Dicer: The technician, an enzyme that chops dsRNA into small interfering RNAs (siRNAs), about 20-25 nucleotides long. RNA-induced silencing complex (RISC): The ensemble, containing Argonaute proteins and the siRNA. Target mRNA: The specific "instrument" to be silenced, carrying the genetic instructions for protein synthesis.
The siRNA within RISC identifies and binds to the complementary sequence on the target mRNA. This binding triggers either:Direct cleavage: Argonaute acts like a molecular scissors, severing the mRNA, preventing protein production. Translation inhibition: RISC recruits other proteins that block ribosomes from translating the mRNA into a protein.
From Labs to Life: The Diverse Applications of RNAi
The ability to silence genes with high specificity unlocks various applications across different fields:
Unlocking Gene Function: Researchers use RNAi to study gene function in various organisms, from model systems like fruit flies to complex human cells. Silencing specific genes reveals their roles in development, disease, and other biological processes.
Therapeutic Potential: RNAi holds immense promise for treating various diseases. siRNA-based drugs are being developed to target genes involved in cancer, viral infections, neurodegenerative diseases, and more. Several clinical trials are underway, showcasing the potential for personalized medicine.
Crop Improvement: In agriculture, RNAi offers sustainable solutions for pest control and crop development. Silencing genes in insects can create pest-resistant crops, while altering plant genes can improve yield, nutritional value, and stress tolerance.
Beyond the Obvious: RNAi applications extend beyond these core areas. It's being explored for gene therapy, stem cell research, and functional genomics, pushing the boundaries of scientific exploration.
Despite its exciting potential, RNAi raises ethical concerns. Off-target effects, unintended silencing of non-target genes, and potential environmental risks need careful consideration. Open and responsible research, coupled with public discourse, is crucial to ensure we harness this powerful tool for good.
RNAi, a testament to biological elegance, has revolutionized our understanding of gene regulation and holds immense potential for transforming various fields. As advancements continue, the future of RNAi seems bright, promising to silence not just genes, but also diseases, food insecurity, and limitations in scientific exploration. The symphony of life, once thought unchangeable, now echoes with the possibility of fine-tuning its notes, thanks to the power of RNA interference.
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jcmarchi · 4 months
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Shedding new light on sugars, the “dark matter” of cellular biology - Technology Org
New Post has been published on https://thedigitalinsider.com/shedding-new-light-on-sugars-the-dark-matter-of-cellular-biology-technology-org/
Shedding new light on sugars, the “dark matter” of cellular biology - Technology Org
Scientists at Université de Montréal’s Department of Chemistry have developed a new fluorogenic probe that can be used to detect and study interactions between two families of biomolecules essential to life: sugars and proteins.
Our idea was to label sugar molecules with a chromophore, a chemical that gives a molecule its colour,” explained Cecioni. “The chromophore is actually fluorogenic, which means that it can become fluorescent if the binding of sugar with the lectin is efficiently captured. Image credit: Cecioni Lab
The findings by professor Samy Cecioni and his students, which open the door to a wide range of applications, were published in mid-October in the prestigious European journal Angewandte Chemie.
Found in all living cells
Sugar is omnipresent in our lives, present in almost all the foods we eat. But the importance of these simple carbohydrates extends far beyond tasty desserts. Sugars are vital to virtually all biological processes in living organisms and there is a vast diversity of naturally occurring sugar molecules.
“All of the cells that make up living organisms are covered in a layer of sugar-based molecules known as glycans,” said Cecioni. “Sugars are therefore on the front line of almost all physiological processes and play a fundamental role in maintaining health and preventing disease.”
“For a long time,” he added, “scientists believed that the complex sugars found on the surface of cells were simply decorative. But we now know that these sugars interact with many other types of molecules, particularly lectins, a large family of proteins.”
Driving disease, from flu to cancer
Like sugars, lectins are found in all living organisms. These proteins have the unique ability to recognize and temporarily attach themselves to sugars. Such interactions occur in many biological processes, such as during the immune response triggered by an infection.
Lectins are attracting a lot of attention these days. This is because scientists have discovered that the phenomenon of lectins “sticking” to sugars plays a key role in the appearance of numerous diseases.
“The more we study the interactions between sugars and lectins, the more we realize how important they are in disease processes,” said Cecioni. “Studies have shown how such interactions are involved in bacteria colonizing our lungs, viruses invading our cells, even cancer cells tricking our immune system into thinking they’re healthy cells.”
Difficult to detect…until now
There are still many missing pieces in the puzzle of how interactions between sugars and lectins unfold because they are so difficult to study. This is because these interactions are transient and weak, making detection a real challenge.
