Journal of Biological Methods (JBM)
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163 research outputs found
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Silk coating as a novel delivery system and reversible adhesive for stiffening and shaping flexible probes
No full textThe performance of any implantable electrode depends not only on its recording or stimulation capabilities but also on its position in relation to the target site. Electrode displacement during or after implantation represents a major issue as it might result in tissue damage or incorrect recording or stimulation location, complicating the interpretation of experimental data. Although thin-film electrode arrays have overcome some of the main limitations of more traditional, stiffer probes, their intrinsic flexibility and unilateral contacts represent a new challenge: they tend to bend during insertion and are difficult to implant simultaneously while maintaining a specific relative position. Here, we present a method that addresses all these issues using a coating of silk fibroin, a versatile protein derived from silkworm cocoons. The method is demonstrated by acquiring electromyographic (EMG) recordings in Manduca sexta, a soft-bodied animal that exemplifies the issues of electrode insertion and placement in delicate and deformable tissues
Ocular surgical models for immune and angiogenic responses
No full textCorneal transplantation serves as a reproducible and simple surgical model to study mechanisms regulating immunity and angiogenesis. The simplicity of the model allows for systematic analysis of different mechanisms involved in immune and angiogenic privilege and their failures. This protocol describes how to induce neovessels and inflammation in an actively regulated avascular and immune-privileged site. This involves placing intra-stromal corneal sutures for two weeks, disrupting the privileges, and performing corneal transplantation subsequently. Privileged and non-privileged recipient responses to donor cornea can be compared to identify key immunological mechanisms that underlie angiogenesis and graft rejection. This protocol can also be adapted to the growing repertoire of genetic models available in the mouse, and is a valuable tool to elucidate molecular mechanisms mediating acceptance or failure of corneal graft. The model could be used to assess the potential of therapeutic molecules to enhance graft survival in vivo
Co-culture of placental explants with isolated CD4 and CD8 T cells: a functional model to define the consequences of placental inflammation
No full textAppropriate placental function is essential for successful pregnancy and placental dysfunction is associated with fetal growth restriction (FGR) and stillbirth. Villitis of unknown etiology (VUE) and chronic intervillositis of unknown etiology (CIUE) are immune-mediated conditions characterised by placental infiltrates of macrophages, CD4 and CD8 T cells. VUE and CIUE occur more frequently in the placentas of pregnancies complicated by FGR. The mechanisms by which this inflammation induces placental dysfunction are yet to be defined. We aimed to develop an in vitro model of placental inflammation to investigate functional consequences of immune cells in the placental environment. Fragments of placental tissue were co-cultured with CD4 and CD8 T cells isolated from whole blood. CellTrackerTM fluorescence was used to identify T cells in cultured explants. Tissue histology, endocrine and nutrient transport function was assessed using established methods. This novel preparation will enable future investigations into immune cell interactions with placenta
Assessing phytase activity
No full textPhytases are nutritionally important for increased bioavailability of dietary minerals and phosphate for monogastric animals including humans. Release of minerals and phosphate is accomplished by the enzymatic stepwise degradation of phytate (inositol hexaphosphate, IP6). Activity determinations of phytase is often based on analysis of total released phosphate (Pi), but phytase activity in its purest form represents released product per time from IP6 only. Microbial and plant preparations often also contain mixtures of phosphatases and organic phosphate compounds; hence some released phosphate in enzymatic assays may originate from non-phytase phosphatases degrading non-phytate molecules. Moreover, even purified enzyme extracts assessed via Pi release may result in errors, since commercial IP6 commonly contains contamination of lower inositol phosphates, and further, the products of phytase IP6 hydrolysis are also substrates for the phytase. These facts motivate a quantitative comparative study. We compared enzyme activity determination in phytase assay samples at four different time points, based on analyzing the substrate IP6 versus the product Pi using different selected methods. The calculated activities varied substantially. For example, at 15 min into enzymatic assay, variations from 152 mU/ml (by IP6 analysis on HPIC) to 275-586 mU/ml (by Pi analysis using several methods) was detected. Our work emphasizes the importance of defining the type of activity assessed, showing that phytase activity based on released Pi may yield false positive results and/or overestimations. We propose to differentiate between phytase activity, being the activity by which IP6 is degraded, and total inositol phosphatase activity, corresponding to total released phosphate during the enzymatic reaction
