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Cambridge, MA, United States

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Cambridge, MA, United States

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News Article | November 28, 2016
Site: www.eurekalert.org

Each animal species hosts its own, unique community of microbes that can significantly improve its health and fitness. That is the implication of a laboratory study that investigated four different animal groups and their associated microbiota. The research found that each species within the group has a distinctive microbial community. Additional experiments with two of the groups - one mammal and one insect - demonstrated that individuals possessing their natural microbiota digested food more efficiently and had greater survival than those that were implanted with the microbial communities of closely related species. "Previous research has tended to concentrate on the negative effects of microbes. In this case we are showing that whole communities of microbes have positive effects as well," said Vanderbilt graduate student Andrew Brooks, co-first author of the study. The paper describing the study's results is titled "Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History" and it was published Nov. 18 in the journal PLOS Biology. "We coined the term phylosymbiosis a couple of years ago to denote the fact that evolution can act on host species and change their microbial communities," said Seth Bordenstein, associate professor of biological sciences and pathology, microbiology, and immunology at Vanderbilt University, who directed the study. Postdoctoral researcher Kevin Kohl and Robert Brucker at Harvard University were other co-first authors, and another participant, Edward Van Opstal, is a graduate student at Vanderbilt. All animals teem with thousands of different species of microbes collectively called the microbiome. Biologists are actively investigating the extent to which these invisible communities play a significant role in the host animal's life and evolution. Answering this question is complicated by a number of factors including environment, diet, age, sex, host genetics and the wide variety of behaviors of the microbial species involved. In the attempt to unravel the evolutionary relationship between hosts and their microbiomes, the Vanderbilt biologists investigated four groups of animals: deer mice, fruit flies, mosquitoes and jewel wasps. First, the researchers characterized the microbiota of 24 closely related species in the four groups. Then they used statistical analyses to determine that the microbial communities form a "tree of life" that parallels that of their hosts. They also applied the same analysis to existing data on the microbiomes of great apes and found a similar pattern. "The evidence indicates that the relationship between hosts and microbiomes is not always random but can be shaped by host evolution," said Bordenstein. Next the biologists raised colonies of deer mice and jewel wasps in the laboratory under highly controlled conditions. In each group, they transplanted the microbiomes from closely related species into some of the individuals and then compared how rapidly they grew and how long they lived compared to those who had their microbiota removed and those that retained their natural set of microbes. In this fashion, they discovered that when the microbial communities from house mice and different deer mice species were transplanted into one species of deer mouse, its ability to digest food was significantly reduced. As a result, they had to eat more mouse chow to get the energy they required. Similarly, when jewel wasps received transplants of microbial communities from related wasp species, they had lower survival rates than those that had their natural microbiota. "Plants and animals evolved in a planet dominated by microbial life," said Bordenstein. "So they had no choice but to tolerate microbes and, as we are now discovering, they also evolved the capacity to 'garden' them in order to enhance their health and fitness." Further information can be found at the Bordenstein Lab. This research was supported by National Science Foundation grants 1456778, 1046149, 1400456, National Institutes of Health grant 5T32GM080178, and the Rowland Institute at Harvard University Junior Fellowship.


