Posts Tagged ‘biology’

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by PETER DOCKRILL

When somebody mentions anaesthetics, we probably think straight away of pain relief, but there’s a lot more going on in these complex chemical compounds than the simple negation of discomfort.

While there’s a range of chemicals that can induce anaesthesia in humans, just how these unrelated compounds trigger a lack of consciousness remains somewhat unclear.

And the mystery deepens when you consider it isn’t only animals that are affected by anaesthetics – plants are, too.

Humans in ancient societies were using things like herbs for various sedative purposes thousands of years ago, but the roots of modern anaesthesia began around the mid-19th century, when physicians began administering diethyl ether to patients during surgical procedures.

It was only a few decades later that scientists realised plants were similarly affected by ether, leading French physiologist Claude Bernard to conclude plants and animals shared a common biological essence that could be disrupted by anaesthetics.

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A century and a half later, scientists are still investigating this strange commonality – basically by slipping plants the mickey and seeing what it does to them.

In a new study by Japanese and European researchers, the team filmed a number of plants that exhibit the phenomenon of rapid plant movement to see what kinds of anaesthetic chemicals affected them.

The sensitive plant (Mimosa pudica) usually closes its leaves in response to touch stimuli; but when exposed to diethyl ether, the dosed-up plants completely lost this response, becoming motionless, with the movement response only returning to normal after 7 hours.

In a separate experiment with the sensitive plants, a lidocaine solution also immobilised the leaves.

Similarly, the Venus flytrap (Dionaea muscipula) lost its ability to close its trap when exposed to diethyl ether – despite repeated prongings by the researchers – but the mechanism recovered in just 15 minutes.

Another carnivorous plant, Cape sundew (Drosera capensis), captures prey via sticky tentacles on its leaves, but experiments showed they lost the ability to bend their leaves and tentacles when exposed to the ether.

As for why plants are incapacitated by these chemicals, the researchers hypothesise it is to do with the inhibition of action potentials, preventing electrical impulses that help plants’ biological systems function.

“[B]ioelectricity and action potentials animate not only humans and animals but also plants,” the researchers explain.

“That animals/humans and also plants are animated via action potentials is of great importance for our ultimate understanding of the elusive nature of plant movements and plant-specific cognition/intelligence based plant behaviour.”

Ultimately, the team thinks these similarities between plant and animal reactions to anaesthetic compounds could lead to future research where plants might function as a substitute model or test system to explore human anaesthesia – something scientists are still pretty uncertain about.

It’s not easy being green, perhaps, but at least they shouldn’t feel any pain.

The findings are reported in Annals of Botany.

https://www.sciencealert.com/plants-respond-anaesthetics-weird-movement-action-brain

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cientific studies on the cleaning power of spit, a lone fruit fly’s ability to spoil wine, and cannibals’ caloric intake garnered top honors at the 28th Ig Nobel Prize ceremony. The seriously silly citations, which “honor achievements that first make people laugh, and then think,” were awarded on Sept. 13 at Harvard University’s Sanders Theatre. Entertaining emcee Marc Abrahams and the savvy satirists of the Annals of Improbable Research produced the ceremony.

The coveted Chemistry Prize went to Portuguese researchers who quantified the cleaning power of human saliva. Nearly 30 years ago, conservators Paula Romão and Adília Alarcão teamed up with late University of Lisbon chemist César Viana to find out why conservators preferred their own saliva to any other solvent for cleaning certain objects—with the goal of finding a more hygienic substitute. Compared with popular solvents, saliva was the superior cleaning agent, particularly for gilded surfaces. The researchers attributed the polishing power to the enzyme α-amylase and suggested solutions of this hydrolase might achieve a spit shine similar to spit (Stud. Conserv. 1990, DOI: 10.1179/sic.1990.35.3.153).

A fruit fly in a glass of wine is always an unwelcome guest. But it turns out that as little as 1 ng of Drosophila melanogaster’s pheromone (Z)-4-undecenal can spoil a glass of pinot blanc. That discovery, from researchers led by Swedish University of Agricultural Sciences’ Peter Witzgall, received the Ig Nobel’s Biology Prize. Only female fruit flies carry the pheromone, so males can swim in spirits without delivering the offending flavor, but the Newscripts gang still prefers to drink wine without flies (J. Chem. Ecol. 2018, DOI: 10.1007/s10886-018-0950-4).

