Antimalarial Dibenzannulated Medium-Ring Keto Lactams

We discovered dibenzannulated medium-ring keto lactams (11,12-dihydro-5H-dibenzo[b,g]azonine-6,13-diones) as a new antimalarial chemotype. Most of these had chromatographic LogD7.4 values ranging from <0 to 3 and good kinetic solubilities (12.5 to >100 μg/mL at pH 6.5). The more polar compounds in the series (LogD7.4 values of <2) had the best metabolic stability (CLint values of <50 μL/min/mg protein in human liver microsomes). Most of the compounds had relatively low cytotoxicity, with IC50 values >30 μM, and there was no correlation between antiplasmodial activity and cytotoxicity. The four most potent compounds had Plasmodium falciparum IC50 values of 4.2 to 9.4 nM and in vitro selectivity indices of 670 to >12,000. They were more than 4 orders-of-magnitude less potent against three other protozoal pathogens (Trypanosoma brucei rhodesiense, Trypanosoma cruzi, and Leishmania donovani) but did have relatively high potency against Toxoplasma gondii, with IC50 values ranging from 80 to 200 nM. These keto lactams are converted into their poorly soluble 4(1H)-quinolone transannular condensation products in vitro in culture medium and in vivo in mouse blood. The similar antiplasmodial potencies of three keto lactam-quinolone pairs suggest that the quinolones likely contribute to the antimalarial activity of the lactams.

High-sensitivity electronic Stark spectrometer featuring a laser-driven light source

We report developmental details of a high-sensitivity Stark absorption spectrometer featuring a laser-driven light source. The light source exhibits intensity fluctuations of ∼0.3% over timescales ranging from 1 min to 12 h, minimal drift (≤0.1%/h), and very little 1/f noise at frequencies greater than 200 Hz, which are comparable to or better than an arc-driven light source. Additional features of the spectrometer include balanced detection with multiplex sampling, which yielded lower noise in A, and constant wavelength or wavenumber (energy) spectral bandpass modes. We achieve noise amplitudes of ∼7 × 10-4 and ∼6 × 10-6 in measurements of single A and ΔA spectra (with 92 data points) taking ∼7 and ∼19 min, respectively.

Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes

Aggregates of conjugated organic molecules (i.e., dyes) may exhibit relatively large one- and two-exciton interaction energies, which has motivated theoretical studies on their potential use in quantum information science (QIS). In practice, one way of realizing large one- and two-exciton interaction energies is by maximizing the transition dipole moment (μ) and difference static dipole moment (Δd) of the constituent dyes. In this work, we characterized the electronic structure and excited-state dynamics of monomers and aggregates of four asymmetric polymethine dyes templated via DNA. Using steady-state and time-resolved absorption and fluorescence spectroscopy along with quantum-chemical calculations, we found the asymmetric polymethine dye monomers exhibited a large μ, an appreciable Δd, and a long excited-state lifetime (τ_p). We formed dimers of all four dyes and observed that one dye, Dy 754, displayed the strongest propensity for aggregation and exciton delocalization. Motivated by these results, we undertook a more comprehensive survey of Dy 754 dimer and tetramer aggregates using steady-state absorption and circular dichroism spectroscopy. Modeling these spectra revealed an appreciable excitonic hopping parameter (J). Lastly, we used femtosecond transient absorption spectroscopy to characterize τ_p of the dimer and tetramer, which we observed to be exceedingly short. This work revealed that asymmetric polymethine dyes exhibited μ, Δd, monomer τ_p, and J values promising for QIS; however, further work is needed to overcome excited-state quenching and achieve long aggregate τ_p.

Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines

Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (μ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.

Queueing theory model of mTOR complexes' impact on Akt-mediated adipocytes response to insulin

A queueing theory based model of mTOR complexes impact on Akt-mediated cell response to insulin is presented in this paper. The model includes several aspects including the effect of insulin on the transport of glucose from the blood into the adipocytes with the participation of GLUT4, and the role of the GAPDH enzyme as a regulator of mTORC1 activity. A genetic algorithm was used to optimize the model parameters. It can be observed that mTORC1 activity is related to the amount of GLUT4 involved in glucose transport. The results show the relationship between the amount of GAPDH in the cell and mTORC1 activity. Moreover, obtained results suggest that mTORC1 inhibitors may be an effective agent in the fight against type 2 diabetes. However, these results are based on theoretical knowledge and appropriate experimental tests should be performed before making firm conclusions.

