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 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.

July to September 2020 IRP Award Winners


METHODS FOR DETERMINING BASE LOCATIONS IN A POLYNUCLEOTIDE

Patent Numbers: US 10,760,117

Current UCSC Inventors:
Miten Jain, Assistant Research ScientistBiomolecular 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.

 Miten Jain on a motorcycle Hugh Olsen Mark Akeson

 


SYSTEM FOR CONTINUOUS MUTAGENESIS IN VIVO TO FACILITATE DIRECTED EVOLUTION

Patent Numbers: US 10,760,071

Manel Camps

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

Patent Numbers: US 10,706,956US 10,726,945

UCSC Inventor: David Haussler

Inventor previously at UCSC: John Sanborn


PATHWAY RECOGNITION ALGORITHM USING DATA INTEGRATION ON GENOMIC MODELS (PARADIGM)

Patent Numbers: US 10,770,169

UCSC Inventors: David Haussler; Josh Stuart

Inventors previously at UCSC: Charles Vaske; Stephen Benz


4-((2-HYDROXY-3-METHOXYBENZYL)AMINO)BENZENESULFONAMIDE DERIVATIVES AS POTENT AND SELECTIVE INHIBITORS OF 12-LIPOXYGENASE

Patent Numbers: US 10,752,581

UCSC Inventor: Ted Holman

April to June 2020 IRP Award Winners


INTERACTIVE INCREMENTAL SYNTHESIS FLOW FOR INTEGRATED CIRCUIT DESIGN

Patent Numbers: US 10,614,188

Current UCSC Inventor:Jose Renau
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.

 

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Z-SCHEME MICROBIAL PHOTOELECTROCHEMICAL SYSTEM (MPS) FOR WASTEWATER-TO-CHEMICAL FUEL CONVERSION

Patent Numbers: US 10,683,218

Yat Li

Current UCSC Inventor:
Yat Li, Professor - Chemistry & Biochemistry

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.

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SYSTEM AND METHOD FOR A HYBRID CURRENT-MODE AND VOLTAGE-MODE INTEGRATED CIRCUIT

Patent Numbers: US 10,691,162

Matt Guthaus

Current UCSC Inventor:
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.   

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NANOPIPETTE DEVICE AND METHOD FOR SUBCELLULAR ANALYSIS

Patent Numbers: US 10,696,962

Nader Pourmand

Current UCSC Inventor:
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.

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Honorary Mentions

ANGULARLY UNBOUNDED THREE-AXIS SPACECRAFT SIMULATOR

Patent Number: US 10,621,883

Inventor previously at UCSC: Simone Chesi

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. 

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January to March 2020 IRP Award Winners


THREE-DIMENSIONAL HIERARCHICAL POROUS CARBON FOAMS FOR SUPERCAPACITORS

Patent Numbers: US 10,526,203

Current UCSC Inventor:Yat Li
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.

 

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METHODS OF REMOVING PERCHLORATE FROM WATER AND VESSELS AND SYSTEMS FOR PRACTICING THE SAME

Patent Numbers: US 10,597,312

Scott Oliver

Current UCSC Inventor:
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.

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Honorary Mentions


Patent(s) Issued as Continuation of Patent Previously Recognized

METHODS FOR GENOME ASSEMBLY AND HAPLOTYPE PHASING

Patent Numbers: US 10,529,443

Current UCSC Inventor: Richard E. Green, Associate Professor - Biomolecular Science & Engineering
Inventor previously at UCSC: Liana F. Lareau


PIERICIDIN BACTERIAL INHIBITORS

Patent Numbers: US 10,588,897

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

Patent Numbers: US 10,443,101Jeremy Sanford

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.

 

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FLUORESCENCE ASSAY FOR INTESTINAL PERMEABILITY

Patent Numbers: US 10,488,418

Bakthan Singaram

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.

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DETERMINATION OF THE OPTIMAL FLUID PULSES FOR ENHANCEMENT OF RESERVOIR PERMEABILITY AND PRODUCTIVITY

Patent Numbers: US 10,513,909

Emily Brodsky

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.

