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  • richardmitnick 11:25 am on June 10, 2020 Permalink | Reply
    Tags: "Scientists marry two powerful techniques to pinpoint locations of individual molecules in their cellular neighborhoods", (CET)-cryogenic electron tomography, , CIASM -correlated imaging by annotation with single molecules, Finding order in a cellular soup-Even in relatively simple bacterial cells location is everything, Microscopy, , , Two types of protein molecules- PopZ and SpmX   

    From SLAC National Accelerator Lab: “Scientists marry two powerful techniques to pinpoint locations of individual molecules in their cellular neighborhoods” 

    From SLAC National Accelerator Lab

    June 8, 2020
    Glennda Chui

    Researchers expect the new method to answer fundamental questions in biology and materials science. First up: Images showing molecules that help guide cell division in bacteria.

    Scientists have married two of today’s most powerful microscopy techniques to make images that pinpoint, for the first time, the identities and precise locations of individual proteins within the detailed context of bacterial cells. This information is crucial for learning how protein molecules work together to organize cell division and carry out other important tasks, such as enabling microbes to sniff out food and danger.

    The new method has already unearthed new information about bacterial proteins and their nearby cellular neighborhoods. Researchers say it also has potential to answer fundamental questions about the molecular machinery of viruses, parasites, and processes like photosynthesis.

    “This is a big leap for biology, and I think there are many, many systems that will benefit from this kind of imaging,” said Stanford Professor Lucy Shapiro, whose research group participated in the study.

    The new hybrid method, called correlated imaging by annotation with single molecules, or CIASM (pronounced “chasm”), was developed by Peter Dahlberg, a postdoctoral researcher in the lab of Professor W. E. Moerner at Stanford University.

    It’s a variation on a technique called low temperature single-molecule microscopy, invented by Moerner three decades ago, which attaches glowing labels to molecules so they can be individually identified. This method underlies super-resolution fluorescence microscopy, the topic of Moerner’s 2014 Nobel Prize in Chemistry.

    What Dahlberg did was find a way to make this type of fluorescence imaging work at sub-freezing temperatures so the same samples could also be examined with cryogenic electron tomography (CET). CET uses streams of electrons to make 3D images of flash-frozen cells and their components at near-atomic resolution. Combining CET with the fluorescent imaging allows scientists to see the tagged molecules in the context of the surrounding cell, a crucial perspective for understanding their role in the cellular machinery.

    1
    With a technique called cryoelectron tomography, scientists can create detailed 3D images of cells, such as this Caulobacter bacterium, and highlight their components – in this case, the cell membranes (red and blue), protein shell (green), protein factories known as ribosomes (yellow) and storage granules (orange). But until now, smaller structures and individual molecules could not be identified and precisely located within these images. A new imaging technique developed at Stanford fills this gap, revealing small molecules that are not visible here. (Peter Dahlberg et al., PNAS, 8 June 2020)

    “We can label specific molecules of interest so that the light we see comes only from those molecules, and then we find where they are within about 10 nanometers, or billionths of a meter. This gives us a much more accurate picture of what’s going on,” Dahlberg said. “We have taken the ultra-precise snapshots provided by CET and added a little bit of color.”

    He added, “It is exciting to develop new imaging methods. When you are done, you get to take a step back and look at all the new questions you can attack.”

    With CIASM, the research team was able to pinpoint the locations of three types of proteins in high-resolution CET images of bacteria taken at the Department of Energy’s SLAC National Accelerator Laboratory. The results were reported in the Proceedings of the National Academy of Sciences today.

    “Every method has its advantages and disadvantages,“ Moerner said, “and this is a nice situation where we can combine two methods to learn more.”

    Finding order in a cellular soup

    Even in relatively simple bacterial cells, location is everything, said Saumya Saurabh, a postdoctoral researcher in Shapiro’s lab who played a leading role in the research.

    “People tend to think of bacteria as sacks of proteins with no organization,” he said. “But it turns out that’s not true, and in fact many of the molecules in bacteria are precisely located in both space and time. If they’re not in the right position, the cell dies. What Pete’s work is finally allowing us to do is look inside with molecular resolution and find out when and where these molecules are located with respect to each other.”

    2
    Scientists thought a seemingly empty area at one end of this Caulobacter cell might hold two proteins involved in cell division. By labeling the proteins with fluorescent tags and then imaging those same samples with cryoelectron tomography, they were able to confirm this location and show exactly how the proteins were arranged. (Peter Dahlberg et al., PNAS, 8 June 2020)

    Caulobacter crescentus, for instance, a well-studied species of freshwater bacteria, is known for dividing into two very different types of daughter cells: One swims freely, while the other forms a stalk and attaches to a surface. How each daughter cell gets what it needs to follow its unique path has been a longstanding mystery.

    Scientists had previously identified small areas at either end of the dividing cell that might contain proteins that play key roles in this lopsided cell division. One of the proteins, PopZ, is found at both ends of the dividing cell, while the other, SpmX (“Spam-X”) is found only in the half that will develop a stalk.

    For this study, Saurabh and graduate student Jiarui Wang labeled proteins in Caulobacter with fluorescent tags. Then Dahlberg froze these samples, performed single-molecule fluorescence imaging on them with the help of graduate student Annina Sartor, and took them to the Stanford-SLAC Cryo-EM facilities for CET imaging directed by Wah Chiu, a professor at Stanford and SLAC.

    3
    A rotating 3D image of the seemingly empty pocket at one end of a Caulobacter cell now shows the precise locations of PopZ molecules. The pocket looks lumpy because it has been manually colored in to highlight the area where researchers thought the molecules might be, but couldn’t identify directly in cryoelectron tomography. (Peter Dahlberg et al., PNAS, 8 June 2020)

    Mapping a protein hangout

    The combined images not only confirmed that both proteins were in the areas scientists had suspected, but also revealed exactly how they were arranged: SpmX was embedded in the cell’s inner membrane and protruded into the cell’s interior, where it came into direct contact with PopZ.

