Stepwise modulation of apical orientational cell adhesions for vertebrate neurulation

Neurulation transforms the neuroectoderm into the neural tube. This transformation relies on reorganising the configurational relationships between the orientations of intrinsic polarities of neighbouring cells. These orientational intercellular relationships are established, maintained, and modulated by orientational cell adhesions (OCAs). Here, using zebrafish (Danio rerio) neurulation as a major model, we propose a new perspective on how OCAs contribute to the parallel, antiparallel, and opposing intercellular relationships that underlie the neural plate–keel–rod–tube transformation, a stepwise process of cell aggregation followed by cord hollowing. We also discuss how OCAs in neurulation may be regulated by various adhesion molecules, including cadherins, Eph/Ephrins, Claudins, Occludins, Crumbs, Na⁺/K⁺-ATPase, and integrins. By comparing neurulation among species, we reveal that antiparallel OCAs represent a conserved mechanism for the fusion of the neural tube. Throughout, we highlight some outstanding questions regarding OCAs in neurulation. Answers to these questions will help us understand better the mechanisms of tubulogenesis of many tissues.     

Optimized microplate β-1,3-glucanase assay system for Trichoderma spp. screening

β-1,3-glucanase is an important cell wall-degrading enzyme involved in mycoparasitism by Trichoderma spp. during antagonism against phytopathogenic fungi. A simple microplate-based method to assay β-1,3-glucanase activity is described here as an alternative to an expensive tube-assay method. The reaction volume of the micro-assay was reduced to 130 µl from the 1150 µl used in the standard β-1,3-glucanase macro-assay. Statistical analyses showed significant difference in sensitivity between the micro- and the macro-assay. The micro-method was optimized using the Response Surface Quadratic Model. The sensitivity of the optimized micro-method was shown to be four-fold greater than the macro-assay and two-fold higher than the micro-assay. The optimized micro-assay was significantly more sensitive in all of the twenty examined isolates during Trichoderma spp. β-1,3-glucanase screening. We conclude that this modified and optimized method is more convenient, faster, cheaper and more reproducible than the traditional tube-assay.     

A sensitive radioimmunoassay for detecting products translated from cloned DNA fragments.

A simple and sensitive radioimmunoassay using E. coli β-galactosidase as a model protein has been developed for the detection of specific translation products of foreign gene fragments cloned into plasmid or phage vectors. This immunoassay is based upon the coupling to an insoluble matrix of F(ab)′₂ fragments derived from the specific antiserum by pepsin digestion. The in situ analysis of phage plaques or of bacterial colonies is performed by overlaying the phage plaques or lysed bacterial colonies with a cellulose filter to which F(ab)′₂ fragments have been chemically coupled. The antigen bound to the filter is detected by subsequent incubations with undigested antiserum and with ¹²⁵I-labeled Staphylococcus aureus protein A followed by autoradiography. By coupling the F(ab)′₂ fragments to the wells of a plastic microtiter plate, liquid cultures can be analyzed quantitatively for the presence of antigen, making possible the analysis of heterogeneous cultures by sib selection. The detection threshold of the microtiter plate assay for liquid culture is shown to be <2 × 10⁸ molecules, or about 1 molecule of β-galactosidase per cell. The in situ immunoassay for bacterial colonies, which permits examination of about 1000 clones per plate, can easily detect microcolonies producing about 10 molecules of β-galactosidase per cell, while the in situ phage plaque assay, also capable of screening about 1000 plaques per plate, is even more sensitive, detecting <1 × 10⁷ molecules per bacteriophage plaque.     

Spiral Plate Method for Bacterial Determination

A method is described for determining the number of bacteria in a solution by the use of a machine which deposits a known volume of sample on a rotating agar plate in an ever decreasing amount in the form of an Archimedes spiral. After the sample is incubated, different colony densities are apparent on the surface of the plate. A modified counting grid is described which relates area of the plate of volume of sample. By counting an appropriate area of the plate, the number of bacteria in the sample is estimated. This method was compared to the pour plate procedure with the use of pure and mixed cultures in water and milk. The results did not demonstrate a significant difference in variance between duplicates at the α = 0.01 level when concentrations of 600 to 12 × 10⁵ bacteria per ml were used, but the spiral plate method gave counts that were higher than counts obtained by the pour plate method. The time and materials required for this method are substantially less than those required for the conventional aerobic pour plate procedure.     