 

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POLYPEPTIDE GLYCOPEPTIDE FRAGMENTS FROM THE V1/V2 AND V3 DOMAINS OF THE HIV-1 ENVELOPE PROTEIN gp120

Patent Numbers: US 10,517,942

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.

Philip BermanRebecca DuBois

  

 

 

 

 

 

 

 

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Honorary Mentions


Patent(s) Issued as Continuation of Patent Previously Recognized

V1/V2 FRAGMENTS OF A HIV-1 ENVELOPE GLYCOPROTEIN

Patent Numbers: US 10,507,239

Current UCSC Inventor: Philip Berman, Distinguished Professor
Inventors previously at UCSC: Gwen Tatsuno, Bin Yu, Javier Morales, Kate Mesa


NANOPIPETTE APPARATUS FOR MANIPULATING CELLS

Patent Numbers: US 10,513,434

Current UCSC Inventor: Nader Pourmand, Professor
Inventors previously at UCSC: R. Adam Seger, Paolo Actis, Boaz Vilozny


July to September 2019 IRP Award Winners


CIRCUIT BREAKER FOR DC APPLICATIONS

Patent Numbers: US 10,389,104Keith Corzine

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.

 

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LC RESONANT CLOCK RESOURCE MINIMIZATION USING COMPENSATION CAPACITANCE

Patent Numbers: US 10,418,939

Matt Guthaus

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.

 

 

 

circuit


Honorary Mentions

NANOPORE SEQUENCING OF POLYNUCLEOTIDES WITH MULTIPLE PASSES

Patent Numbers: US 10,421,998

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

Patent Numbers: US 10,344,327

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


NANOPORE DEVICE FOR REVERSIBLE ION AND MOLECULE SENSING OR MIGRATION

Patent Numbers: US 10,345,260

Current UCSC Inventor: Nader Pourmand, Professor
Other Inventors: Boaz Vilozny, Paolo Actis, R. Adam Seger

 


April to June 2019 IRP Award Winners


NON-ENZYMATIC SALT MEDIATED SYNTHESIS OF POLYNUCLEIC ACIDS

Patent Numbers: US 10,280,191

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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

Patent Numbers: US 10,266,488

tedholman.jpg

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.

 


INHIBITORS OF HUMAN 12/15-LIPOXYGENASE

Patent Numbers: US 10,287,279

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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

Patent Numbers: US 10,274,483

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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

Patent Numbers: US 10,301,626

Current UCSC Inventors:
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.   

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METHODS OF PRODUCING NUCLEIC ACID LIBRARIES AND COMPOSITIONS AND KITS FOR PRACTICING SAME

Patent Numbers: US 10,280,449

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Current UCSC Inventor:
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

Patent Numbers: US 10,249,384, US 10,268,800

Current UCSC Inventor:
David Haussler, Distinguished Professor - Biomolecular Engineering

Inventor Previously at UCSC: John Sanborn


ROBUST SINGLE PHASE DC/AC INVERTER FOR HIGHLY VARYING DC VOLTAGES

Patent Numbers: US 10,263,541

Current UCSC Inventor:
Ricardo San Felice Professor - ECE

Inventor Previously at UCSC: Jun Chai


January to March 2019 IRP Award Winners


METHOD OF GENERATING A DYNAMIC PATHWAY MAP

Patent Numbers: US 10,192,641

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.