Atomic Force Microscopy Cantilever-Based Nanoindentation: Mechanical Property Measurements at the Nanoscale in Air and Fluid

An atomic force microscope (AFM) fundamentally measures the interaction between a nanoscale AFM probe tip and the sample surface. If the force applied by the probe tip and its contact area with the sample can be quantified, it is possible to determine the nanoscale mechanical properties (e.g., elastic or Young's modulus) of the surface being probed. A detailed procedure for performing quantitative AFM cantilever-based nanoindentation experiments is provided here, with representative examples of how the technique can be applied to determine the elastic moduli of a wide variety of sample types, ranging from kPa to GPa. These include live mesenchymal stem cells (MSCs) and nuclei in physiological buffer, resin-embedded dehydrated loblolly pine cross-sections, and Bakken shales of varying composition. Additionally, AFM cantilever-based nanoindentation is used to probe the rupture strength (i.e., breakthrough force) of phospholipid bilayers. Important practical considerations such as method choice and development, probe selection and calibration, region of interest identification, sample heterogeneity, feature size and aspect ratio, tip wear, surface roughness, and data analysis and measurement statistics are discussed to aid proper implementation of the technique. Finally, co-localization of AFM-derived nanomechanical maps with electron microscopy techniques that provide additional information regarding elemental composition is demonstrated.

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm^-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.

Electrochemically induced amorphous-to-rock-salt phase transformation in niobium oxide electrode for Li-ion batteries

Intercalation-type metal oxides are promising negative electrode materials for safe rechargeable lithium-ion batteries due to the reduced risk of Li plating at low voltages. Nevertheless, their lower energy and power density along with cycling instability remain bottlenecks for their implementation, especially for fast-charging applications. Here, we report a nanostructured rock-salt Nb₂O₅ electrode formed through an amorphous-to-crystalline transformation during repeated electrochemical cycling with Li⁺. This electrode can reversibly cycle three lithiums per Nb₂O₅, corresponding to a capacity of 269 mAh g^-1 at 20 mA g^-1, and retains a capacity of 191 mAh g^-1 at a high rate of 1 A g^-1. It exhibits superb cycling stability with a capacity of 225 mAh g^-1 at 200 mA g^-1 for 400 cycles, and a Coulombic efficiency of 99.93%. We attribute the enhanced performance to the cubic rock-salt framework, which promotes low-energy migration paths. Our work suggests that inducing crystallization of amorphous nanomaterials through electrochemical cycling is a promising avenue for creating unconventional high-performance metal oxide electrode materials.

Co-localizing Kelvin Probe Force Microscopy with Other Microscopies and Spectroscopies: Selected Applications in Corrosion Characterization of Alloys

Kelvin probe force microscopy (KPFM), sometimes referred to as surface potential microscopy, is the nanoscale version of the venerable scanning Kelvin probe, both of which measure the Volta potential difference (VPD) between an oscillating probe tip and a sample surface by applying a nulling voltage equal in magnitude but opposite in sign to the tip-sample potential difference. By scanning a conductive KPFM probe over a sample surface, nanoscale variations in surface topography and potential can be mapped, identifying likely anodic and cathodic regions, as well as quantifying the inherent material driving force for galvanic corrosion. Subsequent co-localization of KPFM Volta potential maps with advanced scanning electron microscopy (SEM) techniques, including back scattered electron (BSE) images, energy dispersive spectroscopy (EDS) elemental composition maps, and electron backscattered diffraction (EBSD) inverse pole figures can provide further insight into structure-property-performance relationships. Here, the results of several studies co-localizing KPFM with SEM on a wide variety of alloys of technological interest are presented, demonstrating the utility of combining these techniques at the nanoscale to elucidate corrosion initiation and propagation. Important points to consider and potential pitfalls to avoid in such investigations are also highlighted: in particular, probe calibration and the potential confounding effects on the measured VPDs of the testing environment and sample surface, including ambient humidity (i.e., adsorbed water), surface reactions/oxidation, and polishing debris or other contaminants. Additionally, an example is provided of co-localizing a third technique, scanning confocal Raman microscopy, to demonstrate the general applicability and utility of the co-localization method to provide further structural insight beyond that afforded by electron microscopy-based techniques.

Characterizing Mode Anharmonicity and Huang-Rhys Factors Using Models of Femtosecond Coherence Spectra

Femtosecond laser pulses readily produce coherent quantum beats in transient-absorption spectra. These oscillatory signals often arise from molecular vibrations and therefore may contain information about the excited-state potential energy surface near the Franck-Condon region. Here, by fitting the measured spectra of two laser dyes to microscopic models of femtosecond coherence spectra (FCS) arising from molecular vibrations, we classify coherent quantum-beat signals as fundamentals or overtones and quantify their Huang-Rhys factors and anharmonicity values. We discuss the extracted Huang-Rhys factors in the context of quantum-chemical computations. This work solidifies the use of FCS for analysis of coherent quantum beats arising from molecular vibrations, which will aid studies of molecular aggregates and photosynthetic proteins.

