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News Article | April 13, 2016
Site: www.nature.com

Last month, in an extraordinary dispute before the US Patent and Trademark Office (USPTO), university lawyers laid out their clients' legal strategies for claiming patents that cover the celebrated gene-editing technology CRISPR–Cas9. Over the next year, the USPTO will receive volumes of evidence centred on who first invented the technology. Battles over scientific priority are as old as science itself. But the CRISPR–Cas9 patent dispute is unusual because it pits two leading research institutions against one another for the control and industrial development of a foundational technology: the University of California, Berkeley (UC Berkeley), and the Broad Institute of MIT and Harvard in Cambridge, Massachusetts. As scientific institutions increase their involvement in the commercialization of research1, it is worth considering the potential consequences for science if more institutions follow the path of UC Berkeley and the Broad Institute. In May 2012, researchers at UC Berkeley, led by Jennifer Doudna and her collaborator, Emmanuelle Charpentier (then located at the University of Vienna in Austria) filed a patent application in the United States for CRISPR–Cas9. Seven months later, Feng Zhang, a researcher at the Broad Institute, filed a competing application that covered similar uses of the technology. After Zhang's lawyers requested that his application be fast-tracked, the USPTO awarded one patent to Zhang in April 2014, followed by a dozen more in the subsequent 12 months. Meanwhile, the application made by Doudna and her colleagues languished. Last April, Doudna's lawyers requested that the USPTO conduct a specialized legal trial, known as a patent interference, to determine the ownership of the US patents that cover the CRISPR–Cas9 system. This January, the USPTO formally agreed to carry out the proceeding. One conspicuous aspect of this case, in my opinion, is the degree to which UC Berkeley and the Broad Institute have weighed in on what is essentially a dispute over scientific priority. The Broad Institute has produced press releases, videos and a slick feature on its website that stress the importance of Zhang's contributions to the development of the CRISPR–Cas9 technology. And earlier this year, the central positioning of Zhang's work in a historical perspective of CRISPR published in Cell2 by the president and director of the Broad Institute, Eric Lander, prompted a storm of angry responses from scientists, including Doudna and Charpentier. Meanwhile, at UC Berkeley, a press release that discussed the potential of CRISPR described Doudna as “the inventor of the CRISPR–Cas9 technology”. The financial stakes are high. The CRISPR–Cas9 patents are widely viewed to be worth hundreds of millions, if not billions, of dollars. Both organizations have invested directly in spin-off companies that were co-founded by their researchers — the Broad Institute in Editas Medicine, co-founded by Zhang, and UC Berkeley in Caribou Biosciences, co-founded by Doudna. A report submitted by Editas in January to the US Securities and Exchange Commission lists the Broad Institute and other Harvard-affiliated institutions as owning a major equity stake in the company: about 4.2% of its common shares. Efforts to commercialize the research output from universities played out differently in the past. Since 1980, US universities have been able to patent the inventions of their researchers, thanks to the Bayh–Dole Act — legislation that determines the ownership of intellectual property arising from federally funded research. But for the most part, institutions have kept their distance from disputes over scientific priority. In fact, after factoring in the costs of filing patents and staffing, university technology-transfer offices have generally been money losers for their institutions3. Even in the case of lucrative patents, commercial development has frequently been left to venture capitalists and the researchers themselves. Take the Cohen–Boyer patents, which covered early gene-splicing technology and netted Stanford University and the University of California, San Francisco (UCSF), both in California, hundreds of millions of dollars in licensing fees during the 1980s and 1990s. In this instance, Genentech, the company in South San Francisco, California, that was formed to commercialize the underlying technology, sprung from the efforts of Herbert Boyer, one of the founding researchers, and the financier Robert Swanson. The company was neither owned by, nor an exclusive licensee of, Stanford or UCSF. Research institutions in general are starting to play a bigger part in shepherding their researchers' projects through the commercialization process. A 2014 report from the Association of University Technology Managers in Oakbrook Terrace, Illinois — an organization that supports managers of intellectual property at academic research institutions, non-profit organizations and government agencies worldwide — documented that universities are increasing equity investments in their researchers' start-up companies. Of the patent licences granted by universities in 2014, 10% were tied to such investments1, compared with 6.7% in 1999 (ref. 4). I am concerned that such involvement in commercialization has the potential to clash with the broader, educational mission of research institutions. Universities worldwide have long strived to foster a culture of scientific collaboration. Even when universities have obtained broad patents, as the Carnegie Institute of Washington in Washington DC did in the early 2000s for a gene-expression control technology known as RNA interference, licences have been cheap and easy for researchers to obtain5. In other cases, scientists have simply ignored patents that cover fundamental technologies6. Academic research institutions now seem less shy about taking each other to court for patent infringement. In 2011, the University of Utah in Salt Lake City sued the Max Planck Society for the Advancement of Science in Germany over claims to a patent that covered a technology called short interfering RNA, which inhibits gene expression (see go.nature.com/vyujnp). And over the past four years, Stanford University and the Chinese University of Hong Kong in Sha Tin have engaged in a heated patent litigation over prenatal genetic diagnostic blood tests, a market that was worth US$530 million in 2013. In the current era of budget tightening, universities of all stripes might be tempted to use licensing fees as another funding mechanism. The University of South Florida in Tampa, for example — a public institution that had its state funding cut by $48 million in 2012 — holds a substantial number of patents that have not yet been licensed and has a famously low ratio of patent-licence revenue to research expenditure7. If its financial situation were to deteriorate further, the university might be compelled to extract licence fees from other research institutions for those patents. It would be wrong to suggest that patents, writ large, are failing educational research institutions. In the cases of gene splicing, RNA interference and human embryonic stem cells, patents have been major earners for institutions and researchers without damaging the scientific enterprise5. But an obvious danger of increasing the focus on commercialization is that educational institutions will view scientific research as a path to profit, above all else. It is not hard to imagine that patent disputes might lead to university administrators pushing certain views on their scientists, denigrating collaboration with researchers from competing institutions and tasking tenure committees with valuing patents over publications. Where scientific advances have the potential to be profitable, universities should support researchers to bring that work to fruition. This might include helping them to secure patents. But it is my view that serious commercialization efforts — such as granting exclusive licences or receiving equity ownership in researchers' start-ups — should be left to industry. The CRISPR–Cas9 dispute could have played out very differently. Zhang and Doudna were both co-founders of Editas. And UC Berkeley and the Broad Institute could have filed patent applications that listed the research teams from both institutions as co-inventors. Any resulting patents could then have been freely or cheaply licensed to other research institutions, or used to fund a joint academic organization dedicated to studying the technology. The patents could also have been widely, but not exclusively, licensed to a variety of industry competitors — promoting a robust, competitive market for commercial CRISPR–Cas9 applications and creating a funding stream for further academic research. Biomedical research in educational institutions has long prided itself on a culture of openness and sharing — one that both Zhang and Doudna have exercised by donating various components of the CRISPR–Cas9 system to the open-science consortium Addgene in Cambridge, Massachusetts. The incentives that patents create for educational institutions should not be allowed to erode scientific collaboration.