Two of Cecioni’s students, master’s candidate Cécile Bousch and Ph.D. candidate Brandon Vreulz, had the idea of using light to detect these interactions. The three researchers set to work to create a sort of chemical probe capable of “freezing” the meeting between sugar and lectin and making it visible through fluorescence.
The interaction between sugar and lectin can be described using a “lock and key” relationship, where the “key” is the sugar and the “lock” is the lectin. Chemists have already created molecules capable of blocking this lock-and-key interaction, and can now to identify exactly what sugars are binding to lectins of high interest to human health.
“Our idea was to label sugar molecules with a chromophore, a chemical that gives a molecule its colour,” explained Cecioni. “The chromophore is actually fluorogenic, which means that it can become fluorescent if the binding of sugar with the lectin is efficiently captured. Scientists can then study the mechanisms underlying these interactions and the disturbances that can arise.”
Cecioni and his students are confident their technique can be used with other types of molecules. It may even be possible to control the colour of new fluorescently labelled probes that are created.
By making it possible to visualize interactions between molecules, this discovery is giving researchers a valuable new tool for studying biological interactions, many of which are critical to human health.
Source: University of Montreal
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academiawho · 4 days
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130 Day Productivity Challenge!
24 March '24 - Day 93
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Worked on my mistakes from past tests. I mapped out the chapters for upcoming tests.
I solved PYQs from Biomolecules and did an NCERT reading with that in mind. I read through Structural Organization. Solved some questions to revise the unit of Cell.
I had a physics brush up class today and also got my doubts cleared along with revising AC and EM Waves.
Hope your day went well💛
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Investigating cell killers: An advanced system for size-dependent cytotoxicity analysis of silica
Metal nanomaterials have become an indispensable part of industrial and medical fields due to their unique and versatile properties. Their size, which imparts them with the desired physiochemical properties, is also the reason for environmental and health concerns. The nano-sized particles in nanomaterials have shown high reactivity towards biomolecules and often even toxicity towards biological cells. Scientists have attributed this behavior of metal nanoparticles in interaction with biomolecules to phenomena like inflammation or oxidative stress. However, to ensure the safe usage of metal nanoparticles, there is a need to explore molecular mechanisms responsible for the toxicity and understand how the uptake of nanoparticles by cells varies based on their shape, size, morphology, and other aspects.
Read more.
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Hello! I am a molecular biologist, and I was wondering if I could get your opinion on some of my theories on Gallifreyans.
I haven't read through everything on your blog yet, but I'm working my way through it (lol). So some of this may not be quite accurate with what you have set up thus far.
Basically, I want to briefly discuss alternative splicing! Anyway, in metazoans, alternative splicing outcomes can be regulated in a time and tissue specific manner by legitimately hundreds of biomolecules such as RNA binding proteins, chromatin remodelers, hormones, etc etc. It is subject to epigenetic regulation as alternative splicing and transcription are coupled (and splicing largely occurs cotranscriptionally), so details such as DNA methylation, nucleosome positioning, histone modifications, etc can change the balance of different mRNA isoforms. This is largely because these factors will either help recruit splicing factors (or inhibit their recruitment) or because it will slow RNA Polymerase II elongation.
Onto my theories. I have been thinking for a little while that the lindos hormone can perhaps modulate splicing, triggering the production of regeneration-specific isoforms. Perhaps their bodies work so fast that isoforms promoting totipotency trigger a temporary transition away from the cells' differentiated states.
I also think it could be possible that they have some novel ability to, say, "unsplice," which humans cannot do. This could potentially allow them to use already made transcripts and then completely change them to produce unique proteins without needing to transcribe another mRNA. This could feasibly allow them to rapidly change what proteins are in each cell (perhaps quick enough that it occurs within the regeneration itself). Although, there would be some instability while now unused proteins get degraded or the splicing/unsplicing ratio stabilizes (the molding period). This would require intense regulation as well as unsplicing and resplicing would now be posttranscriptional, but I digress.
Sorry to bother you with the long post, I just had too many nerdy ideas going through my head. Thanks!
-gallifreyanhotfive
Molecular Biology: 'Unsplicing'
Oh, you thrill me with your biology talk! Molecular biology is not a speciality so apologies in advance for any limited response.
🔬 Lindos and Its Variations
Something to be covered in the new Anatomy and Physiology guide is a wider look at the role of Lindos in Time Lords, so we're hitting the nail on the head here.
Under stress, injury, or during the process of regeneration, the lindal gland significantly increases its production of the hormone Lindoneogen like a caffeine-fueled scientist, resulting in a corresponding surge in lindos cell production. There are several forms of lindos cells, including:
Lindopoetic Progenitor Cells (LPCs): Dormant cells that spring into action upon Lindoneogen stimulation.
Lindopoietic Stem Cells (LSCs): Residing in the yellow bone marrow, ready to differentiate under the guidance of Lindoneogen and the catalytic influence of artron, into ...
Lindoblasts and Phagolindotropes: Specialised cells responsible for regenerating tissue and recycling cellular components from the previous incarnation.
Haemolindocytes: Circulating cells that endow Gallifreyan blood with its regenerative properties.
💡Splicing and Lindoneogen
Lindoneogen could play a key role in alternative splicing, creating specific mRNA isoforms vital for regeneration. This implies that Lindoneogen is not just a cellular signal but also a molecular tool for crafting the necessary protein portfolio for regeneration. So Lindoneogen may trigger the production of specific mRNA isoforms that are vital for the regeneration process, which could lead to the expression of proteins that facilitate the transition of cells into a more pluripotent state.
🖇️Unsplicing
Love this idea. 'Unsplicing' as your concept presents would be particularly relevant during regeneration. It could allow cells to quickly alter their protein expression profiles without the lag of new mRNA transcription. This rapid adaptation would be pretty handy for the efficient transition of cells to suit the requirements of the new incarnation.
🔗Integrating with Lindos Cells
This concept of 'unsplicing' could be particularly prominent in the function of phagolindotropes. As these cells are responsible for consuming the previous incarnation’s cells and replacing them with new ones, their ability to 'unsplice' and rapidly change protein expression would be pretty useful. This mechanism might also support the functions of lindoblasts and haemolindocytes in tissue regeneration and blood adaptability.
🏫 So ...
The addition of splicing and unsplicing mechanisms to the lindos theory suggests a more complex and dynamic process than simple cellular proliferation and differentiation, with dynamic genetic adaptations at the molecular level highlighting the advanced biological capabilities of Gallifreyans. Good work, Batman!
→🫀Gallifreyan Anatomy and Physiology Guide (WIP) →⚕️Gallifreyan Emergency Medicine/Monitoring Guides →📝Source list (WIP)
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science-lover33 · 7 months
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Exploring the Marvels of Biological Macromolecules: The Molecular Machinery of Life (Part 1)
In the captivating realm of biochemistry, biological macromolecules stand as the cornerstone of life itself. These intricately structured molecules, each with its unique role, orchestrate the complex symphony of biological processes. Let's dive deep into the world of macromolecules and unravel their astounding intricacies.
Carbohydrates, a group of organic compounds, are fundamental biomolecules in biochemistry. These compounds, composed of carbon (C), hydrogen (H), and oxygen (O) atoms, play multifaceted roles in various biological processes, acting as both an essential energy source and critical structural elements.
Monosaccharides: The Building Blocks
At the most basic level, carbohydrates are composed of monosaccharides, which are simple sugars. Glucose, fructose, and galactose are examples of monosaccharides. They serve as the fundamental building blocks from which more complex carbohydrates are constructed.
Polysaccharides: Storage and Structure
Carbohydrates manifest as polysaccharides, intricate macromolecules created by linking numerous monosaccharide units. Glycogen, found in animals, and starch, prevalent in plants, are storage forms of glucose. In contrast, cellulose, another glucose-based polysaccharide, forms the structural component of plant cell walls.
Energy Production: Glucose Metabolism
Carbohydrates' primary function within biological systems is to provide energy. Glucose, a hexose sugar, undergoes catabolic processes such as glycolysis and cellular respiration to generate adenosine triphosphate (ATP), the cellular energy currency. The controlled release of energy from carbohydrates fuels vital cellular functions.
Regulation of Blood Glucose: Hormonal Control
Maintaining blood glucose levels within a narrow range is crucial for homeostasis. Hormones like insulin and glucagon intricately regulate glucose levels, ensuring cells have a steady supply of this essential fuel source.
Structural Carbohydrates: Cellulose and Chitin
Carbohydrates also contribute to the structural integrity of cells and organisms. Cellulose, a linear polymer of glucose, forms the rigid cell walls of plants. Similarly, chitin, composed of N-acetylglucosamine units, provides structural support in the exoskeletons of arthropods and the cell walls of fungi.
Glycoproteins and Glycolipids: Molecular Signaling
Carbohydrates are often attached to proteins (glycoproteins) and lipids (glycolipids) on cell surfaces. These complex molecules participate in cell recognition and molecular signaling, which is crucial for various cellular processes, including immune responses and cell adhesion.
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rainacademia · 2 years
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september 3rd
made masala chai for myself after weeks
I did not go to the library today, and i regret it only because I missed the chance to get caught in the rain and romanticise my life a little bit more
timed my self solving chemistry problems and turns out im very slow paced, could solve only 25 sums in 45 mins, so my goal for now is to increase it to 35 within 45.
studying and solving questions from biomolecules right now, after which I'll attempt to solve questions from Cell Division to test how much I remember.
