Resarch Tools

Research Tools

Research tools are essential for next generation biomedicine. New research tools that enable scientific discoveries are developed at UMassMed and are now available to the public. Browse through our UMassMed Research Tools inventions by scrolling though or by clicking these categories: 

1) Antibodies and Enzymes2) Animal Models3) Genome Wide Tools4High Throughput Screening Tools5) Bioluminescence, Labeling and Imaging,  6) Stem Cells Tools7) Tissue Engineering.

 

 

  

 

  

Browse Our Research Tools Innovations:

 

Antibodies and Enzymes 

 

Title: Nucleic Acid-guided, Thermostable Restriction Enzyme for DNA and RNA. UMMS15-41.

  • Our invention is a method for the creation of a thermostable, programmable restriction enzyme that can be used to cleave ssRNA, ssDNA, dsRNA, or dsDNA at a specific site determined by the sequence of the small DNA guide bound to Thermus thermophilus Argonaute (TtAgo) protein. This invention is a method that can be used as a molecular biology research tool for cloning and/ manipulating DNA or RNA for research use.

Title: Monoclonal Antibodies Specific for mCherry. UMMS15-10. 

Title: Monoclonal Antibodies that bind Citrullinated Human Fibrinogen. UMMS15-07. 

  • Mouse monoclonal antibodies that recognize the citrullinated form of human fibrinogen.

Title: Monoclonal Antibodies Specific for Streptavidin. UMMS14-67.

Title: Zebrafish Fli1b Rabbit Polyclonal Antibody. UMMS12-60. 

Title: Zebrafish Etv2 Rabbit Polyclonal Antibody. UMMS12-59.

  • Rabbit polyclonal antibody that recognizes the amino terminal half of zebrafish ETV2, a transcription factor that is essential for vascular development in all vertebrates. Etv2 is also knows as ER71, Etsrp, or Ets 1b protein.

Title: A Polyclonal Antibody that Recognizes the Zebrafish Homolog of Flt4 (zfFlt4). UMMS12-58.

Title: Rabbit & Guinea Pig Polyclonal Antibodies to the Circadian Proteins; NPAS2/MOP4, BMAL1/Arnt3/Arnt1/Mop3, Per2, CLOCK, PER1, Casein Kinase 1 delta, and Casein Kinase 1 epsilon. UMMS12-49.

  • Rabbit and Guinea Pig polyclonal antibodies to circadian protein available for licensing. 

    1. anti-NPAS2: antigen is amino acids 597-916
    2. anti-BMAL1: antigen is amino acids 382-586
    3. anti-PER2: antigen is amino acids 1-200
    4. anti-CLOCK: antigen is amino acids 363-855
    5. anti-PER1: antigen is amino acids 1-23
    6. anti-CASEIN KINASE 1 DELTA: antigen is amino acids 243-415
    7. anti-CASEIN KINASE 1 EPSILON: antigen is residues 202-416

Title: anti-OC-STAMP Antibody. UMMS11-56.

  • Chicken polyclonal antibody that recognizes OC-STAMP is available for licensing.  Antigen is human OC-STAMP amino acids 141-161, the extracellular domain. OC-STAMP plays a role in osteoclast fusion and bone formation.

Title: Activated p38 MAPK Isolated From Bacterial Cell Culture. UMMS11-06.

  • DE3 E-coli cells that express a his-tagged p38 MAPK construct yielding phosphorylated p38 MAPK without the secondary step of treating with MKK6.

Title: Rabbit Polyclonal Antibody to mPer1. UMMS08-33.

Title: Rabbit Polyclonal Antibody to Per2. UMMS08-32.

Title: Guinea Pig Polyclonal Antibody to BMAL. UMMS08-31.

Title: Rabbit Polyclonal Antibody to CLOCK. UMMS08-30. 

Title: Pericentrin Antibody A102. UMMS08-20.

  • Monoclonal antibody against tyrosine phosphorylated pericertrin (A012), a centrosome protein involved in microtubule organization and cell division cycle regulation. Rabbit pericentrin antibody included.

Title: New Monoclonal Peptide Antibodies to Centriolin. UMMS08-19.