Putting the paleo diet in a new perspective, University of Brighton archaeologist James Cole took home the Nutrition Prize for calculating that Paleolithic people consumed fewer calories from a human-cannibalism diet than from a traditional meat diet. Thus, Cole concludes, Paleolithic cannibals may have dined on their companions for reasons unrelated to their nutritional needs (Sci. Rep. 2017, DOI: 10.1038/srep44707).

A team led by Wilfrid Laurier University psychologist Lindie H. Liang won the Economics Prize “for investigating whether it is effective for employees to use voodoo dolls to retaliate against abusive bosses.” Push in some pins: The findings indicate voodoo doll retaliations make employees feel better (Leadership Q. 2018, DOI: 10.1016/j.leaqua.2018.01.004).

The Newscripts gang previously reported about this year’s winners of the Ig Nobel for medicine, physicians Marc Mitchell and David Wartinger, who found that riding roller coasters can help people pass kidney stones (J. Am. Osteopath. Assoc.2016, DOI: 10.7556/jaoa.2016.128).

The Reproductive Medicine Prize went to urologists John Barry, Bruce Blank, and Michel Boileau, who, in 1980, used postage stamps t
o test nocturnal erections, described in their study “Nocturnal Penile Tumescence Monitoring with Stamps” (Urol. 1980, DOI: 10.1016/0090-4295(80)90414-8).

The Ig Nobel committee also gave out a Medical Education Prize this year, to gastroenterologist Akira Horiuchi for the report “Colonoscopy in the Sitting Position: Lessons Learned from Self-Colonoscopy” (Gastrointest. Endoscopy 2006, DOI: 10.1016/j.gie.2005.10.014).

Lund University cognitive scientists Gabriela-Alina Sauciuc and coworkers claimed the Anthropology Prize “for collecting evidence, in a zoo, that chimpanzees imitate humans about as often, and about as well, as humans imitate chimpanzees” (Primates 2017, DOI: 10.1007/s10329-017-0624-9).

For a landmark paper documenting that most people don’t read the instruction manual when using complicated products, a Queensland University of Technology team led by Alethea L. Blackler garnered the Literature Prize (Interact. Comp. 2014, DOI: 10.1093/iwc/iwu023).

And finally, the Ig Nobel Peace Prize was awarded to a team from the University of Valencia’s University Research Institute on Traffic & Road Safety “for measuring the frequency, motivation, and effects of shouting and cursing while driving an automobile” (J. Sociol. Anthropol. 2016, DOI: 10.12691/jsa-1-1-1).

The Ig Nobel ceremony can be viewed in its entirety at youtube.com/improbableresearch, and National Public Radio’s “Science Friday” will air an edited recording of the ceremony on the day after U.S. Thanksgiving.

https://cen.acs.org/people/awards/2018-Ig-Nobel-Prizes/96/i37

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Listeria bacteria transport electrons through their cell wall into the environment as tiny currents, assisted by ubiquitous flavin molecules (yellow dots). (Amy Cao graphic, copyright UC Berkeley)

By Robert Sanders

While bacteria that produce electricity have been found in exotic environments like mines and the bottoms of lakes, scientists have missed a source closer to home: the human gut.

UC Berkeley scientists discovered that a common diarrhea-causing bacterium, Listeria monocytogenes, produces electricity using an entirely different technique from known electrogenic bacteria, and that hundreds of other bacterial species use this same process.

Many of these sparking bacteria are part of the human gut microbiome, and many, like the bug that causes the food-borne illness listeriosis, which can also cause miscarriages, are pathogenic. The bacteria that cause gangrene (Clostridium perfringens) and hospital-acquired infections (Enterococcus faecalis) and some disease-causing streptococcus bacteria also produce electricity. Other electrogenic bacteria, like Lactobacilli, are important in fermenting yogurt, and many are probiotics.