    “The exact orientation of this protein complex has been debated over the last 12 years,” Saurabh said. “We were able to observe the protein partners with exquisite resolution. Now we have a very precise picture of how these proteins talk to each other in the cell.”

    4
    The image at left shows the locations of two types of protein molecules, PopZ and SpmX, in a cryoelectron tomography image of a Caulobacter cell. At right, a diagram depicts how the proteins are arranged: SpmX is embedded in the cell’s inner membrane and protrudes into the cell’s cytoplasm, where it comes into direct contact with PopZ. These proteins work together during cell division. (Peter Dahlberg et al., PNAS, 8 June 2020)

    The team tested the accuracy of CIASM by using it to confirm the location of a protein called McpA that was known to be part of a chemoreceptor array in the bacteria. “Exquisitely sensitive proteins in this array serve as Caulobacter’s nose,” Saurabh said, “sensing the chemistry of the surrounding environment so they can move away from unpleasant things and move toward the glucose they eat.”

    The array appears as parallel black lines in CET images, and fluorescent tagging of the same images pinpointed the locations of individual McpA proteins within about 10 nanometers.

    A detailed look at quantum dots

    In a separate, parallel study, published in Angewandte Chemie on April 24, the researchers used a similar technique to look at single quantum dots, with some surprising results.

    Quantum dots ­are nanoscale crystals of semiconductor material that naturally fluoresce in colors determined by their size, shape and composition. These dots are used in research to label and track proteins and other biological materials, and have potential applications in future electronics, lighting, quantum computing, medical imaging and other areas.

    In this study, the goal was to see how the finer structural details of individual dots were related to specific details of their optical properties, said Davis Perez, a PhD student in Moerner’s lab.

    “We were able to see some surprising behaviors of the individual quantum dots – for instance, in their response to excitation with laser light,” he said. “But the most exciting aspect to me is that the method we developed to study quantum dots can also be used to study biological systems such as photosynthetic proteins, where energy is transferred between groups of proteins, and see how the photosynthetic machinery operates.”

    Moerner said his lab is working with Chiu to pursue these challenges.

    “It is the early days of combining the two methods, and we are excited to explore more collaborations linking light and electrons,” Chiu said. “This hybrid imaging approach has the potential to uncover structures of molecular components involved in key biological processes in cells spanning all domains of life.”

    Fluorescence microscopy for this study was carried out in the Moerner lab at Stanford.

    The research was supported, in part, by the National Institute of General Medical Sciences and the Department of Energy Office of Science. The Stanford-SLAC Cryo-EM facilities are part of the CryoEM & Bioimaging Division of the Stanford Synchrotron Radiation Lightsource at SLAC.

    See the full article here .


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    SLAC National Accelerator Lab


    SLAC/LCLS


    SLAC/LCLS II projected view


    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

    SSRL and LCLS are DOE Office of Science user facilities.

     
  • richardmitnick 9:00 am on May 13, 2020 Permalink | Reply
    Tags: , , Capturing detailed maps of cells and tissues via a series of photographs., , Microscopy, 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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    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 10:04 am on May 9, 2020 Permalink | Reply
    Tags: "New imaging technology allows visualization of nanoscale structures inside whole cells and tissues", , , , Microscopy, ,   

    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 12:17 pm on March 13, 2020 Permalink | Reply
    Tags: "New microscopy technique uncovers previously hidden information in micrographs of biological cells", Microscopy, , , Using image analysis and machine learning as a tool to directly determine the gene activity in single cells.   

    From University of Glasgow via phys.org: “New microscopy technique uncovers previously hidden information in micrographs of biological cells” 

    U Glasgow bloc

    From University of Glasgow

    via


    phys.org

    March 13, 2020

    1
    Credit: University of Glasgow.

    A new imaging method combined with machine learning uncovers previously hidden information in micrographs of biological cells to reveal quantitative information of gene expression levels.

    Researchers from the University of Glasgow’s James Watt School of Engineering and School of Computing Science describe in a paper published today in Nature Communications how they have used image analysis and machine learning as a tool to directly determine the gene activity in single cells.

    For centuries, microscopy has been one of the most important tools to understand the structure and behaviour of biological cells. However, it has been limited to what is physically possible the see and has mostly been used to describe size, shape and structure. To understand the underlying gene expression activities, other techniques such as polymerase chain reaction required.

    Here the research groups used detailed image analysis to extract more than 1000 mathematical values describing each cell being analysed, generally called morphometric descriptors. Bringing these values together, it is possible to “teach” a computer the relationship between the morphometric values and the actual gene expression levels.

    This approach has similarities to the kinds of ‘machine vision’ already in use in devices like mobile phones and self-driving cars. In those devices, the algorithms are able to identify objects based on large sets of training data. In the research team’s new paper, their technique allowed them to not just distinguish between different types of cells, but also directly predict the gene activity in each cell.

    3
    Credit: University of Glasgow.

    The University of Glasgow’s Nikolaj Gadegaard, Professor of Biomedical Engineering, said: “I have always believed that there was much more information in the micrographs we have collected over the years. With modern computing science techniques, we have now seen that indeed even small changes in the genome is directly reflected in the cells.”

    This technique could pave the way for extracting far more information from microscopy data than is currently possible today.

    See the full article here .

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    About Science X in 100 words

    Science X™ is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004 (Physorg.com), Science X’s readership has grown steadily to include 5 million scientists, researchers, and engineers every month. Science X publishes approximately 200 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Science X community members enjoy access to many personalized features such as social networking, a personal home page set-up, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.
    Mission 12 reasons for reading daily news on Science X Organization Key editors and writersinclude 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

    U Glasgow campus

    The University of Glasgow (Scottish Gaelic: Oilthigh Ghlaschu, Latin: Universitas Glasguensis) is the fourth oldest university in the English-speaking world and one of Scotland’s four ancient universities. It was founded in 1451. Along with the University of Edinburgh, the University was part of the Scottish Enlightenment during the 18th century. It is currently a member of Universitas 21, the international network of research universities, and the Russell Group.