Mouse splenocyte enrichment strategies via negative selection for broadened single-cell transcriptomics

Mammalian splenic tissue is rich in functional immune cells, primarily lymphocytes which can mask low-abundance populations in downstream analyses. This protocol enriches minority immune cell populations from mouse spleen via immunomagnetic negative depletion to generate an untouched enriched cell fraction. Enriched cells are then spiked with untouched splenocytes in a controlled repopulation, validated by flow cytometry and results in a single-cell transcriptomic clustering analysis with a broadened cellular landscape.

Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates

Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble "transverse" and "adjacent" heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting dyes and fluorescence quenching, while the adjacent heterodimers exhibit optical properties consistent with nonexcitonically interacting dyes and disproportionately large Cy5.5 emission, suggestive of energy transfer between dyes. We use transient absorption spectroscopy to show that quenching in the transverse heterodimer occurs via rapid nonradiative decay to the ground state (∼31 ps) and that in the adjacent heterodimer rapid energy transfer from Cy5 to Cy5.5 (∼420 fs) is followed by Cy5.5 excited-state relaxation (∼700 ps). Accessing such drastically different photophysics, which may be tuned on demand for different target applications, highlights the utility of DNA as a template for dye aggregation.

A Comparison of Solid Electrolyte Interphase Formation and Evolution on Highly Oriented Pyrolytic and Disordered Graphite Negative Electrodes in Lithium-Ion Batteries

The presence and stability of solid electrolyte interphase (SEI) on graphitic electrodes is vital to the performance of lithium-ion batteries (LIBs). However, the formation and evolution of SEI remain the least understood area in LIBs due to its dynamic nature, complexity in chemical composition, heterogeneity in morphology, as well as lack of reliable in situ/operando techniques for accurate characterization. In addition, chemical composition and morphology of SEI are not only affected by the choice of electrolyte, but also by the nature of the electrode surface. While introduction of defects into graphitic electrodes has promoted their electrochemical properties, how such structural defects influence SEI formation and evolution remains an open question. Here, utilizing nondestructive operando electrochemical atomic force microscopy (EChem-AFM) the dynamic SEI formation and evolution on a pair of representative graphitic materials with and without defects, namely, highly oriented pyrolytic and disordered graphite electrodes, are systematically monitored and compared. Complementary to the characterization of SEI topographical and mechanical changes during electrochemical cycling by EChem-AFM, chemical analysis and theoretical calculations are conducted to provide mechanistic insights underlying SEI formation and evolution. The results provide guidance to engineer functional SEIs through design of carbon materials with defects for LIBs and beyond.

REVIEW OF DNA VACCINE APPROACHES AGAINST THE PARASITE TOXOPLASMA GONDII

Toxoplasma gondii is an apicomplexan parasite that affects both humans and livestock. Transmitted to humans through ingestion, it is the second-leading cause of foodborne illness-related death. Currently, there exists no approved vaccine for humans or most livestock against the parasite. DNA vaccines, a type of subunit vaccine which uses segments of the pathogen's DNA to generate immunity, have shown varying degrees of experimental efficacy against infection caused by the parasite. This review compiles DNA vaccine efforts against Toxoplasma gondii, segmenting the analysis by parasite antigen, as well as a review of concomitant adjuvant usage. No single antigenic group was consistently more effective within in vivo trials relative to others.

Neurological and Neurobehavioral Disorders Associated with Toxoplasma gondii Infection in Humans

The intracellular parasite Toxoplasma gondii is estimated to infect up to 30% of the world population, leading to lifelong chronic infection of the brain and muscle tissue. Although most latent T. gondii infections in humans have traditionally been considered asymptomatic, studies in rodents suggest phenotypic neurological changes are possible. Consequently, several studies have examined the link between T. gondii infection and diseases such as schizophrenia, epilepsy, depression, bipolar disorder, dysphoria, Alzheimer's disease, Parkinson's disease, and obsessive-compulsive disorder (OCD). To date, there is varying evidence of the relationship of T. gondii to these human neurological or neurobehavioral disorders. A thorough review of T. gondii literature was conducted to highlight and summarize current findings. We found that schizophrenia was most frequently linked to T. gondii infection, while sleep disruption showed no linkage to T. gondii infection, and other conditions having mixed support for a link to T. gondii. However, infection as a cause of human neurobehavioral disease has yet to be firmly established.

Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity

DNA-templated molecular (dye) aggregates are a novel class of materials that have garnered attention in a broad range of areas including light harvesting, sensing, and computing. Using DNA to template dye aggregation is attractive due to the relative ease with which DNA nanostructures can be assembled in solution, the diverse array of nanostructures that can be assembled, and the ability to precisely position dyes to within a few Angstroms of one another. These factors, combined with the programmability of DNA, raise the prospect of designer materials custom tailored for specific applications. Although considerable progress has been made in characterizing the optical properties and associated electronic structures of these materials, less is known about their excited-state dynamics. For example, little is known about how the excited-state lifetime, a parameter essential to many applications, is influenced by structural factors, such as the number of dyes within the aggregate and their spatial arrangement. In this work, we use a combination of transient absorption spectroscopy and global target analysis to measure excited-state lifetimes in a series of DNA-templated cyanine dye aggregates. Specifically, we investigate six distinct dimer, trimer, and tetramer aggregates—based on the ubiquitous cyanine dye Cy5—templated using both duplex and Holliday junction DNA nanostructures. We find that these DNA-templated Cy5 aggregates all exhibit significantly reduced excited-state lifetimes, some by more than 2 orders of magnitude, and observe considerable variation among the lifetimes. We attribute the reduced excited-state lifetimes to enhanced nonradiative decay and proceed to discuss various structural factors, including exciton delocalization, dye separation, and DNA heterogeneity, that may contribute to the observed reduction and variability of excited-state lifetimes. Guided by insights from structural modeling, we find that the reduced lifetimes and enhanced nonradiative decay are most strongly correlated with the distance between the dyes. These results inform potential tradeoffs between dye separation, excitonic coupling strength, and excited-state lifetime that motivate deeper mechanistic understanding, potentially via further dye and dye template design.

Diaryl Ureas as an Antiprotozoal Chemotype

We now describe the physicochemical profiling, in vitro ADME, and antiparasitic activity of eight N,N'-diarylureas to assess their potential as a broad-spectrum antiprotozoal chemotype. Chromatographic LogD_7.4 values ranged from 2.5 to 4.5; kinetic aq. solubilities were ≤6.3 μg/mL, and plasma protein binding ranged from 95 to 99%. All of the compounds had low intrinsic clearance values in human, but not mouse, liver microsomes. Although no N,N'-diarylurea had submicromolar potency against Trypanosoma cruzi, two had submicromolar potencies against Toxoplasma gondii and Trypanosoma brucei rhodesiense, and five had submicromolar potencies against Leishmania donovani. Plasmodium falciparum appeared to be the most susceptible to growth inhibition by this compound series. Most of the N,N'-diarylureas had antiprotozoal selectivities ≥10. One N,N'-diarylurea had demonstrable activity in mouse models of malaria and toxoplasmosis.

Rotaxane rings promote oblique packing and extended lifetimes in DNA-templated molecular dye aggregates

Molecular excitons play a central role in natural and artificial light harvesting, organic electrònics, and nanoscale computing. The structure and dynamics of molecular excitons, critical to each application, are sensitively governed by molecular packing. Deoxyribonucleic acid (DNA) templating is a powerful approach that enables controlled aggregation via sub-nanometer positioning of molecular dyes. However, finer sub-Angstrom control of dye packing is needed to tailor excitonic properties for specific applications. Here, we show that adding rotaxane rings to squaraine dyes templated with DNA promotes an elusive oblique packing arrangement with highly desirable optical properties. Specifically, dimers of these squaraine:rotaxanes exhibit an absorption spectrum with near-equal intensity excitonically split absorption bands. Theoretical analysis indicates that the transitions are mostly electronic in nature and only have similar intensities over a narrow range of packing angles. Compared with squaraine dimers, squaraine:rotaxane dimers also exhibit extended excited-state lifetimes and less structural heterogeneity. The approach proposed here may be generally useful for optimizing excitonic materials for a variety of applications ranging from solar energy conversion to quantum information science.

Impact of grain orientation and phase on Volta potential differences in an additively manufactured titanium alloy

This work introduces a method for co-localized multi-modal imaging of sub-μm features in an additively manufactured (AM) titanium alloy. Ti-6Al-4V parts manufactured by electron beam melting powder bed fusion were subjected to hot isostatic pressing to seal internal porosity and machined to remove contour-hatch interfaces. Electron microscopy and atomic force microscopy-based techniques (electron backscatter diffraction and scanning Kelvin probe force microscopy) were used to measure and categorize the effects of crystallographic texture, misorientation, and phase content on the relative differences in the Volta potential of α-Ti and β-Ti phases. Given the tunability of additive manufacturing processes, recommendations for texture and phase control are discussed. In particular, our findings indicate that the potential for micro-galvanic corrosion initiation can be regulated in AM Ti-6Al-4V parts by minimizing both the total area of {111} prior-β grains and the number of contact points between {111} β grains and α laths that originate from {001} prior-β grains.

High-Performance Flexible Bismuth Telluride Thin Film from Solution Processed Colloidal Nanoplates

Thermoelectric generators are an environmentally friendly and reliable solid-state energy conversion technology. Flexible and low-cost thermoelectric generators are especially suited to power flexible electronics and sensors using body heat or other ambient heat sources. Bismuth telluride based thermoelectric materials exhibit their best performance near room temperature making them an ideal candidate to power wearable electronics and sensors using body heat. In this report Bi2Te3 thin films are deposited on a flexible polyimide substrate using low-cost and scalable manufacturing methods. The synthesized Bi2Te3 nanocrystals have a thickness of 35 ± 15 nm and a lateral dimension of 692 ± 186 nm. Thin films fabricated from these nanocrystals exhibit a peak power factor of 0.35 mW/m·K2 at 433 K, which is among the highest reported values for flexible thermoelectric films. In order to evaluate the flexibility of the thin films, static and dynamic bending tests were performed while monitoring the change in electrical resistivity. After 1000 bending cycles over a 50mm ROC, the change in electrical resistance of the film was 23%. Using our Bi2Te3 solutions, we demonstrated the ability to print thermoelectric thin films with an aerosol jet printer, highlighting the potential of additive manufacturing techniques for fabricating flexible thermoelectric generators.