  • Polyclonal peptide antibodies against Centriolin, a centrosome protein involved in microtubule organization and cell division cycle regulation. Rabbit Centriolin N-terminus and C-terminus antibodies are included.

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Animal Models 

 

Title: Genetically Modified Non-Human Animals and Methods Relating to Complement Dependent Cytotoxicity. UMMS16-63; Patent Pending. 

  • The present invention provides a genetically modified immunodeficient mouse, wherein the genome of the mouse comprises a repaired C5 complement component structural gene such that the 5 genetically modified immunodeficient mouse expresses the C5 complement component structural gene and is characterized by an intact complement system. The present invention relates to immunodeficient non-obese diabetic (NOD), A/J, A/He, AKR, DBA/2, NZB/B1N, BlO.D2/oSn and other mouse strains genetically modified to restore complement-dependent cytotoxicity which is lacking in the unmodified immunodeficient mice.

Title: In vitro and in vivo Transduction of Intact Pre-implantation Mammalian Embryos. UMMS16-29; Patent Pending.

  • This invention simplifies genetic engineering in mammalian (does it matter which ones?) research and commercial settings by introducing nucleic acids into mammalian embryos without the need for conventional mechanical methods, microinjection or electroporation, which can be lethal. The new transgenic platform works simply by exposing AAV viral particles to an “intact” pre-implantation embryo. Using this method minimizes the need for labor-intensive embryo harvesting and transferring into pseudopregnant females.

Title: SerpinA1 Null Mouse as a Model for Alpha-one Antitrypsin Deficiency and Lung Conditions. UMMS15-62; Patent Pending. 

  • The invention provides a novel mouse model with alpha-one antitrypsin deficiency for use as a tool to study lung conditions including emphysema. With the use of the recently developed CRISPR technology, the inventors designed and implemented a strategy to delete all five copies of the SerpinA1 gene at once overcoming previous technical limitations preventing development of SerpinA1 null mice.

Title: Creation of RIPK3 Reporter and Conditional Deletion Mouse Model. UMMS15-05; Patent Pending. 

  • This invention allows investigators to track endogenous RIPK3 expression in live cells and enables tissue-specific inactivation of RIPK3.  Specifically, the last coding exon of the mouse RIPK3 gene is fused in-frame to the enhanced green fluorescent protein (GFP).  LoxP sites flank the last coding exon of RIPK3. Crossing the RIPK3-GFP “floxed” mice to transgenic mice expressing Cre recombinase under the control of tissue-specific promoter enables conditional deletion and inactivation of RIPK3 in distinct tissues.

Title: Conditional ASC-citrine Expressing Inflammasome Reporter Mouse. UMMS14-64. Related Publication.

  • To facilitate the study of inflammasome activation in vivo, this transgenic mouse expresses fluorescent ASC in the Rosa26 locus. This system contains a knock-in of ASC-citrine gene and a proximal floxed stop site enabling conditional expression in a lineage specific manner by breeding mice with different cre expressing lines.

Title: Development of NOD.Cg-Prkdc<scid> Il2rg<tm1Wjl> Tlr4lps-del Sz/Sz ("NSG Tlr4 Mice"). UMMS13-61; Related Publication

  • This invention provides a immunodeficient mouse model based on the NOD strain (referred to as NSG and NRG mice) that can be engrafted with functional human immune systems, including adaptive and innate immune systems. These mice completely lack adaptive immune cells such as T and B cells, as well as NK cells.  To study the response of human innate immune cells to the TLR agonist LPS in the absence of a murine innate immune response, these NSG mice completely lack TLR4 on their innate immune cells.

Title: COMPOSITIONS AND METHODS FOR CHARACTERIZING AND TREATING MUSCULAR DYSTROPHY. UMMS13-53; Patent 9,260,755

  • This invention provides a patented chimeric mouse model for Facioscapulohumeral muscular dystrophy (FSHD) that can be used to further characterize the disease or identify potential therapeutic agents. In a related pending patent application, the invention further discloses inhibitory nucleic acids targeting one or more of SLC34A2, TRIM49, TRIM43, CD177, NAAA, HSPA6, TC2N, or CD34 to treat FSHD.

Title: Transgenic Non-Human Animal and Methods for Stem Cell Engraftment. UMMS10-43; Patent Pending. 

  • A transgenic immunodeficient non-obese diabetic (NOD) mouse homozygous for the SCID mutation and having an IL2 receptor gamma chain deficiency. Administration of human stem cells to the mouse in the absence of conditioning by irradiation results in similar or greater levels of engraftment of human stem cells compared to a non-obese diabetic (NOD) mouse homozygous. 

 

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Genome Wide Tools

 

Title: Method for Efficient Preparation of cDNA Libraries from Small RNAs. UMMS14-04; Patent Pending.

  • A novel method for generating cDNA libraries from unprecedented low quantities (e.g., pg and sub-pg range) of RNA is described herein. Using this method, cDNA libraries can be generated from a range of biofluids as well as from limited tissue volumes isolated from size-limited pathology specimens including biopsy tissue blocks, from small numbers of pure populations of cells isolated from laser capture microdissection of heterogeneous cell populations, and from small numbers of model-organisms. The methods can incorporate one or more novel components including (i) the reduction of gel purification steps, (ii) seamless transition between ligation and RT using sequential reactions in a single tube, and (iii) incorporation of biotinylated nucleotides in the RT reaction to permit efficient purification of cDNA prior to PCR. 

Title: OmniPrep: An Optimized Method for Making Strand-specific Deep Sequencing Libraries from Diverse RNA Inputs and Small Sample Sizes. UMMS14-03; Patent Pending.

  • This invention provides novel methods for generating cDNA libraries that allow for reliable mapping of the 5′ and 3′ ends of transcripts as well as mapping, to a single nucleotide, the length of the poly(A) tail. This technology overcomes the limitations and biases present in current deep-sequencing platforms. 

Title: Hybridization-independent Labeling of Repetitive DNA Sequence Arrays in Fixed or Living Cells. UMMS13-54; Patent Pending. 

  • The present invention discloses a transcription activator-like effector-based strategy, termed “TALEColor”, for labeling specific repetitive DNA sequences in human chromosomes. TALEs were custom designed for human telomeric repeats and fused with any of numerous fluorescent proteins (FPs). TALE-telomere-FP fusion proteins were used to detect telomeric sequence in both living cells and fixed cells. Using human cells with different average telomere lengths, TALEColor signals correlated positively with telomere length. TALEs were also designed to detect centromeric sequences unique to specific chromosomes, enabling localization of these specific human chromosomes in live cells. These methods may have significant potential both for basic chromosome and genome research as well as in clinical applications. 

Title: Genome-wide Mapping of 5' and 3' End Sequences as well as Poly(A) Tail Length of Capped Transcripts with Single-nucleotide Resolution Using High-throughput Sequencing. UMMS13-35; Patent Pending. 

  • This invention provides novel methods for generating cDNA libraries that allow for reliable mapping of the 5′ and 3′ ends of transcripts as well as mapping, to a single nucleotide, the length of the poly(A) tail. This technology overcomes the limitations and biases present in current deep-sequencing platforms.

Title: Purification of Small RNAs from Human Biofluids. UMMS12-57; Patent Pending.  

  • This invention provides methods for isolating circulating small RNAs from plasma/urine, CSF, or tissue samples, the method comprising using an alkaline phenol:chloroform extraction, and methods of use thereof, including for the detection, prognosis, and/or monitoring of disease in a subject. These methods significantly increase the yield of many assayable small RNAs such as miRNA, some by tenfold or more over present standard methods.

Title: Dosage Compensating Transgene Constructs. UMMS12-46; Patent Pending. 

  • The present invention provides silencing vectors that may be useful in "chromosome therapy" for Down syndrome or may be used as a research tool/system to investigate genomic expression changes and the cellular pathology of trisomy 21. This technology is based on the discovery that the imbalanced expression of hundreds of genes across an extra chromosome can be corrected in Down Syndrome patient stem cells by the targeted addition of one gene, XIST, in a specific location.

Title: Capseq - an Enzymatic Method to Enrich and Deep-seq Capped RNA. UMMS12-18; Patent Pending.

