Method of Generating a Dynamic Pathway Map
Awardees: David Haussler, Distinguished Professor of Biomolecular Engineering; Joshua Stuart, Professor of Biomolecular Engineering
Department: Biomolecular Engineering
The invention describes a computational method for inferring the activity of the genetic circuitry inside cancerous cells. It bases its prediction on various types of genomics data collected from a patient’s tumor specimen and on the known network of interactions between the genetic molecules. Highly activated areas of the network provide clues about patient treatment.
A Method for Distance-Vector Routing Using Adaptive Publish-Subscribe Mechanisms
Awardees: JJ Garcia-Luna Aceves, Distinguished Professor of Computer Science and Engineering
Department: Computer Science and Engineering
This invention is a new method to establish and maintain routing tables in wireless networks. It overcomes problems resulting from the increased number of nodes in today’s networks and the way today’s networks have nodes joining and leaving continuously.
It does so by combining a publish-subscribe mechanisms that learns and maintains information about nodes and controllers with an adaptive protocol for routing in wireless ad hoc networks. The adaptive protocol uses distance vectors for routing in computer networks and integrates a sub-set of nodes to serve as controllers.
Molecular Adapter for Capture and Manipulation of Transfer RNA
Awardees: David Bernick, Assistant Professor of Biomolecular Engineering
Department: Biomolecular Engineering
Transfer RNA (tRNA) is an RNA molecule that carries amino acids to a nascent protein strand during translation from a messenger RNA (mRNA) sequence to a protein. tRNA forms three dimensional structures that make it very difficult to work with using standard molecular biology techniques. This patent involves a method of sequencing a tRNA molecule that involves the addition of oligonucleotide adapters, potentially including a cholesterol tag, to tRNA. The sequencing is performed using a nanopore sequencer.
Distributed LC Resonant Tank Clock Tree Synthesis
Awardees: Matthew Guthaus, Professor of Computer Science and Engineering
Department: Computer Science and Engineering
Power consumption is the single most limiting factor in many devices. This invention reduces power consumption, increases device performance, and lengthens battery life for many such devices by design improvements to those chips. It does so by an iterative placement of electronic ballasts that balance the clock network electronic characteristics.
Salt-Tolerant DNA Polymerases
Awardees: David Bernick, Professor of Biomolecular Engineering
Department: Biomolecular Engineering
This patent describes a method of artificially synthesizing DNA (e.g. via polymerase chain reaction – PCR), or as a motor to translocate a strand of DNA using a DNA polymerase enzyme that works in high salt conditions, such as a solution with an halide concentration greater than 5%. The polymerases used in the methods were initially purified from a collection (metagenome) of archaeal and bacterial cells that live in high-salt conditions, enriched for the viruses that infect them.
Practical Two-Frame 3D+2D TV
Awardees: James Davis, Professor of Computer Science
Department: Computer Science
This patent describes a method for making 3D televisions and movie screens viewable without special glasses. These screens currently require viewers to wear special glasses to see the 3D effect. If the glasses are removed then the viewer sees a double image which is essentially unwatchable. The method described here instead provides a normal 2D viewing experience when the glasses are removed.
Robust Single-Phase DC/AC Inverter for Highly Varying DC Voltages
Awardees: Ricardo Sanfelice, Associate Professor of Computer Engineering; Jun Chai, Research Assistant
Department: Computer Engineering
The invention provides a single phase DC/AC inverter with a unique hybrid control circuit. Given an input DC voltage signal, the inverter produces an AC output signal that approximates a given sinusoidal AC reference signal. The invention solves the problem of robustly converting highly varying DC power into desired AC power. Advantageously, the precision with which the AC output signal approximates a desired reference signal can be adjusted via a tunable parameter in the control circuit, conversion is guaranteed under varying input voltages, and the harmonic distortion is almost entirely eliminated at low frequencies.
