A time to sequence

A next-generation human genome sequence

A near-complete sequence outlines a path for a more inclusive reference.

The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project

The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the "community" of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner's proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.

Sharing Data to Build a Medical Information Commons: From Bermuda to the Global Alliance

The Human Genome Project modeled its open science ethos on nematode biology, most famously through daily release of DNA sequence data based on the 1996 Bermuda Principles. That open science philosophy persists, but daily, unfettered release of data has had to adapt to constraints occasioned by the use of data from individual people, broader use of data not only by scientists but also by clinicians and individuals, the global reach of genomic applications and diverse national privacy and research ethics laws, and the rising prominence of a diverse commercial genomics sector. The Global Alliance for Genomics and Health was established to enable the data sharing that is essential for making meaning of genomic variation. Data-sharing policies and practices will continue to evolve as researchers, health professionals, and individuals strive to construct a global medical and scientific information commons.

Falling giants and the rise of gene editing: ethics, private interests and the public good

This paper considers the tensions created in genomic research by public and private for-profit ideals. Our intent is to strengthen the public good at a time when doing science is strongly motivated by market possibilities and opportunities. Focusing on the emergence of gene editing, and in particular CRISPR, we consider how commercialisation encourages hype and hope-a sense that only promise and idealism can achieve progress. At this rate, genomic research reinforces structures that promote, above all else, private interests, but that may attenuate conditions for the public good of science. In the first part, we situate genomics using the aphorism that 'on the shoulders of giants we see farther'; these giants are infrastructures and research cultures rather than individual 'heroes' of science. In this respect, private initiatives are not the only pivot for successful discovery, and indeed, fascination in those could impinge upon the fundamental role of public-supported discovery. To redress these circumstances, we define the extent to which progress presupposes research strategies that are for the public good. In the second part, we use a 'falling giant' narrative to illustrate the risks of over-indulging for-profit initiatives. We therefore offer a counterpoint to commercialised science, using three identifiable 'giants'-scientists, publics and cultures-to illustrate how the public good contributes to genomic discovery.

Evaluating how we evaluate

Evaluation of scientific work underlies the process of career advancement in academic science, with publications being a fundamental metric. Many aspects of the evaluation process for grants and promotions are deeply ingrained in institutions and funding agencies and have been altered very little in the past several decades, despite substantial changes that have taken place in the scientific work force, the funding landscape, and the way that science is being conducted. This article examines how scientific productivity is being evaluated, what it is rewarding, where it falls short, and why richer information than a standard curriculum vitae/biosketch might provide a more accurate picture of scientific and educational contributions. The article also explores how the evaluation process exerts a profound influence on many aspects of the scientific enterprise, including the training of new scientists, the way in which grant resources are distributed, the manner in which new knowledge is published, and the culture of science itself.

Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA

This review is a practical guide for experimentalists interested in specifically labeling internal sequences on double-stranded (ds) DNA molecules for single-molecule experiments. We describe six labeling approaches demonstrated in a single-molecule context and discuss the merits and drawbacks of each approach with particular attention to the amount of specialized training and reagents required. By evaluating each approach according to criteria relevant to single-molecule experiments, including labeling yield and compatibility with cofactors such as Mg(2+), we provide a simple reference for selecting a labeling method for given experimental constraints. Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.

Genome-wide Association: From Confounded to Confident

Genome-wide association studies (GWAS) allow for a large number of samples to be assayed simultaneously, using a genome-wide tagging single nucleotide polymorphism (SNP) approach. The initial boon of success from disease studies such as macular degeneration and inflammatory bowel disease has been mitigated by lack of genome-wide significance for psychiatric disorders and related traits, despite evaluations of large populations. In addition to SNP genotypes, which are common variants typically attributing small or modest relative risk, copy number variations can be detected based on the same data set. Several rare recurrent copy number variations have been associated with psychiatric diseases in genome-wide analyses. Proper and responsible study design, followed by rigorous data quality assessment of genomic matching of cases and controls, is most likely to uncover regions of significant association that replicate in independent cohorts, thereby maximizing the chance of significant and confident association.

Genetic heterogeneity in human disease

Strong evidence suggests that rare mutations of severe effect are responsible for a substantial portion of complex human disease. Evolutionary forces generate vast genetic heterogeneity in human illness by introducing many new variants in each generation. Current sequencing technologies offer the possibility of finding rare disease-causing mutations and the genes that harbor them.

Magnetic resonance detection: spectroscopy and imaging of lab-on-a-chip

This mini-review is focused on the use of nuclear magnetic resonance (NMR) spectroscopy and imaging to study processes on lab-on-a-chip devices. NMR as an analytical tool is unmatched in its impact across nearly every area of science, from biochemistry and medicine to fundamental chemistry and physics. The controls available to the NMR spectroscopist or imager are vast, allowing for everything from high level structural determination of proteins in solution to detailed contrast imaging of organs in-vivo. Unfortunately, the weak nuclear magnetic moment of the nucleus requires that a very large number of spins be present for an inductively detectable signal, making the use of magnetic resonance as a detection modality for microfluidic devices especially challenging. Here we present recent efforts to combat the inherent sensitivity limitation of magnetic resonance for lab-on-a-chip applications. Principles and examples of different approaches are presented that highlight the flexibility and advantages of this type of detection modality.