Microplates with integrated oxygen sensing for medium optimization in animal cell culture

A new approach using microtiter plate cultivation with on-line measurement of dissolved oxygen (DO) was applied for medium optimization of mammalian cell culture. Applying dynamic liquid phase balance, oxygen uptake rates were calculated from the DO level and used as an indicator for culture viability. The developed method was successfully applied to optimization of the concentration of glucose, glutamine and inorganic salts for cultivation of a Chinese Hamster Ovary (CHO) cell line. Using 2³ full factorial central composite design, the optimum medium composition could be identified in one single run. The concentration of inorganic salts had a significant influence on cultivation. The developed method exhibits high potential to improve procedures of medium optimization for animal cell cultivation by allowing the investigation of large sets of potentially important variables in short time and with reduced effort.     

A Method for Identification and Analysis of Non-Overlapping Myeloid Immunophenotypes in Humans

The development of flow cytometric biomarkers in human studies and clinical trials has been slowed by inconsistent sample processing, use of cell surface markers, and reporting of immunophenotypes. Additionally, the function(s) of distinct cell types as biomarkers cannot be accurately defined without the proper identification of homogeneous populations. As such, we developed a method for the identification and analysis of human leukocyte populations by the use of eight 10-color flow cytometric protocols in combination with novel software analyses. This method utilizes un-manipulated biological sample preparation that allows for the direct quantitation of leukocytes and non-overlapping immunophenotypes. We specifically designed myeloid protocols that enable us to define distinct phenotypes that include mature monocytes, granulocytes, circulating dendritic cells, immature myeloid cells, and myeloid derived suppressor cells (MDSCs). We also identified CD123 as an additional distinguishing marker for the phenotypic characterization of immature LIN^-CD33⁺HLA-DR^- MDSCs. Our approach permits the comprehensive analysis of all peripheral blood leukocytes and yields data that is highly amenable for standardization across inter-laboratory comparisons for human studies.     

Development of a rapid,small-scale DNA repair assay for use on clinical samples

Double-strand breaks (DSBs) are the most lethal form of DNA damage. They can be repaired by one of two pathways, homologous recombination and non-homologous end joining (NHEJ). A NHEJ assay has previously been reported which measures joining using cell-free extracts and a linearised plasmid as DNA substrate. This assay was designed for 3 × 10⁹ cells grown in vitro and utilised radioactively labelled substrate. We have scaled down the method to use smaller cell numbers in a variety of cell lines. Altering the cellular extraction procedure decreased background DNA contamination. The cleaner preparations allowed us to use SYBR Green I staining to identify joined products, which was as sensitive as ³²P-end-labelled DNA. NHEJ was found in established tumour cell lines from different originating tissues, though actual levels and fidelity of repair differed. This method also allowed end joining to be assessed in clinical specimens (human blood, brain and bladder tumours) within 24 h of receiving samples. The application of this method will allow investigation of the role of DSB DNA repair pathways in human tumours.     

A comparative study of freezing single cells and spheroids: Towards a new model system for optimizing freezing protocols for cryobanking of human tumours

Cryopreservation of human tumour cells and tissue is a valuable tool for retrospective analysis and for the transport and handling of biopsy material. Tumour tissue consists of different cell types, which have different optimal freezing conditions, and extracellular matrix. A well-defined and authentic model system is required for developing new freezing protocols and media. This work describes the use of L929 and PC-3 spheroids as new model systems for freezing human tumours. Cell suspension and spheroids were frozen in different vessels (1 ml cryovials and a special, cryo-compatible 30 × 25 μl multi well plate) at slow rate (1 °C/min). Freezing media were combinations of culture or tumour transport medium (Liforlab^®) with the cryoprotective agents, Me₂SO, trehalose and modified starch. We also present a new method of evaluating the viability of three dimensional multicellular systems to compare thawed spheroids objectively. Best viability (70%) of L929 spheroids occurred with a combination of Liforlab^® and starch hydrolysis product. The best cryopreservation results for spheroids were found with extracellular cryoprotectants, while optimum viability of single cells was achieved with Me₂SO.     