    In common with universities of the pre-modern era, Glasgow originally educated students primarily from wealthy backgrounds, however it became a pioneer[citation needed] in British higher education in the 19th century by also providing for the needs of students from the growing urban and commercial middle class. Glasgow University served all of these students by preparing them for professions: the law, medicine, civil service, teaching, and the church. It also trained smaller but growing numbers for careers in science and engineering.[4]

    Originally located in the city’s High Street, since 1870 the main University campus has been located at Gilmorehill in the West End of the city.[5] Additionally, a number of university buildings are located elsewhere, such as the University Marine Biological Station Millport on the Island of Cumbrae in the Firth of Clyde and the Crichton Campus in Dumfries.

    Alumni or former staff of the University include philosopher Francis Hutcheson, engineer James Watt, philosopher and economist Adam Smith, physicist Lord Kelvin, surgeon Joseph Lister, 1st Baron Lister, seven Nobel laureates, and two British Prime Ministers.

     
  • richardmitnick 1:47 pm on February 21, 2020 Permalink | Reply
    Tags: "Otago physicists grab individual atoms in ground-breaking experiment", , , , Microscopy, , The experiment improves on current knowledge by offering a previously unseen view into the microscopic world surprising researchers with the results., The University of Otago, Trapping and cooling of three atoms to a temperature of about a millionth of a Kelvin using highly focused laser beams in a hyper-evacuated (vacuum) chamber.   

    From The University of Otago, NZ: “Otago physicists grab individual atoms in ground-breaking experiment” 

    1

    From The University of Otago

    20 February 2020

    Associate Professor Mikkel Andersen
    Department of Physics
    University of Otago
    Tel +64 3 479 7805
    Email mikkel.andersen@otago.ac.nz

    Mark Hathaway
    Senior Communications Adviser
    University of Otago
    Mob +64 21 279 5016
    Email mark.hathaway@otago.ac.nz

    1
    LASER-cooled atom cloud viewed through microscope camera.

    In a first for quantum physics, University of Otago researchers have “held” individual atoms in place and observed previously unseen complex atomic interactions.

    A myriad of equipment including lasers, mirrors, a vacuum chamber, and microscopes assembled in Otago’s Department of Physics, plus a lot of time, energy, and expertise, have provided the ingredients to investigate this quantum process, which until now was only understood through statistical averaging from experiments involving large numbers of atoms.

    The experiment improves on current knowledge by offering a previously unseen view into the microscopic world, surprising researchers with the results.

    “Our method involves the individual trapping and cooling of three atoms to a temperature of about a millionth of a Kelvin using highly focused laser beams in a hyper-evacuated (vacuum) chamber, around the size of a toaster. We slowly combine the traps containing the atoms to produce controlled interactions that we measure,” says Associate Professor Mikkel F. Andersen of Otago’s Department of Physics.

    1
    Mikkel Andersen (left) and Marvin Weyland in the physics lab.

    When the three atoms approach each other, two form a molecule, and all receive a kick from the energy released in the process. A microscope camera allows the process to be magnified and viewed.

    “Two atoms alone can’t form a molecule, it takes at least three to do chemistry. Our work is the first time this basic process has been studied in isolation, and it turns out that it gave several surprising results that were not expected from previous measurement in large clouds of atoms,” says Postdoctoral Researcher Marvin Weyland, who spearheaded the experiment.

    For example, the researchers were able to see the exact outcome of individual processes, and observed a new process where two of the atoms leave the experiment together. Until now, this level of detail has been impossible to observe in experiments with many atoms.

    “By working at this molecular level, we now know more about how atoms collide and react with one another. With development, this technique could provide a way to build and control single molecules of particular chemicals,” Weyland adds.

    Associate Professor Andersen admits the technique and level of detail can be difficult to comprehend to those outside the world of quantum physics, however he believes the applications of this science will be useful in development of future quantum technologies that might impact society as much as earlier quantum technologies that enabled modern computers and the Internet.

    “Research on being able to build on a smaller and smaller scale has powered much of the technological development over the past decades. For example, it is the sole reason that today’s cellphones have more computing power than the supercomputers of the 1980s. Our research tries to pave the way for being able to build at the very smallest scale possible, namely the atomic scale, and I am thrilled to see how our discoveries will influence technological advancements in the future,” Associate Professor Andersen says.

    The experiment findings [Physical Review Letters] showed that it took much longer than expected to form a molecule compared with other experiments and theoretical calculations, which currently are insufficient to explain this phenomenon. While the researchers suggest mechanisms which may explain the discrepancy, they highlight a need for further theoretical developments in this area of experimental quantum mechanics.

    This completely New Zealand-based research was primarily carried out by members of the University of Otago’s Department of Physics, with assistance from theoretical physicists at Massey University.

    See the full article here.

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    The University of Otago, founded in 1869 by an ordinance of the Otago Provincial Council, is New Zealand’s oldest university. The new University was given 100,000 acres of pastoral land as an endowment and authorised to grant degrees in Arts, Medicine, Law and Music.

    The University opened in July 1871 with a staff of just three Professors, one to teach Classics and English Language and Literature, another having responsibility for Mathematics and Natural Philosophy, and the third to cover Mental and Moral Philosophy and Political Economy. The following year a Professor of Natural Science joined the staff. With a further endowment provided in 1872, the syllabus was widened and new lectureships established: lectures in Law started in 1873, and in 1875 courses began in Medicine. Lectures in Mining were given from 1872, and in 1878 a School of Mines was established.

    The University was originally housed in a building (later the Stock Exchange) on the site of John Wickliffe House in Princes Street but it moved to its present site with the completion of the northern parts of the Clocktower and Geology buildings in 1878 and 1879.

    The School of Dentistry was founded in 1907 and the School of Home Science (later Consumer and Applied Sciences) in 1911. Teaching in Accountancy and Commerce subjects began in 1912. Various new chairs and lectureships were established in the years between the two world wars, and in 1946 teaching began in the Faculty of Theology. The School of Physical Education was opened in 1947.

    A federal University of New Zealand was established by statute in 1870 and became the examining and degree-granting body for all New Zealand university institutions until 1961. The University of Otago had conferred just one Bachelor of Arts degree, on Mr Alexander Watt Williamson, when in 1874 it became an affiliated college of the University of New Zealand.

