Validation of a non-invasive prenatal test for fetal RhD, C, c, E, K and Fya antigens.

We developed and validated a next generation sequencing-(NGS) based NIPT assay using quantitative counting template (QCT) technology to detect RhD, C, c, E, K (Kell), and Fya (Duffy) fetal antigen genotypes from maternal blood samples in the ethnically diverse U.S. population. Quantitative counting template (QCT) technology is utilized to enable quantification and detection of paternally derived fetal antigen alleles in cell-free DNA with high sensitivity and specificity. In an analytical validation, fetal antigen status was determined for 1061 preclinical samples with a sensitivity of 100% (95% CI 99-100%) and specificity of 100% (95% CI 99-100%). Independent analysis of two duplicate plasma samples was conducted for 1683 clinical samples, demonstrating precision of 99.9%. Importantly, in clinical practice the no-results rate was 0% for 711 RhD-negative non-alloimmunized pregnant people and 0.1% for 769 alloimmunized pregnancies. In a clinical validation, NIPT results were 100% concordant with corresponding neonatal antigen genotype/serology for 23 RhD-negative pregnant individuals and 93 antigen evaluations in 30 alloimmunized pregnancies. Overall, this NGS-based fetal antigen NIPT assay had high performance that was comparable to invasive diagnostic assays in a validation study of a diverse U.S. population as early as 10 weeks of gestation, without the need for a sample from the biological partner. These results suggest that NGS-based fetal antigen NIPT may identify more fetuses at risk for hemolytic disease than current clinical practice, which relies on paternal genotyping and invasive diagnostics and therefore is limited by adherence rates and incorrect results due to non-paternity. Clinical adoption of NIPT for the detection of fetal antigens for both alloimmunized and RhD-negative non-alloimmunized pregnant individuals may streamline care and reduce unnecessary treatment, monitoring, and patient anxiety.

FishShapes v1: Functionally relevant measurements of teleost shape and size on three dimensions.

Teleost fishes account for 96% of all fish species and exhibit a spectacular variety of body forms. Teleost lineages range from deep bodied to elongate (e.g., eels, needlefish), laterally compressed (e.g., ribbonfish) to globular (e.g., pufferfish), and include uniquely shaped lineages such as seahorses, flatfishes, and ocean sunfishes. Adaptive body shape convergence within fishes has long been hypothesized but the nature of the relationships between fish form and ecological and environmental variables remain largely unknown at the macroevolutionary scale. To facilitate the investigation of the interacting factors influencing teleost body shape evolution we measured eight functionally relevant linear traits on adult-sized specimens along with specimen mass. Linear measurements of standard length, maximum body depth, maximum fish width, lower jaw length, mouth width, head depth, minimum caudal peduncle depth, and minimum caudal peduncle width were taken in millimeters with calipers, or tape measures for oversized specimens. We measured these traits on a total of 16,523 specimens (1-3 specimens per species) at the Smithsonian National Museum of Natural History and took approximately 7000 person hours of data collection to complete. The data went through a three-step error-checking process to clean and validate the data and then species averages were calculated. We present the complete specimen data set, which encompasses approximately one-fifth of extant teleost species diversity, spanning ~90% of teleost families and ~96% of orders. The species and family names are compatible with the taxonomy used by FishBase and the order information with the phylogenetically informed taxonomy of Betancur-R and colleagues published in 2014. This dataset is licensed under Creative Commons CC0 1.0 Universal (CC0 1.0) but please cite this paper when using the data or a subset of it.

A novel high-throughput molecular counting method with single base-pair resolution enables accurate single-gene NIPT.

Next-generation DNA sequencing is currently limited by an inability to accurately count the number of input DNA molecules. Molecular counting is particularly needed when accurate quantification is required for diagnostic purposes, such as in single gene non-invasive prenatal testing (sgNIPT) and liquid biopsy. We developed Quantitative Counting Template (QCT) molecular counting to reconstruct the number of input DNA molecules using sequencing data. We then used QCT molecular counting to develop sgNIPTs of sickle cell disease, cystic fibrosis, spinal muscular atrophy, alpha-thalassemia, and beta-thalassemia. The analytical sensitivity and specificity of sgNIPT was >98% and >99%, respectively. Validation of sgNIPTs was further performed with maternal blood samples collected during pregnancy, and sgNIPTs were 100% concordant with newborn follow-up.

Rewiring bacterial two-component systems by modular DNA-binding domain swapping.

Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways and valuable sensors for synthetic biology. However, most TCSs remain uncharacterized or difficult to harness for applications. Major challenges are that many TCS output promoters are unknown, subject to cross-regulation, or silent in heterologous hosts. Here, we demonstrate that the two largest families of response regulator DNA-binding domains can be interchanged with remarkable flexibility, enabling the corresponding TCSs to be rewired to synthetic output promoters. We exploit this plasticity to eliminate cross-regulation, un-silence a gram-negative TCS in a gram-positive host, and engineer a system with over 1,300-fold activation. Finally, we apply DNA-binding domain swapping to screen uncharacterized Shewanella oneidensis TCSs in Escherichia coli, leading to the discovery of a previously uncharacterized pH sensor. This work should accelerate fundamental TCS studies and enable the engineering of a large family of genetically encoded sensors with diverse applications.

Phosphatase activity tunes two-component system sensor detection threshold.

Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways in biology, and a major source of sensors for biotechnology. However, the input concentrations to which biosensors respond are often mismatched with application requirements. Here, we utilize a mathematical model to show that TCS detection thresholds increase with the phosphatase activity of the sensor histidine kinase. We experimentally validate this result in engineered Bacillus subtilis nitrate and E. coli aspartate TCS sensors by tuning their detection threshold up to two orders of magnitude. We go on to apply our TCS tuning method to recently described tetrathionate and thiosulfate sensors by mutating a widely conserved residue previously shown to impact phosphatase activity. Finally, we apply TCS tuning to engineer B. subtilis to sense and report a wide range of fertilizer concentrations in soil. This work will enable the engineering of tailor-made biosensors for diverse synthetic biology applications.

Engineering Diagnostic and Therapeutic Gut Bacteria.

Genetically engineered bacteria have the potential to diagnose and treat a wide range of diseases linked to the gastrointestinal tract, or gut. Such engineered microbes will be less expensive and invasive than current diagnostics and more effective and safe than current therapeutics. Recent advances in synthetic biology have dramatically improved the reliability with which bacteria can be engineered with the sensors, genetic circuits, and output (actuator) genes necessary for diagnostic and therapeutic functions. However, to deploy such bacteria in vivo, researchers must identify appropriate gut-adapted strains and consider performance metrics such as sensor detection thresholds, circuit computation speed, growth rate effects, and the evolutionary stability of engineered genetic systems. Other recent reviews have focused on engineering bacteria to target cancer or genetically modifying the endogenous gut microbiota in situ. Here, we develop a standard approach for engineering "smart probiotics," which both diagnose and treat disease, as well as "diagnostic gut bacteria" and "drug factory probiotics," which perform only the former and latter function, respectively. We focus on the use of cutting-edge synthetic biology tools, gut-specific design considerations, and current and future engineering challenges.

An open-hardware platform for optogenetics and photobiology.

In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under $400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.

Understanding the Surface Hopping View of Electronic Transitions and Decoherence.

We present a current, up-to-date review of the surface hopping methodology for solving nonadiabatic problems, 25 years after Tully published the fewest switches surface hopping algorithm. After reviewing the original motivation for and failures of the algorithm, we give a detailed examination of modern advances, focusing on both theoretical and practical issues. We highlight how one can partially derive surface hopping from the Schrödinger equation in the adiabatic basis, how one can change basis within the surface hopping algorithm, and how one should understand and apply the notions of decoherence and wavepacket bifurcation. The question of time reversibility and detailed balance is also examined at length. Recent applications to photoexcited conjugated polymers are discussed briefly.

FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units.

Flow cytometry is widely used to measure gene expression and other molecular biological processes with single cell resolution via fluorescent probes. Flow cytometers output data in arbitrary units (a.u.) that vary with the probe, instrument, and settings. Arbitrary units can be converted to the calibrated unit molecules of equivalent fluorophore (MEF) using commercially available calibration particles. However, there is no convenient, nonproprietary tool available to perform this calibration. Consequently, most researchers report data in a.u., limiting interpretation. Here, we report a software tool named FlowCal to overcome current limitations. FlowCal can be run using an intuitive Microsoft Excel interface, or customizable Python scripts. The software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Additionally, FlowCal automatically gates data, calculates common statistics, and produces publication quality plots. We validate FlowCal by calibrating a.u. measurements of E. coli expressing superfolder GFP (sfGFP) collected at 10 different detector sensitivity (gain) settings to a single MEF value. Additionally, we reduce day-to-day variability in replicate E. coli sfGFP expression measurements due to instrument drift by 33%, and calibrate S. cerevisiae Venus expression data to MEF units. Finally, we demonstrate a simple method for using FlowCal to calibrate fluorescence units across different cytometers. FlowCal should ease the quantitative analysis of flow cytometry data within and across laboratories and facilitate the adoption of standard fluorescence units in synthetic biology and beyond.