Abstract: From the tension of contracting muscle fibers to hydrodynamic stresses within flowing blood, molecules within our bodies are subject to a wide variety of mechanical forces that directly influence their form and function. By analyzing the responses of single molecules under conditions where they experience such forces we can develop a better understanding of many biological processes, and potentially, develop more accurately acting drugs. But up until now experimental analysis of single molecule interactions under force have been expensive, tedious and difficult to perform because it requires use of sophisticated equipment, such as an atomic force microscope or optical tweezers, which only permit analysis of one molecule at a time. Now, a research team led by Wesley Wong at Harvard's Wyss Institute for Biologically Inspired Engineering and Boston Children's Hospital has made a major advance by developing an inexpensive method that permits analysis of the force responses of thousands of similar molecules simultaneously. They report in Nature Communications how programmable DNA nanoswitches can be used in combination with a newly designed miniaturized Centrifuge Force Microscope (CFM) as a highly reliable tool to observe thousands of individual molecules and their responses to mechanical forces in parallel. "This new combined approach will allow us and others to examine how single molecule complexes behave when they are thrown out of their equilibrium by the tunable force generated in our newly designed CFM. By basing this instrument on something that most researchers already have and use -- the benchtop centrifuge -- we hope to make single-molecule force measurements accessible to almost everyone," said Wong, Ph.D., who is a Wyss Institute Associate Faculty member and the study's senior author. He is also Assistant Professor at Harvard Medical School in the Departments of Biological Chemistry & Molecular Pharmacology and Pediatrics, and Investigator in the Program in Cellular and Molecular Medicine at Boston Children's Hospital. Earlier efforts led by Wong at the Rowland Institute at Harvard introduced the first CFM in 2010, which was a highly specialized instrument that carried out high-throughput precision force measurements on single molecules by tethering them to beads and pulling at them using centrifugal force. In his latest CFM iteration, Wong and his team developed a way to carry out the same technique with similar precision using a small inexpensive microscope made from easy-to-assemble elements and 3D printed parts that can be inserted into the swinging bucket of a standard benchtop centrifuge found in virtually all biomedical research laboratories. In addition, the team increased the robustness and accuracy of the assay by integrating thousands of so-called DNA nanoswitches, linear DNA strands with pairs of interacting molecules that are associated with two sequences in their middle and that, in addition, by binding to each other create an internal DNA loop; the nanoswitches' ends are tethered to the surface of the sample on one side and to beads on the other. "By applying a defined range of centrifugal forces to the beads we can provoke the rupture of the molecular complexes generating the looped DNA structures which will be registered by the camera-coupled lens. Importantly, using DNA nanoswitches as a stable scaffold allows us to repeat this process multiple times with the very same molecule in temperature-controlled conditions which greatly enhances our accuracy in determining the heterogeneity that a single molecular interaction can display," said Darren Yang, the first author of the study and a Graduate Student in Wong's team. In future research, bead-associated DNA nanoswitches can be employed to repeatedly assemble and rupture many different biomolecular complexes and to define the mechanical forces that control them. "The integrated DNA nanoswitches are very modular, and can be functionalized with many different biomolecules in essentially a plug-and-play fashion, to enable a wide variety of molecular interactions to be studied with high throughput and reliability," added Wong. Next, the Wyss scientists are planning to apply their DNA nanoswitch-enhanced miniature CFM to the investigation of select biomedically relevant and force-dependent molecular interactions such as protein interactions governing blood clotting or hearing. "Wong's team has created a new technology platform that greatly reduces the cost of single molecule force analysis and makes it widely accessible to the scientific community. In addition to increasing our understanding of basic molecular structure-function relations, it may prove to be a valuable tool for drug development," said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Vascular Biology program at Boston Children's Hospital, and Professor of Bioengineering at SEAS. About Wyss Institute for Biologically Inspired Engineering at Harvard The Wyss Institute for Biologically Inspired Engineering at Harvard University uses Nature's design principles to develop bioinspired materials and devices that will transform medicine and create a more sustainable world. Wyss researchers are developing innovative new engineering solutions for healthcare, energy, architecture, robotics, and manufacturing that are translated into commercial products and therapies through collaborations with clinical investigators, corporate alliances, and formation of new startups. The Wyss Institute creates transformative technological breakthroughs by engaging in high risk research, and crosses disciplinary and institutional barriers, working as an alliance that includes Harvard's Schools of Medicine, Engineering, Arts & Sciences and Design, and in partnership with Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Boston Children's Hospital, Dana-Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, Charité -- Universitätsmedizin Berlin, University of Zurich and Massachusetts Institute of Technology. About Harvard Medical School Harvard Medical School has more than 7,500 full-time faculty working in 11 academic departments located at the School's Boston campus or in one of 47 hospital-based clinical departments at 16 Harvard-affiliated teaching hospitals and research institutes. Those affiliates include Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Cambridge Health Alliance, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Pilgrim Health Care, Hebrew Senior Life, Joslin Diabetes Center, Judge Baker Children's Center, Massachusetts Eye and Ear Infirmary, Massachusetts General Hospital, McLean Hospital, Mount Auburn Hospital, Schepens Eye Research Institute, Spaulding Rehabilitation Hospital and VA Boston Healthcare System. About Boston Children's Hospital Boston Children's Hospital is home to the world's largest research enterprise based at a pediatric medical center, where its discoveries have benefited both children and adults since 1869. More than 1,100 scientists, including seven members of the National Academy of Sciences, 14 members of the Institute of Medicine and 14 members of the Howard Hughes Medical Institute comprise Boston Children's research community. Founded as a 20-bed hospital for children, Boston Children's today is a 395-bed comprehensive center for pediatric and adolescent health care. Boston Children's is also the primary pediatric teaching affiliate of Harvard Medical School. For more information about research and clinical innovation at Boston Children's Hospital, visit: http://vectorblog.org. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.