    In 1961 the University of New Zealand was disestablished, and the power to confer degrees was restored to the University of Otago by the University of Otago Amendment Act 1961.

    Since 1961, when its roll was about 3,000, the University has expanded considerably (in 2016 there were over 20,000 students enrolled) and has broadened its range of qualifications to include undergraduate programmes in Surveying, Pharmacy, Medical Laboratory Science, Teacher Education, Physiotherapy, Applied Science, Dental Technology, Radiation Therapy, Dental Hygiene and Dental Therapy (now combined in an Oral Health programme), Biomedical Sciences, Social Work, and Performing Arts, as well as specialised postgraduate programmes in a variety of disciplines.

    Although the University’s main campus is in Dunedin, it also has Health Sciences campuses in Christchurch (University of Otago, Christchurch) and Wellington (University of Otago, Wellington) (established in 1972 and 1977 respectively), an information and teaching centre in central Auckland (1996), and an information office in Wellington (2001).

    The Dunedin College of Education merged with the University on 1 January 2007, and this added a further campus in Invercargill.

     
    • alexa 3:13 pm on April 2, 2020 Permalink | Reply

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  • richardmitnick 11:40 am on October 30, 2019 Permalink | Reply
    Tags: , , Microscopy, , , Stretched S-DNA   

    From Sandia Lab: “Advanced microscopy reveals unusual DNA structure” 

    From Sandia Lab

    October 30, 2019
    Melissae Fellet
    mfellet@sandia.gov
    505-845-7478

    Sandia scientist pushes technology’s limits to see fundamental feature of stretched S-DNA.

    1
    Adam Backer, an optical scientist at Sandia National Laboratories, helped develop an advanced microscopy technique that revealed highly tilted base pairs in a stretched form of DNA. (Photo by Randy Montoya).

    An advanced imaging technique reveals new structural details of S-DNA, ladder-like DNA that forms when the molecule experiences extreme tension. This work conducted at Sandia National Laboratories and Vrije University in the Netherlands provides the first experimental evidence that S-DNA contains highly tilted base pairs.

    The predictable pairing and stacking of the DNA base pairs help to define the molecule’s double-helical shape. Understanding how the base pairs realign when DNA is stretched might provide insight into a range of biological processes and improve the design and performance of nanodevices built with DNA. Tilted base pairs in stretched S-DNA have been previously predicted using computer simulations, but never conclusively demonstrated in experiments until now, according to a recent article in Science Advances.

    DNA is most commonly known as the molecular carrier of genetic information. However, in research labs around the world, it also has another use: construction material for nanoscale devices. To do this, scientists prepare computer-generated sequences of single-stranded DNA so that certain sections form base pairs with other sections. This forces the strand to bend and fold like origami. Researchers have used this principle to fold DNA into microscopic smiley faces, nanomachines with moving hinges and pistons and “smart” materials that spontaneously adjust to changes in the surrounding chemical environment.

    “To build an airplane or a bridge, it’s important to know the structure, strength and stretchiness of every material that went into it,” said Adam Backer, an optical scientist at Sandia and lead author of the study. “The same thing is true when designing nanostructures with DNA.”

    While much is known about the mechanical properties of DNA’s double helix, mysteries remain about the details of its shape when the molecule is stretched in a laboratory to form the ladder-like structure of S-DNA. Standard ways of visualizing DNA structure cannot track structural changes while the molecule untwists.

    Seeing stretched DNA

    To characterize the structure and stretchiness of S-DNA, Backer worked with colleagues in the Physics of Living Systems research group at LaserLaB Amsterdam at Vrije University. The researchers described their process in the journal article. Using instrumentation developed by his colleagues, Backer first attached a microscopic bead to each end of a short piece of viral DNA. These beads served as handles to manipulate a single molecule of DNA.

    Next, the researchers trapped the beaded DNA in a narrow fluid-filled chamber using two tightly focused laser beams. Because the beads stay trapped inside the laser beams, the researchers could move the beads in the chamber by redirecting the laser beams. This enabled them to stretch the attached DNA to form S-DNA. This technique for manipulating microscopic particles, called optical tweezers, also provided precise control over the amount of stretching force applied to a single DNA molecule.

    However, the structural changes occurring within the stretched DNA molecule were too small to be directly observed with a standard optical microscope. To address this challenge, Backer helped his colleagues combine an imaging method called fluorescence polarization microscopy with the optical tweezers instrument. First, they added small, rod-like fluorescent dye molecules to the solution containing optically trapped DNA. In unstretched DNA, the dye molecules sandwich themselves between neighboring sets of base pairs and align perpendicular to the central axis of the double helix. If a stretching force causes the DNA base pairs to tilt, the dyes would also tilt.

    Next, the researchers used the fluorescent signals from the dyes to determine if the base pairs in stretched DNA tilted. The fluorescent dyes emit green fluorescent light when they interact with light waves from a laser beam pointing along the same axis as the dye molecules. The researchers changed the orientation of the light waves by rotating the polarization of a laser beam through various angles. Then, they stretched the DNA and watched for green fluorescent signals to appear under the microscope. From these measurements, and computational analysis methods developed at Sandia, the researchers determined that the dyes, and thus the base pairs, aligned at a 54-degree angle relative to the DNA’s central axis.

    “This experiment provides the most direct evidence to date supporting the hypothesis that S-DNA contains tilted base pairs,” said Backer. “To gain this fundamentally new understanding of DNA, it was necessary to combine a number of cutting-edge technologies and bring scientists from a range of different technical disciplines together to work toward a common goal.”

    There is widespread speculation among scientists that structures resembling S-DNA may form during the daily activities of human cells, but, at present, the biological purpose of S-DNA is still unknown. S-DNA might facilitate the repair of damaged or broken DNA, helping to guard against cell death and cancer. Backer hopes this clearer understanding of the physical principles governing DNA deformation will guide further research into the role of S-DNA in cells.

