A non-sequential method for constructing trees and hierarchical classifications

Summary A procedure is presented that forms an unrooted tree-like structure from a matrix of pairwise differences. The tree is not formed a portion at a time, as methods now in use generally do, but is formed en toto without intervening estimates of branch lengths. The method is based on a relaxed additivity (four-point metric) constraint. From the tree, a classification may be formed.     

Insect diets as mixtures: optimization for a polyphagous weevil

Development or improvement of artificial insect diets can be tedious, convoluted and often under-appreciated. Using n-dimensional mixture designs, we identified a set of response-optimized meridic diets that contain fewer ingredients than the current commercial diet for Diaprepes abbreviatus, a polyphagous weevil pest of the Caribbean and southern U.S. A diet blend optimized to produce maximum adult weight was predicted to produce adult D. abbreviatus that weigh 28% more compared with adults reared on the standard commercial diet. Diet blends that produced greater individual adult weights resulted in lower survival compared with those blends that yielded adults of more modest proportions. In contrast, a simplified high cottonseed meal blend produced smaller adults more similar to field-collected individuals, and produced the greatest number of adults and the greatest biomass at relatively low cost compared with diets that yielded adult weevils of greater weight. We think that many insect-rearing programs would benefit from application of mixture design methods to situations where diet optimization is desired for researcher-selected criteria. This approach is broadly applicable to any problem that can be conceptualized as a mixture problem.     

A simple method for examining organotypic CNS cultures with nomarski optics

Summary This paper describes a method for examination of living organotypic cultures of CNS with Nomarski differential interference-contrast optics. Cultures grown in Maximow assemblies. which promote the best differentiation of the tissue but are optically faulty, are transferred for Nomarski observation to a simple sandwich chamber which combines the optical perfection of the usual sandwich chamber with the flexibility and safeguarding of sterility characteristic of the Maximow assembly. Thus cultures can be transferred repeatedly between their maintenance and observation chambers. In the resulting microscopic images, it is posible to visualize delicate unmyelinated fibers, myelinated cell bodies and other features which are normally impossible to demonstrate in living cultures as well as to improve the images of other structures such as large neuronal perikarya and myelinated axons. This work was supported in part by NIH Grant NS 11425     

A new method for studying the interaction between chlorpromazine and phospholipid bilayer

The spectroscopic and transmission electron microscopy (TEM) studies of interaction between chlorpromazine (CPZ) and dimyristoyl phosphatidylglycerol (DMPG) bilayer by using gold nanoparticles (AuNPs) as probes are reported. The DMPG bilayer-protected AuNPs were prepared by a simple one-step method. The DMPG bilayer tethered on the AuNPs was considered as a biomembrane model. The addition of CPZ affected the surface plasmon resonance (SPR) and morphology of the prepared AuNPs, and this effect was monitored by UV-vis spectroscopy and TEM. The interaction between CPZ and DMPG bialyer was CPZ concentration-dependent, and the possible mechanism was discussed. This simple and facile method may be quite general and work for other surface active drug-biomembrane or protein-biomembrane interactions.     

A simple method for the addition of rotenone in Arabidopsis thaliana leaves

A simple and reproducible method for the treatment of Arabidopsis thaliana leaves with rotenone is presented. Rosette leaves were incubated with rotenone and Triton X-100 for at least 15 h. Treated leaves showed increased expression of COX19 and BCS1a, 2 genes known to be induced in Arabidopsis cell cultures after rotenone treatment. Moreover, rotenone/Triton X-100 incubated leaves presented an inhibition of oxygen uptake. The simplicity of the procedure shows this methodology is useful for studying the effect of the addition of rotenone to a photosynthetic tissue in situ.     

A precise spectrophotometric method for measuring sodium dodecyl sulfate concentration

Sodium dodecyl sulfate (SDS) is used to denature and solubilize proteins, especially membrane and other hydrophobic proteins. A quantitative method to determine the concentration of SDS using the dye Stains-All is known. However, this method lacks the accuracy and reproducibility necessary for use with protein solutions where SDS concentration is a critical factor, so we modified this method after examining multiple parameters (solvent, pH, buffers, and light exposure). The improved method is simple to implement, robust, accurate, and (most important) precise.     

Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM): A novel method for biomolecular screening

Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a new separation-based affinity method. It has kinetic capabilities exceeding those of surface plasmon resonance (SPR) and does not require immobilization of molecules on the surface. Another distinctive feature of NECEEM is that--if it is combined with an advanced method for the mixing solutions inside a capillary, termed transverse diffusion of laminar flow profiles (TDLFP)--it requires only nanoliter volumes of solutions. The proven applications of NECEEM to biomolecular screening include 1) measuring kinetic and thermodynamic parameters of protein-ligand interactions, 2) quantitative affinity analyses of proteins and hybridization analyses of DNA and RNA, and 3) selection of binding ligands from combinatorial libraries. NECEEM is easy to automate and parallelize. Because of its simplicity and analytical power, NECEEM has the potential to become a workhorse in studies of biomolecular interactions. The author reviews theoretical bases of NECEEM and its applications to biomolecular screening.     

A careful disorderliness in the proteome: sites for interaction and targets for future therapies

The community of scientists interested in studying intrinsically unstructured (or disordered) proteins has emerged in recent years. What began as a controversial idea has become an established phenomenon. The new, greater focus on proteins that are in some way normally unstructured promises to provide a greater understanding of protein function, particularly with respect to protein-protein interactions. These regions also offer new possibilities into how interactions can be targeted by small molecules.     

A method for proteomic identification of membrane-bound proteins containing Asn-linked oligosaccharides

Glycosylated proteins on the cell surface have been shown to be essential for cell-cell interactions in development and differentiation. Our ultimate goal is to identify Asn-linked oligosaccharides that are directly involved in these critical in vivo functions. Because such oligosaccharides would be expected to reside on the integral plasma membrane proteins, and conventional two-dimensional gel techniques are ineffective at separating such proteins, we have developed a new approach to their identification on a proteomics scale from Caenorhabditis elegans. Membrane proteins are solubilized in guanidine-HCl, precipitated, and digested with trypsin. The glycopeptides are then separated by lectin chromatography. Next, glycopeptidase F digestion removes the oligosaccharides from the peptides and converts to Asp each Asn to which one was attached. The peptides are then analyzed by matrix-assisted laser desorption/ionization quadrupole time-of-flight (MALDI-Q-TOF) mass spectrometry. Thus, the membrane glycoproteins are identified through the sequence tags of these peptides and the conversion of at least one deduced Asn residue to Asp at the Asn-X-Ser/Thr consensus sequence. To validate the utility of this approach, we have identified 13 membrane-bound N-glycosylated proteins from the major peaks observed on MALDI-Q-TOF analysis of our total glycopeptide fraction.     

A low-toxicity method for the separation of lanosterol and dihydrolanosterol from commercial mixtures

We describe an inexpensive, low-toxicity and high-yielding method for the production of pure lanosterol and dihydrolanosterol from the commercially available mixture. Optimum conditions are presented for the one-pot production of the intermediate 24,25 vicinal diol of lanosterol acetate (via either epoxidation or hydroxyhalogenation) which is readily separated from the unreacted dihydrolanosterol acetate. The lanosterol diol can then be converted to pure (>97%) lanosterol. Hypophosphorous acid was used for both the conversion of the epoxide to the diol, and as a catalyst for the hydroxyhalogenation by N-halosuccinimides of the olefinic bond.     

A method for examining temporal changes in cyanobacterial harmful algal bloom spatial extent using satellite remote sensing

Cyanobacterial harmful algal blooms (CyanoHAB) are thought to be increasing globally over the past few decades, but relatively little quantitative information is available about the spatial extent of blooms. Satellite remote sensing provides a potential technology for identifying cyanoHABs in multiple water bodies and across geo-political boundaries. An assessment method was developed using MEdium Resolution Imaging Spectrometer (MERIS) imagery to quantify cyanoHAB surface area extent, transferable to different spatial areas, in Florida, Ohio, and California for the test period of 2008 to 2012. Temporal assessment was used to evaluate changes in satellite resolvable inland waterbodies for each state of interest. To further assess cyanoHAB risk within the states, the World Health Organization’s (WHO) recreational guidance level thresholds were used to categorize surface area of cyanoHABs into three risk categories: low, moderate, and high-risk bloom area. Results showed that in Florida, the area of cyanoHABs increased largely due to observed increases in high-risk bloom area. California exhibited a slight decrease in cyanoHAB extent, primarily attributed to decreases in Northern California. In Ohio (excluding Lake Erie), little change in cyanoHAB surface area was observed. This study uses satellite remote sensing to quantify changes in inland cyanoHAB surface area across numerous water bodies within an entire state. The temporal assessment method developed here will be relevant into the future as it is transferable to the Ocean Land Colour Instrument (OLCI) on Sentinel-3A/3B missions.     

