Tagged: Genetics Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 12:51 pm on February 13, 2018 Permalink | Reply
    Tags: , , DropSynth, Genetics, ,   

    From UCLA Newsroom: “UCLA scientists develop low-cost way to build gene sequences” 

    UCLA Newsroom

    February 12, 2018
    Sarah C.P. Williams

    UCLA scientists used DropSynth to make thousands of bacterial genes with different versions of phosphopantetheine adenylyltransferase, or PPAT (pictured). Sriram Kosuri/UCLA.

    A new technique pioneered by UCLA researchers could enable scientists in any typical biochemistry laboratory to make their own gene sequences for only about $2 per gene. Researchers now generally buy gene sequences from commercial vendors for $50 to $100 per gene.

    The approach, DropSynth, which is described in the January issue of the journal Science, makes it possible to produce thousands of genes at once. Scientists use gene sequences to screen for gene’s roles in diseases and important biological processes.

    “Our method gives any lab that wants the power to build its own DNA sequences,” said Sriram Kosuri, a UCLA assistant professor of chemistry and biochemistry and senior author of the study. “This is the first time that, without a million dollars, an average lab can make 10,000 genes from scratch.”

    Increasingly, scientists studying a wide range of subjects in medicine — from antibiotic resistance to cancer — are conducting “high-throughput” experiments, meaning that they simultaneously screen hundreds or thousands of groups of cells. Analyzing large numbers of cells, each with slight differences in their DNA, for their ability to carry out a behavior or survive a drug treatment can reveal the importance of particular genes, or sections of genes, in those abilities.

    Such experiments require not only large numbers of genes but also that those genes are sequenced. Over the past 10 years, advances in sequencing have enabled researchers to simultaneously determine the sequences of many strands of DNA. So the cost of sequencing has plummeted, even as the process of generating genes has remained comparatively slow and expensive.

    “There’s an ongoing need to develop new gene synthesis techniques,” said Calin Plesa, a UCLA postdoctoral research fellow and co-first author of the paper. “The more DNA you can synthesize, the more hypotheses you can test.”

    The current methods for synthesizing genes, he said, either limit the length of a gene to about 200 base pairs — the sets of nucleotides that made up DNA — or are prohibitively expensive for most labs.

    The new method involves isolating small sections of thousands of genes in tiny droplets of water suspended in an oil. Each section of DNA is assigned a molecular “bar code,” which identifies the longer gene to which it belongs.

    Then, the sections, which initially are present in only very small amounts, are copied many times to increase their number. Finally, small beads are used to sort the mixture of DNA fragments into the right combinations to make longer genes, and the sections are combined. The result is a mixture of thousands of the desired genes, which can be used in experiments.

    To show that technique worked, the scientists used DropSynth to make thousands of bacterial genes — each as long as 669 base pairs in length. Each gene encoded a different bacterium’s version of the metabolic protein phosphopantetheine adenylyltransferase, or PPAT, which bacteria need to survive. Because PPAT is critical to bacteria that cause everything from sinus infections to pneumonia and food poisoning, it’s being studied as a potential antibiotic target.

    The researchers created a mixture of the thousands of versions of PPAT with DropSynth, and then added each gene to a version of E. coli that lacked PPAT and tested which ones allowed E. coli to survive. The surviving cells could then be used to screen potential antibiotics very quickly and at a low cost.

    DropSynth could potentially also be useful in engineering new proteins. Currently, scientists can use computer programs to design proteins that meet certain parameters, such as the ability to bind to certain molecules, but DropSynth could offer researchers hundreds or even thousands of options from which to choose the proteins that best fit their needs.

    The team is still working on reducing DropSynth’s error rate. In the meantime, though, the scientists have made the instructions publicly available on their website. All of the chemical substances needed to replicate the approach are commercially available.

    The study’s other authors are graduate students Nathan Lubock and Angus Sidore of UCLA, and Di Zhang of the University of Pennsylvania.

    Funding for the study was provided by the Netherlands Organisation for Scientific Research, the Human Frontier Science Program, the National Science Foundation, the National Institutes of Health, the Searle Scholars Program, the U.S. Department of Energy, and Linda and Fred Wudl.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    UC LA Campus

    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

  • richardmitnick 8:31 am on January 31, 2018 Permalink | Reply
    Tags: , , , Genetics, Multipurpose enhancers and promoters in embryonic development   

    From EMBL: “Multipurpose enhancers and promoters in embryonic development” 

    EMBL European Molecular Biology Laboratory bloc

    European Molecular Biology Laboratory

    30 January 2018
    Iris Kruijen

    Enhancer activity (green) and promoter activity (purple) in the same regulatory element. IMAGE: EMBL / Eileen Furlong.

    EMBL scientists show that some promoters can act as enhancers and vice versa.

    During gene expression, the information stored in our DNA is transcribed: turned into instructions to produce RNA and proteins that perform specific functions within each cell. DNA regions called promoters are located at the beginning of genes, and determine the starting point where transcription is initiated. Other snippets of DNA called enhancers control when and where specific genes are expressed. Enhancers are often located far away from genes and must relay their regulatory information to a gene’s promoter.

    Now, Olga Mikhaylichenko and colleagues in Eileen Furlong’s group at EMBL have gained new insights into the role of enhancers and promoters during embryonic development, a life stage where very tight regulation of gene expression is essential. Furlong explains the main findings of the paper, that explores the balance between enhancer and promoter activity within individual regulatory elements in vivo, and that was published in Genes & Development on January 29, 2018.

    What is the key finding in this paper?

    “It used to be thought that there was a black-and-white distinction between enhancers and promoters: they can only act as one or the other. Our paper shows that there is actually a large grey area in-between, with elements that can perform both functions to varying degrees. The level of enhancer or promoter activity is reflected by both the amount and the direction of transcription from the regulatory element, so whether the element can be read in one or two directions, unidirectional or bidirectional. We also developed a new framework to measure enhancer and promoter activity for the same element, in the same embryo (see figure), which we suggest should become the standard for future studies.”

    Why is this important?

    “First of all, we were able to show that things are not as black and white as they seemed. Enhancers and promoters are in various states of evolution with some having exclusive promoter function, others having predominantly enhancer function, and yet other elements, distal enhancers, having weak promoter activity.

    One of the findings that I am most excited about is when we looked at activity in the other direction, asking if gene promoters can act as developmental enhancers. Here, we found that promoters that are bidirectionally transcribed can function as both strong enhancers and promoters, for the same gene. This suggests that they regulate both the levels (promoters) and spatial expression (enhancer) of the gene. Interestingly, promoters that are unidirectionally transcribed cannot perform this function.