    When Backer joined Sandia as a Truman Fellow in November 2016, he had the opportunity to start an independent research program of his own design. He had developed a method for polarization microscopy during graduate school at Stanford University and thought the technique had potential. Said Backer: “At Sandia I wanted to push this technique as far as it could go. The fact that this work has led to results with potential relevance to fields such as biology and nanotechnology has been extraordinary.”

    See the full article here .


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    Sandia Campus
    Sandia National Laboratory

    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.
    i1
    i2
    i3

     
  • richardmitnick 3:03 pm on May 3, 2019 Permalink | Reply
    Tags: , , Microscopy,   

    From UC Santa Cruz: “Microscope expert develops powerful new tools for biologists” 

    UC Santa Cruz

    From UC Santa Cruz

    May 01, 2019
    Tim Stephens
    stephens@ucsc.edu

    With Sara Abrahamsson’s arrival in the Baskin School of Engineering, UC Santa Cruz is becoming a hotbed of advanced microscopy and microscope development.

    1
    Sara Abrahamsson at the nanofabrication facility where her team makes their custom-designed optics components. (Photo by Gustav Pettersson)

    For biologists, the golden age of microscopy is now. Powerful techniques developed in recent decades enable scientists to study living cells in unprecedented detail, and new techniques continue to push the limits of light microscopes.

    Sara Abrahamsson, an assistant professor of electrical and computer engineering at UC Santa Cruz, is at the forefront of innovations in optical microscopy. She invented a technique called aberration-corrected multi-focus microscopy (MFM), which enables 3-dimensional imaging of living cells. More recently (in 2017), she showed that MFM can be combined with another technique, called structured illumination microscopy (SIM), that provides “super-resolution” beyond the classical limits of light microscopes.

    2
    The aberration-corrected multi-focus microscopy (MFM) technology developed by Abrahamsson requires custom-made diffractive gratings. (Photo by Carolyn Lagattuta)

    “The 2017 paper [BOE] was a proof-of-concept study. Now we want to build the microscope and show that it works for 3-D imaging of living cells with super-resolution,” said Abrahamsson, who won a $700,000 major research instrumentation grant from the National Science Foundation to fund the project.

    Her collaborators in the Department of Molecular, Cell, and Developmental (MCD) Biology are thrilled to be working with Abrahamsson. “Sara is a uniquely talented inventor of microscopes,” said Grant Hartzog, professor of MCD biology.

    Hartzog is one of several UCSC biologists who will be using Abrahamsson’s optical technology to study chromatin (the complex of DNA, RNA, and proteins that forms chromosomes) in the cells of various organisms. He explained that Abrahamsson’s MFM technique improves on the widely used technology of confocal microscopy. A confocal microscope blocks out-of-focus light to obtain sharp images of thin sections at different depths in a sample.

    “You can take multiple slices and build up a 3-D image. The problem is the time that elapses between each image when you’re taking multiple slices of a living cell. Because the components of the cell are in constant motion, the resulting image is blurry,” Hartzog said. “Sara figured out how to focus the light so you can collect all the slices in one shot for an instant 3-D image. That’s really important for imaging living cells.”

    UCSC Microscopy Center

    Abrahamsson’s lab has already built one multi-focus microscope and installed it in the UCSC Life Sciences Microscopy Center, where Hartzog and others have started using it and optimizing their techniques. A SIM system currently under construction will add super-resolution capabilities to the multi-focus microscope.

    3
    The M25 multi-focus microscope uses separate cameras to capture images from 25 focal planes at different depths in a sample. (Photo by Eduardo Hirata)

    Super-resolution is important because the dimensions of the structures of interest to the biologists are so small. The resolution of a light microscope is limited by the wavelengths of visible light to about 200 nanometers. Chromatin structures are much smaller than that, on the order of 10 to 30 nanometers in diameter.

    But scientists have developed ways to get past the classical limits of optical microscopy. Structured illumination microscopy is one of several super-resolution techniques that have been developed, with the first practical implementations appearing in the 1990s. By combining multi-focus and structured illumination microscopy, Abrahamsson’s lab is pushing the technology to the limit in terms of both speed and spatial resolution.

    Meanwhile, Abrahamsson’s graduate student Eduardo Hirata-Miyasaki has developed an extended version of MFM, called the M25, which increases the number of focal planes (or “slices”) from nine to 25 and uses separate cameras to capture the images from each focal plane. This instrument does not have super-resolution capability, but is super-fast. It can record live 3-D volumes at more than 100 frames per second and is designed for functional imaging of living neural circuits of the brain and spinal cord.

    “Thanks to the advances in CMOS sensor technology, we can improve the optical design of the MFM system to create a fast and sensitive method for live 3-D imaging,” said Hirata, who presented the new system at a recent Focus on Microscopy conference in London.

    Custom-designed optics

    The MF-SIM microscope requires building and combining two highly specialized, custom-designed optical systems. Abrahamsson’s team designs and fabricates their own optics components, using a nanofabrication facility at UC Santa Barbara to make the diffractive gratings needed for multi-focus microscopy.

    Hirata explained that the diffractive gratings can be easily customized depending on the region of interest and the target depth of the sample. “The M25 images simultaneously at 25 different depths, and we can vary the separation between those focal planes. Having more focal planes allows us to image greater volumes with higher resolutions,” he said.

    The biologists working with Abrahamsson’s lab are using a range of different organisms in their research. Hartzog and Hinrich Boeger study the effects of chromatin packaging on RNA transcription in yeast cells; Needhi Bhalla studies chromosome dynamics during cell division in C. elegans worms; and William Sullivan studies what happens to damaged chromosomes in fruit flies.

    Abrahamsson did some of her early work at the Advanced Imaging Center at HHMI’s Janelia Research Campus in Ashburn, Virginia, and one of Sullivan’s students went there last year to use their specialized systems. The results only reinforced the need for Abrahamsson’s MF-SIM technology.

    “We’re looking at what happens when a chromosome is broken, which can lead to cancerous cells,” said Sullivan, a professor of MCD biology. “We want to follow this in real time in three dimensions, but we haven’t been able to do that. What Sara’s doing is really pretty ground-breaking.”

