A microperifusion system with environmental control for studying insulin secretion by pancreatic tissue.

A continuous flow reactor (perifusion system) was fabricated and tested for measuring the kinetics of insulin secretion from isolated pancreatic islets of Langerhans in response to step changes in the glucose concentration and oxygen partial pressure in the perfusate flowing around the islets. The system was capable of making rapid changes in perfusate glucose concentration and pO2, had rapid dynamic response for measuring the change in insulin secretion rate as a result of these changes in perfusate, and was suitable for studying very small volumes of tissue. Initial experiments with this system demonstrated that (1) the response of isolated rat islets to glucose stimulation was very fast, with the first phase peak occurring in as little as about 10 s, (2) bulk perfusate oxygen partial pressure levels of 30 mmHg or less reduced the second-phase insulin secretion rate in graded fashion, (3) the reduction in secretion rate began within 1 min following an oxygen partial pressure decrease, and (4) the reduction in secretion rate was reversible, with a burst of insulin secretion occurring during the first minute after partial pressure restoration.     

A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays.

A procedure for immobilization of well-defined quantities of oligodeoxyribonucleotides (ODNs) to a versatile nylon support is described. The solid support, a nylon-6/6 bead, is covalently coated with poly(ethyleneimine) to provide a reactive spacer-arm for attachment of ODNs. 5'-Aminohexyl-tailed ODNs are selectively activated using 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and then covalently attached to the bead via the triazine moiety. The modified nylon support has a low level of binding of nonspecific nucleic acid and efficiently captures both RNA and DNA targets.     

A versatile microstirrer and oxygen electrode system for a spectrophotometer cuvette.

A microstirring device is described which measures only 1 × 1 × 0.4 cm outsidedimensions and is thus suitable for insertion beneath most spectrophotometer cuvettes without displacing the cuvette from the light path and without the need for modification of the spectrophotometer. The top of the cuvette remains accessible for a specially designed cuvette lid and electrode. This combined equipment is particularly suitable for the simultaneous measurement of two parameters, one with the electrode and the other by spectrophotometry. The design of the lid also permits the addition of reactants, including O₂, during monitoring. The equipment has been used to measure the oxygen-binding isotherm of human hemoglobin using 0.1 mg of protein. The curve so obtained was identical with curves found in the literature and obtained under the same conditions of pH, temperature, etc.     

A versatile system for detecting transposition in Arabidopsis

The maize transposable element Activator (Ac) has been shown to be active in a number of dicots, including Arabidopsis thaliana, whose small genome and short generation time have favored its wide adoption as a model organism for molecular genetic approaches to plant physiology and development. Using the Ac element and several bacterial and plant marker genes, we have devised a versatile system for identifying plants in which a transposon has excised and reinserted elsewhere in the genome. The transposons have been designed to facilitate the identification of insertions downstream of promoters and in the vicinity of enhancers by the inclusion of a β-glucuronidase (GUS) gene either lacking a promoter or having a minimal promoter sequence. The system permits the transposon and the source of transposase to be maintained either stably in separate plants or in the same plant. Plants in which transposition is occurring can be identified by the frequent somatic activation of the GUS gene. The herbicide chlorsulfuron is used as a selective agent to identify progeny plants in which the transposon has excised from its original insertion site within a chlorsulfuron-resistant acetolactate synthase gene. Additional selectable markers permit the identification of plants containing a transposed element, but lacking transposase. Here we describe our initial characterization of the system and demonstrate its reliability and efficiency in identifying plants with transposed elements.     

A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous end-joining enzyme LIG4. We also engineer deletions and inversions for a 50 kb Pten genomic region in mouse liver. We discover diverse yet sequence-specific indels at the rearrangement fusion sites. Moreover, we detect Cas9 cleavage at the fourth nucleotide on the non-complementary strand, leading to staggered instead of blunt DNA breaks. These reporters allow mechanisms of chromosomal rearrangements to be investigated.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0680-7) contains supplementary material, which is available to authorized users.     

A versatile and efficient gene-targeting system for Aspergillus nidulans

Aspergillus nidulans is an important experimental organism, and it is a model organism for the genus Aspergillus that includes serious pathogens as well as commercially important organisms. Gene targeting by homologous recombination during transformation is possible in A. nidulans, but the frequency of correct gene targeting is variable and often low. We have identified the A. nidulans homolog (nkuA) of the human KU70 gene that is essential for nonhomologous end joining of DNA in double-strand break repair. Deletion of nkuA (nkuA delta) greatly reduces the frequency of nonhomologous integration of transforming DNA fragments, leading to dramatically improved gene targeting. We have also developed heterologous markers that are selectable in A. nidulans but do not direct integration at any site in the A. nidulans genome. In combination, nkuA delta and the heterologous selectable markers make up a very efficient gene-targeting system. In experiments involving scores of genes, 90% or more of the transformants carried a single insertion of the transforming DNA at the correct site. The system works with linear and circular transforming molecules and it works for tagging genes with fluorescent moieties, replacing genes, and replacing promoters. This system is efficient enough to make genomewide gene-targeting projects feasible.     

