Directed Molecular Evolution Of Macromolecules (e.g., Rna, Dna, Proteins, Etc.) Patents (Class 506/1)
  • Patent number: 10436785
    Abstract: The invention provides antibodies that bind specifically to human indoleamine 2,3-dioxygenase 1 (IDO1), and methods of using the same. The antibodies are capable of binding to a sequence comprising SEQ ID NO: 1 and specifically bind to human IDO1 in formalin fixed paraffin embedded tissues. The antibodies are useful in a number of different analytical techniques, including immunohistochemistry (IHC) and immunocytochemistry (ICC).
    Type: Grant
    Filed: November 29, 2016
    Date of Patent: October 8, 2019
    Assignee: Spring BioScience Corporation
    Inventors: Fernando Jose Rebelo do Couto, Zhiming Liao, Yifei Zhu
  • Patent number: 10427126
    Abstract: The present invention provides a system and method for assessing a synthetic peptide population including interrogating a population of peptide features in the presence of a receptor having an affinity for a binder sequence. The population of peptide features is synthesized over a plurality of synthesis periods and includes a plurality of control peptide features synthesized to have an amino acid sequence including the binder sequence. The control peptide features include a first feature synthesized beginning with a first one of the synthesis periods, and a second feature synthesized beginning after the first one of the synthesis periods such that synthesis of the second control peptide feature is delayed by at least one synthesis period. The method further includes detecting a signal output characteristic of an interaction of the receptor with the control peptide features, the signal output indicative of the fidelity of synthesis of the population of peptide features.
    Type: Grant
    Filed: September 8, 2016
    Date of Patent: October 1, 2019
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Ryan Bannen, Sarah Barilovits, Jigar Patel, Eric Sullivan, John Tan
  • Patent number: 10294471
    Abstract: A method for selecting and isolating aptamers that target M-Ig proteins with a microdevice including at least a first selection chamber is provided. The method includes preparing a first sample of M-Ig proteins from a serum; placing the M-Ig proteins in the first selection chamber; introducing a first group of oligomers including at least an M-Ig targeting oligomer into the first selection chamber, whereby the M-Ig targeting oligomer binds to the first sample of M-Ig proteins. The method further includes removing unbound oligomers of the first sample from the first selection chamber to isolate the M-Ig targeting oligomer.
    Type: Grant
    Filed: January 24, 2017
    Date of Patent: May 21, 2019
    Inventors: Qiao Lin, Milan N. Stojanovic, Timothy R. Olsen, Tilla S. Worgall
  • Patent number: 9988608
    Abstract: A method of producing novel bacteriophages with expanded host-range and bacteriophages with expanded host ranges are disclosed. The method produces mutant phage strains which are infectious to a second host and can be more infectious to their natural host than in their natural state. The method includes repeatedly passaging a selected phage strain into bacterial cultures that contain varied ratios of its natural host bacterial strain with a bacterial strain that the phage of interest is unable to infect; the target-host. After each passage the resulting phage are purified and screened for activity against the target-host via double-overlay assays. When mutant phages that are shown to infect the target-host are discovered, they are further propagated in culture that contains only the target-host to produce a stock of the resulting mutant phage.
    Type: Grant
    Filed: October 14, 2015
    Date of Patent: June 5, 2018
    Assignee: National Technology & Engineering Solutions of Sandia, LLC
    Inventors: Kevin K. Crown, Joshua Santarpia
  • Patent number: 9657339
    Abstract: A method for amplifying a target nucleic acid is disclosed, which includes: (a) fragmenting a nucleic acid sample to create a target fragment comprising a target nucleic acid and two probe-complementary portions; (b) contacting said fragmented nucleic acid sample with a probe comprising two target fragment-complementary portions complementary to the probe-complementary portions of the target fragment; (c) rendering the fragmented nucleic acid sample single-stranded; (d) allowing the probe-complementary portions to hybridise with the target-fragment complementary portions; (e) if the probe in step (b) is not immobilised, immobilising the probe-target fragment hybrid on a solid phase via immobilisation moiety; (f) separating non-immobilised nucleic acid fragments from the solid phase; (g) contacting the solid phase with a ligase to ligate ligatable 5? and 3? ends of the target fragment whereby the target fragment is circularized; and (h) amplifying said circularized target fragment.
