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  • richardmitnick 8:23 am on May 26, 2020 Permalink | Reply
    Tags: "Cosmic rays may have left indelible imprint on early life Stanford physicist says", , Biology, ,   

    From Stanford University: “Cosmic rays may have left indelible imprint on early life, Stanford physicist says” 

    Stanford University Name
    From Stanford University

    May 20, 2020
    Taylor Kubota
    Stanford News Service
    (650) 724-7707
    tkubota@stanford.edu

    Physicists propose that the influence of cosmic rays on early life may explain nature’s preference for a uniform “handedness” among biology’s critical molecules.

    Before there were animals, bacteria or even DNA on Earth, self-replicating molecules were slowly evolving their way from simple matter to life beneath a constant shower of energetic particles from space.

    Cosmic rays produced by high-energy astrophysics sources (ASPERA collaboration – AStroParticle ERAnet)

    1
    Magnetically polarized radiation preferentially ionized one type of “handedness” leading to a slightly different mutation rate between the two mirror proto-lifeforms. Over time, right-handed molecules out-evolved their left-handed counterparts. (Image credit: Simons Foundation)

    In a new paper, [Astrophysical Journal Letters], a Stanford professor and a former postdoctoral scholar speculate that this interaction between ancient proto-organisms and cosmic rays may be responsible for a crucial structural preference, called chirality, in biological molecules. If their idea is correct, it suggests that all life throughout the universe could share the same chiral preference.

    Chirality, also known as handedness, is the existence of mirror-image versions of molecules. Like the left and right hand, two chiral forms of a single molecule reflect each other in shape but don’t line up if stacked. In every major biomolecule – amino acids, DNA, RNA – life only uses one form of molecular handedness. If the mirror version of a molecule is substituted for the regular version within a biological system, the system will often malfunction or stop functioning entirely. In the case of DNA, a single wrong handed sugar would disrupt the stable helical structure of the molecule.

    Louis Pasteur first discovered this biological homochirality in 1848. Since then, scientists have debated whether the handedness of life was driven by random chance or some unknown deterministic influence. Pasteur hypothesized that, if life is asymmetric, then it may be due to an asymmetry in the fundamental interactions of physics that exist throughout the cosmos.

    “We propose that the biological handedness we witness now on Earth is due to evolution amidst magnetically polarized radiation, where a tiny difference in the mutation rate may have promoted the evolution of DNA-based life, rather than its mirror image,” said Noémie Globus, lead author of the paper and a former Koret Fellow at the Kavli Institute for Particle Astrophysics and Cosmology (KIPAC).

    See the full article here .


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    Stanford University campus. No image credit

    Stanford University

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

    Stanford University Seal

     
  • richardmitnick 9:00 am on May 13, 2020 Permalink | Reply
    Tags: , Biology, Capturing detailed maps of cells and tissues via a series of photographs., , , Our body has a natural system for balancing these free radicals with antioxidants, Oxidative stress is caused by an overabundance of free radicals.,   

    From University of New South Wales: “Colour of cells a ‘thermometer’ for molecular imbalance, study finds” 

    U NSW bloc

    From University of New South Wales

    13 May 2020
    Sherry Landow
    UNSW Media & Content
    02 9385 9555
    s.landow@unsw.edu.au

    Non-invasive colour analysis of cells could one day be used in diagnostics, a proof-of-concept study has shown.

    1
    Professor Ewa Goldys and her team used an adapted microscope to capture detailed maps of cells and tissues via a series of photographs. Image: Supplied.

    An imbalance of unstable molecular species called ‘free radicals’ will change the colour of cells – and a new imaging technique could one day allow scientists to detect and decode this colour without needing to take samples from the body, a new study by UNSW Sydney researchers has found. The paper was published online yesterday in Redox Biology.

    “In our study of cell cultures and tissues in the lab, we found that colour is like a thermometer for oxidative stress,” says UNSW Engineering Professor Ewa Goldys, lead author of the study and Deputy Director of the ARC Centre of Excellence for Nanoscale Biophotonics.

    Oxidative stress is caused by an overabundance of free radicals, which can cause damage to cells, DNA and proteins if left unchecked. Poor diet, alcohol consumption and obesity are some factors that can lead to the overproduction of free radicals.

    Our body has a natural system for balancing these free radicals with antioxidants, but too many free radicals will make it harder for the body to repair damaged cells. Oxidative stress can cause chronic inflammation and is linked to many diseases, such as heart disease, diabetes and cancer.

    “Oxidative stress isn’t disease-specific, but its restoration to healthy levels is an excellent measure of how well a therapeutic approach is working,” says Prof Goldys.

    Despite the important role of oxidative stress to our health, it is often overlooked in medical diagnostics. This is largely because it’s difficult to measure on cells ‘in-vivo’ – within the body.

    Current methods for testing oxidative stress involve extracting cells from the body and testing their response in a lab. While some cells can be easily removed, such as blood, this method isn’t an option for other parts of the body.

    To solve this problem, Prof Goldys and her team adapted a standard fluorescent microscope – a microscope that detects natural fluorescent emissions from cells – to test whether cell and tissue colour is impacted by oxidative stress. They also developed a UV-free version of this technology for instances when UV is too dangerous to use, like in ophthalmology and reproductive health.

    The microscopic camera works by emitting bursts of low-level LED light at various wavelengths onto cells and tissues. The light is absorbed by fluorescent molecules, which then emit their own light in response.

    This fluorescent light allows the researchers to capture detailed maps of cells and tissues via a series of photographs. The microscope then decodes what the colours mean at a molecular level.

    “The microscope has a device that precisely captures the colours in the cells,” explains Prof Goldys.