The requisite electronic structure theory to describe photoexcited nonadiabatic dynamics: nonadiabatic derivative couplings and diabatic electronic couplings.

Electronically photoexcited dynamics are complicated because there are so many different relaxation pathways: fluorescence, phosphorescence, radiationless decay, electon transfer, etc. In practice, to model photoexcited systems is a very difficult enterprise, requiring accurate and very efficient tools in both electronic structure theory and nonadiabatic chemical dynamics. Moreover, these theoretical tools are not traditional tools. On the one hand, the electronic structure tools involve couplings between electonic states (rather than typical single state energies and gradients). On the other hand, the dynamics tools involve propagating nuclei on multiple potential energy surfaces (rather than the usual ground state dynamics). In this Account, we review recent developments in electronic structure theory as directly applicable for modeling photoexcited systems. In particular, we focus on how one may evaluate the couplings between two different electronic states. These couplings come in two flavors. If we order states energetically, the resulting adiabatic states are coupled via derivative couplings. Derivative couplings capture how electronic wave functions change as a function of nuclear geometry and can usually be calculated with straightforward tools from analytic gradient theory. One nuance arises, however, in the context of time-dependent density functional theory (TD-DFT): how do we evaluate derivative couplings between TD-DFT excited states (which are tricky, because no wave function is available)? This conundrum was recently solved, and we review the solution below. We also discuss the solution to a second, pesky problem of origin dependence, whereby the derivative couplings do not (strictly) satisfy translation variance, which can lead to a lack of momentum conservation. Apart from adiabatic states, if we order states according to their electronic character, the resulting diabatic states are coupled via electronic or diabatic couplings. The couplings between diabatic states |ΞA⟩ and |ΞB⟩ are just the simple matrix elements, ⟨ΞA|H|ΞB⟩. A difficulty arises, however, because constructing exactly diabatic states is formally impossible and constructing quasi-diabatic states is not unique. To that end, we review recent advances in localized diabatization, which is one approach for generating adiabatic-to-diabatic (ATD) transformations. We also highlight outstanding questions in the arena of diabatization, especially how to generate multiple globally stable diabatic surfaces.

Surface hopping outperforms secular Redfield theory when reorganization energies range from small to moderate (and nuclei are classical).

We evaluate the accuracy of Tully's surface hopping algorithm for the spin-boson model in the limit of small to moderate reorganization energy. We calculate transition rates between diabatic surfaces in the exciton basis and compare against exact results from the hierarchical equations of motion; we also compare against approximate rates from the secular Redfield equation and Ehrenfest dynamics. We show that decoherence-corrected surface hopping performs very well in this regime, agreeing with secular Redfield theory for very weak system-bath coupling and outperforming secular Redfield theory for moderate system-bath coupling. Surface hopping can also be extended beyond the Markovian limits of standard Redfield theory. Given previous work [B. R. Landry and J. E. Subotnik, J. Chem. Phys. 137, 22A513 (2012)] that establishes the accuracy of decoherence-corrected surface-hopping in the Marcus regime, this work suggests that surface hopping may well have a very wide range of applicability.

Can surface hopping sans decoherence recover Marcus theory? Understanding the role of friction in a surface hopping view of electron transfer.

We compare the dynamics of Fewest Switches Surface Hopping (FSSH) in different parameter regimes of the spin-boson model. We show that for exceptional regions of the spin-boson parameter space, FSSH dynamics are in fact time-reversible. In these rare instances, FSSH does recover the correct Marcus rate scaling (as a function of diabatic coupling) without the addition of decoherence. In regions where dynamics are irreversible, however, FSSH does not recover the correct Marcus rate scaling. Finally, by comparing the friction dependence of rates predicted by various decoherence schemes to an analytic result by Zusman, we provide yet more evidence that the method of introducing decoherence has a qualitative effect on the accuracy of results and this effect must be treated carefully.

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals.

