sciencesyd

[sciencesyd]

hold up everyone—new bacteria discovered named “Chonkus” that can help us with our mistakes!

[sciencesyd]

I'm fascinated by microbiomes, the communities of bacteria, unicellular fungi, and other tiny living beings that populate various parts of animal bodies. We literally can't function without them; our gut micriobiome, for example, is crucial to our ability to digest food.

It's long been thought that the brain was kept sterile by the blood-brain barrier. However, this recent study shows that fish have a brain microbiome, so it's not entirely out of the realm of possibility we might, too. It's tough to study, because accessing the brain opens up the risk of outside contamination confounding the results of the study.

But if it is true, the implications could be huge. There's already a growing body of evidence that our gut microbiome has a significant impact on our mental health and mood through what's known as the Gut-Brain Axis. This is a series of connections between these parts of the body that includes the nervous, endocrine, immune, and other systems. Given there's about one microbial cell for every human cell in our bodies, it wouldn't be at all surprising that our microbial communities have a bigger influence on our lives than we think.

Because it's quite dangerous to study a living human brain, it will be difficult to determine whether we do have cranial microbiomes. But I'll be keeping my eye out for any further news along these lines.

[sciencesyd]

"A new study evaluated a low-cost yet effective way to combat bacterial resistance using curcumin–the natural yellow plant compound in turmeric.

In 2017, a tragic death in a Nevada hospital was linked to a new strain of bacteria that had developed a resistance to 26 different antibiotics. Called ‘superbugs’, such antibiotic-resistant bacteria (including MRSA) remains a pressing public health threat.

Now researchers at Texas A&M University have shown that curcumin, the compound that gives turmeric its characteristic bright yellow color, can be used to reduce this antibiotic resistance.

They showed that when curcumin is intentionally given to bacteria as food, and then activated by light, it can trigger deleterious reactions within these microbes, eventually killing them. They demonstrated that this process reduces the number of antibiotic-resistant strains and renders conventional antibiotics effective again.

The results of the study were published this week in the journal Scientific Reports.

“We need alternative ways to either kill the superbugs or find a novel way to modify natural processes within the bacteria so that antibiotics start to act again,” said Dr. Vanderlei Bagnato, professor in the Department of Biomedical Engineering and senior author on the study.

Photodynamic inactivation, a technique that has shown promise in combating bacterial resistance, uses light and light-sensitive molecules, called photosensitizers, to produce reactive oxygen species that can kill microorganisms by disrupting their metabolic processes.

In the new experiments, the team used curcumin, which is also a natural food for bacteria. They tested this technique on strains of Staphylococcus aureus (MRSA) that are resistant to amoxicillin, erythromycin, and gentamicin.

The researchers exposed the bacteria to many cycles of light exposure and then compared the minimum concentration of antibiotics needed to kill the bacteria after light exposure versus those that did not get light exposure.

“When we have a mixed population of bacteria where some are resistant, we can use photodynamic inactivation to narrow the bacterial distribution, leaving behind strains that are more or less similar in their response to antibiotics,” Bagnato told Texas A&M News.

“It’s much easier now to predict the precise antibiotic dose needed to remove the infection.”

MORE PROGRESS ON SUPERBUGS: • The Humble Potato Could Hold Key to Beating Hospital Superbugs and Crop Diseases • Compounds in Amber Could Help Fight Drug-Resistant Bacteria Superbugs, Say Scientists • When Antibiotics Failed, She Found a Natural Enemy of the Superbug to Save Husband’s Life

The team noted that photodynamic inactivation using curcumin has tremendous potential as an adjuvant or additional therapy with antibiotics for diseases, like pneumonia, caused by antibiotic-resistant bacteria.

“Photodynamic inactivation offers a cost-effective treatment option, which is crucial for reducing medical expenses not only in developing countries but also in the United States,” said Dr. Vladislav Yakovlev, professor in the Department of Biomedical Engineering and author on the study..."

-via Good News Network, February 8, 2025

[sciencesyd]

Italy's Phlegraean Fields is a hotspot of volcanic activity—an ever-shifting landscape pocketed with acidic hot springs. This huge caldera is a part of the Campanian volcanic arc, which includes Mount Vesuvius, whose eruption wiped out the Roman city of Pompeii in 79 C.E. Yet, despite the hostile and scalding conditions of this environment, some microorganisms thrive. Researchers at Michigan State University are taking notice, hoping to uncover new information about how a particular alga survives in such extreme conditions. In a paper published in Plant Physiology, researchers in the MSU-DOE Plant Research Laboratory and the Walker lab—in collaboration with the Shachar-Hill lab of the Department of Plant Biology—are studying Cyanidioschyzon merolae, or C. merolae, and its unique ability to photosynthesize its own food. Understanding how C. merolae operates in such extreme conditions can help scientists better extrapolate—or improve upon—the process of photosynthesis, a function vital to all life on Earth.

Continue Reading.

[sciencesyd]

research.exe

You open your eyes and find yourself in a room illuminated by bright fluorescent lights.  Where am I?, you wonder, as you begin to scan the room.  To your right, you find a beaten-up, black leather couch with a sagging indentation in the seat cushion (it’s seen better days).  Directly in front of the couch, two rows of tables with thick black tabletops project out from the wall.  Wired shelves jut-out from the center of each table, almost touching the ceiling; each stuffed to the brim with boxes, glass flasks, tubes with blue-caps, and miscellaneous writing utensils.  You think, Huh, I wonder who’s lab this is?

OBJECTIVE: COMPLETE YOUR EXPERIMENT (0/4)

Oh, you think. Maybe this is my lab. You walk past the table closest to you, hesitantly inspecting its surface for any clues about the experiment you have to do. You see papers scattered about and various empty test tubes, but nothing really calls to you.  You turn your attention to the wired shelves above the desk, spotting what looks like a small plastic fish tank with a neon-pink top.  It looks just like the one you received as a child when you won a fish at the county fair

You approach the tank expecting to find a brightly colored fish, only to find that, disappointingly, there is none.  In fact, the tank is curiously lacking water.  You lean-in to  inspect the contents of the tank more closely, but immediately jump back in a fright.  Inside is a spider.  A very, very, dead, spider. 

Please tell me this is not a part of my experiment.

THIS IS NOT YOUR EXPERIMENT

Oh, thank God, you think as you let out a sigh of relief and retreat to the second table.  Your eyes start to wander up its shelves until you notice a rhythmic hum coming from behind you.  Intrigued, you turn around to a boxy machine, about the size of your torso, with a plexiglass front that is swirling a foil covered flask filled with dark yellow liquid.  A memory of you sitting across a desk from your new supervisor comes to mind; you remember her mentioning she would start culturing your bacteria so that you could start your experiments the following day. 

You think to yourself, This is probably for me, and reach towards the handle of the machine to open the plexiglass front.  Before you touch the handle, you see your bare, gloveless, hand, and think, That’s a problem.  You turn back to the table; scan the surface:  scientific glass paraphernalia, a small rack containing pipettes, various boxes of pipette tips, and – Ah! A box of gloves! You grab two and slip them on.  

Now, protected, you turn back to the machine and open the plexiglass cover, causing a warm, slightly smelly odor to waft out.  The machine instantly slows its rotating motion until the liquid in the flask stops swirling.  You grab the flask, feeling its warmth through the gloves.  

BACTERIA SUCCESSFULLY GROWN, COMPLETE EXPERIMENT (¼)

You hold up the glass towards the fluorescent lights and notice that the yellow liquid is quite cloudy.  You bring it to the table, remove the foil covering the top of the glass and –

GAME OVER YOU CONTAMINATED YOUR BACTERIAL CULTURE.  WHERE IS YOUR CONE OF STERILITY?

You open your eyes and find yourself in a room with fluorescent lights. Cautiously, you inspect the room: a beaten-up black leather couch, two rows of tables, over-stuffed shelves, and a very dead-spider in a tank.

OBJECTIVE: COMPLETE YOUR EXPERIMENT (0/4)

Let’s try this again. Steering clear of the table with the dead spider, you now walk to the second table and snag a pair of gloves.  As you stretch the gloves over your hands, you think back to when you last heard the term, “cone of sterility.”  You recall being in your microbiology class, using a Bunsen Burner to create a sterile work surface.  

And now when you look down, there’s a Bunsen burner accompanied with a metal striker next to the box of gloves.  How could you have missed this?  You open the valve connected to the burner and spark the striker, instantly igniting a bright blue flame.

Satisfied, you collect your bacterial culture from the machine once again.   