News Article | December 26, 2016
Site: www.bbc.co.uk

Astronomer Vera Rubin, whose pioneering work contributed to the theory of dark matter, has died at the age of 88, her son says. Allan Rubin said she died on Sunday of natural causes, AP reported. She was living in Princeton, New Jersey. Her studies earned her numerous honours, including being the second female astronomer to be elected to the US National Academy of Sciences. But many questioned why she was never awarded a Nobel Prize. In 1974, Rubin helped provide further convincing evidence that the stars at the edges of galaxies moved faster than expected. Gravity calculations using only visible matter in galaxies showed that the outer stars should have been moving more slowly. To reconcile her observations with the law of gravity, scientists proposed there was matter we cannot see and called it dark matter. Dark matter is an unidentified type of matter comprising approximately 27% of the mass and energy in the observable universe. Vera Rubin's interest in astronomy began as a young girl and grew with the involvement of her father, who helped her build a telescope and took her to meetings of amateur astronomers, according to a profile of the American Museum of Natural History. She was the only astronomy major to graduate from the prestigious women's college Vassar in 1948. When she sought to enrol as a graduate student at Princeton, she was told that women were not allowed in the university's graduate astronomy programme, a policy that was not abandoned until 1975. So she applied to Cornell University, where she studied physics. She then went on to Georgetown University, where she earned her doctorate in 1954. Later she moved on to work at the Carnegie Institute of Washington. In 1993 she was awarded the US National Medal of Science.