Strategy for automated analysis of dynamic metabolic mixtures by NMR. Application to an insect venom

Elucidation of the composition of chemical-biological samples is a main focus of systems biology and metabolomics. Due to the inherent complexity of these mixtures, reliable, efficient, and potentially automatable methods are needed to identify the underlying metabolites and natural products. Because of its rich chemical information content, nuclear magnetic resonance (NMR) spectroscopy has a unique potential for this task. Here we present a generalization and application of a recently introduced NMR data collection, processing, and analysis strategy that circumvents the need for extensive purification and hyphenation prior to analysis. It uses covariance TOCSY NMR spectra measured on a 1-mm high-temperature cryogenic probe that are analyzed by a spectral trace clustering algorithm yielding 1D NMR spectra of the individual components for their unambiguous identification. The method is demonstrated on a metabolic model mixture and is then applied to the unpurified venom mixture of an individual walking stick insect that contains several slowly interconverting and closely related metabolites.

para-Hydrogen-Induced Polarization in Heterogeneous Hydrogenation Reactions

We demonstrate the creation and observation of para-hydrogen-induced polarization in heterogeneous hydrogenation reactions. Wilkinson's catalyst, RhCl(PPh3)3, supported on either modified silica gel or a polymer, is shown to hydrogenate styrene into ethylbenzene and to produce enhanced spin polarizations, observed through NMR, when the reaction was performed with H2 gas enriched in the para spin isomer. Furthermore, gaseous phase para-hydrogenation of propylene to propane with two catalysts, the Wilkinson's catalyst supported on modified silica gel and Rh(cod)(sulfos) (cod = cycloocta-1,5-diene; sulfos = -O3S(C6H4)CH2C(CH2PPh2)3) supported on silica gel, demonstrates heterogeneous catalytic conversion resulting in large spin polarizations. These experiments serve as a direct verification of the mechanism of heterogeneous hydrogenation reactions involving immobilized metal complexes and can be potentially developed into a practical tool for producing catalyst-free fluids with highly polarized nuclear spins for a broad range of hyperpolarized NMR and MRI applications.

Separation and analysis of nanomole quantities of heparin oligosaccharides using on-line capillary isotachophoresis coupled with NMR detection

Glycosaminoglycans (GAGs) are important in a number of biological processes and are structurally altered in many pathological conditions. The complete determination of GAG primary structures has been hampered by the lack of sensitive and specific analytical techniques. Nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for GAG structure elucidation despite its relatively poor limits of detection. Solenoidal microcoils have greatly enhanced the mass limits of detection of NMR, enabling the on-line coupling of microseparation and concentration techniques such as capillary isotachophoresis (cITP), which can separate and concentrate analytes by 2-3 orders of magnitude. We have successfully used cITP coupled with on-line NMR detection to separate and concentrate nanomole quantities of heparin oligosaccharides. This sensitive on-line measurement approach has the potential to provide new insights into the relationships between biological function and GAG microstructures.

Hyphenation of Gas Chromatography to Microcoil 1H Nuclear Magnetic Resonance Spectroscopy

Whereas the hyphenation of gas chromatography (GC) with mass spectrometry is of great importance, little is known about the coupling to nuclear magnetic resonance spectroscopy (NMR). The investigation of this technique is an attractive proposition because of the valuable information given by NMR on molecular structure. The experiments shown here are to our knowledge the first hyphenating capillary GC to microcoil NMR. In contrast to liquids, gases have rarely been investigated by NMR, mainly due to the experimental difficulties in handling gases and the low signal-to-noise-ratio (SNR) of the NMR signal obtained at atmospheric pressure. With advances in NMR sensitivity (higher magnetic fields and solenoidal microprobes), this limitation can be largely overcome. In this paper, we describe the use of a custom-built solenoidal NMR microprobe with an active volume of 2 microL for the NMR detection of several compounds at 400 MHz, first in a mixture, and then with full coupling to capillary GC to identify them separately. The injected amounts of each analyte in the hyphenated experiments are in the range of 15-50 micromol, resulting in reasonable SNR for sample masses of 1-2 microg.

Exploring uncharted terrain in nature's structure space using capillary NMR spectroscopy: 13 steroids from 50 fireflies

Capillary NMR spectroscopy (CapNMR) was used to characterize 13 new cardenolides and related steroids from a severely mass-limited natural products sample derived from a rare firefly, Lucidota atra. These analyses were carried out on only partially purified samples, each containing 20-100 mug of up to three steroids. Compared to other NMR spectroscopic techniques, CapNMR provided an up to 3-fold gain in sensitivity while maintaining very high spectral quality, which was essential for the identification of the L. atra steroids. We show that CapNMR allows for routine 1H and 13C NMR spectroscopic characterization of small molecule samples containing as little as 40 nmol of material.