    Type: Grant
    Filed: December 3, 2010
    Date of Patent: May 23, 2017
    Assignee: Agilent Technologies, Inc.
    Inventors: Fredrik Roos, Henrik Johansson, Magnus Isaksson, Mats Nilsson, Olle (Olof) Ericsson, Simon Fredriksson
  • Patent number: 9617590
    Abstract: This disclosure describes, in one aspect, a method for preparing DNA molecule for sequencing. Generally, the method includes fragmenting the DNA molecule into double-stranded fragments; amplifying at least a portion of the double-stranded fragments; circularizing the fragments so that the first end of the fragment comprises a first loop connecting the strands and the second end of the fragment comprises a second loop connecting the strands; annealing a first sequencing primer to the first loop oriented to sequence at least a portion of one strand of the fragment; and annealing a second sequencing primer to the second loop oriented to sequence at least a portion of the other strand of the fragment. In another aspect, this disclosure describes a method for sequencing a DNA molecule.
    Type: Grant
    Filed: September 28, 2012
    Date of Patent: April 11, 2017
    Assignee: STC.UNM
    Inventors: Jeremy Edwards, Payman Zarkesh-Ha, Steven R. J. Brueck
  • Patent number: 9556428
    Abstract: A eukaryotic expression vector capable of displaying a multi-chain polypeptide on the surface of a host cell is provided, such that the biological activity of the multi-chain polypeptide is exhibited at the surface of the host cell. Such a vector allows for the display of complex biologically active polypeptides, e.g., biologically active multi-chain polypeptides such as immunoglobulin Fab fragments. The present invention describes and enables the successful display of a multi-chain polypeptide on the surface of a eukaryotic host cell. Preferred vectors are described for expressing the chains of a multi-chain polypeptide in a host cell separately and independently (e.g., under separate vector control elements, and/or on separate expression vectors, thus forming a matched vector set).
    Type: Grant
    Filed: May 21, 2015
    Date of Patent: January 31, 2017
    Assignee: Dyax Corp.
    Inventors: Simon E. Hufton, Hendricus Renerus Jacobus Mattheus Hoogenboom
  • Patent number: 9382535
    Abstract: Methods useful in constructing libraries that collectively display members of diverse families of peptides, polypeptides or proteins and the libraries produced using those methods. Methods of screening those libraries and the peptides, polypeptides or proteins identified by such screens.
    Type: Grant
    Filed: February 28, 2006
    Date of Patent: July 5, 2016
    Assignee: Dyax Corp.
    Inventors: Robert C. Ladner, Edward H. Cohen, Horacio G. Nastri, Kristin L. Rookey, Rene Hoet
  • Patent number: 9296777
    Abstract: Embodiments of the invention are to compounds, methods, and compositions for use in the treatment of viral infections. More specifically embodiments of the invention are 2?,4?-substituted nucleoside compounds useful for the treatment of viral infections, such as HIV, HCV, and HBV infections.
    Type: Grant
    Filed: April 30, 2014
    Date of Patent: March 29, 2016
    Inventors: Michael Joseph Sofia, Jinfa Du
  • Patent number: 9267952
    Abstract: The present invention relates generally to novel applications in combating infectious disease, cancer, allergy and autoimmune diseases. In one aspect, the invention relates to identifying one or more protein binding moieties of interest. In another aspect, the present invention relates to identifying one or more candidate vaccines.
    Type: Grant
    Filed: November 4, 2009
    Date of Patent: February 23, 2016
    Assignee: MorphoSys AG
    Inventor: Markus Enzelberger
  • Patent number: 9206473
    Abstract: A method of rapidly producing a double-stranded target DNA is disclosed. The method includes the step of producing multiple single stranded primary DNA constructs having (a) partially overlapping and complementary internal regions that together define the target DNA, and (b) flanking regions on either side of the internal regions containing a PCR primer recognition site and a restriction enzyme recognition site. The primary DNA constructs are amplified to form a pool of double-stranded primary constructs, and a restriction enzyme is used to cleave off the flanking regions. The target double-stranded DNA is then assembled from the cleaved fragments. Hundreds of thousands of oligonucleotides can be synthesized and quickly and efficiently assembled into many different individual double-stranded DNA target sequences using this method.