    Having the microscopy experts here on campus makes a big difference, he added.

    “There’s always a lot of back and forth, the biologists talking to the engineers to figure out how to get the end result we want,” Sullivan said. “Being able to just take our samples downstairs, instead of traveling to Janelia with live flies, we can make much faster progress.”

    Abrahamsson’s expertise in optics is in high demand, and she is developing and teaching new courses in optics and microscopy for students at UC Santa Cruz. She is also starting a project with researchers at NASA’s Jet Propulsion Laboratory working on a planned space probe. In all these projects, Abrahamsson is excited not only about the new technology, but also about what scientists will be able to learn with it.

    “I can’t wait to see my collaborators take the first data set of living cells on the MF-SIM that we are building. Who knows what they are going to be able to discover with it?” she said.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    UCSC Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)

    .

    UCO Lick Shane Telescope
    UCO Lick Shane Telescope interior
    Shane Telescope at UCO Lick Observatory, UCSC

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    UC Santa Cruz campus
    The University of California, Santa Cruz, opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

    UCSC is the home base for the Lick Observatory.

    Lick Observatory's Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building
    Lick Observatory’s Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building

    Search for extraterrestrial intelligence expands at Lick Observatory
    New instrument scans the sky for pulses of infrared light
    March 23, 2015
    By Hilary Lebow
    1
    The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch) UCSC Lick Nickel telescope

    Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

    “Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego who led the development of the new instrument while at the University of Toronto’s Dunlap Institute for Astronomy & Astrophysics.

    Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by UC Berkeley researchers. The infrared project takes advantage of new technology not available for that first optical search.

    Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

    Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

    “The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

    The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

    Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

    “We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

    Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

    “This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

    NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

    “Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

    NIROSETI will be fully operational by early summer and will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

    The NIROSETI team also includes Geoffrey Marcy and Andrew Siemion from UC Berkeley; Patrick Dorval, a Dunlap undergraduate, and Elliot Meyer, a Dunlap graduate student; and Richard Treffers of Starman Systems. Funding for the project comes from the generous support of Bill and Susan Bloomfield.

     
  • richardmitnick 9:16 am on August 21, 2018 Permalink | Reply
    Tags: , Building phylogenetic trees, Chronograms, , , , , Investigating Earth’s earliest life, Kelsey Moore, Microscopy, ,   

    From MIT News: Women in STEM- “Investigating Earth’s earliest life” Kelsey Moore 

    MIT News
    MIT Widget

    From MIT News

    August 18, 2018
    Fatima Husain

    1
    Kelsey Moore. Image: Ian MacLellan

    Graduate student Kelsey Moore uses genetic and fossil evidence to study the first stages of evolution on our planet.

    In the second grade, Kelsey Moore became acquainted with geologic time. Her teachers instructed the class to unroll a giant strip of felt down a long hallway in the school. Most of the felt was solid black, but at the very end, the students caught a glimpse of red.

    That tiny red strip represented the time on Earth in which humans have lived, the teachers said. The lesson sparked Moore’s curiosity. What happened on Earth before there were humans? How could she find out?

    A little over a decade later, Moore enrolled in her first geoscience class at Smith College and discovered she now had the tools to begin to answer those very questions.

    Moore zeroed in on geobiology, the study of how the physical Earth and biosphere interact. During the first semester of her sophomore year of college, she took a class that she says “totally blew my mind.”

    “I knew I wanted to learn about Earth history. But then I took this invertebrate paleontology class and realized how much we can learn about life and how life has evolved,” Moore says. A few lectures into the semester, she mustered the courage to ask her professor, Sara Pruss in Smith’s Department of Geosciences, for a research position in the lab.

    Now a fourth-year graduate student at MIT, Moore works in the geobiology lab of Associate Professor Tanja Bosak in MIT’s Department of Earth, Atmospheric, and Planetary Sciences. In addition to carrying out her own research, Moore, who is also a Graduate Resident Tutor in the Simmons Hall undergraduate dorm, makes it a priority to help guide the lab’s undergraduate researchers and teach them the techniques they need to know.

    Time travel

    “We have a natural curiosity about how we got here, and how the Earth became what it is. There’s so much unknown about the early biosphere on Earth when you go back 2 billion, 3 billion, 4 billion years,” Moore says.

    Moore studies early life on Earth by focusing on ancient microbes from the Proterozoic, the period of Earth’s history that spans 2.5 billion to 542 million years ago — between the time when oxygen began to appear in the atmosphere up until the advent and proliferation of complex life. Early in her graduate studies, Moore and Bosak collaborated with Greg Fournier, the Cecil and Ida Green Assistant Professor of Geobiology, on research tracking cyanobacterial evolution. Their research is supported by the Simons Collaboration on the Origins of Life.

    An image of Cyanobacteria, Tolypothrix

    The question of when cyanobacteria gained the ability to perform oxygenic photosynthesis, which produces oxygen and is how many plants on Earth today get their energy, is still under debate. To track cyanobacterial evolution, MIT researchers draw from genetics and micropaleontology. Moore works on molecular clock models, which track genetic mutations over time to measure evolutionary divergence in organisms.

    Clad with a white lab coat, lab glasses, and bright purple gloves, Moore sifts through multiple cyanobacteria under a microscope to find modern analogs to ancient cyanobacterial fossils. The process can be time-consuming.

    “I do a lot of microscopy,” Moore says with a laugh. Once she’s identified an analog, Moore cultures that particular type of cyanobacteria, a process which can sometimes take months. After the strain is enriched and cultured, Moore extracts DNA from the cyanobacteria. “We sequence modern organisms to get their genomes, reconstruct them, and build phylogenetic trees,” Moore says.

    By tying information together from ancient fossils and modern analogs using molecular clocks, Moore hopes to build a chronogram — a type of phylogenetic tree with a time component that eventually traces back to when cyanobacteria evolved the ability to split water and produce oxygen.

    Moore also studies the process of fossilization, on Earth and potentially other planets. She is collaborating with researchers at NASA’s Jet Propulsion Laboratory to help them prepare for the upcoming Mars 2020 rover mission.

