The UC Santa Cruz Office of Research has created the Inventor Recognition Program (IRP) to acknowledge researchers on a quarterly basis for their U.S. patent awards and to showcase the groundbreaking research that is conducted on the UCSC campus every day. Launched in December 2016, the IRP is meant to recognize the hard work of UCSC faculty, students, and staff and to help them realize the value of their inventions by commercializing their inventions and discoveries.
Current UCSC Inventor: Seth Rubin, Professor – Chemistry & Biochemistry
Inventor Previously at UCSC:
Keelan Guiley
Cyclin-dependent kinases (Cdks) are enzymes that play a part in regulating the cell cycle. Cdks bind to cyclins (Cyc), forming complexes that can phosphorylate other proteins. p27 is a protein that can further regulate Cdk-cyclin complexes.
Cdk-cyclin complexes are implicated in the cancer cell-cycle progression. Cdk4 and Cdk6 inhibitors have been developed in the past decade for cancer treatment. These inhibitors have been developed in screens against recombinant Cdk4-CycD dimeric complex. However, it is important to also consider how p27 affects Cdk-cyclin complexes, and screen for inhibitors for cancer treatments in light of p27.
This patent includes a polypeptide for an engineered p27, where the engineered p27 forms a trimeric protein complex with Cdk4/Cdk6 and CycD. The p27-Cdk4/6-CycD complex can be used to screen against new inhibitors that are effective in different cancer types.
VELOCIMETRY-BASED IDENTIFICATION OF SINGLE PROTEINS AND OTHER PARTICLES
Current UCSC Inventor: Holger Schmidt, Distinguished Professor – Electrical and Computer Engineering
The demand for assays on the molecular level has increased. Molecular analysis techniques are used for diagnosis, treatment, and drug development. However, current approaches are limited when there are low copy numbers or very little sample material. There is an unmet need for low abundance detection and detection at single cell protein concentrations without requiring complex, bulky, and expensive devices and systems.
This patent, in collaboration with a researcher at Brigham Young University, describes ways to detect, identify, and manipulate individual molecules based on their velocity as they move through an optically interrogated channel.
The technology described in this patent has been licensed by and is being commercialized by Fluxus in Sunnyvale.
Inventors previously at UCSC: Michael Wehner, Keng-Yu Lin, Natalie King
Millimeter scale internal combustion engines can potentially replace batteries in effectively any small portable powered system. These systems would use liquid hydrocarbon fuels, which hold more energy per weight than certain batteries. Instead of charging, such systems would require changing fuel capsules, an instantaneous solution.
However, the polymer combustion engines that have been developed require connection to external controls. Such engines have to be controlled either manually or using active valves that are individually programmed to open and close at predetermined times. These auxiliary systems are far larger and heavier than the micro-engines themselves, diminishing the micro-engines’ usefulness.
This patent describes passive microfluidic valves that allow, modulate, or block flow based on predetermined system parameters such as flow rate or pressure difference. The valves can also be configured to either allow or block flow in the reverse direction. Such valves allow for controlling combustion reactions at small scales.
NOISE REDUCTION IN HIGH FREQUENCY AMPLIFIERS USING TRANSMISSION LINES TO PROVIDE FEEDBACK
Ken Pedrotti, Professor and Chair – Electrical and Computer Engineering
Inventor Previously at UCSC:
Tianchi Zeng
Receivers are used in wireless systems. They accept and make sense of signals that are transmitted. Low noise amplifiers (LNAs) are used to pick up weak signals and amplify them without also significantly amplifying noise. LNAs can be incorporated in receivers. Reducing LNA noise can increase the transmission range or reduce power consumption, resulting in higher performance or reduced system cost.
This patent includes approaches to reduce the noise in LNAs by using a transmission line feedback path. These LNAs can be implemented in many applications, such as receivers.
EXTRA-COMPACT KEY WITH REUSABLE COMMON KEY FOR ENCRYPTION
Hamid Sadjadpour, Professor – Electrical and Computer Engineering
Cryptography has been used for centuries to transmit messages such that only the intended recipient, and not any eavesdroppers, can read them. Encryption scrambles the data being transferred. Only sender and the recipient have the keys to make sense of the scrambled data.
Aspects of this patent involve techniques for compact key encoding of data for public storage, such as cloud storage, with either higher levels or security, smaller keys, or both. Perfect secrecy can be accomplished with a much smaller key size than file size and with less complexity than previously introduced. The encrypted or encoded data takes no more space than the plaintext, because a random bit is not inserted at any position, as in previous works.
Furthermore, the new approaches assume no limitations on the eavesdropper storage size or computational capability and are perfectly secure with probability one. In these techniques, both the user and the eavesdropper are assumed to have unlimited storage and computational complexity capabilities.
TECHNIQUES FOR LOOP-FREE DYNAMIC ON-DEMAND AND PROACTIVE ROUTING IN COMMUNICATIONS NETWORKS
JJ Garcia-Luna-Aceves, Distinguished Professor Emeritus – Computer Science and Engineering
Inventor Previously at UCSC: Ehsan Hemmati
In networks, such as computer networks, routing loops can occur when there is a mistake about the path that data should take to be transmitted to its destination. Routing loops can cause data to bounce back and forth between the same nodes in a network, thus negatively affecting the network.
This patent includes ways to establish loop-free routes in communications networks by utilizing a reference distance field.
TECHNIQUES FOR VIRTUAL TIME SLOTTING OF COMMUNICATIONS PACKETS
JJ Garcia-Luna-Aceves, Distinguished Professor Emeritus – Computer Science and Engineering
When nodes in a data communications network compete for access to a shared channel, collisions can occur. Carrier-sense multiple access (CSMA) is a method used to avoid collisions. The transmitting node senses whether the shared channel is already active. However, there are circumstances where carrier sensing is neither possible nor easy.
This patent includes techniques for reducing collisions when sharing common radio channels in ad hoc networks at nodes with reduced radio capacity by virtual time slotting (VTS) of communications packets or sharing of information on channel congestion or some combination.
PLATINUM OXIDE NANOPARTICLES FOR ELECTROCHEMICAL HYDROGEN EVOLUTION AND METHODS FOR MAKING ND USING THE SAME
Shaowei Chen, Professor – Chemistry & Biochemistry
Inventor Previously at UCSC:
Forrest Nichols
Electrochemical hydrogen generation provides potential use for future renewable energy storage and conversion. Hydrogen evolution reaction (HER) generally refers to a method of generating hydrogen gas from water, and is an important process in electrochemical energy conversion and storage. Platinum (Pt) is a leading catalyst for HER. However, Pt is high in cost and low in supply, so there is a need to optimize its use.
This patent includes platinum oxide nanoparticles deposited on graphitic carbon nitride nanosheets. These catalyst compositions can be used in HER more efficiently.
Honorable Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
NANOPORE DEVICE FOR REVERSIBLE ION AND MOLECULE SENSING OR MIGRATION
Current UCSC Inventor: Keith Corzine, Professor – Electrical and Computer Engineering
Light emission from a semiconductor device can be an indicator of how that device is operating. This patent, in collaboration with researchers at the Naval Postgraduate School, describes methods for determining the temperature and current of semiconductor devices by measuring light emitted from those devices. The patent also describes methods for measuring light emitted to estimate the long-term degradation for those devices.
CRYSTALLIZATION OF TWO-DIMENSIONAL STRUCTURES COMPRISING MULTIPLE THIN FILMS
Current UCSC Inventor: Nobby Kobayashi, Professor – Electrical and Computer Engineering
Thin film structures, materials, techniques are used for a variety of industrial applications, such as thin film transistors. Demand for better performing electronic devices requires advances to thin film approaches, including compatible structures and scalable processes. This patent, in collaboration with a researcher at Shimane University, includes new methods to form thin structures on non-single-crystalline substrates, such as glass, or on single-crystalline substrates that are highly-incompatible, such as silicon.