    Type: Grant
    Filed: November 1, 2011
    Date of Patent: December 8, 2015
    Assignee: Wisconsin Alumni Research Foundation
    Inventors: Michael R. Sussman, Kathryn E. Richmond, Matt J. Rodesch
  • Patent number: 9127076
    Abstract: This invention relates in part to modifying BtBooster (BtB) peptides, in part to increase their stability in insect midgut digestive juices. Some preferred embodiments of BtB have removed proteinase cleavage sites resulting in increased stability of the modified BtB in the insect gut, while retaining the ability to enhance B.t. proteins for improved insect control. In some preferred embodiments, the protease-stable BtB is used in combination with B.t. spores and/or crystals comprising a Cry protein. Also reported herein is the significant and increased enhancement of Bt toxins against relatively Bt-tolerant insects (Helicoverpa zea, Spodoptera exigua and Agrotis ipsilon), when used with BtBs. We also describe increased toxin enhancement with cadherin fragments that are stabilized against over-digestion by insect midgut proteinases. We also report enhancement of Bt Cry1F toxin by cadherin fragments.
    Type: Grant
    Filed: August 11, 2008
    Date of Patent: September 8, 2015
    Assignee: The University of Georgia Research Foundation
    Inventors: Mohd Amir-Fursan Abdullah, Michael J. Adang
  • Patent number: 9127090
    Abstract: A fibronectin type III (Fn3) polypeptide monobody, a nucleic acid molecule encoding said monobody, and a variegated nucleic acid library encoding said monobody, are provided by the invention. Also provided are methods of preparing a Fn3 polypeptide monobody, and kits to perform said methods. Further provided is a method of identifying the amino acid sequence of a polypeptide molecule capable of binding to a specific binding partner (SBP) so as to form a polypeptide:SSP complex, and a method of identifying the amino acid sequence of a polypeptide molecule capable of catalyzing a chemical reaction with a catalyzed rate constant, kcat, and an uncatalyzed rate constant, kuncat, such that the ratio of kcat/kuncat is greater than 10.
    Type: Grant
    Filed: June 29, 2011
    Date of Patent: September 8, 2015
    Assignee: Novartis AG
    Inventor: Shohei Koide
  • Publication number: 20150148237
    Abstract: The present disclosure describes the identification and use of aptamers and photoaptamers having slower dissociation rate constants than those obtained using previously described methods. Specifically, the present disclosure describes methods for the identification and use of aptamers to one or more targets within a histological or cytological sample, which have slow rates of dissociation. The aptamers may be used to assess localization, relative density, and presence or absence of one or more targets in cytological and histological samples. Targets may be selected that are specific and diagnostic of a given disease state for which the sample was collected. The aptamers may also be used to introduce target specific signal moieties. In addition to target identification, the aptamers may be used to amplify signal generation through a variety of methods.
    Type: Application
    Filed: January 27, 2015
    Publication date: May 28, 2015
    Inventors: Dominic Zichi, Sheri K. Wilcox, Chris Bock, Daniel J. Schneider, Bruce Eaton, Larry Gold, Thale C. Jarvis, Jeffrey D. Carter
  • Publication number: 20150139977
    Abstract: The invention relates to enzymes having xylanase, mannanase and/or glucanase activity, e.g., catalyzing hydrolysis of internal ?-1,4-xylosidic linkages or endo-?-1,4-glucanase linkages; and/or degrading a linear polysaccharide beta-1,4-xylan into xylose. Thus, the invention provides methods and processes for breaking down hemicellulose, which is a major component of the cell wall of plants, including methods and processes for hydrolyzing hemicelluloses in any plant or wood or wood product, wood waste, paper pulp, paper product or paper waste or byproduct. In addition, methods of designing new xylanases, mannanases and/or glucanases and methods of use thereof are also provided. The xylanases, mannanases and/or glucanases have increased activity and stability at increased pH and temperature.