BACTERIA SUCCESSFULLY GROWN COMPLETE EXPERIMENT (1/4)

You bring the flask to your desk and remove its foil covering.  As you stare at the flask you think, What do I do now? 

You scan the table for clues and notice drawers underneath the desk.   You open the first drawer on your right to find a red, spiral-bound notebook. 

NOTEBOOK FOUND

You open the notebook and find pages filled with handwritten notes, tables, and calculations.  You flip through, page after page, stopping at the last entry titled, Protocol for PCR.  As you read through the protocol, a memory flashes through your mind.  Your supervisor is rattling off the steps you need to complete for your experiment while you frantically write down her every word.  You nod in triumph. Now I’m getting somewhere.

After reading through the first portion of the protocol, you get out the various test tubes and pipettes you’ll need for the experiment.  Apparently, you first need to get the DNA from your bacteria. 

Using your pipette, you transfer 0.5 mL of bacterial culture from your flask to one, small plastic tube.  You pause.  Was that right?

Feeling confident that you did, in fact, do that right, you continue to transfer 0.5 mL of culture into more tubes, getting into a bit of a groove.  After your fifth transfer, you twist to grab another 0.5 mL sample, causing your elbow to bump into  your flask, splattering the culture on you and the table –

GAME OVER YOU DESTROYED YOUR BACTERIAL CULTURE AND CONTAMINATED YOURSELF.  WHY WEREN’T YOU WEARING A LAB COAT?

You open your eyes and find yourself in a room with fluorescent lights.  You storm over to the second table, slip on a pair of gloves, and fling open the drawer with the notebook.  As you grab the notebook from the drawer, you ask yourself, , in a mocking tone, Why weren’t you wearing a lab coat?”.  I never needed to in my last lab! 

Frustrated, you open more drawers until you find a neatly folded white lab coat.   You pull your arms through its sleeves and secure the buttons on the front. Happy now?, you ask no one.

You flip open your notebook to your protocol and arrange your workspace accordingly, Bunsen burner included.  You turn to the incubator, open its cover, and take out the flask of bacterial culture.  

BACTERIA SUCCESSFULLY GROWN COMPLETE EXPERIMENT (1/4)

You place the flask on your desk, out of elbow-knocking range, and take a breath to steady yourself.  You remove its foil cover and, with great care and precision, begin pipetting samples of the culture into various tube.  As you move through your protocol,  you complete a series of repetitive steps:  adding reagents to tubes, placing them into a machine that spins them, discarding some of the liquid, adding more reagents – all in order to burst open the bacteria and to isolate their DNA.  After one final spin of the tubes, you are left with what appears to be a teardrop of liquid at the bottom of each tube.

DNA OBTAINED COMPLETE EXPERIMENT (2/4)

Yes!, you think, while doing a little fist pump.  You’re getting pretty good at this.  You refer to your notebook for the next steps and determine you must now prepare your DNA samples for PCR Amplification.  I know how to do this!, you think.  You did this in your previous lab.

You look through the shelves for a familiar box and grab the one labeled, Taq PCR Kit.  Hello old friend. You open the box, remove its bottled contents and dexterously mix your reagents into one small test tube. You then separate the contents equally into even smaller test tubes and finish-off by adding a  microscopic amount of bacterial DNA into each of the tiny test tubes.  After securing the caps to the top of each one, you think,  time to get these guys into the thermocycler.

You spot the laboratory-grade toaster-oven-like machine on a table across the room.  You rest your tubes on the table, lift up the top of the machine, and expose a metal sheet with a series of small, circular cutouts.  Carefully, you place each tube into its own circular slot and close the machine’s lid.  You look at the small screen on the front of the machine, touching a series of digital buttons to find the preloaded program needed to run so that your DNA samples will magically double in number with the power of heat and enzymes.  After pressing OK, the machine begins to hum and a timer appears on its screen, counting down from 01:18:00. 

Confident in your progress, you walk back to your station to scan your notebook for your next step.  You spot the words, Gel Electrophoresis, along with a series of  calculations for reagents you need to mix to create a small gelatinous square.  You fumble through the shelves until you find the reagents in question along with the equipment to make the gel.  After mixing and quickly microwaving the reagents in a flask, you pour the concoction into a rectangular mold the size of a notecard.  You have just finished placing what looks like a comb with 6 very wide teeth into the top of the rectangle when you hear a ding.