    Hints from other studies suggest that these general features are conserved from fruit flies to humans. Our findings uncover a new aspect of promoter and enhancer function during embryogenesis, and provide interesting insights into how these elements might have evolved to regulate robust embryonic development.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    EMBL European Molecular Biology Laboratory campus

    EMBL is Europe’s flagship laboratory for the life sciences, with more than 80 independent groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its 1800 employees, from many nations, operate across five sites: the main laboratory in Heidelberg, and outstations in Grenoble; Hamburg; Hinxton, near Cambridge (the European Bioinformatics Institute), and Monterotondo, near Rome. Founded in 1974, EMBL is an inter-governmental organisation funded by public research monies from its member states. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Around 200 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

  • richardmitnick 1:19 pm on January 30, 2018 Permalink | Reply
    Tags: , , Cell differentiation, , Genetics, , Polycomb Repressive Complex 2 (PRC2)   

    From LBNL: “Silencing Is Golden: Scientists Image Molecules Vital for Gene Regulation” 

    Berkeley Logo

    Berkeley Lab

    January 29, 2018
    Dan Krotz
    (510) 486-4019

    Structure of the human Polycomb Repressive Complex 2 (PRC2) bound to cofactors obtained by cryo-electron microscopy. Both cofactors mimic the histone protein tail to stabilize and stimulate the enzymatic activity of PRC2. (Credit: Vignesh Kasinath)

    All the trillions of cells in our body share the same genetic information and are derived from a single, fertilized egg. When this initial cell multiplies during fetal development, its daughter cells become more and more specialized. This process, called cell differentiation, gives rise to all the various cell types, such as nerve, muscle, or blood cells, which are diverse in shape and function and make up tissues and organs. How can the same genetic blueprint lead to such diversity? The answer lies in the way that genes are switched on or off during the course of development.

    Scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) have been studying the molecules that act at the genetic level to give rise to different types of cells. Some of these molecules are a complex of proteins called the Polycomb Repressive Complex 2 (PRC2) that is involved in “silencing” genes so that they are not “read” by the cellular machinery that decodes genetic information, effectively keeping the genetic information in the “off” state.

    In two new studies, a team of researchers led by Eva Nogales, senior faculty scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, has gained insight into the structure of PRC2 and the ways in which it is regulated to affect gene silencing. Their work was reported on January 18 in the journal Science and on January 29 in Nature Structural and Molecular Biology by Eva Nogales and postdoctoral researchers Vignesh Kasinath and Simon Poepsel.

    Both publications provide a structural framework to understand PRC2 function, and in the case of the latter, the structures are the first to illustrate how a molecule of this type engages with its substrate. The structural descriptions of human PRC2 with its natural partners in the cell lend important insight into the mechanism by which the PRC2 complex regulates gene expression. This information could provide new possibilities for the development of therapies for cancer.

    PRC2 is a gene regulator that is vital for normal development. Genomic DNA is packaged into nucleosomes, which are formed by histone proteins that have DNA wrapped around them. Histone proteins have long polypeptide tails that can be modified by the addition and removal of small chemical groups. These modifications influence the interaction of nucleosomes with each other and other protein complexes in the nucleus. The function of PRC2 in the cell is to make a particular chemical change in one of the histones. The genes in the regions of the genome that have been modified by PRC2 are switched off, or become silenced.

    This montage of the full PRC2 with two nucleosomes is based on the superposition of the cryo-EM maps of PRC2 with and without the nucleosomes to show the consistency of the observed nucleosome binding configuration with the full PRC2 structure. (Credit: Simon Poepsel)

    “Not surprisingly, elaborate mechanisms have evolved to ensure that PRC2 marks the correct regions for silencing at the right time,” said Nogales, who is also a Howard Hughes Medical Investigator and professor of Biochemistry, Biophysics and Structural Biology at the University of California, Berkeley. Failure of this regulation not only impairs the process of development, but also contributes to the reversal of cell differentiation and the uncontrolled cell growth that are the hallmarks of cancer. “Therefore,” Nogales continued, “gaining insight into how PRC2 function is adjusted both in space and time is crucial to understanding cell development.”

    Nogales and her team use structural biology to elucidate how biomolecules, particularly proteins and nucleic acids (DNA, RNA), are organized and combine to form functional biological assemblies. Obtaining detailed insights into their three-dimensional shape will not only help to understand how they function but also how this function is regulated in the cell. These two studies rely on cryo-electron microscopy for imaging the biomolecules, a technique that can see large biomolecules on a very small scale and in multiple conformations. Kasinath and Poepsel, have now solved the structure of PRC2, which provides a framework to understand how this complex is regulated to modify histone proteins.

    The first study, published January 18 in Science by Kasinath, Poepsel, Nogales, and coworkers, visualized the architecture of the complete PRC2 in atomic detail. First author Vignesh Kasinath said, “It took three years of work to obtain this high-resolution structure of all the parts, or subunits, that make up a functional PRC2, as well as visualize how additional protein subunits, called cofactors, may help regulate its activity. Remarkably, both cofactors mimic the histone protein tail in their binding to PRC2 suggesting that cofactors and histone tails together work hand-in-hand to regulate PRC2 function. This structural work holds great promise for new drug development to fight PRC2 dysfunction in cancer.”

    This work is complemented by a second study that presents snapshots of PRC2 binding to the histone proteins that it modifies as a signal for gene silencing. The structures, which have been published in Nature Structural and Molecular Biology on January 29 by Poepsel, Kasinath and Nogales this week, illustrate beautifully the action of this sophisticated complex. “PRC2 can simultaneously engage two nucleosomes,” said Poepsel, first author of this study. “Our cryo-EM images help us understand how the complex can recognize the presence of a histone modification in one nucleosome and place the same tag onto a neighboring nucleosome.” This cascade of activity enables PRC2 to spread this modification over the entire neighboring gene loci, thereby marking it for silencing. Nogales added, “The visualization of such interactions is notoriously hard. We have made an important step forward in our general understanding of how gene regulators can bind to and recognize nucleosomes.”

    PRC2 is essential to gene regulation and expression in all multicellular organisms. The findings from both studies open up tremendous possibilities for combatting cancer while simultaneously expanding our knowledge of gene regulation at a molecular level. “Because PRC2 is deregulated in cancers, it makes a good target for potential therapeutics,” said Nogales. The fundamental understanding of PRC2 arising from these studies will have broad implications in both plant and animal biology.

    This work was funded by the Howard Hughes Medical Institute and Eli Lilly. This research used cryo-electron microscopy (cryo-EM) and made use of the unique resources of the Bay Area Cryo-EM Facility. Image analysis relied on heavy computational work that was carried out at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility.

    NERSC Cray XC40 Cori II supercomputer

    LBL NERSC Cray XC30 Edison supercomputer

    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.