Experimental model for stimulation of cultured human osteoblast-like cells by high frequency vibration

Reliable and reproducible experimental methods for studying enhancement of osteoblast proliferation and metabolic activity in vitro provide invaluable tools for the research of biochemical processes involved in bone turnover in vivo. Some of the current methods used for this purpose are based on the ability of the osteoblasts to react metabolically to mechanical stimulation. These methods are based on the hypothesis that intracellular metabolic pathways could be influenced by the excitation of cytoskeletal components by mechanical cell deformation. Based on the same assumptions we developed a new experimental approach of biomechanical stimulation of cultured osteoblast-like cells by vibration. This method is based on the use of a specially designed vibration device that consists of an electric shaker with horizontally mounted well plate containing cell cultures. We used a first passage explant outgrowth of human osteoblast-like cell cultures, originating from samples of cancelous bone, collected from femoral necks of six donors during surgical arthroplasties of osteoarthritic hips. Well plates with replicates of cultured cells were exposed to a sine shaped vibration protocol in a frequency range of 20–60 Hz with displacement amplitude of 25 (±5) μm. We found that vibration at a distinct set of mechanical parameters of 20 Hz frequency and peak to peak acceleration of 0.5 ± 0.1 m/sec² is optimal for cell proliferation, and at 60 Hz frequency with peak to peak acceleration of 1.3 ± 0.1 m/sec² for metabolic activity. The presented easily reproducible experimental model should improve and simplify further research on the interactions between mechanical stimuli and intracellular biochemical pathways in osteoblasts. This revised version was published online in September 2006 with corrections to the Cover Date.     

A procedure for the measurement of intracellular deoxyribonucleoside triphosphate pools by thin layer chromatography

Excellent separation of ³²P-labeled deoxynucleoside triphosphates from other biological compounds has been achieved using continuous-flow thin layer chromatography on poly (ethylene) imine-cellulose layers. Large pools of ribose nucleotides are removed by periodate oxidation of the formic acid-soluble extract from labeled cells. This extract is directly spotted on the thin layer plates and developed in one direction with phosphoric acid. The plate is then reversed in an ammonium sulfate solvent. Several samples can be measured on a single plate. Pools from 10⁶ cells (10^?13 moles dNTP) can be measured quickly and easily. It should be possible to quantitate these results. The method is general and should be applicable to nucleotide pool studies in both bacterial and animal systems.     

Ice-Cap: A Method for Growing Arabidopsis and Tomato Plants in 96-well Plates for High-Throughput Genotyping

It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping project is to collect a tissue sample from each individual plant. The traditional approach to this task is to sample plants one-at-a-time. If one wishes to genotype hundreds or thousands of individuals, however, using this strategy results in a significant bottleneck in the genotyping pipeline. The Ice-Cap method that we describe here provides a high-throughput solution to this challenge by allowing one scientist to collect tissue from several thousand seedlings in a single day ^1,2. This level of throughput is made possible by the fact that tissue is harvested from plants 96-at-a-time, rather than one-at-a-time.The Ice-Cap method provides an integrated platform for performing seedling growth, tissue harvest, and DNA extraction. The basis for Ice-Cap is the growth of seedlings in a stacked pair of 96-well plates. The wells of the upper plate contain plugs of agar growth media on which individual seedlings germinate. The roots grow down through the agar media, exit the upper plate through a hole, and pass into a lower plate containing water. To harvest tissue for DNA extraction, the water in the lower plate containing root tissue is rapidly frozen while the seedlings in the upper plate remain at room temperature. The upper plate is then peeled away from the lower plate, yielding one plate with 96 root tissue samples frozen in ice and one plate with 96 viable seedlings. The technique is named "Ice-Cap" because it uses ice to capture the root tissue. The 96-well plate containing the seedlings can then wrapped in foil and transferred to low temperature. This process suspends further growth of the seedlings, but does not affect their viability. Once genotype analysis has been completed, seedlings with the desired genotype can be transferred from the 96-well plate to soil for further propagation. We have demonstrated the utility of the Ice-Cap method using Arabidopsis thaliana, tomato, and rice seedlings. We expect that the method should also be applicable to other species of plants with seeds small enough to fit into the wells of 96-well plates.     

High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the phenolic polymer lignin, that is also difficult to digest ¹. In order to improve the digestibility of plant materials we need to discover the main bottlenecks for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification ². These tasks require a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90°C. The pretreatment solution is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme mixture for a variable length of time at 50°C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH colorimetric method.     