🎧: still, the japanese house
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humancelltournament · 7 months
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Propaganda!
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A lysosome is a membrane-bound organelle found in many animal cells. They are spherical vesicles that contain hydrolytic enzymes that can break down many kinds of biomolecules. A lysosome has a specific composition, of both its membrane proteins, and its lumenal proteins. Besides degradation of polymers, the lysosome is involved in various cell processes, including secretion, plasma membrane repair, apoptosis, cell signaling, and energy metabolism.
Glucagon is a peptide hormone, produced by alpha cells of the pancreas. It raises the concentration of glucose and fatty acids in the bloodstream and is considered to be the main catabolic hormone of the body. It is also used as a medication to treat a number of health conditions. Its effect is opposite to that of insulin, which lowers extracellular glucose. It is produced from proglucagon, encoded by the GCG gene.
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berry-notes · 6 months
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30/9/23- Saturday
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The pictures are mine please don’t repost without permission!! Tasks📌
[x] cell- the functional unit
[x] biomolecules
[ ] biological nomenclature
[ ] anatomy in frogs
Vent ahead:-
hey there everyone! I hope everyone had a good day. Today was a bit meh day for me. I decide to wake up at 5:30 but my period pain said, no, so I ended up sleeping in till 7. I have my last midterm (biology) on Tuesday so I have been studying non stop for it. I managed to finish two of the hardest chapters so yay for me. Only 6 more to tackle before exams.
I ended up making hot chocolate and took a small walk in the neighbourhood but as it started to rain I had to come back unfortunately. I journaled for a bit as well and jam to GUTS once again. I am in love with that album <333
I think I will probably study till late night today and finish the rest of my tasks. And once again my clothes are covered by my dogs hair :,) n e ways
I hope you all had a wonderful day! Goodnight
signing off
-molly
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naturalrights-retard · 10 months
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A new University of Iowa study provides the first experimental evidence that exposure to glyphosate, even at officially designated “safe” levels, disrupts the gut microbiome in mammals.
Glyphosate is the active ingredient in Monsanto’s (owned by Bayer) widely used line of broad-spectrum herbicides.
Consisting of trillions of benign, ever-resident microorganisms (bacteria, yeast, fungi, and even viruses), the gut microbiome helps animals digest food, fight infections, produce vitamin K and other important biomolecules, and metabolize medicines.
Intestinal microbes, especially certain bacterial species, may also benefit the immune system and heart health while reducing cancer risk and positively affecting healthy aging and longevity. The term “microbiome” refers to these organisms and also to their collective genomes.
Investigators at the University of Iowa found that at levels approximating the U.S. Acceptable Daily Intake (ADI) — 1.75 milligrams per kilogram of body weight per day — glyphosate altered the gut microbiome composition and induced “a pro-inflammatory environment.”
They determined this by measuring the loss of beneficial Lactobacillus and Bifidobacterium bacterial species, and the simultaneous blocking of microbial gene pathways that produce anti-inflammatory short-chain fatty acids.
Changes in gut microbe populations were also accompanied by higher levels of pro-inflammatory markers such as Lipocalin-2 and CD4/IL17A-positive immune system cells, and an increase in fecal pH.
Lipocalin-2 is a biomarker for various forms of kidney diseases, heart failure and obesity-related illnesses. The IL-17 family of cytokines promotes protective immunity against many pathogens but also, paradoxically, drives inflammatory pathology during infection and autoimmunity.
According to the authors of the study, published in the June issue of Environmental Toxicology and Pharmacology, a rising fecal pH inhibits the normal production of anti-inflammatory short-chain fatty acids.
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Did life exist on Mars? Other planets? With AI's help, we may know soon
Scientists have discovered a simple and reliable test for signs of past or present life on other planets – “the holy grail of astrobiology.”
In the journal Proceedings of the National Academy of Sciences, a seven-member team, funded by the John Templeton Foundation and led by Jim Cleaves and Robert Hazen of the Carnegie Institution for Science, reports that, with 90% accuracy, their artificial intelligence-based method distinguished modern and ancient biological samples from those of abiotic origin.
“This routine analytical method has the potential to revolutionize the search for extraterrestrial life and deepen our understanding of both the origin and chemistry of the earliest life on Earth,” says Dr. Hazen.  “It opens the way to using smart sensors on robotic spacecraft, landers and rovers to search for signs of life before the samples return to Earth.”
Most immediately, the new test could reveal the history of mysterious, ancient rocks on Earth, and possibly that of samples already collected by the Mars Curiosity rover’s Sample Analysis at Mars (SAM) instrument. The latter tests could be conducted using an onboard analytical instrument nicknamed “SAM” (for Sample Analysis at Mars.  (NASA photos at https://bit.ly/3P8V8II).