  • This invention discloses novel methods for the enzymatic enrichment and detection of RNA 5' ends that eliminates contaminating RNA sequences and dramatically enriches for RNAs that contain the nuclease resistant 5' cap structure.  The invention avoids the tedious and inefficient column purification procedure and can clone mRNA from as little as 500 ng. The cloned sequences are anchored at the 5' end of capped RNAs thus simplifying the bioinformatics analysis to compare samples.

Title: DEDUCING EXON CONNECTIVITY BY RNA-TEMPLATED DNA. UMMS09-38; Patent 8,975,019

  • This invention discloses a method for studying mRNA sequences without disrupting transcript connectivity or relative abundance. Contrary to existing methods to study mRNA splicing, this method directly assesses the relative abundance of isoforms, with information regarding multiple ligases and mRNA exon connectivity. Improved understanding of isoforms may facilitate further study of developmental disease or cancer.

Title: METHODS OF IDENTIFYING INTERACTIONS BETWEEN GENOMIC LOCI. UMMS08-44; Patent 9,434,985.

  • This invention provides a new protocol to describe long range physical interaction of genome loci within and between chromosomes. Long range regulatory elements in the genomes are known to interact. This interaction is important for genome biology, as it can control aspects of the genome, such as stability and dosage compensation. Contrary to the previous methods for describing long range genome interactions, Hi-C does not require prior understanding of one genomic loci, making it a truly genome wide characterization. This invention may reveal important aspects of genomic interaction in disease. 

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High Throughput Screening Tools

  

 

Title: Discovery and Targeting of Host Factors that Modulate Hepatitis B Virus Replication. UMMS15-60; Patent Pending.  

  • This invention discloses the first ever genetic screen to identify Hepatitis B virus host factors. The invention further encompasses the factors, such as Zinc finger, CCHC domain containing 14 (ZCCHC14), identified by those methods and methods of treating Hepatitis B virus infections by targeting those factors.

Title: Using Cas9 Coupled Histone Effector to Investigate Enhancer Function. UMMS15-23; Patent Pending. 

  • The invention uses CRISPR targeting to provides a rapid high throughput system to determine the contribution of distal cis-regulatory elements to development and disease. This method is faster and more versatile than using TALE of ZFN effectors. This level of genome control has previously not been achieved with other RNA-guided regulatory technologies such as RNAi.

Title: A Versatile Microplate Design for High Performance Spectroscopic Applications. UMMS14-19; Patent Pending.

  • This novel technology describes a microplate for use in high-throughput determinations of protein stability, protein-DNA/RNA binding, and protein-protein associations. The disclosed invention overcomes the limitations of other microplate designs including meniscus formation, variable path length for each well, and compatibility with use in the UV and far-UV region. The invention uses two optical flats, which for example can be quartz glass, and a spacer having a plurality of holes defined in the spacer to make optical measurements.

Title: BCR Adapter lgM (BCRAM) for the BCR/TLR Delivery of Autoantigens to Polyclonal Murine and Human B Cell Populations. UMMS13-65; Patent Pending.

  • This technology provides a model for autoantigen activation of B cells that can be used to research and treat the development/progression of autoimmune diseases, such as systemic lupus erythematosus (SLE).  This novel research tool enables the identification of suitable drug targets and provides methods for production of autoantigens.  Specifically, a BCR adapter IgM (BCRAM) is described to exemplify delivery of autoantigens to polyclonal B cell populations resulting in immunoactivation by Toll-like receptor activation.

Title: SCREENING METHODS FOR SPINAL MUSCULAR ATOPHY. UMMS12-67; Patent 9,212,209

  • This technology provides vectors that increase survival of motor neuron (SMN) protein production by an SMN2 gene and methods for treatment of spinal muscular atrophy (SMA). Further discloses is a clonal second generation SMN-luciferase reporter cell line that combines the strengths of both the promoter-based assay and a previous splicing reporter. This assay is much more robust, has lower well-to-well variation, and displays more stable luciferase expression that does not change with serial passage that can be used to identify potential therapeutic agents for SMA. 

Title: An IFNβ Reporter Cell Line, clone SZ34. UMMS12-01. 