“The fact that so many bugs that interact with humans, either as pathogens or in probiotics or in our microbiota or involved in fermentation of human products, are electrogenic — that had been missed before,” said Dan Portnoy, a UC Berkeley professor of molecular and cell biology and of plant and microbial biology. “It could tell us a lot about how these bacteria infect us or help us have a healthy gut.”

The discovery will be good news for those currently trying to create living batteries from microbes. Such “green” bioenergetic technologies could, for example, generate electricity from bacteria in waste treatment plants.

The research will be posted online Sept. 12 in advance of Oct. 4 print publication in the journal Nature.

Breathing metal

Bacteria generate electricity for the same reason we breathe oxygen: to remove electrons produced during metabolism and support energy production. Whereas animals and plants transfer their electrons to oxygen inside the mitochondria of every cell, bacteria in environments with no oxygen — including our gut, but also alcohol and cheese fermentation vats and acidic mines — have to find another electron acceptor. In geologic environments, that has often been a mineral — iron or manganese, for example — outside the cell. In some sense, these bacteria “breathe” iron or manganese.

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A microbial battery made with newly discovered electrogenic bacteria. Electrodes (CE, WE) are placed in jars full of bacteria, producing up to half a millivolt of electricity. Ajo-Franklin photo.

Transferring electrons out of the cell to a mineral requires a cascade of special chemical reactions, the so-called extracellular electron transfer chain, which carries the electrons as a tiny electrical current. Some scientists have tapped that chain to make a battery: stick an electrode in a flask of these bacteria and you can generate electricity.

The newly discovered extracellular electron transfer system is actually simpler than the already known transfer chain, and seems to be used by bacteria only when necessary, perhaps when oxygen levels are low. So far, this simpler electron transfer chain has been found in bacteria with a single cell wall — microbes classified as gram-positive bacteria — that live in an environment with lots of flavin, which are derivatives of vitamin B2.

“It seems that the cell structure of these bacteria and the vitamin-rich ecological niche that they occupy makes it significantly easier and more cost effective to transfer electrons out of the cell,” said first author Sam Light, a postdoctoral fellow. “Thus, we think that the conventionally studied mineral-respiring bacteria are using extracellular electron transfer because it is crucial for survival, whereas these newly identified bacteria are using it because it is ‘easy.’”

To see how robust this system is, Light teamed up with Caroline Ajo-Franklin from Lawrence Berkeley National Laboratory, who explores the interactions between living microbes and inorganic materials for possible applications in carbon capture and sequestration and bio-solar energy generation.

She used an electrode to measure the electric current that streams from the bacteria — up to 500 microamps — confirming that it is indeed electrogenic. In fact, they make about as much electricity — some 100,000 electrons per second per cell — as known electrogenic bacteria.

Light is particularly intrigued by the presence of this system in Lactobacillus, bacteria crucial to the production of cheese, yogurt and sauerkraut. Perhaps, he suggests, electron transport plays a role in the taste of cheese and sauerkraut.

“This is a whole big part of the physiology of bacteria that people didn’t realize existed, and that could be potentially manipulated,” he said.

Light and Portnoy have many more questions about how and why these bacteria developed such a unique system. Simplicity — it’s easier to transfer electrons through one cell wall rather than through two — and opportunity — taking advantage of ubiquitous flavin molecules to get rid of electrons – appear to have enabled these bacteria to find a way to survive in both oxygen-rich and oxygen-poor environments.

Other co-authors are Lin Su and Jose A. Cornejo of Berkeley Lab and Rafael Rivera-Lugo, Alexander Louie and Anthony T. Iavarone of UC Berkeley. The research was funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health and the Office of Naval Research.

http://news.berkeley.edu/2018/09/12/gut-bacterias-shocking-secret-they-produce-electricity/

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Someday doctors may prescribe sugar pills for certain chronic pain patients based on their brain anatomy and psychology. And the pills will reduce their pain as effectively as any powerful drug on the market, according to new research.

Northwestern Medicine scientists have shown they can reliably predict which chronic pain patients will respond to a sugar placebo pill based on the patients’ brain anatomy and psychological characteristics.