News Article | March 17, 2016
Site: phys.org

The benchtop CFM device, consisting of the CFM unit itself (on the top), parts for transmitting the camera signal as well as a battery (on the right), fits into two standard buckets of a common laboratory centrifuge that are balanced by counterweights in the respective opposite buckets. Credit: Wyss Institute at Harvard University. From the tension of contracting muscle fibers to hydrodynamic stresses within flowing blood, molecules within our bodies are subject to a wide variety of mechanical forces that directly influence their form and function. By analyzing the responses of single molecules under conditions where they experience such forces we can develop a better understanding of many biological processes, and potentially, develop more accurately acting drugs. But up until now experimental analysis of single molecule interactions under force have been expensive, tedious and difficult to perform because it requires use of sophisticated equipment, such as an atomic force microscope or optical tweezers, which only permit analysis of one molecule at a time. Now, a research team led by Wesley Wong at Harvard's Wyss Institute for Biologically Inspired Engineering and Boston Children's Hospital has made a major advance by developing an inexpensive method that permits analysis of the force responses of thousands of similar molecules simultaneously. They report in Nature Communications how programmable DNA nanoswitches can be used in combination with a newly designed miniaturized Centrifuge Force Microscope (CFM) as a highly reliable tool to observe thousands of individual molecules and their responses to mechanical forces in parallel. "This new combined approach will allow us and others to examine how single molecule complexes behave when they are thrown out of their equilibrium by the tunable force generated in our newly designed CFM. By basing this instrument on something that most researchers already have and use—the benchtop centrifuge—we hope to make single-molecule force measurements accessible to almost everyone," said Wong, Ph.D., who is a Wyss Institute Associate Faculty member and the study's senior author. He is also Assistant Professor at Harvard Medical School in the Departments of Biological Chemistry & Molecular Pharmacology and Pediatrics, and Investigator in the Program in Cellular and Molecular Medicine at Boston Children's Hospital. Earlier efforts led by Wong at the Rowland Institute at Harvard introduced the first CFM in 2010, which was a highly specialized instrument that carried out high-throughput precision force measurements on single molecules by tethering them to beads and pulling at them using centrifugal force. In his latest CFM iteration, Wong and his team developed a way to carry out the same technique with similar precision using a small inexpensive microscope made from easy-to-assemble elements and 3D printed parts that can be inserted into the swinging bucket of a standard benchtop centrifuge found in virtually all biomedical research laboratories. In addition, the team increased the robustness and accuracy of the assay by integrating thousands of so-called DNA nanoswitches, linear DNA strands with pairs of interacting molecules that are associated with two sequences in their middle and that, in addition, by binding to each other create an internal DNA loop; the nanoswitches' ends are tethered to the surface of the sample on one side and to beads on the other. "By applying a defined range of centrifugal forces to the beads we can provoke the rupture of the molecular complexes generating the looped DNA structures which will be registered by the camera-coupled lens. Importantly, using DNA nanoswitches as a stable scaffold allows us to repeat this process multiple times with the very same molecule in temperature-controlled conditions which greatly enhances our accuracy in determining the heterogeneity that a single molecular interaction can display," said Darren Yang, the first author of the study and a Graduate Student in Wong's team. In future research, bead-associated DNA nanoswitches can be employed to repeatedly assemble and rupture many different biomolecular complexes and to define the mechanical forces that control them. "The integrated DNA nanoswitches are very modular, and can be functionalized with many different biomolecules in essentially a plug-and-play fashion, to enable a wide variety of molecular interactions to be studied with high throughput and reliability," added Wong. Next, the Wyss scientists are planning to apply their DNA nanoswitch-enhanced miniature CFM to the investigation of select biomedically relevant and force-dependent molecular interactions such as protein interactions governing blood clotting or hearing. "Wong's team has created a new technology platform that greatly reduces the cost of single molecule force analysis and makes it widely accessible to the scientific community. In addition to increasing our understanding of basic molecular structure-function relations, it may prove to be a valuable tool for drug development," said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and the Vascular Biology program at Boston Children's Hospital, and Professor of Bioengineering at SEAS. Explore further: Single-molecule manipulation for the masses


Wilson L.,Rowland Institute at Harvard | Zhang R.,Rowland Institute at Harvard
Optics Express | Year: 2012

The Rayleigh-Sommerfeld back-propagation method is a fast and highly flexible volume reconstruction scheme for digital holographic microscopy. We present a new method for 3D localization of weakly scattering objects using this technique. A well-known aspect of classical optics (the Gouy phase shift) can be used to discriminate between objects lying on either side of the holographic image plane. This results in an unambiguous model-free measurement of the axial coordinate of microscopic samples and is demonstrated both on an individual colloidal sphere, and on a more complex object -a layer of such particles in close contact. © 2012 Optical Society of America.