A versatile oxygenator and perfusion system for magnetic resonance studies

A compact, reusable membrane oxygenator has been constructed for the perfusion of cultured cells and isolated organs. While the oxygenator was designed to be compatible with nuclear magnetic resonance (NMR) spectroscopy studies, it can also be used for any experiment which requires warming and oxygenation of perfusates. For the NMR studies, the oxygenator can be positioned at the opening of the magnet bore which allows oxygenation and warming of the perfusate immediately prior to delivery to the tissue, therefore eliminating problems with heat or oxygen loss which may occur with the long perfusion lines. (c) 1996 John Wiley & Sons, Inc.     

A versatile lentiviral expression system to identify mammalian protein-protein interactions

Protein-protein interactions (PPIs) are central to our understanding of protein function, biological processes and signaling pathways. Affinity purification coupled with mass spectrometry (AP-MS) is a powerful approach for detecting PPIs and protein complexes and relies on the purification of bait proteins using bait-specific binding reagents. These binding reagents may recognize bait proteins directly or affinity tags that are fused to bait proteins. A limitation of the latter approach is that expression of affinity tagged baits is largely constrained to engineered or unnatural cell lines, which results in the AP-MS identification of PPIs that may not accurately reflect those seen in nature. Therefore, generating cell lines stably expressing affinity tagged bait proteins in a broad range of cell types and cell lines is important for identifying PPIs that are dependent on different contexts. To facilitate the identification of PPIs across many mammalian cell types, we developed the mammalian affinity purification and lentiviral expression (MAPLE) system. MAPLE uses recombinant lentiviral technology to stably and efficiently express affinity tagged complementary DNA (cDNA) in mammalian cells, including cells that are difficult to transfect and non-dividing cells. The MAPLE vectors contain a versatile affinity (VA) tag for multi-step protein purification schemes and subcellular localization studies. In this methods article, we present a step-by-step overview of the MAPLE system workflow.     

A versatile vector system for multiple gene expression in plants

Today, cloning vectors that have been specifically designed to facilitate the fusion, overexpression or down-regulation of a variety of genes in plant cells are available from various sources. In most cases, their basic design allows the cloning of a single target gene, typically under a specific promoter, in parallel with the expression of selection and/or marker genes from the same vector. However, new and versatile systems now exist that expand the user's choice to a large number of promoters and terminators, and various autofluorescent tags confer the ability to express multiple genes from a single transformation vector.     

Sulfonates-PMMA nanoparticles conjugates: A versatile system for multimodal application

We report herein the viability of a novel nanoparticles (NPs) conjugated system, namely the attachment, based on ionic and hydrophobic interactions, of different sulfonated organic salts to positively charged poly(methylmethacrylate) (PMMA)-based core-shell nanoparticles (EA0) having an high density of ammonium groups on their shells. In this context three different applications of the sulfonates@EA0 systems have been described. In detail, their ability as cytotoxic drugs and pro-drugs carriers was evaluated in vitro on NCI-H460 cell line and in vivo against human ovarian carcinoma IGROV-1 cells. Besides, 8-hydroxypyrene-1,3,6-trisulfonic acid, trisodium salt (HPTS) was chosen for NPs loading, and its internalization as bioimaging probe was evaluated on Hep G2 cells. Overall, the available data support the interest for these PMMA NPs@sulfonates systems as a promising formulation for theranostic applications. In vivo biological data strongly support the potential value of these core-shell NPs as delivery system for negatively charged drugs or biologically active molecules. Additionally, we have demonstrated the ability of these PMMA core-shell nanoparticles to act as efficient carriers of fluorophores. In principle, thanks to the high PMMA NPs external charge density, sequential and very easy post-loading of different sulfonates is achievable, thus allowing the preparation of nanocarriers either with bi-modal drug delivery behaviour or as theranostic systems.     

A versatile microfiltration device

A versatile vacuum microfiltration device was designed for separation of small volumes of liquid from samples of cells or subcellular organelles through membrane filters. It is especially useful for separation of small samples from radioactive tracer when low blank values are mandatory for the performance of the measurement. In the present communication the microfiltration device was used for the separation of organelles from incubation medium labeled with 45Ca2+ for measurement of uptake of 45Ca2+ by small samples of liver or pancreatic islet mitochondria or of pancreatic islet secretory granules. Measurement of 45Ca2+ uptake was possible in samples containing less than 1 microgram of protein even if the sample was incubated with only 10,000 cpm of 45CaCl2. Blank values ranged only between 2.6 and 4.7% of the test values. The device should be useful for a variety of applications in many research areas where sample volumes are small.     

A simple,versatile feeder layer system for Brassica oleracea protoplast culture

Protoplasts from cauliflower (Brassica oleracea ssp. botrytis) and broccoli (ssp. italica) leaves and hypocotyls were successfully cultured on membrane filters over a feeder layer of cells from a B. campestris suspension culture. Cells from rice, tomato and tobacco suspensions were not as effective as the B. campestris cells. Plants were recovered from protoplasts of previously recalcitrant Brassica genotypes. Protoplasts cultured in low numbers (10–100) on the feeder layer divided and formed colonies capable of plant regeneration, as did fused protoplasts.Abbreviations BA 6-benzylaminopurine - 2,4-D 2,4-dichlorophenoxyacetic acid - IAA indole-3-acetic acid - NAA naphthaleneacetic acid - PCV packed cell volume