“Their brain is already tuned to respond,” said senior study author A. Vania Apkarian, professor of physiology at Northwestern University Feinberg School of Medicine. “They have the appropriate psychology and biology that puts them in a cognitive state that as soon as you say, ‘this may make your pain better,’ their pain gets better.”

There’s no need to fool the patient, Apkarian said.

“You can tell them, ‘I’m giving you a drug that has no physiological effect but your brain will respond to it,'” he said. “You don’t need to hide it. There is a biology behind the placebo response.”

The study was published Sept. 12 in Nature Communications.

The findings have three potential benefits:

Prescribing non-active drugs rather than active drugs. “It’s much better to give someone a non-active drug rather than an active drug and get the same result,” Apkarian said. “Most pharmacological treatments have long-term adverse effects or addictive properties. Placebo becomes as good an option for treatment as any drug we have on the market.”

Eliminating the placebo effect from drug trials. “Drug trials would need to recruit fewer people, and identifying the physiological effects would be much easier,” Apkarian said. “You’ve taken away a big component of noise in the study.”

Reduced health care costs. A sugar pill prescription for chronic pain patients would result in vast cost savings for patients and the health care system, Apkarian said.

How the study worked

About 60 chronic back pain patients were randomized into two arms of the study. In one arm, subjects didn’t know if they got the drug or the placebo. Researchers didn’t study the people who got the real drug. The other study arm included people who came to the clinic but didn’t get a placebo or drug. They were the control group.

The individuals whose pain decreased as a result of the sugar pill had a similar brain anatomy and psychological traits. The right side of their emotional brain was larger than the left, and they had a larger cortical sensory area than people who were not responsive to the placebo. The chronic pain placebo responders also were emotionally self-aware, sensitive to painful situations and mindful of their environment.

“Clinicians who are treating chronic pain patients should seriously consider that some will get as good a response to a sugar pill as any other drug,” Apkarian said. “They should use it and see the outcome. This opens up a whole new field.”

https://news.northwestern.edu/stories/2018/september/sugar-pills-relieve-pain-for-chronic-pain-patients/


Motion sensor “camera traps” unobtrusively take pictures of animals in their natural environment, oftentimes yielding images not otherwise observable. The artificial intelligence system automatically processes such images, here correctly reporting this as a picture of two impala standing.

A new paper in the Proceedings of the National Academy of Sciences (PNAS) reports how a cutting-edge artificial intelligence technique called deep learning can automatically identify, count and describe animals in their natural habitats.

Photographs that are automatically collected by motion-sensor cameras can then be automatically described by deep neural networks. The result is a system that can automate animal identification for up to 99.3 percent of images while still performing at the same 96.6 percent accuracy rate of crowdsourced teams of human volunteers.

“This technology lets us accurately, unobtrusively and inexpensively collect wildlife data, which could help catalyze the transformation of many fields of ecology, wildlife biology, zoology, conservation biology and animal behavior into ‘big data’ sciences. This will dramatically improve our ability to both study and conserve wildlife and precious ecosystems,” says Jeff Clune, the senior author of the paper. He is the Harris Associate Professor at the University of Wyoming and a senior research manager at Uber’s Artificial Intelligence Labs.

The paper was written by Clune; his Ph.D. student Mohammad Sadegh Norouzzadeh; his former Ph.D. student Anh Nguyen (now at Auburn University); Margaret Kosmala (Harvard University); Ali Swanson (University of Oxford); and Meredith Palmer and Craig Packer (both from the University of Minnesota).

Deep neural networks are a form of computational intelligence loosely inspired by how animal brains see and understand the world. They require vast amounts of training data to work well, and the data must be accurately labeled (e.g., each image being correctly tagged with which species of animal is present, how many there are, etc.).

This study obtained the necessary data from Snapshot Serengeti, a citizen science project on the http://www.zooniverse.org platform. Snapshot Serengeti has deployed a large number of “camera traps” (motion-sensor cameras) in Tanzania that collect millions of images of animals in their natural habitat, such as lions, leopards, cheetahs and elephants. The information in these photographs is only useful once it has been converted into text and numbers. For years, the best method for extracting such information was to ask crowdsourced teams of human volunteers to label each image manually. The study published today harnessed 3.2 million labeled images produced in this manner by more than 50,000 human volunteers over several years.