“We’ll need to tweak our method to match SAM’s protocols, but it’s possible that we already have data in hand to determine if there are molecules on Mars from an organic Martian biosphere.”
“The search for extraterrestrial life remains one of the most tantalizing endeavors in modern science,” says lead author Jim Cleaves of the Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC.  
“The implications of this new research are many, but there are three big takeaways: First, at some deep level, biochemistry differs from abiotic organic chemistry; second, we can look at Mars and ancient Earth samples to tell if they were once alive; and third, it is likely this new method could distinguish alternative biospheres from those of Earth, with significant implications for future astrobiology missions.”
The innovative analytical method does not rely simply on identifying a specific molecule or group of compounds in a sample.
Instead, the researchers demonstrated that AI can differentiate biotic from abiotic samples by
detecting subtle differences within a sample’s molecular patterns as revealed by pyrolysis gas chromatography analysis (which separates and identifies a sample’s component parts), followed by mass spectrometry (which determines the molecular weights of those components).
Vast multidimensional data from the molecular analyses of 134 known abiotic or biotic carbon-rich samples were used to train AI to predict a new sample’s origin. With approximately 90% accuracy, AI successfully identified samples that had originated from:
Living things, such as modern shells, teeth, bones, insects, leaves, rice, human hair, and cells preserved in fine-grained rock
Remnants of ancient life altered by geological processing (e.g. coal, oil, amber, and carbon-rich fossils), or
Samples with abiotic origins, such as pure laboratory chemicals (e.g., amino acids) and
carbon-rich meteorites.
The authors add that until now the origins of many ancient carbon-bearing samples have been difficult to determine because collections of organic molecules, whether biotic or abiotic, tend to degrade over time. 
Surprisingly, in spite of significant decay and alteration, the new analytical method detected signs of biology preserved in some instances over hundreds of millions of years. 
Says Dr. Hazen: “We began with the idea that the chemistry of life differs fundamentally from that of the inanimate world; that there are ‘chemical rules of life’ that influence the diversity and distribution of biomolecules. If we could deduce those rules, we can use them to guide our efforts to model life’s origins or to detect subtle signs of life on other worlds.”
“These results mean that we may be able to find a lifeform from another planet, another biosphere, even if it is very different from the life we know on Earth.  And, if we do find signs of life elsewhere, we can tell if life on Earth and other planets derived from a common or different origin.”
“Put another way, the method should be able to detect alien biochemistries, as well as Earth life. That is a big deal because it's relatively easy to spot the molecular biomarkers of Earth life, but we cannot assume that alien life will use DNA, amino acids, etc. Our method looks for patterns in molecular distributions that arise from life's demand for "functional" molecules.
“What really astonished us was that we trained our machine-learning model to predict only two sample types – biotic or abiotic – but the method discovered three distinct populations: abiotic, living biotic, and fossil biotic.  In other words, it could tell more recent biological samples from fossil samples – a newly plucked leaf or vegetable, say, versus something that died long ago. This surprising finding gives us optimism that other attributes such as photosynthetic life or eukaryotes (cells with a nucleus) might also be distinguished.”
To explain the role of AI, co-author Anirudh Prabhu of the Carnegie Institution for Science uses the idea of separating coins using different attributes – monetary value, metal, year, weight or radius, for example – then going further to find combinations of attributes that create more nuanced separations and groupings. “And when hundreds of such attributes are involved, AI algorithms are invaluable to collate the information and create highly nuanced insights.”
Adds Dr. Cleaves: “From a chemical standpoint, the differences between biotic and abiotic samples relate to things like water solubility, molecular weights, volatility and so on.”
"The simple way I would think about this is that a cell has a membrane and an interior, called the cytosol; the membrane is pretty water-insoluble, while the cell's content is pretty water-soluble. That arrangement keeps the membrane assembled as it tries to minimize its components' contacts with water and also keeps the ‘inside components’ from leaking across the membrane.”
“The inside components can also stay dissolved in water despite being extremely large molecules like chromosomes and proteins,” he says. 
“So, if one breaks a living cell or tissue into its components, one gets a mix of very water-soluble molecules and very water-insoluble molecules spread across a spectrum. Things like petroleum and coal have lost most of the water-soluble material over their long histories.”
“Abiological samples can have unique distributions across this spectrum relative to each other, but they are also distinct from the biological distributions."
The technique may soon resolve a number of scientific mysteries on Earth, including the origin of 3.5 billion-year-old black sediments from Western Australia (photo at https://bit.ly/3YWbZ4Z) — hotly debated rocks that some researchers contend hold Earth’s oldest fossil microbes, while others claim they are devoid of life signs.
Other samples from ancient rocks in Northern Canada, South Africa, and China evoke similar debates. 