    Type: Application
    Filed: October 22, 2014
    Publication date: May 21, 2015
    Inventors: David Weiner, David Blum, Alexander Varvak, Shaun Healey, Kristine Chang, Geoff Hazlewood, Thomas Todaro, Grace Desantis, Hwai Chang, Connie Jo Hansen, Scott W. Beaver, Thomas Woodward, Charles Hancock
  • Publication number: 20150133305
    Abstract: The present invention is directed to methods, for example phage display assays, for bioengineering peptides that bind to individual distinct nucleotides. Also provided are peptides engineered by such methods. Specifically, cyclic peptides that bind individual distinct nucleotides are provided herein.
    Type: Application
    Filed: November 7, 2008
    Publication date: May 14, 2015
    Inventors: Mineo Yamakawa, Joseph V. Kosmoski, Deane C. Little
  • Publication number: 20150133307
    Abstract: Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.
    Type: Application
    Filed: September 26, 2014
    Publication date: May 14, 2015
    Inventors: Xiyun Zhang, Russell Javiniar Sarmiento, Donald Scott Baskerville, Gjalt W. Huisman
  • Publication number: 20150133308
    Abstract: The present invention relates to a method for improving a repebody protein comprising repeat modules and a nucleotide library encoding a repebody protein library for improving the repebody protein. More particularly, the present invention relates to a method for improving a repebody protein using a module evolution method of sequentially mutating repeat modules constituting the repebody protein, and a nucleotide library encoding a repebody protein library used to improve the protein. According to the module evolution method of the present invention, an improved repebody protein can be screened which has a high binding affinity and accordingly increased specificity and activity, and thus it is easy to express a repebody used as an inhibitor, a therapeutic agent, and an analysis means against a target substance.
    Type: Application
    Filed: November 11, 2014
    Publication date: May 14, 2015
    Inventors: Hak-Sung Kim, Joong-Jae Lee, Hyun-Ho Kyeong, Jung-Min Choi, Da-Eun Hwang, Hae-Kap Cheong, Hyun Jung Kim, Eun-Kyeong Jo, Chul-Su Yang, Jae-Min Yuk
  • Publication number: 20150133306
    Abstract: The invention provides a method for preparing a compound or a product having one or more characteristics that meet or exceed a user specification, the process comprising the step of selecting a first combination of chemical inputs, optionally together with physical inputs, and supplying those inputs to a reaction space, thereby to generate a first product; analysing one or more characteristics of the product generated; comparing the one or more characteristics against a user specification; using a genetic algorithm selecting a second combination of chemical inputs, optionally together with physical inputs, wherein the second combination differs from the first combination, and supplying those inputs to the reaction space, thereby to generate a second product; analysing one or more characteristics of the second product generated; comparing the one or more characteristics generated against the user specification; repeating the selecting and analysing steps for further individual combinations of chemical and/or p
    Type: Application
    Filed: May 24, 2013
    Publication date: May 14, 2015
    Inventor: Leroy Cronin
  • Publication number: 20150119254
    Abstract: An object of the present invention is to develop and provide a method for efficiently producing a nucleic acid aptamer, particularly, a DNA aptamer, having higher specificity and binding activity against a target substance than those of nucleic acid aptamers obtained by conventional methods. The present invention provides a transcribable or replicable nucleic acid aptamer comprising a natural nucleotide and a non-natural nucleotide having an artificial base-pairable artificial base. The present invention also provides a method for sequencing a non-natural nucleotide-containing single-stranded nucleic acid molecule selected from a single-stranded nucleic acid library.