    “We then use a big data approach to digitally ‘unmix’ the colour into its molecular components – red, green and blue, for example.”

    The team developed a way to quantify each colour component by assigning it with a value. Once these values are tallied, scientists can measure oxidisation levels without need for cell extraction and analytical procedures.

    “Once you have numbers, you can test all sorts of things,” says Prof Goldys, who was awarded a prestigious Eureka Award in 2016 for her discovery that the colours of cells and tissues can be subtle indicators of health and disease.

    While their adapted microscope is not yet on the market, Prof Goldys is undertaking steps to begin the clinical trial in two years’ time. First, she will conduct an animal study, then seek TGA approval for the adapted microscope to be used in human studies, before starting a human trial in a selected disease condition.

    If these steps are successful, the adapted microscope could become a common tool used in medical practices and scientific research.

    In the meantime, Prof Goldys is excited about her next project, which will focus on how this technology can help monitor eye disease – particularly glaucoma.

    Alongside researchers including UNSW Scientia Fellow Dr Nicole Carnt, the team are developing a bespoke camera that will photograph the back of the eye via the pupil. This camera will help ophthalmologists measure the oxidative stress of cells and tissues in the retina.

    “The findings could change how we monitor and treat eye diseases,” says Prof Goldys.

    “Early detection could hopefully help medical staff and patients slow disease progression.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    U NSW Campus

    Welcome to UNSW Australia (The University of New South Wales), one of Australia’s leading research and teaching universities. At UNSW, we take pride in the broad range and high quality of our teaching programs. Our teaching gains strength and currency from our research activities, strong industry links and our international nature; UNSW has a strong regional and global engagement.

    In developing new ideas and promoting lasting knowledge we are creating an academic environment where outstanding students and scholars from around the world can be inspired to excel in their programs of study and research. Partnerships with both local and global communities allow UNSW to share knowledge, debate and research outcomes. UNSW’s public events include concert performances, open days and public forums on issues such as the environment, healthcare and global politics. We encourage you to explore the UNSW website so you can find out more about what we do.

     
  • richardmitnick 10:46 am on May 9, 2020 Permalink | Reply
    Tags: "Survival in the Atacama Desert", , Biology, Chroococcidiopsis – a cyanobacteria commonly found in deserts – and gypsum in Chile’s Atacama Desert., ,   

    From COSMOS: “Survival in the Atacama Desert” 

    Cosmos Magazine bloc

    From COSMOS

    05 May 2020
    Nick Carne

    1
    Gypsum rocks in Chile’s Atacama Desert. Credit:Jocelyne DiRuggiero

    It’s not quite life on Mars, but it may be a pointer.

    US researchers have shown that, as some had suspected, microorganisms can survive in the harshest of conditions by extracting water from the rocks they colonise.

    A team from the University of California (UC) and Johns Hopkins University (JHU) studied interactions between Chroococcidiopsis – a cyanobacteria commonly found in deserts – and gypsum in Chile’s Atacama Desert.

    1
    An international team of scientists has found that a strange type of bacteria can turn light into fuel in incredibly dim environments. Similar bacteria could someday help humans colonize Mars and expand our search for life on other planets, researchers said in a statement released with the new work.

    Organisms called cyanobacteria absorb sunlight to create energy, releasing oxygen in the process. But until now, researchers thought these bacteria could absorb only specific, higher-energy wavelengths of light. The new work reveals that at least one species of cyanobacteria, called Chroococcidiopsis thermalis — which lives in some of the world’s most extreme environments — can absorb redder (less energetic) wavelengths of light, thus allowing it to thrive in dark conditions, such as deep underwater in hot springs. [Extreme Life on Earth: 8 Bizarre Creatures]

    “This work redefines the minimum energy needed in light to drive photosynthesis,” Jennifer Morton, a researcher at Australian National University (ANU) and a co-author of the new work, said in the statement. “This type of photosynthesis may well be happening in your garden, under a rock.” (In fact, a related species has even been found living inside rocks in the desert.)

    When grown in far-red light, this cyanobacteria, called Chroococcidiopsis thermalis, can still photosynthesize where others falter. Credit: T. Darienko/CC BY-SA 4.0

    Or below it, to be precise. The Chroococcidiopsis exist beneath a thin layer of rock that gives them a measure of protection against the high solar irradiance, extreme dryness and battering winds in what is the world’s driest non-polar region.

    When gypsum samples were studied back in the lab, the most striking discovery was that the microorganisms change the very nature of the rock. By extracting water, they cause a phase transformation of the material – from gypsum to anhydrite, a dehydrated mineral.

    Intrigued, the researchers ran some experiments, allowing the organisms to colonise half-millimetre cubes of rock, called coupons, under two different conditions: one in the presence of water, to mimic a high-humidity environment, and the other completely dry.

    Amid moisture, they found, the gypsum did not transform to the anhydrite phase.

    The cyanobacteria “didn’t need water from the rock, they got it from their surroundings”, says David Kisailus, from UC Irvine. “But when they were put under stressed conditions, the microbes had no alternative but to extract water from the gypsum, inducing this phase transformation in the material.”

    Kisailus’s team used a combination of advanced microscopy and spectroscopy to examine the interactions between the biological and geological counterparts, finding that the organisms bore into the rock by excreting a biofilm containing organic acids.

    UCI’s Wei Huang then used a modified electron microscope equipped with a Raman spectrometer to discover that the cyanobacteria used the acid to penetrate the gypsum in specific crystallographic directions – only along certain planes where they could more easily access the water existing between faces of calcium and sulfate ions.

