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Pennsylvania State University

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33 articles published in JoVE

Biochemistry

Advancing High-Resolution Imaging of Virus Assemblies in Liquid and Ice Liza-Anastasia DiCecco*^1,2, Samantha Berry*¹, G. M. Jonaid*^1,3, Maria J. Solares^1,4, Liam Kaylor^1,4, Jennifer L. Gray⁵, Carol Bator⁶, William J. Dearnaley¹, Michael Spilman⁷, Madeline J. Dressel-Dukes⁸, Kathryn Grandfield², Sarah M. McDonald Esstman⁹, Deborah F. Kelly^1,5,6 ¹Department of Biomedical Engineering, Pennsylvania State University, ²Department of Materials Science and Engineering, McMaster University, ³Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, ⁴Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, ⁵Materials Research Institute, Pennsylvania State University, ⁶Huck Institutes of the Life Sciences, Pennsylvania State University, ⁷Applications team, Direct Electron, ⁸Application Scientist, Protochips, Inc., ⁹Department of Biology, Wake Forest University Here protocols are described to prepare virus assemblies suitable for liquid-EM and cryo-EM analysis at the nanoscale using transmission electron microscopy.
Neuroscience

Size Exclusion Chromatography for Separating Extracellular Vesicles from Conditioned Cell Culture Media Madison T. Jones¹, Samantha W. Manioci¹, Ashley E. Russell^1,2 ¹Department of Biology, School of Science, Penn State Erie, The Behrend College, ²Magee Womens Research Institute—Allied Member The protocol here demonstrates that extracellular vesicles can be adequately separated from conditioned cell culture media using size exclusion chromatography.
Biochemistry

Sample Preparation using a Lipid Monolayer Method for Electron Crystallographic Studies Chloe D. Truong^1,2, Dewight R. Williams³, Mary Zhu¹, Joseph Che-Yen Wang⁴, Po-Lin Chiu^1,2 ¹School of Molecular Sciences, Arizona State University, ²Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, ³Eyring Materials Center, Arizona State University, ⁴Department of Microbiology and Immunology, The Pennsylvania State University Lipid monolayers have been used as a foundation for forming two-dimensional (2D) protein crystals for structural studies for decades. They are stable at the air-water interface and can serve as a thin supporting material for electron imaging. Here we present the proven steps on preparing lipid monolayers for biological studies.
Environment

The Role of Fabric in Frictional Properties of Phyllosilicate-Rich Tectonic Faults Cristiano Collettini^1,4, Telemaco Tesei², Fabio Trippetta¹, Marco M. Scuderi¹, Eliza Richardson³, Chris Marone^1,3, Giacomo Pozzi⁴, Cecilia Viti⁵ ¹Dipartimento di Scienze della Terra, Sapienza Università di Roma, ²Dipartimento di Geoscienze, Università di Padova, ³Department of Geoscience, The Pennsylvania State University, ⁴Istituto Nazionale di Geofisica e Vulcanologia, ⁵Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, Università di Siena Friction of phyllosilicates-rich faults sheared in their in situ geometry is significantly lower than friction of their powdered equivalents.
Bioengineering

Photodegradable Hydrogel Interfaces for Bacteria Screening, Selection, and Isolation Niloufar Fattahi¹, Niloy Barua¹, André J. van der Vlies², Ryan R. Hansen¹ ¹Tim Taylor Department of Chemical Engineering, Kansas State University, ²Department of Materials Science and Engineering, The Pennsylvania State University The use of photodegradable hydrogels to isolate bacterial cells by utilizing a high-resolution light pattering tool is reported. Essential experimental procedures, results, and advantages of the process are reviewed. The method enables rapid and inexpensive isolation of targeted bacteria showing rare or unique functions from heterogeneous communities or populations.
Chemistry