    Type: Application
    Filed: November 15, 2012
    Publication date: April 30, 2015
    Inventors: Ichiro Hirao, Michiko Hirao, Rie Yamashige, Shigeyuki Yokoyama
  • Publication number: 20150110836
    Abstract: The present disclosure provides compositions and methods for the generation of an antibody or immunogenic composition, such as a vaccine, through epitope focusing by variable effective antigen surface concentration. Generally, the composition and methods of the disclosure comprise three steps: a “design process” comprising one or more in silico bioinformatics steps to select and generate a library of potential antigens for use in the immunogenic composition; a “formulation process”, comprising in vitro testing of potential antigens, using various biochemical assays, and further combining two or more antigens to generate one or more immunogenic compositions; and an “administering” step, whereby the immunogenic composition is administered to a host animal, immune cell, subject or patient. Further steps may also be included, such as the isolation and production of antibodies raised by host immune response to the immunogenic composition.
    Type: Application
    Filed: May 21, 2013
    Publication date: April 23, 2015
    Inventor: Jacob E. Glanville
  • Publication number: 20150104433
    Abstract: The present invention relates to a method for preparing an expression vector encoding a tailored recombinase, which tailored recombinase is capable of recombining asymmetric target sequences within the long terminal repeat (LTR) of proviral DNA of a plurality of retrovirus strains inserted into the genome of a host cell, as well as to the obtained expression vector, cells transfected with this, expressed recombinase and pharmaceutical compositions comprising the expression vector, cells and/or recombinase. Pharmaceutical compositions are useful, e.g., in treatment and/or prevention of retrovirus infection. In particular, asymmetric target sequences present in a plurality of HIV strains are disclosed, as well as tailored recombinases capable of combining these sequences (Tre 3.0 and 4.0) and expression vectors encoding them.
    Type: Application
    Filed: December 4, 2014
    Publication date: April 16, 2015
    Inventors: Joachim Hauber, Jan Chemnitz, Frank Buchholz, Janet Chusainow
  • Patent number: 9006148
    Abstract: Methods of using a progressive cavity pump as a bioreactor are disclosed. Methods of isolating a biological product, such as pancreatic islet cells, using the bioreactor are also disclosed.
    Type: Grant
    Filed: September 13, 2012
    Date of Patent: April 14, 2015
    Inventor: Harvey Zar
  • Publication number: 20150093758
    Abstract: Disclosed herein are novel synthetic prostate specific antigen (PSA)-targeted capture agents that specifically bind PSA. In certain embodiments, these PSA capture agents are biligand or triligand capture agents containing two or three target-binding moieties, respectively.
    Type: Application
    Filed: July 28, 2014
    Publication date: April 2, 2015
    Inventors: James R. Heath, Heather Dawn Agnew, Suresh Mark Pitram
  • Publication number: 20150059011
    Abstract: Methods are provided to select plants and populations of epigenetically fixed crop plants with improved yield.
    Type: Application
    Filed: October 30, 2014
    Publication date: February 26, 2015
    Inventor: Marc DeBlock
  • Publication number: 20150031549
    Abstract: The invention relates to a method for selecting a sequence set from a library of expressed nucleic acid sequences, wherein cells are provided, each cell comprises an expressed nucleic acid sequence expressed as a target protein. The cells are encapsulated by treating them with a cationic polysaccharide and subsequently treating them with an anionic polysaccharide, yielding encapsulated cells, perforating the membrane of the encapsulated cells, yielding solubilized compartments, contacting them with a ligand to said target protein, the ligand bearing a detectable label, and selecting a subset of solubilized compartments as a function of detectable label and isolating the expressed nucleic acid sequences from the selection as a selected sequence set.
    Type: Application
    Filed: January 9, 2013
    Publication date: January 29, 2015
    Inventors: Daniel Scott, Andreas Plückthun
  • Publication number: 20150024944
    Abstract: The present disclosure provides methods of integrating therapeutic protein and antibody generation and/or selection, evolution and expression in a eukaryotic host for manufacturing in a single system. Therapeutic proteins, including antibodies, are generated, optimized and manufactured in the same eukaryotic host system. The disclosed system of Comprehensive Integrated Antibody Optimization (CIAO!™) allows for simultaneous evolution of protein performance and expression optimization.