    “Researchers have suspected for a long time that microorganisms might be able to extract water from minerals, but this is the first demonstration of it,” says JHU biologist Jocelyne DiRuggiero

    “This is an amazing survival strategy for microorganisms living at the dry limit for life, and it will guide our search for life elsewhere.”

    The findings are reported in a paper in the journal Proceedings of the National Academy of Science.

    See the full article here .


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    • Skyscapes for the Soul 4:37 pm on May 9, 2020 Permalink | Reply

      A post about life in the Atacama desert is of great interest. It had long been a place on my bucket list – until Murray Foote visited and mentioned the altitude. Ugh, this low desert rat would not survive such heights. Nice though to hear that other researchers can bring me interesting news from there.

      Like

  • richardmitnick 10:04 am on May 9, 2020 Permalink | Reply
    Tags: "New imaging technology allows visualization of nanoscale structures inside whole cells and tissues", , Biology, , , ,   

    From Purdue University: “New imaging technology allows visualization of nanoscale structures inside whole cells and tissues” 

    From Purdue University

    1
    This image shows a 3D super-resolution reconstruction of dendrites in primary visual cortex. (Image provided)

    Since Robert Hooke’s first description of a cell in Micrographia 350 years ago, microscopy has played an important role in understanding the rules of life.

    However, the smallest resolvable feature, the resolution, is restricted by the wave nature of light. This century-old barrier has restricted understanding of cellular functions, interactions and dynamics, particularly at the sub-micron to nanometer scale.

    Super-resolution fluorescence microscopy overcomes this fundamental limit, offering up to tenfold improvement in resolution, and allows scientists to visualize the inner workings of cells and biomolecules at unprecedented spatial resolution.

    Such resolving capability is impeded, however, when observing inside whole-cell or tissue specimens, such as the ones often analyzed during the studies of the cancer or the brain. Light signals, emitted from molecules inside a specimen, travel through different parts of cell or tissue structures at different speeds and result in aberrations, which will deteriorate the image.

    Now, Purdue University researchers have developed a new technology to overcome this challenge.

    “Our technology allows us to measure wavefront distortions induced by the specimen, either a cell or a tissue, directly from the signals generated by single molecules – tiny light sources attached to the cellular structures of interest,” said Fang Huang, an assistant professor of biomedical engineering in Purdue’s College of Engineering. “By knowing the distortion induced, we can pinpoint the positions of individual molecules at high precision and accuracy. We obtain thousands to millions of coordinates of individual molecules within a cell or tissue volume and use these coordinates to reveal the nanoscale architectures of specimen constituents.”

    The Purdue team’s technology is recently published in Nature Methods. A video showing an animated 3D super-resolution is available at https://youtu.be/c9j621vUFBM. This tool from Purdue researchers allows visualization of nanoscale structures inside whole cells and tissues. It could allow for better understanding for diseases affecting the brain and regenerative therapies.

    “During three-dimensional super-resolution imaging, we record thousands to millions of emission patterns of single fluorescent molecules,” said Fan Xu, a postdoctoral associate in Huang’s lab and a co-first author of the publication. “These emission patterns can be regarded as random observations at various axial positions sampled from the underlying 3D point-spread function describing the shapes of these emission patterns at different depths, which we aim to retrieve. Our technology uses two steps: assignment and update, to iteratively retrieve the wavefront distortion and the 3D responses from the recorded single molecule dataset containing emission patterns of molecules at arbitrary locations.”

    The Purdue technology allows finding the positions of biomolecules with a precision down to a few nanometers inside whole cells and tissues and therefore, resolving cellular and tissue architectures with high resolution and fidelity.

    “This advancement expands the routine applicability of super-resolution microscopy from selected cellular targets near coverslips to intra- and extra-cellular targets deep inside tissues,” said Donghan Ma, a postdoctoral researcher in Huang’s lab and a co-first author of the publication. “This newfound capacity of visualization could allow for better understanding for neurodegenerative diseases such as Alzheimer’s, and many other diseases affecting the brain and various parts inside the body.”

    The National Institutes of Health provided major support for the research.

    Other members of the research team include Gary Landreth, a professor from Indiana University’s School of Medicine; Sarah Calve, an associate professor of biomedical engineering in Purdue’s College of Engineering (currently an associate professor of mechanical engineering at the University of Colorado Boulder); Peng Yin, a professor from Harvard Medical School; and Alexander Chubykin, an assistant professor of biological sciences at Purdue. The complete list of authors can be found in Nature Methods.

    “This technical advancement is startling and will fundamentally change the precision with which we evaluate the pathological features of Alzheimer’s disease,” Landreth said. “We are able to see smaller and smaller objects and their interactions with each other, which helps reveal structure complexities we have not appreciated before.”

    Calve said the technology is a step forward in regenerative therapies to help promote repair within the body.

    “This development is critical for understanding tissue biology and being able to visualize structural changes,” Calve said.

    Chubykin, whose lab focuses on autism and diseases affecting the brain, said the high-resolution imaging technology provides a new method for understanding impairments in the brain.

    “This is a tremendous breakthrough in terms of functional and structural analyses,” Chubykin said. “We can see a much more detailed view of the brain and even mark specific neurons with genetic tools for further study.”

    The team worked with the Purdue Research Foundation Office of Technology Commercialization to patent the technology. The office recently moved into the Convergence Center for Innovation and Collaboration in Discovery Park District, adjacent to the Purdue campus.

    The inventors are looking for partners to commercialize their technology. For more information on licensing this innovation, contact Dipak Narula of OTC at dnarula@prf.org.

    See the full article here .

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    Purdue University is a public research university in West Lafayette, Indiana, and the flagship campus of the Purdue University system. The university was founded in 1869 after Lafayette businessman John Purdue donated land and money to establish a college of science, technology, and agriculture in his name. The first classes were held on September 16, 1874, with six instructors and 39 students.