Picometer-Precision Atomic Position Tracking through Electron Microscopy Leixin Miao¹, Adrian Chmielewski¹, Debangshu Mukherjee², Nasim Alem¹ ¹Department of Materials Science & Engineering, The Pennsylvania State University, ²Center for Nanophase Materials Sciences, Oak Ridge National Laboratory This work presents a workflow for atomic position tracking in atomic resolution transmission electron microscopy imaging. This workflow is performed using an open-source Matlab app (EASY-STEM).
Biology

Pupal and Adult Injections for RNAi and CRISPR Gene Editing in Nasonia vitripennis Elena Dalla Benetta*¹, Duverney Chaverra-Rodriguez*¹, Jason L. Rasgon², Omar S. Akbari¹ ¹Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, ²Department of Entomology, The Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, The Pennsylvania State University Here, we describe methods for efficient pupal and adult injections in Nasonia vitripennis as accessible alternatives to embryo microinjection, enabling functional analysis of genes of interest using either RNA-silencing via RNA interference (RNAi) or gene knockout via CRISPR/Cas9 genome editing.
Behavior

A Standardized Protocol for Preference Testing to Assess Fish Welfare Cairsty DePasquale¹, Jennifer Sturgill¹, Victoria A. Braithwaite² ¹Department of Biology, Pennsylvania State University - Altoona, ²Department of Ecosystem Science & Management, Pennsylvania State University A fundamental aspect of assessing the welfare of animals in captivity is to ask whether the animals have what they want. Here, we present a protocol to determine housing preference in the zebrafish (Danio rerio) with respect to the presence/absence of environmental enrichment and access to flowing of water.
Behavior

Assessment of Midline Lingual Point-Pressure Somatosensation Using Von Frey Hair Monofilaments Nicole M. Etter¹, Scott P. Breen^2,3, Maya I. M. Alcala^2,3, Gregory R. Ziegler³, John E. Hayes^2,3 ¹Department of Communication Sciences and Disorders, College of Health and Human Development, The Pennsylvania State University, ²Sensory Evaluation Center, The Pennsylvania State University, ³Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University This work describes a standard method to assess tactile sensation at the midline of the tongue tip. Using Von Frey Hair (VFH) monofilaments, this protocol provides estimates of detection and discrimination threshold estimates for oral point pressure (OPP).
Biochemistry

Kinase Inhibitor Screening In Self-assembled Human Protein Microarrays Fernanda Festa^1,2, Joshua Labaer¹ ¹Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, ²Department of Pediatrics, and Biochemistry/Molecular Biology, College of Medicine, Pennsylvania State University A detailed protocol for the generation of self-assembled human protein microarrays for the screening of kinase inhibitors is presented.
Immunology and Infection

An Immunohistopathologic Study to Profile the Folate Receptor Beta Macrophage and Vascular Immune Microenvironment in Giant Cell Arteritis Shirley Albano-Aluquin¹, Jozef Malysz², Michal Kidacki³, Manohar Ratnam⁴, Nancy J. Olsen¹ ¹Department of Medicine, Penn State University, ²Department of Pathology, Penn State University, ³Penn State College of Medicine, ⁴Department of Oncology, Wayne State University School of Medicine The protocol illustrates the use of histopathologic examination and immunohistochemistry to profile the folate receptor beta macrophage and its relationship with the total immune cell infiltrate in temporal artery biopsies in giant cell arteritis.
Environment

Wastewater Irrigation Impacts on Soil Hydraulic Conductivity: Coupled Field Sampling and Laboratory Determination of Saturated Hydraulic Conductivity Jack E. Watson¹, Tyson Robb², Danielle Andrews-Brown³, Melissa Miller¹ ¹Department of Ecosystem Science and Management, Pennsylvania State University, ²Department of Geography and Environmental Sustainability, State University of New York, Oneonta, ³Department of Geology and Environmental Science, University of Pittsburgh Here we present a methodology which matches a soil sample size and a hydraulic conductivity measurement device to prevent the so-called wall flow along the inside of the soil container from being erroneously included in water flow measurements. Its use is demonstrated with samples collected from a wastewater irrigation site.
Immunology and Infection

Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry Krista M. Armbruster¹, Timothy C. Meredith¹ ¹Department of Biochemistry and Molecular Biology, Pennsylvania State University The enrichment of bacterial lipoproteins using a non-ionic surfactant phase partitioning method is described for direct use in TLR assays or other applications. Further steps are detailed to prepare N-terminal tryptic lipopeptides for structural characterization by mass spectrometry.
Environment

Continuous Hydrologic and Water Quality Monitoring of Vernal Ponds Odette Mina^1,2, Heather E. Gall¹, Joseph W. Chandler¹, Jeremy Harper³, Malcolm Taylor¹ ¹Department of Agricultural and Biological Engineering, Pennsylvania State University, ²Energy and Environmental Sustainability Laboratory, Pennsylvania State University, ³Department of Ecosystem Science and Management, Pennsylvania State University Understanding the ecosystem services and processes provided by vernal ponds and the impacts of anthropogenic activities on their ability to provide these services requires intensive hydrologic monitoring. This sampling protocol using in-situ monitoring equipment was developed to understand the impact of anthropogenic activities on water levels and quality.
Chemistry

Determination of Thermodynamic Properties of Alkaline Earth-liquid Metal Alloys Using the Electromotive Force Technique Thomas P. Nigl¹, Nathan D. Smith¹, Timothy Lichtenstein¹, Jarrod Gesualdi¹, Kuldeep Kumar¹, Hojong Kim¹ ¹Department of Materials Science and Engineering, The Pennsylvania State University This protocol describes the measurement of the electromotive force of alkaline-earth elements in liquid metal alloys at high temperatures (723-1,123 K) to determine their thermodynamic properties, including activity, partial molar entropy, partial molar enthalpy, and phase transition temperatures, over a wide composition range.
Bioengineering

PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions Djoshkun Shengjuler¹, Simou Sun², Paul S. Cremer^1,2, Craig E. Cameron¹ ¹Department of Biochemistry and Molecular Biology, The Pennsylvania State University, ²Department of Chemistry, The Pennsylvania State University Here we present a supported lipid bilayer in the context of a microfluidic platform to study protein-phosphoinositide interactions using a label-free method based on pH modulation.
Immunology and Infection

Isolation, Characterization, and Purification of Macrophages from Tissues Affected by Obesity-related Inflammation Joselyn N. Allen¹, Adwitia Dey¹, Ruth Nissly², James Fraser¹, Shan Yu¹, Gayathri Balandaram¹, Jeffrey M. Peters¹, Pamela A. Hankey-Giblin¹ ¹Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, ²Microscopy and Cytometry Facility, The Huck Institutes of Life Sciences, Pennsylvania State University This protocol allows a researcher to isolate and characterize tissue-resident macrophages in various hallmark inflamed tissues extracted from diet-induced models of metabolic disorders.
Immunology and Infection

Inoculating Anopheles gambiae Mosquitoes with Beads to Induce and Measure the Melanization Immune Response Antoine M. G. Barreaux^1,2, Priscille Barreaux^1,2, Matthew B. Thomas², Jacob C. Koella¹ ¹Laboratoire d'écologie et d'épidémioloigie parasitaire, Institut de biologie, Université de Neuchâtel, ²Merkle Lab, Department of Entomology, Pennsylvania State University Through inoculation with beads, the described technique enables the stimulation of the mosquito melanization response in the hemolymph circulating system. The amount of melanin covering the beads can be measured after dissection as a measure of the immune response.
Engineering

Characterization of Full Set Material Constants and Their Temperature Dependence for Piezoelectric Materials Using Resonant Ultrasound Spectroscopy Liguo Tang¹, Wenwu Cao² ¹Key Laboratory of Underwater Acoustic Communication and Marine Information Technology, Xiamen University, ²Department of Mathematics and Material Research Institute, The Pennsylvania State University This protocol describes the procedure of measuring the temperature dependence of the full set material constants of piezoelectric materials using resonant ultrasound spectroscopy (RUS).
Developmental Biology

Differentiation of the SH-SY5Y Human Neuroblastoma Cell Line Mackenzie M. Shipley¹, Colleen A. Mangold¹, Moriah L. Szpara¹ ¹Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University It is critical in neurobiology and neurovirology to have a reliable, replicable in vitro system that serves as a translational model for what occurs in vivo in human neurons. This protocol describes how to culture and differentiate SH-SY5Y human neuroblastoma cells into viable neurons for use in in vitro applications.
Medicine

Povidone Iodine Rectal Preparation at Time of Prostate Needle Biopsy is a Simple and Reproducible Means to Reduce Risk of Procedural Infection Jay D. Raman¹, Kathleen K. Lehman¹, Kalyan Dewan², Girish Kirimanjeswara² ¹Division of Urology, Penn State Milton S. Hershey Medical Center, ²Department of Veterinary and Biomedical Sciences, Penn State University Here, we present a protocol for use at the time of transrectal ultrasound guided prostate needle biopsy (TRUS PNB) that is a simple and cost-effective means to reduce infections following the procedure.
Environment

The Use of an Automated System (GreenFeed) to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals Alexander N. Hristov¹, Joonpyo Oh¹, Fabio Giallongo¹, Tyler Frederick¹, Holley Weeks¹, Patrick R. Zimmerman², Michael T. Harper¹, Rada A. Hristova³, R. Scott Zimmerman², Antonio F. Branco⁴ ¹Department of Animal Science, Pennsylvania State University, ²C-Lock, Inc. Rapid City, SD, ³Color Productions, State College, PA, ⁴Departamento de Zootecnia, Universidade Estadual de Maringá Accuracy and precision of the techniques used to measure methane emissions from ruminant animals are critically important for the success of greenhouse gas mitigation efforts. This manuscript describes the principles and operation of an automated system to monitor methane and carbon dioxide mass fluxes from the breath of ruminant animals.
Behavior

Applying Stereotactic Injection Technique to Study Genetic Effects on Animal Behaviors Colleen McSweeney¹, Yingwei Mao¹ ¹Department of Biology, The Pennsylvania State University Stereotactic injection of lentiviruses expressing cDNAs or shRNAs can modulate gene expression in specific brain areas of mice. Here, we present a protocol to combine stereotactic injections with behavioral tasks, such as the Open Field Test (OFT) and the Forced Swim Test (FST).
Bioengineering

Molecular Entanglement and Electrospinnability of Biopolymers Lingyan Kong¹, Gregory R. Ziegler¹ ¹Department of Food Science, Pennsylvania State University Electrospinning is a fascinating technique used to fabricate micro- to nano-scale fibers from a wide variety of materials. Molecular entanglement of the constituent polymers in the spinning dope is essential for successful electrospinning. We present a protocol for utilizing rheology to evaluate the electrospinnability of two biopolymers, starch and pullulan.
Medicine

Dried Blood Spot Collection of Health Biomarkers to Maximize Participation in Population Studies Michael W. Ostler¹, James H. Porter^1,2, Orfeu M. Buxton^1,2,3,4 ¹Center for Population and Development Studies, Harvard School of Public Health, ² Biomarkers are directly-measured biological indicators of disease or health. In population and social sciences, biomarkers need to be easy to obtain, transport, and analyze. Dried Blood Spot (DBS) collection meets this need, can be collected in the field with high response rates and analyzed for a variety of biomarkers.
Immunology and Infection

Accelerated Type 1 Diabetes Induction in Mice by Adoptive Transfer of Diabetogenic CD4+ T Cells Gregory Berry¹, Hanspeter Waldner¹ ¹Department of Microbiology & Immunology, Pennsylvania State University College of Medicine We provide a reproducible method to induce type 1 diabetes (T1D) in mice within two weeks by the adoptive transfer of islet antigen-specific, primary CD4+ T cells.
Engineering