    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Vignesh Kasinath was supported by a postdoctoral fellowship from Helen Hay Whitney and Simon Poepsel was supported by the Alexander von Humboldt foundation (Germany) as a Feodor-Lynen postdoctoral fellow.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    A U.S. Department of Energy National Laboratory Operated by the University of California

    University of California Seal

    DOE Seal

  • richardmitnick 9:14 am on January 22, 2018 Permalink | Reply
    Tags: , , Cambridge Rindge and Latin School (CRLS), Genetics, Harvard Life Sciences Outreach Program,   

    From Harvard Gazette “Learning to understand their own DNA” 

    Harvard University
    Harvard University

    Harvard Gazette

    January 19, 2018
    Deborah Blackwell

    Cambridge Rindge and Latin student Hannah Thomsen isolates her DNA for sequencing during an Amgen biotech lab inside the Science Center. Kris Snibbe/Harvard Staff Photographer.

    Harvard opens its labs to help local high school students decode biotech

    On the fourth floor of Harvard’s Science Center, high school biology students from Cambridge Rindge and Latin School (CRLS) put on safety goggles and gloves, and step up to lab tables conveniently set up with pipettes, centrifuges, and other implements.

    Then they get to work isolating their own DNA.

    “This is real-life science, the stuff that people who work in biotech are actually doing in their labs, and the fact that kids get to do this at the high school level is amazing,” said Janira Arocho, a biology teacher at CRLS. “I didn’t get to do this type of stuff until I was in college.”

    Teaching younger students the tools of modern science is the goal of the Amgen Biotech Experience (ABE,) a STEM (science, technology, engineering, and mathematics) program that opens the field of biotechnology to high schoolers and their teachers, while at the same time teaching them how to approach science as critical thinkers and innovators — and a lot about who they are.

    “It’s normally really, really challenging to give them a good sense of what happens just by lecturing about it,” said Tara Bennett Bristow, site director of the Massachusetts ABE. “The ABE program is not only helping to increase their scientific literacy in biotechnology, it’s exposing them in a hands-on fashion, which generates enthusiasm.”

    In its sixth year in Massachusetts, the local branch of the program is a partnership between the Harvard and the Amgen Foundation. A foundation grant through the University’s Life Sciences Outreach Program provides the kits of materials and equipment for students to do labs that mirror the process of therapeutic research and development, and Massachusetts teachers participating in the program complete summer training workshops at Harvard.

    Arocho, who has participated in the program for several years, said with the training, “I was able to learn everything my students would be doing ahead of time, as opposed to learning along with them in my own classroom.”

    More than 80,000 students around the world — 6,000 of them from Massachusetts high schools, along with 100 of their teachers — participated in ABE last year. At Harvard, which in July received another three-year grant to continue ABE programing, about 500 CRLS students are able to use the undergraduate biology teaching laboratories, where their own teacher leads the lab and graduate students and postdoctoral fellows are on site for assistance.

    CRLS students Hannah Thomsen (from left) and Elizabeth Lucas-Foley work with their Biology teacher Janira Arocho, GSAS student Alyson Ramirez, and CRLS students Peter Fulweiler and Kerri Sands. Kris Snibbe/Harvard Staff Photographer.

    n one lab in December, the CRLS students isolated their own DNA (their results were sent out for sequencing, and reports returned to them several days later for analysis). In another, the students produced a red fluorescent protein — used in the field for in vivo imaging — with common biotech tools.

    Alia Qatarneh, the site coordinator of the ABE program at Harvard, leads teacher ABE workshops, training, and student labs. Qatarneh said she is particularly excited that the program was just implemented at her alma mater, Boston Latin School, where she was able to teach an ABE lab to four advanced placement biology classes last fall.

    “It was amazing to go back to Boston Latin and think of my own experience as a high school student. I was so into science and loved hands-on things, but didn’t take AP biology because I was scared,” she said. “If I were a high school student and I had a chance to hold pipettes, to change the genetic makeup of bacteria to make it glow in the dark, how cool would that be?”

    An assessment by the nonprofit research firm WestEd found that the ABE program substantially adds to students’ knowledge of biotechnology, and increases their interest and confidence in their scientific abilities. The program is open and for free participating high school biology students, including those with learning disabilities, and even those without an interest in science.

    “Students may say, ‘Wow biotech, I didn’t know that this field existed. I thought that if I liked science I had to be a doctor, and now I have this whole different path in front of me,’” Qatarneh said.

    Arocho said her students love going to Harvard, seeing what the labs look like, and doing their work there. “Alia always starts by telling them that this is the exact same lab that the Harvard freshman are doing, and the exact same place, so they do get excited about that,” she said.

    CRLS junior Peter Fulweiler, one of Arocho’s students, said the best part is taking what he learned in the classroom and putting it all together in the lab.

    “I love the hands-on part of this. It’s really interesting, because it’s not like we are reading instructions; we are making an attempt to actually understand what we are learning by doing it,” he said. “The bonus is that we get to find out where we are from on our mothers’ side.”

    Science teacher Lawrence Spezzano is one of 10 instructors at Boston Latin now implementing the ABE program. He said it allows for flexibility and differentiation, and enhances learning opportunities as well as classroom logistics.

    “The program was perfect. As an AP biology teacher struggling to fit more labs and biotechnology into a time-constrained curriculum, the mapped-out process is creative and engaging to both me and my students,” Spezzano said.

    Kerri Sands, a junior at CRLS, said she has always dreamed of being a geneticist. She wants to eventually change the future of medicine, and now feels like she can.

    “I just love the science of this, the lab is like my home. I love the whole experience of everything from the micro pipetting to the centrifuging. I love it all,” she said. “This has made my passion for science even stronger.”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Harvard University campus
    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

  • richardmitnick 2:17 pm on December 31, 2017 Permalink | Reply
    Tags: Genetics, , HiCRep method to accurately assess the reproducibility of data from Hi-C experiments, New insights into how the genome works inside of a cell, New statistical method for evaluating reproducibility in studies of genome organization" 2017, , Quite often correlation is treated as a proxy of reproducibility in many scientific disciplines but they actually are not the same thing, , With the massive amount of data that is being produced in whole-genome studies it is vital to ensure the quality of the data   

    From Pennsylvania State University: “New statistical method for evaluating reproducibility in studies of genome organization” 2017 

    Penn State Bloc

    Pennsylvania State University

    03 October 2017
    Qunhua Li:
    (814) 863-7395

    Barbara K. Kennedy:
    (814) 863-4682

    Sam Sholtis

    A new, statistical method to evaluate the reproducibility of data from Hi-C — a cutting-edge tool for studying how the genome works in three dimensions inside of a cell — will help ensure that the data in these “big data” studies is reliable.