    The main campus in West Lafayette offers more than 200 majors for undergraduates, over 69 masters and doctoral programs, and professional degrees in pharmacy and veterinary medicine. In addition, Purdue has 18 intercollegiate sports teams and more than 900 student organizations. Purdue is a member of the Big Ten Conference and enrolls the second largest student body of any university in Indiana, as well as the fourth largest foreign student population of any university in the United States.

     
  • richardmitnick 12:33 pm on May 8, 2020 Permalink | Reply
    Tags: "Scanning with golden bow ties", , Biology, , , , Terahertz scanners   

    From COSMOS: “Scanning with golden bow ties” 

    Cosmos Magazine bloc

    From COSMOS

    08 May 2020
    Phil Dooley

    Detectors would operate in terahertz region.

    1
    Credits: DIMITAR JEVTICS

    Australian and British physicists have unveiled their design for a high-precision detector they say could enable a new generation of safe compact scanners.

    As described in a paper in the journal Science, it is based around tiny “bow ties”, each comprising two triangles of solid gold connected by two nanowires.

    This design allows it to operate in the terahertz region of the electromagnetic spectrum, between microwaves and infrared. Terahertz scanning offers a safer low-energy alternative to X-rays: it is not powerful enough to ionise materials.

    However, it still penetrates materials such as plastics, wood and paper, is absorbed by water, and is reflected by metals, giving the technology the capability to analyse a wide range of samples.

    The bow ties also are able to detect the polarisation of the terahertz radiation, which adds another dimension to the detector’s versatility.

    “The polarisation gives you much more useful information, especially about biological molecules, for example their chirality,” says Chennupati Jagadish from the Australian National University (ANU).

    “Complex molecules have their own terahertz fingerprints, so this technology can be used for finding cancer biomarkers, locating explosives or measuring moisture levels in crops.”

    The device is the result of a collaboration between ANU and Oxford University in England and Scotland’s Strathclyde University.

    Importantly, the researchers say, it overcomes a limitation in the resolution, or detail, of conventional terahertz imaging, which is linked to its millimetre-scale wavelength – a million times larger than X-rays, with nanometre-scale wavelengths.

    The design gets around this limitation with the microscopic scale of the bow ties. The pair of nanowires at their heart are indium phosphide wires one hundredth the size of a human hair: around 280 nanometres in diameter and ten micrometres long.

    Although each detector is much smaller than the terahertz waves (around 300 microns), an array of bow ties can be used to create a near-field image that bypasses the diffraction limit of the terahertz radiation’s wavelength.

    To detect the polarisation of the radiation, the team combined two bow ties, set at right angles to each other, with their central nanowires crossing but not in contact – one bow tie is set slightly above the other.

    Although a simplistic-sounding design, the vertically offset configuration took three years of collaboration to devise and manufacture.

    The nanowires were created at ANU, the triangles were added at Oxford as antennae to boost the signal level (gold being the obvious choice due to its high conductivity), then the devices were assembled at Strathclyde.

    The team is now developing nano-scale electronics to connect to the detector, so the whole device can be built onto a single chip, in contrast with existing bulky terahertz scanners.

    See the full article here .


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    Please help promote STEM in your local schools.

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  • richardmitnick 12:07 pm on May 5, 2020 Permalink | Reply
    Tags: "'When chemistry became biology': looking for the origins of life in hot springs", , Biology, ,   

    From University of New South Wales: “‘When chemistry became biology’: looking for the origins of life in hot springs” 

    U NSW bloc

    From University of New South Wales

    05 May 2020

    Sherry Landow
    UNSW Media & Content
    02 9385 9555
    s.landow@unsw.edu.au

    Hot springs may have been the ‘spark’ that helped organic matter turn into life – these UNSW Sydney scientists have put this hypothesis to the test in New Zealand.

    1
    Hot springs in New Zealand took Dr Anna Wang and Mr Luke Steller a step closer to the complex geological processes that happened on early Earth. Image: ABC Catalyst.

    50 years ago, a meteorite landed in Victoria carrying many of the building blocks for life, including amino acids, nucleobases and lipids. These organic molecules formed when compounds in stardust, which had collected on the meteorite, reacted under low temperatures and UV light as it passed through space.

    Many astrobiologists think life on Earth could have been kickstarted when meteorites carrying similar organic matter fell to the planet around four billion years ago.

    The big question is how this organic matter along with what was already on Earth – called prebiotic ‘soup’ – turned into life.

    “We think hot springs on the Earth’s surface hold the answer,” says Mr Luke Steller, PhD candidate at UNSW’s Australian Centre for Astrobiology. “Their elevated temperature and exposure to the atmosphere allow for a unique process that underwater environments don’t offer.

    “The cycle of dehydration (by evaporation) and rehydration (by splashing from geysers or pools) in hot springs allows small lipid bubbles called ‘vesicles’ to form around molecules.

    “Vesicles containing the right genetic material could have conceivably been ‘protocells’ – the ancestors of modern living cells.”

    Mr Steller is currently collaborating with Dr Anna Wang, Scientia Fellow in the School of Chemistry, to trace when – and how – chemistry became biology.

    Late last year, Mr Steller and Dr Wang travelled to Rotorua in New Zealand with ABC Catalyst to recreate this protocell formation in a real hot spring environment. The Catalyst episode, ‘Asteroid Hunters’, airs tonight.

    “Almost any sort of chemical reaction could happen in a hot spring,” says Dr Wang.

    “If you combine that with the extra-terrestrial material bombarding the planet four billion years ago, they become the most chemically-exciting places on Earth.”

    It starts with a bubble

    Vesicles, also known as lipid membranes, play a vital role in protecting the genetic molecules in our cells and, potentially, the ancestors to all cells.

    “A bubble around some molecules is the first step towards an individual organism,” says Mr Steller. “This entity, a protocell, could be capable of competing with other protocells and start undergoing Darwinian evolution.

    “Without a barrier, there is nothing to separate the genetic material from anything else – it would be dilute and part of a homogeneous soup.”

    The researchers were inspired by the efforts of Prof David Deamer and Dr Bruce Damer from the University of California, Santa Cruz, to test vesicle formation in a real-world lab.

    Mr Steller and Dr Wang prepared vials of lipids (fatty acids) like those found in meteorites and RNA – a nucleic acid essential for life. RNA is theorised to have been present in early Earth.

    Combined with hot spring water (containing dissolved minerals and salts), this mixture is an example of a prebiotic soup that might have led to the first replicating cell.

    “When we first mixed the prebiotic soup with the hot spring water and submerged the vials into a hot spring, the high temperatures dried out the ingredients,” says Mr Steller. “This process of drying down the lipids and RNA together ‘trapped’ the concentrated RNA between the lipid layers.”

    When the soup was rehydrated – a process that occurs naturally in hot springs by splashing – the researchers saw vesicles containing concentrated RNA form.

    “By having these wet-dry cycles, all the important organic molecules floating around gets crammed inside one little place. This can help the molecules interact and chemically react.

    “Being compartmentalised, these vesicles suddenly have their own ‘identities’ and can start competing, increasing in complexity and evolving towards something life-like.”

    2
    Hot springs in Rotorua, New Zealand. Image: ABC Catalyst.

    A messy laboratory

    Hot springs take astrobiologists a step closer to the complex geological processes that happened on early Earth.

    “Early Earth was a messy place,” says Mr Steller. “There were many different minerals and water chemistries present, and clays bubbling around in hot spring pools.

    “There was a lot of splashing, lightning and different fluids and gases all getting churned up, boiled and mixed around.”

    Travelling to Rotorua offered an opportunity for the researchers to ‘ground-proof’ experiments and show that concepts demonstrated in the lab are robust enough to stay true in messier environments.

    “Conducting prebiotic experiments in clean glass test tubes doesn’t really represent what happened on early Earth,” says Mr Steller.

    “While we can’t go back in time, we have geological evidence that hot springs were present on early Earth. In some ways, visiting hot springs feels like going back to the source.”

    The building blocks of life

    Dr Wang is fascinated by the first self-assembly step to life on Earth: where chemicals were able to come together and transition into biology.

    She recently received a prestigious $1.7m international life science grant to create self-propagating synthetic cells.

    “In origin of life studies, we ask questions like: ‘What physics were necessary for self-assembly?’, ‘What was the geological context that could have helped all those processes?’, and ‘What help did we get from outer space that could have helped catalyse this life?’

    “All of these factors came together once – and it was so successful that it was able to persist through billions of years and evolve into all of life that we see today.

    “There is shared chemistry to plants, viruses, bacteria, and us. Understanding how it all came about could help us build better microreactors for manufacturing biological goods, or to identify potential drug targets for disease.”

    Mr Steller is part of a wider team at UNSW assisting NASA in understanding how life may have been preserved on other planets in our solar system.

    “The origin of life is part of humanity’s narrative,” he says.

    “Learning more about it isn’t only beneficial for science, it’s helping us develop our understanding of who we are and our place in the universe.”

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    U NSW Campus

    Welcome to UNSW Australia (The University of New South Wales), one of Australia’s leading research and teaching universities. At UNSW, we take pride in the broad range and high quality of our teaching programs. Our teaching gains strength and currency from our research activities, strong industry links and our international nature; UNSW has a strong regional and global engagement.

    In developing new ideas and promoting lasting knowledge we are creating an academic environment where outstanding students and scholars from around the world can be inspired to excel in their programs of study and research. Partnerships with both local and global communities allow UNSW to share knowledge, debate and research outcomes. UNSW’s public events include concert performances, open days and public forums on issues such as the environment, healthcare and global politics. We encourage you to explore the UNSW website so you can find out more about what we do.

     
  • richardmitnick 10:01 am on March 19, 2020 Permalink | Reply
    Tags: "Scientists Have Discovered the Origins of the Building Blocks of Life", , , Biology, ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life., ,   

    From Rutgers University: “Scientists Have Discovered the Origins of the Building Blocks of Life” 

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    Our Great Seal.

    From Rutgers University

    March 16, 2020

    Todd Bates
    848-932-0550
    todd.bates@rutgers.edu

    Rutgers researchers retraced the evolution of enzymes over billions of years.

    1
    This image shows a fold (shape) that may have been one of the earliest proteins in the evolution of metabolism. Image: Vikas Nanda/Rutgers University

    Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

    Their study, which predicts what the earliest proteins looked like 3.5 billion to 2.5 billion years ago, is published in the journal Proceedings of the National Academy of Sciences.

    The scientists retraced, like a many thousand piece puzzle, the evolution of enzymes (proteins) from the present to the deep past. The solution to the puzzle required two missing pieces, and life on Earth could not exist without them. By constructing a network connected by their roles in metabolism, this team discovered the missing pieces.

    “We know very little about how life started on our planet. This work allowed us to glimpse deep in time and propose the earliest metabolic proteins,” said co-author Vikas Nanda, a professor of Biochemistry and Molecular Biology at Rutgers Robert Wood Johnson Medical School and a resident faculty member at the Center for Advanced Biotechnology and Medicine. “Our predictions will be tested in the laboratory to better understand the origins of life on Earth and to inform how life may originate elsewhere. We are building models of proteins in the lab and testing whether they can trigger reactions critical for early metabolism.”