    Type: Application
    Filed: September 9, 2014
    Publication date: January 22, 2015
    Inventor: Jay Milton Short
  • Patent number: 8912127
    Abstract: The invention relates to a method for generating a gene mosaic by somatic in vivo recombination, comprising: e) in a single step procedure (vii) transforming a cell with at least one gene A having a sequence homology of less than 99.5% to another gene to be recombined that is an integral part of the cell genome or presented in the framework of a genetic construct, (viii) recombining said genes, (ix) generating a gene mosaic of the genes at an integration site of a target genome, wherein said at least one gene A has a single flanking target sequence either at the 5? end or 3? end anchoring to the 5? or 3? end of said integration site, and f) selecting clones comprising the gene mosaic, as well as a method of producing a diversity of gene mosaics and gene assembly.
    Type: Grant
    Filed: April 8, 2011
    Date of Patent: December 16, 2014
    Assignee: Eviagenics, S.A.
    Inventors: Rudy Pandjaitan, Alejandro Luque
  • Publication number: 20140357497
    Abstract: Methods, systems, and computer programs for designing probes or primers for nucleic acid sequencing, generating libraries of nucleic acid sequences, and mapping genomic sequences are provided herein,
    Type: Application
    Filed: April 26, 2012
    Publication date: December 4, 2014
    Inventors: Kun Zhang, Athurva Gore
  • Publication number: 20140349855
    Abstract: A proteinaceous particle, for example a bacteriophage, ribosome or cell, displaying on its surface a T-cell receptor (TCR). The displayed TCR is preferably a heterodimer having a non-native disulfide bond between constant domain residues. Such display particles may be used for the creation of diverse TCR libraries for the identification of high affinity TCRs. Several high affinities are disclosed.
    Type: Application
    Filed: April 10, 2014
    Publication date: November 27, 2014
    Inventors: Bent Karsten Jakobsen, Torben Bent Andersen, Peter Eamon Molloy, Yi Li
  • Publication number: 20140342918
    Abstract: The disclosure relates to a switchable aptamer having a high affinity for a selected target such as a virus, cell or antibody when in the presence of a binding ion and a low affinity for said target in the absence of said binding ion. The switchable aptamer may be isolated from a pool comprising a mixture of aptamers by incubating the pool with the target ligand and a binding ion to form target-aptamer complexes; separating unbound aptamer molecules from the target-aptamer complexes; contacting the target-aptamer complexes with a chelating agent having affinity for the binding ion wherein a switchable aptamer specific to said target is released from the target-aptamer complexes; and isolating the switchable aptamer released in the preceding step.
    Type: Application
    Filed: May 14, 2014
    Publication date: November 20, 2014
    Inventors: Maxim V. Berezovski, Mohamed Wehbe, Mahmoud Aziz Mahmoud Labib, Darija Muharemagic, Anna S. Zamay, Shahrokh Ghobadloo
  • Publication number: 20140323315
    Abstract: The present invention relates, inter alia, to polyspecificity reagents, methods of making the same, and methods of using the same in, inter alia, the selection, screening, enrichment, and identification of non-polyspecific, and thus developable, polypeptides.
    Type: Application
    Filed: April 29, 2014
    Publication date: October 30, 2014
    Applicant: Adimab, LLC
    Inventors: Piotr Bobrowicz, Amber D. Hanna, Jerry M. Thomas
  • Publication number: 20140302999
    Abstract: The present invention is directed to a method for obtaining an in vitro pharmacological model of a recombinant protein drug in a given host. A plurality of biomolecules are selected which are known or suspected to influence pharmacology of the recombinant protein in the host via a binding interaction with the recombinant protein. The recombinant protein is contacted with each selected biomolecule and the binding kinetics parameters for each interaction are determined using a binding assay. These steps are then repeated with all selected biomolecules to produce a plurality of binding kinetics parameters for the selected biomolecules. The combined results provide an in vitro pharmacological model of the recombinant protein in the host. The in vitro pharmacological model may then be used in several applications, such as optimizing new batches of recombinant protein drugs, developing biosimilar or bio-better drug candidates.
    Type: Application
    Filed: November 2, 2012
    Publication date: October 9, 2014
    Inventor: Magdalena Leszczyniecka
  • Publication number: 20140302998
    Abstract: The present application provides stable peptide-based Akt capture agents and the use thereof as detection, diagnosis, and treatment agents. The application further provides novel methods of developing stable peptide-based capture agents, including Akt capture agents, using iterative on-bead in situ click chemistry.
