University of Kansas

10 ARTICLES PUBLISHED IN JoVE

Biology

A Protocol for Computer-Based Protein Structure and Function Prediction

Ambrish Roy^1,2, Dong Xu¹, Jonathan Poisson¹, Yang Zhang^1,2

¹Center for Computational Medicine and Bioinformatics, University of Michigan , ²Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas

Guidelines for computer based structural and functional characterization of protein using the I-TASSER pipeline is described. Starting from query protein sequence, 3D models are generated using multiple threading alignments and iterative structural assembly simulations. Functional inferences are thereafter drawn based on matches to proteins with known structure and functions.

Environment

Reliable Method for Assessing Seed Germination, Dormancy, and Mortality under Field Conditions

Brian A. Pace¹, Helen M. Alexander², D. Jason Emry³, Kristin L. Mercer¹

¹Department of Horticulture and Crop Science, Ohio State University, ²Department of Ecology and Evolutionary Biology, University of Kansas, ³Department of Biology, Washburn University

Here we present a protocol for assessing seed survivorship, germination and dormancy under field conditions using buried, labeled seed strips and tetrazolium chloride (TZ) viability testing.

Behavior

Central and Divided Visual Field Presentation of Emotional Images to Measure Hemispheric Differences in Motivated Attention

Aminda J. O'Hare¹, Ruth Ann Atchley², Keith M. Young³

¹Department of Psychology, University of Massachusetts Dartmouth, ²Department of Psychology, University of Kansas, ³Department of Psychology, University of Minnesota Duluth

This study compared central versus divided visual field presentations of emotional images to assess differences in motivated attention between the two hemispheres. The late positive potential (LPP) was recorded using electroencephalography (EEG) and event-related potentials (ERPs) methodologies to assess motivated attention.

JoVE Core

Treatment with Vancomycin Loaded Calcium Sulphate and Autogenous Bone in an Improved Rabbit Model of Bone Infection

Yang Zhang^*1, Lifeng Shen^*2, Ping'er Wang³, Weixing Xi⁴, Zhongming Yu¹, Xiaowen Huang¹, Xuping Wang¹, Dan Shou¹

¹Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, ²Department of Orthopaedic Surgery, Tongde Hospital of Zhejiang Province, ³Institute of Orthopaedics and Traumatology, First Affiliated Hospital of Zhejiang Chinese Medical University, ⁴Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province

This study presents an improved rabbit model infected with Staphylococcus aureus by blocking the same amount of bacteria in bone marrow. Vancomycin loaded calcium sulphate and autogenous bone are used for antibiotic and bone repair treatment. The protocol could be helpful for studying bone infection and regeneration.

Engineering

A Soft Tooling Process Chain for Injection Molding of a 3D Component with Micro Pillars

Yang Zhang¹, David Bue Pedersen¹, Michael Mischkot¹, Matteo Calaon¹, Federico Baruffi¹, Guido Tosello¹

¹Department of Mechanical Engineering, Technical University of Denmark

A protocol for fabricating injection molding inserts for complex geometry with micro features on surfaces employing Additive Manufacturing (AM) is presented.

Engineering

Microfluidic Fabrication Techniques for High-Pressure Testing of Microscale Supercritical CO₂ Foam Transport in Fractured Unconventional Reservoirs

Hooman Hosseini¹, Feng Guo², Reza Barati Ghahfarokhi¹, Saman A. Aryana²

¹Department of Chemical and Petroleum Engineering, University of Kansas, ²Department of Chemical Engineering, University of Wyoming

This paper describes a protocol along with a comparative study of two microfluidic fabrication techniques, namely photolithography/wet-etching/thermal-bonding and Selective Laser-induced Etching (SLE), that are suitable for high-pressure conditions. These techniques constitute enabling platforms for direct observation of fluid flow in surrogate permeable media and fractured systems under reservoir conditions.

Bioengineering

Tetrameric Fluorescent Antigen Arrays for Single-Step Identification of Antigen-Specific B Cells

Kyle D. Apley^*1, J. Daniel Griffin^*1, Stephanie N. Johnson¹, Cory J. Berkland^1,2,3, Brandon J. DeKosky^1,2,3

¹Department of Pharmaceutical Chemistry, University of Kansas, ²Bioengineering Graduate Program, University of Kansas, ³Department of Chemical and Petroleum Engineering, University of Kansas

This protocol details the customizable production and use of fluorescent probes for labeling antigen-specific B cells.

Developmental Biology

Generation of a Mouse Artificial Decidualization Model with Ovariectomy for Endometrial Decidualization Research

Yang Zhang^*1,2,3, Zhe Zhang^*1,2,3, Nannan Kang^1,2,3, Xiaoqiang Sheng^1,2,3

¹Center for Reproductive Medicine and Obstetrics and Gynecology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, ²State Key Laboratory of Reproductive Medicine, Nanjing Medical University, ³Center for Molecular Reproductive Medicine, Nanjing University

Here, we describe the method of generating an artificial decidualization model using the ovariectomized mouse, a classic endometrial decidualization experiment in the research field of endometrial decidualization.

Cancer Research

Rapid In Vitro Cytotoxicity Evaluation of Jurkat Expressing Chimeric Antigen Receptor using Fluorescent Imaging

Siddharth Subham^*1,2,3, John D. Jeppson^*1, Benjamin K. Gibbs⁴, Jacqueline Babai², Riza Alker¹, Andrew K. Godwin^4,5,6, David Akhavan^1,2,3

¹Department of Radiation Oncology, University of Kansas Cancer Center, ²Department of Cancer Biology, University of Kansas Cancer Center, ³BioEngineering Program, University of Kansas, ⁴Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, ⁵University of Kansas Cancer Center, ⁶Kansas Institute for Precision Medicine, University of Kansas Medical Center

A protocol to evaluate quantitative tumor cell killing by Jurkat cells expressing chimeric antigen receptor (CAR) targeting single tumor antigen. This protocol can be used as a screening platform for rapid optimization of CAR hinge constructs prior to confirmation in peripheral blood-derived T cells.

Bioengineering

Hyperpolarized ¹²⁹Xe Lung MRI and Spectroscopy in Mechanically Ventilated Mice

Mariah L. Costa^1,2,3, Joseph W. Plummer^1,2, Abdullah S. Bdaiwi¹, Brice J. Albert⁴, Elizabeth M. Fugate³, Peter J. Niedbalski^5,6,7, Diana M. Lindquist^3,8, Zackary I. Cleveland^1,2,3,8,9

¹Center for Pulmonary Imaging Research, Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, ²Department of Biomedical Engineering, University of Cincinnati, ³Imaging Research Center, Department of Radiology, Cincinnati Children's Hospital Medical Center, ⁴Analytical Technology Group, Aurorium, ⁵Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of Kansas Medical Center, ⁶Department of Bioengineering, University of Kansas, ⁷Hoglund Biomedical Imaging Center, University of Kansas Medical Center, ⁸Department of Pediatrics, University of Cincinnati, ⁹Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center

Hyperpolarized xenon MRI can quantify regional lung microstructure (air-space dimensions) and physiology (ventilation and gas exchange) in translational research and clinical care. Although challenging, it can provide comparable pulmonary insights in preclinical studies. This protocol describes the infrastructure and procedures needed to perform routine xenon lung MRI in mice.