Turner L.,Rowland Institute at Harvard | Stern A.S.,Rowland Institute at Harvard | Berg H.C.,Rowland Institute at Harvard
Journal of Bacteriology | Year: 2012

Bacterial flagellar filaments grow at their distal ends, from flagellin that travels through a central channel~2 nm in diameter. The flagellin is extruded from the cytoplasm by a pump powered by a proton motive force (PMF). We measured filament growth in cells near the mid-exponential-phase with flagellin bearing a specific cysteine-for-serine substitution, allowing filaments to be labeled with sulfhydryl-specific fluorescent dyes. We labeled filaments first with a green maleimide dye and then, following an additional period of growth, with a red maleimide dye. The contour lengths of the green and red segments were measured. The average lengths of red segments (~2.3 μm) were the same regardless of the lengths of the green segments from which they grew (ranging from less than 1 to more than 9 μmin length). Thus, flagellar filaments do not grow at a rate that decreases exponentially with length, as formerly supposed. If flagellar filaments were broken by viscous shear, the broken filaments continued to grow. Identical results were obtained whether flagellin was expressed from fliC on the chromosome under the control of its native promoter or on a plasmid under the control of the arabinose promoter. © 2012, American Society for Microbiology.


Hoch J.C.,University of Connecticut Health Center | Maciejewski M.W.,University of Connecticut Health Center | Mobli M.,University of Queensland | Schuyler A.D.,University of Connecticut Health Center | Stern A.S.,Rowland Institute at Harvard
Accounts of Chemical Research | Year: 2014

NMR spectroscopy is one of the most powerful and versatile analytic tools available to chemists. The discrete Fourier transform (DFT) played a seminal role in the development of modern NMR, including the multidimensional methods that are essential for characterizing complex biomolecules. However, it suffers from well-known limitations: chiefly the difficulty in obtaining high-resolution spectral estimates from short data records. Because the time required to perform an experiment is proportional to the number of data samples, this problem imposes a sampling burden for multidimensional NMR experiments. At high magnetic field, where spectral dispersion is greatest, the problem becomes particularly acute. Consequently multidimensional NMR experiments that rely on the DFT must either sacrifice resolution in order to be completed in reasonable time or use inordinate amounts of time to achieve the potential resolution afforded by high-field magnets.Maximum entropy (MaxEnt) reconstruction is a non-Fourier method of spectrum analysis that can provide high-resolution spectral estimates from short data records. It can also be used with nonuniformly sampled data sets. Since resolution is substantially determined by the largest evolution time sampled, nonuniform sampling enables high resolution while avoiding the need to uniformly sample at large numbers of evolution times. The Nyquist sampling theorem does not apply to nonuniformly sampled data, and artifacts that occur with the use of nonuniform sampling can be viewed as frequency-aliased signals. Strategies for suppressing nonuniform sampling artifacts include the careful design of the sampling scheme and special methods for computing the spectrum. Researchers now routinely report that they can complete an N-dimensional NMR experiment 3N-1 times faster (a 3D experiment in one ninth of the time). As a result, high-resolution three- and four-dimensional experiments that were prohibitively time consuming are now practical. Conversely, tailored sampling in the indirect dimensions has led to improved sensitivity.Further advances in nonuniform sampling strategies could enable further reductions in sampling requirements for high resolution NMR spectra, and the combination of these strategies with robust non-Fourier methods of spectrum analysis (such as MaxEnt) represent a profound change in the way researchers conduct multidimensional experiments. The potential benefits will enable more advanced applications of multidimensional NMR spectroscopy to study biological macromolecules, metabolomics, natural products, dynamic systems, and other areas where resolution, sensitivity, or experiment time are limiting. Just as the development of multidimensional NMR methods presaged multidimensional methods in other areas of spectroscopy, we anticipate that nonuniform sampling approaches will find applications in other forms of spectroscopy. © 2014 American Chemical Society.