Fully inkjet-printed multilayered graphene-based flexible electrodes for repeatable electrochemical response

Graphene has proven to be useful in biosensing applications. However, one of the main hurdles with printed graphene-based electrodes is achieving repeatable electrochemical performance from one printed electrode to another. We have developed a consistent fabrication process to control the sheet resistance of inkjet-printed graphene electrodes, thereby accomplishing repeatable electrochemical performance. Herein, we investigated the electrochemical properties of multilayered graphene (MLG) electrodes fully inkjet-printed (IJP) on flexible Kapton substrates. The electrodes were fabricated by inkjet printing three materials – (1) a conductive silver ink for electrical contact, (2) an insulating dielectric ink, and (3) MLG ink as the sensing material. The selected materials and fabrication methods provided great control over the ink rheology and material deposition, which enabled stable and repeatable electrochemical response: bending tests revealed the electrochemical behavior of these sensors remained consistent over 1000 bend cycles. Due to the abundance of structural defects (e.g., edge defects) present in the exfoliated graphene platelets, cyclic voltammetry (CV) of the graphene electrodes showed good electron transfer (k = 1.125 × 10⁻² cm s⁻¹) with a detection limit (0.01 mM) for the ferric/ferrocyanide redox couple, [Fe(CN)₆]^−3/−4, which is comparable or superior to modified graphene or graphene oxide-based sensors. Additionally, the potentiometric response of the electrodes displayed good sensitivity over the pH range of 4–10. Moreover, a fully IJP three-electrode device (MLG, platinum, and Ag/AgCl) also showed quasi-reversibility compared to a single IJP MLG electrode device. These findings demonstrate significant promise for scalable fabrication of a flexible, low cost, and fully-IJP wearable sensor system needed for space, military, and commercial biosensing applications.

A fully inkjet printed and flexible multilayer graphene based three electrode device showed electrochemical reversibility.

Stochastic Simulation of Cellular Metabolism

Increased technological methods have enabled the investigation of biology at nanoscale levels. Such systems require the use of computational methods to comprehend the complex interactions that occur. The dynamics of metabolic systems have been traditionally described utilizing differential equations without fully capturing the heterogeneity of biological systems. Stochastic modeling approaches have recently emerged with the capacity to incorporate the statistical properties of such systems. However, the processing of stochastic algorithms is a computationally intensive task with intrinsic limitations. Alternatively, the queueing theory approach, historically used in the evaluation of telecommunication networks, can significantly reduce the computational power required to generate simulated results while simultaneously reducing the expansion of errors. We present here the application of queueing theory to simulate stochastic metabolic networks with high efficiency. With the use of glycolysis as a well understood biological model, we demonstrate the power of the proposed modeling methods discussed herein. Furthermore, we describe the simulation and pharmacological inhibition of glycolysis to provide an example of modeling capabilities.

Structure-Activity Relationship of Antischistosomal Ozonide Carboxylic Acids

Semisynthetic artemisinins and other bioactive peroxides are best known for their powerful antimalarial activities, and they also show substantial activity against schistosomes-another hemoglobin-degrading pathogen. Building on this discovery, we now describe the initial structure-activity relationship (SAR) of antischistosomal ozonide carboxylic acids OZ418 (2) and OZ165 (3). Irrespective of lipophilicity, these ozonide weak acids have relatively low aqueous solubilities and high protein binding values. Ozonides with para-substituted carboxymethoxy and N-benzylglycine substituents had high antischistosomal efficacies. It was possible to increase solubility, decrease protein binding, and maintain the high antischistosomal activity in mice infected with juvenile and adult Schistosoma mansoni by incorporating a weak base functional group in these compounds. In some cases, adding polar functional groups and heteroatoms to the spiroadamantane substructure increased the solubility and metabolic stability, but in all cases decreased the antischistosomal activity.

Activity of diphenyl ether benzyl amines against Human African Trypanosomiasis

Insect-borne parasite Trypanosoma brucei plagues humans and other animals, eliciting the disease Human African trypanosomiasis, also known as African sleeping sickness. This disease poses the biggest threat to the people in Sub-Saharan Africa. Given the high toxicity and difficulties with administration of currently available drugs, a novel treatment is needed. Building on known Human African trypanosomiasis structure-activity relationship (SAR), we now describe a number of functionally simple diphenyl ether analogs which give low micromolar activity (IC₅₀ = 0.16-0.96 μM) against T. b. rhodesiense. The best compound shows favorable selectivity against the L6 cell line (SI = 750) and even greater selectivity (SI = 1200) against four human cell lines. The data herein provides direction for the ongoing optimization of antitrypanosomal diphenyl ethers.