Insights into cyclodextrin interactions during sample stacking using capillary isotachophoresis with on-line microcoil NMR detection

On-line capillary isotachophoresis (cITP)-NMR experiments were used to probe the interactions of the pharmaceutical compounds S-alprenolol, S-atenolol, R-propranolol, R-salbutamol and S-terbutaline with beta-cyclodextrin (beta-CD) during cITP concentration. In cITP, ionic analytes are concentrated and separated on the basis of their electrophoretic mobility. Because neutral molecules have an electrophoretic mobility of zero, they are normally not concentrated or separated in electrophoretic experiments like cITP. Most of the analytes studied were concentrated by cITP sample stacking by a factor of around 300. For analytes that formed a strong inclusion complex, beta-CD co-concentrated during cITP sample stacking. However, once the focusing process was complete, a discrete diffusional boundary formed between the cITP-focused analyte band and the leading and trailing electrolyte, which restricted diffusion into and out of the analyte band.

High-Throughput Microcoil NMR of Compound Libraries Using Zero-Dispersion Segmented Flow Analysis

An automated system for loading samples into a microcoil NMR probe has been developed using segmented flow analysis. This approach enhanced 2-fold the throughput of the published direct injection and flow injection methods, improved sample utilization 3-fold, and was applicable to high-field NMR facilities with long transfer lines between the sample handler and NMR magnet. Sample volumes of 2 microL (10-30 mM, approximately 10 microg) were drawn from a 96-well microtiter plate by a sample handler, then pumped to a 0.5-microL microcoil NMR probe as a queue of closely spaced "plugs" separated by an immiscible fluorocarbon fluid. Individual sample plugs were detected by their NMR signal and automatically positioned for stopped-flow data acquisition. The sample in the NMR coil could be changed within 35 s by advancing the queue. The fluorocarbon liquid wetted the wall of the Teflon transfer line, preventing the DMSO samples from contacting the capillary wall and thus reducing sample losses to below 5% after passage through the 3-m transfer line. With a wash plug of solvent between samples, sample-to-sample carryover was <1%. Significantly, the samples did not disperse into the carrier liquid during loading or during acquisitions of several days for trace analysis. For automated high-throughput analysis using a 16-second acquisition time, spectra were recorded at a rate of 1.5 min/sample and total deuterated solvent consumption was <0.5 mL (1 US dollar) per 96-well plate.

Development of a Functionalized Xenon Biosensor

NMR-based biosensors that utilize laser-polarized xenon offer potential advantages beyond current sensing technologies. These advantages include the capacity to simultaneously detect multiple analytes, the applicability to in vivo spectroscopy and imaging, and the possibility of "remote" amplified detection. Here, we present a detailed NMR characterization of the binding of a biotin-derivatized caged-xenon sensor to avidin. Binding of "functionalized" xenon to avidin leads to a change in the chemical shift of the encapsulated xenon in addition to a broadening of the resonance, both of which serve as NMR markers of ligand-target interaction. A control experiment in which the biotin-binding site of avidin was blocked with native biotin showed no such spectral changes, confirming that only specific binding, rather than nonspecific contact, between avidin and functionalized xenon leads to the effects on the xenon NMR spectrum. The exchange rate of xenon (between solution and cage) and the xenon spin-lattice relaxation rate were not changed significantly upon binding. We describe two methods for enhancing the signal from functionalized xenon by exploiting the laser-polarized xenon magnetization reservoir. We also show that the xenon chemical shifts are distinct for xenon encapsulated in different diastereomeric cage molecules. This demonstrates the potential for tuning the encapsulated xenon chemical shift, which is a key requirement for being able to multiplex the biosensor.

Biomolecular NMR using a microcoil NMR probe--new technique for the chemical shift assignment of aromatic side chains in proteins

A specially designed microcoil probe for use in biomolecular NMR spectroscopy is presented. The microcoil probe shows a mass-based sensitivity increase of a minimal factor of 7.5, allowing for the first time routine biomolecular NMR spectroscopy with microgram amounts of proteins. In addition, the exceptional radio frequency capabilities of this probe allowed us to record an aliphatic-aromatic HCCH-TOCSY spectrum for the first time. Using this spectrum, the side chains of aliphatic and aromatic amino acids can be completely assigned using only a single experiment. Using the conserved hypothetical protein TM0979 from Thermotoga maritima, we demonstrate the capabilities of this microcoil NMR probe to completely pursue the sequence specific backbone assignment with less than 500 microg of (13)C,(15)N labeled protein.