Fluorescent foci quantitation for high-throughput analysis
No full textA number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells
Isolation and sequencing of active origins of DNA replication by nascent strand capture and release (NSCR)
No full textNascent strand capture and release (NSCR) is a method for isolation of short nascent strands to identify origins of DNA replication. The protocol provided involves isolation of total DNA, denaturation, size fractionation on a sucrose gradient, 5’-biotinylation of the appropriate size nucleic acids, binding to a streptavidin coated column or magnetic beads, intensive washing, and specific release only the RNA containing chimeric nascent strand DNA using RNaseI. The method has been applied to mammalian cells derived from proliferative tissues and cell culture but could be used for any system where DNA replication is primed by a small RNA resulting in chimeric RNA-DNA molecules
Inducing gene expression by targeting promoter sequences using small activating RNAs
No full textVector-based systems comprised of exogenous nucleic acid sequences remain the standard for ectopic expression of a particular gene. Such systems offer robust overexpression, but have inherent drawbacks such the tedious process of construction, excluding sequences (e.g. introns and untranslated regions) important for gene function and potential insertional mutagenesis of host genome associated with the use of viral vectors. We and others have recently reported that short double-stranded RNAs (dsRNAs) can induce endogenous gene expression by targeting promoter sequences in a phenomenon referred to as RNA activation (RNAa) and such dsRNAs are termed small activating RNAs (saRNAs). To date, RNAa has been successfully utilized to induce the expression of different genes such as tumor suppressor genes. Here, we describe a detailed protocol for target selection and dsRNA design with associated experiments to facilitate RNAa in cultured cells. This technique may be applied to selectively activate endogenous gene expression for studying gene function, interrogating molecular pathways and reprogramming cell fate
A reliable protocol for the stable transformation of non-embryogenic cells cultures of grapevine (Vitis vinifera L.) and Taxus x media
No full textOne of the major intent of metabolic engineering in cell culture systems is to increase yields of secondary metabolites. Efficient transformation methods are a priority to successfully apply metabolic engineering to cell cultures of plants that produce bioactive or therapeutic compounds, such as Vitis vinifera and Taxus x media. The aim of this study was to establish a reliable method to transform non-embryogenic cell cultures of these species. The V. vinifera cv. Gamay/cv. Monastrell cell lines and Taxus x media were used for Agrobacterium-mediated transformation using the Gateway-compatible Agrobacterium sp. binary vector system for fast reliable DNA cloning. The Taxus x media and Vitis cell lines were maintained in culture for more than 4 and 15 months, respectively, with no loss of reporter gene expression or antibiotic resistance. The introduced genes had no discernible effect on cell growth, or led to extracellular accumulation of phytoalexin trans-Resveratrol (t-R) in response to elicitation with methylated cyclodextrins (MBCD) and methyl jasmonate (MeJA) in the grapevine transgenic cell lines compared to the parental control. The method described herein provides an excellent tool to exploit exponentially growing genomic resources to enhance, optimize or diversify the production of bioactive compounds generated by grapevine and yew cell cultures, and offers a better understanding of many grapevine and yew biology areas
Cell-based assays using calcein acetoxymethyl ester show variation in fluorescence with treatment conditions
No full textThe use of fluorogenic compounds in cell and molecular biology has increased in both frequency and range of applications. However, such compounds may introduce artifacts in intracellular fluorescence and cell number estimations as a consequence of interaction with exogenous stimulants, necessitating the use of adequate controls for accurate measurements and valid conclusions. Using calcein acetoxymethyl ester (AM) in combination with various exogenous cellular treatments, we report that the standard practice of direct normalization of experimental values to controls is insufficient for fluorogenic measurements. Treatments applied to cells may influence intracellular conversion of the fluorogenic compound, thereby enhancing or decreasing fluorescence relative to controls. We hereby encourage caution and recommend normalization of cellular fluorescence within each treatment group before comparison to controls