    Type: Application
    Filed: July 11, 2012
    Publication date: October 9, 2014
    Inventors: James R. Heath, Arundhati Nag, Samir Das, Kaycie M. Deyle, Steven Wesley Millward, Paul Edward Kearney
  • Patent number: 8835162
    Abstract: The invention provides a method of incorporating nonstandard amino acids into a protein by utilizing a modified aminoacyl-tRNA synthetase to charge the nonstandard amino acid to a modified tRNA, which forms strict Watson-Crick base-pairing with a codon that normally forms wobble base-pairing with natural tRNAs.
    Type: Grant
    Filed: December 28, 2012
    Date of Patent: September 16, 2014
    Assignee: California Institute of Technology
    Inventors: Inchan Kwon, David Tirrell
  • Publication number: 20140256557
    Abstract: The disclosure relates to a method of generating a diverse set of variants to screen improved and novel properties within the variant population, a system for creating the diverse set of variants, and the variant peptides.
    Type: Application
    Filed: May 19, 2014
    Publication date: September 11, 2014
    Applicant: Codexis, Inc.
    Inventor: Richard Fox
  • Publication number: 20140249035
    Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.
    Type: Application
    Filed: April 18, 2014
    Publication date: September 4, 2014
    Applicant: Codexis Mayflower Holdings, LLC
    Inventor: Richard John Fox
  • Publication number: 20140243209
    Abstract: The present invention provides a method for detecting an interaction, which method can solve not only the problem of false negatives but also the problem of false positives.
    Type: Application
    Filed: September 28, 2012
    Publication date: August 28, 2014
    Applicant: The University of Tokyo
    Inventors: Etsuko Miyamoto, Shigeo Fujimori
  • Publication number: 20140243208
    Abstract: The invention encompasses compositions and methods for selecting aptamers.
    Type: Application
    Filed: July 23, 2012
    Publication date: August 28, 2014
    Applicant: Mediomics, LLC
    Inventors: Yie-Hwa Chang, Ling Tian, Rongsheng Wang
  • Publication number: 20140221216
    Abstract: The present invention provides methods for identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. More specifically, some embodiments of the present invention provide methods for building sequence-activity models comprising multiplicative terms and using the models to guide directed evolution. In some embodiments, the sequence-activity models include one or more interaction terms, each of which including an interaction coefficient representing the contribution to activity of two or more defined residues. In some embodiments, the models describe relation between protein or nucleic acid sequences and protein activities. In some embodiments, the present invention also provides methods for preparing sequence-activity models, including but not limited to stepwise addition or subtraction techniques, Bayesian regression, ensemble regression and other methods.
    Type: Application
    Filed: January 29, 2014
    Publication date: August 7, 2014
    Inventors: Gregory Allan Cope, Nicholas John Agard
  • Publication number: 20140213459
    Abstract: The present invention relates to methods for improving the folding stability of antibodies, to antibodies with improved folding stability, nucleic acid and vectors encoding such antibodies, and to uses of such antibodies, nucleic acid and vectors.
    Type: Application
    Filed: May 29, 2012
    Publication date: July 31, 2014
    Inventor: Roland Beckmann
  • Publication number: 20140213460
    Abstract: Methods relating to obtaining libraries of YY1-binding long non-coding RNAs, libraries obtained thereby, and methods of use thereof.
    Type: Application
    Filed: July 3, 2012
    Publication date: July 31, 2014
    Inventors: Jeannie T. Lee, Yesu Jeon
  • Publication number: 20140206846
    Abstract: The present invention relates to antibody-based dual targeting molecules, and to methods for generating such dual targeting molecules, including a library-based approach.
    Type: Application
    Filed: May 29, 2012
    Publication date: July 24, 2014
    Inventor: Roland Beckmann
  • Publication number: 20140200145
    Abstract: The invention relates to a method for metabolic evolution of a variant of a natural small aromatic molecule product of a metabolic pathway, by somatic in vivo assembly and recombination of said metabolic pathway employing a gene mosaic of at least one gene A, which comprises a) in a single step procedure (i) transforming a cell with at least one gene A having a sequence homology of less than 99.