“We’re applying our methods right now to address these long-standing questions about the biogenicity of the organic material in these rocks,” Hazen says.
And new ideas have poured forth about the potential contributions of this new approach in other fields such as biology, paleontology and archaeology. 
“If AI can easily distinguish biotic from abiotic, as well as modern from ancient life, then what other insights might we gain? For example, could we tease out whether an ancient fossil cell had a nucleus, or was photosynthetic?” says Dr. Hazen.
“Could it analyze charred remains and discriminate different kinds of wood from an archeological site? It’s as if we are just dipping our toes in the water of a vast ocean of possibilities.” 
IMAGE....This image taken by NASA's Perseverance rover on Aug. 6, 2021, shows the hole drilled in a Martian rock in preparation for the rover's first attempt to collect a sample. It was taken by one of the rover’s hazard cameras in what the rover's science team has nicknamed a "paver rock" in the "Crater Floor Fractured Rough" area of Jezero Crater. CREDIT NASA/JPL-Caltech
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🧪 (this is such a fun idea!)
So in my lab, we study cells in biofilms. Biofilms are surface-adhered aggregates of microbes living in a matrix of biomolecules that they secrete. The really cool things is that even though a biofilm is a community of individual microbes, not an organism, it actually takes on a lot of multicellular properties. The current thinking is that multicellularity might have arisen as a result of cells living together in biofilms.
The specialization that occurs within biofilms is analogous to differentiation. Biofilms are heterogeneous, even when they are comprised of a clonal population (in which all the cells are genetically identical). There's a division of labor that occurs as a result of stochastic gene expression: one subpopulation of cells might only excrete exopolysaccharides, for example, while another works exclusively at nucleic acid metabolism. This division of labor isn't a result of environmental factors; it's a result of communication between the cells in the biofilm.
But this goes even further - in biofilms, cooperation is actually prioritized over competition between cells, which for a long time was hard to explain from an evolutionary standpoint. Biofilms commonly have cannibalism pathways: as the biofilm matures, the community signals cell types that are no longer needed to lyse -- and they do! After that, the remaining cells - especially the types that are most useful/energetically expensive to the community - will metabolize the remains of the lysed cells. This is darn similar to apoptosis, or pre-programmed cell death, in multicellular organisms. Apoptosis is the process that forms a baby's fingers and eyelids - the tissue tells particular cells to lyse so that gaps in the tissue can be created, then take in the nutrients they leave behind. It's also how pre-cancerous cells are frequently kept in check - the surrounding cells signal cells behaving abnormally to lyse.
Biofilms! Actually fit a number of the traditional "definition by description" criteria for living organisms as a unit rather than as individual cells! Biofilms adapt to their environments, grow and develop, and respond to stimulus. They evolve, after a fashion. Cell-to-cell communication allows biofilms to perform group behaviors all at once in a coordinated way, much as a multicellular tissue would.
This isn't to say that biofilms ought to be considered living organisms; clearly, they are composed of individual, typically prokaryotic microbes. But current thinking is that this is where the multicellular compact (cooperate, don't compete) began! Communities like this are very likely the predecessor to organisms in which millions of cells communicate and differentiate and cooperate. It's a really good transitional state, which is why I love studying communities like this.
If you happen to have institutional access, here is a really great paper on the subject.
Why does this point me to God? Because God gave us these crazy little communities that swap DNA back and forth and talk to each other and die for each other and then he gave us bodies that behave the same way! Just like the Bible is full of repeated ideas and motifs, just like good literature returns and returns to sets of themes, just like music does variations on a line or a theme or a chorus, so too with nature. The study of evolutionary biology is, at least in some respects, digging deep into what those themes are and using them to draw conclusions. Everything is everything; my body's cells and the cells in my petri dishes are more similar than I might ever have guessed.
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jcmarchi · 18 days
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Scientists Train AI to Make More of Life’s Building Blocks - Technology Org
New Post has been published on https://thedigitalinsider.com/scientists-train-ai-to-make-more-of-lifes-building-blocks-technology-org/
Scientists Train AI to Make More of Life’s Building Blocks - Technology Org
A new research paper in Science details an artificial intelligence (AI) upgrade that significantly enhances scientists’ ability to model and generate biomolecules, the building blocks of life. 
Recent breakthroughs in AI now allow scientists to create protein molecules unlike any found in nature. Image credit: Ian Haydon, UW Medicine Institute for Protein Design
This breakthrough is the work of academic researchers at the Institute for Protein Design at the University of Washington School of Medicine, who have made their new tools freely accessible to the scientific community.  
In the rapidly evolving field of AI-driven science, this advance builds upon the success of AlphaFold (a tool from Google DeepMind), and RoseTTAFold and RFdiffusion (both developed at the institute). 