Dual Microcoil NMR Probe Coupled to Cyclic CE for Continuous Separation and Analyte Isolation

Capillary electrophoresis (CE)-nuclear magnetic resonance (NMR) spectroscopy combines the separation efficiency of CE and the information-rich detection capabilities of NMR. However, the temporally narrow CE peaks reduce NMR sensitivity and prevent on-line multidimensional NMR acquisitions. In this work, cyclic CE with multicoil NMR instrumentation is developed to perform CE in multiple closed loops. As a proof of concept, a two-loop five-junction capillary configuration creates two connected yet independently operable fluidic loops. With appropriate voltage switching, analytes can be directed as desired around or between the loops, and a particular analyte band can be parked in one NMR detector coil while CE continues in the second loop and monitored with a second NMR detector coil. The separation of a mixture of amino acids (Ala, Val, Thr) is achieved in two cycles. After one CE cycle, Ala is separated and COSY data are recorded in one loop while Val and Thr are separated in the second loop. At the end of the second cycle, both Val and Thr are separated and multidimensional NMR spectra acquired. With this instrumentation and appropriate protocols, two-dimensional NMR data acquisition and CE separation are achieved simultaneously.

Hyphenation of Capillary HPLC to Microcoil 1H NMR Spectroscopy for the Determination of Tocopherol Homologues

Highly selective reversed phases (C(30) phases) are self-packed in 250 microm inner diameter fused-silica capillaries and employed for capillary HPLC separation of shape-constrained natural compounds (tocopherol homologues, vitamin E). Miniaturized hyphenated systems such as capillary HPLC-ESI-MS (positive ionization mode) and, with special emphasis, continuous-flow capillary HPLC- NMR are used for structural determination of the separated compounds. Despite the small amount of sample available (1.33 microg of each tocopherol), the authors have been able to monitor the capillary HPLC separation under continuous-flow (1)H NMR conditions, thus allowing an immediate peak identification. Further structural assignment was carried out in the stopped-flow NMR mode as shown, for example, by a 2D (1)H,(1)H COSY NMR spectrum of alpha-tocopherol. We demonstrate in this paper the considerable potential of hyphenated capillary separations coupled to MS and NMR for the investigation of restricted amounts of sample.

High-Throughput Nuclear Magnetic Resonance Analysis Using a Multiple Coil Flow Probe

An automated method for high-throughput nuclear magnetic resonance (NMR) spectroscopy has been developed using a four-coil Multiplex NMR probe. The probe is constructed with solenoidal microcoils optimized for detection of small volume, mass-limited samples and a flow-through design. Four samples can be simultaneously injected into the Multiplex probe with a robotics liquid handler and then analyzed in rapid succession using a selective excitation experiment. Due to the simultaneous injection of four samples and the reduced analysis time with rapid selective excitation, the analysis rate achieved thus far is as low as 1 sample/34 s for 1D 1H NMR.

NMR detection with multiple solenoidal microcoils for continuous-flow capillary electrophoresis

Nuclear magnetic resonance (NMR) spectroscopy represents a promising on-line detector for capillary electrophoresis (CE). The inherent poor sensitivity of NMR mandates the use of NMR probes with the highest mass sensitivity, such as those containing solenoidal microcoils, for CE/NMR hyphenation. However, electrophoretic current degrades the resolution of NMR spectra obtained from solenoidal coils. A new method to avoid microcoil NMR spectral degradation during continuous-flow CE is demonstrated using a unique multiple solenoidal coil NMR probe. The electrophoretic flow from a single separation capillary is split into multiple outlets, each possessing its own NMR detection coil. While the CE electrophoretic flow is directed through one outlet, stopped-flow, high-resolution NMR spectra are obtained from the coil at the other outlet. The electrophoretic flow and NMR measurements are cycled between the outlets to allow a continuous CE separation with "stopped-flow" detection. As a new approach for improving multiple coil probe performance, the magnetic field homogeneity is automatically adjusted (via the shim coils of the magnet) for the active coil. The multiple microcoil CE/NMR coupling has been used to analyze a <3 nmole mixture of amines while obtaining between 1 and 2 Hz line width, demonstrating the ability to avoid electrophoretic current-induced line broadening.

High-resolution capillary tube NMR. A miniaturized 5-microL high-sensitivity TXI probe for mass-limited samples, off-line LC NMR, and HT NMR

A new triple-resonance (TXI) (1H, 13C, 15N) high-resolution nuclear magnetic resonance (NMR) capillary probe with 2.5-microL NMR-active sample volume (V(obs)) was built and tested for applications with mass- and volume-limited samples and for coupling of microbore liquid chromatography to NMR. This is the first microliter probe with optimized coil geometry for use with individual capillary tubes with an outer diameter of 1 mm. The 90 degree pulse lengths of the 1-mm microliter probe were below 2 micros for proton, below 8 micros for carbon, and below 20 micros for nitrogen, and a spectral line width at signal half-height below 1 Hz was obtained. Compared to a conventional 5-mm probe, the new 600-MHz 1-mm TXI microliter probe with z-gradient shows an increase in mass sensitivity by a factor of 5, corresponding to a 25-fold reduction in measuring time. The consumption of costly deuterated solvent is reduced by at least 2 orders of magnitude. The 1-mm TXI microliter probe with z-gradient allows the measurement of one-dimensional 1H NMR and two-dimensional heteronuclear NMR spectra with a few nanomoles (micrograms) of compound with high sensitivity, speed, and quality. This is a breakthrough for discrete sample NMR spectroscopy with paramount importance for structure elucidation in natural compound chemistry and metabolic research. It offers also advantages for linking chromatographic methods to NMR in a nindustrial environment. Capillary tube NMR may find new applications in areas where high sample throughput is essential, e.g., in the quality control of large sample arrays from parallel chemistry, screening, and compound depositories. It has the potential to increase the sample throughput by 1 order of magnitude or more if new hardware for fast sample handling and exchange becomes available.

Capillary isotachophoresis/NMR: extension to trace impurity analysis and improved instrumental coupling

Building upon its promising initial performance, the online coupling of capillary isotachophoresis (cITP) to nuclear magnetic resonance (NMR) is extended to trace impurity analysis. By simultaneously concentrating and separating dilute charged species on the basis of their electrophoretic mobility, cITP greatly facilitates NMR structural elucidation. cITP/NMR appears particularly attractive for identifying trace charged synthetic and natural organic compounds obscured by large excesses of other components. A 9.4 microL injection of 200 microM (1.9 nmol) atenolol in a 1000-fold excess of sucrose (200 mM) is analyzed by cITP/NMR. A microcoil, the most mass sensitive NMR probe, serves as the detector as it provides optimal NMR observation of the capillary-scale separation. cITP successfully isolates the atenolol from the sucrose while concentrating it 200-fold to 40 mM before presentation to the 30 nL observe volume microcoil, thereby enabling rapid 1H NMR spectral acquisition of atenolol (experimental time of 10 s) without obstruction from sucrose. For this particular probe and sample, the stacking efficiency is near the theoretical limit as 67% of the sample occupies the 1 mm long microcoil during peak maximum. A multiple-coil probe with two serial 1 mm long microcoils arranged 1 cm apart has been developed to facilitate peak trapping and sample band positioning during cITP/NMR.

Influence of pressure upon coupling pressurized capillary electrochromatography with nuclear magnetic resonance spectroscopy

In this work, the influence of supplementary pressure on the separation efficiency of pressurized capillary electrochromatography (pCEC) was examined. At low pressures of up to 30 bar, which is more than sufficient to prevent bubble formation, no significant loss in separation efficiency is observed. Even at 100 bar, the efficiency of pCEC is still significantly better than without application of an electric field. In addition, analysis times are drastically reduced compared to both capillary electrochromatography (CEC) and capillary HPLC. On the basis of these results, an improved interface for capillary NMR coupling is described and used for the separation and identification of a mixture of unsaturated fatty acid methyl esters. Under these conditions, the analysis time could be shortened by up to a factor of 10 when pCEC is coupled to NMR spectroscopy.

Analysis of multiple samples using multiplex sample NMR: selective excitation and chemical shift imaging approaches

Two improved approaches for the rapid analysis of multiple samples using multiplex sample NMR are described. In the first approach, frequency-selective 90 degrees radio frequency pulses and large pulsed field gradients are applied to excite and detect multiple samples in rapid succession. This method is advantageous for samples with relatively long longitudinal (T1) relaxation times. In the second approach, chemical shift imaging is applied to acquire both the spectral and spatial information of multiple samples simultaneously. Chemical shift imaging is more time-consuming than selective excitation; however, it is advantageous for detecting samples with short T1's and for signal averaging. Both approaches demonstrate the potential of multiplex sample NMR for carrying out high-throughput NMR detection.

Monitoring temperature changes in capillary electrophoresis with nanoliter-volume NMR thermometry

Nanoliter-volume proton nuclear magnetic resonance (NMR) spectroscopy is used to monitor the electrolyte temperature during capillary electrophoresis (CE). By measuring the shift in the proton resonance frequency of the water signal, the intracapillary temperature can be recorded noninvasively with subsecond temporal resolution and spatial resolution on the order of 1 mm. Thermal changes of more than 65 degrees C are observed under both equilibrium and nonequilibrium conditions for typical CE separation conditions. Several capillary and buffer combinations are examined with external cooling by both liquid and air convection. Additionally, NMR thermometry allows nonequilibrium temperatures in analyte bands to be monitored during a separation. As one example, a plug of 1 mM NaCl is injected into a capillary filled with 50 mM borate buffer. Upon reaching the NMR detector, the temperature in the NaCl band is more than 20 degrees C higher than the temperature in the surrounding buffer. Such observations have direct applicability to a variety of studies, including experiments which utilize sample stacking and isotachophoresis.