    A Rutgers-led team of scientists called ENIGMA (Evolution of Nanomachines in Geospheres and Microbial Ancestors) is conducting the research with a NASA grant and via membership in the NASA Astrobiology Program. The ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life.

    “We think life was built from very small building blocks and emerged like a Lego set to make cells and more complex organisms like us,” said senior author Paul G. Falkowski, ENIGMA principal investigator and a distinguished professor at Rutgers University–New Brunswick who leads the Environmental Biophysics and Molecular Ecology Laboratory. “We think we have found the building blocks of life – the Lego set that led, ultimately, to the evolution of cells, animals and plants.”

    The Rutgers team focused on two protein “folds” that are likely the first structures in early metabolism. They are a ferredoxin fold that binds iron-sulfur compounds, and a “Rossmann” fold, which binds nucleotides (the building blocks of DNA and RNA). These are two pieces of the puzzle that must fit in the evolution of life.

    Proteins are chains of amino acids and a chain’s 3D path in space is called a fold. Ferredoxins are metals found in modern proteins and shuttle electrons around cells to promote metabolism. Electrons flow through solids, liquids and gases and power living systems, and the same electrical force must be present in any other planetary system with a chance to support life.

    There is evidence the two folds may have shared a common ancestor and, if true, the ancestor may have been the first metabolic enzyme of life.

    The lead author is Hagai Raanan, a former post-doctoral associate in the Environmental Biophysics and Molecular Ecology Laboratory. Rutgers co-authors include Saroj Poudel, a post-doctoral associate, and Douglas H. Pike, a doctoral student in the ENIGMA project.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    rutgers-campus

    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

     
  • richardmitnick 8:20 am on March 17, 2020 Permalink | Reply
    Tags: "Ocean acidification impacts oysters’ memory of environmental stress", , Biology, Study of the Olympia oyster and the Pacific oyster.,   

    From University of Washington: “Ocean acidification impacts oysters’ memory of environmental stress” 

    From University of Washington

    March 12, 2020
    Dan DiNicola
    School of Aquatic and Fishery Sciences

    1
    Empty Pacific oyster shells are placed on a mat after being sampled. The effect of acidified waters on multiple generations of Pacific oysters can influence aquaculture in Washington and globally.Yaamini Venkataraman/University of Washington.

    As oceans absorb more carbon dioxide, they are becoming increasingly acidic and shifting the delicate balance that supports marine life. How species will cope with ocean acidification and the other consequences of global climate change is still very much unknown and could have sweeping consequences.

    Researchers from the University of Washington School of Aquatic and Fishery Sciences have discovered that ocean acidification impacts the ability of some oysters to pass down “memories” of environmental trauma to their offspring.

    The two papers were published in December in Ecological Applications and the Journal of Shellfish Research.

    “Warming and acidifying oceans negatively influence many marine species. However, some species that live in extreme environments, such as the intertidal, may be more resilient than others to these changes,” said Laura Spencer, one of the two lead authors and a graduate student in aquatic and fishery sciences. “Some species may even be able to pass on memories of harsh conditions to their offspring, making them more capable of surviving in similarly harsh environments.”

    2
    A bed of Pacific and Olympia oysters in Puget Sound, Washington.Laura Spencer/University of Washington.

    Researchers studied two species of ecologically and commercially valuable oysters found throughout Puget Sound: the Olympia oyster and the Pacific oyster. Although oyster larvae are sensitive to acidifying oceans, adult oysters commonly occur in intertidal areas and estuaries where they must endure constantly fluctuating water conditions.

    It is this hardiness that has researchers hopeful that oysters can withstand an increasingly acidic ocean. If their resilience to stressors can be passed down to their offspring, it could promote an increased tolerance among the future population.

    In Spencer’s study, Olympia oysters were exposed to a combination of elevated temperatures and acidified conditions during winter months, mimicking what might happen under climate change. The higher water temperatures caused the oysters to spawn earlier; however, these effects were canceled out when combined with acidified conditions. Researchers then reared and transplanted the exposed oysters’ offspring to four estuaries in Puget Sound. They observed that the offspring whose parents were exposed to acidified conditions in the lab had higher survival rates in two of the four bays.

    3
    Olympia oysters being measured for size and sampled for reproductive tissue after pH exposure.Laura Spencer/University of Washington.

    “We found that Olympia oyster adults were relatively resilient to acidification and warming when exposed during the winter,” said Spencer. “Most interestingly, we found evidence that adult exposure to acidified conditions can benefit offspring by improving survival.”

    This carryover effect demonstrates that the experiences of oyster parents have a direct impact on how their offspring perform, and juvenile oysters may be more resilient in certain environments when their parents have been pre-conditioned by similar stressors.

    In the other study, adult Pacific oysters were similarly exposed to acidified conditions in the lab. The oysters were then placed back in ambient water to recover before spawning. Researchers observed that the embryonic and larval offspring of female oysters exposed to these experimental conditions experienced poorer survival than a similar control group.

    4
    An approximately 12-day-old oyster larvae feeding on algae, viewed under the microscopeLaura Spencer/University of Washington.

    “The conditions one generation of Pacific oysters experience can affect how their children perform,” said lead author Yaamini Venkataraman, a graduate student in aquatic and fishery sciences. “Even if oysters are not in stressful conditions when they reproduce, their previous stressful experiences can impact their offspring.”

