Modeling transthyretin (TTR) amyloid diseases, from monomer to amyloid fibrils.

ATTR amyloidosis is caused by deposition of large, insoluble aggregates (amyloid fibrils) of cross-ß-sheet TTR protein molecules on the intercellular surfaces of tissues. The process of amyloid formation from monomeric TTR protein molecules to amyloid deposits has not been fully characterized and is therefore modeled in this paper. Two models are considered: 1) TTR monomers in the blood spontaneously fold into a ß-sheet conformation, aggregate into short proto-fibrils that then circulate in the blood until they find a complementary tissue where the proto-fibrils accumulate to form the large, insoluble amyloid fibrils found in affected tissues. 2) TTR monomers in the native or ß-sheet conformation circulate in the blood until they find a tissue binding site and deposit in the tissue or tissues forming amyloid deposits in situ. These models only differ on where the selection for ß-sheet complementarity occurs, in the blood where wt-wt, wt-v, and v-v interactions determine selectivity, or on the tissue surface where tissue-wt and tissure-v interactions also determine selectivity. Statistical modeling in both cases thus involves selectivity in fibril aggregation and tissue binding. Because binding of protein molecules into fibrils and binding of fibrils to tissues occurs through multiple weak non-covalent bonds, strong complementarity between ß-sheet molecules and between fibrils and tissues is required to explain the insolubility and tissue selectivity of ATTR amyloidosis. Observation of differing tissue selectivity and thence disease phenotypes from either pure wildtype TTR protein or a mix of wildtype and variant molecules in amyloid fibrils evidences the requirement for fibril-tissue complementarity. Understanding the process that forms fibrils and binds fibrils to tissues may lead to new possibilities for interrupting the process and preventing or curing ATTR amyloidosis.

Comparison of the Dynamic Thermal Gradient to Temperature-Programmed Conditions in Gas Chromatography Using a Stochastic Transport Model.

This paper compares dynamic (i.e., temporally changing) thermal gradient gas chromatography (GC) to temperature-programmed GC using a previously published stochastic transport model to simulate peak characteristics for the separation of C12-C40 hydrocarbons. All comparisons are made using chromatographic conditions that give approximately equal analyte retention times (tR). As shown previously, a static thermal gradient does not improve resolution (Rs) equally for all analytes, which highlights the need for a dynamic thermal gradient. An optimal dynamic thermal gradient should result in constant analyte velocities at any instant in time for those analytes that are actively being separated (i.e., analytes that have low retention factors). The average separation temperature for each analyte is used to determine the thermal gradient profile at different times in the temperature ramp. Because many of the analytes require a similar thermal gradient profile when actively being separated, the thermal gradient profile in this study was held fixed; however, the temperature of the entire thermal gradient was raised over time. From the simulations performed in this study, optimized dynamic thermal gradient conditions are shown to improve Rs by up to 13% over comparative temperature-programmed conditions, even with a perfect injection (i.e., zero injection bandwidth). In the dynamic thermal gradient simulations, all analytes showed improvements in Rs along with slightly shorter tR values compared to simulations for traditional temperature-programmed conditions.

Comparison of Static Thermal Gradient to Isothermal Conditions in Gas Chromatography Using a Stochastic Transport Model.

This paper compares static (i.e., temporally unchanging) thermal gradient gas chromatography (GC) to isothermal GC using a stochastic transport model to simulate peak characteristics for the separation of C12-C14 hydrocarbons resulting from variations in injection bandwidth. All comparisons are made using chromatographic conditions that give approximately equal analyte retention times so that the resolution and number of theoretical plates can be clearly compared between simulations. Simulations show that resolution can be significantly improved using a linear thermal gradient along the entire column length. This is mainly achieved by partially compensating for loss in resolution from the increase in mobile phase velocity, which approximates an ideal, basic separation. The slope of the linear thermal gradient required to maximize resolution is a function of the retention parameters, which are specific to each analyte pair; a single static, thermal gradient will not affect all analytes equally. A static, non-linear thermal gradient that creates constant analyte velocities at all column locations provides the largest observed gains in resolution. From the simulations performed in this study, optimized linear thermal gradient conditions are shown to improve the resolution by as much as 8.8% over comparative isothermal conditions, even with a perfect injection (i.e., zero initial bandwidth).