Gene circuits are dynamical systems that regulate cellular behaviors, often using protein signals as inputs and outputs. Here we have developed an optogenetic 'function generator' method for programming tailor-made gene expression signals in live bacterial cells. We designed precomputed light sequences based on experimentally calibrated mathematical models of light-switchable two-component systems and used them to drive intracellular protein levels to match user-defined reference time courses. We used this approach to generate accelerated and linearized dynamics, sinusoidal oscillations with desired amplitudes and periods, and a complex waveform, all with unprecedented accuracy and precision. We also combined the function generator with a dual fluorescent protein reporter system, analogous to a dual-channel oscilloscope, to reveal that a synthetic repressible promoter linearly transforms repressor signals with an approximate 7-min delay. Our approach will enable a new generation of dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the predictive design and rigorous understanding of biological systems.

Quantifying the Lifetime of Triplet Energy Transfer Processes in Organic Chromophores: A Case Study of 4-(2-Naphthylmethyl)benzaldehyde.

We simulate the dynamics of triplet-triplet energy transfer in a donor-bridge-acceptor system [4-(2-naphthylmethyl)benzaldehyde] with surface hopping, using electronic energies, gradients, and derivative couplings that are calculated on the fly. Using Boys localization to diabatize electronic states, we calculate energy transfer rates that agree favorably with experiment. The atomistic nature of our dynamical investigation produces several unique insights into this energy transfer reaction including an approximation of the decoherence time for the energy transfer process and the observation that the reaction pathway passes through a conical intersection.

Communication: The correct interpretation of surface hopping trajectories: how to calculate electronic properties.

In a recent paper, we presented a road map for how Tully's fewest switches surface hopping (FSSH) algorithm can be derived, under certain circumstances, from the mixed quantum-classical Liouville equation. In this communication, we now demonstrate how this new interpretation of surface hopping can yield significantly enhanced results for electronic properties in nonadiabatic calculations. Specifically, we calculate diabatic populations for the spin-boson problem using FSSH trajectories. We show that, for some Hamiltonians, without changing the FSSH algorithm at all but rather simply reinterpreting the ensemble of surface hopping trajectories, we recover excellent results and remove any and all ambiguity about the initial condition problem.

Can we derive Tully's surface-hopping algorithm from the semiclassical quantum Liouville equation? Almost, but only with decoherence.

In this article, we demonstrate that Tully's fewest-switches surface hopping (FSSH) algorithm approximately obeys the mixed quantum-classical Liouville equation (QCLE), provided that several conditions are satisfied--some major conditions, and some minor. The major conditions are: (1) nuclei must be moving quickly with large momenta; (2) there cannot be explicit recoherences or interference effects between nuclear wave packets; (3) force-based decoherence must be added to the FSSH algorithm, and the trajectories can no longer rigorously be independent (though approximations for independent trajectories are possible). We furthermore expect that FSSH (with decoherence) will be most robust when nonadiabatic transitions in an adiabatic basis are dictated primarily by derivative couplings that are presumably localized to crossing regions, rather than by small but pervasive off-diagonal force matrix elements. In the end, our results emphasize the strengths of and possibilities for the FSSH algorithm when decoherence is included, while also demonstrating the limitations of the FSSH algorithm and its inherent inability to follow the QCLE exactly.

Use of degradation tags to control protein levels in the Cyanobacterium Synechocystis sp. Strain PCC 6803.

We generated a collection of ssrA-based C-terminal protein degradation tags with different degradation strengths. The steady-state fluorescence levels of different enhanced yellow fluorescent protein (eYFP) tag variants in a Synechocystis sp. indicated a tunable range from 1% to 50% of untagged eYFP.

How to recover Marcus theory with fewest switches surface hopping: add just a touch of decoherence.

We present a slightly improved version of our augmented fewest switches surface hopping (A-FSSH) algorithm and apply it to the calculation of transition rates between diabatic electronic states within the spin-boson model. We compare A-FSSH rates with (i) Marcus rates from the golden rule, (ii) Tully-style FSSH rates, and (iii) FSSH rates using a simple, intuitive decoherence criterion. We show that unlike FSSH, A-FSSH recovers the correct scaling with diabatic coupling (quadratic in V) as well as the lack of dependence on harmonic frequency ω for small enough values of ω and large enough temperatures.

Communication: Standard surface hopping predicts incorrect scaling for Marcus' golden-rule rate: the decoherence problem cannot be ignored.

We evaluate the accuracy of Tully's surface hopping algorithm for the spin-boson model for the case of a small diabatic coupling parameter (V). We calculate the transition rates between diabatic surfaces, and we compare our results to the expected Marcus rates. We show that standard surface hopping yields an incorrect scaling with diabatic coupling (linear in V), which we demonstrate is due to an incorrect treatment of decoherence. By modifying standard surface hopping to include decoherence events, we recover the correct scaling (~V(2)).