Richards C.T.,Rowland Institute at Harvard | Clemente C.J.,Rowland Institute at Harvard
Bioinspiration and Biomimetics | Year: 2012

To explore the interplay between muscle function and propulsor shape in swimming animals, we built a robotic foot to mimic the morphology and hind limb kinematics of Xenopus laevis frogs. Four foot shapes ranging from low aspect ratio (AR = 0.74) to high (AR = 5) were compared to test whether low-AR feet produce higher propulsive drag force resulting in faster swimming. Using feedback loops, two complementary control modes were used to rotate the foot: force was transmitted to the foot either from (1) a living plantaris longus (PL) muscle stimulated in vitro or (2) an in silico mathematical model of the PL. To mimic forward swimming, foot translation was calculated in real time from fluid force measured at the foot. Therefore, bio-robot swimming emerged from musclefluid interactions via the feedback loop. Among in vitro-robotic trials, muscle impulse ranged from 0.12 ± 0.002 to 0.18 ± 0.007 N s and swimming velocities from 0.41 ± 0.01 to 0.43 ± 0.00 m s 1, similar to in vivo values from prior studies. Trends in in silico-robotic data mirrored in vitro-robotic observations. Increasing AR caused a small (∼10%) increase in peak bio-robot swimming velocity. In contrast, muscle forcevelocity effects were strongly dependent on foot shape. Between low- and high-AR feet, muscle impulse increased ∼50%, while peak shortening velocity decreased ∼50% resulting in a ∼20% increase in net work. However, muscle-propulsion efficiency (body center of mass work/muscle work) remained independent of AR. Thus, we demonstrate how our experimental technique is useful for quantifying the complex interplay among limb morphology, muscle mechanics and hydrodynamics. © 2012 IOP Publishing Ltd.


Wilson L.G.,University of Edinburgh | Wilson L.G.,Rowland Institute at Harvard | Poon W.C.K.,University of Edinburgh
Physical Chemistry Chemical Physics | Year: 2011

We introduce active, probe-based microrheological techniques for measuring the flow and deformation of complex fluids. These techniques are ideal for mechanical characterization either when little sample is available, or when samples show significant spatial heterogeneity. We review recent results, paying particular attention to comparing and contrasting rheological parameters obtained from micro- and macro-rheological techniques. © the Owner Societies 2011.


Martinez V.A.,University of Edinburgh | Schwarz-Linek J.,University of Edinburgh | Reufer M.,University of Edinburgh | Wilson L.G.,University of York | And 3 more authors.
Proceedings of the National Academy of Sciences of the United States of America | Year: 2014

It is widely believed that the swimming speed, v, of many flagellated bacteria is a nonmonotonic function of the concentration, c, of high-molecular-weight linear polymers in aqueous solution, showing peaked v(c) curves. Pores in the polymer solution were suggested as the explanation. Quantifying this picture led to a theory that predicted peaked v(c) curves. Using high-throughput methods for characterizing motility, we measured v and the angular frequency of cell body rotation, Ω, of motile Escherichia coli as a function of polymer concentration in polyvinylpyrrolidone (PVP) and Ficoll solutions of different molecular weights. We find that nonmonotonic v(c) curves are typically due to low-molecular-weight impurities. After purification by dialysis, the measured v(c) and Ω(c) relations for all but the highest-molecular-weight PVP can be described in detail by Newtonian hydrodynamics. There is clear evidence for non-Newtonian effects in the highest-molecular-weight PVP solution. Calculations suggest that this is due to the fast-rotating flagella seeing a lower viscosity than the cell body, so that flagella can be seen as nano-rheometers for probing the non-Newtonian behavior of high polymer solutions on a molecular scale.


Buchanan S.M.,Rowland Institute at Harvard | Kain J.S.,Rowland Institute at Harvard | De Bivorta B.L.,Rowland Institute at Harvard | De Bivorta B.L.,Harvard University
Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Genetically identical individuals display variability in their physiology, morphology, and behaviors, even when reared in essentially identical environments, but there is little mechanistic understanding of the basis of such variation. Here, we investigated whether Drosophila melanogaster displays individual-to-individual variation in locomotor behaviors. We developed a new high-throughout platform capable of measuring the exploratory behavior of hundreds of individual flies simultaneously. With this approach, we find that, during exploratory walking, individual flies exhibit significant bias in their left vs. right locomotor choices, with some flies being strongly left biased or right biased. This idiosyncrasy was present in all genotypes examined, including wild-derived populations and inbred isogenic laboratory strains. The biases of individual flies persist for their lifetime and are non-heritable: i.e., mating two left-biased individuals does not yield left-biased progeny. This locomotor handedness is uncorrelated with other asymmetries, such as the handedness of gut twisting, leg-length asymmetry, and wing-folding preference. Using transgenics and mutants, we find that the magnitude of locomotor handedness is under the control of columnar neurons within the central complex, a brain region implicated in motor planning and execution. When these neurons are silenced, exploratory laterality increases, with more extreme leftiness and rightiness. This observation intriguingly implies that the brain may be able to dynamically regulate behavioral individuality. © 2015, National Academy of Sciences. All rights reserved.

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