Simulating Capillary Gas Chromatographic Separations including Thermal Gradient Conditions.

This article presents a method of simulating molecular transport in capillary gas chromatography (GC) applicable to isothermal, temperature-programmed, and thermal gradient conditions. The approach accounts for parameter differences that can occur across an analyte band including pressure, mobile phase velocity, temperature, and retention factor. The model was validated experimentally using a GC column comprised of microchannels in a stainless-steel plate capable of isothermal, temperature-programmed, and thermal gradient GC separations. The parameters governing retention and dispersion in the transport model were fitted with 12 experimental isothermal separations. The transport model was validated with experimental data for three analytes using four temperature-programmed and three thermal gradient GC separations. The simulated peaks (elution time and dispersion) give reasonable predictions of observed separations. The magnitudes of the maximum error between simulated peak elution time and experiment were 2.6 and 4.2% for temperature-programmed and thermal gradient GC, respectively. The magnitudes of the maximum error between the simulated peak width and experiment were 15.4 and 5.8% for temperature-programmed and thermal gradient GC, respectively. These relatively low errors give confidence that the model reflects the behavior of the transport processes and provides meaningful predictions for GC separations. This transport model allows for an evaluation of analyte separation characteristics of the analyte band at any position along the length of the GC column in addition to peak characteristics at the column exit. The transport model enables investigation of column conditions that influence separation behavior and opens exploration of optimal column design and heating conditions.

Transformation of matter in living organisms during growth and evolution.

Growth of an organism involves transformations of the state of matter from unstructured food or photosynthate into the highly organized matter in the living organism. Biological evolution involves random changes in the structure of DNA that lead to changes in the organization of the matter in an organism. Thermodynamic data show the organized biomass in living organisms has the same thermodynamic properties as a random mixture of the same elemental composition and is not in an energetically metastable, low entropy state. Therefore, the central thesis of this work is that building biological structures and organization from foodstuffs incurs no direct thermodynamic cost. The implication is that growth and evolution occur with little or no thermodynamic cost. In consequence, the fundamental difference between living biomass and lifeless organic sludge is in the information constraints that direct and govern the organization of the system. These constraints within a living organism override random processes to produce an organized distribution of biomass within the organism. Similarly, the information in DNA constrains the outcome of biological evolution across organisms within a population of a species in a predictable way that leads to convergent evolution. Although individuals and molecules act or are acted upon in a random manner, the outcome in a constrained system is predictable within an organism and across organisms. As a consequence evolution will produce similar outcomes at the macro level in similar environments. Stochastic determinism is proposed as a method that could be used to model convergent evolution.

Portable capillary liquid chromatography for pharmaceutical and illicit drug analysis.

A newly developed portable capillary liquid chromatograph was investigated for the separation of various pharmaceutical and illicit drug compounds. The system consists of two high-pressure syringe pumps capable of delivering capillary-scale flow rates at pressures up to 10 000 psi. Capillary liquid chromatography columns packed with sub-2 µm particles are housed in cartridges that can be inserted into the system and easily connected through high-pressure fluidic contact points by simply applying a specific, predetermined torque rather than using standard fittings and less precise sealing protocols. Several over-the-counter analgesic drug separations are demonstrated, along with a simple online measurement of tablet dissolution. Twenty illicit drug compounds were also separated across six targeted drug panels. The results described in this study demonstrate the capability of this compact liquid chromatography instrument to address several important drug-related applications while simplifying system operation, and greatly reducing solvent usage and waste generation essential for onsite analysis.

Stainless-Steel Column for Robust, High-Temperature Microchip Gas Chromatography.

