Biomolecular theorem proving on a chip: a novel microfluidic solution to a classical logic problem

Biomolecules inside a microfluidic system can be used to solve computational problems, such as theorem proving, which is an important class of logical reasoning problems. In this article, the Boolean variables (literals) were represented using single-stranded DNA molecules, and theorem proving was performed by the hybridization and ligation of these variables into a double-stranded "solution" DNA. Then, a novel sequential reaction mixing method in a microfluidic chip was designed to solve a theorem proving problem, where a reaction loop and three additional chambers were integrated and controlled by pneumatic valves. DNA hybridization, ligation, toehold-mediated DNA strand displacement, exonuclease I digestion, and fluorescence detection of the double-stranded DNA were sequentially performed using this platform. Depending on the computational result, detection of the correct answer was demonstrated based on the presence of a fluorescence signal. This result is the first demonstration that microfluidics can be used to facilitate DNA-based logical inference.     

Single-cell recording and stimulation with a 16k micro-nail electrode array integrated on a 0.18 μm CMOS chip

To cope with the growing needs in research towards the understanding of cellular function and network dynamics, advanced micro-electrode arrays (MEAs) based on integrated complementary metal oxide semiconductor (CMOS) circuits have been increasingly reported. Although such arrays contain a large number of sensors for recording and/or stimulation, the size of the electrodes on these chips are often larger than a typical mammalian cell. Therefore, true single-cell recording and stimulation remains challenging. Single-cell resolution can be obtained by decreasing the size of the electrodes, which inherently increases the characteristic impedance and noise. Here, we present an array of 16,384 active sensors monolithically integrated on chip, realized in 0.18 μm CMOS technology for recording and stimulation of individual cells. Successful recording of electrical activity of cardiac cells with the chip, validated with intracellular whole-cell patch clamp recordings are presented, illustrating single-cell readout capability. Further, by applying a single-electrode stimulation protocol, we could pace individual cardiac cells, demonstrating single-cell addressability. This novel electrode array could help pave the way towards solving complex interactions of mammalian cellular networks.     

Noncontrast dynamic MRA in intracranial arteriovenous malformation (AVM), comparison with time of flight (TOF) and digital subtraction angiography (DSA)

Digital subtraction angiography (DSA) remains the gold standard to diagnose intracranial arteriovenous malformations (AVMs) but is invasive. Existing magnetic resonance angiography (MRA) is suboptimal for assessing the hemodynamics of AVMs. The objective of this study was to evaluate the clinical utility of a novel noncontrast four-dimensional (4D) dynamic MRA (dMRA) in the evaluation of intracranial AVMs through comparison with DSA and time-of-flight (TOF) MRA. Nineteen patients (12 women, mean age 26.2±10.7 years) with intracranial AVMs were examined with 4D dMRA, TOF and DSA. Spetzler-Martin grading scale was evaluated using each of the above three methods independently by two raters. Diagnostic confidence scores for three components of AVMs (feeding artery, nidus and draining vein) were also rated. Kendall's coefficient of concordance was calculated to evaluate the reliability between two raters within each modality (dMRA, TOF, TOF plus dMRA). The Wilcoxon signed-rank test was applied to compare the diagnostic confidence scores between each pair of the three modalities. dMRA was able to detect 16 out of 19 AVMs, and the ratings of AVM size and location matched those of DSA. The diagnostic confidence scores by dMRA were adequate for nidus (3.5/5), moderate for feeding arteries (2.5/5) and poor for draining veins (1.5/5). The hemodynamic information provided by dMRA improved diagnostic confidence scores by TOF MRA. As a completely noninvasive method, 4D dMRA offers hemodynamic information with a temporal resolution of 50-100 ms for the evaluation of AVMs and can complement existing methods such as DSA and TOF MRA.     

Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures

Verification by imaging of the structure of 3D DNA constructs, both bare and conjugated to metal nanoparticles, is challenging. We demonstrate here two transmission electron microscopy (TEM) based methods to distinguish between fully formed tetrahedra, synthesized from DNA conjugated with gold nanoparticles (GNPs) at their vertices, and structures which are only partially formed. When deposited on a surface, fully formed tetrahedra are expected to retain their 3D pyramidal structure, while partially formed structures are expected to form a 2D structure. The first method by which 3D and 2D structures were distinguished was imaging them at different defocusing values. While for 2D structures all the four GNPs acquire Fresnel fringes at the same defocusing value, for 3D structures at least one particle is at a different plane with respect to the others, and so it acquires Fresnel fringes at a different defocusing value. The second method we show is imaging of the structures at different angles. While a single TEM image gives only a 2D projection of the structure, by combining information achieved from imaging at several tilting angles one may verify the structural construct.     

Direct measurement of the interactions of amide solvents with single-walled carbon nanotubes using isothermal titration calorimetry

The interaction enthalpy of amide solvents with single-walled carbon nanotube (SWCNT) dispersions is measured using isothermal titration calorimetry (ITC). N,N-Dimethyl-formamide (DMF) and N-methyl-2-pyrilidone (NMP) were used to make dispersions of highly purified (6,5) SWCNTs. Using isothermal titration calorimetry, the ΔH and K(A) terms related to the solvent-nanotube interactions were measured, and ΔG and ΔS of the interaction were determined. It was found that the interaction enthalpy of NMP with SWCNTs dispersed in DMF was exothermic. The addition of a second solvent into a NMP or DMF dispersion produced spontaneous exfoliation of SWCNT bundles as the solvent properties became more favorable. During the titration, a positive change in interaction entropy within the dispersed system due to the unbundling of SWCNTs was measured. From blank titrations of pure DMF into pure NMP and the reverse, dilution enthalpies were also calculated and compared to the literature, along with the corresponding enthalpic interaction coefficients, h(xx) and h(xxx). From our results, ITC appears to be a viable technique for measuring the interaction of solvent molecules with the surface of SWCNTs and for measuring the effect of mixed solvent properties on SWCNT dispersions.     

HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.     

An Operations Research Approach to the Problem of the Sugarcane Selection

Selection for superior clones is the most important aspect of sugar cane improvement programs, and is a long and expensive process. While studies have investigated different components of selection independently, there has not been a whole system approach to improve the process. This study observes the problem as an integrated system, where if one parameter changes the state of the whole system changes. A computer based stochastic simulation model that accurately represents the selection was developed. This paper describes the simulation model, showing its accuracy as well as how a combination of dynamic programming and branch and bound can be applied to the model to optimise the selection system, giving a new application of these techniques. The model can be directly applied to any region targeted by sugarcane breeding programs or to other clonally propagated crops.     

Improving the Sensitivity of a Quartz Crystal Microbalance for Biosensing by Using Porous Gold

 A quartz crystal microbalance can be used as a biosensor if biological receptor molecules (ligands) are attached to the crystal. To improve the sensitivity, the surface area of the gold electrodes on the crystal was increased by rendering the electrodes porous. This increased the response up to a factor of 3. A protein model system with human anti-myoglobin as ligand and sheep skeletal myoglobin at different concentrations as analyte was used. The quartz crystal was mounted in a flow-cell, where immobilisation, binding and regeneration of the surface were carried out. The kinetics of the model system was monitored under various experimental conditions. Received February 2, 2000. Revision June 30, 2000.     

Total Synthesis of (+)-6-epi-Ophiobolin A

The ophiobolin sesterterpenes are notable plant pathogens which have recently elicited significant chemical and biological attention because of their intriguing carbogenic frameworks, reactive functionalities, and emerging anticancer profiles. Reported herein is a total synthesis of (+)-6-epi-ophiobolin A in 14 steps, a task which addresses construction of the synthetically challenging spirocyclic tetrahydrofuran motif as well as several other key stereochemical problems. This work demonstrates a streamlined synthetic platform to complex ophiobolins leveraging disparate termination modes of a radical polycyclization cascade for divergent elaboration and functionalization.