    Schematic representation of the HiCRep method. HiCRep uses two steps to accurately assess the reproducibility of data from Hi-C experiments. Step 1: Data from Hi-C experiments (represented in triangle graphs) is first smoothed in order to allow researchers to see trends in the data more clearly. Step 2: The data is stratified based on distance to account for the overabundance of nearby interactions in Hi-C data. Credit: Li Laboratory, Penn State University

    “Hi-C captures the physical interactions among different regions of the genome,” said Qunhua Li, assistant professor of statistics at Penn State and lead author of the paper. “These interactions play a role in determining what makes a muscle cell a muscle cell instead of a nerve or cancer cell. However, standard measures to assess data reproducibility often cannot tell if two samples come from the same cell type or from completely unrelated cell types. This makes it difficult to judge if the data is reproducible. We have developed a novel method to accurately evaluate the reproducibility of Hi-C data, which will allow researchers to more confidently interpret the biology from the data.”

    The new method, called HiCRep, developed by a team of researchers at Penn State and the University of Washington, is the first to account for a unique feature of Hi-C data — interactions between regions of the genome that are close together are far more likely to happen by chance and therefore create spurious, or false, similarity between unrelated samples. A paper describing the new method appears in the journal Genome Research.

    “With the massive amount of data that is being produced in whole-genome studies, it is vital to ensure the quality of the data,” said Li. “With high-throughput technologies like Hi-C, we are in a position to gain new insight into how the genome works inside of a cell, but only if the data is reliable and reproducible.”

    Inside the nucleus of a cell there is a massive amount of genetic material in the form of chromosomes — extremely long molecules made of DNA and proteins. The chromosomes, which contain genes and the regulatory DNA sequences that control when and where the genes are used, are organized and packaged into a structure called chromatin. The cell’s fate, whether it becomes a muscle or nerve cell, for example, depends, at least in part, on which parts of the chromatin structure is accessible for genes to be expressed, which parts are closed, and how these regions interact. HiC identifies these interactions by locking the interacting regions of the genome together, isolating them, and then sequencing them to find out where they came from in the genome.

    The HiCRep method is able to accurately reconstruct the biological relationship between different cell types, where other methods fail. Credit: Li Laboratory, Penn State University

    “It’s kind of like a giant bowl of spaghetti in which every place the noodles touch could be a biologically important interaction,” said Li. “Hi-C finds all of these interactions, but the vast majority of them occur between regions of the genome that are very close to each other on the chromosomes and do not have specific biological functions. A consequence of this is that the strength of signals heavily depends on the distance between the interaction regions. This makes it extremely difficult for commonly-used reproducibility measures, such as correlation coefficients, to differentiate Hi-C data because this pattern can look very similar even between very different cell types. Our new method takes this feature of Hi-C into account and allows us to reliably distinguish different cell types.”

    “This reteaches us a basic statistical lesson that is often overlooked in the field,” said Li. “Quite often, correlation is treated as a proxy of reproducibility in many scientific disciplines, but they actually are not the same thing. Correlation is about how strongly two objects are related. Two irrelevant objects can have high correlation by being related to a common factor. This is the case here. Distance is the hidden common factor in the Hi-C data that drives the correlation, making the correlation fail to reflect the information of interest. Ironically, while this phenomenon, known as the confounding effect in statistical terms, is discussed in every elementary statistics course, it is still quite striking to see how often it is overlooked in practice, even among well-trained scientists.“

    The researchers designed HiCRep to systematically account for this distance-dependent feature of Hi-C data. In order to accomplish this, the researchers first smooth the data to allow them to see trends in the data more clearly. They then developed a new measure of similarity that is able to more easily distinguish data from different cell types by stratifying the interactions based on the distance between the two regions. “This is like studying the effect of drug treatment for a population with very different ages. Stratifying by age helps us focus on the drug effect. For our case, stratifying by distance helps us focus on the true relationship between samples.”

    To test their method, the research team evaluated Hi-C data from several different cell types using HiCRep and two traditional methods. Where the traditional methods were tripped up by spurious correlations based on the excess of nearby interactions, HiCRep was able to reliably differentiate the cell types. Additionally, HiCRep could quantify the amount of difference between cell types and accurately reconstruct which cells were more closely related to one another.

    In addition to Li, the research team includes Tao Yang, Feipeng Zhang, Fan Song, Ross C. Hardison, and Feng Yue at Penn State; and Galip Gürkan Yardımcı and William Stafford Noble at the University of Washington. The research was supported by the U.S. National Institutes of Health, a Computation, Bioinformatics, and Statistics (CBIOS) training grant at Penn State, and the Huck Institutes of the Life Sciences at Penn State.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Penn State Campus


    We teach students that the real measure of success is what you do to improve the lives of others, and they learn to be hard-working leaders with a global perspective. We conduct research to improve lives. We add millions to the economy through projects in our state and beyond. We help communities by sharing our faculty expertise and research.

    Penn State lives close by no matter where you are. Our campuses are located from one side of Pennsylvania to the other. Through Penn State World Campus, students can take courses and work toward degrees online from anywhere on the globe that has Internet service.

    We support students in many ways, including advising and counseling services for school and life; diversity and inclusion services; social media sites; safety services; and emergency assistance.

    Our network of more than a half-million alumni is accessible to students when they want advice and to learn about job networking and mentor opportunities as well as what to expect in the future. Through our alumni, Penn State lives all over the world.

    The best part of Penn State is our people. Our students, faculty, staff, alumni, and friends in communities near our campuses and across the globe are dedicated to education and fostering a diverse and inclusive environment.

  • richardmitnick 2:27 pm on December 19, 2017 Permalink | Reply
    Tags: 20 “loading” molecules called aminoacyl-tRNA synthetases, , Charles Carter, Genetics, Kurt Gödel's Theorem and the Chemistry of Life, Peter Wills, protein-like molecules rather than RNA may have been the planet’s first self-replicators, ,   

    From Quanta: “The End of the RNA World Is Near, Biochemists Argue” 

    Quanta Magazine
    Quanta Magazine

    December 19, 2017
    Jordana Cepelewicz

    A popular theory holds that life emerged from a rich chemical soup in which RNA was the original self-replicator. But a combination of peptides and RNA might have been more effective.
    Novikov Aleksey

    Four billion years ago, the first molecular precursors to life emerged, swirling about in Earth’s primordial soup of chemicals. Although the identity of these molecules remains a subject of fractious debate, scientists agree that the molecules would have had to perform two major functions: storing information and catalyzing chemical reactions. The modern cell assigns these responsibilities to its DNA and its proteins, respectively — but according to the narrative that dominates origin-of-life research and biology-textbook descriptions today, RNA was the first to play that role, paving the way for DNA and proteins to take over later.