METHODS OF PRODUCING NUCLEIC ACID LIBRARIES AND COMPOSITIONS AND KITS FOR PRACTICING SAME
This patent describes the production of nucleic acid (e.g. DNA or RNA) libraries from single stranded nucleic acids through the use of single stranded nucleic acid binding proteins. These libraries can then be used for downstream analysis like PCR or DNA sequencing. Importantly, this method allows accurate sequencing of nucleic acids from low quality samples such as ancient DNA and follicle-free hair.
The technology described in this patent has been licensed by and is being commercialized byClaret Biosciencein Santa Cruz.
Roberto Manduchi, Professor - Computer Science and Engineering
Many people living with low vision use screen magnifiers to read documents and web pages on a computer. Screen magnifiers give users visual access to graphical information and allow them to appreciate even complex layouts displayed on the screen, like a magnifying glass. Conventional screen magnification technology can be slow and a burden to a user in that it requires continuous manual scrolling (using the mouse or trackpad) in order to move the focus of magnification (located at the mouse cursor). This patent includes alternative methods and systems for magnifying text or graphics on a screen, as a more modern aid for reading of the text or graphics.
Marco Rolandi, Professor - Electrical and Computer Engineering
Inventor Previously at UCSC: John Felts
This patent describes a closed cell foam made of chitin, the main component of shrimp shells and other aquaculture waste. It also describes methods of making the foam and resulting products. The foam is biodegradable and can be used in any of a number of products.
Ali Yanik, Associate Professor, Electrical and Computer Engineering
Inventors Previously at UCSC: Xiangchao Zhu, Evan Peterson, Yixiang Li
Microfluidic devices provide control and manipulation of fluids in microfluidic channels and are useful for processing, detecting or analyzing particles of interest in a fluid sample. Applications of microfluidics include immunoaffinity assays, which are designed to detect and isolate analytes of interest, such as low-abundance rare cells, among a larger population of cells in a sample. Traditionally, rare cells have been difficult to effectively and efficiently detect against a large population of background cells. This patent describes advanced ways to isolate targets in a microfluidic channel using a unique arrangement of acoustic waves and capture agents.
SYSTEM AND METHOD FOR SENSING VOLATILE ORGANIC COMPOUNDS
Current UCSC Inventor: Peter Weiss-Penzias, Faculty Researcher, Chemistry & Biochemistry; Microbiology and Environmental Toxicity; Earth and Planetary Sciences
Inventor Previously at UCSC: Mauricio Rojas-Andrade
The patent describes an accurate and low cost sensor for the detection of volatile organic compounds such as ethanol. The gas sensor makes use of a metal oxide nanostructure layer that has a resistance that varies in response to the concentration of the volatile organic compound. This invention is particularly useful in breweries, wineries, and composting facilities that are in need of such sensors.
Honorable Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
NETWORK CONGESTION REDUCTION USING BOOLEAN CONSTRAINED MULTIPATH ROUTING
Current UCSC Inventor: Holger Schmidt, Distinguished Professor – Electrical and Computer Engineering
Liquid-core waveguides can be used to detect various particles. In particular, these waveguides find use in detecting biological samples such as nucleic acids and proteins. There are several drawbacks to current liquid-core waveguide technologies. One drawback is that particles near the walls of the liquid-core waveguides are not detected sufficiently or at all. This patent includes improved ways to detect particles by using a liquid-core waveguide that can better capture generated light and its transport to a photodetector.
APPARATUS AND METHOD FOR EFFICIENT DEPLOYMENT OF NODES IN A NETWORK
Current UCSC Inventor: Katia Obraczka, Professor – Computer Science and Engineering; Kerry Veenstra, Lecturer – Computer Science and Engineering
Outdoor camera networks have many applications, such as surveillance. Choosing the positions of camera nodes in three dimensional regions can be challenging. Landforms such as mountains and hills might block the cameras’ line of sight views. Conventional methods for choosing where to place nodes are computationally inefficient. This patent includes ways to efficiently choose where to place nodes in a network.
CARBON-DOPED NICKEL OXIDE CATALYST AND METHODS FOR MAKING AND USING THEREOF
Current UCSC Inventor: Yat Li, Professor – Chemistry and Biochemistry
Inventors Previously at UCSC: Tianyi Kou, Mingpeng Chen
Water electrolysis (water splitting) is a sustainable and environmentally friendly way to generate hydrogen fuel. Using alkaline electrolytes for hydrogen evolution reaction (HER) avoids some of the issues that arise with using acidic electrolytes. However, using alkaline electrolytes poses its own problems as well. This patent includes ways to utilize nickel oxide to form alkaline HER catalysts. Nickel oxide can be doped with carbon, which overcomes the issues that come with using it as an alkaline HER catalyst.
METHODS OF PRODUCING RIBOSOMAL RIBONUCLEIC ACID COMPLEXES
Ribosomal ribonucleic acid (rRNA) sequencing is a method that can be used to identify organisms present within a given sample. For example, 16S rRNA sequencing is used to study phylogeny and taxonomy from samples that are difficult or impossible to study. Sequencing rRNA with next-generation sequencing is a cost-effective way to identify organisms that may not be found using other ways. This patent includes methods of making nucleic acid complexes that involve combining, under certain conditions, a sample including rRNA, a probe complement oligonucleotide, and an oligonucleotide probe. The rRNA of the nucleic acid complex produced can then be sequenced via nanopore sequencing to determine whether and how much of an organism is in a sample.
ELECTRO-PLASMONIC NANOANTENNA FOR EXTRACELLULAR OPTICAL DETECTION OF ELECTROGENIC SIGNALS
Current UCSC Inventor: A. Ali Yanik, Associate Professor – Electrical and Computer Engineering
Inventors Previously at UCSC: Ahsan Habib, Xiangchao Zhu
There are several benefits to using light to detect electrophysiological signals, such as those that come from neuronal activity. Light offers, among other things, excellent spatiotemporal resolution – light can be utilized to detect when and where activities occur. In order to use light to detect such signals, however, electrogenic activity must be converted to photonic signals. There are translators capable of converting electrogenic activity to photonic signals. However, conventional translators are limited because they may not be sensitive enough. This patent includes an electro-plasmonic nanoantenna that overcomes the limitations of conventional translators.
COMPACT KEY WITH REUSABLE COMMON KEY FOR ENCRYPTION
Current UCSC Inventors: Hamid Sadjadpour, Professor – Electrical and Computer Engineering
Aspects of this patent involve techniques for compact key encoding of data for public storage, such as cloud storage, that provides a substantially higher level of security, including perfect security in some cases, or substantially smaller keys than in previous approaches, or some combination. This patent improves upon the inventor’s previous work. Perfect secrecy can be accomplished with a much smaller key size than file size and with less complexity than previously introduced. Furthermore, the encrypted or encoded data takes no more space than the plaintext, because a random bit is not inserted at any position, as in previous works.
SYSTEM FOR DETERMINING RESERVOIR PROPERTIES FROM LONG-TERM TEMPERATURE MONITORING
Current UCSC Inventor: Emily Brodsky, Professor – Earth and Planetary Sciences
In applications such as geothermal engineering and environmental engineering, there is a need to determine in situ the properties of underground reservoirs that allow fluid to flow. Conventional approaches to determine such properties typically require invasive and difficult to analyze tests, or measure indirect variables that may not be directly related to the flow properties. This patent, in collaboration with a researcher at Cornell University, includes ways to passively determine reservoir properties. The resulting estimates of reservoir properties are more accurate and efficient.