A new chemotype with promise against Trypanosoma cruzi

Pyridyl benzamide 2 is a potent inhibitor of Trypanosoma cruzi, but not other protozoan parasites, and had a selectivity-index of ≥10. The initial structure-activity relationship (SAR) indicates that benzamide and sulfonamide functional groups, and N-methylpiperazine and sterically unhindered 3-pyridyl substructures are required for high activity against T. cruzi. Compound 2 and its active analogs had low to moderate metabolic stabilities in human and mouse liver microsomes.

Assessment of Gene Expression Biomarkers in the Chilean Pencil Catfish, Trichomycterus areolatus, from the Choapa River Basin, Coquimbo Chile

The objective of this study was to describe changes in the gene expression in the Chilean catfish, Trichomycterus areolatus, based on their geographic location within the Choapa River. Genes of choice included those that are biomarkers of exposure to metals, oxidative stress, and endocrine disruption. Male and female T. areolatus were sampled from four sites in January 2015 differently impacted by human activities. In males, but not females, hepatic gene expression of heat shock protein (HSP70) and cytochrome P450 1A (CYP1A) were significantly elevated at the site adjacent to the small city of Salamanca, relative to the other sites. In females, hepatic HSP70, the aryl hydrocarbon receptor (AHR), and the estrogen responsive genes, vitellogenin (VTG) and estrogen receptor alpha (ERα), were significantly lower at the site located furthest downstream. A similar downstream pattern of lower expression levels also was found in ovarian tissue for the genes, HSP70 and ERα. Gill gene expression showed a unique pattern in females as levels of metallothionein were elevated at the site furthest downstream. While analytical chemistry of water samples provided limited evidence of agrichemical contamination, the gene expression data are consistent with an exposure to agrichemicals and metals. T. areolatus may be a valuable sentinel organism and its use as a bioindicator species in some rivers within Chile can provide considerable insight, particularly in situations analytical chemistry is limited by environmental constraints.

DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes

Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.

An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases

The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch's small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development.

Large Davydov Splitting and Strong Fluorescence Suppression: An Investigation of Exciton Delocalization in DNA-Templated Holliday Junction Dye Aggregates

Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.

Novel Toxoplasma gondii inhibitor chemotypes

We profiled three novel T. gondii inhibitors identified from an antimalarial phenotypic high throughput screen (HTS) campaign: styryl 4-oxo-1,3-benzoxazin-4-one KG3, tetrahydrobenzo[b]pyran KG7, and benzoquinone hydrazone KG8. These compounds inhibit T. gondii in vitro with IC₅₀ values ranging from 0.3 to 2μM, comparable to that of 0.25 to 1.5μM for the control drug pyrimethamine. KG3 had no measurable cytotoxicity against five mammalian cell lines, whereas KG7 and KG8 inhibited the growth of 2 of 5 cell lines with KG8 being the least selective for T. gondii. None of the compounds were mutagenic in an Ames assay. Experimental gLogD_7.4 and calculated PSA values for the three compounds were well within the ranges predicted to be favorable for good ADME, even though each compound had relatively low aqueous solubility. All three compounds were metabolically unstable, especially KG3 and KG7. Multiple IP doses of 5mg/kg KG7 and KG8 increased survival in a T. gondii mouse model. Despite their liabilities, we suggest that these compounds are useful starting points for chemical prospecting, scaffold-hopping, and optimization.

Progress in antischistosomal N,N'-diaryl urea SAR

N,N'-Diaryl ureas have recently emerged as a new antischistosomal chemotype. We now describe physicochemical profiling, in vitro ADME, plasma exposure, and ex vivo and in vivo activities against Schistosoma mansoni for twenty new N,N'-diaryl ureas designed primarily to increase aqueous solubility, but also to maximize structural diversity. Replacement of one of the 4-fluoro-3-trifluoromethylphenyl substructures of lead N,N'-diaryl urea 1 with azaheterocycles and benzoic acids, benzamides, or benzonitriles decreased lipophilicity, and in most cases, increased aqueous solubility. There was no clear relationship between lipophilicity and metabolic stability, although all compounds with 3-trifluoromethyl-4-pyridyl substructures were metabolically stable. N,N'-diaryl ureas containing 4-fluoro-3-trifluoromethylphenyl, 3-trifluoromethyl-4-pyridyl, 2,2-difluorobenzodioxole, or 4-benzonitrile substructures had high activity against ex vivo S. mansoni and relatively low cytotoxicity. N,N-diaryl ureas with 3-trifluoromethyl-4-pyridyl and 2,2-difluorobenzodioxole substructures had the highest exposures whereas those with 4-fluoro-3-trifluoromethylphenyl substructures had the best in vivo antischistosomal activities. There was no direct correlation between compound exposure and in vivo activity.