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Joshua Stuart
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David 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

Patent Numbers: US 10,201,603

Current UCSC Inventors:
Phillip Berman, Distinguished Professor - Biomolecular Engineering
Sara O’Rourke, Assistant Project Scientist - Chemistry & Biochemistry
William Scott, Professor - Chemistry & Biochemistry

COMPOSITIONS, DEVICES, SYSTEMS AND METHODS FOR USING A NANOPORE

Patent Numbers: US 10,208,342

Current UCSC Inventors:
Mark Akeson, Professor - Biomolecular Engineering
David Deamer, Research Professor - Biomolecular Engineering

Other Inventors: William Dunbar, Noah Wilson, Kate Lieberman

COMPOSITIONS, DEVICES, SYSTEMS AND METHODS FOR USING A NANOPORE

Patent Numbers: US 10,196,688

Current UCSC Inventors:
Mark Akeson, Professor - Biomolecular Engineering
David Deamer, Research Professor - Biomolecular Engineering

Other Inventors: Mark Dunbar, Roger Chen, Noah Wilson

COMPOSITIONS, DEVICES, SYSTEMS AND METHODS FOR USING A NANOPORE

Patent Numbers: US 10,202,645

Current UCSC Inventors:
Mark Akeson, Professor - Biomolecular Engineering
David Deamer, Research Professor - Biomolecular Engineering

Other Inventors: Daniel Branton, Seiko Endo

COMPOSITIONS AND METHODS EMPLOYING WOLBACHIA fTSZ AS A TARGET FOR ALBENDAZOLE SULFONE

Patent Numbers: US 10,220,022

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

Patent Numbers: US 10,242,155

Current UCSC Inventors:
David Haussler, Distinguished Professor - Biomolecular Engineering

Other Inventors: John Sanborn


October to December 2018 IRP Award Winners


A METHOD FOR DISTANCE-VECTOR ROUTING USING ADAPTIVE PUBLISH-SUBSCRIBE MECHANISMS

JJ Garcia-Luna Aceves
JJ Garcia-Luna Aceves

Patent Numbers: US 10,091,094

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

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David Bernick

Patent Numbers: US 10,131,944

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-MODE CLOCK DISTRIBUTION

Patent Numbers: US 10,097,168

Current UCSC Inventors: Matthew Guthaus, Professor 
Other Inventors: Riadul Islam 

METHOD FOR GENOME ASSEMBLY AND HAPLOTYPE PHASINGS

Patent Numbers: US 10,089,437

Current UCSC Inventors: Ed Green
Other Inventors: Seico Benner; Bill Dunbar; Noah Wilson; Nicholas Hurt 


July to September 2018 IRP Award Winners


PIERICIDIN BACTERIAL INHIBITORS

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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.

 

 


DISTRIBUTED LC RESONANT TANK CLOCK TREE SYNTHESIS

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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.

 

 


SALT-TOLERANT DNA POLYMERASES

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

 

NUCLEOTIDE SEQUENCING USING AND ARRAY OF INDEPENDENTLY ADDRESSABLE NANOPORES

Patent Numbers: US 10,081,835

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

 

METHOD FOR USING A NANOPORE

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

 

COMPOSITIONS AND METHODS EMPLOYING WOLBACHIA FTSZ AS A TARGET FOR ALBENDAZOLE SULFONE

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 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

 

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)

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

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.

DUAL-NANOPORE ELECTRONICS CONFIGURATION TO CO-TRAP INDIVIDUAL DNA MOLECULES FOR SEQUENCING AND SINGLE MOLECULE SCIENCE

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


CURRENT MODE CLOCK DISTRIBUTION

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.

 

 


SELF-BIASED AND SUNSTAINABLE ELECTROHYDROGENESIS DEVICE

Photo of Yat Li

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.


THERAPEUTIC COMPOSITIONS AND METHODS FOR TREATING HIV INCLUDING IDENTIFICATION AND MANIPULATION OF PARTICULAR DOMAINS ASSOCIATED WITH IMMUNOGENICITY

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


HIV-1 GP 120 V1N2 ANTIGENS AND IMMUNOLOGICAL USES THEREOF

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.

  


SWITCHABLE LED LIGHTBULB

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. 


 

TWO CHAMBERED DUAL_PORE DEVICE

Photo of David Haussler

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.

 


BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA

Photo of David Haussler
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, Associate Professor of Chemistry & Biochemistry

Patent Number: 9,573,977

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

Photo of Joel Kubby
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

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

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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

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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)

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

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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

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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)
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

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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.