PCR COMPLETE COMPLETE EXPERIMENT (3/4)

Almost done!, you think to yourself as you hurry over to the machine and remove the tubes.  

You walk back to the gel with your tubes to notice that it has gone from liquid to solid.  It’s just like Jell-O, only so much more toxic.

Needing to remove the comb to reveal the indents into which  your DNA must go, you carefully wiggle the comb to loosen it from the gel.  

Nothing happens.  You wiggle harder. Why isn’t this working? You wiggle it even harder only to completely slice through your gel with its teeth.

No, no, no! You begin to panic, waiting for the inevitable GAME OVER, which you’ve already seen twice before.

But nothing happens. With a sigh of relief, you toss the gel in the container labeled, “WASTE,” and you weigh, mix, pour, and set your gel once again.  You re-attempt removing the comb, being extra careful this time, and it comes out with ease. You place the gel within its mold into a small container that has electrodes plugged into it, filling the container with enough solution to help transmit the electrical current through the gel to separate and visualize the DNA within it. 

You pop open the lids of each tiny tube and pipette a small sample of purple solution into each one (this will help you visualize the DNA within the gel under UV light). You transfer each sample into its own divet that you made with the comb, leaving the last one for your DNA ladder - your molecular ruler that measures the length of the DNA in the other wells. You put the lid over the box, switch on the electrical power supply, set the white, plastic time, and stare at it anxiously as it counts down from 30:00.

After what felt like an eternity, your timer beeps.  You turn off the machine and remove the lid. 

GEL ELECTROPHORESIS COMPLETE EXPERIMENT COMPLETED (4/4) CHECK RESULTS

You carefully remove the gel from the liquid, placing it on the square UV light box next to the container.  This is it, you think.  You place a clear, UV resistant cover over the gel, flip on the UV light, you hold your breath.  You peer at the gel, seeing small illuminated stripes down the right side as expected, but the rest of the gel is completely blank.  But I followed all the –

GAME OVER START OVER? Y / N

[sciencesyd]

Skip Google for Research

As Google has worked to overtake the internet, its search algorithm has not just gotten worse.  It has been designed to prioritize advertisers and popular pages often times excluding pages and content that better matches your search terms 

As a writer in need of information for my stories, I find this unacceptable.  As a proponent of availability of information so the populace can actually educate itself, it is unforgivable.

Below is a concise list of useful research sites compiled by Edward Clark over on Facebook. I was familiar with some, but not all of these.

⁂

Google is so powerful that it “hides” other search systems from us. We just don’t know the existence of most of them. Meanwhile, there are still a huge number of excellent searchers in the world who specialize in books, science, other smart information. Keep a list of sites you never heard of.

www.refseek.com - Academic Resource Search. More than a billion sources: encyclopedia, monographies, magazines.

www.worldcat.org - a search for the contents of 20 thousand worldwide libraries. Find out where lies the nearest rare book you need.

https://link.springer.com - access to more than 10 million scientific documents: books, articles, research protocols.

www.bioline.org.br is a library of scientific bioscience journals published in developing countries.

http://repec.org - volunteers from 102 countries have collected almost 4 million publications on economics and related science.

www.science.gov is an American state search engine on 2200+ scientific sites. More than 200 million articles are indexed.

www.pdfdrive.com is the largest website for free download of books in PDF format. Claiming over 225 million names.

www.base-search.net is one of the most powerful researches on academic studies texts. More than 100 million scientific documents, 70% of them are free

[sciencesyd]

Hey. Your brain needs to de-frag. Literally it needs you to sit there and space out.

If you want your memory or executive function to improve, stare out a window at the skyline or sidewalk or trees or birds on the electrical wires for like 20+ minutes per day. (With no other stimulation like a podcast or TV if you can manage but hey baby steps innit). If you're fortunate enough to have safe outside with any bits of nature, go stare closely at a 1 meter square of grass and trip out on the bugs and shapes of grasses and stuff.

Literally this will make you smarter. Our brains HAVE TO HAVE this zone out time to do important stuff behind the scenes. This does not happen during sleep, it's something else.

That weird pressurized feeling you get sometimes might be your brain on no defrag.

Give your brain a Daily Dose Of De-Frag.

[sciencesyd]

An aquarium in Japan was closed for renovations, and their resident sunfish got depressed not seeing visitors. So the staff put some uniforms with printed faces against the tank, and it immediately recovered.