This paper reports the first results of a robust, high-performance, stainless-steel microchip gas-chromatography (GC) column that is capable of analyzing complex real-world mixtures as well as operating at very high temperatures. Using a serpentine design, a 10 m column with an approximately semicircular cross-section with a 52 µm hydraulic diameter ( Dh) was produced in a 17 × 6.3 × 0.1 cm rectangular steel chip. The channels were produced using a multilayer-chemical-etch and diffusion-bonding process, and metal nuts were brazed onto the inlet and outlet ports allowing for column interfacing with ferrules and fused silica capillary tubing. After deactivating the metal surface, channels were statically coated with a ≈0.1 µm layer of 5% phenyl-1% vinyl-methylpolysiloxane (SE-54) stationary phase and cross-linked with dicumyl peroxide. By using n-tridecane ( n-C13) as a test analyte with a retention factor ( k) of 5, a total of 44 500 plates (≈4500 plates per meter) was obtained isothermally at 120 °C. The column was thermally stable to at least 350 °C, and rapid temperature programming (35 °C/min) was demonstrated for the boiling-point range from n-C5 to n-C44 (ASTM D2887 simulated-distillation standard). The column was also tested for separation of two complex mixtures: gasoline headspace and kerosene. These initial experiments demonstrate that the planar stainless-steel column with proper interfacing can be a viable alternative platform for portable, robust microchip GC that is capable of high-temperature operation for low-volatility-compound analysis.

Accounting for measurement error in log regression models with applications to accelerated testing.

In regression settings, parameter estimates will be biased when the explanatory variables are measured with error. This bias can significantly affect modeling goals. In particular, accelerated lifetime testing involves an extrapolation of the fitted model, and a small amount of bias in parameter estimates may result in a significant increase in the bias of the extrapolated predictions. Additionally, bias may arise when the stochastic component of a log regression model is assumed to be multiplicative when the actual underlying stochastic component is additive. To account for these possible sources of bias, a log regression model with measurement error and additive error is approximated by a weighted regression model which can be estimated using Iteratively Re-weighted Least Squares. Using the reduced Eyring equation in an accelerated testing setting, the model is compared to previously accepted approaches to modeling accelerated testing data with both simulations and real data.

Extending the upper temperature range of gas chromatography with all-silicon microchip columns using a heater/clamp assembly.

Miniaturization of gas chromatography (GC) instrumentation is of interest because it addresses current and future issues relating to compactness, portability and field application. While incremental advancements continue to be reported in GC with columns fabricated in microchips (referred to in this paper as "microchip columns"), the current performance is far from acceptable. This lower performance compared to conventional GC is due to factors such as pooling of the stationary phase in corners of non-cylindrical channels, adsorption of sensitive compounds on incompletely deactivated surfaces, shorter column lengths and less than optimum interfacing to injector and detector. In this work, a GC system utilizing microchip columns was developed that solves the latter challenge, i.e., microchip interfacing to injector and detector. A microchip compression clamp was constructed to heat the microchip (i.e., primary heater), and seal the injector and detector fused silica interface tubing to the inlet and outlet ports of the microchip channels with minimum extra-column dead volume. This clamp allowed occasional operation up to 375°C and routine operation up to 300°C. The compression clamp was constructed of a low expansion alloy, Kovar™, to minimize leaking due to thermal expansion mismatch at the interface during repeated thermal cycling, and it was tested over several months for more than one hundred injections without forming leaks. A 5.9m long microcolumn with rectangular cross section of 158µm×80µm, which approximately matches a 100µm i.d. cylindrical fused silica column, was fabricated in a silicon wafer using deep reactive ion etching (DRIE) and high temperature fusion bonding; finally, the channel was coated statically with a 1% vinyl, 5% phenyl, 94% methylpolysiloxane stationary phase. High temperature separations of C10-C40 n-alkanes and a commercial diesel sample were demonstrated using the system under both temperature programmed GC (TPGC) and thermal gradient GC (TGGC) conditions. TGGC analysis of a complex essential oil sample was also demonstrated. Addition of a secondary heater and polyimide insulation proved to be helpful in achieving the desired elution temperature without having to raise the primary heater temperature above 300°C for high boiling point compounds.

Dual-wavelength light-emitting diode-based ultraviolet absorption detector for nano-flow capillary liquid chromatography.