Two-dimensional fluorescence correlation in capillary electrophoresis for peak resolution and species identification

A new spectroscopic dimension-fluorescence intensity correlation--is introduced to enhance peak resolution and species identification in capillary electrophoresis. In two-dimensional correlation CE, a conventional electropherogram is spread into two dimensions through cross-correlation analysis of fluorescence time response. A laser that is sinusoidally modulated in intensity is used as the excitation source. Three channels of information are collected during a CE run: the steady-state intensity, the ac amplitude, and the phase-resolved fluorescence intensity. The correlation between two chosen channels is then evaluated. A two-dimensional correlation electropherogram consists of a plot of the correlation intensity versus two axes of migration time. Through correlation analysis, species discrimination and peak resolution are significantly enhanced without having to physically separate the solutes. Two-dimensional correlation CE showed complete resolution between two overlapping sample peaks with a resolution of 0.28 in the conventional one-dimensional electropherogram. In separations of polycyclic aromatic hydrocarbons by micellar electrokinetic chromatography (MEKC), two-dimensional correlation analysis resolved all overlapping elution peaks unseparable by one-dimensional MEKC, demonstrating the utility of 2D correlation in separation method development. The capability of 2D correlation CE in species identification is demonstrated with a sequence of 39 consecutively injected peaks containing four fluorescent dyes. Species identification in sequencing is achieved without complex data treatment in two-dimensional correlation CE.

Long-range (1)H-(15)N heteronuclear shift correlation at natural abundance

Despite the inherently low sensitivity of (15)N NMR because of its low gyromagnetic ratio (gamma(N)) and its relatively low natural abundance (0.37%), this important nuclide still has useful potential as a structural probe even at natural abundance. Inverse-detected NMR methods coupled with major advances in NMR probe designs have made it possible to acquire long-range (1)H-(15)N heteronuclear shift correlation data on samples as small as a micromole overnight. Chemical shift referencing schemes for (15)N and the range of (15)N shifts are discussed, followed by a discussion of the currently available pulse sequences, pulse calibration, parametrization and processing of long-range (1)H-(15)N data, and the implications of probe selection. These topics are followed by a review of the applications contained in the literature that have utilized (1)H-(15)N heteronuclear shift correlation experiments at natural abundance, with emphasis placed on the observed long-range coupling pathways.

Electrochemistry in nanovials fabricated by combining screen printing and laser micromachining

The coupling of screen-printing and laser micromachining technology has been used to create a nanovial with "built-in" working and reference electrodes. The volume of the nanovial was calculated to be 7.2 nL using dimensions determined by SEM. The electrochemical nanovial was characterized using the ferri/ferrocyanide redox couple. Cyclic voltammetry and chronoamperometry experiments were performed with electrochemical nanovials utilizing 5% (v/v) glycerin in the solutions and a humidified headspace to control evaporation of the small-volume samples. Chronoamperometry experiments gave results consistent with a diffusion-limited process and revealed a working electrode surface area of 2.6 x 10(4) micron 2. The ultrasmall-volume cells represent a simple, reliable, low-cost approach for the fabrication of complete electrochemical nanovials.

A microcoil NMR probe for coupling microscale HPLC with on-line NMR spectroscopy

An HPLC NMR system is presented that integrates a commercial microbore HPLC system using a 0.5-mm column with a 500-MHz proton NMR spectrometer using a custom NMR probe with an observe volume of 1.1 microL and a coil fill factor of 68%. Careful attention to capillary connections and NMR flow cell design allows on-line NMR detection with no significant loss in separation efficiency when compared with a UV chromatogram. HPLC NMR is performed on mixtures of amino acids and small peptides with analyte injection amounts as small as 750 ng; the separations are accomplished in less than 10 min and individual NMR spectra are acquired with 12 s time resolution. Stopped-flow NMR is achieved by diversion of the chromatographic flow after observation of the beginning of the analyte band within the NMR flow cell. Isolation of the compound of interest within the NMR detection cell allows multidimensional experiments to be performed. A stopped-flow COSY spectrum of the peptide Phe-Ala is acquired in 3.5 h with an injected amount of 5 micrograms.

Multiple solenoidal microcoil probes for high-sensitivity, high-throughput nuclear magnetic resonance spectroscopy

Two designs for incorporating multiple solenoidal microcoils into a single probe head are presented to increase the throughput of high-resolution NMR. Through a combination of radio frequency switches and low-noise amplifiers, multiple NMR spectra can be acquired in the same time as a single spectrum from a conventional probe consisting of one coil. Since this method does not compromise sensitivity with regard to the individual microcoils, throughput increases linearly with the number of coils. Only one receiver is needed, and data acquisition parameters can be optimized for each sample. Specifically, a four-coil system has been implemented for proton NMR at 250 MHz using a wide-bore magnet, with an observe volume of 28 nL for each microcoil. Signal cross-contamination was approximately 0.2% between individual coils, and simultaneous one- and two-dimensional spectra have been obtained from samples of fructose, galactose, adenosine triphosphate, and chloroquine (7 nmol of each compound). A more compact two-coil configuration has also been designed for operation at 500 MHz, with observe volumes of 5 and 31 nL for the two coils. One- and two-dimensional spectra were acquired from samples of 1-butanol (55 nmol) and ethylbenzene (250 nmol).