Fiore C.L.,University of New Hampshire | Baker D.M.,Carnegie Institute of Washington | Lesser M.P.,University of New Hampshire
PLoS ONE | Year: 2013

Background:Sponges have long been known to be ecologically important members of the benthic fauna on coral reefs. Recently, it has been shown that sponges are also important contributors to the nitrogen biogeochemistry of coral reefs. The studies that have been done show that most sponges are net sources of dissolved inorganic nitrogen (DIN; NH4 + and NO3 -) and that nitrification, mediated by their symbiotic prokaryotes, is the primary process involved in supplying DIN to adjacent reefs.Methodology/Principal Findings:A natural experiment was conducted with the Caribbean sponge Xestospongia muta from three different locations (Florida Keys, USA; Lee Stocking Island, Bahamas and Little Cayman, Cayman Islands). The DIN fluxes of sponges were studied using nutrient analysis, stable isotope ratios, and isotope tracer experiments. Results showed that the fluxes of DIN were variable between locations and that X. muta can be either a source or sink of DIN. Stable isotope values of sponge and symbiotic bacterial fractions indicate that the prokaryotic community is capable of taking up both NH4 + and NO3 - while the differences in δ15N between the sponge and bacterial fractions from the NH4 + tracer experiment suggest that there is translocation of labeled N from the symbiotic bacteria to the host.Conclusions/Significance:Nitrogen cycling in X. muta appears to be more complex than previous studies have shown and our results suggest that anaerobic processes such as denitrification or anammox occur in these sponges in addition to aerobic nitrification. Furthermore, the metabolism of this sponge and its prokaryotic symbionts may have a significant impact on the nitrogen biogeochemistry on Caribbean coral reefs by releasing large amounts of DIN, including higher NH4 + concentrations that previously reported. © 2013 Fiore et al.


Bochanski J.J.,Pennsylvania State University | Bochanski J.J.,Massachusetts Institute of Technology | Hawley S.L.,University of Washington | West A.A.,Boston University | West A.A.,Carnegie Institute of Washington
Astronomical Journal | Year: 2011

We present a statistical parallax analysis of low-mass dwarfs from the Sloan Digital Sky Survey. We calculate absolute r-band magnitudes (Mr ) as a function of color and spectral type and investigate changes in M r with location in the Milky Way. We find that magnetically active M dwarfs are intrinsically brighter in Mr than their inactive counterparts at the same color or spectral type. Metallicity, as traced by the proxy ζ, also affects Mr , with metal-poor stars having fainter absolute magnitudes than higher metallicity M dwarfs at the same color or spectral type. Additionally, we measure the velocity ellipsoid and solar reflex motion for each subsample of M dwarfs. We find good agreement between our measured solar peculiar motion and previous results for similar populations, as well as some evidence for differing motions of early and late M-type populations in U and W velocities that cannot be attributed to asymmetric drift. The reflex solar motion and the velocity dispersions both show that younger populations, as traced by magnetic activity and location near the Galactic plane, have experienced less dynamical heating. We introduce a new parameter, the independent position altitude (IPA), to investigate populations as a function of vertical height from the Galactic plane. M dwarfs at all types exhibit an increase in velocity dispersion when analyzed in comparable IPA subgroups. © 2011. The American Astronomical Society. All rights reserved.


Vogt S.S.,University of California at Santa Cruz | Butler R.P.,Carnegie Institute of Washington | Haghighipour N.,University of Hawaii at Manoa
Astronomische Nachrichten | Year: 2012

We present an analysis of the significantly expanded HARPS 2011 radial velocity data set for GJ 581 that was presented by Forveille et al. (2011). Our analysis reaches substantially different conclusions regarding the evidence for a Super-Earth-mass planet in the star's Habitable Zone. We were able to reproduce their reported χ 2 ν and RMS values only after removing some outliers from their models and refitting the trimmed down RV set. A suite of 4000 N-body simulations of their Keplerian model all resulted in unstable systems and revealed that their reported 3.6σ detection of e = 0.32 for the eccentricity of GJ 581e is manifestly incompatible with the system's dynamical stability. Furthermore, their Keplerian model, when integrated only over the time baseline of the observations, significantly increases the χ 2 ν and demonstrates the need for including non-Keplerian orbital precession when modeling this system. We find that a four-planet model with all of the planets on circular or nearly circular orbits provides both an excellent self-consistent fit to their RV data and also results in a very stable configuration. The periodogram of the residuals to a 4-planet all-circular-orbit model reveals significant peaks that suggest one or more additional planets in this system. We conclude that the present 240-point HARPS data set, when analyzed in its entirety, and modeled with fully self-consistent stable orbits, by and of itself does offer significant support for a fifth signal in the data with a period near 32 days. This signal has a false alarm probability of <4% and is consistent with a planet of minimum mass 2.2 M ⊕, orbiting squarely in the star's habitable zone at 0.13 AU, where liquid water on planetary surfaces is a distinct possibility. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Sun Y.,Argonne National Laboratory | Ren Y.,Argonne National Laboratory | Haeffner D.R.,Argonne National Laboratory | Almer J.D.,Argonne National Laboratory | And 3 more authors.
Nano Letters | Year: 2010