    This hypothesis, proposed in the 1960s and dubbed the “RNA world” two decades later, is usually viewed as the most likely explanation for how life got its start. Alternative “worlds” abound, but they’re often seen as fallback theories, flights of fancy or whimsical thought experiments.

    That’s mainly because, theorizing aside, the RNA world is fortified by much more experimental evidence than any of its competitors have accumulated. Last month, Quanta Magazine reported on an alternative theory suggesting that protein-like molecules, rather than RNA, may have been the planet’s first self-replicators. But its findings were purely computational; the researchers have only just begun experiments to seek support for their claims.

    Now, a pair of researchers has put forth another theory — this time involving the coevolution of RNA and peptides — that they hope will shake the RNA world’s hold.

    Recent papers published in Biosystems and Molecular Biology and Evolution delineated why the RNA world hypothesis does not provide a sufficient foundation for the evolutionary events that followed. Instead, said Charles Carter, a structural biologist at the University of North Carolina, Chapel Hill, who co-authored the papers, the model represents “an expedient proposal.” “There’s no way that a single polymer could carry out all of the necessary processes we now characterize as part of life,” he added.

    And that single polymer certainly couldn’t be RNA, according to his team’s studies. The main objection to the molecule concerns catalysis: Some research has shown that for life to take hold, the mystery polymer would have had to coordinate the rates of chemical reactions that could differ in speed by as much as 20 orders of magnitude. Even if RNA could somehow do this in the prebiotic world, its capabilities as a catalyst would have been adapted to the searing temperatures — around 100 degrees Celsius — that abounded on early Earth. Once the planet started to cool, Carter claims, RNA wouldn’t have been able to evolve and keep up the work of synchronization. Before long, the symphony of chemical reactions would have fallen into disarray.

    Perhaps most importantly, an RNA-only world could not explain the emergence of the genetic code, which nearly all living organisms today use to translate genetic information into proteins. The code takes each of the 64 possible three-nucleotide RNA sequences and maps them to one of the 20 amino acids used to build proteins. Finding a set of rules robust enough to do that would take far too long with RNA alone, said Peter Wills, Carter’s co-author at the University of Auckland in New Zealand — if the RNA world could even reach that point, which he deemed highly unlikely. In Wills’ view, RNA might have been able to catalyze its own formation, making it “chemically reflexive,” but it lacked what he called “computational reflexivity.”

    “A system that uses information the way organisms use genetic information — to synthesize their own components — must contain reflexive information,” Wills said. He defined reflexive information as information that, “when decoded by the system, makes the components that perform exactly that particular decoding.” The RNA of the RNA world hypothesis, he added, is just chemistry because it has no means of controlling its chemistry. “The RNA world doesn’t tell you anything about genetics,” he said.

    Nature had to find a different route, a better shortcut to the genetic code. Carter and Wills think they’ve uncovered that shortcut. It depends on a tight feedback loop — one that would not have developed from RNA alone but instead from a peptide-RNA complex.

    Bringing Peptides Into the Mix

    Carter found hints of that complex in the mid-1970s, when he learned in graduate school that certain structures seen in most proteins are “right-handed.” That is, the atoms in the structures could have two equivalent mirror-image arrangements, but the structures all use just one. Most of the nucleic acids and sugars that make up DNA and RNA are right-handed, too. Carter began to think of RNA and polypeptides as complementary structures, and he modeled a complex in which “they were made for each other, like a hand in a glove.”

    This implied an elementary kind of coding, a basis for the exchange of information between the RNA and the polypeptide. He was on his way to sketching what that might have looked like, working backward from the far more sophisticated modern genetic code. When the RNA world, coined in 1986, rose to prominence, Carter admitted, “I was pretty ticked off.” He felt that his peptide-RNA world, proposed a decade earlier, had been totally ignored.

    Since then, he, Wills and others have collaborated on a theory that circles back to that research. Their main goal was to figure out the very simple genetic code that preceded today’s more specific and complicated one. And so they turned not just to computation but also to genetics.

    At the center of their theory are 20 “loading” molecules called aminoacyl-tRNA synthetases. These catalytic enzymes allow RNA to bond with specific amino acids in keeping with the rules of the genetic code. “In a sense, the genetic code is ‘written’ in the specificity of the active sites” of those enzymes, said Jannie Hofmeyr, a biochemist at Stellenbosch University in South Africa, who was not involved in the study.

    Lucy Reading-Ikkanda/Quanta Magazine

    Previous research showed that the 20 enzymes could be divided evenly into two groups of 10 based on their structure and sequence. These two enzyme classes, it turned out, have certain sequences that code for mutually exclusive amino acids — meaning that the enzymes had to have arisen from complementary strands of the same ancient gene. Carter, Wills and their colleagues found that in this scenario, RNA coded for peptides using a set of just two rules (or, in other words, using just two types of amino acids). The resulting peptide products ended up enforcing the very rules that governed the translation process, thus forming the tight feedback loop the researchers knew would be the linchpin of the theory.

    Gödel’s Theorem and the Chemistry of Life

    Carter sees strong parallels between this kind of loop and the mathematical one described by the philosopher and mathematician Kurt Gödel, whose “incompleteness” theorem states that in any logical system that can represent itself, statements will inevitably arise that cannot be shown to be true or false within that system. “I believe that the analogy to Gödel’s theorem furnishes a quite strong argument for inevitability,” Carter said.

    In their recent papers, Carter and Wills show that their peptide-RNA world solves gaps in origin-of-life history that RNA alone can’t explain. “They provide solid theoretical and experimental evidence that peptides and RNA were jointly involved in the origin of the genetic code right from the start,” Hofmeyr said, “and that metabolism, construction through transcription and translation, and replication must have coevolved.”

    Of course, the Carter-Wills model begins with the genetic code, the existence of which presupposes complex chemical reactions involving molecules like transfer RNA and the loading enzymes. The researchers claim that the events leading up to their proposed scenario involved RNA and peptides interacting (in the complex that Carter described in the 1970s, for example). Yet that suggestion still leaves many open questions about how that chemistry began and what it looked like.

    To answer these questions, theories abound that move far beyond the RNA world. In fact, some scientists take an approach precisely opposite to that of Carter and Wills: They think instead that the earliest stages of life did not need to begin with anything resembling the kind of chemistry seen today. Doron Lancet, a genomics researcher at the Weizmann Institute of Science in Israel, posits an alternative theory that rests on assemblies of lipids that catalyze the entrance and exit of various molecules. Information is carried not by genetic sequences, but rather by the lipid composition of such assemblies.