Nonlinear Blending: A Useful General Concept for the Assessment of Combination Drug Synergy

Human diseases may involve cellular signaling networks that contain redundant pathways, so that blocking a single pathway in the system cannot achieve the desired effect. As such, the use of drugs in combination are particularly effective interventions in networked systems. However, common synergy measures are often inadequate to quantify the effect of two different drugs in complex cellular systems. This article proposes a general approach to quantifying the synergy of two drugs in combination. This approach is called strong nonlinear blending. Drugs with different relative potencies, different effect maxima, or situations of potentiation or coalism pose no problem for strong nonlinear blending as a way to assess the increased response benefit to be gained by combining two drugs. This is important as testing drug combinations in complex biological systems are likely to produce a wide variety of possible response surfaces. It is also shown that for monotone increasing (or decreasing) dose response surfaces that strong nonlinear blending is equivalent to improved potency along a ray of constant dose ratio. This is important because fixed dose ratios form the basis for many preclinical and clinical combination drug experiments. Two examples are given involving HIV and cancer chemotherapy combination drug experiments.     

A facile method for the direct synthesis of lanthionine containing cyclic peptides

A series of disulfide bridged peptides were designed as potential inhibitors of protein-protein interactions. Following solid phase synthesis, completely deprotected linear peptides were first oxidized to their disulfide analogs and then transformed into their lanthionine equivalents via a base-assisted reaction in water. Peptides consisting of cystine bridges of length i, i+3, with and without discrimination of the chiral centers, were studied for this transformation. Lanthionine peptides were also obtained directly from the reduced linear peptides under mild alkaline treatment, and the reaction proceeded via disulfide bond formation. The extent of conversion of a disulfide bridge into its lanthionine counterpart varied according to the primary sequence. Product characterization revealed diastereomeric lanthionine formation. The presence of D-amino acids, peptide conformation, and/or position of the cystine bridge are among the factors determining the facility of this reaction. Elimination of the backbone proton beta to the sulfur atom followed by intramolecular thiol Michael addition is the most likely mechanism for this transformation.     

A facile method for the direct synthesis of lanthionine containing cyclic peptides

Summary A series of disulfide bridged peptides were designed as potential inhibitors of protein-protein interactions. Following solid phase synthesis, completely deprotected linear peptides were first oxidized to their disulfide analogs and then transformed into their lanthionine equivalents via a base-assisted reaction in water. Peptides consisting of cystine bridges of lengthi, i+3, with and without discrimination of the chiral centers, were studied for this transformation. Lanthionine peptides were also obtained directly from the reduced linear peptides under mild alkaline treatment, and the reaction proceeded via disulfide bond formation. The extent of conversion of a disulfide bridge into its lanthionine counterpart varied according to the primary sequence. Product characterization revealed diastereomeric lanthionine formation. The presence of D-amino acids, peptide conformation, and/or position of the cystine bridge are among the factors determining the facility of this reaction. Elimination of the backbone proton beta to the sulfur atom followed by intramolecular thiol Michael addition is the most likely mechanism for this transformation.     

A mechanism-based, solution-phase method for screening combinatorial mixtures of potential platinum anticancer drugs

 We report a new, mechanism-based approach to the screening of pools of potential platinum antitumor drugs. A platinum complex of L-lysine, [Pt(Lys)Cl₂] or Kplatin, was selected from mixtures of platinum-amino acid compounds based on the ability of its DNA adducts to bind HMG1 in a gel mobility shift assay. Kplatin, unlike most other platinum antitumor drug candidates, is an (N,O)-chelated complex which binds DNA forming two isomeric 1,2-d(GpG) intrastrand DNA cross-links. Kplatin-modified DNA is specifically recognized by HMG1, HMG1 domain B, and testis-specific HMG, all of which bind to the major cisplatin-DNA adducts. Kplatin is toxic towards the human tumor cell lines HeLa and KM12 with LC₅₀ values of 59.2±7.8 μM and 74 μM, respectively. Received: 16 July 1997 / Accepted 31 October 1997     

A sensitive method for examining whole-cell biochemical composition in single cells of filamentous fungi using synchrotron FTIR spectromicroscopy

Cell function is related to cell composition. The asexual state of filamentous fungi (molds and mildews) has two main life cycle stages: vegetative hyphae for substrate colonization and nutrient acquisition, and asexual spores for survival and dispersal. Hyphal composition changes over a few tens of microns during growth and maturation; spores are different from hyphae. Most biochemical analyses are restricted to studying a few components at high spatial resolution (e.g. histochemistry) or many compounds at low spatial resolution (e.g. GC-MS). Synchrotron FTIR spectromicroscopy can be used to study fungal cell biology by fingerprinting varieties of carbohydrates, proteins, and lipids at about 6 microm spatial resolution. FTIR can distinguish fungal species and changes during hyphal growth, and reveals that even fungi grown under optimal vs mildly stressed conditions exhibit dramatic biochemical changes without obvious morphological effects. Here we compare hypha and spore composition of two fungi, Neurospora and Rhizopus. There are clear biochemical changes when Neurospora hyphae commit to spore development, during spore maturation and following germination, many of which are consistent with results from molecular genetics, but have not been shown before at high spatial resolution. Rhizopus spores develop within a fluid-containing sporangium that becomes dry at maturity. Rhizopus spores had similar protein content and significantly more carbohydrate than the sporangial fluid, both of which are novel findings.     

Ribonucleic acid mass and concentration in individual nerve cells: A new method for quantitative determinations

A method is presented which allows quantitative determinations to be made of the total quantity and mean concentration of ribonucleic acid (RNA) in the individual nerve cell. The cells are dissected out, after which they are extracted enzymically. The extract of each cell is placed separately on a cellphane strip. This serves as a cuvette in the subsequent photographic-photometric determination of the amount of RNA present in the extract. Since the volume of the cell is determined, the mean concentration is also obtained.A number of experiments shows that the method is subject to errors amounting to less than ±5% when applied to large and medium-sized nerve cells.An account is given of analyses of motor anterior horn cells and spinal ganglion cells.     

A new method for fish leucocyte counting and partial differentiation by flow cytometry

A simple and rapid method for analysis of fish blood cells is presented. Carp (Cyprinus carpio) blood was diluted 200 times with Hanks' solution containing 1 microg/ml of DiOC6(3) which is a fluorescent, lipophilic dye. After staining for 10 min, the blood cells were measured by a flow cytometer (FACS). Several blood cell populations were identified by different FL-1 (green fluorescence), FSC (forward scatter), and SSC (side scatter) properties. FL-1 v. SSC or FSC v. SSC dot-plot of stained blood cells displayed five separate cell populations: erythrocytes: a mixture of thrombocytes plus lymphocytes; monocytes; neutrophils; and basophils. The number of each type of blood cell counted by the FACS was in good agreement with those counted microscopically.     

A method for obtaining equilibrium tautomeric mixtures of reducing sugars via glycosylamines using nonaqueous media

Equilibrium tautomeric mixtures of several mono- and disaccharides are obtained in anhydrous form, without the use of water, by reacting the commercially available reducing sugars with ammonia gas in dry methanol, followed by the concentration of the resultant solution to dryness. Mutarotation and hydrolysis of the initially formed glycosylamine in the resultant medium account for the transformation. Equilibrium anomeric mixtures enriched in the beta-form of commercially available sugars such as alpha-D-glucose and alpha-lactose have not only vastly increased solubility, but are also synthetically valuable as these can be readily converted to the methyl/benzyl/trimethylsilyl ether and other derivatives for further transformations.     

A method for assaying perchlorate concentration in microbial cultures using the fluorescent dye resazurin

Low concentrations (μg/L) of the perchlorate anion, ClO₄⁻, have been measured in surface and ground water supplies in many locations throughout the United States. Perchlorate is known to affect the function of the thyroid gland in mammals and its toxicity primarily results from its inhibition of thyroid hormone output. The major sources of perchlorate contamination in surface and ground waters are defense contractors, military installations, propellant manufacturers and agriculture. The currently accepted method of perchlorate analysis, recommended by the US EPA, is neither fast nor easy to use and requires purchase of an expensive high performance ion chromatograph (IC). The novel method described here uses dye resazurin to measure perchlorate reduction by bacterial cultures and bacterial consortia in a high-throughput, multi-well, culture plate format. The method is based on the observation that perchlorate reduction and the decrease of resazurin fluorescence occur simultaneously in perchlorate degrading cultures. The bioassays were performed in anaerobic serum bottles or 96-well plates with constant shaking, using a minimal ATCC medium with 10 mM acetate as electron donor/carbon source and 200 ppm perchlorate as an electron acceptor. Fluorescence measurements with excitation at 570 nm and emission at 590 nm were taken in 20 min intervals. Changes in perchlorate concentration were confirmed using IC. Based on the experimental data, a simple model showing the correlation between perchlorate concentration in microbial culture and resazurin fluorescence level was proposed. Other dyes including redox indicators, reactive azo dyes and electron shuttle chemicals were also tested for comparison and were found less useful.