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Elves--an Expert System For X-ray Crystallography Of Biological Macromolecules

Elves is a computer expert system for X-ray crystallography of biological macromolecules. Elves automates and accelerates every step of X-ray data analysis, from processing X-ray diffraction images to guiding and refining a molecular model. Elves requires the use of CCP4, which must be obtained under separate license from a third party. Elves also uses common data analysis programs such as Mosflm. Elves also has novel functionalities, such as Spotter to identify and display particular diffraction spots, sendhome to transmit data frames over the internet, and table1.com to tabulate statistics for publication. Elves sequentially runs each step of X-ray structure determination using a generalized regimen. The problem-solving strategy is based on empirical rules and procedures for overcoming common problems. Optimized parameters are passed from each program to the next. These values can be evaluated by the user or simply accepted automatically at each stage. The overall effect is to systematize, optimize and accelerate the process of X-ray structure analysis in biomedical research. Elves can accept English language inputs or shell script inputs. After locating the data and the necessary programs on the file system, Elves writes program-input scripts, runs programs, examines the output and iteratively repeats this cycle to optimize input parameters. This optimization is generally beyond the capability of human users of the underlying programs. This systematic X-ray data analysis reduces the frequency of mistakes. In addition, Elves operates faster and more reliably than a human user, even when the user employs a graphical interface. Complicated analytical calculations that can take months for human users to complete can be performed in a matter of hours using Elves. To date, Elves has been used to help determine the crystal structure of over fourteen proteins. Novel structures have been solved in as little as five hours from the start of X-ray data collection at a synchrotron source; a typical investigator not using Elves would take weeks to months to complete the same work.


96 Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} The CRISPR-Cas system is now understood to confer bacteria and archaea with acquired immunity against phage and viruses. CRISPR-Cas systems consist of Cas proteins, which are involved in acquisition, targeting and cleavage of foreign DNA or RNA, and a CRISPR array, which includes direct repeats flanking short spacer sequences that guide Cas proteins to their targets. The programmable nature of these systems has facilitated their use as a versatile technology that is revolutionizing the field of genome manipulation. There is a need in the art for additional CRISPR-Cas systems with improved cleavage and manipulation under a variety of conditions and ones that are particularly thermostable under those conditions.     UC researchers discovered a new type of RNA-guided endonuclease (GeoCas9) and variants of GeoCas9.  GeoCas9 was found to be stable and enzymatically active in a temperature range of from 15°C to 75°C and has extended lifetime in human plasma.  With evidence that GeoCas9 maintains cleavage activity at mesophilic temperatures, the ability of GeoCas9 to edit mammalian genomes was then assessed.  The researchers found that when comparing the editing efficiency for both GeoCas9 and SpyCas9, similar editing efficiencies by both proteins were observed, demonstrating that GeoCas9 is an effective alternative to SpyCas9 for genome editing in mammalian cells.  Similar to CRISPR-Cas9, GeoCas9 enzymes are expected to have a wide variety of applications in genome editing and nucleic acid manipulation.   

Configurations for Integrated MRI-linear Accelerators

Researchers at Stanford and University of California, Berkeley, have developed an integrated MRI-Linac hybrid system that can increase the efficacy of image-guided radiotherapy (IGRT). This system allows more aggressive treatment strategies that employ dose escalation, tighter geometric margins and sharper dose gradients which can improve clinical outcomes. This radiotherapy treatment apparatus includes a treatment beam (charged by Linac, particle, proton, or electron beam), a magnetic field disposed parallel collinear to the treatment beam, and a target that is disposed along the treatment beam. MRI is ideal for IGRT, however, there is magnetic field and RF interference between the linear accelerator and MRI scanner. The configurations of this system overcome this issue.

CB6 for Highly Sensitive Molecular Detection Using HyperCEST NMR

Hyperpolarized 129Xe chemical exchange saturation transfer (HyperCEST) nuclear magnetic resonance (NMR), used to detect cancer markers, small molecule analytes, and cell surface glycans, relies on the targeted delivery of xenon hosts to a region of interest or small chemical shift difference between bound and unbound xenon sensors. Cryptophane-A (CryA) xenon hosts, used in the past, are hydrophobic, costly, and difficult to functionalize. CB6 is an excellent xenon host for activated 129Xe NMR detection because it produces a distinctive signal, has better exchange parameters for HyperCEST when compared to CryA, is soluble in most buffers and biological environments, and is commercially available. One major limitation of CB6 sensors is the difficult chemical functionalization to generalize them for diverse spectroscopic applications. To address this problem, researchers at Lawrence Berkeley National Laboratory and University of California, Berkeley, have designed, synthesized, and implemented a chemically-activated cucurbit[6]uril (CB6) platform for 129Xe HyperCEST NMR that blocks 129Xe@CB6 interactions with greater control to eliminate background signals until the CB6 reaches a region of interest, where it is then released to produce a 129Xe @CB6 signal. This technology will enable detection of increasingly lower concentrations of targets as the molecular systems become more optimized. 

Advanced Chemical Sensing Method and Apparatus

Conventional chemical sensors or chemical resistors detect the molecule concentration by monitoring the resistance change caused by the reaction near the sensing material surface. One of the problems with these systems is with drift, when over time the analyte molecules poison the device’s sensing surface, causing weaker performance on selectivity and sensitivity. This often requires rigorous and timely calibrations to the sensor, which involves human intervention, and often times complete sensor replacement. To address this problem, researchers at the University of California, Berkeley, have developed a vertical platform that dramatically improves the sensor’s ability to manage and recover from the poison environments. By examining and manipulating the sensing plane vis-à-vis the near field surface, researchers have demonstrated an effective and robust chemical sensing platform for a range of gas sensing applications.

Contraceptive Compounds

Steroid hormones regulate human physiology and cellular metabolism by either slowly changing gene expression, or by a binding to a plasma membrane receptor, which leads to the activation of ion channels. The latter represents a fast signaling event that plays role in sperm activation or insulin secretion. For example, the female hormone progesterone (P4) activates the principal calcium channel of sperm (CatSper) via this fast pathway. By testing different steroids and steroid-like molecules, UC Berkeley researchers discovered that pregnenolone sulfate (PS), a sulfated steroid hormone similar in structure to P4, is another steroid hormone that can activate CatSper in human spermatozoa. In addition, the researchers discovered two specific and nontoxic compounds found in plants that antagonize physiological function of P4 and PS, and prevent spermatozoa from reaching full fertilizing potential. These compounds can serve as contraceptives since they reduced the number of hyperactive spermatozoa, thus preventing sperm from reaching and fertilizing an egg.  

Self-Cleaning Mass Sensor For Particulate Matter Monitoring

Airborne particulates (such as vehicle exhaust, dust, and metallics) are a health hazard.  Monitors for measuring particulate matter (PM) concentrations in air are typically designed for stationary industrial use; and while they are quite sensitive, they are also bulky, heavy, and expensive.  Accordingly, there is a need for PM concentration monitors that are inexpensive and portable so that they can be more pervasive, and also used by mass-market consumers. Recently, various types of portable PM monitors have been developed.  One class of monitor uses optical technology to measure particulates flowing through (not deposited on) the device.  This optical technology is not sensitive to extremely small particles (with diameters of 200 nanometers or less), yet these small particles are a serious health hazard.  Another class of PM monitor uses various technologies to measure the mass of particles deposited on (not flowing through) the device.  This type of monitor can be quite sensitive, but eventually, it can become overloaded with deposited particles.  Moreover, multiple layers of particles can eliminate the possibility of determining the chemical nature of the particles. To address these shortcomings, researchers at UC Berkeley have developed a means of periodically cleaning deposited particles from mass-sensing components of deposit-based PM sensors.  The Berkeley technology results in PM sensors that are not only portable and low-cost, but also have long-lasting functionality.

Enzymatic Synthesis Of Cyclic Dinucleotides

96 Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} GGDEF domain-containing enzymes are diguanylate cyclases that produce cyclic di-GMP (cdiG), a second messenger that modulates the key bacterial lifestyle transition from a motile to sessile biofilm-forming state. The ubiquity of genes encoding GGDEF proteins in bacterial genomes has established the dominance of cdiG signaling in bacteria. A subfamily of GGDEF enzymes synthesizes the asymmetric signaling molecule cyclic AMP-GMP. Hybrid CDN-producing and promiscuous substrate-binding (Hypr) GGDEF enzymes are widely distributed and found in other deltaproteobacteria and have roles that include regulation of cAG signaling.  GGDEF enzymes that produce cyclic dinucleotides are especially of interest.    UC Berkeley researcher have developed a new method of preparing and using cyclic dinucleotides (CDNs) by contacting a CDN producing-enzyme (e.g., a GGDEF enzyme) with a precursor of a CDN under conditions sufficient to convert the precursor into a CDN. This method produces a variety of non-naturally occurring, asymmetric and symmetric CDNs and can be performed in vitro or in a genetically modified host cell. Also provided are CDN compositions that find use in a variety of applications such as modulating an immune response in an individual.