Distortion of plant cell plate formation by the intracellular-calcium antagonist TMB-8

Summary Caulonema tip cells ofFunaria deposit new oblique cross walls of specific morphology and placement by a highly defined reorientation mechanism. In the presence of the purported intracellular Ca²⁺ antagonist 8-(N,N-diethylamino)octyl-3,4,5-trimethoxybenzoate (TMB-8), these cross walls form in the proper place but exhibit a distorted morphology. Video microscopy indicates that the deformation takes place during the reorientation of the cell plate from a perpendicular to an oblique configuration. Electron micrographs of TMB-8 treated cells indicate a stabilization of phragmoplast microtubules and a greater amount of vesicles and membrane in the developing cell plate. TMB-8 treated cells also show intense chlortetracycline fluorescence from mitochondria, vesicles and endoplasmic reticulum as compared to untreated cells indicating that TMB-8 is blocking release of Ca²⁺ from intracellular stores. It is concluded that this may cause distortation of cross walls as they form by delaying vesicle fusion, stabilizing microtubules, and increasing the amount of new wall material in the developing cell plate.Abbreviations CTC chlortetracycline - OsFeCN osmium ferricyanide method - TMB-8 8-(N,N-diethylamino)octyl-3,4,5-trimethoxybenzoate     

Live Imaging of Innate Immune and Preneoplastic Cell Interactions Using an Inducible Gal4/UAS Expression System in Larval Zebrafish Skin

Here we describe a method to conditionally induce epithelial cell transformation by the use of the 4-Hydroxytamoxifen (4-OHT) inducible KalTA4-ER^T2/UAS expression system¹ in zebrafish larvae, and the subsequent live imaging of innate immune cell interaction with HRAS^G12V expressing skin cells. The KalTA4-ER^T2/UAS system is both inducible and reversible which allows us to induce cell transformation with precise temporal/spatial resolution in vivo. This provides us with a unique opportunity to live image how individual preneoplastic cells interact with host tissues as soon as they emerge, then follow their progression as well as regression. Recent studies in zebrafish larvae have shown a trophic function of innate immunity in the earliest stages of tumorigenesis^2,3. Our inducible system would allow us to live image the onset of cellular transformation and the subsequent host response, which may lead to important insights on the underlying mechanisms for the regulation of oncogenic trophic inflammatory responses. We also discuss how one might adapt our protocol to achieve temporal and spatial control of ectopic gene expression in any tissue of interest.     

Human Neuroendocrine Tumor Cell Lines as a Three-Dimensional Model for the Study of Human Neuroendocrine Tumor Therapy

Neuroendocrine tumors (NETs) are rare tumors, with an incidence of two per 100, 000 individuals per year, and they account for 0.5% of all human malignancies.¹ Other than surgery for the minority of patients who present with localized disease, there is little or no survival benefit of systemic therapy. Therefore, there is a great need to better understand the biology of NETs, and in particular define new therapeutic targets for patients with nonresectable or metastatic neuroendocrine tumors. 3D cell culture is becoming a popular method for drug screening due to its relevance in modeling the in vivo tumor tissue organization and microenvironment.^2,3 The 3D multicellular spheroids could provide valuable information in a more timely and less expensive manner than directly proceeding from 2D cell culture experiments to animal (murine) models.To facilitate the discovery of new therapeutics for NET patients, we have developed an in vitro 3D multicellular spheroids model using the human NET cell lines. The NET cells are plated in a non-adhesive agarose-coated 24-well plate and incubated under physiological conditions (5% CO₂, 37 °C) with a very slow agitation for 16-24 hr after plating. The cells form multicellular spheroids starting on the 3^rd or 4^th day. The spheroids become more spherical by the 6^th day, at which point the drug treatments are initiated. The efficacy of the drug treatments on the NET spheroids is monitored based on the morphology, shape and size of the spheroids with a phase-contrast light microscope. The size of the spheroids is estimated automatically using a custom-developed MATLAB program based on an active contour algorithm. Further, we demonstrate a simple method to process the HistoGel embedding on these 3D spheroids, allowing the use of standard histological and immunohistochemical techniques. This is the first report on generating 3D spheroids using NET cell lines to examine the effect of therapeutic drugs. We have also performed histology on these 3D spheroids, and displayed an example of a single drug''s effect on growth and proliferation of the NET spheroids. Our results support that the NET spheroids are valuable for further studies of NET biology and drug development.     

