Skip to Main

Research

Grand-Funded Projects

Trauma Research and Combat Casualty Care Collaborative TRC4

A research entity singularly focused on addressing the critical need for improved trauma care in the United States.

CORT-Provided Research Support

CORT research support provides state-of-the-art services that augment the capabilities, availability, and budgets of individual CORT investigators.

Histology

Our laboratory has extensive experience in histology tissue processing, routine histology stains, and immunofluorescent histology, with a focus on musculoskeletal tissues including bone, muscle, and skin. We are equipped with two cryostats for frozen tissue sectioning. Commonly performed stains include H&E, Masson's Trichrome, picrosirius red, safranin O, and oil red O. We routinely conduct immunofluorescent histology for various antigens related to bone development, vasculature, nerve, and muscle, preparing samples for both confocal and epifluorescent microscopy.

Microscopy Core

Microscopy

Our laboratory houses a Leica Stellaris Confocal Microscope fitted with a tunable white light laser and up to 63x objective, allowing for very high-resolution imaging of multiple fluorophores simultaneously. We also have a DM750 brightfield microscope equipped with a polarizing light filter for imaging the birefringence of picrosirius red-stained samples.

Micro-CT and X-Ray Core

Micro-CT and X-Ray

Our lab is home to a KubTec X-Ray Cabinet and a Bruker Skyscan 1272 Micro-Computed Tomography scanner. Micro-CT imaging allows for high-resolution scanning of small objects, and our laboratory has expertise in imaging the mouse skeleton, fractures, and ectopic bone formation. Our laboratory routinely utilizes Micro-CT analysis software such as CT Vox, CT An, and ORS Dragonfly software for bone volume assessment, porosity, trabecular volume and thickness, cortical thickness, and tibial length.

Bioinformatics

We employ two experienced bioinformaticians specializing in the analysis of transcriptomics data and the development of machine learning programs. Our expertise includes single-cell RNA-sequencing, single-nucleus ATAC-sequencing, and spatial transcriptomics. We routinely analyze single-cell RNA-sequencing data, processing both in-house and publicly available datasets (e.g., NCBI GEO). Our analysis capabilities encompass differential gene expression/visualization (Seurat), data integration (Harmony, SCT), trajectory analysis (Monocle, slingshot, Velocyto), cell-cell communication (CellChat, NicheNetr), differentiation state analysis (CytoTRACE), automated cell identification (scCATCH), and pathway analysis (enrichR, ClusterProfiler). Additionally, we utilize data management pipelines (BPCells, qs) for improved analysis speeds.

Surgery Core

Surgery

The Levi Laboratory is proficient in mouse surgical models of the musculoskeletal system. We have a dedicated surgery room with two surgery bays, a tissue harvest bay, and a dissecting microscope equipped with a computer monitor for microsurgery procedures. We have developed reliable and reproducible surgical models to study traumatic injuries, including a burn/tenotomy model of heterotopic ossification. We also utilize well-validated models of traumatic injury, such as hip arthroplasty models of heterotopic ossification, volumetric muscle loss and ischemia/reperfusion models of muscle fibrosis, digit tip amputation models for studying regeneration, and mouse parabiosis. The Levi Laboratory is well-trained in developing new surgical techniques and offers guidance in developing surgical protocols for institutional approval.