DNA variation in a 5-Mb region of the X chromosome and estimates of sex-specific/type-specific mutation rates

We describe a new approach for the study of human genome variation, based on our solid-phase fluorescence chemical mismatch-cleavage method. Multiplex screening rates >/=80 kb/36-lane gels are achieved, and accuracy of mismatch location is within +/-2 bp. The density of differences between DNA from any two humans is sufficiently low, and the estimate of their position is accurate enough, to avoid sequencing of most polymorphic sites when defining their allelic state. Furthermore, highly variable sequences, such as microsatellites, are distinguished easily, so that separate consideration can be given to loci that do and do not fit the definition of infinite mutation sites. We examined a 5-Mb region of Xq22 to define the haplotypes of 23 men (9 Europeans, 9 Ashkenazim, and 5 Pygmies) by reference to DNA from one Italian man. Fifty-eight 1.5-kb segments revealed 102 segregating sites. Seven of these are shared by all three groups, two by Pygmies and Europeans, two by Pygmies and Ashkenazim, and 19 by Ashkenazim and Europeans. Europeans are the least polymorphic, and Pygmies are the most polymorphic. Conserved allelic associations were recognizable within 40-kb DNA segments, and so was recombination in the longer intervals separating such segments. The men showed only three segregating sites in a 16.5-kb unique region of the Y chromosome. Divergence between X- and Y-chromosome sequences of humans and chimpanzees indicated higher male mutation rates for different types of mutations. These rates for the X chromosomes were very similar to those estimated for the X-linked factor IX gene in the U.K. population.

An Effective Approach for Analyzing “Prefinished” Genomic Sequence Data

Ongoing efforts to sequence the human genome are already generating large amounts of data, with substantial increases anticipated over the next few years. In most cases, a shotgun sequencing strategy is being used, which rapidly yields most of the primary sequence in incompletely assembled sequence contigs (“prefinished” sequence) and more slowly produces the final, completely assembled sequence (“finished” sequence). Thus, in general, prefinished sequence is produced in excess of finished sequence, and this trend is certain to continue and even accelerate over the next few years. Even at a prefinished stage, genomic sequence represents a rich source of important biological information that is of great interest to many investigators. However, analyzing such data is a challenging and daunting task, both because of its sheer volume and because it can change on a day-by-day basis. To facilitate the discovery and characterization of genes and other important elements within prefinished sequence, we have developed an analytical strategy and system that uses readily available software tools in new combinations. Implementation of this strategy for the analysis of prefinished sequence data from human chromosome 7 has demonstrated that this is a convenient, inexpensive, and extensible solution to the problem of analyzing the large amounts of preliminary data being produced by large-scale sequencing efforts. Our approach is accessible to any investigator who wishes to assimilate additional information about particular sequence data en route to developing richer annotations of a finished sequence.

[Our software system is available via an extensive web supplement to this article at http://www.ncbi.nlm.nih.gov/Kuehl/prefinished.]

The emerging importance of genetics in epidemiologic research. I. Basic concepts in human genetics and laboratory technology

PURPOSE

To define a general framework of current approaches to the discovery of disease-associated genes and the role of genetic factors in influencing disease risk through the integration of genome technology and traditional epidemiologic methods.

METHODS

An overview of basic concepts in human genetics, laboratory methodology for measuring genetic variation believed to influence common diseases, and issues concerning preparation and utilization of genetic materials is provided as a foundation for genetic epidemiologic research.

RESULTS

Identification and characterization of human genetic variation is providing new risk factors for disease in the form of DNA sequence variation. The availability of genetic material from participants in large epidemiologic studies and appropriate informed consent represents an invaluable resource for exploring genetic and environmental influences on disease risk.

CONCLUSIONS

Advances in genome technology coupled with vast amounts of genetic data resulting from the Human Genome Project are broadening the scope of epidemiologic research and providing tools to identify individuals at increased risk of disease. Combining diverse expertise from the fields of epidemiology and human genetics provides unique opportunities to localize disease-susceptibility genes and examine molecular mechanisms of complex disease etiology.