Encapsulation and Permeability Characteristics of Plasma Polymerized Hollow Particles Anaram Shahravan¹, Themis Matsoukas¹ ¹Department of Chemical Engineering, The Pennsylvania State University We have used plasma enhanced chemical vapor deposition to deposit thin films ranging from a few nm to several 100 nm on nano-sized particles of various materials. We subsequently etch the core material to produce hollow nanoshells whose permeability is controlled by the thickness of the shell. We characterize the permeability of these coatings to small solutes and demonstrate that these barriers can provide sustained release of the core material over several days.
Immunology and Infection

Directed Differentiation of Induced Pluripotent Stem Cells towards T Lymphocytes Fengyang Lei¹, Rizwanul Haque¹, Xiaofang Xiong¹, Jianxun Song¹ ¹Department of Microbiology and Immunology, Pennsylvania State University College of Medicine Generation of T lymphocytes from induced pluripotent stem (iPS) cells gives an alternative approach of using embryonic stem cells for T cell-based immunotherapy. The method shows that by utilizing either in vitro or in vivo induction system, iPS cells are able to differentiate into both conventional and antigen-specific T lymphocytes.
Neuroscience

A Polished and Reinforced Thinned-skull Window for Long-term Imaging of the Mouse Brain Andy Y. Shih¹, Celine Mateo¹, Patrick J. Drew^2,3, Philbert S. Tsai¹, David Kleinfeld^1,4 ¹Department of Physics, University of California, San Diego, ²Department of Engineering Science and Mechanics, Pennsylvania State University, ³Department of Neurosurgery, Pennsylvania State University, ⁴Section of Neurobiology, University of California, San Diego We present a method to form an imaging window in the mouse skull that spans millimeters and is stable for months without inflammation of the brain. This method is well suited for longitudinal studies of blood flow, cellular dynamics, and cell/vascular structure using two-photon microscopy.
Biology

Isolation of CD133+ Liver Stem Cells for Clonal Expansion C. Bart Rountree¹, Wei Ding¹, Hein Dang¹, Colleen VanKirk², Gay M. Crooks³ ¹Department of Pediatrics and Pharmacology, Pennsylvania State College of Medicine, ²Department of Pharmacology, Pennsylvania State College of Medicine, ³Department of Pediatrics, University of California Los Angeles, School of Medicine Here we describe the isolation of CD133 expressing liver stem cells and cancer stem cells from whole murine liver, a process that requires tissue digestion, cell enrichment, and flow cytometry isolation. We include methods for advanced single cell isolation and clonal expansion.
Biology

Primer-Free Aptamer Selection Using A Random DNA Library Weihua Pan¹, Ping Xin¹, Susan Patrick¹, Stacey Dean², Christine Keating², Gary Clawson^3,4 ¹Department of Pathology, Hershey Medical Center, Pennsylvania State University, ²Department of Chemistry, Pennsylvania State University, ³Departments of Pathology, and Biochemistry and Molecular Biology, Hershey Medical Center, Pennsylvania State University, ⁴Materials Research Institute, Pennsylvania State University SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere with the selection process (false positives and negatives). Here we present a primer-free protocol.
Neuroscience

Low-stress Route Learning Using the Lashley III Maze in Mice Amanda Bressler¹, David Blizard², Anne Andrews^3,4,5,6 ¹Department of Chemistry, Pennsylvania State University, ²Center for Developmental and Health Genetics, Pennsylvania State University, ³Department of Veterinary and Biomedical Sciences, Pennsylvania State University, ⁴Huck Institute of the Life Sciences, Pennsylvania State University, ⁵California NanoSystems Institute, University of California, Los Angeles, ⁶Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles The Lashley III maze is a route-learning task that does not rely on aversive stimuli or visual cues. It is thus a highly attractive option for evaluating learning and memory, especially in aging mice or otherwise where stress is a consideration.
Biology

Measuring Plant Cell Wall Extension (Creep) Induced by Acidic pH and by Alpha-Expansin Daniel M. Durachko¹, Daniel J. Cosgrove¹ ¹Department of Biology, Penn State University We demonstrate the use of a constant-force extensometer to measure long-term extension (creep) of plant cell wall specimens induced by acidic buffers and expansin protein.

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