  • Equipment List
    • Fluorescent and confocal microscopy
    • MicroCT scanners
    • IVIS imaging devices
    • 10X RNA sequencing facilities
    •  mouse genomics core.
    • Leica confocal microscope and Bruker
    • SKYSCAN 1272 CMOS EDITION - High-resolution 3D X-ray Microscopy
    • Cytation 5- digital microscope and microplate reader
    • 4D-Nuclefector System
    • PARAMETER Cabinet X-ray System
  • Injury Models
    • Burn
    • Tenotomy
    • Muscle Crush
    • Volumentric Muscle Loss
    • Fracture
    • Calvarial Defect
  • Mouse Genotypes - Brekken Lab
    Mouse LineOptional Information
    KPC p48-Cre; KrasLSL-G12D/+; Trp53LSL-R172H/+; mixed background
    KIC KrasLSL−G12D/+Ink4afl/flPtf1aCre/+
    KPfC KrasLSL-G12D/+; Trp53lox/lox; PdxCre/+ 
    KC KrasLSL-G12D/+; PdxCre/+ 
    TBK1 KO KPC TBK1 ∆/∆ (KD) X KPC: p48-Cre; LSL-KrasG12D; P53-172H/+; mixed background
    TBK1 KO TBK1 ∆/∆ (KD); mixed background: these mice were received under an MTA, need permission to transfer
    Gas6 KO Global knockout of Gas6
    Csf1r-Cre Cre active in Csf1r+ myeloid cells
    Vegfr2Floxed mice received va MTA; permission required for transfer
    Ptn null FVB Homozygous KO 
    B2GP1-null beta2gylcoprotein-1
    Pymt Het pymt+/- males; PyMT expressed in mammary gland, hence forms mammary tumor
    Pymt Ptn null Homozygous KO PTN, PyMT heteroxygous +/- males
    Fvb WT  
    Ptn null B6 Homozygous KO 
    Mer KO Global Mer-/- in C57BL/6 background
    PDGFRA-creERT;DTA Inducible genetic ablation of PDGFRa+ cells
    KIC; confetti Conffetti reporter on KIC tumor cells
    KPfC; confetti Conffetti reporter on KPfC tumor cells
    wt1creERT; confetti Wt1 is promoter for mesothelial cells and stellate cells
    FSF-KRAS;P53frt/+  
    AXL KO KIC same as AXL LacZ/LacZ KIC
    Axl KO KPfC AXL LacZ/LacZ;KrasLSL-G12D/+; Trp53lox/lox; PdxCre/+ 
    AXL LacZ/LacZ B6 Global AXL KO in C57BL/6 Background
    AXL LacZ/LacZ FVB Global AXL KO in FVB background
    AXL LacZ/LacZ KIC AXL-LacZ/LacZ X TBK1 ∆/∆ (KD) X KIC: p48-Cre; LSL-KrasG12D; Ink4a/Arflox/lox
    OT-II OVA MHC-II Knock-in mice, CD4 TCR can recognize OVA peptide
    mTmG; Immorto mTmG reporter bred into Immorto mouse
  • Mouse Genotypes - Dellinger Lab
    Mouse LineOptional Information
    Prox1-CreERT2 (knock-in) Cre active in lymphatics, hepatocytes, cardiomyocytes, skeletal muscle, neurons
    Prox1-CreERT2 (transgenic) Cre active in lymphatics, hepatocytes, cardiomyocytes, skeletal muscle, neurons
    Lyve1-CreERT2 (transgenic)  
    Vegfc-CreERT2  
    Lyve1-Cre (knock-in) Cre active in lymphatics and blood endothelial cells in the liver, lung, kidney, pancreas, yolk sac
    LSL-KrasG12D  
    LSL-Pik3caH1047R  
    Vegfr3-Chy (mixed) These mice develop fewer lymphatics than wild-type mice
    Prox1-tdTomato Lymphatic reporter mouse
    TetO-KrasG12D  
    TetO-Vegfc Transgene that induces growth of lymphatics in tissue-specific manner
    TetO-Vegfd Transgene that induces growth of lymphatics in tissue-specific manner
    Osx-tTA-TetO-Cre Cre and tTA active in bone cells
    Vegfc-flox/flox  
    Stat3-flox/flox  
    mT/mG  
    LSL-rtTA  
    LSL-dnMEK Cre-inducible dominant negative MEK
  • Mouse Genotypes - Huang Lab
    • NSG
  • Mouse Genotypes - Levi Lab
    • Hox TSP2
    • LysMCre TSP1
    • TSP1/TSP2
    • AviliCre
    • DDR2 flox
    • DDR2-CreER2
    • DDR2LacZ
    • Fgf18 flox
    • Fgfr1,2,3 flox
    • Hoxa11 GFP
    • Hoxa11CreER
    • PV cre
    • C57BL/6J
    • PDGFRaCreER
    • Rosa Luseap/Luseap (LUC)
    • Arf6-floxed
    • Arkadia-floxed
    • FKbp10-floxed
    • GPR81
    • KOGPR81-Floxed
    • Hif1a-floxed
    • Hif1a-floxed;TdTom
    • Hoxa11CreER; Arf6-floxed
    • Hoxa11CreER; Arkadia-floxed; tdTom
