IRP Patent Awardees

July to September 2018 IRP Award Winner




Victoria Auerbuch Stone

Patent Numbers: US 10,080,745

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.




Matthew Guthaus

Patent Numbers: US 10,073,937

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.




David Bernick
David Bernick

Patent Numbers: US 10,059,984

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


Patent Numbers: US 10,081,835

Current UCSC Inventors: Mark Akeson, Professor; David Deamer, Professor 
Other Inventors: Bill Dunbar; Roger Chen; Noah Wilson



Patent Numbers: US 10,059,988

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



Patent Numbers: US 10,028,936

Current UCSC Inventors: Bill Sullivan, Professor 
Other Inventors: Laura Serbus; Fredric  Landmann; Catharina Lindley; Pamela White



April to June 2018 IRP Award Winner

Practical Two-Frame 3D+2D TV

Photo of James Davis

James Davis, Professor Computer Science

Patent Numbers: 10,003,789

Inventor: James Davis, Professor 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.

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

Photo of Rebecca Braslau

Rebecca Braslau, Professor Chemistry

& Biochemistry

Patent Numbers: 9,896,532

Inventor: Rebecca Braslau, Professor Chemisty & 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.





Photo of David Haussler

Jun Chai, Research Assistant


Photo of David Haussler

Ricardo Sanfelice, Associate Professor,

Department of Computer Engineering


Patent Numbers: 9,876,442

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)


Patent Numbers: 9,910,955

Inventor: Ed Green, Associate Professor, Biomolecular Engineering

Inventors No Longer at UCSC


Patent Numbers: 9,886,561

Inventor: Andrew Hospodor, Ignacio Corderi

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.


Patent Numbers: 9,863,912

Inventor: William Dunbar, Jungsuk Kim

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


October to December 2017 IRP Award Winners


Photo of David Haussler

Matthew Guthaus, Associate Professor

Computer Engineering

Patent Numbers: 9,787,293

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.




Photo of David Haussler

Yat Li, Associate Professor, Department

of Chemistry and Biochemistry

Patent Numbers: 9,825,321

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.


Photo of David Haussler

Phillip Berman, Distinguished Professor

Biomolecular Engineering

Patent Numbers: 9,782,472

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


Photo of Phillip Berman

Phillip Berman, Distinguished Professor

Biomolecular Engineering

Patent Numbers: 9,731,002

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.



Patent Number: 9,144,129

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. 



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Holger Schmidt, Associate Dean for Research

Electrical Engineering

Patent Numbers: 9,696,277

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.



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David Haussler, UCSC Genomics Institute

Patent Numbers: 9,721,062

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)

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David Haussler, UC Santa Cruz Genomics Institute

Patent Numbers: 9,646,134; 9,652,587

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

An archived photo of Hartmut Sadrozinski and Abe Seiden
Abe Seiden and Hartmut Sadrozinski from the SCIPP archives

Patent Number: 9,613,993

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 (Research Physicist and Adjunct Professor) and Abraham Seiden (Research Professor)
Hartmut Sadrozinski and Abraham Seiden, Santa Cruz Institute for Particle Physics
Nicolo Cartiglia, Research Associate
Nicolo 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

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Seth Rubin, Associater Professor of Chemistry & Biochemistry

Patent Number: 9,573,977

Inventor: Seth Rubin, Associater 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

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Joel Kubby, Professor of Electrical Engineering
Photo of Xiadong Tao
Xiadong Tao, Assistant Project Scientist — Electrical Engineering

Patent Number: 9,535,247

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

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Nader Pourmand, Associate Professor of Biomolecular Engineering

Patent Number: 9,598,281

Inventor: Nader PourmandAssociate 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

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Roger Linington, Research Fellow

Patent Number: 9,596,855

Inventors: Roger Linington, Research Fellow (now at Simon Fraser University); Fitnat Yildiz, Professor, Microbiology & Environmental Toxicology 

Photo of Fitnat Yildiz
Fitnat Yildiz, Professor of Microbiology & Environmental Toxicology

ntibiotic 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

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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)

Patent Number: 9,411,930

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.

The Appetite Stimulating Protein

Patent Number: 9,394,343

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)
Photo of Pamela White

Pamela White, a graduate student in the Sullivan Lab (Photo by Steve Kurtz)

Patent Number: 9,439,889

Inventors: William Sullivan (Professor), Catharina Casper-Lindley (Senior Scientist), and Pamela White (Graduate Student)

Department: Molecular, Cell, & Developmental Biology

A way to screen for bacteria in worms that are responsible for several life-threatening diseases in third world countries.

A New Route To B-Lactam Structures

Joseph Konopelski, professor of chemistry

Patent Number: 9,469,610

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.