IRP Patent Awardees

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 recogonize 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.

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

Title: David Haussler, Distinguished Professor, Biomolecular Engineering and Scientific Director, UC Santa Cruz Genomics Institute

Department: Biomolecular Engineering, 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

Names & Titles: Hartmut Sadrozinski (Research Physicist and Adjunct Professor), Abraham Seiden, (Research Professor), and Nicolo Cartiglia (Research Associate)

Hartmut Sadrozinski (Research Physicist and Adjunct Professor) and Abraham Seiden (Research Professor)
Hartmut Sadrozinski and Abraham Seiden, Santa Cruz Institute for Particle Physics
Department: Santa Cruz Institute for Particle Physics (SCIPP) and UC Santa Cruz Physics Department
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

Name: Seth Rubin

Title: Associate Professor

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
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Xiadong Tao, Assistant Project Scientist — Electrical Engineering

Names & Titles: Joel Kubby (Professor) and 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

Name: Nader Pourmand

Title: Associate Professor 

Department: Biomolecular Science and Engineering

The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Dr. Pourmand and his team have developed a single-cell interrogation platform based on scanning ion conductance microscopy for continuous sampling of intracellular content from individual cells. Among many other functionalities, for the nanobiopsy, this platform uses a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. Researchers might use this platform to understand cancer and other diseases which might provide a foundation for dynamic subcellular genomic analysis.


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

Names and Titles: Roger Linington, Research Fellow (now at Simon Fraser University) and Fitnat Yildiz, Professor

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Fitnat Yildiz, Professor of Microbiology & Environmental Toxicology

Department: 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

Photo of Mark Akeson
Mark Akeson, professor of Biomolecular Engineering

Name: Mark Akeson

Title: Professor

Department: Biomolecular Science & Engineering

The invention is one of a series of patents from the biomolecular engineering department concerning sequencing of DNA using a nanoscale hole or 'nanopore'. When a voltage is applied across the nanopore, DNA is pulled through the hole in single file order. The bases that make up the DNA are read as they transit the pore. In this particular patent, the inventors combined voltage feedback control with an enzyme to precisely regulate movement of the DNA. This results in improved DNA sequencing accuracy.



July to September 2016 IRP Patent Awardees

Faster, Better Genome Assembly

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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)

Name: Edward Green

Title: Associate Professor

Department: Biomolecular Engineering

Assembling genomes is like solving a giant, 3 billion-piece jigsaw puzzle. The invention describes a streamlined way to figure out which pieces are near other pieces so the puzzle can be reconstructed more accurately and quickly. Licensed by Dovetail Genomics in Santa Cruz, the invention has been used to assemble the genomes of hundreds of plant and animals. With this information, scientists can begin to unravel the biology inherent in each.

In the spring, several new initiatives from the UC Office of the President will be rolled out across the 10 campuses to further innovation, commercialization, and entrepreneurship and highlight the growing body of research providing public benefit. The IATC office will lead the implementation of these initiatives with various leaders around campus to bring these opportunities to the entire university community.


The Appetite Stimulating Protein

Name: Glenn Millhauser 

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Glenn Millhauser, a professor in the Department of Chemistry & Biochemistry (Photo by Steve Kurtz)

Title:  Distinguished Professor

Department: Chemistry & Biochemistry

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

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Catharina Casper-Lindley, a senior scientist in the lab of Professor William Sullivan, professor of Molecular, Cell, & Developmental Biology (Photo by Steve Kurtz)
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Pamela White, a graduate student in the Sullivan Lab (Photo by Steve Kurtz)

Names & Titles: 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

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Joseph Konopelski, professor of chemistry

Name: Joe Konopelski 

Title: Professor

Department: 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.