    Just like the model proposed by Carter and Wills, Lancet’s ideas involve not one type of molecule but a huge variety of them. “More and more bits of evidence are accumulating,” Lancet said, “that can make an alternative hypothesis be right.” The jury is still out on what actually transpired at life’s origins, but the tide seems to be turning away from a story dedicated solely to RNA.

    “We should put only a few of our eggs in the RNA world basket,” Hofmeyr said.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

    • stewarthoughblog 2:02 am on December 20, 2017 Permalink | Reply

      It is about time that RNA nonsense comes to an end. There is admittedly considerable scientific knowledge that has and can still be gained by studying RNA macromolecules, but the desperation of naturalists proposing it either as the source of first life is intellectually insulting. RNA’s complexity may be assemblable in intelligent design highly managed labs environments, but ridiculous to consider possible in any geochemically relevant primordial environment. RNA is easily mutated, highly reactive, and only an intermediate macromolecule restricted by the protein catch-22.

      Frustratingly, the desperation continues with propositions of lipid collective assembly, but at least science appears to coming to its senses about RNA.


  • richardmitnick 1:03 pm on December 16, 2017 Permalink | Reply
    Tags: , , Experiments with zebrafish, Gdf3, Genetic instructions from mom set the pattern for embryonic development, Genetics, If gdf3 is not supplied to the egg by the mother the fertilized egg cannot produce two of the three major types of cells required for development, mRNAs-messenger RNAs, Ndr1 and Ndr2 are required to form the mesoderm and endoderm, , TGF-beta family of cell-signaling molecules, Vg1   

    From Princeton University Research Blog: “Genetic instructions from mom set the pattern for embryonic development” 

    Princeton University
    Princeton University Research Blog

    December 15, 2017
    Department of Molecular Biology

    No image caption or credit.

    A new study indicates an essential role for a maternally inherited gene in embryonic development. The study found that zebrafish that failed to inherit specific genetic instructions from mom developed fatal defects earlier in development, even if the fish could make their own version of the gene. The study by researchers at Princeton University was published Nov. 15 in the journal eLife.

    When female animals form egg cells inside their ovaries, they deposit messenger RNAs (mRNAs) – a sort of genetic instruction set – in the egg cell cytoplasm. After fertilization, these maternally supplied mRNAs can be translated into proteins required for the early stages of embryonic development, before the embryo is able to produce mRNAs and proteins of its own.

    More than thirty years ago, researchers discovered that mRNAs encoding a protein called Vg1 are deposited in the cytoplasm of frog eggs. “vg1 is famous for being one of the first recognized maternal mRNAs,” said Rebecca Burdine, associate professor of molecular biology at Princeton. “Many papers have been written on how this RNA is localized and regulated, but it was never clear what the Vg1 protein actually does in the developing embryo.”

    Compared to a normal zebrafish embryo (right), an embryo lacking gdf3 (left) inherited from mom shows major defects resulting from its inability to form mesoderm and endoderm cells early in development. Credit: Pelliccia et al., 2017.

    In the study, Burdine and two graduate students Jose Pelliccia and Granton Jindal used CRISPR/Cas9 gene editing to remove Vg1, known as Gdf3 in zebrafish. Embryos that couldn’t produce any Gdf3 of their own–but received a healthy portion of the gdf3 mRNA from their mothers–developed perfectly normally. But embryos that didn’t receive maternal gdf3 mRNA showed major defects early on in their development, dying just three days after fertilization.

    “If gdf3 is not supplied to the egg by the mother, the fertilized egg cannot produce two of the three major types of cells required for development,” Burdine said. “The embryos lack all [cell types known as] mesoderm and endoderm and are left with skin and some neural tissue, [which derive from the third major cell type, the ectoderm].”

    Vg1/Gdf3 is a member of the TGF-beta family of cell-signaling molecules. Two other members of this family, Ndr1 and Ndr2, are required to form the mesoderm and endoderm early in zebrafish development. Embryos lacking maternally supplied gdf3 look very similar to embryos lacking both of these proteins, which are analogous to the Nodal 1 and 2 proteins in mammals.

    The researchers found that maternal gdf3 is required for Ndr1 and Ndr2 to signal at the levels necessary to properly induce the formation of mesoderm and endoderm cells in early zebrafish embryos. In the absence of gdf3, Ndr1 and Ndr2 signaling is dramatically reduced and embryonic development goes awry.

    Nodal signaling is also required later in zebrafish development when it helps to establish differences between the left and right sides of the developing embryo. It does this, in part, by directing the formation of an organ known as Kupffer’s vesicle, whose asymmetric shape helps determine the embryo’s left and right sides. Subsequently, Nodal signaling induces the expression of a third Nodal protein, called southpaw, in a group of mesoderm cells on the left-hand side of the embryo.

    To investigate whether maternally supplied gdf3 mRNA also plays a role in left-right patterning, the researchers used a series of experimental tricks to supply embryos with enough Gdf3 protein to form the mesoderm and endoderm and survive until the later stages of embryonic development.

    As predicted, these embryos showed defects in left-right patterning. Their Kupffer’s vesicles were abnormally symmetric in shape, and southpaw expression was greatly reduced, suggesting that gdf3 is also required for optimal Nodal signaling during later stages of embryonic development. At this stage, however, embryonic gdf3 seems to be capable of doing the job if maternally supplied gdf3 is absent.

    Nodal and Vg1 proteins are known to bind to each other in other species. “Thus, we hypothesize that Gdf3 combines with Ndr1 and Ndr2 to facilitate Nodal signaling during zebrafish development, acting as an essential factor in embryonic patterning,” said Pelliccia, a graduate student in molecular biology. Co-author Jindal earned his Ph.D. in chemical and biological engineering in 2017.

    At the same time as Burdine and colleagues, two other research groups, led by Joe Yost at the University of Utah and Alex Schier at Harvard University, made similar findings on the role of gdf3 during zebrafish development. “All three groups worked together to co-submit and co-publish in eLife, allowing the students involved to all get credit for their hard work,” Burdine said. “It’s a great example of how science should be done.”

    The research was funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (grant R01HD048584) and the National Science Foundation (graduate research fellowship DGE 1148900).

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition
    Princeton University Campus

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

    Princeton Shield

  • richardmitnick 5:02 pm on December 14, 2017 Permalink | Reply
    Tags: Amino acids are the building blocks of proteins, , Est1 is a subunit of a protein (an enzyme) called telomerase, Genetics, Identifing previously undiscovered activities for a protein, , ,   

    From Salk: “Revealing the best-kept secrets of proteins” 

    Salk Institute bloc

    Salk Institute for Biological Studies

    December 14, 2017
    No writer credit

    From left: John Lubin, Vicki Lundblad and Tim Tucey. Credit: Salk Institute

    Salk scientists develop new approach to identify important undiscovered functions of proteins.