Coherent Exciton Delocalization in a Two-State DNA-Templated Dye Aggregate System

Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.

Detection of Intestinal Pathogens in River, Shore, and Drinking Water in Lima, Peru

Water quality management is an ongoing struggle for many locations worldwide. Current testing of water supplies can be time-consuming, expensive, and lack sensitivity. This study describes an alternative, easy-to-use, and inexpensive method to water sampling and testing at remote locations. This method was employed to detect a number of intestinal pathogens in various locations of Lima, Peru. A total of 34 PCR primer pairs were tested for specificity and high-yield amplification for 12 different pathogens using known DNA templates. Select primers for each pathogen were then tested for minimum detection limits of DNA. Water samples were collected from 22 locations. PCR was used to detect the presence of a pathogen, virulence factors, or differentiate between pathogenic species. In 22 water samples, cholera toxin gene was detected in 4.5% of samples, C. perfringens DNA was detected in 50% of samples, E. histolytica DNA was detected in 54.5% of samples, Giardia intestinalis DNA was detected in 4.5% of samples, Leptospira spp. DNA was detected in 29% of samples, and T. gondii DNA was detected in 31.8% of samples. DNA from three pathogens, C. perfringens, E. histolytica, and T. gondii, were found in residential samples, which accounted for 10 out of 22 samples.

Modeling and Analysis of Intercalant Effects on Circular DNA Conformation

The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medications, rapid screening of structural changes to DNA can provide important insight into their mechanism of interaction. In this study, we report changes to circular DNA conformation from intercalation with ethidium bromide using all-atom molecular dynamics simulations and characterized experimentally by translocation through a silicon nitride solid-state nanopore. Our measurements reveal three distinct current blockade levels and a 6-fold increase in translocation times for ethidium bromide-treated circular DNA as compared to untreated circular DNA. We attribute these increases to changes in the supercoiled configuration hypothesized to be branched or looped structures formed in the circular DNA molecule. Further evidence of the conformational changes is demonstrated by qualitative atomic force microscopy analysis. These results expand the current methodology for predicting and characterizing DNA tertiary structure and advance nanopore technology as a platform for deciphering structural changes of other important biomolecules.

De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome

Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included.

Excitonic AND Logic Gates on DNA Brick Nanobreadboards

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes

Caveolin-1 (CAV1) is a vital scaffold protein heterogeneously expressed in both healthy and malignant tissue. We focus on the role of CAV1 when overexpressed in T-cell leukemia. Previously, we have shown that CAV1 is involved in cell-to-cell communication, cellular proliferation, and immune synapse formation; however, the molecular mechanisms have not been elucidated. We hypothesize that the role of CAV1 in immune synapse formation contributes to immune regulation during leukemic progression, thereby warranting studies of the role of CAV1 in CD4⁺ T-cells in relation to antigen-presenting cells. To address this need, we developed a computational model of a CD4⁺ immune effector T-cell to mimic cellular dynamics and molecular signaling under healthy and immunocompromised conditions (i.e., leukemic conditions). Using the Cell Collective computational modeling software, the CD4⁺ T-cell model was constructed and simulated under CAV1^+/+, CAV1^+/−, and CAV1^−/− conditions to produce a hypothetical immune response. This model allowed us to predict and examine the heterogeneous effects and mechanisms of CAV1 in silico. Experimental results indicate a signature of molecules involved in cellular proliferation, cell survival, and cytoskeletal rearrangement that were highly affected by CAV1 knock out. With this comprehensive model of a CD4⁺ T-cell, we then validated in vivo protein expression levels. Based on this study, we modeled a CD4⁺ T-cell, manipulated gene expression in immunocompromised versus competent settings, validated these manipulations in an in vivo murine model, and corroborated acute T-cell leukemia gene expression profiles in human beings. Moreover, we can model an immunocompetent versus an immunocompromised microenvironment to better understand how signaling is regulated in patients with leukemia.

De novo Assembly and Analysis of the Northern Leopard Frog Rana pipiens Transcriptome

The northern leopard frog Rana (Lithobates) pipiens is an important animal model, being used extensively in cancer, neurology, physiology, and biomechanical studies. R. pipiens is a native North American frog whose range extends from northern Canada to southwest United States, but over the past few decades its populations have declined significantly and is now considered uncommon in large portions of the United States and Canada. To aid in the study and conservation of R. pipiens, this paper describes the first R. pipiens transcriptome. The R. pipiens transcriptome was annotated using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG). Differential expression analysis revealed universal and tissue specific genes, and endocrine-related genes were identified. Transcriptome assemblies and other sequence data are available for download.