Current UCSC Inventor: Nobby Kobayashi, Professor – Electrical and Computer Engineering
Hydrogen (H2) is a promising clean fuel that can be generated by splitting water with sunlight. One advantageous way to utilize sunlight to generate H2 is by splitting water using a photoelectrochemical cell (PEC). However, this method has its own drawbacks. Hydrogen bubbles can interfere with sunlight propagation and degrade performance. This patent addresses this issue by including PECs that differ in design from conventional PECs. The PECs included spatially and temporally decouple generation of sunlight-driven electron-hole pairs from the transfer of electrical charges from/to liquid electrolyte (e.g., water) to produce H2. In contrast to conventional PEC designs where these two processes occur simultaneously on the same surface of a photoelectrode, this PEC design has these processes take place on opposite surfaces of the photoelectrode.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
STRUCTURAL MATCHING FOR FAST RE-SYNTHESIS OF ELECTRONIC CIRCUITS
Current UCSC Inventor: J.J. Garcia-Luna-Aceves, Distinguished Professor – Computer Science and Engineering; Luca de Alfaro, Professor – Computer Science and Engineering
Inventor Previously at UCSC: Molly Zhang
When nodes in a data communications network compete for access to a shared wireless medium, collisions can occur. The carrier-sense multiple access (CSMA) protocol is used to avoid data packet collisions on shared common radio channels. However, there are several circumstances in which using the CSMA protocol is not ideal. This patent includes ways to reduce packet collisions on shared channels in data communications networks by using virtual time slotting or shared congestion information or some combination.
METHODS OF PRODUCING COBALT NANOPARTICLES AND HOLLOW GOLD NANOSPHERES AND KITS FOR PRACTICING SAME
Current UCSC Inventor: Jin Zhang, Distinguished Professor – Chemistry & Biochemistry; Sarah Lindley, Research Fellow – Chemistry & Biochemistry
Inventors Previously at UCSC: Staci Adams, Frank Song, Ying-Chih Pu, Weichun Zhang
Noble metal nanostructures are important and have many applications, such as photothermal therapy treatments for cancer. Being able to control various properties of metal nanostructures, such as their size, is desirable because different applications require different properties.
The hollow gold nanosphere (HGN) are a type of metal nanostructure that has performed strongly in various applications. Cobalt nanoparticles can be used to produce HGNs. This patent includes methods of making cobalt nanoparticles of a pre-selected diameter by selecting a corresponding temperature. By using these methods, the diameter of the resulting HGNs can also be controlled.
INHIBITORS OF PLATELET FUNCTION AND METHODS FOR USE OF THE SAME
Current UCSC Inventor: Ted Holman, Professor – Chemistry & Biochemistry
Platelet aggregation helps stop blood flow. For instance, platelet aggregation is crucial to stopping blood flow after an injury such as a cut. However, for those with dangerous diseases such as thrombosis, platelet aggregation can be deadly. This patent, which resulted from a collaboration with researchers at the University of Michigan, includes compounds and methods for inhibiting platelet aggregation.
METHODS AND COMPOSITIONS FOR TREATING INFLAMMATORY DISEASES
Current UCSC Inventor: Susan Carpenter, Professor – Molecular, Cell, & Developmental Biology
Inventors previously at UCSC:
Apple Vollmers, Sergio Covarrubias
Immune responses help fight against infections. An uncontrolled immune response, however, can be deadly. Sepsis is one such inflammatory disease that can lead to organ failure and death, which is why it is crucial to develop new sepsis therapies. This patent involves inhibitors of gastric adenocarcinoma predictive long intergenic noncoding (GAPLINC) RNA, a type of long noncoding RNA (lncRNA), and are based on the discovery that GAPLINC plays a role in regulating inflammation.
SYSTEM AND METHOD FOR ARTIFICIAL INTELLIGENCE STORY GENERATION ALLOWING CONTENT INTRODUCTION
Inventors Previously at UCSC: Snigdha Chaturvedi, Faeze Brahman, Alexandru Petrusca
There are several challenges to automatic story generation, including composing a passage of text that is coherent and fluent. This patent includes techniques for artificial intelligence (AI) assisted story generation. The techniques give the user more control over the generated story by allowing the user to introduce content as the story progresses. The experience is an interactive one and the resulting story is more satisfactory to the user.
BARCODED SOLID SUPPORTS AND METHODS OF MAKING AND USING SAME
Current UCSC Inventors: Ed Green, Professor – Biomolecular Engineering; Balaji Sundararaman, Graduate Student – Biomolecular Engineering
Barcodes are identifiable nucleic acid sequences that can be coupled to a target nucleic acid, either directly or indirectly. Doing so assists in analyzing the nucleic acids of interest. This patent includes ways to make barcoded solid supports. These methods have a variety of applications, such as cancer diagnostics.
Current UCSC Inventor: Ed Green, Associate Professor - Biomolecular Engineering
In order to sequence nucleic acids, such as DNA, using certain sequencing methods, the nucleic acids first have to be prepared. This patent includes ways of utilizing oligonucleotides to prepare target nucleic acids for sequencing.
PHYSICALLY OPERABLE AND MECHANICALLY RECONFIGURABLE LIGHT SOURCES
Current UCSC Inventor: Holger Schmidt, Distinguished Professor – Electrical and Computer Engineering
In optofluidics, it may be necessary to adjust the amount of light coming from a light source, or to control whether the light source is even activated. For example, a laser may need to be activated, deactivated, and/or tuned. This patent includes a new approach to reconfigure light sources.
METHOD FOR DETERMINING RELATEDNESS OF GENOMIC SAMPLES USING PARTIAL SEQUENCE INFORMATION
Current UCSC Inventor: Ed Green, Associate Professor - Biomolecular Engineering
Inventor previously at UCSC:
Samuel H. Vohr
Determining whether two DNA samples come from the same individual can be difficult when there is a limited amount of DNA present. This challenge can arise, for example, when analyzing DNA from individuals who lived thousands of years ago. This patent includes a new method for determining whether two DNA samples come from the same individual. The method involves utilizing very low amounts of DNA and even partial sequences of DNA fragments.
COMPACT KEY ENCODING OF DATA FOR PUBLIC EXPOSURE SUCH AS CLOUD STORAGE
Current UCSC Inventor: Hamid Sadjadpour, Professor – Electrical and Computer Engineering
Inventor previously at UCSC:
Mohsen Karimzadeh Kiskani
Aspects of this patent involve techniques for compact key encoding of data for public storage, such as cloud storage, that provides a substantially higher level of security, including perfect security in some cases, or substantially smaller keys than in previous approaches, or some combination.
DUAL-CAPACITOR RESONANT CIRCUIT FOR USE WITH QUASI-RESONANT ZERO-CURRENT-SWITCHING DC-DC CONVERTERS
Current UCSC Inventor: Leila Parsa, Professor – Electrical and Computer Engineering
There is a need for DC-DC converters which provide for efficient energy transfer, particularly when it comes to utilizing renewable energy sources such as solar photovoltaics and wind turbines. Aspects of this patent include a DC-DC converter with a dual-capacitor resonant circuit. Such a converter has several benefits over other converters.
FLUORESCENCE-BASED REPORTERS FOR MUTAGENESIS DETECTION IN E. COLI
Current UCSC Inventor: Manel Camps, Associate Professor - Microbiology and Environmental Toxicology
Inventor previously at UCSC:
Jennifer Allen
When model organisms are exposed to chemicals, occurrence of DNA mutations can provide insight on various things, such as whether a chemical would cause birth defects or cancer. Mutagenesis can also be used to study various DNA processes. This patent includes a method for using fluorescence-based reporters to detect mutagenesis in E. coli.
CATALYSIS OF HYDROGEN EVOLUTION REACTION USING RUTHENIUM ION COMPLEXED CARBON NITRIDE MATERIALS
Current UCSC Inventor: Shaowei Chen, Professor – Chemistry and Biochemistry
Inventors previously at UCSC:
Yi Peng, Bingzhang Lu
Hydrogen evolution reaction (HER) generally refers to a method of generating hydrogen gas from water. Catalysts such as platinum are used to carry out HER. However, catalysts currently used can be expensive or catalyze HER inefficiently. Aspects of this patent include the incorporation of ruthenium ion into a carbon nitride nanosheet and subsequently incorporating graphene oxide into the nanosheet; the resulting composite can be used to catalyze HER.
NANOPORE SENSOR FOR ENZYME-MEDIATED PROTEIN TRANSLOCATION
Current UCSC Inventor: Mark Akeson, Professor – Biomolecular Engineering
Inventors previously at UCSC:
Jeffrey Matthew Nivala, Douglas Benjamin Marks
Nanopores have popularly been used to sequence DNA. It is harder, however, to sequence proteins with nanopores due to the structural characteristics and nonuniform charges of proteins. This patent describes a method of unfolding and passing proteins through nanopores in a controlled, sequential manner so that the amino acid sequences of proteins can be analyzed.
DYNAMIC TUNING OF CONTENTION WINDOWS IN COMPUTER NETWORKS
Current UCSC Inventor: Katia Obraczka, Professor – Computer Science and Engineering
Inventor previously at UCSC:
Yalda Edalat
When multiple nodes in a communications network send data at the same time, a collision occurs, disrupting data transmission and negatively impacting the communications network. Collision prevention for wireless networks focuses on avoiding collisions, a method which can involve delaying data transmission. This patent describes techniques for determining the appropriate amount of time to delay data transmission in order to avoid collisions.
PLASMOFLUIDIC MICROLENSES FOR LABEL-FREE OPTICAL SORTING OF BIOPARTICLES
Current UCSC Inventor: A. Ali Yanik, Associate Professor – Electrical and Computer Engineering; Yixiang Li, Graduate Student – Electrical and Computer Engineering
Inventor previously at UCSC:
Xiangchao Zhu
Optical chromatography is a technique used to separate microscopic particles. For example, it can be used to separate bioparticles such as human blood components. Optical chromatography is a useful technique because it can distinguish between bioparticles having subtle differences. This patent includes a microlens that improves existing optical chromatography techniques.
SEMANTIC INTERIOR MAPOLOGY: A TOOL BOX FOR INDOOR SCENE DESCRIPTION FROM ARCHITECTURAL FLOOR PLANS
Roberto Manduchi, Professor – Computer Science and Engineering
Inventor previously at UCSC:
Viet Trinh
This patent describes Semantic Interior Mapology (SIM) toolbox, computer implemented systems or methods that can convert floor plans and contents of a room (such as furniture) to vectorized form. For example, a floor plan of a building can be converted to an interactive 3D view.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
METHODS OF PRODUCING NUCLEIC ACID LIBRARIES AND COMPOSITIONS AND KITS FOR PRACTICING SAME
Current UCSC Inventors: JJ Garcia-Luna-Aceves, Professor - Computer Science and Engineering
In network routing, the traditional collision avoidance handshake consists of a request-to-send (RTS), clear-to-send (CTS), a data packet, and an acknowledgment (ACK). This invention augments that process using pilots, which are sent by a receiving node after it sends a CTS or by a sending node after it sends its data packet. The result is that multiple access interference between data packets or ACKs is avoided.
This solution is particularly effective in a system that relies on single half duplex channels which can fail due to hidden terminals, exposed transmitters, and exposed receivers.
METHOD AND APPARATUS FOR EFFICIENT COMMUNICATION PACKET GENERATION IN INTERNET OF THINGS (IOT)
Current UCSC Inventor: Katia Obraczka, Professor - Computer Science and Engineering
This invention resulted from a collaboration with investigators from the University of Brasilia and the Federal University of Pernambuco in Brazil. The Internet’s TCP/IP protocol architecture is a layered system design. As such, the functions performed by the TCP/IP protocol suite are implemented at different protocol layers, where each layer provides a specific set of services to the layer above through a well-defined interface. Using this interface, data being received or sent is passed up or down the stack on its way through the network. However, layered design approaches can increase overhead, as each layer incurs additional communication (e.g., additional header field) and processing costs. Furthermore, limiting the flow between layers to data plane information restricts the sharing of control information across layers and may lead to functions being duplicated at different layers. The technology described in this patent is referred to as the IoT Unified Services framework, or IoTUS for short. It involves generating communication packets for use by IoT nodes. The packets are generated by presenting an API to each protocol in a protocol stack. A single packet buffer is configured to hold headers for all the protocols that are directed to a destination node. Then memory pointers are stored in tables maintained by the porotocols. When a input from the first protocol reaches the API, the single packet buffer is updated, as is the table in the second protocol. It has the effect of facilitating and promoting information and functional sharing among the layers of the network protocol stack, resulting in more energy and storage-efficient IoT networks.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventors: Jin Zhang, Professor - Chemistry & Biochemistry
Inventors previously at UCSC: Jason Cooper; Sheraz Gul
Quantum dots are important materials in solid state lighting and biological labeling. Their optical/electronic properties can be altered by changing their size or by adding other elements. However, adding new elements to the quantum dot results in a charge imbalance that impairs their function. This patent describes improved versions of quantum dots that include a trivalent cation, (e.g. Al3+, Ga3+, In3+, or Tl3+) to correct the charge imbalance. The new structures also include an organic capping ligand to enhance water solubility of the nanocrystal.
Current UCSC Inventor: Keith Corzine, Professor - Electrical and Computer Engineering
Inventor previously at UCSC: Vahid Dargahi
Conversion of direct current (DC) to alternating current (AC) is necessary in situations where AC appliances and devices are run in a system that is powered by DC, such as a solar powered home or a nuclear powered vessel. This is often done using a modular multilevel converter. These are formed of cascaded submodules of circuits. However, such a system can be subject to circulating electrical current through the submodules. This decreases output power, requires components with higher current ratings, and increases heat in the system. The patent describes a system that introduces pulse width modulation insulated gate bipolar transistors to the modules, which eliminates the circulating current in the submodules.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
DETERMINATION OF THE OPTIMAL FLUID PULSES FOR ENHANCEMENT OF RESERVOIR PERMEABILITY AND PRODUCTIVITY
Current UCSC Inventor: Ed Green, Associate Professor - Biomolecular Engineering
The invention is a method of identifying DNA segments that are close to one another on the same chromosome. This facilitates phasing, or determining which variants on those segments are derived from the same copy of the chromosome (e.g., both segments are on the maternally inherited chromosome) or different copies (e.g., one segment is on the maternally inherited chromosome and the other is on the paternally inherited chromosome). This particular method involves the formation of protein-nucleic acid crosslinks that protect the nucleic acid molecule from damage and preserve physical linkage before adding a barcode tag and performing next generation nucleic acid sequencing.
COMPLEMENTARY CONJUGATED POLYELECTROLYTE COMPLEXES AS ELECTRONIC ENERGY RELAYS
Current UCSC Inventors: Alexander Ayzner, Associate Professor - Chemistry & Biochemistry
This patent relates to light harvesting antennae which can be incorporated into artificial photosynthesis systems. The particular system involves the use of conjugated polyelectrolytes which are semiconducting polymers with charged sidechains. The polyelectrolytes form complexes where one conjugated polyelectrolyte acts as an electron donor and the other conjugated polyelectrolyte acts as an electron acceptor. The electron acceptor can be poly(alkylcarboxythiphene), and any conjugated polyelectrolyte that forms a donor/acceptor pair with the poly(alkylcarboxythiphene) can be used.
HYDROXYEICOSATRIENOIC ACID COMPOUNDS AND THEIR USE AS THERAPEUTIC AGENTS
Current UCSC Inventors: Ted Holman, Professor - Chemistry & Biochemistry
Invented in collaboration with investigators at the University of Michigan, this patent describes 12(S)-hydroxyeicosatrienoic acid (12(S)-HETrE) compounds that can be used in treating any of a number of pathological conditions including thrombotic conditions such as myocardial infarction or stroke.
NETWORK CONGESTION REDUCTION USING BOOLEAN CONSTRAINED MULTIPATH ROUTING
Current UCSC Inventors: Brad Smith, Associate Professor - Computer Engineering
This patent describes a method of routing data packets through the use of Boolean expressions. In particular, the method involves computing for a source node and all destination nodes in a data network a set of routes that satisfy policy constraints expressed as Boolean variables and selecting from that set of routes a route that satisfies the policy constraints but that have sufficient bandwidth. This invention then allows selection of paths that satisfy particular policies but that also reduce congestion.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventor: Scott Lokey, Professor -Chemistry & Biochemistry
This patent describes a set of hexapeptide scaffolds that can enter cells and interact with drug targets inside the cell that are inaccessible to conventional small molecule therapeutics. The specific peptides are cyclic with Z – Y – X – Pro – Y – Phe motif where Pro represents the amino acid proline, Phe represents the amino acid phenylalanine, and where X, Y, and Z are variable amino acid structures.
PYRROLOQUINOLIN COMPOUNDS AND METHODS OF USING SAME
Current UCSC Inventors: Phil Crews, Professor - Chemistry & Biochemistry Nicholas Lorig-Roach, Graduate Student - Biomolecular Engineering
Inventors previously at UCSC: Sheng Lin, Erin McCauley, Karen Tenney
This invention resulted from a collaboration with Dr. Fred Valeriote at the Henry Ford Medical Center. The patent describes the isolation and derivatization of compounds derived from marine sponges that could have efficacy in inhibiting cell proliferative disorders such as cancers.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
Current UCSC Inventor: Jose Renau, Professor - Computer Science and Engineering
Electronic Design Automation is employed to design circuitry is that too complex to be designed solely by humans. These include Very-Large Scale Integration (VLSI) circuits and Field Programmable Gate Arrays (FPGA). The patent involves a computer based method of speeding up design cycles for highly complex FPGAs. This method involves automatically detecting a section of a circuit design that can be re-used in later designs and automatically re-using those sections in those later designs.
NON-MIGRATORY INTERNAL PLASTICIZERS ATTACHED TO A PENDANT COVALENT LINKAGE
Current UCSC Inventor: Rebecca Braslau, Professor - Chemistry & Biochemistry</sp
Inventor previously at UCSC: Chad Higa
Plasticizers such as phthalates are added to plastics such as polyvinylchlorides and polystyrenes to make them softer. However, phthalates leach from discarded plastics over time and into the environment. Phthalates frequently mimic hormones and act as endocrine disruptors in humans as well as in wildlife. The patent describes a plasticizer that softens the plastic, but stays covalently bonded to the polymer and therefore does not leach from the plastic.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventor: Holger Schmidt, Professor - Electrical and Computer Engineering
The patent describes an optical waveguide that includes a microfluidic channel with a pneumatically controlled lifting gate valve that can block or release fluid flow as well as alter the light path within the waveguide. Such systems can be used in any of a number of microfluidic systems including lab-on-a-chip style optofluidic chips that can be used to detect biological entities such as viruses with greater speed and precision than PCR or antibody based methods.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
Current UCSC Inventors: Miten Jain, Assistant Research Scientist - Biomolecular Engineering Hugh Olsen, Project Scientist - Biomolecular Engineering Mark Akeson, Professor - Biomolecular Science & Engineering
This patent describes a method of detecting modified cytosine residues in genomic DNA using nanopore sequencing. In particular, the method detects 5-methylcytosines, 5-hydroxymethyl cytosines, 5-formylcytosines, and 5-carboxylcytosines and involves treating the DNA with a deaminase and a glycosylase. These create an abasic site in the DNA which can be readily detected using nanopore sequencing.
SYSTEM FOR CONTINUOUS MUTAGENESIS IN VIVO TO FACILITATE DIRECTED EVOLUTION
Current UCSC Inventor: Manel Camps, Associate Professor - Microbiology & Environmental Toxicology
This patent describes a system of performing in vivo mutagenesis in a continuous culture without selection of mutants resulting in more efficient directed evolution. In particular the patent describes a an error prone DNA polymerase with particular mutations and a method of using it to perform directed evolution in E. coli cells. The method involves coexpressing the mutant polymerase with a gene that is the target of the directed evolution in E. coli. DNA plasmids including the mutation can readily be purified from E. coli and tested on selective media.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
Current UCSC Inventor: Jose Renau, Professor - Computer Science and Engineering
Inventor Previously at UCSC: Rafael Trapani Posignolo
The invention described in this patent is an automated method of designing integrated circuits called LiveSynth. The method involves dividing a circuit design into multiple regions with invariant boundaries that do not have their functionality changed during synthesis. LiveSynth is then able to find these regions - called invariant cones – in which no further optimization is necessary during the original synthesis. The result is a significantly more productive method of hardware design. More changes can be explored per unit time and suboptimal designs are quickly identified and moved on from.
Z-SCHEME MICROBIAL PHOTOELECTROCHEMICAL SYSTEM (MPS) FOR WASTEWATER-TO-CHEMICAL FUEL CONVERSION
The invention described in this patent is an electrolysis device that converts wastewater to hydrogen fuel and clean water. The components include what is called a bio-photoanode containing electrogenic bacteria and semiconductor photocathode. Wastewater is flowed through the device. Solar light shining on the photocathode results in a flow of protons to the photocathode which are converted into hydrogen gas. In the meantime, the bacteria in the biophotoanode break down organic matter in the wastewater.
SYSTEM AND METHOD FOR A HYBRID CURRENT-MODE AND VOLTAGE-MODE INTEGRATED CIRCUIT
Matt Guthaus, Professor - Computer Science and Engineering
Inventor Previously at UCSC: Riadul Islam
This patent describes a clock circuit that includes current mode to voltage mode converters in a network tree formation and a global current mode transmitter that provides a current mode clock signal to each current mode to voltage mode converters. Most existing VLSI designs have voltage mode clock networks that consume significant amounts of power and require clock buffers to ensure that signals arrive simultaneously. Current mode signaling does not need such buffers, but is not optimal for all uses. The circuit converts a global current mode clock to a local voltage mode clock for optimal accuracy and power use.
NANOPIPETTE DEVICE AND METHOD FOR SUBCELLULAR ANALYSIS
Nader Pourmand, Professor - Biomolecular Science & Engineering
Inventors Previously at UCSC: Paolo Actis; Michelle Maalouf
This patent describes a nanopipette apparatus that can be used to interrogate individual living cells. A nanopipette is a capillary tube of around 100 nanometer diameter that can be used to aspirate, inject, and detect proteins, small molecules, and nucleic acids while keeping the cells alive. The nanopipette includes electrodes inside and outside of the capillary and further includes a circuit that controls the voltage between the electrodes and detects ionic current. This system also includes a computer program to semi-automatically identify and position the nanopipette on a cell of interest to be analyzed.
This patent, which resulted from a collaboration with the US Department of the Navy, describes a method of using a 3-axis gimbal to simulate spacecraft rotational dynamics. As a spherical air bearing on the inner gimbal approaches the limit of free travel, the three-axis gimbal’s position is changed to move away from the limit of free travel. This then simulates angularly unbounded rotation of a spacecraft.
January to March 2020 IRP Award Winners
THREE-DIMENSIONAL HIERARCHICAL POROUS CARBON FOAMS FOR SUPERCAPACITORS
Current UCSC Inventor: Yat Li, Professor - Chemistry & Biochemistry
Inventors Previously at UCSC: Feng Zhang; Tianyu Liu
This patent describes a method of making porous carbon foams. Porous carbon foams are important for storing electric charges at ultrafast charging and discharging rates and are important for use in supercapacitors. This particular method involves mixing an SiO2 particle dispersion with a chitosan solution. Chitosan is a readily available biopolymer derived from shrimp shells and is available at very low cost.
METHODS OF REMOVING PERCHLORATE FROM WATER AND VESSELS AND SYSTEMS FOR PRACTICING THE SAME
Scott R. J. Oliver, Professor - Chemistry & Biochemistry
Inventor Previously at UCSC:
Ian Colinas
Perchlorate is a harmful pollutant resulting from the manufacture of rocket fuel and explosives and also occurs in bleach as well as some fertilizers. This patent describes a method of removing perchlorate from ground water. The method involves passing the contaminated water over a material made up of silver ions and nitrate ions bound by a framework molecule called 4-4' bipyridine. The material captures the perchlorate ions. This method has an advantage over other methods of removing perchlorate from water in that the capture material can be recharged – perchlorate ions can be removed into a smaller volume of liquid – and reused to capture more perchlorate.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventor: Victora Auerbuch Stone, Professor - Microbiology & Environmental Toxicology Inventors previously at UCSC: Roger Linington, Weng Ruh Wong, Miles Duncan
October to December 2019 IRP Award Winners
EXONIC SPLICING ENHANCERS AND EXONIC SPLICING SILENCERS
Current UCSC Inventor: Jeremy Sanford, Associate Professor - Molecular, Cell & Developmental Biology
Inventor Previously at UCSC: Timothy Sterne-Weiler
Sequences in RNA exons can act as enhancers or silencers of mRNA splicing. Mutations in these sequences can result in improper suppression of splicing. These mutations are often present in rare genomic diseases and correlate closely with improper splicing of disease related genes. This patent describes antisense RNA compositions that can be used to correct the improper splicing and potentially ameliorate the disease. This particular patent describes use of sequences that bind an ACUAGG sequence. Additional patents in the series bind to other sequences.
Current UCSC Inventor: Bakthan Singaram, Professor - Chemistry and Biochemistry
Inventors Previously at UCSC:
Angel Resendez, Dominic-Luc Webb
Similar to US Patent Number 10,274,483, his invention describes a method of measuring lactulose and/or mannitol in a biological fluid from a subject, such as a urine sample. According to this method, the subject consumes riboflavin along with lactulose and/or mannitol. The sample is then later collected and combined with a solution that includes an organoboranic compound coupled to a fluorescent molecule such as 4,4’-N,N’-bis-(benzyl-2-boronic acid)-dipyridinium dibromide (also known as oBBV). The lactulose and/or mannitol will result in the emission of fluorescent light in an intensity that depends on the concentration of the lactulose or mannitol. The fluorescence emission of riboflavin is used to normalize the emission of the lactulose or mannitol to improve accuracy. Lactulose and mannitol have long been used to measure small intestine permeability, but measurement of these compounds has historically been performed using expensive equipment such as mass spectrometers.
DETERMINATION OF THE OPTIMAL FLUID PULSES FOR ENHANCEMENT OF RESERVOIR PERMEABILITY AND PRODUCTIVITY
Current UCSC Inventor: Emily Brodsky, Professor - Earth and Planetary Sciences
Inventor Previously at UCSC:
Thibault Candela
Increasing the permeability near an underground well can be important for a wide array of uses, including geothermal power production, injection of gases below ground for storage, and environmental remediation. In these situations, pores and wells can clog during use with a wide array of elements. Usually, mechanical forcing is used to clear these sites, but the results are usually mixed. This invention provides a method of calculating an optimal fluid pulse oscillation to most effectively increase the permeability of the well.
POLYPEPTIDE GLYCOPEPTIDE FRAGMENTS FROM THE V1/V2 AND V3 DOMAINS OF THE HIV-1 ENVELOPE PROTEIN gp120
Current UCSC Inventors: Philip Berman, Distinguished Professor - Biomolecular Science & Engineering
Rebecca DuBois, Assistant Professor - Biomolecular Science & Engineering
Inventors Previously at UCSC:
Gabriel Byrne; Rachel Doran; Javier Morales; Bin Yu; Gerardo Perez; Kate Mesa, David Alexander
This patent describes a potential HIV-1 vaccine immunogen that is engineered to elicit the production of broadly neutralizing antibodies against HIV-1. Prior to the discovery that resulted in this invention, it was believed that trimeric envelope proteins were recognized by broadly neutralizing antibodies. However, this invention showed that monomers were capable of recognition by broadly neutralizing antibodies if the monomers are properly glycosylated by being generated in an appropriate cell line and/or one that is treated with a compound that limits glycosylation to particular sugars. One such polypeptide monomer is described in detail. It includes a V1/V2 domain of HIV-1 gp120 fused to a V3 stem domain of gp120. This construct does not include the C2 domain of gp120. Preferably, the construct is glycosylated by mannose-5 or mannose-9 at asparagine (N) amino acids.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventor: Keith Corzine, Professor - Electrical & Computer Engineering
This patent was prosecuted in collaboration with Clemson University, where Dr. Corzine worked prior to coming to UC Santa Cruz. The invention involves a DC circuit breaker that can automatically detect and isolate an electrical fault between a power source and a load. DC circuit breakers are difficult to design because such circuits contain a constant current and breaking the circuit causes a sustained arc and ensuing risk of fire and damage to the wiring. This circuit breaker involves at least two magnetically coupled inductors that detect faults via increases in power without reacting to routine step changes in load. It has advantages over other DC circuit breakers in that it contains fewer parts, resulting in cheaper and more reliable manufacture.
LC RESONANT CLOCK RESOURCE MINIMIZATION USING COMPENSATION CAPACITANCE
Current UCSC Inventor: Matt Guthaus, Professor - Computer Science & Engineering
Inventor Previously at UCSC:
Ping-Yao Lin
This invention describes Very Large Scale Integration (VLSI) Chips that consume substantially less power than similar chips. The power savings has been achieved by using a specialized set of capacitors and inductors to maintain the chip’s clock rate throughout the chop at a lower power than with comparable chips.
Honorary Mentions
NANOPORE SEQUENCING OF POLYNUCLEOTIDES WITH MULTIPLE PASSES
Inventor Previously at UCSC: Arthur Rand, former Graduate Student - Biomolecular Science & Engineering
This invention provides a method of sequencing a long-read DNA sequence by threading the DNA molecule back and forth through a nanopore, a technique described as “flossing” in the issued patent.
Patent(s) Issued as Continuation of Patent Previously Recognized
COMPOSITIONS, DEVICES, SYSTEMS, AND METHODS FOR USING A NANOPORE
Current UCSC Inventor: David Deamer, Research Professor - Biomolecular Engineering
This invention resulted from a collaboration with investigators at Université Pierre et Marie Curie. The invention comprises a cell-, protein-, and lipid-free method for preparing an RNA polymer from its component mononucleotides. The method involves repeated drying and resolubilizing a solution containing mononucleotides (rAMP, rCMP, rGMP, rUMP) and other components. An RNA polymer of a desired length and sequence can be made by the addition of a template polynucleotide (such as a DNA oligonucleotide.) This method promises rapid, inexpensive, large scale synthesis of RNA molecules for research or therapeutic use, such as siRNA and miRNA.
4-((2-hydroxy-3-methoxybenzyl)amino)benzenesulfonamide DERIVATIVES AS POTENT AND SELECTIVE INHIBITORS OF 12-LIPOXYGENASE
Current UCSC Inventor: Ted Holman, Professor - Chemistry & Biochemistry
This invention resulted from a collaboration with investigators at Eastern Virginia Medical School, Thomas Jefferson University, and the National Institutes of Health. The invention involves potential drug compounds that inhibit lipoxygenases – enzymes that transform fatty acids into cell signaling agents. The compounds described in this patent inhibit a particular lipoxygenase known as arachidonate 12-lipoxygenase, or 12-LOX. 12-LOX activity is implicated in a wide range of conditions including cancer, diabetes, cardiovascular disease, transplanted organ rejection, and Alzheimer’s disease. The compounds potently and selectively inhibit 12-LOX, excluding the other lipoxygenases. These compounds are in development.
Current UCSC Inventor: Ted Holman, Professor - Chemistry & Biochemistry
This invention resulted from a collaboration with investigators at Boston Children’s Hospital and the National Institutes of Health. The invention involves potential drug compounds that inhibit a lipoxygenase known as human reticulocyte 15-lipoxygenase-1 or 12/15-LOX. Similar to 12-LOX, 12/15-LOX is implicated in a wide range of conditions such as stroke, atherogenesis, cancer, diabetes, and Alzheimer’s disease, among others. Also similar to the above patent, these compounds potently and specifically inhibit 12/15-LOX excluding the other lipoxygenases.
FLOURESCENCE METHOD FOR SENSING CHLORINATED DISACCHARICES
Current UCSC Inventor: Bakthan Singaram, Professor - Chemistry & Biochemistry
Inventors Previously at UCSC: Angel Resendez, Dominic-Luc Webb
This invention describes a method of measuring sucralose (the main ingredient in Splenda®) in a biological fluid, such as a urine sample. According to the method, the sample is treated with a reagent that removes chlorine atoms from the sucralose molecule and then the sample is combined with a solution that includes a boronic acid derivative and a fluorescent molecule such as 4,4’-N,N’-bis-(benzyl-2-boronic acid)-dipyridinium dibromide (also known as oBBV). Sucralose, if present, will result in the emission of fluorescent light in an intensity that depends on the concentration of sucralose. Sucralose has long been used to measure colon permeability by feeding sucralose to a patient and identifying sucralose in the urine, but measurement of sucralose has historically been performed using expensive equipment such as mass spectrometers. This assay provides a rapid and low cost measurement of sucralose.
CATALYTIC STRANDS OF MINIMAL HAMMERHEAD RIBOZYMES AND METHODS FOR USING THE SAME
William Scott, Professor - Chemistry & Biochemistry
Sara O’Rourke, Assistant Project Scientist - Chemistry & Biochemistry
Most enzymes that catalyze chemical reactions are proteins. Ribozymes are ribonucleic acid (RNA) molecules that catalyze chemical reactions. A hammerhead ribozyme is a particular type of ribozyme that can cut another RNA molecule at a specific place. The invention described in this patent is an engineered hammerhead ribozyme that includes the minimal number of components of the hammerhead ribozyme required for the ribozyme to still function as a fully active catalyst. The ribozyme can be synthesized to cleave a selected target strand, such as a critical site in the HIV genome. As a result, this hammerhead ribozyme could be used in an HIV treatment.
METHODS OF PRODUCING NUCLEIC ACID LIBRARIES AND COMPOSITIONS AND KITS FOR PRACTICING SAME
Chris Vollmers, Assistant Professor - Biomolecular Engineering
Inventor Previously at UCSC: Charles Cole
This invention involves a method of creating nucleic acid libraries for high throughput sequencing of nucleic acids too long to be sequenced by some sequencing techniques (e.g. the Illumina® sequencer). The method (called TMIseq) involves tagging sequences of interest with primers that both facilitate high throughput sequencing and that also identify individual nucleic acid molecules. The tagging is followed by treating the tagged sequences with an enzyme known as a Tn5 transposase. The Tn5 transposase is associated with either a forward or reverse sequencing primer and fragments the sequence of interest into a more readily sequenced length and inserts the sequencing primer onto the end of the fragment. Fragments with both a forward and reverse sequencing primer can be sequenced. This invention can be used for any of a number of sequences of interest and the patent describes the sequencing of a human antibody heavy chain repertoire using the method.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
BAMBAM: PARALLEL COMPARITIVE ANALYSIS OF HIGH THROUGHPUT SEQUENCING DATA
Current UCSC Inventors: David Haussler, Distinguished Professor - Biomolecular Engineering Joshua Stuart, Professor - Biomolecular Engineering
Other Inventors: Charles Vaske, Steven Benz
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.
Joshua StuartDavid Haussler
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
METHOD THERAPUTIC COMPOSITIONS AND METHODS FOR TREATING HIV INCLUDING IDENTIFICATION AND MANIPULATION OF PARTICULAR DOMAINS ASSOCIATED WITH IMMUNOGENICITY
Current UCSC Inventors: William Sullivan, Professor - Molecular, Cell, and Developmental Biology Catharina Lindley, Research Grant Program Officer - Biomolecular Engineering
Other Inventors: Laura Serbus, Frederic Landmann, Pamela White
BAMBAM: PARALLEL COMPARITIVE ANALYSIS OF HIGH THROUGHPUT SEQUENCING DATA
Current UCSC Inventors: JJ Garcia-Luna Aceves, Distinguished Professor Other Inventors: Li Qian
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
Current UCSC Inventors: David Bernick, Assistant Professor Other Inventors: Andrew Smith
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.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
Current UCSC Inventors: Victoria Auerbuch Stone, Associate Professor Microbiology and Environmental Toxicology Other Inventors: Roger Linington; Eng Ruh Wong; Miles Duncan
The bacterial type III secretion system is a needle-like apparatus used by many Gram-negative pathogens like Salmonella, Yersinia, and Pseudomonas to inject toxins into a host cell to facilitate infection. This patent describes using a small molecule compound called Piericidin and a derivative of it called Mer-A 2062B to inhibit the type III secretion system.
Current UCSC Inventors: Matthew Guthaus, Professor Computer 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.
Current UCSC Inventors: David Bernick, Assistant Adjunct Professor Biomolecular Engineering Other Inventors: Andrew Holmes; Jeff Nivala
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.
Honorary Mentions
Patent(s) Issued as Continuation of Patent Previously Recognized
NUCLEOTIDE SEQUENCING USING AND ARRAY OF INDEPENDENTLY ADDRESSABLE NANOPORES
Current UCSC Inventors:Mark Akeson, Professor; David Deamer, Professor; Kathy Lieberman, Project Scientist; Robin Abu-Shumays, Research Associate Other Inventors: Seico Benner; Bill Dunbar; Noah Wilson; Nicholas Hurt
COMPOSITIONS AND METHODS EMPLOYING WOLBACHIA FTSZ AS A TARGET FOR ALBENDAZOLE SULFONE
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.
These screens display separate images for the left and right eyes, and the human brain mixes the signals from each eye to produce a 3D experience. This invention modifies the individual images provided to each eye by mixing content from the left and right images together. When viewed through 3D glasses, the brain continues to produce a 3D experience, but when viewed without glasses, this new mixture is perceived as a standard 2D video.
January to March 2018 IRP Award Winners
Deactivation of Urushiol: the causation agent of contact dermatitis from Poison Oak and Ivy
Inventor: Rebecca Braslau, Professor Chemistry & Biochemistry
Urushiol exposure from the oil of Poison Oak, Ivy, Sumac and Dogwood leads to contact dermatitis for approximately 70% of the population. Urushiol is an invisible, tenacious oil that can elicit painful rashes and blistering upon exposure to skin at tiny concentrations, and is resistant to removal by normal washings with soap and water. The patent describes chemistry to chemically convert urushiol to a benign species that can no longer cause contact dermatitis. This treatment is envisioned to be useful for contaminated surfaces, such as clothing, furniture, vehicles, fire-fighting and search & rescue equipment, and gardening tools.
ROBUST SINGLE-PHASE DC/AC INVERTER FOR HIGHLY VARYING DC VOLTAGES
Inventor: Ricardo Sanfelice, Associate Professor; Jun Chai, Graduate Research Assistant; 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.
Honorary Mention
(Patent(s) Issued as Continuation of Patent Previously Recognized)
METHODS FOR GENOME ASSEMBLY AND HAPLOTYPE PHASING
Patent Numbers: 9,910,955
Inventor: Ed Green, Associate Professor, Biomolecular Engineering
Inventors No Longer at UCSC
EFFICIENT ENCODING AND STORAGE AND RETRIEVVAL OF GENOMIC DATA
This invention provides a method of encoding duplicated nucleic acid sequence data such that it can be compressed for storage, but later accessed by a researcher.
DUAL-NANOPORE ELECTRONICS CONFIGURATION TO CO-TRAP INDIVIDUAL DNA MOLECULES FOR SEQUENCING AND SINGLE MOLECULE SCIENCE
This invention describes a device used in polymer sequencing (such as DNA sequencing) that works by passing the polymer through a set of two nanopores and controlling the movement of the polymer through the nanopores by adjusting the voltage around the nanopores
Inventor: Matthew Guthaus, Associate Professor Computer Engineering; Riadul Islam (previously PhD Student at UCSC)
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.demand for clean energy.
SELF-BIASED AND SUNSTAINABLE ELECTROHYDROGENESIS DEVICE
Inventor: Yat Li, Associate Professor Department of Chemistry and Biochemistry; Hanyu Wang; Gongming Wang
The rapid growth of global population leads to the increasing demand for energy and clean water. Water splitting represents a promising solution for generating hydrogen gas, a clean chemical fuel that can be used in fuel cells. However, fresh water is also a valuable resource for human survival. A better approach would be to use wastewater instead of clean water. This invention describes a microbial-photoelectrochemical device that can simultaneously remove organic waste in the municipal wastewater and recover the wasted energy in organic matters for hydrogen production, with the help of sunlight. It provides a new solution that can address the need for wastewater treatment and the increasing demand for clean energy.
THERAPEUTIC COMPOSITIONS AND METHODS FOR TREATING HIV INCLUDING IDENTIFICATION AND MANIPULATION OF PARTICULAR DOMAINS ASSOCIATED WITH IMMUNOGENICITY
Inventor: Phillip Berman, Distinguished Professor, Biomolecular Engineering; Sara O’Rourke, Researcher, Biomolecular Engineering; William Scott, Professor, Chemistry & Biochemistry
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.
July to Sept 2017 IRP Award Winners
HIV-1 GP 120 V1N2 ANTIGENS AND IMMUNOLOGICAL USES THEREOF
Inventor: Phillip Berman, Distinguished Professor; Kate Mesa, Lab Manager; Bin Yu, Specialist
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.
Inventor: David Munday, Lecturer 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.
Inventor:Holger Schmidt, Associate Dean for Research, 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
Inventor: David Haussler, Distinguished Professor, Biomolecular Engineering and Scientific Director, UC Santa Cruz Genomics Institute
The purpose of this invention 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.
April to June 2017 IRP Patent Awardees
BamBam: Parallel Comparative Analysis of High-Throughput Sequencing Data (two patents)
Inventor: David Haussler, Distinguished Professor, Biomolecular Engineering and Scientific Director, UC Santa Cruz Genomics Institute
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.
Segmented AC-Coupled Readout From Continuous Collection Electrodes in Semiconductor Sensor
Abe Seiden and Hartmut Sadrozinski from the SCIPP archives
Inventors: Hartmut Sadrozinski Research Physicist and Adjunct Professor, Santa Cruz Institute for Particle Physics (SCIPP); Abraham Seiden, Research Professor, SCIPP; Nicolo Cartiglia Research Associate, SCIPP;
Hartmut Sadrozinski and Abraham Seiden, Santa Cruz Institute for Particle PhysicsNicolo Cartiglia, Santa Cruz Institute for Particle Physics (SCIPP)
Semiconductor sensors have an ubiquitous and necessary implementation in a number of important applications from atomic particle research to medical imaging. This invention provides significant enhancements to these sensors such as stronger imaging for cancer diagnosis and treatment, increased precision for detection in particle accelerators (such as those used to detect the Higgs boson), and has broad commercial potential including for use in drones and autonomous vehicles. The technology radically simplifies the design and delivers improved performance compared to existing ultra fast semiconductor detectors (UFSD), and in doing so substantially cuts costs. The first prototypes were tested at UC Santa Cruz’ SCIPP labs by their undergraduates and subsequent prototypes are now being tailored for use in cancer hospitals and the Large Hadron Collider.
January to March 2017 IRP Patent Awardees
Method for preventing neoplastic transformation by inhibition of retinoblastoma protein inactivation
Seth Rubin, Associate Professor of Chemistry & Biochemistry
Inventor: Seth Rubin, Associate Professor of Chemistry & Biochemistry
Department: Chemistry & Biochemistry Department
The patent describes a new strategy to inhibit cancer cell proliferation by targeting proteins that control cell division. A common problem in cancer is that a protein called the retinoblastoma protein (Rb) is improperly inactivated. Rb normally prevents cell division by binding another protein called E2F. In cancer cells, Rb cannot bind E2F because it has undergone a chemical modification. Our approach reactivates Rb with chemical compounds that stabilize its binding to E2F, and we have established an assay to identify these potential therapeutic compounds.
Interferometric focusing of guide-stars for direct wavefront sensing
Joel Kubby, Professor of Electrical EngineeringXiadong Tao, Assistant Project Scientist — Electrical Engineering
Inventors: Joel Kubby, Professor Electrical Engineering; 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
Nader Pourmand, Associate Professor of Biomolecular Engineering
Inventor: Nader Pourmand, Associate Professor, 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.
Small molecule inhibitors of biofilm formation and the novel use of previously identified compounds for inhibition of biofilm formation and applications for drug therapy and medical device coating
Inventors: Roger Linington, Research Fellow (now at Simon Fraser University); Fitnat Yildiz, Professor, Microbiology & Environmental Toxicology
Fitnat Yildiz, Professor of Microbiology & Environmental Toxicology
Antibiotic resistance is a major emerging threat for global healthcare. In many cases, pathogenic bacteria can adhere to natural and non-natural surfaces in the body as persistent surface-associated assemblages called biofilms. These biofilm states are less susceptible to antibiotic treatment, increasing the likelihood of re-emergence of infection after the end of the course of antibiotics, and resulting in higher risk of the development of antibiotic resistance. By directly targeting the formation and persistence of these biofilm colonies, this new invention provides a promising complementary approach to treating bacterial infections. The new compounds covered under this patent are potent inhibitors of biofilm formation with very low mammalian cell cytotoxicity, making them valuable for both infection control and medical device coating applications.
October to December 2016 IRP Patent Awardees
Compositions, Devices, Systems, And Methods For Using A Nanopore
Mark Akeson, professor of Biomolecular Engineering
Name: Mark Akeson, Professor, 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.
July to September 2016 IRP Patent Awardees
Faster, Better Genome Assembly
Ed Green's startup, Dovetail Genomics, opened its doors in summer 2013 in a bio-incubator space on campus, and now employs about 20 people in its own office in Santa Cruz. (Photo by Steve Kurtz)
Inventor: Edward Green, Associate Professor, 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.
Inventor: Glenn Millhauser, Distinguished Professor, Chemistry & Biology
Glenn Millhauser, a professor in the Department of Chemistry & Biochemistry (Photo by Steve Kurtz)
A primary area of our research deals with metabolic signaling in the brain, with specific attention to the Agouti-Related Protein. AgRP is a small, hormone-like protein that plays a critical role in the neuronal pathways that give the sensation of hunger and controls how our bodies store energy. In 2002, our lab used Nuclear Magnetic Resonance to solve the AgRP structure. Since then, we’ve been trying to understand the functional importance of the protein’s domains.
We are also very interested in the protein’s therapeutic potential. Understandably, most of the modern focus on controlling metabolic function deals with weight loss. However, there are very important clinical scenarios where weight gain is essential. Cancer patients undergoing chemotherapy and AIDS sufferers often develop a life threatening condition called cachexia (similar to anorexia). These patients not only lose the desire to eat, but their bodies also experience extreme atrophy with profound loss of muscle tissue. With cachexia brought on by chemotherapy it’s the classic case of the treatment being worse than the disease. There are few drugs for treating cachexia; once the condition sets in, it is very difficult to reverse. Fortunately as demonstrated in animal models, AgRP is uniquely capable of reversing cachexia with restoration of appetite and subsequent weight gain.
Building on our interest in AgRP functional domains, and motivated by the need for clinical treatments, we developed a new strategy for enhancing AgRP function through mutagenesis. Our most potent proteins stimulate feeding at more than double that of wild-type AgRP. This protein and its variants could prove to be remarkably useful as drugs for enhancing the outcome of cancer and AIDS treatments.
Methods Employing Wolbachia FTSZ As A Target For Albendazole Sulfone
Catharina Casper-Lindley, a senior scientist in the lab of Professor William Sullivan, professor of Molecular, Cell, & Developmental Biology (Photo by Steve Kurtz)
Pamela White, a graduate student in the Sullivan Lab (Photo by Steve Kurtz)
Inventor: Joe Konopelski, Professor, Chemistry & Biochemistry
Suitably constructed, the b-lactam ring, represents the core of a vast array of antibiotics, including some used to treat drug-resistant bacterial strains. During the course of another project we discovered a new route to b-lactam structures from readily available starting materials. Our discovery could be of use to the drug development community, particularly as antibiotic resistance is such an important problem.
Aspects of this patent involve techniques for compact key encoding of data for public storage, such as cloud storage, that provides a substantially higher level of security, including perfect security in some cases, or substantially smaller keys than in previous approaches, or some combination. This patent improves upon the inventor’s previous work. Perfect secrecy can be accomplished with a much smaller key size than file size and with less complexity than previously introduced. Furthermore, the encrypted or encoded data takes no more space than the plaintext, because a random bit is not inserted at any position, as in previous works.