    In the bustling setting of the cell, proteins encounter each other by the thousands. Despite the hubbub, each one manages to selectively interact with just the right partners, thanks to specific contact regions on its surface that are still far more mysterious than might be expected, given decades of research into protein structure and function.

    Now, Salk Institute scientists have developed a new method to discover which surface contacts on proteins are critical for these cellular interactions. The novel approach shows that essential new functions can be uncovered even for well-studied proteins, and has significant implications for therapeutic drug development, which depends heavily on how drugs physically interact with their cellular targets. The paper appeared in the early online version of Genetics in late November, and is slated for publication in the January print edition of the journal.

    “This paper illustrates the power of this methodology,” says senior author Vicki Lundblad, holder of the Ralph S. and Becky O’Conner Chair. “It can not only identify previously undiscovered activities for a protein, but it can also pinpoint the exact amino acids on a protein surface that perform these new functions.”

    Amino acids are the building blocks of proteins. Their specific linear arrangement determines the identity of a protein, and clusters of them on the protein’s surface serve as contacts, regulating how that protein interacts with other proteins and molecules. Lundblad and her colleagues suspected that, despite decades of work deciphering the mysteries of proteins, the extent of this regulatory landscape on the surface of proteins had remained mostly unexplored. Long ago, her group unexpectedly discovered one such regulatory amino acid cluster, while searching one-by-one through 300,000 mutant yeast cells. Although that work opened up a new area of research in the field of telomere biology, Lundblad was determined to figure out a more robust methodology that could rapidly uncover many more of these unexplored protein surfaces.

    Enter John Lubin, now a PhD student in Lundblad’s lab, who began working with her as an undergraduate.

    “My task was to figure out how to search through 30 mutant yeast cells, instead of 300,000, to discover new activities for a protein,” says Lubin, the paper’s co–first author. Timothy Tucey, the other co–first author, was a postdoctoral researcher in Lundblad’s group and is now at Monash University.

    Together they turned to a protein called Est1, which Lundblad had discovered in yeast as a postdoctoral researcher in 1989. Est1 is a subunit of a protein (an enzyme) called telomerase, which keeps the protective caps at the ends of chromosomes (known as telomeres) from getting too short. As the first subunit of telomerase to be discovered, Est1 has been subjected to intensive study by many research groups.

    The Salk team’s approach involved introducing a small, but customized, set of mutations into yeast cells that would selectively disrupt surface contacts on the cells’ Est1 protein. The team then analyzed the cells to see what effect, if any, the various mutations had. Abnormalities resulting from a specific mutation would suggest what the role of the unmutated version was. To do so, they used a genetic trick, by flooding the cells with each mutant protein, and looking for the rare mutant protein that could interfere with cell function, as their previous work had shown that this would preferentially target the protein surface.

    Lundblad’s team discovered four functions for Est1 through this approach. Impairment of any of these four functions by mutations to Est1’s surface amino acids, the scientists found, resulted in cells that had critically short telomeres, indicating specific roles for the Est1 contacts in the telomerase complex.

    “What has us excited about this technique is that it can be applied to numerous proteins,” says Lundblad. “In particular, many therapeutic drugs rely on being able to access a very specific location on a protein surface, which we suspect can be uncovered by this method.”

    Using this approach, her team has already uncovered new functions for a set of proteins that regulate the stability of the genome, and has also applied for grants that fund research into drug targets.

    The work was funded by the National Institutes of Health, the National Science Foundation, the Rose Hills Foundation and the Glenn Center for Aging Research.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Salk Institute Campus

    Every cure has a starting point. Like Dr. Jonas Salk when he conquered polio, Salk scientists are dedicated to innovative biological research. Exploring the molecular basis of diseases makes curing them more likely. In an outstanding and unique environment we gather the foremost scientific minds in the world and give them the freedom to work collaboratively and think creatively. For over 50 years this wide-ranging scientific inquiry has yielded life-changing discoveries impacting human health. We are home to Nobel Laureates and members of the National Academy of Sciences who train and mentor the next generation of international scientists. We lead biological research. We prize discovery. Salk is where cures begin.

  • richardmitnick 3:28 pm on December 14, 2017 Permalink | Reply
    Tags: , , Genetics, Single-stranded DNA and RNA origami go live,   

    From Wyss: “Single-stranded DNA and RNA origami go live” 

    Harvard bloc tiny
    Wyss Institute bloc
    Wyss Institute

    December 14, 2017
    Benjamin Boettner

    Single-stranded origami technology is based on design rules that can be used to cross DNA strands in and out of single stranded regions to build large nanostructures. Credit: Molgraphics.

    Like genetic DNA (and RNA) in nature, these engineered nanotechnological devices are also made up of strands that are comprised of the four bases known in shorthand as A, C, T, and G. Regions within those strands can spontaneously fold and bind to each other via short complementary base sequences in which As from one sequence specifically bind to Ts from another sequence, and Cs to Gs. Researchers at the Wyss Institute of Biologically Inspired Engineering and elsewhere have used these features to design self-assembling nanostructures such as scaffolded DNA origami and DNA bricks with ever-growing sizes and complexities that are becoming useful for diverse applications. However, the translation of these structures into medical and industrial applications is still challenging, partially because these multi-stranded systems are prone to local defects due to missing stands. In addition, they self-assemble from hundreds to thousands of individual DNA sequences that each need to be verified and tested for high-precision applications, and whose expensive synthesis often produces undesired side products.

    Now, a novel approach published in Science by a collaborative team of researchers from the Wyss Institute, Arizona State University, and Autodesk for the first time enables the design of complex single-stranded DNA and RNA origami that can autonomously fold into diverse, stable, user-defined structures. In contrast to the synthesis of multi-stranded nanostructures, these entirely new types of origami are folded from one single strand, which can be replicated in living cells, allowing their potential low-cost production at large scales and with high purities, opening entirely new opportunities for diverse applications such as drug delivery and nanofabrication.

    Earlier generations of larger-sized origami are composed of a central scaffold strand whose folding and stability requires more than two hundred short staple strands that bridge distant parts of the scaffold and fix them in space. “In contrast to traditional scaffolded origamis, which are assembled from hundreds of components, our new approach allows us to reliably design and synthesize stable single-stranded and self-folding origami,” said Wyss Institute Core Faculty member and corresponding author Peng Yin, Ph.D. “Our fundamentally new approach relies on single-strand folding, rather than multi-component assembly, to produce large nanostructures. This, together with the ability to basically clone and multiply the single component strand in bacteria, presents a game-changing advance in DNA nanotechnology that greatly enhances single-stranded origami’s potential for real-world applications.” Yin is also co-lead of the Wyss Institute’s Molecular Robotics Initiative and Professor of Systems Biology at Harvard Medical School (HMS).

