Journal of Biological Methods (JBM)
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163 research outputs found
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The answer depends on the question: Optimal conditions for western blot characterization of muscle collagen type 1 depends on desired isoform
No full textFibrillar collagen type 1 is the most abundant type of collagen within the body and is a critical component of extracellular infrastructure. In order to assess collagen synthesis and extracellular accumulation in fibrotic disorders, improved methods are needed to detect changes in procollagen versus mature collagen at the protein level. Using Western blot methodology, we systematically examined: (1) gel composition (Tris-glycine vs. bis-Tris, gradient vs. non-gradient, sodium dodecyl sulfate (SDS) vs. no SDS); (2) sample preparation (SDS vs. no SDS, β-mercaptoethanol (BME) vs. no BME, boiling vs. no boiling); and (3) running buffer composition (SDS vs. no SDS). Our results indicate full native gel conditions prevent resolution of all collagen type 1 bands. The best resolution of type 1 procollagens is achieved using 4%–12% Tris-glycine gels without the presence of SDS in the gel itself, although SDS in the running and sample buffers are needed. Also, BME must not be added to the sample buffer and samples should not be boiled. For characterization of mature collagen 1(I), both 8% and gradients type gels are appropriate, although still without SDS, yet with SDS included in both running and sample buffers, BME must be added to the sample buffer, and samples should not be boiled. Boiling is to be avoided as the antigenic site recognized by the monoclonal antibody used is sensitive to thermal denaturation, as is the case with many monoclonal antibodies available on the market. Thus, the exact parameters employed are dependent upon the collagen protein product that the scientist desires to identify
A standardized methodology for longitudinal assessment of corneal endothelial morphometry in eye banked corneas
No full textEye banked research-grade human donor corneas serve as principal ex vivo source for studying the mechanisms that underlie corneal endothelial cell damage/death and survival. Wide-field specular microscopy can be used for corneal endothelial visualization and allows for indirect assessment of endothelial cell function by analyzing endothelial cell density and morphometric parameters. However, a standardized approach is needed to observe corneal endothelial changes over time. This protocol describes reliable ex vivo methods for consecutive analyses of human donor corneal endothelial cell density and morphometric parameters change using a wide-field dual imaging specular microscope. This protocol involves tissue warming, acquisition and analysis of specular endothelial images, assessment of corneal layers with the new Enhance mode, optical pachymetry measurement, and qualitative image quality grading scales. This quantitative and qualitative evaluation of donor corneas allows for a systematic analysis of endothelial dynamic responses to ex vivo induced stress and can be used as a valuable tool to better elucidate specular findings and mechanisms mediating corneal endothelial cell loss in corneal disease and after transplantation
Real time mitochondrial dimension measurements
No full textMitochondrial volume is correlated with cell function and internal cell processes. Changes in mitochondrial volume were associated with advanced states of cardiac disease. Thus, measurements of mitochondrial dimension deformations are important to the understanding of cell function and its deterioration. Existing methods either allow measurements of the volume of isolated mitochondria, which are an inferior model to that of isolated cells, or they allow short time measurements that are toxic to the cells. Recent studies have discovered that mitochondrial deformation along a given cell axis can be measured by using the Fourier transformation on the variation in transmitted light intensity induced by the periodic lattice of myofilaments alternating with mitochondrial rows. However, this method was used only offline and in a line scan mode, making it impossible to measure both axes. We designed an open source program in LabVIEW to take advantage of the transmitted light diffraction technique and quantify mitochondrial two dimension (2D) deformation in cardiomyocytes, in situ in real time for long periods (more than several seconds). We validated the program on synthetic and on experimental images from rabbit and rat ventricular myocytes. The program can analyze offline and real time simultaneous 2D mitochondrial deformation dynamics as well as also sarcomere length dynamics. Moreover, the program can accurately analyze images acquired from different cameras. Quantification of mitochondrial 2D deformations is a powerful tool for exploring cell biophysics and bioenergetics mechanisms and will lay the foundation for a future clinical tool for quantifying mitochondrial volume changes associated with different cardiac diseases
Small RNA-seq: The RNA 5
No full textThe preparation of small RNA cDNA sequencing libraries depends on the unbiased ligation of adapters to the RNA ends. Small RNA with 5’ recessed ends are poor substrates for enzymatic adapter ligation, but this 5’ adapter ligation problem can go undetected if the library preparation steps are not monitored. Here we illustrate the severity of the 5’ RNA end ligation problem using several pre-miRNA-like hairpins that allow us to expand the definition of the problem to include 5’ ends close to a hairpin stem, whether recessed or in a short extension. The ribosome profiling method can avoid a difficult 5’ adapter ligation, but the enzyme typically used to circularize the cDNA has been reported to be biased, calling into question the benefit of this workaround. Using the TS2126 RNA ligase 1 (a.k.a. CircLigase) as the circularizing enzyme, we devised a bias test for the circularization of first strand cDNA. All possible dinucleotides were circle-ligated with similar efficiency. To re-linearize the first strand cDNA in the ribosome profiling approach, we introduce an improved method wherein a single ribonucleotide is placed between the sequencing primer binding sites in the reverse transcriptase primer, which later serves as the point of re-linearization by RNase A. We incorporate this step into the ribosomal profiling method and describe a complete improved library preparation method, Coligo-seq, for the sequencing of small RNA with secondary structure close to the 5’ end. This method accepts a variety of 5’ modified RNA, including 5’ monophosphorylated RNA, as demonstrated by the construction of a HeLa cell microRNA cDNA library
