METHODS AND SYSTEMS OF CHARACTERIZING AND COUNTING MICROBIOLOGICAL COLONIES
A means to rapidly count colonies of microorganisms on nutrient plates was developed. The practice may be used to speed many practices, procedures, and tests used in biology, microbiology, and medicine that rely in whole or in part on the ability to culture, enumerate, and assess microorganisms. The measurement tool, measurement process, and method of analysis will enable previously unattainable research into bacterial activity. The method is novel and valuable because it makes use of sensitive optical metrology to resolve growth of microorganisms much sooner than can be done with traditional methods. In short, white-light interferometry (WLI) is used to obtain high resolution 3-D profiles of microorganisms that have been placed on nutrient enriched agar plates. The resulting profiles have very fine sub-micron depth resolution and the ability to see single cells and microorganisms. Images may be captured at high magnification to observe a single microbe as it grows into a microcolony or images may be captured at low magnification to observe many microorganisms at once. Images are captured non-destructively which enables monitoring over time without apparent disruption microbial growth, activity, and processes. Traditional colony counting methods take 24 hrs for fast growing bacteria and up to 3 weeks for some species. This invention will allow researchers and clinicians to count colony forming units in a bacterial culture sample as early as 1-4 hrs after being applied to an agar plate. This invention would also require less material (smaller and fewer plates) and fewer resources (less incubation space and less time for incubation). A company that makes and sells WLI optical profilers would be able to modify their product hardware and software to accommodate this method. It could be sold as an add-on to their existing instrument. Traditionally, WLI instruments have been used to examine non-living hard surfaces (e.g., printed circuit boards, hard disks, machined parts, etc.). Licensing this technology would allow a maker of white-light interferometry instruments to expand into new markets, especially biomedical research and clinical testing. Users of this invention would benefit by performing colony counting much faster while using few resources and providing other relevant and significant morphological details that are not measurable by other means. This invention can be summarized as three major parts: A method to prepare, image, and analyze microbial cultures with WLI such that CFUs and other morphological traits can be rapidly assessed Culture plates with surface properties and optical characteristics that enhance and enable WLI imaging An integrated WLI imaging system for bacterial culture analysis that may include: modifications to existing WLI instruments or components such as sample holders or imaging stages, automated or semi-automated analysis routines implemented in software, and customized culture plates designed for WLI imaging. Full details of experiments done to demonstrate this invention are included in the appended manuscript.
Methods and Apparatuses for Cross-Ontologial Analytics
This invention disclosure presents a method and system that exploits the impact that Endocrine Disrupting Chemicals (EDCs) exert on gene products through receptor binding to refine the predictive power of Quantitative Structure-Activity Relationships (QSAR) modeling in identifying EDCs and to discover biomarkers associated with identified EDCs. The approach focuses on two main tasks: . Develop a framework to assess the toxicity of chemicals in terms of their impact at the gene/protein level . Use the impact of chemicals at the gene/protein level to identify biomarkers.
Serum markers for type II diabetes mellitus
A method for identifying persons with increased risk of developing type 2 diabetes mellitus utilizing selected biomarkers described hereafter either alone or in combination. The present invention allows for broad based, reliable, screening of large population bases and provides other advantages, including the formulation of effective strategies for characterizing, archiving, and contrasting data from multiple sample types under varying conditions. diabetes has not been previously reported in the literature.
PRODUCTION OF ORGANIC ACIDS FROM ASPERGILLUS CIS-ACONITIC ACID DECARBOXYLASE (CADA) DELETION STRAINS
Methods and Compositions for Degradation of Lignocellulosic Material
The present invention provides methods and compositions for the conversion of plant biomass to fermentable sugars that can be converted to useful products. The methods include methods for degrading lignocellulosic material using enzyme mixtures to liberate sugars. The compositions of the invention include enzyme combinations that break down lignocellulose. The invention includes methods to identify the optimum ratios and compositions of enzymes with which to degrade each lignocellulosic material. These methods entail tests to identify the optimum enzyme composition and ratios for efficient conversion of any lignocellulosic substrate to its constituent sugars. While the multi-enzyme product may contain many types of enzymes, mixtures comprising enzymes that increase or enhance sugar release from biomass are preferred, including hemicellulases. The enzymes of the multi-enzyme product can be provided by a variety of sources. In one embodiment, the enzymes can be produced by a growing microorganism, especially a fungus, which produce the enzymes naturally or by virtue of being genetically modified to express the enzyme or enzymes.