Current Mode Clock Distribution
Awardees: Matthew Guthaus, Associate Professor of Computer Engineering; Riadul Islam (previously Ph.D. Student at UCSC)
Department: Computer Engineering
In a high-performance computer system design, the clock network consumes a significant amount of power and causes the most switching noise. High power consumption requires larger batteries while switching noise degrades the accuracy of sensitive sensor measurements in modern Systems-on-Chips. Prof. Matthew Guthaus, faculty in Computer Engineering, and his graduate student Riadul Islam, now a faculty at University of Michigan Dearborn, have developed the concept of a current-mode clock distribution to address these problems. Current-mode clocking senses current flow rather than a traditional voltage swing in clock wires and thereby eliminates most of the noise and power problems in traditional clock distribution schemes. Current-mode clocking simultaneously increases the potential maximum speeds of computer chips for performance improvements.
Therapeutic Compositions and Methods For Treating HIV Including Identification and Manipulation of Particular Domains Associated With Immunogenicity
Awardees: Phillip Berman, Distinguished Professor; Sara O’Rourke, Associate Project Scientist; William Scott, Professor
Department: Biomolecular Engineering
This patent describes HIV viral proteins with engineered mutations. In particular, the engineered mutations help expose antibody epitopes in the viral proteins that raise broadly neutralizing antibody responses, which could in turn result in a more effective HIV vaccine.
HIV-1 Gp 120 V1n2 Antigens And Immunological Uses Thereof
Awardees: Phillip Berman, Distinguished Professor; Kate Mesa, Lab Manager; Bin Yu, Specialist
Department: Biomolecular Engineering
This patent describes small, properly folded and glycosylated fragments of the HIV envelope glycoprotein, gp120, that appear to be useful components of an HIV vaccine. Over the last decade scientists have identified 3-4 sites on the 510 amino acid envelope protein recognized by protective antibodies. However these sites contain specific sugar molecules (mannose-5) and fail to promote a strong immune responses in the context of the full length gp120 molecule. Thus new ways are required to target antibody responses to these key sites rather than the dozen or more sites recognized by non-protective antibodies. This patent describes properly folded and glycosylated fragments of gp120, and methods for their production. When included in an HIV vaccine, these fragments can focus the immune response to sites recognized by protective antibodies.
Switchable LED Lightbulb
Awardee: David Munday, Lecturer
Department: Computer Engineering
The US patent office recently issued a patent to a senior design student team and Professor David Munday for inventing a new LED lightbulb capable of multiple brightness settings all within the same bulb. Most commercial LED light bulbs are manufactured for a given brightness level, but this bulb is adjustable through a number of possible controls including onboard buttons, wifi control, and automatic brightness control.
Two-Chambered Dual-Pore Device
Awardee: Holger Schmidt, Associate Dean for Research and Professor of Electrical Engineering
Department: Electrical Engineering
Nanopores form the basis of several approaches to next generation DNA sequencing technology. The basic idea behind this is to identify the bases that make up DNA one by one as they move through a nanoscopic opening. This invention describes how to improve control over the molecules to be tested by using two coupled nanopores, and how to implement this principle on a compact semiconductor chip.
BamBam: Parallel Comparative Analysis of High-Throughput Sequencing Data (two patents)
Awardee: David Haussler, Distinguished Professor and Scientific Director, UC Santa Cruz Genomics Institute
Department: Biomolecular Engineering
The purpose of the inventions encompassed by these two patents is to more efficiently compare biological sequences from two distinct samples. The analysis of biological sequence information usually involves the manipulation of enormous data files, which in turn results in long processing times to generate a meaningful comparison between the biological sequences. The inventions described in these two patents provides a more efficient way to compare biological sequences from distinct samples from a patient (e.g. normal tissue vs. tumor tissue) and generate patient-specific treatment instructions based on those sequences. The 9,646,134 patent concerns genomic information while the 9,652,587 patent also encompasses proteomic and transcriptomic information.
Interferometric Focusing of Guide-Stars for Direct Wavefront Sensing
Awardees: Joel Kubby, Professor; Xiaodong Tao, Assistant Project Scientist
Department: Electrical Engineering
The optimal performance of an optical microscope is difficult to achieve due to aberrations caused by tissues. In order to compensate for these aberrations, we applied adaptive optics with direct wavefront sensing using fluorescent “guide-stars” embedded in tissues for wavefront measurement. A scattering effect within the tissues limits the intensity of the guide star and reduces the signal to noise ratio of wavefront measurement. This patent describes the use of interferometric focusing of excitation light onto a guide-star deep within tissue to increase the fluorescence intensity of the guide-star which in turn overcomes the signal loss caused by scattering.
