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Past Issue in 2022
Volume: 12, Issue: 0
Biochemistry
Evaluation of Urine Proteins by Capillary Electrophoresis
Capillary electrophoresis (CE) is a laboratory method usually used to separate proteins in body fluids such as serum, cerebrospinal fluid, or urine. Separation of proteins in urine can have clinical applications for evaluating samples from healthy dogs and dogs with proteinuria in a qualitative way, which would not be possible with gel electrophoresis. Other advantages of CE over gel electrophoresis in serum include the reduced separation time (2 min vs. 20 min in a gel), reduction of waste harmful to humans and the environment, and ability to obtain a curve without the need for additional staining. This protocol is divided into four steps. Firstly, urine needs to be prepared prior to dialysis. Secondly, urine needs to undergo dialysis to eliminate compounds that could interfere with separation, and to concentrate the urine. The third step is CE using specific equipment. The last step is to separate the fractions of the phoretograms obtained in the previous step. This method is mostly an automatized process, easily reproducible, and that can be performed in any laboratory, as a part of the diagnostic or follow-up of patients with renal disease.Graphical abstract:
Purification of Crimean Congo Hemorrhagic Fever Virus (CCHFV) Nucleocapsid Protein Using Detergent Gradient and Free Thawing
Protein aggregation remains a major challenge in the purification of recombinant proteins in both eukaryotic and prokaryotic expression systems. One such protein is the nucleocapsid protein of Crimean Congo Hemorrhagic fever virus (CCHFV), which has high aggregation tendency and rapidly precipitates upon purification by NiNTA chromatography. Using the detergent gradient purification approach reported here, the freshly purified protein by NiNTA chromatography was mixed with the dilution buffer containing a high detergent concentration, followed by overnight freezing at -80 °C. Thawing the resulting mixture at room temperature triggered the formation of a detergent concentration gradient containing the active protein in the low detergent concentration zone towards the top of the gradient. The inactive aggregates migrated to the high detergent concentration zone towards the bottom of the gradient. The method prevented further aggregation and retained the activity of the native protein despite numerous freeze–thaw cycles. This simple approach creates an appropriate microenvironment towards the top of the gradient for correctly folded proteins, and it prevents aggregation by rapidly separating the preformed early aggregates from the correctly folded protein in the mixture. This unique approach will be of potential importance for the biotechnological industry, as well as other fields of protein biochemistry that routinely purify recombinant proteins and face the challenges of protein aggregation.Graphical abstract:
Biophysics
Visualization, Quantification, and Modeling of Endogenous RNA Polymerase II Phosphorylation at a Single-copy Gene in Living Cells
In eukaryotic cells, RNA Polymerase II (RNAP2) is the enzyme in charge of transcribing mRNA from DNA. RNAP2 possesses an extended carboxy-terminal domain (CTD) that gets dynamically phosphorylated as RNAP2 progresses through the transcription cycle, therefore regulating each step of transcription from recruitment to termination. Although RNAP2 residue-specific phosphorylation has been characterized in fixed cells by immunoprecipitation-based assays, or in live cells by using tandem gene arrays, these assays can mask heterogeneity and limit temporal and spatial resolution. Our protocol employs multi-colored complementary fluorescent antibody-based (Fab) probes to specifically detect the CTD of the RNAP2 (CTD-RNAP2), and its phosphorylated form at the serine 5 residue (Ser5ph-RNAP2) at a single-copy HIV-1 reporter gene. Together with high-resolution fluorescence microscopy, single-molecule tracking analysis, and rigorous computational modeling, our system allows us to visualize, quantify, and predict endogenous RNAP2 phosphorylation dynamics and mRNA synthesis at a single-copy gene, in living cells, and throughout the transcription cycle.Graphical abstract: Schematic of the steps for visualizing, quantifying, and predicting RNAP2 phosphorylation at a single-copy gene.
Cancer Biology
CRISPR/Cas9-mediated Gene Knockout Followed by Negative Selection Leads to a Complete TCR Depletion in orthoCAR19 T Cells
Genome-editing technologies, especially CRISPR (clustered regularly interspaced short palindrome repeats)/Cas9 (CRISPR-associated protein 9), endows researchers the ability to make efficient, simple, and precise genomic DNA changes in many eukaryotic cell types. CRISPR/Cas9-mediated efficient gene knockout holds huge potential to improve the efficacy and safety of chimeric antigen receptor (CAR) T cell-based immunotherapies. Here, we describe an optimized approach for a complete loss of endogenous T cell receptor (TCR) protein expression, by CRISPR/Cas9-mediated TCR α constant (TRAC) and TCR β constant (TRBC) gene knockout, followed by subsequent CD3 negative selection in engineered human orthoCAR19 T cells. We believe this method can be expanded beyond CAR T cell application, and target other cell surface receptors.Graphical abstract: Schematic overview of the two-step process of endogenous TCR depletion in engineered human orthoCAR19 T cells using (1) CRISPR/Cas9-mediated gene knockout followed by (2) CD3 negative selection.
Computational Biology and Bioinformatics
TRACES: a Freely Accessible, Semi-automated Pipeline for Detection, Tracking, and Quantification of Fluorescently Labeled Cellular Structures
Subcellular structures exhibit diverse behaviors in different cellular processes, including changes in morphology, abundance, and relative spatial distribution. Faithfully tracking and quantifying these changes are essential to understand their functions. However, most freely accessible methods lack integrated features for tracking multiple objects in different spectral channels simultaneously. To overcome these limitations, we have developed TRACES (Tracking of Active Cellular Structures), a customizable and open-source pipeline capable of detecting, tracking, and quantifying fluorescently labeled cellular structures in up to three spectral channels simultaneously at single-cell level. Here, we detail step-by-step instructions for performing the TRACES pipeline, including image acquisition and segmentation, object identification and tracking, and data quantification and visualization. We believe that TRACES will be a valuable tool for cell biologists, enabling them to track and measure the spatiotemporal dynamics of subcellular structures in a robust and semi-automated manner.
Drug Discovery
Generation of a Human Conditionally Immortalized Cell-based Multicellular Spheroidal Blood-Brain Barrier Model for Permeability Evaluation of Macromolecules
There is an urgent need for the development of brain drug delivery carriers based on middle-sized or macromolecules, to which in vitro blood-brain barrier (BBB) models are expected to contribute significantly through evaluation of BBB permeability. As part of efforts to develop such models, we have been working on human conditionally immortalized cell-based multicellular spheroidal BBB models (hiMCS-BBB models), and we herein introduce the model development protocol. Briefly, astrocytes are first seeded in an ultra-low attachment 3D cell culture plate, to make the central core (Day 0). Next, pericytes are added over the core, to form an outer layer (Day 1). Then, brain microvascular endothelial cells are further added to each well, to create the outmost monolayer serving as the BBB (Day 2). Finally, the spheroids cultured for two days (on Day 4) can be used for assays of interest (e.g., antibody permeability assays). Neither special equipment nor techniques are required to produce hiMCS-BBB models. Therefore, the protocol presented here will not only facilitate the model sharing among the BBB community but also provide some technical clues contributing to the development of similar MCS-BBB models using other cell sources, such as primary or iPS-derived BBB cells. Graphical abstract:
Immunology
Cost Effective Method for gDNA Isolation from the Cecal Content and High Yield Procedure for RNA Isolation from the Colonic Tissue of Mice
Microbiome studies are quickly gaining momentum. Since most of the resident microbes (consisting of bacteria, fungi, and viruses) are difficult to culture, sequencing the microbial genome is the method of choice to characterize them. It is therefore important to have efficient methodology for gDNA isolation of gut microbes. Mouse models are widely used to understand human disease etiology while avoiding human ethics-related complications. However, the widely used kit-based methods are costly, and sometimes yields (in terms of quality and quantity) are sub-optimal. To overcome this problem, we developed a straightforward, standardized DNA isolation procedure from mouse cecal content for further microbiome-related studies. The reagents we used to standardize the procedure are readily available even in a not-so-well-equipped laboratory, and the reagents are not expensive. The yield and quality of the DNA are also better than those obtained by the readily available kit-based methods.Additionally, we modified the kit-based method of RNA isolation from the colon tissue sample of the mouse for better yield. Churning the tissue with liquid nitrogen at the beginning of the procedure improves RNA quality and quantity.Graphical abstract:
Microbiology
Cryptococcus neoformans Virulence Assay Using a Galleria mellonella Larvae Model System
Cryptococcus neoformans is a human pathogenic fungus that can cause pulmonary infections and meningitis in both immunocompromised and otherwise healthy individuals. Limited treatment options and a high mortality rate underlie the necessity for extensive research of the virulence of C. neoformans. Here we describe a detailed protocol for using the Galleria mellonella (Greater Wax Moth) larvae as a model organism for the virulence analysis of the cryptococcal infections. This protocol describes in detail the evaluation of G. mellonella larvae viability and the alternatives for troubleshooting the infection procedure. This protocol can be easily modified to study different inocula or fungal species, or the effects of a drug or antifungal agent on fungal disease within the larvae. We describe modified alternative versions of the protocol that allow using G. mellonella to study fungal diseases with different inocula and at different temperatures.
Molecular Biology
DSP-crosslinking and Immunoprecipitation to Isolate Weak Protein Complex
Detecting protein-protein interactions (PPIs) is one of the most used approaches to reveal the molecular regulation of protein of interests (POIs). Immunoprecipitation of POIs followed by mass spectrometry or western blot analysis enables us to detect co-precipitated POI-binding proteins. However, some binding proteins are lost during cell lysis or immunoprecipitation if the protein binding affinity is weak. Crosslinking POI and its binding proteins stabilizes the PPI and increases the chance of detecting the interacting proteins. Here, we introduce the method of DSP (dithiobis(succinimidyl propionate))-mediated crosslinking, followed by tandem immunoprecipitation (FLAG and HA tags). The eluted proteins interacting with POI can be analyzed by mass spectrometry or western blotting. This method has the potential to be applied to various cytoplasmic proteins.Graphical abstract:
Neuroscience
A Step-by-step Protocol for Obtaining Mature Microglia from Mice
In mice, microglial precursors in the yolk sac migrate to the brain parenchyma through the head neuroepithelial layer between embryonic days 8.5 (E8.5)–E16.5 and acquire their unique identity with a ramified form. Based on the microglial developmental process, we dissected the neuroepithelial layer (NEL) of E13.5 mice, which is composed of microglial progenitor and neuroepithelial cells. The NEL was bankable and expandable. In addition, microglial precursors were matured according to NEL culture duration. The matured microglia (MG; CD11b-positive cells) were easily isolated from the cultured NEL using a magnetic-activated cell sorting system and named NEL-MG. In conclusion, we obtained higher yields of adult-like microglia (mature microglia: NEL-MG) compared to previous in vitro surrogates such as neonatal microglia and microglial cell lines. Graphical abstract: