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Ado- Trastuzumab-Emtansine is approved by EMA and FDA for treatment of HER-2-positive metastatic breast cancer. The drug combines the cytotoxic activity of emtansine with trastuzumab [1,2,3]. Here we are describing 50- year old woman with 3-ple positive left breast cancer with metastasis to left axillary lymph nodes treated with the drug. The patient had normal liver and spleen structure on CT of the abdomen with I.V. contrast, along with a normal liver function test. However she did have a mild elevation of her indirect bilirubin after the initiation of the drug. Despite the normal liver and spleen and absence of Cirrhosis the patient developed drug induced spider angiomas on the upper chest, upper back, shoulders along with palmar erythema. The association of the Ado-Trastuzumab-Emtansine with spider angiomas and palmar erythema in those with normal liver and spleen function, with only a mild elevation of indirect bilirubin is discussed in the article [1].

Non-targeted analysis (NTA) methods are widely used for chemical discovery but seldom employed for quantitation due to a lack of robust methods to estimate chemical concentrations with confidence limits. Herein, we present and evaluate new statistical methods for quantitative NTA (qNTA) using high-resolution mass spectrometry (HRMS) data from EPA's Non-Targeted Analysis Collaborative Trial (ENTACT). Experimental intensities of ENTACT analytes were observed at multiple concentrations using a semi-automated NTA workflow. Chemical concentrations and corresponding confidence limits were first estimated using traditional calibration curves. Two qNTA estimation methods were then implemented using experimental response factor (RF) data (where RF = intensity/concentration). The bounded response factor method used a non-parametric bootstrap procedure to estimate select quantiles of training set RF distributions. Quantile estimates then were applied to test set HRMS intensities to inversely estimate concentrations with confidence limits. The ionization efficiency estimation method restricted the distribution of likely RFs for each analyte using ionization efficiency predictions. Given the intended future use for chemical risk characterization, predicted upper confidence limits (protective values) were compared to known chemical concentrations. Using traditional calibration curves, 95% of upper confidence limits were within ~tenfold of the true concentrations. The error increased to ~60-fold (ESI+) and ~120-fold (ESI-) for the ionization efficiency estimation method and to ~150-fold (ESI+) and ~130-fold (ESI-) for the bounded response factor method. This work demonstrates successful implementation of confidence limit estimation strategies to support qNTA studies and marks a crucial step towards translating NTA data in a risk-based context.

Phthalates are widely used as plasticizers in polyvinyl chloride (PVC) plastics and solvents in many consumer products, resulting in the constant exposure of humans to these chemicals. Although many phthalate metabolites have been targeted in quantitative analysis for exposure assessment, there still remain many which are unknown and thus unmonitored. Due to its discovery based nature, non-targeted analysis using high-resolution mass spectrometry (HRMS) is increasingly used to screen and identify previously unknown metabolites as exposure biomarkers. In this study, we developed a new non-targeted analysis approach for identification of phthalate metabolites based on a comprehensive study of the fragmentation pathways in electrospray ionization (ESI) quadrupole-time-of-flight mass spectrometry (QTOF-MS). The method uses three structurally specific fragment ions as diagnostic filters to identify precursor ions associated with phthalate metabolites as well as distinguish between the types of phthalate metabolites identified. It was found that the fragmentation pathway of phthalate oxidative metabolites is significantly different from non-oxidative metabolites. The fragment ions generated at various collision energies (CE) from 0 to 40 V were investigated to understand their cleavage mechanisms. All phthalate metabolites including oxidative and non-oxidative metabolites produce a specific ion at m/z 121.0295, representing the deprotonated benzoate ion [C(6)H(5)COO](-). Most phthalate metabolites can produce a specific ion at m/z 147.0088, the deprotonated o-phthalic anhydride ion. However, phthalate carboxylate metabolites can only produce the [M-H-R](-) ion at m/z 165.0193 and do not produce the fragment at m/z 147.0088. Based on these findings, four fragmentation pathways of phthalate metabolites have also been proposed in this study and applied to improve the identification of new metabolites in non-targeted analysis. With this workflow, eight unknown precursor ions were identified in the pooled urine sample, but only one followed the fragmentation pathway. It was interpreted as unreported new phthalate metabolite by the MS/MS spectrum and its predicted retention time supported the interpretation. The developed method can identify new phthalate metabolites in human urine with a detection limit of less than 50 ppb.

Non-targeted analysis (NTA) is a rapidly evolving analytical technique with numerous opportunities to improve and expand instrumental and data analysis methods. In this work, NTA was performed on eight synthetic mixtures containing 1264 unique chemical substances from the U.S. Environmental Protection Agency's Non-Targeted Analysis Collaborative Trial (ENTACT). These mixtures were analyzed by atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) using both positive and negative polarities for a total of four modes. Out of the 1264 ENTACT chemical substances, 1116 were detected in at least one ionization mode, 185 chemicals were detected using all four ionization modes, whereas 148 were not detected. Forty-four chemicals were detected only by APCI, and 181 were detected only by ESI. Molecular descriptors and physicochemical properties were used to assess which ionization type was preferred for a given compound. One ToxPrint substructure (naphthalene group) was found to be enriched in compounds only detected using APCI, and eight ToxPrints (e.g., several alcohol moieties) were enriched in compounds only detected using ESI. Examination of physicochemical parameters for ENTACT chemicals suggests that those with higher aqueous solubility preferentially ionized by ESI-. While ESI typically detects a larger number of compounds, APCI offers chromatograms with less background, fewer co-elutions, and additional chemical space coverage, suggesting both should be considered for broader coverage in future NTA research. Graphical abstract.

High-resolution mass spectrometry (HRMS) enables rapid chemical annotation via accurate mass measurements and matching of experimentally derived spectra with reference spectra. Reference libraries are generated from chemical standards and are therefore limited in size relative to known chemical space. To address this limitation, in silico spectra (i.e., MS/MS or MS2 spectra), predicted via Competitive Fragmentation Modeling-ID (CFM-ID) algorithms, were generated for compounds within the U.S. Environmental Protection Agency’s (EPA) Distributed Structure-Searchable Toxicity (DSSTox) database (totaling, at the time of analysis, ~ 765,000 substances). Experimental spectra from EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT) mixtures (n = 10) were then used to evaluate the performance of the in silico spectra. Overall, MS2 spectra were acquired for 377 unique compounds from the ENTACT mixtures. Approximately 53% of these compounds were correctly identified using a commercial reference library, whereas up to 50% were correctly identified as the top hit using the in silico library. Together, the reference and in silico libraries were able to correctly identify 73% of the 377 ENTACT substances. When using the in silico spectra for candidate filtering, an examination of binary classifiers showed a true positive rate (TPR) of 0.90 associated with false positive rates (FPRs) of 0.10 to 0.85, depending on the sample and method of candidate filtering. Taken together, these findings show the abilities of in silico spectra to correctly identify true positives in complex samples (at rates comparable to those observed with reference spectra), and efficiently filter large numbers of potential false positives from further consideration. Graphical abstract Electronic supplementary material The online version of this article (10.1007/s00216-019-02351-7) contains supplementary material, which is available to authorized users.

Non-targeted analysis (NTA) encompasses a rapidly evolving set of mass spectrometry techniques aimed at characterizing the chemical composition of complex samples, identifying unknown compounds, and/or classifying samples, without prior knowledge regarding the chemical content of the samples. Recent advances in NTA are the result of improved and more accessible instrumentation for data generation and analysis tools for data evaluation and interpretation. As researchers continue to develop NTA approaches in various scientific fields, there is a growing need to identify, disseminate, and adopt community-wide method reporting guidelines. In 2018, NTA researchers formed the Benchmarking and Publications for Non-Targeted Analysis Working Group (BP4NTA) to address this need. Consisting of participants from around the world and representing fields ranging from environmental science and food chemistry to 'omics and toxicology, BP4NTA provides resources addressing a variety of challenges associated with NTA. Thus far, BP4NTA group members have aimed to establish a consensus on NTA-related terms and concepts and to create consistency in reporting practices by providing resources on a public Web site, including consensus definitions, reference content, and lists of available tools. Moving forward, BP4NTA will provide a setting for NTA researchers to continue discussing emerging challenges and contribute to additional harmonization efforts.

It has been known that a high-brightness electron beam emits broadband synchrotron radiation when traversing a curved orbit. The radiation reaction at wavelengths comparable to the bunch length or to the wavelength of a phase space modulated beam may lead to collective instabilities. In this paper, we investigate a potential single-pass instability mechanism of coherent-radiation-induced longitudinal multibunch beam breakup (BBU) instability in the presence of a closely spaced microbunch train in an undulator, particularly when the microbunch spacing is close to the resonant wavelength of the undulator. This problem is formulated based on the macroparticle model together with the slippage constraint on the beam-wave interaction. The set of coupled differential equations for individual microbunches can be solved analytically for the first few microbunches with linearization of the coherent radiation wakefield, and numerically in general nonlinear cases for unequal spacing or nonuniform filling charges. The underlying mechanisms, including the slippage effect, the potential-well effect leading to extra focusing, dependence of microbunch spacing and filling patterns, are discussed. The analysis is then applied to the recently proposed steady-state microbunching (SSMB) mechanism with two examples serving for the high average coherent radiation power sources for extreme ultraviolet (EUV) and infrared wavelength regions. For the specific scenario considered in this paper, it is found that when the microbunch spacing is close to the fundamental resonant wavelength, the coherent radiation can provide extra longitudinal focusing for the individual microbunches, leading to more stable multibunch oscillations. For the preliminary nominal SSMB designs with the average beam current of 1 A, our studies show that the single-pass longitudinal BBU instability should not be a severe issue.

With the increasing availability of high-resolution mass spectrometers, suspect screening and non-targeted analysis are becoming popular compound identification tools for environmental researchers. Samples of interest often contain a large (unknown) number of chemicals spanning the detectable mass range of the instrument. In an effort to separate these chemicals prior to injection into the mass spectrometer, a chromatography method is often utilized. There are numerous types of gas and liquid chromatographs that can be coupled to commercially available mass spectrometers. Depending on the type of instrument used for analysis, the researcher is likely to observe a different subset of compounds based on the amenability of those chemicals to the selected experimental techniques and equipment. It would be advantageous if this subset of chemicals could be predicted prior to conducting the experiment, in order to minimize potential false-positive and false-negative identifications. In this work, we utilize experimental datasets to predict the amenability of chemical compounds to detection with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). The assembled dataset totals 5517 unique chemicals either explicitly detected or not detected with LC-ESI-MS. The resulting detected/not-detected matrix has been modeled using specific molecular descriptors to predict which chemicals are amenable to LC-ESI-MS, and to which form(s) of ionization. Random forest models, including a measure of the applicability domain of the model for both positive and negative modes of the electrospray ionization source, were successfully developed. The outcome of this work will help to inform future suspect screening and non-targeted analyses of chemicals by better defining the potential LC-ESI-MS detectable chemical landscape of interest.

Originating from the stochastic nature of the photon emission process, the diffusion of the electron longitudinal coordinate exists even if the global phase slippage of a storage ring is zero, as we cannot zero all the local phase slippages simultaneously. This quantum diffusion is viewed as the most fundamental limit of the lowest bunch length realizable in an electron storage ring from the single-particle dynamics perspective. Here, we present an analysis of this effect using the Courant-Snyder parametrization in the longitudinal dimension. Analytical formulas for the longitudinal emittance, energy spread, and bunch length are derived. The same formalism is used to discuss the application of multiple radio frequency systems for longitudinal strong focusing. The presented work is expected to be useful in the development of novel light source mechanisms like steady-state microbunching, where a short bunch length or small longitudinal emittance is needed.

Low longitudinal emittance means small energy spread and short bunch length, which makes high-power short-wavelength coherent radiation possible. In a storage ring, due to quantum excitation, the equilibrium longitudinal emittance is mainly the overall contribution of all bend-related elements, such as bends, undulators and laser modulators. By introducing longitudinal Twiss function and analyzing the 6D one-turn map in 3D Twiss form, the longitudinal emittance contribution of all these elements is theoretically studied in this paper, and a general method for minimizing the storage ring equilibrium longitudinal emittance is proposed. An integrated optimization of longitudinal beta function shows, the longitudinal emittance scales as the third power of bending angle, and can be as low as subpicometer with a beam energy of 400 MeV in an ultimate state.

There is an increasing need for comparable and harmonized retention times (tR) in liquid chromatography (LC) among different laboratories, to provide supplementary evidence for the identity of compounds in high-resolution mass spectrometry (HRMS)-based suspect and nontarget screening investigations. In this study, a rigorously tested, flexible, and less system-dependent unified retention time index (RTI) approach for LC is presented, based on the calibration of the elution pattern. Two sets of 18 calibrants were selected for each of ESI+ and ESI-based on the maximum overlap with the retention times and chemical similarity indices from a total set of 2123 compounds. The resulting calibration set, with RTI set to range between 1 and 1000, was proposed as the most appropriate RTI system after rigorous evaluation, coordinated by the NORMAN network. The validation of the proposed RTI system was done externally on different instrumentation and LC conditions. The RTI can also be used to check the reproducibility and quality of LC conditions. Two quantitative structure-retention relationship (QSRR)-based models were built based on the developed RTI systems, which assist in the removal of false-positive annotations. The applicability domains of the QSRR models allowed completing the identification process with higher confidence for substances within the domain, while indicating those substances for which results should be treated with caution. The proposed RTI system was used to improve confidence in suspect and nontarget screening and increase the comparability between laboratories as demonstrated for two examples. All RTI-related calculations can be performed online at http://rti.chem.uoa.gr/., The authors acknowledge the contributions of Birgit Beck (Eawag) during this work. They also acknowledge the partial financial support from the NORMAN Association. R.A. acknowledges the scholarship and financial support from the Hellenic Foundation for Research and Innovation (HFRI) and the General Secretariat for Research and Technology (GSRT), under the HFRI Ph.D. Fellowship grant (GA. no. 14484). E.L.S. was supported by the Luxembourg National Research Fund (FNR, Grant A18/BM/12341006).

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, requires iron for survival. In Mtb, MhuD is the cytosolic protein that degrades imported heme. MhuD is distinct, in both sequence and structure, from canonical heme oxygenases (HOs) but homologous with IsdG-type proteins. Canonical HO is found mainly in eukaryotes, while IsdG-type proteins are predominantly found in prokaryotes, including pathogens. While there are several published structures of MhuD and other IsdG-type proteins in complex with the heme substrate, no structures of IsdG-type proteins in complex with a product have been reported, unlike the case for HOs. We recently showed that the Mtb variant MhuD-R26S produces biliverdin IXα (αBV) rather than the wild-type mycobilin isomers. Given that mycobilin and other IsdG-type protein products like staphylobilin are difficult to isolate in quantities sufficient for structure determination, here we use the MhuD-R26S variant and its product αBV as a proxy to study the IsdG-type protein-product complex. First, we show that αBV has a nanomolar affinity for MhuD and the R26S variant. Second, we determined the MhuD-R26S-αBV complex structure to 2.5 Å, which reveals two notable features: (1) two αBV molecules bound per active site and (2) a novel α-helix (α3) that was not observed in previous MhuD-heme structures. Finally, through molecular dynamics simulations, we show that α3 is stable with the proximal αBV alone. MhuD's high affinity for the product and the observed structural and electrostatic changes that accompany substrate turnover suggest that there may be an unidentified class of proteins that are responsible for the extraction of products from MhuD and other IsdG-type proteins.

Non-targeted analysis (NTA) methods are increasingly used to discover contaminants of emerging concern (CECs), but the extent to which these methods can support exposure and health studies remains to be determined. EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) was launched in 2016 to address this need. As part of ENTACT, 1269 unique substances from EPA's ToxCast library were combined to make ten synthetic mixtures, with each mixture containing between 95 and 365 substances. As a participant in the trial, we first performed blinded NTA on each mixture using liquid chromatography (LC) coupled with high-resolution mass spectrometry (HRMS). We then performed an unblinded evaluation to identify limitations of our NTA method. Overall, at least 60% of spiked substances could be observed using selected methods. Discounting spiked isomers, true positive rates from the blinded and unblinded analyses reached a maximum of 46% and 65%, respectively. An overall reproducibility rate of 75% was observed for substances spiked into more than one mixture and observed at least once. Considerable discordance in substance identification was observed when comparing a subset of our results derived from two separate reversed-phase chromatography methods. We conclude that a single NTA method, even when optimized, can likely characterize only a subset of ToxCast substances (and, by extension, other CECs). Rigorous quality control and self-evaluation practices should be required of labs generating NTA data to support exposure and health studies. Accurate and transparent communication of performance results will best enable meaningful interpretations and defensible use of NTA data. Graphical abstract ᅟ.

Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency&rsquo, s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.

The use of particle accelerators as photon sources has enabled advances in science and technology1. Currently the workhorses of such sources are storage-ring-based synchrotron radiation facilities2–4 and linear-accelerator-based free-electron lasers5–14. Synchrotron radiation facilities deliver photons with high repetition rates but relatively low power, owing to their temporally incoherent nature. Free-electron lasers produce radiation with high peak brightness, but their repetition rate is limited by the driving sources. The steady-state microbunching15–22 (SSMB) mechanism has been proposed to generate high-repetition, high-power radiation at wavelengths ranging from the terahertz scale to the extreme ultraviolet. This is accomplished by using microbunching-enabled multiparticle coherent enhancement of the radiation in an electron storage ring on a steady-state turn-by-turn basis. A crucial step in unveiling the potential of SSMB as a future photon source is the demonstration of its mechanism in a real machine. Here we report an experimental demonstration of the SSMB mechanism. We show that electron bunches stored in a quasi-isochronous ring can yield sub-micrometre microbunching and coherent radiation, one complete revolution after energy modulation induced by a 1,064-nanometre-wavelength laser. Our results verify that the optical phases of electrons can be correlated turn by turn at a precision of sub-laser wavelengths. On the basis of this phase correlation, we expect that SSMB will be realized by applying a phase-locked laser that interacts with the electrons turn by turn. This demonstration represents a milestone towards the implementation of an SSMB-based high-repetition, high-power photon source. The mechanism of steady-state electron microbunching is demonstrated, providing a basis that will enable its full implementation in electron storage rings to generate high-repetition, high-power coherent radiation.

The mechanism of steady-state microbunching (SSMB) has been proposed [D. F. Ratner and A. W. Chao, Phys. Rev. Lett. 105, 154801 (2010)PRLTAO0031-900710.1103/PhysRevLett.105.154801] to generate high-power coherent radiation at a high repetition rate or in continuous-wave mode using electron storage rings. In this paper, the related single-particle dynamics are theoretically and numerically studied, and important results are presented. The investigated effects are longitudinal quantum radiation excitation, nonlinear momentum compaction, and linear and nonlinear coupling of the transverse and longitudinal motion. Although this analysis is oriented toward SSMB, some of the analyzed effects are also crucial in cases such as coherent harmonic generation, bunch slicing, bunch compression, free-electron laser beam transport lines, and quasi-isochronous rings, which involve precise longitudinal phase-space manipulations.

This paper reports the observation of beam energy widening and distortion from Gaussian due to a nonvanishing horizontal chromaticity at a quasi-isochronous storage ring. The result originates from an average path-length dependence on the betatron oscillation amplitudes, which is intimately correlated to the transverse chromaticities. It is the first experimental validation of the impact of such a nonlinear transverse-longitudinal coupling effect on the equilibrium beam characteristics in a storage ring. The results could be important for quasi-isochronous rings, steady-state microbunching, nonscaling fixed-field alternate gradient accelerators, etc., where very small momentum compaction or large chromaticity is required.

In a Steady-State Microbunching light source, a 100 nanosecond long pulse is enhanced in a cavity to megawatts average power. A novel enhancement scheme is invented. Modeling and simulation are conducted to demonstrate its feasibility.

Environmental chemicals comprise a major portion of the human exposome, with some shown to impact the health of susceptible populations, including pregnant women and developing fetuses. The placenta and cord blood serve as important biological windows into the maternal and fetal environments. In this article we review how environmental chemicals (defined here to include man-made chemicals [e.g., flame retardants, pesticides/ herbicides, per- and polyfluoroalkyl substances], toxins, metals, and other xenobiotic compounds) contribute to the prenatal exposome and highlight future directions to advance this research field. Our findings from a survey of recent literature indicate the need to better understand the breadth of environmental chemicals that reach the placenta and cord blood, as well as the linkages between prenatal exposures, mechanisms of toxicity, and subsequent health outcomes. Research efforts tailored towards addressing these needs will provide a more comprehensive understanding of how environmental chemicals impact maternal and fetal health.

Non-targeted analysis (NTA) methods are being increasingly used to aid in the identification of unknown compounds in the environment, a problem that has challenged environmental chemists for decades. Despite its increased use, quality assurance practices for NTA have not been well established. Furthermore, capabilities and limitations of certain NTA methods have not been thoroughly evaluated. Standard reference material dust (SRM 2585) was used here to evaluate the ability of NTA to identify previously reported compounds, as well as a suite of 365 chemicals that were spiked at various stages of the analytical procedure. Analysis of the unaltered SRM 2585 extracts revealed that several previously reported compounds can be identified by NTA, and that correct identification was dependent on concentration. A manual inspection of unknown features in SRM 2585 revealed the presence of two chlorinated and fluorinated compounds in high abundance, likely precursors to perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS). A retrospective analysis of data from the American Healthy Homes Survey revealed that these compounds were present in 42% of sampled homes. Spiking the dust at various stages of sample preparation revealed losses from extraction, cleanup, and instrumental analysis; the log K(ow) for individual compounds influenced the overall recovery levels but no pattern could be discerned from the various degrees of interference that the matrix had on the ionization efficiency of the spiked chemicals. Analysis of the matrix-free chemical mixture at low, medium, and high concentrations led to more correct identifications than analysis at one, very high concentration. Varying the spiked amount and identifying reported compounds at known concentrations allowed an estimation of the lower limits of identification (LOIs) for NTA, analogous to limits of detection in targeted analysis. The LOIs were much lower than levels in dust that would be likely to cause bioactivity in humans, indicating that NTA is useful for identifying and monitoring compounds that may be of toxicological concern. Graphical abstract.

Cryptosporidiosis is a diarrheal disease predominantly caused by Cryptosporidium parvum ( Cp) and Cryptosporidium hominis ( Ch), apicomplexan parasites which infect the intestinal epithelial cells of their human hosts. The only approved drug for cryptosporidiosis is nitazoxanide, which shows limited efficacy in immunocompromised children, the most vulnerable patient population. Thus, new therapeutics and in vitro infection models are urgently needed to address the current unmet medical need. Toward this aim, we have developed novel cytopathic effect (CPE)-based Cp and Ch assays in human colonic tumor (HCT-8) cells and compared them to traditional imaging formats. Further model validation was achieved through screening a collection of FDA-approved drugs and confirming many previously known anti- Cryptosporidium hits as well as identifying a few novel candidates. Collectively, our data reveals this model to be a simple, functional, and homogeneous gain of signal format amenable to high throughput screening, opening new avenues for the discovery of novel anticryptosporidials.

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, requires iron for survival. In Mtb, MhuD is the cytosolic protein that degrades imported heme. MhuD is distinct, both in sequence and structure, from canonical heme oxygenases (HOs) but homologous with IsdG-type proteins. Canonical HO is found mainly in eukaryotes, while IsdG-type proteins are predominantly found in prokaryotes including pathogens. While there are several published structures of MhuD and other IsdG-type proteins in complex with heme substrate, no structures have been reported of IsdG-type proteins in complex with product, unlike HOs. We recently showed that the Mtb variant MhuD-R26S produces biliverdin IXα (αBV) rather than the wild-type mycobilin isomers as product. Given that mycobilin and other IsdG-type protein products like staphylobilin are difficult to isolate in quantities sufficient for structure determination, here we use the MhuD-R26S variant and its product αBV as a proxy to study the IsdG-type protein/product complex. First we show that αBV has nanomolar affinity for MhuD and the R26S variant. Second we determined the MhuD-R26S-αBV complex structure to 2.5 Å, which reveals two notable features (1) two αBV molecules bound per active site and (2) a novel α-helix (α3) unobserved in previous MhuD-heme structures. Finally, through molecular dynamics simulations we show that α3 is stable with the proximal αBV alone. With MhuD’s high affinity for product along with observed structural and electrostatic changes that accompany substrate turnover suggest that there may be an unidentified class of proteins responsible for product extraction from MhuD and other IsdG-type proteins.

Mycobacterium tuberculosis heme-degrading protein MhuD degrades heme to mycobilin isomers and iron, while its closest homologues from Staphylococcus aureus, IsdG and IsdI, degrade heme to staphylobilin isomers, formaldehyde, and iron. Superposition of the structures of the heme-bound complexes reveals that the heme molecule in the MhuD active site is rotated ∼90° about the tetrapyrrole plane with respect to IsdG and IsdI active site heme molecules. Therefore, the variation in IsdG/IsdI and MhuD chromophore products may be attributed to the different heme orientations. In MhuD, two arginines, Arg22 and Arg26, stabilize the heme propionates and may account for the heme orientation. Herein, we demonstrate that the MhuD-R26S variant alters the resulting chromophore product from mycobilin to biliverdin IXα (α-BV), whereas the R22S variant does not. Surprisingly, unlike canonical heme oxygenase (HO) that also degrades heme to α-BV, the MhuD-R26S variant produces the C1 product formaldehyde rather than carbon monoxide as observed for HO. The MhuD-R26S variant is an important tool for further probing the mechanism of action of MhuD and for studying the fate of the MhuD product in mycobacterium.

The highly contagious disease tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis (Mtb), which has been evolving drug resistance at an alarming rate. Like all human pathogens, Mtb requires iron for growth and virulence. Consequently, Mtb iron transport is an emerging drug target. However, the development of anti-TB drugs aimed at these metabolic pathways have been restricted by the dearth of information on Mtb iron acquisition. In this review, we describe the multiple strategies utilized by Mtb to acquire ferric iron and heme-iron. Mtb iron uptake is a complex process, requiring biosynthesis and subsequent export of Mtb siderophores, followed by ferric iron scavenging and ferric-siderophore import into Mtb. Additionally, Mtb possesses two possible heme uptake pathways, and an Mtb-specific mechanism of heme degradation that yields iron and novel heme-degradation products. We conclude with perspectives for potential therapeutics that could directly target Mtb heme and iron uptake machineries. We also highlight how hijacking Mtb heme and iron acquisition pathways for drug import may facilitate drug transport through the notoriously impregnable Mtb cell-wall.

The apicomplexan parasite Cryptosporidium is the second most important diarrheal pathogen causing life-threatening diarrhea in children, which is also associated with long-term growth faltering and cognitive deficiency. Cryptosporidiosis is a parasitic disease of public health concern caused by Cryptosporidium parvum and Cryptosporidium hominis. Currently, nitazoxanide is the only approved treatment for cryptosporidium infections. Unfortunately, it has limited efficacy in the most vulnerable patients, thus there is an urgent need for a safe and efficacious cryptosporidiosis drug. In this work, we present our current perspectives on the target product profile for novel cryptosporidiosis therapies and the perceived challenges and possible mitigation plans at different stages in the cryptosporidiosis drug discovery process.

MhuD is a protein found in mycobacteria that can bind up to two heme molecules per protein monomer and catalyze the degradation of heme to mycobilin in vitro. Here the K(d1) for heme dissociation from heme-bound MhuD was determined to be 7.6 ± 0.8 nM and the K(d2) for heme dissocation from diheme-bound MhuD was determined to be 3.3 ± 1.1 μM. These data strongly suggest that MhuD is a competent heme oxygenase in vivo.

We consider a compact storage-ring-based EUV light source with the recently proposed electron beam manipulation technique. Theoretical analysis and numerical simulations demonstrated that this technique can be used for the generation of megawatt-scale level, fully temporal coherent EUV in storage rings.

Spiropyrazolopyridone 1 was identified, as a novel dengue virus (DENV) inhibitor, from a DENV serotype 2 (DENV-2) high-throughput phenotypic screen. As a general trend within this chemical class, chiral resolution of the racemate revealed that R enantiomer was significantly more potent than the S. Cell-based lead optimization of the spiropyrazolopyridones focusing on improving the physicochemical properties is described. As a result, an optimal compound 14a, with balanced in vitro potency and pharmacokinetic profile, achieved about 1.9 log viremia reduction at 3 × 50 mg/kg (bid) or 3 × 100 mg/kg (QD) oral doses in the dengue in vivo mouse efficacy model.

Effects of the chromaticity on head-tail instabilities for broadband impedances are comprehensively studied, using the two particle model, the Vlasov analysis and computer simulations. We show both in the two particle model and the Vlasov analysis with the trapezoidal (semiconstant) wake model that we can derive universal contour plots for the growth factor as a function of the two dimensionless parameters: the wakefield strength, $\mathrm{\ensuremath{\Upsilon}}$, and the difference of the betatron phase advances between the head and the tail, $\ensuremath{\chi}$. They reveal how the chromaticity affects strong head-tail instabilities and excites head-tail instabilities. We also apply the LEP (Large Electron-Positron Collider) broadband resonator model to the Vlasov approach and find that the results are in very good agreement with those of the trapezoidal wake model. The theoretical findings are also reinforced by the simulation results. The trapezoidal wake model turns out to be a very useful tool since it significantly simplifies the time domain analysis and provides well-behaved impedance at the same time.

A feasibility study of fusion reactors based on accelerators is carried out. We consider a novel scheme where a beam from the accelerator hits the target plasma on the resonance of the fusion reaction and establish characteristic criteria for a workable reactor. We consider the reactions $ d + t \rightarrow n + \alpha, d + {}^3H_e \rightarrow p + \alpha$, and $p + {}^{11}B \rightarrow 3 \alpha$ in this study. The critical temperature of the plasma is determined from overcoming the stopping power of the beam with the fusion energy gain. The needed plasma lifetime is determined from the width of the resonance, the beam velocity and the plasma density. We estimate the critical beam flux by balancing the energy of fusion production against the plasma thermo-energy and the loss due to stopping power for the case of an inert plasma. The product of critical flux and plasma lifetime is independent of plasma density and has a weak dependence on temperature. Even though the critical temperatures for these reactions are lower than those for the thermonuclear reactors, the critical flux is in the range of $10^{22} - 10^{24}/\rm{cm^2/s}$ for the plasma density $\rho_t = 10^{15}/{\rm cm^3}$ in the case of an inert plasma. Several approaches to control the growth of the two-stream instability are discussed. We have also considered several scenarios for practical implementation which will require further studies. Finally, we consider the case where the injected beam at the resonance energy maintains the plasma temperature and prolongs its lifetime to reach a steady state. The equations for power balance and particle number conservation are given for this case., Comment: To be published in Nuclear Fusion as a letter, 7 pages, 2 figures

As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge.

Mycobacterium heme utilization degrader (MhuD) is a heme-degrading protein from Mycobacterium tuberculosis responsible for extracting the essential nutrient iron from host-derived heme. MhuD has been previously shown to produce unique organic products compared to those of canonical heme oxygenases (HOs) as well as those of the IsdG/I heme-degrading enzymes from Staphylococcus aureus. Here, we report the X-ray crystal structure of cyanide-inhibited MhuD (MhuD–heme–CN) as well as detailed 1H nuclear magnetic resonance (NMR), UV/vis absorption, and magnetic circular dichroism (MCD) spectroscopic characterization of this species. There is no evidence for an ordered network of water molecules on the distal side of the heme substrate in the X-ray crystal structure, as was previously reported for canonical HOs. The degree of heme ruffling in the crystal structure of MhuD is greater than that observed for HO and less than that observed for IsdI. As a consequence, the Fe 3dxz-, 3dyz-, and 3dxy-based MOs are very close in energy, and the room-temperature 1H NMR spectrum of MhuD–heme–CN is consistent with population of both a 2Eg electronic state with a (dxy)2(dxz,dyz)3 electron configuration, similar to the ground state of canonical HOs, and a 2B2g state with a (dxz,dyz)4(dxy)1 electron configuration, similar to the ground state of cyanide-inhibited IsdI. Variable temperature, variable field MCD saturation magnetization data establishes that MhuD–heme–CN has a 2B2g electronic ground state with a low-lying 2Eg excited state. Our crystallographic and spectroscopic data suggest that there are both structural and electronic contributions to the α-meso regioselectivity of MhuD-catalyzed heme cleavage. The structural distortion of the heme substrate observed in the X-ray crystal structure of MhuD–heme–CN is likely to favor cleavage at the α- and γ-meso carbons, whereas the spin density distribution may favor selective oxygenation of the α-meso carbon., X-ray crystallography has revealed that M. tuberculosis MhuD stabilizes a ruffled heme substrate. 1H nuclear magnetic resonance and variable temperature, variable field magnetic circular dichroism spectroscopic characterization of this species have demonstrated that MhuD stabilizes an unusual heme electronic structure with a 2B2g electronic ground state and a thermally accessible 2Eg excited state. The data presented here strongly suggests that the α-meso regioselectivity of MhuD-catalyzed porphyrin cleavage depends on both structural and electronic factors.

The recent increase in extensively drug-resistant bacterial pathogens and the associated increase of morbidity and mortality demonstrate the immediate need for new antibiotic backbones with novel mechanisms of action. Here, we report the development of the PepSAVI-MS pipeline for bioactive peptide discovery. This highly versatile platform employs mass spectrometry and statistics to identify bioactive peptide targets from complex biological samples. We validate the use of this platform through the successful identification of known bioactive peptides from a botanical species, Viola odorata. Using this pipeline, we have widened the known antimicrobial spectrum for V. odorata cyclotides, including antibacterial activity of cycloviolacin O2 against A. baumannii. We further demonstrate the broad applicability of the platform through the identification of novel anticancer activities for cycloviolacins by their cytotoxicity against ovarian, breast, and prostate cancer cell lines.

Diarrhoeal disease is responsible for 8.6% of global child mortality. Recent epidemiological studies found the protozoan parasite Cryptosporidium to be a leading cause of paediatric diarrhoea, with particularly grave impact on infants and immunocompromised individuals. There is neither a vaccine nor an effective treatment. Here we establish a drug discovery process built on scalable phenotypic assays and mouse models that take advantage of transgenic parasites. Screening a library of compounds with anti-parasitic activity, we identify pyrazolopyridines as inhibitors of Cryptosporidium parvum and Cryptosporidium hominis. Oral treatment with the pyrazolopyridine KDU731 results in a potent reduction in intestinal infection of immunocompromised mice. Treatment also leads to rapid resolution of diarrhoea and dehydration in neonatal calves, a clinical model of cryptosporidiosis that closely resembles human infection. Our results suggest that the Cryptosporidium lipid kinase PI(4)K (phosphatidylinositol-4-OH kinase) is a target for pyrazolopyridines and that KDU731 warrants further preclinical evaluation as a drug candidate for the treatment of cryptosporidiosis.

As we consider the tremendous physics reaches of the big future circular electron–positron and proton–proton colliders, it might be advisable to keep a close track of what accelerator challenges they face. Good progresses are being made, and yet it is reported here that substantial investments in funding, manpower, as well as a long sustained time to the R&D efforts will be required in preparation to realize these dream colliders.

A recently proposed technique in storage ring accelerators is applied to provide potential high-power sources of photon radiation. The technique is based on the steady-state microbunching (SSMB) mechanism. As examples of this application, one may consider a high-power DUV photon source for research in atomic and molecular physics or a high-power EUV radiation source for industrial lithography. A less challenging proof-of-principle test to produce IR radiation using an existing storage ring is also considered.