Nanopipette Apparatus for Manipulating Cells
Awardee: Nader Pourmand, Associate Professor
Department: Biomolecular Science and Engineering
The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Dr. Pourmand and his team have developed a single-cell interrogation platform based on scanning ion conductance microscopy for continuous sampling of intracellular content from individual cells. Among many other functionalities, for the nanobiopsy, this platform uses a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. Researchers might use this platform to understand cancer and other diseases which might provide a foundation for dynamic subcellular genomic analysis.
Compositions, Devices, Systems, And Methods For Using A Nanopore
Awardee: Mark Akeson, Professor
Department: Biomolecular Science & Engineering
The invention is one of a series of patents from the biomolecular engineering department concerning sequencing of DNA using a nanoscale hole or “nanopore.” When a voltage is applied across the nanopore, DNA is pulled through the hole in single file order. The bases that make up the DNA are read as they transit the pore. In this particular patent, the inventors combined voltage feedback control with an enzyme to precisely regulate movement of the DNA. This results in improved DNA sequencing accuracy.
Faster, Better Genome Assembly
Awardee: Edward Green, Associate Professor
Department: Biomolecular Engineering
Assembling genomes is like solving a giant, 3 billion-piece jigsaw puzzle. The invention describes a streamlined way to figure out which pieces are near other pieces so the puzzle can be reconstructed more accurately and quickly. Licensed by Dovetail Genomics in Santa Cruz, the invention has been used to assemble the genomes of hundreds of plant and animals. With this information, scientists can begin to unravel the biology inherent in each.
In the spring, several new initiatives from the UC Office of the President will be rolled out across the 10 campuses to further innovation, commercialization, and entrepreneurship and highlight the growing body of research providing public benefit. The IATC office will lead the implementation of these initiatives with various leaders around campus to bring these opportunities to the entire university community.
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Method of Generating a Dynamic Pathway Map
Awardees: David Haussler, Distinguished Professor of Biomolecular Engineering; Joshua Stuart, Professor of Biomolecular Engineering
Department: Biomolecular Engineering
The invention describes a computational method for inferring the activity of the genetic circuitry inside cancerous cells. It bases its prediction on various types of genomics data collected from a patient’s tumor specimen and on the known network of interactions between the genetic molecules. Highly activated areas of the network provide clues about patient treatment.
A Method for Distance-Vector Routing Using Adaptive Publish-Subscribe Mechanisms
Awardees: JJ Garcia-Luna Aceves, Distinguished Professor of Computer Science and Engineering
Department: Computer Science and Engineering
This invention is a new method to establish and maintain routing tables in wireless networks. It overcomes problems resulting from the increased number of nodes in today’s networks and the way today’s networks have nodes joining and leaving continuously.
It does so by combining a publish-subscribe mechanisms that learns and maintains information about nodes and controllers with an adaptive protocol for routing in wireless ad hoc networks. The adaptive protocol uses distance vectors for routing in computer networks and integrates a sub-set of nodes to serve as controllers.
Molecular Adapter for Capture and Manipulation of Transfer RNA
Awardees: David Bernick, Assistant Professor of Biomolecular Engineering
Department: Biomolecular Engineering
Transfer RNA (tRNA) is an RNA molecule that carries amino acids to a nascent protein strand during translation from a messenger RNA (mRNA) sequence to a protein. tRNA forms three dimensional structures that make it very difficult to work with using standard molecular biology techniques. This patent involves a method of sequencing a tRNA molecule that involves the addition of oligonucleotide adapters, potentially including a cholesterol tag, to tRNA. The sequencing is performed using a nanopore sequencer.
Distributed LC Resonant Tank Clock Tree Synthesis
Awardees: Matthew Guthaus, Professor of Computer Science and Engineering
Department: Computer Science and Engineering
Power consumption is the single most limiting factor in many devices. This invention reduces power consumption, increases device performance, and lengthens battery life for many such devices by design improvements to those chips. It does so by an iterative placement of electronic ballasts that balance the clock network electronic characteristics.
Salt-Tolerant DNA Polymerases
Awardees: David Bernick, Professor of Biomolecular Engineering
Department: Biomolecular Engineering
This patent describes a method of artificially synthesizing DNA (e.g. via polymerase chain reaction – PCR), or as a motor to translocate a strand of DNA using a DNA polymerase enzyme that works in high salt conditions, such as a solution with an halide concentration greater than 5%. The polymerases used in the methods were initially purified from a collection (metagenome) of archaeal and bacterial cells that live in high-salt conditions, enriched for the viruses that infect them.
Practical Two-Frame 3D+2D TV
Awardees: James Davis, Professor of Computer Science
Department: Computer Science
This patent describes a method for making 3D televisions and movie screens viewable without special glasses. These screens currently require viewers to wear special glasses to see the 3D effect. If the glasses are removed then the viewer sees a double image which is essentially unwatchable. The method described here instead provides a normal 2D viewing experience when the glasses are removed.
Robust Single-Phase DC/AC Inverter for Highly Varying DC Voltages
Awardees: Ricardo Sanfelice, Associate Professor of Computer Engineering; Jun Chai, Research Assistant
Department: Computer Engineering
The invention provides a single phase DC/AC inverter with a unique hybrid control circuit. Given an input DC voltage signal, the inverter produces an AC output signal that approximates a given sinusoidal AC reference signal. The invention solves the problem of robustly converting highly varying DC power into desired AC power. Advantageously, the precision with which the AC output signal approximates a desired reference signal can be adjusted via a tunable parameter in the control circuit, conversion is guaranteed under varying input voltages, and the harmonic distortion is almost entirely eliminated at low frequencies.
Current Mode Clock Distribution
Awardees: Matthew Guthaus, Associate Professor of Computer Engineering; Riadul Islam (previously Ph.D. Student at UCSC)
Department: Computer Engineering
In a high-performance computer system design, the clock network consumes a significant amount of power and causes the most switching noise. High power consumption requires larger batteries while switching noise degrades the accuracy of sensitive sensor measurements in modern Systems-on-Chips. Prof. Matthew Guthaus, faculty in Computer Engineering, and his graduate student Riadul Islam, now a faculty at University of Michigan Dearborn, have developed the concept of a current-mode clock distribution to address these problems. Current-mode clocking senses current flow rather than a traditional voltage swing in clock wires and thereby eliminates most of the noise and power problems in traditional clock distribution schemes. Current-mode clocking simultaneously increases the potential maximum speeds of computer chips for performance improvements.
Therapeutic Compositions and Methods For Treating HIV Including Identification and Manipulation of Particular Domains Associated With Immunogenicity
Awardees: Phillip Berman, Distinguished Professor; Sara O’Rourke, Associate Project Scientist; William Scott, Professor
Department: Biomolecular Engineering
This patent describes HIV viral proteins with engineered mutations. In particular, the engineered mutations help expose antibody epitopes in the viral proteins that raise broadly neutralizing antibody responses, which could in turn result in a more effective HIV vaccine.
HIV-1 Gp 120 V1n2 Antigens And Immunological Uses Thereof
Awardees: Phillip Berman, Distinguished Professor; Kate Mesa, Lab Manager; Bin Yu, Specialist
Department: Biomolecular Engineering
This patent describes small, properly folded and glycosylated fragments of the HIV envelope glycoprotein, gp120, that appear to be useful components of an HIV vaccine. Over the last decade scientists have identified 3-4 sites on the 510 amino acid envelope protein recognized by protective antibodies. However these sites contain specific sugar molecules (mannose-5) and fail to promote a strong immune responses in the context of the full length gp120 molecule. Thus new ways are required to target antibody responses to these key sites rather than the dozen or more sites recognized by non-protective antibodies. This patent describes properly folded and glycosylated fragments of gp120, and methods for their production. When included in an HIV vaccine, these fragments can focus the immune response to sites recognized by protective antibodies.
Switchable LED Lightbulb
Awardee: David Munday, Lecturer
Department: Computer Engineering
The US patent office recently issued a patent to a senior design student team and Professor David Munday for inventing a new LED lightbulb capable of multiple brightness settings all within the same bulb. Most commercial LED light bulbs are manufactured for a given brightness level, but this bulb is adjustable through a number of possible controls including onboard buttons, wifi control, and automatic brightness control.
Two-Chambered Dual-Pore Device
Awardee: Holger Schmidt, Associate Dean for Research and Professor of Electrical Engineering
Department: Electrical Engineering
Nanopores form the basis of several approaches to next generation DNA sequencing technology. The basic idea behind this is to identify the bases that make up DNA one by one as they move through a nanoscopic opening. This invention describes how to improve control over the molecules to be tested by using two coupled nanopores, and how to implement this principle on a compact semiconductor chip.
BamBam: Parallel Comparative Analysis of High-Throughput Sequencing Data (two patents)
Awardee: David Haussler, Distinguished Professor and Scientific Director, UC Santa Cruz Genomics Institute
Department: Biomolecular Engineering
The purpose of the inventions encompassed by these two patents is to more efficiently compare biological sequences from two distinct samples. The analysis of biological sequence information usually involves the manipulation of enormous data files, which in turn results in long processing times to generate a meaningful comparison between the biological sequences. The inventions described in these two patents provides a more efficient way to compare biological sequences from distinct samples from a patient (e.g. normal tissue vs. tumor tissue) and generate patient-specific treatment instructions based on those sequences. The 9,646,134 patent concerns genomic information while the 9,652,587 patent also encompasses proteomic and transcriptomic information.
Interferometric Focusing of Guide-Stars for Direct Wavefront Sensing
Awardees: Joel Kubby, Professor; Xiaodong Tao, Assistant Project Scientist
Department: Electrical Engineering
The optimal performance of an optical microscope is difficult to achieve due to aberrations caused by tissues. In order to compensate for these aberrations, we applied adaptive optics with direct wavefront sensing using fluorescent “guide-stars” embedded in tissues for wavefront measurement. A scattering effect within the tissues limits the intensity of the guide star and reduces the signal to noise ratio of wavefront measurement. This patent describes the use of interferometric focusing of excitation light onto a guide-star deep within tissue to increase the fluorescence intensity of the guide-star which in turn overcomes the signal loss caused by scattering.
Nanopipette Apparatus for Manipulating Cells
Awardee: Nader Pourmand, Associate Professor
Department: Biomolecular Science and Engineering
The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Dr. Pourmand and his team have developed a single-cell interrogation platform based on scanning ion conductance microscopy for continuous sampling of intracellular content from individual cells. Among many other functionalities, for the nanobiopsy, this platform uses a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. Researchers might use this platform to understand cancer and other diseases which might provide a foundation for dynamic subcellular genomic analysis.
Compositions, Devices, Systems, And Methods For Using A Nanopore
Awardee: Mark Akeson, Professor
Department: Biomolecular Science & Engineering
The invention is one of a series of patents from the biomolecular engineering department concerning sequencing of DNA using a nanoscale hole or “nanopore.” When a voltage is applied across the nanopore, DNA is pulled through the hole in single file order. The bases that make up the DNA are read as they transit the pore. In this particular patent, the inventors combined voltage feedback control with an enzyme to precisely regulate movement of the DNA. This results in improved DNA sequencing accuracy.
Faster, Better Genome Assembly
Awardee: Edward Green, Associate Professor
Department: Biomolecular Engineering
Assembling genomes is like solving a giant, 3 billion-piece jigsaw puzzle. The invention describes a streamlined way to figure out which pieces are near other pieces so the puzzle can be reconstructed more accurately and quickly. Licensed by Dovetail Genomics in Santa Cruz, the invention has been used to assemble the genomes of hundreds of plant and animals. With this information, scientists can begin to unravel the biology inherent in each.
In the spring, several new initiatives from the UC Office of the President will be rolled out across the 10 campuses to further innovation, commercialization, and entrepreneurship and highlight the growing body of research providing public benefit. The IATC office will lead the implementation of these initiatives with various leaders around campus to bring these opportunities to the entire university community.