Jilin University View Institution's Website 10 articles published in JoVE Biology Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets Kewei Li1, Yusi Fan1, Yaqing Liu1, Hongmei Liu2, Gongyou Zhang2, Meiyu Duan1, Lan Huang1, Fengfeng Zhou1 1College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 2School of Biology and Engineering, Guizhou Medical University Here, we introduce a protocol for converting transcriptomic data into a mqTrans view, enabling the identification of dark biomarkers. While not differentially expressed in conventional transcriptomic analyses, these biomarkers exhibit differential expression in the mqTrans view. The approach serves as a complementary technique to traditional methods, unveiling previously overlooked biomarkers. Genetics Transient Transduction of the Strobilated Forms of Echinococcus granulosus Mohammad Ali Mohammadi1, Ali Afgar2, Ashkan Faridi3, Seyed Mohammad Mousavi2, Ali Derakhshani2, Mehdi Borhani4, Majid Fasihi Harandi2 1Student Research Committee, School of Medicine, Kerman University of Medical Sciences, 2Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, 3Department of Parasitology and Mycology, Faculty of Medicine, Kurdistan University of Medical Sciences, 4State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University We describe a rapid transient transduction technique in different developmental stages of Echinococcus granulosus using third-generation lentiviral vectors. Neuroscience Craniotomy Procedure for Visualizing Neuronal Activities in Hippocampus of Behaving Mice YangDong Wang1,2,3,4, DanYang Zhu5, BaoYue Liu1,2,3,6, Kiryl D. Piatkevich1,2,3 1School of Life Sciences, Westlake University, 2Westlake Laboratory of Life Sciences and Biomedicine, 3Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 4 This article demonstrates the preparation of a custom-made imaging window supplemented with infusion cannula and its implantation onto the CA1 region of the hippocampus in mice. Medicine Establishing In Situ Closed Circuit Perfusion of Lower Abdominal Organs and Hind Limbs in Mice Ping Ren1,2,3, Chunyan Yang2,4, Laren A. Lofchy2, Guankui Wang2, Fangfang Chen*2,4,5, Dmitri Simberg*2 1Department of Thoracic Surgery, The First Hospital of Jilin University, 2The Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 3Key Laboratory of Zoonoses Research, Ministry of Education, Jilin University, 4Department of Cardiology, China-Japan Union Hospital of Jilin University, 5Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University A protocol is described for in situ perfusion of the mouse lower body, including the bladder, the prostate, sex organs, bone, muscle and foot skin. Medicine Intra-Operative Neural Monitoring of Thyroid Surgery in a Porcine Model Che-Wei Wu1,2,3, Tzu-Yen Huang2, Hui-Chun Chen4, Hsiu-Ya Chen5, Tsung-Yi Tsai2, Pi-Ying Chang5, Yi-Chu Lin2, Hsin-Yi Tseng2, Pao-Chu Hun6, Xiaoli Liu7, Hui Sun7, Gregory W. Randolph8, Gianlorenzo Dionigi9, Feng-Yu Chiang2,3, I-Cheng Lu5,10,11 1Department of Otorhinolaryngology, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, 2Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 3Department of Otorhinolaryngology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, 4Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 5Department of Anesthesiology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 6Laboratory Animal Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, 7Department of Thyroid and Parathyroid Surgery, China-Japan Union Hospital and Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin University, 8Division of Thyroid and Parathyroid Endocrine Surgery, Department of Otolaryngology, Massachusetts Eye and Ear Infirmary; Division of Surgical Oncology, Department of Surgery, Massachusetts General Hospital; Department of Otology and Laryngology, Harvard Medical School, 9Division for Endocrine Surgery, Department of Human Pathology in Adulthood and Child-hood "G. Barresi", University Hospital G. Martino, University of Messina, 10Department of Anesthesiology, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, 11Department of Anesthesiology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University This study aims to develop a standard protocol of intra-operative neural monitoring of thyroid surgery in a porcine model. Here, we present a protocol to demonstrate general anesthesia, to compare different types of electrodes, and to investigate the electrophysiological characteristics of the normal and injured recurrent laryngeal nerves. Cancer Research Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances Xin Feng1, Shaofei Wang1, Quewang Liu1, Han Li2, Jiamei Liu2, Cheng Xu2, Weifeng Yang2, Yayun Shu2, Weiwei Zheng1, Bingxin Yu3, Mingran Qi4, Wenyang Zhou1, Fengfeng Zhou1 1College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, 2College of Software, Jilin University, 3Ultrasonography Department, China-Japan Union Hospital of Jilin University, 4Department of Pathogenobiology, College of Basic Medical Science, Jilin University Existing algorithms generate one solution for a biomarker detection dataset. This protocol demonstrates the existence of multiple similarly effective solutions and presents a user-friendly software to help biomedical researchers investigate their datasets for the proposed challenge. Computer scientists may also provide this feature in their biomarker detection algorithms. Developmental Biology The C. elegans Excretory Canal as a Model for Intracellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis in a Single Cell: labeling by GFP-fusions, RNAi Interaction Screen and Imaging Nan Zhang1,2, Edward Membreno1, Susan Raj1, Hongjie Zhang1,3, Liakot A Khan1, Verena Gobel1 1Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School, 2College of Life Sciences, Jilin University, 3Faculty of Health Sciences, University of Macau The C. elegans excretory canal is a unique single-cell model for the visual in vivo analysis of de novo polarized membrane biogenesis. This protocol describes a combination of standard genetic/RNAi and imaging approaches, adaptable for the identification and characterization of molecules directing unicellular tubulogenesis, and apical membrane and lumen biogenesis. Developmental Biology The C. elegans Intestine As a Model for Intercellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis at the Single-cell Level: Labeling by Antibody Staining, RNAi Loss-of-function Analysis and Imaging Nan Zhang1,2, Liakot A Khan1, Edward Membreno1, Gholamali Jafari1, Siyang Yan1, Hongjie Zhang1,3, Verena Gobel1 1Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital, Harvard Medical School, 2College of Life Sciences, Jilin University, 3Faculty of Health Sciences, University of Macau The transparent C. elegans intestine can serve as an "in vivo tissue chamber" for studying apicobasal membrane and lumen biogenesis at the single-cell and subcellular level during multicellular tubulogenesis. This protocol describes how to combine standard labeling, loss-of-function genetic/RNAi and microscopic approaches to dissect these processes on a molecular level. Biology Single-molecule Imaging of Gene Regulation In vivo Using Cotranslational Activation by Cleavage (CoTrAC) Zach Hensel1, Xiaona Fang1,2,3, Jie Xiao1 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 2Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 3Department of Physics, Jilin University We describe a fluorescence microscopy method, Co-Translational Activation by Cleavage (CoTrAC), to image the production of protein molecules in live cells with single-molecule precision without perturbing the protein's functionality. This method has been used to follow the stochastic expression dynamics of a transcription factor, the λ repressor CI 1. Biology Lens Transplantation in Zebrafish and its Application in the Analysis of Eye Mutants Yan Zhang 1,2, Kyle McCulloch2, Jarema Malicki2 1The Second Teaching Hospital of Jilin University, 2Department of Ophthalmology, Harvard Medical School Lens development involves interactions with other tissues. Several zebrafish eye mutants are characterized by an abnormally small lens size. Here we demonstrate a lens transplantation experiment to determine whether this phenotype is due to intrinsic causes or defective interactions with tissues that surround the lens.