    These two contrasting results are both encouraging and concerning to Washington’s shellfish industry, which generates nearly $150 million a year and provides over 2,700 jobs. While one study revealed that juvenile Olympia oysters benefited and experienced a survival advantage due to parental exposure to acidified conditions, the other study showed the embryonic and larval survival of Pacific oysters decreased with parental exposure. The authors believe these differing results could be species-specific or because the experiments focused on different life stages of oysters.

    Nevertheless, determining how and why some species, such as the Olympia oyster, tolerate ocean acidification and warming helps inform where to focus conservation resources and how to improve growing methods, said Spencer.

    5
    UW doctoral student Yaamini Venkataraman examines oyster reproductive tissue.Photo courtesy of Yaamini Venkataraman.

    “We needed to broaden our understanding of environmental memory when thinking about how oysters or other organisms will persist in the face of climate change,” explained Venkataraman. “The aquaculture industry is part of the fiber of Washington, and understanding how oysters will respond to changes in their environment, like more acidic water conditions, across multiple generations is crucial to sustaining the industry.”

    This recent research shows that as the world’s oceans warm and become more acidic due to climate change, species tolerance or sensitivity can’t be defined by looking solely at one generation of oysters.

    Additional co-authors are Ryan Crim and Stuart Ryan with the Puget Sound Restoration Fund; Micah Horwith, who completed the work with Washington Department of Natural Resources but now works at Washington State Department of Ecology; and Steven Roberts, a UW professor of aquatic and fishery sciences.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 4:04 pm on March 10, 2020 Permalink | Reply
    Tags: "Some domesticated plants ignore beneficial soil microbes", , Biology, Domestication yielded bigger crops often at the expense of plant microbiomes., ,   

    From UC Riverside: “Some domesticated plants ignore beneficial soil microbes” 

    UC Riverside bloc

    From UC Riverside

    March 10, 2020
    Holly Ober

    1
    Domestication yielded bigger crops often at the expense of plant microbiomes.

    While domestication of plants has yielded bigger crops, the process has often had a negative effect on plant microbiomes, making domesticated plants more dependent on fertilizer and other soil amendments than their wild relatives.

    In an effort to make crops more productive and sustainable, researchers recommend reintroduction of genes from the wild relatives of commercial crops that restore domesticated plants’ ability to interact with beneficial soil microbes.

    Thousands of years ago, people harvested small wild plants for food. Eventually, they selectively cultivated the largest ones until the plump cereals, legumes, and fruit we know today evolved. But through millennia of human tending, many cultivated plants lost some ability to interact with soil microbes that provide necessary nutrients. This has made some domesticated plants more dependent on fertilizer, one of the world’s largest sources of nitrogen and phosphorous pollution and a product that consumes fossil fuels to produce.

    “I was surprised how completely hidden these changes can be,” said Joel Sachs, a professor of biology at UC Riverside and senior author of a paper published today in Trends in Ecology and Evolution. “We’re so focused on above ground traits that we’ve been able to massively reshape plants while ignoring a suite of other characteristics and have inadvertently bred plants with degraded capacity to gain benefits from microbes.”

    Bacteria and fungi form intimate associations with plant roots that can dramatically improve plant growth. These microbes help break down soil elements like phosphorous and nitrogen that the plants absorb through their roots. The microbes also get resources from the plants in a mutually beneficial, or symbiotic, relationship. When fertilizer or other soil amendments make nutrients freely available, plants have less need to interact with microbes.

    Sachs and first author Stephanie Porter of Washington State University, Vancouver, reviewed 120 studies of microbial symbiosis in plants and concluded that many types of domesticated plants show a degraded capacity to form symbiotic communities with soil microbes.

    “The message of our paper is that domestication has hidden costs,” Sachs said. “When plants are selected for a small handful of traits like making a bigger seed or faster growth, you can lose a lot of important traits relating to microbes along the way.”

    This evolutionary loss has turned into a loss for the environment as well.

    Excess nitrogen and phosphorous from fertilizer can leach from fields into waterways, leading to algae overgrowth, low oxygen levels, and dead zones. Nitrogen oxide from fertilizer enters the atmosphere, contributing to air pollution. Fossil fuels are also consumed to manufacture fertilizers.

    Some companies have begun selling nitrogen-fixing bacteria as soil amendments to make agriculture more sustainable, but Sachs said these amendments don’t work well because some domesticated plants can no longer pick up those beneficial microbes from the soil.

    “If we’re going to fix these problems, we need to figure out which traits have been lost and which useful traits have been maintained in the wild relative,” Sachs said. “Then breed the wild and domesticated together to recover those traits.”

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    UC Riverside Campus

    The University of California, Riverside is one of 10 universities within the prestigious University of California system, and the only UC located in Inland Southern California.

    Widely recognized as one of the most ethnically diverse research universities in the nation, UCR’s current enrollment is more than 21,000 students, with a goal of 25,000 students by 2020. The campus is in the midst of a tremendous growth spurt with new and remodeled facilities coming on-line on a regular basis.

    We are located approximately 50 miles east of downtown Los Angeles. UCR is also within easy driving distance of dozens of major cultural and recreational sites, as well as desert, mountain and coastal destinations.

     
  • richardmitnick 10:13 am on March 9, 2020 Permalink | Reply
    Tags: , Biology, , ,   

    From University of Toronto: “With new federal funding, U of T researchers aid global effort to understand and control COVID-19” 

    U Toronto Bloc

    From University of Toronto

    March 06, 2020
    Geoffrey Vendeville

    1
    U of T researchers are among several of the 47 research teams pursuing projects related to COVID-19 that are receiving support through a rapid federal funding competition. (Photo by Nick Iwanyshyn.)