“When I told Jeff Clune we had 3.2 million labeled images, he stopped in his tracks,” says Packer, who heads the Snapshot Serengeti project. “We wanted to test whether we could use machine learning to automate the work of human volunteers. Our citizen scientists have done phenomenal work, but we needed to speed up the process to handle ever greater amounts of data. The deep learning algorithm is amazing and far surpassed my expectations. This is a game changer for wildlife ecology.”

Swanson, who founded Snapshot Serengeti, adds: “There are hundreds of camera-trap projects in the world, and very few of them are able to recruit large armies of human volunteers to extract their data. That means that much of the knowledge in these important data sets remains untapped. Although projects are increasingly turning to citizen science for image classification, we’re starting to see it take longer and longer to label each batch of images as the demand for volunteers grows. We believe deep learning will be key in alleviating the bottleneck for camera-trap projects: the effort of converting images into usable data.”

“Not only does the artificial intelligence system tell you which of 48 different species of animal is present, but it also tells you how many there are and what they are doing. It will tell you if they are eating, sleeping, if babies are present, etc.,” adds Kosmala, another Snapshot Serengeti leader. “We estimate that the deep learning technology pipeline we describe would save more than eight years of human labeling effort for each additional 3 million images. That is a lot of valuable volunteer time that can be redeployed to help other projects.”

First-author Sadegh Norouzzadeh points out that “Deep learning is still improving rapidly, and we expect that its performance will only get better in the coming years. Here, we wanted to demonstrate the value of the technology to the wildlife ecology community, but we expect that as more people research how to improve deep learning for this application and publish their datasets, the sky’s the limit. It is exciting to think of all the different ways this technology can help with our important scientific and conservation missions.”

The paper that in PNAS is titled, “Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning.”

http://www.uwyo.edu/uw/news/2018/06/researchers-use-artificial-intelligence-to-identify,-count,-describe-wild-animals.html

The purpose and evolutionary origins of sleep are among the biggest mysteries in neuroscience. Every complex animal, from the humblest fruit fly to the largest blue whale, sleeps — yet scientists can’t explain why any organism would leave itself vulnerable to predators, and unable to eat or mate, for a large portion of the day. Now, researchers have demonstrated for the first time that even an organism without a brain — a kind of jellyfish — shows sleep-like behaviour, suggesting that the origins of sleep are more primitive than thought.

Researchers observed that the rate at which Cassiopea jellyfish pulsed their bell decreased by one-third at night, and the animals were much slower to respond to external stimuli such as food or movement during that time. When deprived of their night-time rest, the jellies were less active the next day.

“Everyone we talk to has an opinion about whether or not jellyfish sleep. It really forces them to grapple with the question of what sleep is,” says Ravi Nath, the paper’s first author and a molecular geneticist at the California Institute of Technology (Caltech) in Pasadena. The study was published in Current Biology.

“This work provides compelling evidence for how early in evolution a sleep-like state evolved,” says Dion Dickman, a neuroscientist at the University of Southern California in Los Angeles.

Mindless sleep
Nath is studying sleep in the worm Caenorhabditis elegans, but whenever he presented his work at research conferences, other scientists scoffed at the idea that such a simple animal could sleep. The question got Nath thinking: how minimal can an animal’s nervous system get before the creature lacks the ability to sleep? Nath’s obsession soon infected his friends and fellow Caltech PhD students Michael Abrams and Claire Bedbrook. Abrams works on jellyfish, and he suggested that one of these creatures would be a suitable model organism, because jellies have neurons but no central nervous system. Instead, their neurons connect in a decentralized neural net.