    • Hoxa11CreER; GLS-floxed
    • Hoxa11CreER; LdhA-floxed
    • Hoxa11CreER; SLC1A5-floxed
    • Hoxa11CreER; Srf-floxed
    • Hoxa11CreER; Tak1-floxed
    • Hoxa11CreER; Vhl-floxed;tdTom
    • Hoxa11CreER;Hif1a-floxed; tdTom
    • PDGFRaCreER; LdhA/B-floxed
    • LdhA/B-floxed
    • LdhA-floxed
    • LysMCre; GPR81 Flox
    • MCT4 KO
    • PDGFRaCreER; FKbp10-floxed
    • PDGFRaCreER; GPR81-Floxed
    • PDGFRaCreER; LdhA/B-Floxed
    • PDGFRaCreER;Hif1a-floxed;TdTom
    • Plod2-floxed
    • Snai1 flox Snai2 flox
    • Srf-floxed
    • Tak1-floxed
    • VHL-floxed
    • Hoxa11CreER; TGFbR2-floxed; tdTom
    • LysMCre
    • Mrp8Cre
    • Mrp8CreTLR9 flox
    • PDGFRaCreER Alk5 flox
    • PDGFRaCreER DDR2 flox
    • PDGFRaCreER FAK flox
    • PDGFRaCreER TGFBR2 flox
    • PDGFRaCreER Yap/Taz flox
    • TGFB1 flox
    • TGFBR 2 flox
    • TLR9 flox
    • Yap flox / Taz flox
    • PDGFRaCreER TdTom
    • Mrp8Cre tdTom
    • CD169iCre tdTom
    • DDR2-CreER2 x Ai14
    • FLT4Cre iDTR
    • FLT4Cre Pik3Ca flox
    • FLT4Cre Pten flox
    • K14CreER
    • PDGFRaCreER Rainbow
    • Prox1eGFP
    • Rainbow
    • TSP2 Reporter
    • Acod1 KO
    • Cthrc1
    • LysMCre Irg1 flox
    • Mrp8Cre Irg1 flox
    • PDGFRaCreER TSP1 flox
    • PDGFRaCreER TSP2 flox
    • TSP2 flox
    • Hoxa11CreER tdTom
    • TSP1 flox
    • P53 flox / Rb flox
    • BMP2 fn
    • Arg1 flox
    • CD169iCre
    • CD169iCre tdTom Piezo1 flox
    • CD4Cre Piezo1 flox
    • Hoxa11CreER Jmjd3 flox
    • LysMCre Arg1 flox
    • LysMCre Jmjd3 flox
    • LysMCre MLL flox
    • LysMCre Piezo1 flo
    • LysMCre SetDB2 flox
    • LysMCre TLR9 flox
    • LysMCre TMEM16F Flox
    • LysMCre Yap/Taz flox
    • Osx Cre
    • PDGFRaCreER Jmjd3 flox
    • PDGFRaCreER Piezo1 flox
    • Piezo 1 flox
    • Piezo 2 flox
    • TMEM 16 KO
    • TMEM16F Flox
    • Trem2
    • LysMCre Notch flox
    • FAK flox
    • Vegfa flox
  • Mouse Genotypes - Tang Lab
    Mouse LineOptional Information
    KCH KrasLSL-G12D/+; PdxCre/+ HMGB1fl/fl; mixed background
    KCR KrasLSL-G12D/+; PdxCre/+ RAGEfl/fl; mixed background
    KCLCN2-flox KrasLSL-G12D/+; PdxCre/+LCN2fl/fl; mixed background, LCN2-flox mice received va MTA; permission required for transfer
    KC KrasLSL-G12D/+; PdxCre/+ 
    KCZip14 KrasLSL-G12D/+; PdxCre/+ ZIP14; mixed background, Zip14 mice received va MTA; permission required for transfer
    GPX4-floxLYZ2 Knockout GPX4 in myeloid cell , GPX4-flox mice received va MTA; permission required for transfer
    Caspase11 KO Global knockout of Caspase11,mice received va MTA; permission required for transfer
    RAGE-floxLYZ2 Knockout RAGE in myeloid cell
    KCGSDMD(m) KrasLSL-G12D/+; PdxCre/+ GSDMD(mutation); mixed background, GSDMD(mutation) mice received va MTA; permission required for transfer
    MRL model for SLE
    Caspase11-floxLYZ2 Knockout Caspase11 in myeloid cell, Caspase11-flox mice received va MTA; permission required for transfer
    ALBcreGPX4 Knockout GPX4 in liver
    ALK KO Global knockout of ALK
    CDK2 KO Global knockout of CDK2, mice received va MTA; permission required for transfer
    CDK2-flox mice received va MTA; permission required for transfer
    TLR4 KO Global knockout of TLR4
    GSDMD KO Global knockout of GSDMD
    Acod1 KO Global knockout of Acod1
    Acod1-flox  mice received va MTA; permission required for transfer
    LDHa-flox  mice received va MTA; permission required for transfer
  • Mouse Genotypes - Wang Lab
    Mouse LineOptional Information
    Atp4b-Cre; p53f/f; Cdh1f/f; YFPf/f gastric pareital cell, leading to gastric adenocarcinoma
    Atp4b-Cre; p53f/f; Cdh1f/f; YFPf/f; Arid1a f/+ and f/f  
    p53f/f; Cdh1f/f; YFP pure C57/BL6
    Cdh1f/f; YFP pure C57/BL6
    p53f/f; YFP pure C57/BL6
Back-to top