    “We’re trying to analyze fossils on Earth to get an idea for how we’re going to look at whatever samples get brought back from Mars, and then to also understand how we can learn from other planets and potentially other life,” Moore says.

    After MIT, Moore hopes to continue research, pursue postdoctoral fellowships, and eventually teach.

    “I really love research. So why stop? I’m going to keep going,” Moore says. She says she wants to teach in an institution that emphasizes giving research opportunities to undergraduate students.

    “Undergrads can be overlooked, but they’re really intelligent people and they’re budding scientists,” Moore says. “So being able to foster that and to see them grow and trust that they are capable in doing research, I think, is my calling.”

    Geology up close

    To study ancient organisms and find fossils, Moore has traveled across the world, to Shark Bay in Australia, Death Valley in the United States, and Bermuda.

    “In order to understand the rocks, you really have to get your nose on the rocks. Go and look at them, and be there. You have to go and stand in the tidal pools and see what’s happening — watch the air bubbles from the cyanobacteria and see them make oxygen,” Moore says. “Those kinds of things are really important in order to understand and fully wrap your brain around how important those interactions are.”

    And in the field, Moore says, researchers have to “roll with the punches.”

    “You don’t have a nice, beautiful, pristine lab set up with all the tools and equipment that you need. You just can’t account for everything,” Moore says. “You have to do what you can with the tools that you have.”

    Mentorship

    As a Graduate Resident Tutor, Moore helps to create supporting living environments for the undergraduate residents of Simmons Hall.

    Each week, she hosts a study break in her apartment in Simmons for her cohort of students — complete with freshly baked treats. “[Baking] is really relaxing for me,” Moore says. “It’s therapeutic.”

    “I think part of the reason I love baking so much is that it’s my creative outlet,” she says. “I know that a lot of people describe baking as like chemistry. But I think you have the opportunity to be more creative and have more fun with it. The creative side of it is something that I love, that I crave outside of research.”

    Part of Moore’s determination to research, trek out in the field, and mentor undergraduates draws from her “biggest science inspiration” — her mother, Michele Moore, a physics professor at Spokane Falls Community College in Spokane, Washington.

    “She was a stay-at-home mom my entire childhood. And then when I was in middle school, she decided to go and get a college degree,” Moore says. When Moore started high school, her mother earned her bachelor’s degree in physics. Then, when Moore started college, her mother earned her PhD. “She was sort of one step ahead of me all the time, and she was a big inspiration for me and gave me the confidence to be a woman in science.”

    See the full article here .


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    Please help promote STEM in your local schools.


    Stem Education Coalition

    MIT Seal

    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

    MIT Campus

     
  • richardmitnick 1:13 pm on July 28, 2018 Permalink | Reply
    Tags: , Guinness World Record for micro view into hidden worlds, Microscopy, Record-breaking microscope developed using methods pioneered by Sheffield scientists,   

    From U Sheffield and Cornell University: “Record-breaking microscope developed using methods pioneered by Sheffield scientists” 

    From U Sheffield

    23 July 2018
    Sean Barton
    Media Relations Officer
    University of Sheffield
    0114 222 9852
    s.barton@sheffield.ac.uk

    1
    A revolutionary microscope that has produced images in the highest resolution ever obtained has been developed by researchers using microscopic techniques pioneered by scientists at the University of Sheffield.

    Revolutionary microscope produces images in the highest resolution ever obtained
    Electron microscope developed using computational algorithms pioneered by University of Sheffield scientists
    Record-breaking microscope could be used to study 3D atomic structure at unprecedented resolution

    The record-breaking electron microscope, built by researchers at Cornell University in the USA, can produce images at a higher resolution than conventional approaches. It could be used to determine the atomic structure of materials that are normally damaged using existing methods.

    The microscope may eventually allow researchers to study 2D materials, such graphene, using unprecedented precision to provide new insights into this burgeoning class of useful materials that have extraordinary physical and electrical properties, and which could revolutionise many modern technologies.

    It may also lead to the development of a method that can image individual atoms in 3D objects without damaging the structure by using ‘slow’ low-energy electrons.

    Electron imaging is usually conducted using expensive lenses and high-energy electrons that damage many types of material. Alternatively, the Cornell research team recorded electrons that had been scattered through high angles to get around these problems.

    Once scattered, the electrons don’t look anything like an image, so the Cornell research team used computational algorithms developed by scientists at the University of Sheffield to work out backwards what the specimen looked like. This is what enabled the microscope to generate the record-breaking high resolution image.

    For many years, this backwards calculation, known as the phase problem, was regarded as impossible to solve for a large image.

    Professor John Rodenburg from the University of Sheffield’s Department of Electronic and Electrical Engineering, who developed the computational algorithms together with his colleague Andrew Maiden, commented:

    “The electron microscope developed by the Cornell research team is the most powerful microscope we’ve ever seen. It is capable of capturing images that have an unprecedented level of detail, which is important because it now paves the way for us to develop new insights into material structure at the atomic scale.

    “Such an advanced electron microscope wasn’t possible previously because although the technique we developed here at the University of Sheffield works well for X-ray and light microscopes, in the case of electron microscopy it needs a near-perfect detector to get good enough quality data. Now, due to the advances in detector technology made by the Cornell team, this record-breaking microscope can successfully run the Sheffield algorithm.”

    Cornell Bloc

    From Cornell Chronicle

    Guinness World Record for micro view into hidden worlds

    2

    July 25, 2018
    Tom Fleischman

    In a recent research paper published in Nature, a group led by physics professors David Muller and Sol Gruner claimed a world record for electron microscope resolution using a high-powered detector and a technique called ptychography. Their technique was shown to measure down to 0.39 ångströms or 0.039 nanometers (one-billionth of a meter).

    Guinness World Records has officially recognized the Cornell collaboration’s achievement, listing it alongside such notables as Robert Pershing Wadlow (at 8 feet, 11.1 inches, the world’s tallest human) and Lee Redmond (longest fingernails, with a combined length of 28 feet, 4 inches).

    Gruner, former director of the Cornell High Energy Synchrotron Source, said he’d always dreamed of making the Guinness grade, but didn’t figure microscopy would be his ticket to fame.

    “I always thought that I’d need to eat 40 hamburgers in five minutes or stand on one foot for days to get into the Guinness book,” he said. “Who would have thought that seeing a few atoms would do the trick?”

    That brings to four the number of current Cornell University-affiliated record-holders. Muller also shares the record for thinnest glass (three atoms thick, 2013); the other records are held in part by applied and engineering physics professor Harold Craighead, who shares records for smallest replica guitar (1997) and lightest object weighed (2004). In addition, the current record for furthest distance covered by a quadruped robot (83.28 miles, in 2015) eclipsed the mark of 40.5 miles set by Cornell’s Ranger robot in 2011.

    See the full Sheffield article here .
    See the full Cornell Chronicle article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

    U Sheffield campus

    The University of Sheffield (informally Sheffield University) is a public research university in Sheffield, South Yorkshire, England. It received its royal charter in 1905 as successor to the University College of Sheffield, which was established in 1897 by the merger of Sheffield Medical School (founded in 1828), Firth College (1879) and Sheffield Technical School (1884).

    Sheffield is a multi-campus university predominantly over two campus areas: the Western Bank and the St George’s. The university is organised into five academic faculties composed of multiple departments. It had 20,005 undergraduate and 8,710 postgraduate students in 2016/17. The annual income of the institution for 2016–17 was £623.6 million of which £155.9 million was from research grants and contracts, with an expenditure of £633.0 million. Sheffield ranks among the top 10 of UK universities for research grant funding.

    Sheffield was placed 75th worldwide according to QS World University Rankings and 104th worldwide according to Times Higher Education World University Rankings. It was ranked 12th in the UK amongst multi-faculty institutions for the quality (GPA) of its research and for its Research Power in the 2014 Research Excellence Framework. In 2011, Sheffield was named ‘University of the Year’ in the Times Higher Education awards. The Times Higher Education Student Experience Survey 2014 ranked the University of Sheffield 1st for student experience, social life, university facilities and accommodation, among other categories.

    It is one of the original red brick universities, a member of the Russell Group of research-intensive universities, the Worldwide Universities Network, the N8 Group of the eight most research intensive universities in Northern England and the White Rose University Consortium. There are eight Nobel laureates affiliated with Sheffield and six of them are the alumni or former long-term staffs of the university.

     
  • richardmitnick 5:10 am on November 15, 2017 Permalink | Reply
    Tags: , , Microscopy   

    From COSMOS: “Need a better microscope? Add mirrors” 

    Cosmos Magazine bloc

    COSMOS Magazine

    15 November 2017
    Andrew Masterson

    1
    Anthony Van Leeuwenhoek’s first microscope, from the seventeenth century, looks nothing like a modern SPIM microscope, but both are products of a quest to improve optics. Stegerphoto.

    From pre-classical times onwards, it could be argued, lens-makers have been the unsung heroes of science.

    As early as 750 BCE the Assyrians were shaping lenses from quartz. From there, the history of optics both underpins and enables discovery in both the macro and micro worlds.

    Where would science be today had it not been for the patient work of myriad lens grinders and optics theorists, including Francis Bacon, Galileo, van Leeuwenhoek, right up to Roberts and Young – inventors in 1951 of photon scanning microscopy – and beyond?

    Even today, the quest for better, clearer, more detailed images from lenses continues apace, with the latest advance, declared in the journal Nature Communications, coming from the US National Institutes of Health and the University of Chicago.

    2
    The images obtained by the combination of the new coverslip and computer algorithms show clearer views of small structures. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    3
    In this diagram, you can see how the mirrored coverslip allows for four simultaneous views. Credit: Yicong Wu, National Institute of Biomedical Imaging and Bioengineering

    A team of researchers, led by Hari Shroff, head of the National Institute of Biomedical Imaging and Bioengineering’s lab section on High Resolution Optical Imaging (HROI), report the solution to a mechanical problem in microscope optics that was, in a way, of their own making.

    Several years ago, Shroff and colleagues developed a new type of microscope that performed “selective plane illumination microscopy” or SPIM. These microscopes use light sheets to illuminate only sections of specimens being examined, thereby doing less damage and better preserving the sample.

    In 2013, Shroff’s team created a SPIM microscope that used two lenses instead of one, which improved image quality and depth perception, In 2016, a third lens was added, allowing improved resolution and 3D-imagery.

    A fourth lens would have boosted matters even more, but at this point van Leeuwenhoek’s twenty-first century heirs hit a snag.

    “Once we incorporated three lenses, we found it became increasingly difficult to add more,” says Shroff. “Not because we reached the limit of our computational abilities, but because we ran out of physical space.”

    Proximity was a real issue. Not only were the three lenses crowded together, but all had to be positioned extremely close to the sample being examined to allow the imaging goal – detailed views of structures within a single cell, say – to be achieved.

    In their new paper, Shroff and his colleagues reveal a solution to the problem that is nothing if not elegant. Rather than try to cram an extra lens in, they have put mirrors on the coverslip – the thin piece of glass that sits on top of the sample.

    The result – especially when coupled with new algorithms in the computerised back-end of a SPIM microscope – is better speed, efficiency and resolution.

    “It’s a lot like looking into a mirror,” Shroff explains. “If you look at a scene in a mirror, you can view perspectives that are otherwise hidden. We used this same principle with the microscope.

    “We can see the sample conventionally using the usual views enabled by the lenses themselves, while at the same time recording the reflected images of the sample provided by the mirror.”

    The addition of the tiny mirrors was not without its own problems. Every microscope raw image contains unwanted data from the source of illumination used to light up the sample. With three lenses, there are three sources of this interference; with mirrors added, these too are multiplied.

    Shroff, however, took this problem to computational imaging researcher Patrick La Riviere at the University of Chicago, who, with his team, was able to modify the processing software to eliminate the extra noise and further improve the signal.

    Francis Bacon, one thinks, would have approved.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

     
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