Cassiopea jellyfish, in particular, caught the trio’s attention. Nicknamed the upside-down jellyfish because of its habit of sitting on the sea floor on its bell, with its tentacles waving upwards, Cassiopea rarely moves on its own. This made it easier for the researchers to design an automated system that used video to track the activity of the pulsing bell. To provide evidence of sleep-like behaviour in Cassiopea (or any other organism), the researchers needed to show a rapidly reversible period of decreased activity, or quiescence, with decreased responsiveness to stimuli. The behaviour also had to be driven by a need to sleep that increased the longer the jellyfish was awake, so that a day of reduced sleep would be followed by increased rest.

Other researchers had already documented a nightly drop in activity in other species of jellyfish, but no jellyfish had been known to display the other aspects of sleep behaviour. In a 35-litre tank, Nath, Abrams and Bedbrook tracked the bell pulses of Cassiopea over six days and nights and found that the rate, which was an average of one pulse per second by day, dropped by almost one-third at night. They also documented night-time pulse-free periods of 10–15 seconds, which didn’t occur during the day.

Restless night
Without an established jellyfish alarm clock, the scientists used a snack of brine shrimp and oyster roe to try to rouse the snoozing Cassiopea. When they dropped food in the tank at night, Cassiopea responded to its treat by returning to a daytime pattern of activity. The team used the jellyfish’s preference for sitting on solid surfaces to test whether quiescent Cassiopea had a delayed response to external stimuli. They slowly lifted the jellyfish off the bottom of the tank using a screen, then pulled it out from under the animal, leaving the jelly floating in the water. It took longer for the creature to begin pulsing and to reorient itself when this happened at night than it did during the day. If the experiment was immediately repeated at night, the jellyfish responded as if it were daytime. Lastly, when the team forced Cassiopea to pull an all-nighter by keeping it awake with repeated pulses of water, they found a 17% drop in activity the following day.

“This work shows that sleep is much older than we thought. The simplicity of these organisms is a door opener to understand why sleep evolved and what it does,” says Thomas Bosch, an evolutionary biologist at Kiel University in Germany. “Sleep can be traced back to these little metazoans — how much further does it go?” he asks.

That’s what Nath, Abrams and Bedbrook want to find out. Amid the chaos of finishing their PhD theses, they have begun searching for ancient genes that might control sleep, in the hope that this might provide hints as to why sleep originally evolved.

https://www.nature.com/news/jellyfish-caught-snoozing-give-clues-to-origin-of-sleep-1.22654

by RUSSELL MCLENDON

Rip Van Winkle, the titular ne’er-do-well of Washington Irving’s 1819 short story, famously spent 20 years napping in a forest. This lengthy slumber, apparently triggered by ghost liquor, caused Van Winkle to sleep through the American Revolutionary War.

Nearly two centuries later, scientists are shedding light on plants that do something similar in real life. A surprisingly diverse mix of plants around the world can live dormant underground for up to 20 years, researchers report in the journal Ecology Letters, a strategy that allows the plants to survive hard times by simply napping until things get better.

At least 114 species from 24 plant families are capable of this trick, in which a plant abandons photosynthesis to focus on survival in the soil. It’s a way for plants to hedge their bets, the study’s authors explain, by accepting certain short-term hardships — like missed opportunities to grow and reproduce — for the longer-term benefits of avoiding mortal dangers on the surface.

“It would seem to be paradoxical that plants would evolve this behavior, because being underground means they cannot photosynthesize, flower or reproduce,” says co-author Michael Hutchings, an ecology professor at the University of Sussex, in a statement. “And yet this study has shown that many plants in a large number of species frequently exhibit prolonged dormancy.”

So how do these Rip Van Winkle plants survive for up to 20 years without sunlight? Many species have found other ways to endure dormancy, Hutchings says, especially “by evolving mechanisms enabling them to obtain carbohydrates and nutrients from soil-based fungal associates.” Befriending soil fungi, he adds, “allows them to survive and even thrive during dormant periods.”

This strategy is used by many orchid species (including the lady’s slipper orchids pictured above), along with a wide variety of other plant types. It typically occurs in only part of a population or species during any given year, the researchers note, so the broader population can keep growing and reproducing while the designated survivors wait underground as backup.

https://www.mnn.com/earth-matters/wilderness-resources/blogs/rip-van-winkle-plants-can-hide-underground-20-years