    The University of Toronto and affiliated institutions will receive almost $6 million for research projects related to COVID-19, with $2.7 million to campus-based researchers, while $3.13 million will go to U of T researchers at affiliated hospitals – part of a $27 million federal investment in research related to the global outbreak.

    Patty Hajdu, Canada’s Minister of Health, announced the results of a rapid research funding competition in Montreal on Friday for projects related to the novel coronavirus, which has so far infected tens of thousands of people around the world.

    The focus of the research at U of T includes the development of rapid and low-cost diagnostics, antiviral compounds and statistical models to forecast disease transmission.

    Vivek Goel, U of T’s vice-president, research and innovation, and strategic initiatives, said U of T researchers have the expertise and experience to make a major contribution to scientists’ understanding of the coronavirus and how to deal with it.

    “U of T and its partners are home to many leading experts in public health, medicine, biology and other fields that can collectively advance our knowledge of this new illness and help mitigate its impact,” said Goel, who was the founding head of Public Health Ontario. “Many of these research projects engage those who are also on the front-lines of our health system, helping to ensure that the research will be relevant and applied immediately and also inform the management of future infectious disease outbreaks.”

    As of March 6, the number of confirmed cases of COVID-19 worldwide has surpassed 100,000, with cases reported on every continent except Antarctica.

    One of the newly funded projects, based at the Sinai Health System, involves U of T researchers Allison McGeer and Samira Mubareka and aims to paint a better picture of how the virus spreads.

    McGeer is a professor at U of T’s Dalla Lana School of Public Health and in the departments of medicine and laboratory medicine and pathobiology in the Faculty of Medicine. She is also the director of the Infectious Disease Epidemiology Research Unit at Mount Sinai Hospital. Mubareka is an assistant professor in the department of laboratory medicine and pathobiology as well as a virologist at Sunnybrook Health Sciences Centre.

    Their team plans to collect data to shed light on how long a patient with the virus is infectious, and how the virus spreads to surfaces and through the air.

    “The importance is with risk management and mitigation,” Mubareka told U of T News.

    She added that removing some of the uncertainty around how the virus spreads can help hospitals make better use of their resources.

    “At some point resources will be finite, and if you have a really good sense of how long people shed [the virus] for, you know how long they will need to be isolated,” Mubareka said.

    The research team also plans to systematically collect samples containing the virus, serum and immune system cells to create a bio-bank that can be shared with researchers working on vaccines or treatments.

    Keith Pardee, an assistant professor at U of T’s Leslie Dan Faculty of Pharmacy, is part of a research team that involves experts in four countries who are collaborating on low-cost and easy-to-use diagnostic tests to improve the triaging of patients.

    During the Zika virus outbreak, the team developed diagnostics within weeks that met the U.S. Centers for Disease Control’s gold standard for use in clinical labs. With COVID-19, the researchers propose to design a suite of diagnostic tools including a “lab-in-a-box kit” that can be used to respond to a large outbreak, a package to help produce diagnostics on-site to support a sustained response and an on-the-spot test for rapid screening of patients – even in places like a cruise ship or airport.

    The team’s goal is to produce tools that will not only be useful in Canada but in countries with health-care systems less capable of handling mass emergencies.

    Another project led by Xiaolin Wei of U of T’s Dalla Lana School of Public Health seeks to produce guidelines to help health-care workers respond to COVID-19 and similar outbreaks in the future. Working with researchers in the Philippines and Sri Lanka, Wei will use front-line experiences in China to develop guidelines and training so health-care workers in these and other low-to-middle-income countries can manage COVID-19 patients and infection control.

    David Fisman, at Dalla Lana and the Institute of Health Policy, Management and Evaluation and the department of medicine in the Faculty of Medicine, is approaching the disease from another angle.

    Fisman and his colleagues – doctors, epidemiologists, public health professionals and statisticians – specialize in data analysis and modelling to help answer three basic questions about an epidemic: When will it peak? When will it end? And how big will it be?

    The team, which has experience dealing with SARS, H1N1 and Ebola, will use mathematical and statistical modelling to forecast the near-term course of the disease, make sense of “messy or noisy” public data and use the information to build simulations that can help guide Canadian health agencies’ decisions.

    Read a Q & A with Professor Fisman

    Other U of T experts who received federal grants for research related to the novel coronavirus are: Isaac Bogoch, of the Faculty of Medicine and the University Health Network; Prabhat Jha, of the Dalla Lana School of Public Health and St. Michael’s Hospital in the Unity Health Toronto network; Sachdev Sidhu, of the Donnelly Centre for Cellular and Biomolecular Research, the department of molecular genetics in the Faculty of Medicine and the Institute of Biomaterials and Biomedical Engineering; and Haibo Zhang, a professor in the department of physiology in the Faculty of Medicine who also works at St. Michael’s Hospital.

    In total, 47 research teams across the country received funding through several agencies and non-profits: the Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada, the Social Sciences and Humanities Research Council of Canada, the Canada Research Coordinating Committee, the International Development Research Centre and Genome Canada.

    In a statement, Theresa Tam, the chief public health officer of Canada, spoke of the importance of research in responding to emerging disease outbreaks.

    “The research to be undertaken by the successful teams will help to answer some of our most pressing questions about COVID-19 and help to develop the tools we need to effectively respond to this global public health emergency,” she said.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Founded in 1827, the University of Toronto has evolved into Canada’s leading institution of learning, discovery and knowledge creation. We are proud to be one of the world’s top research-intensive universities, driven to invent and innovate.

    Our students have the opportunity to learn from and work with preeminent thought leaders through our multidisciplinary network of teaching and research faculty, alumni and partners.

    The ideas, innovations and actions of more than 560,000 graduates continue to have a positive impact on the world.

     
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