Inflammatory monocyte response due to altered wall shear stress in an isolated femoral artery model
No full textArteriogenesis (collateral formation) is accompanied by a pro-inflammatory state that may be related to the wall shear stress (WSS) within the neo-collateral vessels. Examining the pro-inflammatory component in situ or in vivo is complex. In an ex vivo mouse femoral artery perfusion model, we examined the effect of wall shear stress on pro-arteriogenic inflammatory markers and monocyte adhesion. In a femoral artery model with defined pulsatile flow, WSS was controlled (at physiological stress, 1.4×, and 2× physiological stress) during a 24 h perfusion before gene expression levels and monocyte adhesion were assessed. Significant upregulation of expression was found for the cytokine TNFα, adhesion molecule ICAM-1, growth factor TGFβ, and the transcription factor Egr-1 at varying levels of increased WSS compared to physiological control. Further, trends toward upregulation were found for FGF-2, the cytokine MCP-1 and adhesion molecules VCAM-1 and P-selectin with increased WSS. Finally, monocytes adhesion increased in response to increased WSS. We have developed a murine femoral artery model for studying changes in WSS ex vivo and show that the artery responds by upregulating inflammatory cytokines, adhesion molecules and growth factors consistent with previous in vivo findings
Histone deacetylase inhibitor-based chromatin precipitation for identification of targeted genomic loci
No full textHistone deacetylase (HDAC) catalyzes the removal of acetyl marks from histones, effectively regulating gene expression. Genome wide chromatin immunoprecipitation (ChIP) studies have shown HDACs are present on numerous active and repressed genes. However, HDAC inhibitors (HDACi) only regulate a small subset of this population in a cell type dependent fashion. To determine genomic locations directly targeted by HDACi, we developed a chromatin precipitation method using a photoreactive HDAC inhibitor probe (photomate). We validate this method by analyzing several canonical HDACi regulated genes, CDKN1A and FOSL1, and compare it to traditional ChIP using HDAC1 antibodies. We show that HDACi target HDACs bound at the promoter regions but not gene bodies, differing from HDAC1 antibody-based ChIP in the case of CDKN1A. This approach is anticipated to be useful for genome wide studies to identify the subset of genes directly regulated by an HDACi in a given cell type
Large-scale production of lentiviral vectors using multilayer cell factories
No full textLentiviral-mediated gene therapy has been proposed for the treatment of a range of diseases, and due to its genome integration properties, it offers the potential for long-lasting benefit from a once-off treatment. Production methods for pre-clinical studies in animal models, and ultimately for human clinical trials, must be capable of producing large quantities of high-quality lentiviral vector in an efficient and cost-effective manner. We report here a medium-scale method (from 1.5 L to 6 L of vector supernatant) for lentiviral vector production in adherent cell cultures using the NUNCâ„¢ EasyFillâ„¢ Cell Factoryâ„¢ from Thermo Fisher Scientific. Downstream purification uses a Mustang Q XT5 anion exchange capsule from Pall, and an ultracentrifugation step to concentrate the vector. This method is capable of producing lentiviral vector with concentrated titres of 108–109 TU/ml, with reduced manual handling compared to single monolayer flask methods
Patient-derived xenograft model for uterine leiomyoma by sub-renal capsule grafting
No full textUterine leiomyoma (UL) or fibroid is a benign smooth muscle tumor of the myometrium with a lifetime incidence of approximately 70%. ULs often require medical intervention due to severe symptoms such as heavy menstrual bleeding and abdominal pain. Although the most common and effective management of ULs is surgical removal, the invasive surgical procedure imposes physical and psychological burdens on the patients. Moreover, the economic burden of UL on health care system is enormous due to the high cost of surgeries. Thus, therapeutic options with long-term efficacy to replace surgical management are urgently needed. For the development of such medical options, reliable preclinical research models are imperative. Ex vivo culture of UL cells has been the primary research model for decades. However, recent studies demonstrated that primary cell culture is not a suitable model for UL research, as primary cultures of ULs mostly consist of non-tumor fibroblasts. Here we describe the protocol for patient-derived xenograft of UL, which faithfully replicates the phenotypes of human UL in situ
High resolution measurement of membrane receptor endocytosis
No full textWe present a new approach to quantify the half-life of membrane proteins on the cell surface, through tagging the protein with the photoconvertible fluorescent protein, Dendra2. Upon exposure to 405 nm light, Dendra2 is photoconverted from green to red emission. Total internal reflection fluorescence microscopy (TIRF) is applied to limit visualization of fluorescence to proteins located on the plasma membrane. Conversion of Dendra2 works as a pulse chase experiment through monitoring only the population of protein that has been photoconverted. As the protein is endocytosed the red emission decreases due to the protein leaving the TIRF field of view. This method is not impacted by the insertion of new protein into the plasma membrane as newly synthesized protein only exhibits green emission. We used this approach to determine the half-life of ENaC on the plasma membrane illustrating the high temporal resolution capability of this technique compared to current methods