    To first enable the production of single-stranded and stable DNA-based origami with distinct folding patterns, the team had to overcome several challenges. In a large DNA strand that goes through a complex folding process, many sequences need to accurately pair up with sequences that are far away from each other. If this process does not happen in an orderly and precise fashion, the strand gets tangled and forms unspecific knots along the way, rendering it useless. “To avoid this problem, we identified new design rules that we can use to cross DNA strands between different double-stranded regions and developed a web-based automated design tool that allows researchers to integrate many of these events into a folding path leading up to a large knot-free nanocomplex,” said Dongran Han, Ph.D., the study’s first author and a Postdoctoral Fellow on Yin’s team.

    This schematic shows how a single strand of DNA can be programmed to self-fold into a large nanostructure, like, for example, that of a heart. The Wyss Institute researchers used atomic force microscopy to visualize the heart-shaped and a variety of other nanostructures, which can inexpensively and consistently be multiplied using bacteria as nanofactories. Credit: Wyss Institute at Harvard University.

    The largest DNA origami structures created previously were assembled by synthesizing all their constituent sequences individually in vitro and by mixing them together. As a key feature of the new design process, the single-strandedness of the DNA origami allowed the researchers to introduce DNA sequences stably into E. coli bacteria to inexpensively and accurately replicate them with every cell division. “This could greatly facilitate the development of single-stranded origami for high-precision nanotech like drug delivery vehicles, for example, as only a single easy-to-produce molecule needs to be validated and approved,” said Han.

    Finally, the team also adapted single-stranded origami technology to RNA, which as a different nucleic acid material offers certain advantages including, for example, even higher production levels in bacteria, and usefulness for potential intra-cellular and therapeutic RNA applications. Translating the approach to RNA also scales up the size and complexity of synthetic RNA structures 10-fold compared to previous structures made from RNA.

    Their proof-of-concept analysis also proved that protruding DNA loops can be precisely positioned and be used as handles for the attachment of functional proteins. In future developments, single-stranded origami could thus be potentially functionalized by attaching enzymes, fluorescent probes, metal particles, or drugs either to their surfaces or within cavities inside. This could effectively convert single-stranded origami into nanofactories, light-sensing and emitting optical devices, or drug delivery vehicles.

    In this disc-shaped single-stranded DNA origami, visualized with atomic force microscopy, individual protruding hairpins have been introduced at positions that together compose a “smiley face” and that can be functionalized with useful molecules and activities. Credit: Wyss Institute at Harvard University

    “This new advance by the Wyss Institute’s Molecular Robotics Initiative transforms an exciting laboratory research methodology into a potentially transformative technology that can be manufactured at large scale by leveraging the biological machinery of living cells. This work opens a path by which DNA nanotechnology and origami approaches may be translated into products that meet real-world challenges,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children’s Hospital, as well as Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences (SEAS).

    The results announced today establish DNA nanotechnology as a viable alternative approach for applications that have the potential to benefit all of us and the Nation as a whole,” said Jim Kurose, Assistant Director of the National Science Foundation’s (NSF) Directorate for Computer and Information Science and Engineering (CISE). “We are delighted this work was supported by NSF’s Expeditions in Computing program, which has, over the last decade funded large teams of researchers to pursue ambitious, fundamental research agendas that help define and shape the future of computer and information science and engineering, and impact our national competitiveness.

    Besides Yin and Han, the study includes corresponding authors Hao Yan, Ph.D., and Fei Zhang, Ph.D., Director and Assistant Professor at the Biodesign Center for Molecular Design and Biomimetics at Arizona State University, Tempe, respectively, and Byoungkwon An, Ph.D., Principle Research Scientist at Autodesk Research, San Francisco; Shuoxing Jiang, Ph.D., Xiaodong Qi, and Yan Liu, Ph.D., Assistant Professor from the Biodesign Institute; Cameron Myhrvold, Ph.D., Bei Wang, and Mingjie Dai, Ph.D., past and present members of Yin’s team at the Wyss Institute; and Maxwell Bates, who worked with An. The study was funded by the Office of Naval Research, the Army Research Office, the National Science Foundation’s Expeditions in Computing program, and the Wyss Institute for Biologically Inspired Engineering.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Wyss Institute campus

    The Wyss (pronounced “Veese”) Institute for Biologically Inspired Engineering uses Nature’s design principles to develop bioinspired materials and devices that will transform medicine and create a more sustainable world.

    Working as an alliance among Harvard’s Schools of Medicine, Engineering, and Arts & Sciences, and in partnership with Beth Israel Deaconess Medical Center, Boston Children’s Hospital, Brigham and Women’s Hospital, Dana Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Tufts University, and Boston University, the Institute crosses disciplinary and institutional barriers to engage in high-risk research that leads to transformative technological breakthroughs.

  • richardmitnick 9:42 am on November 30, 2017 Permalink | Reply
    Tags: An additional pair of bases—X and Y successfully added to DNA, , , , , Genetics, , Scripps   

    From Science Magazine: “Scientists just added two functional letters to the genetic code” 

    Science Magazine

    Nov. 29, 2017
    Giorgia Guglielmi

    James Cavallini/Science Source

    All life forms on Earth use the same genetic alphabet of the bases A, T, C, and G—nitrogen-containing compounds that constitute the building blocks of DNA and spell out the instructions for making proteins. Now, scientists have developed the first bacterium to use extra letters, or unnatural bases, to build proteins. The new research builds on the team’s previous efforts to expand the natural genetic code. In 2014, the scientists engineered Escherichia coli bacteria (pictured) to incorporate an additional pair of bases—X and Y—into their DNA. The bacteria could store the unnatural bases and pass them onto daughter cells. But to be useful, these bases need to be transcribed into RNA molecules and then translated into proteins. So in the new study the researchers slipped the “alien” pair of bases into bacterial genes that also contained traditional bases. The microbes successfully “read” DNA containing the unnatural bases and transcribed it into RNA molecules. What’s more, the bacteria could use these RNA molecules to produce a variant of green fluorescent protein that contains unnatural amino acids, the team reports today in Nature. The traditional four DNA bases code for 20 amino acids, but the addition of X and Y could produce up to 152 amino acids, which might become building blocks for new drugs and novel materials, the scientists say.

    The scientists behind the work at the Scripps Research Institute have already formed a company to try to use the technique to develop new antibiotics, vaccines and other products, though a lot more work needs to be done before this is practical.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

Compose new post
Next post/Next comment
Previous post/Previous comment
Show/Hide comments
Go to top
Go to login
Show/Hide help
shift + esc
%d bloggers like this: