Journal of Biological Methods (JBM)
Not a member yet
163 research outputs found
Sort by
Embryo microinjection of the lecithotrophic sea urchin Heliocidaris erythrogramma
No full textMicroinjection is a common embryological technique used for many types of experiments, including lineage tracing, manipulating gene expression, or genome editing. Injectable reagents include mRNA overexpression, mis-expression, or dominant-negative experiments to examine a gene of interest, a morpholino antisense oligo to prevent translation of an mRNA or spliceoform of interest and CRISPR-Cas9 reagents. Thus, the technique is broadly useful for basic embryological studies, constructing gene regulatory networks, and directly testing hypotheses about cis-regulatory and coding sequence changes underlying the evolution of development. However, the methods for microinjection in typical planktotrophic marine invertebrates may not work well in the highly modified eggs and embryos of lecithotrophic species. This protocol is optimized for the lecithotrophic sea urchin Heliocidaris erythrogramma
Multi-parametric flow cytometry staining procedure for analyzing tumor-infiltrating immune cells following oncolytic herpes simplex virus immunotherapy in intracranial glioblastoma
No full textMulti-color flow cytometry is a standard laboratory protocol, which is regularly used to analyze tumor-infiltrating immune cell subsets. Oncolytic herpes simplex virus has shown promise in treating various types of cancers, including deadly glioblastoma. Intracranial/intratumoral treatment with oncolytic herpes simplex virus expressing interleukin 12, i.e., immunovirotherapy results in induction of anti-tumor immune responses and tumor infiltration of a variety of immune cells. Multi-color flow cytometry is employed to characterize immune cells in the tumor microenvironment. Here, we describe a step-by-step 11-color flow cytometry protocol to stain tumor-infiltrating immune cells in glioblastoma following oncolytic herpes virotherapy. We also describe a method to identify HSV-1 glycoprotein-B-specific CD8+ T cells using fluorochrome-conjugated major histocompatibility complex multimers. The multimers carry major histocompatibility peptide complexes, which have the ability to interact and bind to T cell receptors present on the surface of T cells; allowing identification of T cells (e.g., CD8+) reactive to a desired antigen. This multimer staining can be used in conjunction with the multi-parametric flow cytometry staining. Brain tumor quadrants are harvested, minced, enzymatically digested, immune cells are isolated by positive selection, single cells are counted and blocked for Fc receptors, cells are incubated with dye and/or color-conjugated antibodies, and flow cytrometry is performed using a BD LSRII flow cytometer. The protocol described herein is also applicable to stain immune cells in other mouse and human tumors or in any desired tissues
A minimally-invasive serial cerebrospinal fluid sampling model in conscious Göttingen minipigs
No full textDrug concentrations in cerebrospinal fluid (CSF) are typically used as a as a surrogate measure of their availability in the CNS, and CSF penetration in animal studies are used for assessment of CNS drug delivery in early preclinical drug development. The minipig is a valid alternative to dogs and non-human primates as non-rodent species in preclinical research, but this species presents anatomical peculiarities that make the serial collection of CSF technically challenging. A minimally-invasive serial cerebrospinal fluid collection model via catheterization of the subarachnoid space in conscious minipigs was developed allowing assessment of longitudinal drug pharmacokinetics in the central nervous system in preclinical research. Shortly, the subarachnoid space was accessed in the anesthetized minipig by puncture with a Tuohy needle; when CSF was flowing through the needle a catheter was advanced and thereafter tunneled and fixed on the back. The PK of peptide A administered subcutaneously was performed and CSF could be sampled in the conscious animals for up to 48 h. When compared to the plasma kinetic data, there was a clear difference in the elimination phase of Pept. A from CSF, with an apparent longer average terminal half-life in CSF. The 3Rs are addressed by reducing the number of animals needed for a pharmacokinetic profile in central nervous system and by improving the validity of the model avoiding biases due to anesthesia, blood contamination, and inter-individual variability
In vivo measurement of enhanced agouti-related peptide release in the paraventricular nucleus of the hypothalamus through Gs activation of agouti-related peptide neurons
No full textAgouti-related peptide (AgRP) neurons of the hypothalamus play a role in hunger-triggered food intake, stability of body weight, and long-term energy balance. A recent study showed that activation of the Gs-linked G protein-coupled receptors (GCPR) expressed by hypothalamic AgRP neurons promotes a sustained increase in food intake. Enhanced AgRP release has been the postulated underlying mechanism. Here, we confirmed that activation of Gs-coupled receptors expressed by AgRP neurons in the arcuate nucleus (ARC) of the hypothalamus, which is the primary brain region for the synthesis and release of AgRP, leads to increased release of AgRP in the paraventricular nucleus of the hypothalamus (PVN). We were unable to confirm changes in AgRP expression or intracellular content using traditional histological techniques. Thus, we developed an assay to measure AgRP in the extracellular fluid in the brain using large molecular weight cut-off microdialysis probes. Our technique enables assessment of brain AgRP pharmacokinetics under physiological conditions and in response to specific pharmacological interventions designed to modulate AgRP signaling
FairSubset: A tool to choose representative subsets of data for use with replicates or groups of different sample sizes
No full textHigh-impact journals are promoting transparency of data. Modern scientific methods can be automated and produce disparate samples sizes. In many cases, it is desirable to retain identical or pre-defined sample sizes between replicates or groups. However, choosing which subset of originally acquired data that best matches the entirety of the data set without introducing bias is not trivial. Here, we released a free online tool, FairSubset, and its constituent Shiny App R code to subset data in an unbiased fashion. Subsets were set at the same N across samples and retained representative average and standard deviation information. The method can be used for quantitation of entire fields of view or other replicates without biasing the data pool toward large N samples. We showed examples of the tool’s use with fluorescence data and DNA-damage related Comet tail quantitation. This FairSubset tool and the method to retain distribution information at the single-datum level may be considered for standardized use in fair publishing practices
Detection of clinically relevant immune checkpoint markers by multicolor flow cytometry
No full textAs checkpoint inhibitor immunotherapies gain traction among cancer researchers and clinicians, the need grows for assays that can definitively phenotype patient immune cells. Herein, we present an 8-color flow cytometry panel for lineage and immune checkpoint markers and validate it using healthy human donor peripheral blood mononuclear cells (PBMCs). Flow cytometry data was generated on a BD LSR Fortessa and supported by Luminex multiplex soluble immunoassay. Our data showed significant variation between donors at both baseline and different stages of activation, as well as a trend in increasing expression of checkpoint markers on stimulated CD4+ and CD8+ T-cells with time. Soluble immune checkpoint quantification assays revealed that LAG-3, TIM-3, CTLA-4, and PD-1 soluble isoforms are upregulated after stimulation. This 8-color flow cytometry panel, supported here by soluble immunoassay, can be used to identify and evaluate immune checkpoints on T-lymphocytes in cryopreserved human PBMC samples. This panel is ideal for characterizing checkpoint expression in clinical samples for which cryopreservation is necessary
A step-by-step beginner
No full textBacterial whole genome sequencing (WGS) is becoming a widely-used technique in research, clinical diagnostic, and public health laboratories. It enables high resolution characterization of bacterial pathogens in terms of properties that include antibiotic resistance, molecular epidemiology, and virulence. The introduction of next-generation sequencing instrumentation has made WGS attainable in terms of costs. However, the lack of a beginner’s protocol for WGS still represents a barrier to its adoption in some settings. Here, we present detailed step-by-step methods for obtaining WGS data from a range of different bacteria (Gram-positive, Gram-negative, and acid-fast) using the Illumina platform. Modifications have been performed with respect to DNA extraction and library normalization to maximize the output from the laboratory consumables invested. The protocol represents a simplified and reproducible method for producing high quality sequencing data. The key advantages of this protocol include: simplicity of the protocol for users with no prior genome sequencing experience and reproducibility of the protocol across a wide range of bacteria
A multivariate statistical analysis of the effects of styrene maleic acid encapsulated RL71 in a xenograft model of triple negative breast cancer
No full textWe have previously shown that the curcumin derivative 3,5-bis(3,4,5-trimethoxybenzylidene)-1-methylpiperidine-4-one (RL71), when encapsulated in styrene maleic acid micelles (SMA-RL71), significantly suppressed the growth of MDAMB-231 xenografts by 67%. Univariate statistical analysis showed that pEGFR/EGFR, pAkt/Akt, pmTOR/mTOR and p4EBP1/4EPBP1 were all significantly decreased in tumors from treated mice compared to SMA controls. In this study, multivariate statistical analyses (MVAs) were performed to identify the molecular networks that worked together to drive tumor suppression, with the aim to determine if this analysis could also be used to predict treatment outcome. Linear discriminant analysis correctly predicted, to 100% certainty, mice that received SMA-RL71 treatment. Additionally, results from multiple linear regression showed that the expression of Ki67, PKC-α, PP2AA-α, PP2AA-β and CaD1 networked together to drive tumor growth suppression. Overall, the MVAs provided evidence for a molecular network of signaling proteins that drives tumor suppression in response to SMA-RL71 treatment, which should be explored further in animal studies of cancer
Comparative analysis of diagnostic platforms for measurement of differentially methylated insulin DNA
No full textCirculating cell-free DNA (cfDNA) has been intensively investigated as a diagnostic and prognostic marker for various cancers. In recent years, presence of unmethylated insulin cfDNA in the circulation has been correlated with pancreatic β-cell death and risk of developing type 1 diabetes. Digital (d)PCR is an increasingly popular method of quantifying insulin cfDNA due to its ability to determine absolute copy numbers, and its increased sensitivity when compared to the more routinely used quantitative PCR. Multiple platforms have been developed to carry out dPCR. However, not all technologies perform comparably, thereby necessitating evaluation of each platform. Here, we compare two dPCR platforms: the QuantStudio 3D (QS3D, Applied Biosystems) and the QX200 (Bio-Rad), to measure copies of unmethylated/methylated insulin plasmids. The QS3D detected greater copy numbers of the plasmids than the QX200 (manual mode), whereas QX200 demonstrated minimal replicate variability, increased throughput, ease of use and the potential for automation. Overall, the performance of QX200, in our hands, was better suited to measure differentially methylated insulin cfDNA.