  • Large-scale and high throughput screen for compounds that module type I interferons identify potential therapeutics that block viral replication. Clone SZ34 is a stabilly transfected human embryonic kidney cell (HEK) with expression plasmids for an IFN-Beta-promoter-driven firefly luciferase reporter gene (IFN-Beta-Luc).

Title: TOLE LIKERECEPTORS-BASED BIOSENSORS. UMMS09-59; Patent 9,409,968

  • This invention discloses methods and compositions to detect Toll-like receptor (TLR) binding to ligands and evaluate compound for screening. Using different biosensor complexes, this technology enables the diagnosis of gram positive or negative infections in a human subject. Each platform utilizes a TLR conjugated to a biosensor that detects a single TLR-ligand binding domain complementary to its cognate ligand. This technology can provide a method to select appropriate treatment for a patient with inflammatory and possibly other conditions.

Title: COMPOUNDS FOR MODULATING TLR2. UMMS09-52 Patent 8,609,6639,271,972

  • Viral infection causes damage to the host via stimulation of production of host cytokines. These processes can culminate in edema and damage to host organs. From screening, this novel invention identifies molecules that could potentially inhibit the cytokine response to viral infection by inhibiting RNA virus-mediated TNF-alpha production. The current invention discloses methods of the system used to screen, a TLR2 and CD14 stable cell line, and molecular inhibitors of Lymphocytic Choriomeningitis Virus (LCMV) induced cytokine production. These newly discovered molecules may facilitate amelioration of symptoms in a broad range of hemorrhagic fever viruses.

Title: Mammalian Cell Lines for High Throughput Screening for mRNA Splicing Inhibitors. UMMS09-06.

  • This invention contains a method for high throughput screening for drug compounds that inhibit mRNA splicing. Using a luciferase based assay system, the inventors developed an assay that can report when splicing has occurred. Drugs that can inhibit major and minor splicesomes can be identified through this method. This technique is applicable to diseases that arise from perturbations in mRNA processing and/or splicing.

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Bioluminescence, Labeling and Imaging 

 

 

Title: T Cell Hybridomas Expressing Luciferase Under the Control of IL-2 Promotor Element. UMMS15-15. 

  • T Cell Hybridomas Expressing Luciferase Under the Control of IL-2 Promotor Elements. 

Title: In Vivo Rechargeable Near Infrared Emitting Mesoporous Persistent Luminescence Nanocomposites. UMMS15-20; Patent Pending. 

  • The invention provides methods to produce novel mesoporous persistent luminescece silica nanoparticles that are uniform and homogeneous for optical imaging applications.

Title: COATED UP-CONVERSION NANOPARTICLES. UMMS12-13; Patent 9,333,271

  • The invention provides novel biocompatible upconversion nanoparticles (UCNP) comprising a core of cubic nanocrystals (e.g., comprising α-Na Lna, Lnb Lnc F4) and an epitaxial shell (e.g., formed from CaF2; wherein Lnb is Yb). The disclosed nanoparticles lack the toxicity of traditional UCNPs and are synthesized in a single reactor vessel making them more amenable to large-scale production. Further provided are methods of whole body imaging and photochemical methods using the disclosed nanoparticles.

    • Inventors: Gang Han
    • Applications:
    • Patent Expiration Dates2034-03-27

Title: LUCIFERIN AMIDES. UMMS12-04; Patent 9,370,588 

  • This technology discloses luciferin amides (e.g., amides derived from firefly luciferin and their analogs) and imaging methods to detect fatty acid amide hydrolase (FAAH) activity in vitro, in live cells, and in vivo. The compounds and methods described are more sensitive and faster than conventional coumarin-based FAAH assays.  These assays may be used to identify therapeutic targets for conditions involving inflammation.

Title: Mutant Luciferases and Synthetic Luciferin Substrates. UMMS11-28; Patent Pending. 

  • This technology provides novel mutant luciferases capable of efficient light emission with aminoluciferins that can be used to monitor gene expression in mammalian cells or perform bioluminescence imaging in whole organisms. This technology is based on the finding that the disclosed genetically-modified luciferases give higher light output in live mammalian cells than D-luciferin over a wide concentration range.