The design of a miniaturized LED-based UV-absorption detector was significantly improved for on-column nanoflow LC. The detector measures approximately 27mm×24mm×10mm and weighs only 30g. Detection limits down to the nanomolar range and linearity across 3 orders of magnitude were obtained using sodium anthraquinone-2-sulfonate as a test analyte. Using two miniaturized detectors, a dual-detector system was assembled containing 255nm and 275nm LEDs with only 216nL volume between the detectors A 100µm slit was used for on-column detection with a 150µm i.d. packed capillary column. Chromatographic separation of a phenol mixture was demonstrated using the dual-detector system, with each detector producing a unique chromatogram. Less than 6% variation in the ratios of absorbances measured at the two wavelengths for specific analytes was obtained across 3 orders of magnitude concentration, which demonstrates the potential of using absorption ratio measurements for target analyte detection. The dual-detector system was used for simple, but accurate, mobile phase flow rate measurement at the exit of the column. With a flow rate range from 200 to 2000nL/min, less than 3% variation was observed.

Discovery and Confirmation of Diagnostic Serum Lipid Biomarkers for Alzheimer's Disease Using Direct Infusion Mass Spectrometry.

Alzheimer's disease (AD) is a neurodegenerative disorder lacking early biochemical diagnosis and treatment. Lipids have been implicated in neurodegenerative disorders including AD. A shotgun lipidomic approach was undertaken to determine if lipid biomarkers exist that can discriminate AD cases from controls. The discovery study involved sera from 29 different stage AD cases and 32 controls. Lipid extraction was performed using organic solvent and the samples were directly infused into a time-of-flight mass spectrometer. Differences between AD cases and controls were detected with 87 statistically significant lipid candidate markers found. These potential lipid markers were reevaluated in a second confirmatory study involving 27 cases and 30 controls. Of the 87 candidates from the first study, 35 continued to be statistically significant in the second confirmatory set. Tandem MS studies were performed and almost all confirmed markers were characterized and classified. Using a Bayesian lasso probit regression model on the confirmed markers, a multi-marker set with AUC = 0.886 was developed comparing all stages of AD with controls. Additionally, using confirmed biomarkers, multi-marker sets with AUCs >0.90 were developed for each specific AD Clinical Dementia Rating versus controls, including the earliest stage of AD. More conservative and likely more realistic statistical analyses still found multi-marker sets that appeared useful in diagnosing AD. Finally, using ordinal modeling a set of markers was developed that staged AD accurately 70% of the time, p = 0.0079. These results suggest that these serum lipidomic biomarkers may help diagnose and perhaps even stage AD.

Compact Ultrahigh-Pressure Nanoflow Capillary Liquid Chromatograph.

A compact ultrahigh-pressure nanoflow liquid chromatograph (LC) was developed with the purpose in mind of creating a portable system that could be easily moved to various testing locations or placed in close proximity to other instruments for optimal coupling, such as with mass spectrometry (MS). The system utilized innovative nanoflow pumps integrated with a very low volume stop-flow injector and mixing tee. The system weighed only 5.9 kg (13 lbs) or 4.5 kg (10 lbs) without a controller and could hold up to 1100 bar (16000 psi) of pressure. The total volume pump capacity was 60 µL. In this study, the sample injection volume was determined by either a 60 nL internal sample groove machined in a high-pressure valve rotor or by a 1 µL external sample loop, although other sample grooves or loops could be selected. The gradient dwell volume was approximately 640 nL, which allowed significant reduction in sample analysis time. Gradient performance was evaluated by determining the gradient step accuracy. A low RSD (0.6%, n = 4) was obtained for day-to-day experiments. Linear gradient reproducibility was evaluated by separating a three-component polycyclic aromatic hydrocarbon mixture on a commercial 150 µm inner diameter capillary column packed with 1.7 µm particles. Good retention-time reproducibility (RSD < 0.17%) demonstrated that the pumping system could successfully generate ultrahigh pressures for use in capillary LC. The system was successfully coupled to an LTQ Orbitrap MS in a simple and efficient way; LC-MS of a trypsin-digested bovine serum albumin (BSA) sample provided narrow peaks, short dwell time, and good peptide coverage.

Global "omics" evaluation of human placental responses to preeclamptic conditions.

BACKGROUND: Preeclampsia (PE) is a leading cause of maternal death. Its cause is still debated but there is general agreement that the placenta plays a central role. Perhaps the most commonly proposed contributors to PE include placental hypoxia, oxidative stress, and increased proinflammatory cytokines. How the placenta responds to these abnormalities has been considered but not as part of a comprehensive analysis of low-molecular-weight biomolecules and their responses to these accepted PE conditions. OBJECTIVE: Using a peptidomic approach, we sought to identify a set of molecules exhibiting differential expression in consequence of provocative agents/chemical mediators of PE applied to healthy human placental tissue. STUDY DESIGN: Known PE conditions were imposed on normal placental tissue from 13 uncomplicated pregnancies and changes in the low-molecular-weight peptidome were evaluated. A t test was used to identify potential markers for each imposed stress. These markers were then submitted to a least absolute shrinkage and selection operator multinomial logistic regression model to identify signatures specific to each stressor. Estimates of model performance on external data were obtained through internal validation. RESULTS: A total of 146 markers were increased/decreased as a consequence of exposure to proposed mediators of PE. Of these 75 changed with hypoxia; 23 with hypoxia-reoxygenation/oxidative stress and 48 from exposure to tumor necrosis factor-α. These markers were chemically characterized using tandem mass spectrometry. Identification rates were: hypoxia, 34%; hypoxia-reoxygenation, 60%; and tumor necrosis factor-α, 50%. Least absolute shrinkage and selection operator modeling specified 16 markers that effectively distinguished all groups, ie, the 3 abnormal conditions and control. Bootstrap estimates of misclassification rates, multiclass area under the curve, and Brier score were 0.108, 0.944, and 0.160, respectively. CONCLUSION: Using this approach we found previously unknown molecular changes in response to individual PE conditions that allowed development biomolecular signatures for exposure to each accepted pathogenic condition.

Detection and confirmation of serum lipid biomarkers for preeclampsia using direct infusion mass spectrometry.

Despite substantial research, the early diagnosis of preeclampsia remains elusive. Lipids are now recognized to be involved in regulation and pathophysiology of some disease. Shotgun lipidomic studies were undertaken to determine whether serum lipid biomarkers exist that predict preeclampsia later in the same in pregnancy. A discovery study was performed using sera collected at 12-14 weeks pregnancy from 27 controls with uncomplicated pregnancies and 29 cases that later developed preeclampsia. Lipids were extracted and analyzed by direct infusion into a TOF mass spectrometer. MS signals, demonstrating apparent differences were selected, their abundances determined, and statistical differences tested. Statistically significant lipid markers were reevaluated in a second confirmatory study having 43 controls and 37 preeclampsia cases. Multi-marker combinations were developed using those lipid biomarkers confirmed in the second study. The initial study detected 45 potential preeclampsia markers. Of these, 23 markers continued to be statistically significant in the second confirmatory set. Most of these markers, representing several lipid classes, were chemically characterized, typically providing lipid class and potential molecular components using MS(2) Several multi-marker panels with areas under the curve >0.85 and high predictive values were developed. Developed panels of serum lipidomic biomarkers appear to be able to identify most women at risk for preeclampsia in a given pregnancy at 12-14 weeks gestation.

Hand-portable liquid chromatographic instrumentation.

Over the last four decades, liquid chromatography (LC) has experienced an evolution to smaller columns and particles, new stationary phases and low flow rate instrumentation. However, the development of person-portable LC has not followed, mainly due to difficulties encountered in miniaturizing pumps and detectors, and in reducing solvent consumption. The recent introduction of small, non-splitting pumping systems and UV-absorption detectors for use with capillary columns has finally provided miniaturized instrumentation suitable for high-performance hand-portable LC. Fully integrated microfabricated LC still remains a significant challenge. Ion chromatography (IC) has been successfully miniaturized and applied for field analysis; however, applications are mostly limited to inorganic and small organic ions. This review covers advancements that make possible more rapid expansion of portable forms of LC and IC.

Hand-Portable Gradient Capillary Liquid Chromatography Pumping System.

In this work, a novel splitless nanoflow gradient generator integrated with a stop-flow injector was developed and evaluated using an on-column UV-absorption detector. The gradient pumping system consisted of two nanoflow pumps controlled by micro stepper motors, a mixer connected to a serpentine tube, and a high-pressure valve. The gradient system weighed only 4 kg (9 lbs) and could generate up to 55 MPa (8000 psi) pressure. The system could operate using a 24 V DC battery and required 1.2 A for operation. The total volume capacity of the pump was 74 µL, and a sample volume of 60 nL could be injected. The system provided accurate nanoflow rates as low as 10 nL/min without employing a splitter, making it ideal for capillary column use. The gradient dwell volume was calculated to be 1.3 µL, which created a delay of approximately 4 min with a typical flow rate of 350 nL/min. Gradient performance was evaluated for gradient step accuracy, and excellent reproducibility was obtained in day-to-day experiments (RSD < 1.2%, n = 4). Linear gradient reproducibility was tested by separating a three-component pesticide mixture on a poly(ethylene glycol) diacrylate (PEGDA) monolithic column. The retention time reproducibility was very good in run-to-run experiments (RSD < 1.42%, n = 4). Finally, excellent separation of five phenols was demonstrated using the nanoflow gradient system.

LED-based UV absorption detector with low detection limits for capillary liquid chromatography.

A 260 nm deep UV LED-based absorption detector with low detection limits was developed and integrated with a small nanoflow pumping system. The detector is small in size (5.2 × 3.0 cm) and weighs only 85 g (without electronics). This detector was specifically designed and optimized for on-column detection to minimize extra-column band broadening. No optical reference was included due to the low drift in the signal. Two ball lenses, one of which was integrated with the LED, were used to increase light throughput through the capillary column. Stray light was minimized by the use of a band-pass filter and an adjustable slit. Signals down to the parts per billion level (nanomolar) were easily detected with a short-term noise level of 4.4 µAU, confirming a low limit of detection and low noise. The detection limit for adenosine-5'-monophosphate was 230 times lower than any previously reported values. Good linearities (3 orders of magnitude) were obtained using sodium anthraquinone-2-sulfonate, adenosine-5'-monophosphate, dl-tryptophan, and phenol. The LC system was demonstrated by performing isocratic separation of phenolic compounds using a monolithic capillary column (16.5 cm × 150 µm i.d.) synthesized from poly(ethylene glycol) diacrylate.

Moving thermal gradients in gas chromatography.

This paper examines the separation effects of a moving thermal gradient on a chromatographic column in gas chromatography. This movement of the gradient has a focusing effect on the analyte bands, limiting band broadening in the column. Here we examine the relationship between the slope of this gradient, the velocity of the gradient and the resulting band width. Additionally we examine how transport of analytes along the column at their analyte specific constant temperatures, determined by the gradient slope and velocity, affects resolution. This examination is based primarily on a theoretical model of partitioning and transport of analyte under low concentration conditions. Preliminary predictions indicate that analytes reach near constant temperatures, relative positions and resolutions in less than 100cm of column transport. Use of longer columns produces very little improvement in resolution for any fixed slope. Properties of the thermal gradient determine a fixed solute band width for each analyte. These widths are nearly reached within the first 40-70cm, after which little broadening or narrowing of the bands occur. The focusing effect of the thermal gradient corrects for broad injections, reduces effects of irregular stationary phase coatings and can be used with short columns for fast analysis. Thermal gradient gas chromatographic instrumentation was constructed and used to illustrate some characteristics predicted from the theoretical results.

Axial thermal gradients in microchip gas chromatography.

Fabrication technologies for microelectromechanical systems (MEMS) allow miniaturization of conventional benchtop gas chromatography (GC) to portable, palm-sized microfabricated GC (µGC) devices, which are suitable for on-site chemical analysis and remote sensing. The separation performance of µGC systems, however, has not been on par with conventional GC. Column efficiency, peak symmetry and resolution are often compromised by column defects and non-ideal injections. The relatively low performance of µGC devices has impeded their further commercialization and broader application. In this work, the separation performance of µGC columns was improved by incorporating thermal gradient gas chromatography (TGGC). The analysis time was ∼20% shorter for TGGC separations compared to conventional temperature-programmed GC (TPGC) when a wide sample band was introduced into the column. Up to 50% reduction in peak tailing was observed for polar analytes, which improved their resolution. The signal-to-noise ratios (S/N) of late-eluting peaks were increased by 3-4 fold. The unique focusing effect of TGGC overcomes many of the previous shortcomings inherent in µGC analyses.