    Type: Application
    Filed: June 20, 2012
    Publication date: July 17, 2014
    Applicant: Eviagenics S.A.
    Inventors: Rudy Pandjaitan, Sarra Sebai, Alejándro Luque
  • Patent number: 8759058
    Abstract: The present invention relates generally to hydrogen production for use in fuel cells, foodstuffs and chemical production, and more particularly, to biologically and photosynthetically produced hydrogen. Specifically, disclosed is a method for producing bacteria and green alga that can produce hydrogen in quantities that exceed four hundred percent of the hydrogen produced by green alga in nature; thus, producing organisms which can serve as hydrogen generators for fuel cells, chemical production and numerous other applications.
    Type: Grant
    Filed: February 24, 2012
    Date of Patent: June 24, 2014
    Inventors: Scott Plummer, Mark Plummer
  • Patent number: 8741810
    Abstract: The present invention relates to a high efficiency method of expressing immunoglobulin molecules in eukaryotic cells. The invention is further drawn to a method of producing immunoglobulin heavy and light chain libraries, particularly using the trimolecular recombination method, for expression in eukaryotic cells. The invention further provides methods of selecting and screening for antigen-specific immunoglobulin molecules, and antigen-specific fragments thereof. The invention also provides kits for producing, screening and selecting antigen-specific immunoglobulin molecules. Finally, the invention provides immunoglobulin molecules, and antigen-specific fragments thereof, produced by the methods provided herein.
    Type: Grant
    Filed: August 17, 2007
    Date of Patent: June 3, 2014
    Assignee: University of Rochester
    Inventors: Maurice Zauderer, Ernest S. Smith
  • Publication number: 20140121115
    Abstract: New rare-cutting endonucleases, also called custom-made meganucleases, which recognize and cleave a specific nucleotide sequence, derived polynucleotide sequences, recombinant vector cell, animal, or plant comprising said polynucleotide sequences, process for producing said rare-cutting endonucleases and any use thereof, more particularly, for genetic engineering, antiviral therapy and gene therapy.
    Type: Application
    Filed: December 21, 2012
    Publication date: May 1, 2014
    Applicant: Cellectis
    Inventors: Sylvain Arnould, Sylvia Bruneau, Jean-Pierre Cabaniols, Patrick Chames, Andre Choulika, Phillipe Duchateau, Jean-Charles Epinat, Agnes Gouble, Emmanuel Lacroix, Frederic Paques, Christophe Perez-Michaut, Julianne Smith, Davie Sourdive
  • Publication number: 20140109249
    Abstract: The present invention relates to methods for the screening, identification and/or application of microorganisms of use in imparting beneficial properties to plants.
    Type: Application
    Filed: October 10, 2013
    Publication date: April 17, 2014
    Applicant: Biodiscovery New Zealand Limited
    Inventors: Susan Jane Turner, Peter John Wigley
  • Publication number: 20140100120
    Abstract: Provided herein are methods for a novel bead-based next-generation “X-aptamer” selection scheme that extends aptamer technology to include X-modified bases, thus resulting in X-aptamers, at any position along the sequence because the aptamers are chemically synthesized via a split-pool scheme on individual beads. Also provides are application to a wide range of commonly used DNA modifications, including, but not limited to, monothioate and dithioate backbone substitutions. This new class of aptamer allows chemical modifications introduced to any of the bases in the aptamer sequence as well as the phosphate backbones and can be extended to other carbohydrate-based systems.
    Type: Application
    Filed: October 10, 2013
    Publication date: April 10, 2014
    Inventors: David G Gorenstein, Weiguo He, David E Volk, Miquel-Angel Elizondo-Riojas, Ross Durland, Johnnie Engelhardt
  • Publication number: 20140094373
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Application
    Filed: October 2, 2013
    Publication date: April 3, 2014
    Applicant: Natera, Inc.
    Inventors: Berhard Zimmermann, Matthew Hill, Philippe Lacroute, Michael Dodd