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Stem Cell Tools

 

Title: Expansion of Human Adipocyte White and "Brite/Beige" Progenitors through Angiogenic Expansion of their Vascular Niche. UMMS14-26; Patent Pending.

  • This invention relates to methods of making human adipose capillary progenitor cells (HACAPS), which are capable of giving rise to either white or "Brown-on-white" (Brite) adipose cells, and enriched populations thereof, for reconstructive and metabolic therapy, and for drug discovery. Further, methods of treating subjects by administering HACAPS are provided. 

Title: Cas9 Effector-mediated Regulation of Transcription and Differentiation in Human Pluripotent Stem Cells. UMMS14-12; Patent Pending. 

  • This invention provides novel methods of and systems for modifying the transcriptional regulation of stem or progenitor cells to promote their differentiation or reprogramming of somatic cells. Further, the labeling and editing of human genomic loci in live cells with three orthogonal CRISPR/Cas9 components allow multicolor detection of genomic loci with high spatial resolution, which provides an avenue for barcoding elements of the human genome in the living state. This technology provides a much needed system that can be used to promote differentiation of a stem, progenitor or precursor cell population and can be used in a directed approach to identify genes related to cell differentiation down desired lineage pathways.

Title: INHIBITIONOFFGFSIGNALING. UMMS13-66; Patent 7,968,527. 

  • The technology discloses methods for inhibiting FGF signaling, a pathway that plays a role in embryogenesis, angiogenesis and cancer. The method comprises contacting the FGF-responsive cell with an exogenous Sulf1-treated heparin compound resulting in reduced cellular proliferation, cellular migration, and angiogenesis. In stem cells, FGF inhibition supresses mesoderm formation and, thereafter, redirects cellular differentiation to ectoderm.

Title: Dual Probe as a Diagnostic and Therapeutic Agent for Stem Cell and Related Applications. UMMS12-33; Patent Pending.

  • To better understand the risks associated with stem cell therapies, this invention provides compounds to track transplanted stem cells in vivo overtime using noninvasive imaging techniques.  Specifically, the invention provides novel multi-modality probes constructed by utilizing (a) the high selectivity of long hydrocarbon chains for binding to plasma membranes of cells, (b) a near-infrared (NIR) dye for optical imaging, and (c) a radionuclide for PET or SPECT imaging.

Title: Mitogen-Activated Protein Kinase Kinase Kinase Kinase (Map4k4) as a Therapeutic Target of Muscular Dystrophies including Duchenne Muscular Dystrophy (DMD). UMMS12-29; Patent Pending. 

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Tissue Engineering

 

 

Title: Surface Mineralization of Metal Alloys Grafted With Zwitterionic Polymer Brushes. UMMS14-35; Patent Pending.

  • The invention provides novel compositions and methods of surface mineralization for metallic or ceramic implants and devices and the resulting enhancement of properties and performance in skeletal tissue engineering, orthopedic applications and dental care. The novel approach utilizes zwitterionic brushes (e.g., of poly(sulfobetaine methacrylate) or pSBMA) covalently grafted on the surface of titanium or its alloy substrates (e.g., Ti6A14V) to promote surface-mineralization of hydroxyapatite with enhanced surface mineral coverage and mineral- substrate interfacial adhesion. The zwitterionic surface brushes, capable of attracting both cationic and anionic precursor ions during hydroxyapatite-mineralization, significantly increase the surface mineral coverage and significantly reinforce the attachment of the surface apatite crystals on the titanium alloy substrate which withstood supersonication treatment.

Title: Extensible and Elastomeric Electrospun Composites with High Mineral Content. UMMS12-80; Patent Pending.

  • This invention provides novel compositions of hydroxyapatite and block copolymers, wherein the co-polymers have degradable hydrophobic blocks and hydrophilic blocks for stable interfacing with hydroxyapatite, resulting in stable polymer-hydroxyapatite suspensions. The super- hydrophilicity, strengthened mechanical integrity, and retained structural integrity of the HA- PELA composite in aqueous environment represent major advantages over the HA-PLA composites for skeletal tissue engineering applications. 

 

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