A simplified micro-method for quantification of fecal excretion of neutral and acidic sterols for outpatient studies in humans.

A simple and precise micro-method for measurement of daily fecal excretion of neutral and acidic sterols has been developed which utilizes sitostanol (24-ethyl-5 alpha-cholestane-3 beta-ol) as fecal flow and recovery marker. Extractions of sterols were performed from 50 microliters of fecal homogenate (feces-water 1:1), and analyses of neutral and acidic sterols were carried out by gas-liquid chromatography. The method is sensitive, precise, and easy to perform; the intra-assay variability yielded coefficients of variations of 1.9% and 3.5% (n = 6) for neutral and acidic sterols, respectively. The results from this method were compared with those obtained with the standard fecal flow marker chromic oxide. The correlation coefficients between the two markers were compared in 16 subjects and were 0.938 and 0.998 for excretion of neutral sterols and acidic sterols, respectively. Comparison of the fecal excretion of neutral and acidic sterols in 12 subjects determined from frozen samples and aliquots (approximately 1 g) sent by ordinary mail to the laboratory (transport time 1 to 5 days) gave identical results using sitostanol as fecal flow marker (818 +/- (SEM) 85 mg/day vs. 838 +/- 89 mg/day for neutral sterols and 417 +/- 59 mg/day vs. 414 +/- 60 mg/day for acidic sterols). The new micro-method is ideally suited for research laboratories in need of a simple, accurate, inexpensive, and high through-put method for measuring daily fecal excretion of neutral and acidic sterols, as well as total cholesterol synthesis, and can be performed on an outpatient basis.     

Development of a simple and sensitive technique for detection of point mutations in the K-ras oncogene

We sought to develop a simple and sensitive method based on mutant allele-specific amplification (MASA) for the detection of point mutations in the k-ras oncogene in blood samples. We used MASA and three nested MASA methods to detect a point mutation (GGT→GAT) in rat DHD cells at codon 12 of exon 1 of the k-ras gene. MASA allowed us to detect one k-ras mutated cell on a background of 10⁷ normal cells. The third nested-MASA (nested-MASA.c) method that we developed allowed us to detect one mutated cell among 10¹⁰ normal cells. Our methods should allow the detection of small amounts of mutant k-ras DNA in tissue, serum, and plasma, combining speed with efficiency and specificity.     

Pressure probe technique for measuring water relations of cells in higher plants

A new method is described for continuously measuring cell turgor pressure (P), hydraulic conductivity (L_p), and volumetric elastic modulus (ε) in higher plant cells, using a pressure probe. This technique permits volume changes, ΔV, and turgor pressure changes, ΔP, to be determined with an accuracy of 10⁻⁵ to 10⁻⁶ μl and 3 to 5·10⁻² bar, respectively.

The main principle of the new method is the same as the pressure probe developed by Zimmermann and Steudle in which pressure is transmitted to a pressure transducer by means of an oil-filled capillary introduced into the cell. In order to use the pressure probe for small tissue cells, the effective compressible volume of the apparatus has to be sufficiently small in comparison to the volume of the cell itself. This is achieved by accurately fixing the oil/cell sap boundary in the very tip of the microcapillary by means of an electronic feedback mechanism, so that the effective volume of the apparatus is reduced to about 2 to 10% of the cell volume. In this way also, errors arising from compressibility of the apparatus and temperature fluctuations can be excluded.

Measurements on tissues cells of Capsicum annuum fruits yield ε values of 2 to 25 bar. Furthermore, ε can be shown to be a function of both cell turgor pressure and cell volume; ε increases with increasing turgor pressure and is higher in larger cells.

     

A microplate spectrofluorometric assay for bacterial biofilms

A spectrofluorometric assay was developed for quantification of bacterial biofilms grown on a microtiter plate. The method involved staining biofilms formed by gram-negative and gram-positive bacteria with wheat germ agglutinin-Alexa Fluor 488 conjugate, which selectively binds to N-acetylglucosamine residues in biofilms. The fluorescence of stained biofilms was measured with a fluorescent plate reader. This method was compared with a widely used microplate colorimetric assay involving crystal violet staining of biofilms formed by both gram-negative and gram-positive bacteria. A strong linear association existed between the two methods (r ²=0.99/0.94). Being more sensitive and specific as compared to colorimetric method, the spectrofluorometric assay provides a better alternative for quantification and characterization of bacterial biofilms.