The paper’s lead authors are postdoctoral scholar Jue Wang and graduate students Rohith Krishna and Woody Ahern — all members of David Baker’s lab. Baker is a professor of biochemistry at UW Medicine and director of the Institute for Protein Design.
In the new study, the scientists first retrained the protein modeling tool RoseTTAFold so it could accurately model how proteins interact with common molecules found in living cells such as DNA, RNA, metal ions, sugars and other small chemicals. 
The team named their new tool RoseTTAFold All-Atom, reasoning that a single AI model trained on data from all the major types of biomolecules would become a useful tool for life sciences research. In the paper, the researchers show that RoseTTAFold All-Atom can predict in detail how particular proteins and DNA stretches interact, how certain drug molecules may bind to human receptors, and more.
“We made RoseTTAFold All-Atom free so that scientists everywhere can make new discoveries about the molecules that run all of biology. It may enable them to understand the molecular mechanisms of many diseases better, and this may unlock new treatments,” said Krishna.
The team then used their upgraded AI model to enhance RFdiffusion, a widely used generative AI system that can create proteins unlike any found in nature. Lab tests confirmed that RFdiffusion All-Atom can generate proteins with pockets that bind to specific compounds, including the steroid digoxigenin, the iron-rich blood molecule heme, and chemicals used by plants to absorb sunlight. 
This demonstrates that AI can generate a wide variety of advanced biological functions.
“Our goal here was to build an AI tool that could generate more sophisticated therapies and other useful molecules. For instance, researchers can now design proteins that shut down specific disease-causing molecules, paving the way for precise and effective treatments,” Ahern said.
“By empowering scientists everywhere to generate biomolecules with unprecedented precision, we’re opening the door to groundbreaking discoveries and practical applications that will shape the future of medicine, materials science, and beyond,” Baker said.
Source: University of Washington
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academiawho · 1 year
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I need tips on how to study/revise for chemistry,especially physical chemistry.
Dear anon, I don't know whether you meant boards or competitive exams, so I covered for both since it is based on common ground anyway.
So👇
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There is no other way that we could do well in physical chemistry except practice. A LOT.
What I understand about this dilemma (that I too have at this point, not fully solved) is that by the time you do at least 15 questions on a topic, you can get a grasp on the important formulae/which topics the questions hail from.
Mole concept : limiting reagent, M, m, w/w or w/v% (this particular option is not that frequent), reactions with stoichiometry coinciding with chemical kinetics, electrochemistry and metallurgy
Atomic Structure : which spectral series is in which region of the spectrum, sums with ratio of wavelengths (largest, smallest, comparison of different series), emission and absorption spectra, parts correlating to the physics part of energy levels and radius of hydrogen-like species
Gaseous state : GRAHAM'S LAW OF DIFFUSION (I cannot stress this enough, do it), the Cv and Cp values for Mono, Di and Polyatomic gases which connects thermo in Chem as well as Physics, mean free path proportionalities
Thermo (unit) : everything. All the laws, equations and graphs. adiabatic, isothermal, isochoric, my head and my tongue. Do every numerical in thermo. It's a weak point for a lot of us and we, right now, have the time to make it... Well, a not weak point.
Equilibrium : learn all the formulae and before you learn the formulae visualise/logically understand how something is happening. Log tables, roots, figure out some way to make decimal operations easier. A lot of sums from this one tpo because it isn't that connected to physics like thermo or electrochemistry
Redox : Make a trick for recognising which one is oxidation and which one is reduction. Balancing reactions must be practiced.
Solid state : Repetitive revision of the lattice examples is the only way we can remember them. Muscle memory can serve us well here. Make charts or stick it up on your wall to look at it every few days if that works for you. The rest are formulae and 4-5 numbers to be remembered. Density sums, chemical formula sums, voids sums <- practice
Solutions : formulae, how you get van't hoff factor for a compound, association and dissociation which is linked with electrochemistry molar conductivity part
Electrochemistry : formulae, graphs, molar conductivity sums, kohlrausch's law sums, electrolyte difference/spotting (will help in equilibrium), the cathode and anode of cells (this rarely comes)
Chemical Kinetics : some zero and first order reaction examples (will connect to radioactivity in nuclei chapter), half life formulae, and the 75% and 99% concentration formulae too (these 2 are not there in the tbk but it makes life easier in both phy and chem), all the graphs (should be able to read them even if they are messed around with or changed a bit)
Surface Chemistry : gold number sums, coagulation power and value orders in sols, recognising positive and negative sols, purification methods, electrophoresis definition (you'd be surprised how many times this came), helm holtz double layer theory, tindal's effect (connects a bit to optics, but vaguely), micelles (connects to bot biomolecules and cell unit). This chapter is very theoretical so keep revising stuff you don't get at first glance
Now briefly about Inorganic and Organic Chemistry:
Inorganic : write all the orders and the logics behind it. Some trends are weird so remember them with some trick (keep the tricks to the minimum in inorganic btw, it messes with your brain otherwise). That's as far as I've gotten with inorganic myself, but we can still work on it. If you have any advice regarding this, please do share.