Identification, mapping, and phylogenomic analysis of four new human members of the T-box gene family: EOMES, TBX6, TBX18, and TBX19

Brachyury(T) is a mouse mutation, first described over 70 years ago, that causes defects in mesoderm formation. Recently several related genes, the T-box gene family, that encode a similar N-terminal DNA binding domain, the T-box, and that play critical roles in human embryonic development have been identified. It has been shown that human TBX5 and TBX3, if mutated, cause developmental disorders, Holt-Oram syndrome (OMIM 142900) and ulnar-mammary syndrome (OMIM 181450), respectively. We have identified four new human members of the T-box gene family, EOMES, TBX6, TBX18, and TBX19, and these genes have been mapped to different chromosomal regions by radiation hybrid mapping. The four T-box genes were classified into four different subfamilies and have also been subjected to phylogenomic analysis. Human EOMES maps at 3p21.3-p21.2. This Tbr1-subfamily gene is likely to play a significant role in early embryogenesis similar to that described for Xenopus eomesodermin. Human TBX6 maps at 16p12-q12. This Tbx6-subfamily gene is likely to participate in paraxial mesoderm formation and somitogenesis in human embryo. TBX18 is a novel member of the Tbx1 subfamily that maps at 6q14-q15. Two subgroups, TBX1/10 and TBX15/18 subgroups, could be distinguished within the Tbx1 subfamily. TBX19 is an orthologue of chick TbxT and maps at 1q23-q24. The genomic organization of TBX19 is highly similar to that of human T(Brachyury), another human member of the same subfamily.

Limited-sample NMR using solenoidal microcoils, perfluorocarbon plugs, and capillary spinning

This study demonstrates three improvements to mass-limited NMR using solenoidal microcoils as detectors: (1) sample confinement using liquid perfluorocarbon plugs to increase the observe factor, (2) design and incorporation of a capillary spinner to improve spectral line widths, and (3) facile sample changing via the use of a capillary insert. The probe is constructed to spin a fused silica capillary of 530 microns i.d., 700 microns o.d. inside a solenoidal coil wound around a 0.8 mm i.d., 1 mm o.d. glass capillary. The smaller capillary contains the sample, and capillaries with different samples can be exchanged easily. In high-resolution limited sample microcoil NMR studies published thus far, the length of the sample plug has been 7-10 times the length of the solenoid to avoid line broadening from volume magnetic susceptibility (chi v) mismatches at both ends of the sample. This arrangement is not efficient since it places most of the sample volume outside of the coil observe volume. It is shown here that the observe factor cannot exceed 23% if the sample plug is bracketed by air, without substantial line broadening occurring. However, if the sample is bracketed by two liquid perfluorocarbon plugs, the observe factor can be increased to 70% while maintaining high spectral resolution. This is equivalent to improving the limit of detection by a factor of 3, or reducing the total data acquisition time for a given signal-to-noise by a factor of 9. It is also shown that, for the 440-nL sample plug used in this study (bracketed by the perflurocarbon plugs), sample spinning can improve the spectral resolution from 1.5 (nonspinning) to 0.6 Hz (spinning). This corresponds to a further improvement in the limit of detection of 2.5, or just over a factor of 6 decrease in data acquisition time.

An integrated nanoliter DNA analysis device

A device was developed that uses microfabricated fluidic channels, heaters, temperature sensors, and fluorescence detectors to analyze nanoliter-size DNA samples. The device is capable of measuring aqueous reagent and DNA-containing solutions, mixing the solutions together, amplifying or digesting the DNA to form discrete products, and separating and detecting those products. No external lenses, heaters, or mechanical pumps are necessary for complete sample processing and analysis. Because all of the components are made using conventional photolithographic production techniques, they operate as a single closed system. The components have the potential for assembly into complex, low-power, integrated analysis systems at low unit cost. The availability of portable, reliable instruments may facilitate the use of DNA analysis in applications such as rapid medical diagnostics and point-of-use agricultural testing.

Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules

New mapping approaches construct ordered restriction maps from fluorescence microscope images of individual, endonuclease-digested DNA molecules. In optical mapping, molecules are elongated and fixed onto derivatized glass surfaces, preserving biochemical accessibility and fragment order after enzymatic digestion. Measurements of relative fluorescence intensity and apparent length determine the sizes of restriction fragments, enabling ordered map construction without electrophoretic analysis. The optical mapping system reported here is based on our physical characterization of an effect using fluid flows developed within tiny, evaporating droplets to elongate and fix DNA molecules onto derivatized surfaces. Such evaporation-driven molecular fixation produces well elongated molecules accessible to restriction endonucleases, and notably, DNA polymerase I. We then developed the robotic means to grid DNA spots in well defined arrays that are digested and analyzed in parallel. To effectively harness this effect for high-throughput genome mapping, we developed: (i) machine vision and automatic image acquisition techniques to work with fixed, digested molecules within gridded samples, and (ii) Bayesian inference approaches that are used to analyze machine vision data, automatically producing high-resolution restriction maps from images of individual DNA molecules. The aggregate significance of this work is the development of an integrated system for mapping small insert clones allowing biochemical data obtained from engineered ensembles of individual molecules to be automatically accumulated and analyzed for map construction. These approaches are sufficiently general for varied biochemical analyses of individual molecules using statistically meaningful population sizes.