A novel method for simulating insulin mediated GLUT4 translocation

Glucose transport in humans is a vital process which is tightly regulated by the endocrine system. Specifically, the insulin hormone triggers a cascade of intracellular signals in target cells mediating the uptake of glucose. Insulin signaling triggers cellular relocalization of the glucose transporter protein GLUT4 to the cell surface, which is primarily responsible for regulated glucose import. Pathology associated with the disruption of this pathway can lead to metabolic disorders, such as type II diabetes mellitus, characterized by the failure of cells to appropriately uptake glucose from the blood. We describe a novel simulation tool of the insulin intracellular response, incorporating the latest findings regarding As160 and GEF interactions. The simulation tool differs from previous computational approaches which employ algebraic or differential equations; instead, the tool incorporates statistical variations of kinetic constants and initial molecular concentrations which more accurately mimic the intracellular environment. Using this approach, we successfully recapitulate observed in vitro insulin responses, plus the effects of Wortmannin-like inhibition of the pathway. The developed tool provides insight into transient changes in molecule concentrations throughout the insulin signaling pathway, and may be employed to identify or evaluate potentially critical components of this pathway, including those associated with insulin resistance. In the future, this highly tractable platform may be useful for simulating other complex cell signaling pathways. Biotechnol. Bioeng. 2014;111: 2454-2465. © 2014 Wiley Periodicals, Inc.

ESTIMATING BACTERIAL DIVERSITY IN SCIRTOTHRIPS DORSALIS (THYSANOPTERA: THRIPIDAE) VIA NEXT GENERATION SEQUENCING

The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations.

Characterization of the Asian Citrus Psyllid Transcriptome

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].

Integrative genomic approaches highlight a family of parasite-specific kinases that regulate host responses

Apicomplexan parasites release factors via specialized secretory organelles (rhoptries, micronemes) that are thought to control host cell responses. In order to explore parasite-mediated modulation of host cell signaling pathways, we exploited a phylogenomic approach to characterize the Toxoplasma gondii kinome, defining a 44 member family of coccidian-specific secreted kinases, some of which have been previously implicated in virulence. Comparative genomic analysis suggests that "ROPK" genes are under positive selection, and expression profiling demonstrates that most are differentially expressed between strains and/or during differentiation. Integrating diverse genomic-scale analyses points to ROP38 as likely to be particularly important in parasite biology. Upregulating expression of this previously uncharacterized gene in transgenic parasites dramatically suppresses transcriptional responses in the infected cell. Specifically, parasite ROP38 downregulates host genes associated with MAPK signaling and the control of apoptosis and proliferation. These results highlight the value of integrative genomic approaches in prioritizing candidates for functional validation.

An insertional trap for conditional gene expression in Toxoplasma gondii: identification of TAF250 as an essential gene

Toxoplasmosis is characterized by fast lytic replication cycles leading to severe tissue lesions. Successful host cell invasion is essential for pathogenesis. The division cycle of Toxoplasma gondii is characterized by an unusual cell cycle progression and a distinct internal budding mechanism. To identify essential genes involved in the lytic cycle we devised an insertional gene trapping strategy using the Tet-transactivator system. In essence, a random, active promoter is displaced with a tetracycline regulatable promoter, which if in an essential gene, will result in a conditionally lethal phenotype upon tetracycline addition. We isolated eight mutants with growth defects, two of which displayed modest invasion defects, one of which had an additional cell cycle defect. The trapped loci were identified using expression microarrays, exploiting the tetracycline dependent expression of the trapped genes. In mutant 3.3H6 we identified TCP-1, a component of the chaperonin protein folding machinery under the control of the Tet promoter. However, this gene was not critical for growth of mutant 3.3H6. Subsequently, we identified a suppressor gene encoding a protein with a hypothetical function by guided cosmid complementation. In mutant 4.3B13, we identified TAF250, an RNA polymerase II complex component, as the trapped, essential gene. Furthermore, by mapping the plasmid insertion boundaries we identified multiple genomic rearrangements, which hint at a potential replication dependent DNA repair mechanism. Furthermore, these rearrangements provide an explanation for inconsistent locus rescue results observed by molecular biological approaches. Taken together, we have added an approach to identify and study essential genes in Toxoplasma.

A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

BACKGROUND

Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators.

RESULTS

Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals) and Plasmodium falciparum (a related parasite responsible for severe human malaria), we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP)-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis) and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at pilot scale to inform future array designs.

CONCLUSIONS

In addition to providing an initial global view of the T. gondii transcriptome across major lineages and permitting detailed resolution of recombination points in a historical sexual cross, the multifunctional nature of this array also allowed opportunities to exploit probes for purposes beyond their intended use, enhancing analyses. This array is in widespread use by the T. gondii research community, and several aspects of the design strategy are likely to be useful for other pathogens.