Organic : understand the mechanism behind any reactions. Not just the way it's given in the textbook, but try to connect all organic chapters to each other. Practice a lot of questions, the direct ones as well as the weird ones. Organic does not have any tricks, it just requires practice and that can be done if we understand how each reaction goes about and why we do it.
Hope this helps you with Physical Chemistry and the like🤗 Thank you for approaching me with this so I could think out loud
Have a nice productive day!
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Zwitterionic polymeric sulfur ylides: A new generation of antifouling and bactericidal materials
Bacteria that gather into biofilms on the surfaces of implants, catheters, breathing tubes, and other medical components are a serious health hazard. In the journal Angewandte Chemie International Edition, a research team from the Netherlands has now introduced a new material based on poly(sulfur ylides) that—when applied as coating—effectively inhibits this process known as "fouling." The coating minimizes the adhesion of bacteria to surfaces and is also a bactericide while not affecting mammalian cells. Bacteria organized into biofilms are especially stubborn and often resistant to antibiotics. It is estimated that 65% of infections acquired in hospitals originate from biofilms. The cause is frequently contamination with infectious bacteria from a patient's skin or pathogens that circulate in the bloodstream. The first step is adhesion of the bacteria to a surface. To inhibit this, exposed surfaces are given antifouling coatings, usually made of polyethylene glycol (PEG). PEG binds to water molecules, which then form a hydration layer—an effective barrier against the undesired adsorption of biomolecules and bacterial cells. However, recent research has revealed that PEG also has disadvantages in that it seems to trigger immune responses.
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leebird-simmer · 2 years
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Internal Structure of a Neuron
The Four Main Families of Organic Chemicals in the Brain
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Inside a Neuron
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Major Neuronal Organelles
- Cell membrane
- Mitochondria
- Nucleus
- Endoplasmic reticulum
- Golgi apparatus
- Cytoplasm: all the fluid inside the neuron (intracellular fluid) including the fluid inside the cell body (soma), inside the dendrites, and inside the axon & axon terminal (called axoplasm).
- Neurofilaments and microtubules are both found in the cell body, dendrites, and axon. Both help the neuron maintain its structure (like a skeleton).
- Lysosomes are cellular organelles that contain acid enzymes to break up waste materials and cellular debris.
- Enzyme = biomolecule responsible for breaking down chemicals
Cell Membrane
- The plasma membrane forms the outer “wall” of each neuron (including the cell body, dendrites, axon, axon terminals).
- Separates intracellular and extracellular fluid
- Regulates movement of substances into and out of the cell: most cannot pass
- Structure:
lipid bilayer (fat molecules) + proteins embedded in membrane
Proteins form receptors that bind different chemicals, including drugs.
Proteins form ion channels, allowing ions in and out of cells, creating electrical currents.
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Mitochondria
- singular: mitochondrion
- look like kidney beans
- “Powerhouse of the cell”
- breaks down nutrients such as glucose to provide cell with energy (adenosine triphosphate, ATP) so it can function
- Many mitochondria scattered throughout the neuron’s cell body, also in its dendrites, axon, and axon terminals.
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Nucleus
- surrounded by nuclear membrane (formed by two lipid bilayer membranes)
- contains genetic information: chromosomes (genes). Each chromosome consists of a single, long DNA molecule associated with proteins.
- Genes: segments of DNA that encode the synthesis of particular proteins.
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Endoplasmic Reticulum
- formed from the lipid bilayer membrane that extends from the nucleus
- Ribosomes: protein structures that act as catalysts for protein synthesis
- Responsible for assembling proteins via method called translation:
later phase of protein synthesis in which the mRNA travels from nucleus to the ER. mRNA is translated into a particular sequence of amino acids to form a protein.
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Information Flow Contained in Genetic Code
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Golgi Apparatus
- a collection of several lipid bilayer membrane-enclosed cisternae (4-6) connected to each other and also to the EPR
- a major site of carbohydrate synthesis
- a sorting and dispatching station for the products of the EPR (proteins)
Nucleus, endoplasmic reticulum, and Golgi apparatus work together to synthesize and distribute proteins. Proteins made at the EPR travel on to the Golgi apparatus where they are labeled by carbohydrates and wrapped inside bags called vesicles. The lipid bags protect the proteins inside from being degraded (broken down) by enzymes within the cell.
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Protein Transport
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Synapse
Neurotransmitters released from the presynaptic site bind to receptors on the postsynaptic site.
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