Enhancing the sensitivity of DNA detection and recovery from agarose gels

By inserting nitrocellulose strips into agarose gels alongside the electrophoresed lanes and passing an electric current perpendicularly in the direction of the strips, highly efficient transfer of DNA bands onto the membrane in the form of concentrated dots is achieved. DNA detection limits by this technique are enhanced, at least three times as visualized by ethidium bromide fluorescence and at least twice more by radiolabeling.     

A fast ‘Monte-Carlo cross-validation’ procedure for large least squares problems with noisy data

Summary We propose a fast Monte-Carlo algorithm for calculating reliable estimates of the trace of the influence matrixA involved in regularization of linear equations or data smoothing problems, where is the regularization or smoothing parameter. This general algorithm is simply as follows: i) generaten pseudo-random valuesw ₁, ...,w _n , from the standard normal distribution (wheren is the number of data points) and letw=(w ₁, ...,w _n ) ^T , ii) compute the residual vectorw–A w, iii) take the normalized inner-product (w ^T (w–A w))/(w ^T w) as an approximation to (1/n)tr(I–A ). We show, both by theoretical bounds and by numerical simulations on some typical problems, that the expected relative precision of these estimates is very good whenn is large enough, and that they can be used in practice for the minimization with respect to of the well known Generalized Cross-Validation (GCV) function. This permits the use of the GCV method for choosing in any particular large-scale application, with only a similar amount of work as the standard residual method. Numerical applications of this procedure to optimal spline smoothing in one or two dimensions show its efficiency.     

A short and stereoselective synthesis of carbocyclic alpha-l-dideoxyhomonucleosides

A stereoselective five-step total synthesis of the hitherto unknown carbocyclic alpha-L-dideoxyhomonu-cleosides starting from readily available (1R,5S)-2-oxabicyclo[3.3.0]oct-6-en-3-one is described.     

Recent developments in the synthesis of 11β-aryl-estrone derivatives

An industrial synthesis of 11β-aryl-estrone derivatives is described, based on the 1,4-addition of the aryl side-chain, as a cuprate, on to a mixture of allylic 5(10) alpha and beta epoxides, followed by hydrolysis and subsequent aromatization.     

Highlights on the Binding of Cobalta-Bis-(Dicarbollide) with Glucose Units

Metalla-bis-dicarbollides, such as the cobalta-bis-dicarbollide (COSAN) anion [Co(C₂B₉H₁₁)₂]⁻, have attracted much attention in biology but a deep understanding of their interactions with cell components is still missing. For this purpose, we studied the interactions of COSAN with the glucose moiety, which is ubiquitous at biological interfaces. Octyl-glucopyranoside surfactant (C8G1) was chosen as a model as it self-assembles in water and creates a hydrated glucose-covered interface. At low COSAN content and below the critical micellar concentration (CMC) of C8G1, COSAN binds to C8G1 monomers through the hydrophobic effect. Above the CMC of C8G1, COSAN adsorbs onto C8G1 micelles through the superchaotropic effect. At high COSAN concentrations, COSAN disrupts C8G1 micelles and the assemblies become similar to COSAN micelles but with a small amount of solubilized C8G1. Therefore, COSAN binds in a versatile way to C8G1 through either the hydrophobic or superchaotropic effect depending on their relative concentrations.     

In situ tissue pathology from spatially encoded mass spectrometry classifiers visualized in real time through augmented reality

Integration between a hand-held mass spectrometry desorption probe based on picosecond infrared laser technology (PIRL-MS) and an optical surgical tracking system demonstrates in situ tissue pathology from point-sampled mass spectrometry data. Spatially encoded pathology classifications are displayed at the site of laser sampling as color-coded pixels in an augmented reality video feed of the surgical field of view. This is enabled by two-way communication between surgical navigation and mass spectrometry data analysis platforms through a custom-built interface. Performance of the system was evaluated using murine models of human cancers sampled in situ in the presence of body fluids with a technical pixel error of 1.0 ± 0.2 mm, suggesting a 84% or 92% (excluding one outlier) cancer type classification rate across different molecular models that distinguish cell-lines of each class of breast, brain, head and neck murine models. Further, through end-point immunohistochemical staining for DNA damage, cell death and neuronal viability, spatially encoded PIRL-MS sampling is shown to produce classifiable mass spectral data from living murine brain tissue, with levels of neuronal damage that are comparable to those induced by a surgical scalpel. This highlights the potential of spatially encoded PIRL-MS analysis for in vivo use during neurosurgical applications of cancer type determination or point-sampling in vivo tissue during tumor bed examination to assess cancer removal. The interface developed herein for the analysis and the display of spatially encoded PIRL-MS data can be adapted to other hand-held mass spectrometry analysis probes currently available.

Integration between a hand-held mass spectrometry desorption probe based on picosecond infrared laser technology (PIRL-MS) and an optical surgical tracking system demonstrates in situ tissue pathology from point-sampled mass spectrometry data.     

Design and synthesis of a new class of membrane-permeable triazaborolopyridinium fluorescent probes

A new class of fluorescent triazaborolopyridinium compounds was synthesized from hydrazones of 2-hydrazinylpyridine (HPY) and evaluated as potential dyes for live-cell imaging applications. The HPY dyes are small, their absorption/emission properties are tunable through variation of pyridyl or hydrazone substituents, and they offer favorable photophysical characteristics featuring large Stokes shifts and general insensitivity to solvent or pH. The stability, neutral charge, cell membrane permeability, and favorable relative influences on the water solubility of HPY conjugates are complementary to existing fluorescent dyes and offer advantages for the development of receptor-targeted small-molecule probes. This potential was assessed through the development of a new class of cysteine-derived HPY-conjugate imaging agents for the kinesin spindle protein (KSP) that is expressed in the cytoplasm during mitosis and is a promising chemotherapeutic target. Conjugates possessing the neutral HPY or charged Alexa Fluor dyes that function as potent, selective allosteric inhibitors of the KSP motor were compared using biochemical and cell-based phenotypic assays and live-cell imaging. These results demonstrate the effectiveness of the HPY dye moiety as a component of probes for an intracellular protein target and highlight the importance of dye structure in determining the pathway of cell entry and the overall performance of small-molecule conjugates as imaging agents.     

Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides

We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.     

On-chip multi-electrochemical sensor array platform for simultaneous screening of nitric oxide and peroxynitrite

In this work we report on the design, microfabrication and analytical performances of a new electrochemical sensor array (ESA) which allows for the first time the simultaneous amperometric detection of nitric oxide (NO) and peroxynitrite (ONOO(-)), two biologically relevant molecules. The on-chip device includes individually addressable sets of gold ultramicroelectrodes (UMEs) of 50 μm diameter, Ag/AgCl reference electrode and gold counter electrode. The electrodes are separated into two groups; each has one reference electrode, one counter electrode and 110 UMEs specifically tailored to detect a specific analyte. The ESA is incorporated on a custom interface with a cell culture well and spring contact pins that can be easily interconnected to an external multichannel potentiostat. Each UME of the network dedicated to the detection of NO is electrochemically modified by electrodepositing thin layers of poly(eugenol) and poly(phenol). The detection of NO is performed amperometrically at 0.8 V vs. Ag/AgCl in phosphate buffer solution (PBS, pH = 7.4) and other buffers adapted to biological cell culture, using a NO-donor. The network of UMEs dedicated to the detection of ONOO(-) is used without further chemical modification of the surface and the uncoated gold electrodes operate at -0.1 V vs. Ag/AgCl to detect the reduction of ONOOH in PBS. The selectivity issue of both sensors against major biologically relevant interfering analytes is examined. Simultaneous detection of NO and ONOO(-) in PBS is also achieved.