Real-time evolution of nanoparticles grown at the semiconductor/electrolyte interface formed between a single crystalline n-type GaAs wafer and an aqueous solution of AgNO3 has been studied by using high-energy synchrotron X-ray diffraction. The results reveal the distinct nucleation and growth steps involved in the growth of anisotropic Ag nanoplates on the surface of the GaAs wafer. For the first time, a quick transit stage is observed to be responsible for the structural transformation of the nuclei to form structurally stable seeds that are critical for guiding their anisotropic growth into nanoplates. Reaction between a GaAs wafer and AgNO3 solution at room temperature primarily produces Ag nanoplates on the surface of the GaAs wafer in the dark and at room temperature. In contrast, X-ray irradiation can induce charge separation in the GaAs wafer to drive the growth of nanoparticles made of silver oxy salt (Ag7NO11) and silver arsenate (Ag 3AsO4) at the semiconductor/electrolyte interface if the GaAs wafer is illuminated by the X-ray and reaction time is long enough. © 2010 American Chemical Society.


Rodigas T.J.,University of Arizona | Rodigas T.J.,Carnegie Institute of Washington | Malhotra R.,University of Arizona | Hinz P.M.,University of Arizona
Astrophysical Journal | Year: 2014

Planets can affect debris disk structure by creating gaps, sharp edges, warps, and other potentially observable signatures. However, there is currently no simple way for observers to deduce a disk-shepherding planet's properties from the observed features of the disk. Here we present a single equation that relates a shepherding planet's maximum mass to the debris ring's observed width in scattered light, along with a procedure to estimate the planet's eccentricity and minimum semimajor axis. We accomplish this by performing dynamical N-body simulations of model systems containing a star, a single planet, and an exterior disk of parent bodies and dust grains to determine the resulting debris disk properties over a wide range of input parameters. We find that the relationship between planet mass and debris disk width is linear, with increasing planet mass producing broader debris rings. We apply our methods to five imaged debris rings to constrain the putative planet masses and orbits in each system. Observers can use our empirically derived equation as a guide for future direct imaging searches for planets in debris disk systems. In the fortuitous case of an imaged planet orbiting interior to an imaged disk, the planet's maximum mass can be estimated independent of atmospheric models. © 2014. The American Astronomical Society. All rights reserved..


Jones D.O.,Boston University | Jones D.O.,Carnegie Institute of Washington | West A.A.,Boston University | Foster J.B.,Boston University
Astronomical Journal | Year: 2011

We use spectra of more than 56,000M dwarfs from the Sloan Digital Sky Survey (SDSS) to create a high-latitude extinction map of the local Galaxy. Our technique compares spectra from the stars in the SDSSData Release 7M dwarf sample in low-extinction lines of sight, as determined by Schlegel etal., to other SDSSM dwarf spectra in order to derive improved distance estimates and accurate line-of-sight extinctions. Unlike most previous studies, which have used a two-color method to determine extinction, we fit extinction curves to fluxes across the spectral range from 5700 to 9200 for every star in our sample. Our result is an AV map that extends from a few tens ofpc to approximately 2kpc away from the Sun. We also use a similar technique to create a map of RV values within approximately 1kpc of the Sun and find that they are consistent with the widely accepted diffuse interstellar medium value of 3.1. Using our extinction data, we derive a dust scale height for the local Galaxy of 119 15pc and find evidence for a local dust cavity. © 2011. The American Astronomical Society. All rights reserved.


Patent
Carnegie Institute Of Washington | Date: 2014-11-06

The invention provides fusion proteins comprising at least one fluorescent protein that is linked to at least one transporter protein that changes three-dimensional conformation upon specifically transporting its substrate. The transporter protein may be a nitrate transporter, a peptide transporter, or a hormone transporter. The invention provides fusion proteins comprising at least one fluorescent protein that is linked to at least one mechanosensitive ion channel protein. The invention also provides for methods of using the fusion proteins of the present invention and nucleic acids encoding the fusion proteins.


Patent
Carnegie Institute Of Washington | Date: 2015-02-27

The present invention relates generally to an integrated system, apparatus and method that allows for the continuous culturing of microorganisms under high pressure conditions and at a wide range of temperatures. More specifically, the system is configured to be gas tight and operate under aerobic or anaerobic conditions. The system is also configured to permit periodic sampling of the incubated organisms under such conditions with minimal physical/chemical disturbance inside the reactor and minimal impacts of shear forces on the collected biomass.

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