Dynamical topological phase realized in a trapped-ion quantum simulator.

Nascent platforms for programmable quantum simulation offer unprecedented access to new regimes of far-from-equilibrium quantum many-body dynamics in almost isolated systems. Here achieving precise control over quantum many-body entanglement is an essential task for quantum sensing and computation. Extensive theoretical work indicates that these capabilities can enable dynamical phases and critical phenomena that show topologically robust methods to create, protect and manipulate quantum entanglement that self-correct against large classes of errors. However, so far, experimental realizations have been confined to classical (non-entangled) symmetry-breaking orders1-5. In this work, we demonstrate an emergent dynamical symmetry-protected topological phase6, in a quasiperiodically driven array of ten 171Yb+ hyperfine qubits in Quantinuum's System Model H1 trapped-ion quantum processor7. This phase shows edge qubits that are dynamically protected from control errors, cross-talk and stray fields. Crucially, this edge protection relies purely on emergent dynamical symmetries that are absolutely stable to generic coherent perturbations. This property is special to quasiperiodically driven systems: as we demonstrate, the analogous edge states of a periodically driven qubit array are vulnerable to symmetry-breaking errors and quickly decohere. Our work paves the way for implementation of more complex dynamical topological orders8,9 that would enable error-resilient manipulation of quantum information.

Reverse vaccinology-based identification of a novel surface lipoprotein that is an effective vaccine antigen against bovine infections caused by Pasteurella multocida.

Pasteurella multocida can infect a multitude of wild and domesticated animals, with infections in cattle resulting in hemorrhagic septicemia (HS) or contributing to bovine respiratory disease (BRD) complex. Current cattle vaccines against P. multocida consist of inactivated bacteria, which only offer limited and serogroup specific protection. Here, we describe a newly identified surface lipoprotein, PmSLP, that is present in nearly all annotated P. multocida strains isolated from cattle. Bovine associated variants span three of the four identified phylogenetic clusters, with PmSLP-1 and PmSLP-2 being restricted to BRD associated isolates and PmSLP-3 being restricted to isolates associated with HS. Recombinantly expressed, soluble PmSLP-1 (BRD-PmSLP) and PmSLP-3 (HS-PmSLP) vaccines were both able to provide full protection in a mouse sepsis model against the matched P. multocida strain, however no cross-protection and minimal serum IgG cross-reactivity was identified. Full protection against both challenge strains was achieved with a bivalent vaccine containing both BRD-PmSLP and HS-PmSLP, with serum IgG from immunized mice being highly reactive to both variants. Year-long stability studies with lyophilized antigen stored under various temperatures show no appreciable difference in biophysical properties or loss of efficacy in the mouse challenge model. PmSLP-1 and PmSLP-3 vaccines were each evaluated for immunogenicity in two independent cattle trials involving animals of different age ranges and breeds. In all four trials, vaccination with PmSLP resulted in an increase in antigen specific serum IgG over baseline. In a blinded cattle challenge study with a recently isolated HS strain, the matched HS-PmSLP vaccine showed strong efficacy (75-87.5% survival compared to 0% in the control group). Together, these data suggest that cattle vaccines composed of PmSLP antigens can be a practical and effective solution for preventing HS and BRD related P. multocida infections.

IL-1/MyD88-Dependent G-CSF and IL-6 Secretion Mediates Postburn Anemia.

The anemia of critical illness (ACI) is a nearly universal pathophysiological consequence of burn injury and a primary reason burn patients require massive quantities of transfused blood. Inflammatory processes are expected to drive postburn ACI and prevent meaningful erythropoietic stimulation through iron or erythropoietin supplementation, but to this day no specific inflammatory pathways have been identified as a critical mechanism. In this study, we examined whether secretion of G-CSF and IL-6 mediates distinct features of postburn ACI and interrogated inflammatory mechanisms that could be responsible for their secretion. Our analysis of mouse and human skin samples identified the burn wound as a primary source of G-CSF and IL-6 secretion. We show that G-CSF and IL-6 are secreted independently through an IL-1/MyD88-dependent mechanism, and we ruled out TLR2 and TLR4 as critical receptors. Our results indicate that IL-1/MyD88-dependent G-CSF secretion plays a key role in impairing medullary erythropoiesis and IL-6 secretion plays a key role in limiting the access of erythroid cells to iron. Importantly, we found that IL-1α/ß neutralizing Abs broadly attenuated features of postburn ACI that could be attributed to G-CSF or IL-6 secretion and rescued deficits of circulating RBC counts, hemoglobin, and hematocrit caused by burn injury. We conclude that wound-based IL-1/MyD88 signaling mediates postburn ACI through induction of G-CSF and IL-6 secretion.

Quantum Hall effect based on Weyl orbits in Cd3As2.

Discovered decades ago, the quantum Hall effect remains one of the most studied phenomena in condensed matter physics and is relevant for research areas such as topological phases, strong electron correlations and quantum computing1-5. The quantized electron transport that is characteristic of the quantum Hall effect typically originates from chiral edge states-ballistic conducting channels that emerge when two-dimensional electron systems are subjected to large magnetic fields2. However, whether the quantum Hall effect can be extended to higher dimensions without simply stacking two-dimensional systems is unknown. Here we report evidence of a new type of quantum Hall effect, based on Weyl orbits in nanostructures of the three-dimensional topological semimetal Cd3As2. The Weyl orbits consist of Fermi arcs (open arc-like surface states) on opposite surfaces of the sample connected by one-dimensional chiral Landau levels along the magnetic field through the bulk6,7. This transport through the bulk results in an additional contribution (compared to stacked two-dimensional systems and which depends on the sample thickness) to the quantum phase of the Weyl orbit. Consequently, chiral states can emerge even in the bulk. To measure these quantum phase shifts and search for the associated chiral modes in the bulk, we conduct transport experiments using wedge-shaped Cd3As2 nanostructures with variable thickness. We find that the quantum Hall transport is strongly modulated by the sample thickness. The dependence of the Landau levels on the magnitude and direction of the magnetic field and on the sample thickness agrees with theoretical predictions based on the modified Lifshitz-Onsager relation for the Weyl orbits. Nanostructures of topological semimetals thus provide a way of exploring quantum Hall physics in three-dimensional materials with enhanced tunability.

d-Mon: A Transmon with Strong Anharmonicity Based on Planar c-Axis Tunneling Junction between d-Wave and s-Wave Superconductors.

We propose a novel qubit architecture based on a planar c-axis Josephson junction between a thin flake d-wave superconductor, such as a high-T_{c} cuprate Bi_{2}Sr_{2}CaCu_{2}O_{8+x}, and a conventional s-wave superconductor. When operated in the transmon regime the device-that we call "d mon"-becomes insensitive to offset charge fluctuations and, importantly, exhibits at the same time energy level spectrum with strong anharmonicity that is widely tunable through the device geometry and applied magnetic flux. Crucially, unlike previous qubit designs based on d-wave superconductors the proposed device operates in a regime where quasiparticles are fully gapped and can be therefore expected to achieve long coherence times.

Predictors of middle school students' perceptions of automated writing evaluation.

This study examined middle school students' perceptions of an automated writing evaluation (AWE) system, MI Write. We summarize students' perceptions of MI Write's usability, usefulness, and desirability both quantitatively and qualitatively. We then estimate hierarchical entry regression models that account for district context, classroom climate, demographic factors (i.e., gender, special education status, limited English proficiency status, socioeconomic status, grade), students' writing-related beliefs and affect, and students' writing proficiency as predictors of students' perceptions. Controlling for districts, students reporting more optimal classroom climate also reported higher usability, usefulness, and desirability for MI Write. Also, model results revealed that eighth graders, students with limited English proficiency, and students of lower socioeconomic status perceived MI Write relatively more useable; students with lower socioeconomic status also perceived MI Write relatively more useful and desirable. Students who liked writing more and more strongly believed that writing is a recursive process viewed MI Write as more useable, useful, and desirable. Students with greater writing proficiency viewed MI Write as less useable and useful; writing proficiency was not related to desirability perceptions. We conclude with a discussion of implications and future directions.

Transitions in the Learnability of Global Charges from Local Measurements.

We consider monitored quantum systems with a global conserved charge, and ask how efficiently an observer ("eavesdropper") can learn the global charge of such systems from local projective measurements. We find phase transitions as a function of the measurement rate, depending on how much information about the quantum dynamics the eavesdropper has access to. For random unitary circuits with U(1) symmetry, we present an optimal classical classifier to reconstruct the global charge from local measurement outcomes only. We demonstrate the existence of phase transitions in the performance of this classifier in the thermodynamic limit. We also study numerically improved classifiers by including some knowledge about the unitary gates pattern.

Field Theory of Charge Sharpening in Symmetric Monitored Quantum Circuits.

Monitored quantum circuits (MRCs) exhibit a measurement-induced phase transition between area-law and volume-law entanglement scaling. MRCs with a conserved charge additionally exhibit two distinct volume-law entangled phases that cannot be characterized by equilibrium notions of symmetry-breaking or topological order, but rather by the nonequilibrium dynamics and steady-state distribution of charge fluctuations. These include a charge-fuzzy phase in which charge information is rapidly scrambled leading to slowly decaying spatial fluctuations of charge in the steady state, and a charge-sharp phase in which measurements collapse quantum fluctuations of charge without destroying the volume-law entanglement of neutral degrees of freedom. By taking a continuous-time, weak-measurement limit, we construct a controlled replica field theory description of these phases and their intervening charge-sharpening transition in one spatial dimension. We find that the charge fuzzy phase is a critical phase with continuously evolving critical exponents that terminates in a modified Kosterlitz-Thouless transition to the short-range correlated charge-sharp phase. We numerically corroborate these scaling predictions also hold for discrete-time projective-measurement circuit models using large-scale matrix-product state simulations, and discuss generalizations to higher dimensions.

Entanglement from Tensor Networks on a Trapped-Ion Quantum Computer.

The ability to selectively measure, initialize, and reuse qubits during a quantum circuit enables a mapping of the spatial structure of certain tensor-network states onto the dynamics of quantum circuits, thereby achieving dramatic resource savings when simulating quantum systems with limited entanglement. We experimentally demonstrate a significant benefit of this approach to quantum simulation: the entanglement structure of an infinite system-specifically the half-chain entanglement spectrum-is conveniently encoded within a small register of "bond qubits" and can be extracted with relative ease. Using Honeywell's model H0 quantum computer equipped with selective midcircuit measurement and reset, we quantitatively determine the near-critical entanglement entropy of a correlated spin chain directly in the thermodynamic limit and show that its phase transition becomes quickly resolved upon expanding the bond-qubit register.

Transport evidence for Fermi-arc-mediated chirality transfer in the Dirac semimetal Cd3As2.

The dispersion of charge carriers in a metal is distinctly different from that of free electrons owing to their interactions with the crystal lattice. These interactions may lead to quasiparticles mimicking the massless relativistic dynamics of high-energy particle physics, and they can twist the quantum phase of electrons into topologically non-trivial knots-producing protected surface states with anomalous electromagnetic properties. These effects intertwine in materials known as Weyl semimetals, and in their crystal-symmetry-protected analogues, Dirac semimetals. The latter show a linear electronic dispersion in three dimensions described by two copies of the Weyl equation (a theoretical description of massless relativistic fermions). At the surface of a crystal, the broken translational symmetry creates topological surface states, so-called Fermi arcs, which have no counterparts in high-energy physics or conventional condensed matter systems. Here we present Shubnikov-de Haas oscillations in focused-ion-beam-prepared microstructures of Cd3As2 that are consistent with the theoretically predicted 'Weyl orbits', a kind of cyclotron motion that weaves together Fermi-arc and chiral bulk states. In contrast to conventional cyclotron orbits, this motion is driven by the transfer of chirality from one Weyl node to another, rather than momentum transfer of the Lorentz force. Our observations provide evidence for direct access to the topological properties of charge in a transport experiment, a first step towards their potential application.

The association between primary care use and potentially-preventable hospitalization among dual eligibles age 65 and over.

BACKGROUND: Individuals dually-enrolled in Medicare and Medicaid (dual eligibles) are disproportionately sicker, have higher health care costs, and are hospitalized more often for ambulatory care sensitive conditions (ACSCs) than other Medicare beneficiaries. Primary care may reduce ACSC hospitalizations, but this has not been well studied among dual eligibles. We examined the relationship between primary care and ACSC hospitalization among dual eligibles age 65 and older. METHODS: In this observational study, we used 100% Medicare claims data for dual eligibles ages 65 and over from 2012 to 2018 to estimate the likelihood of ACSC hospitalization as a function of primary care visits and other factors. We used linear probability models stratified by rurality, with subgroup analyses for dual eligibles with diabetes or congestive heart failure. RESULTS: Each additional primary care visit was associated with an 0.05 and 0.09 percentage point decrease in the probability of ACSC hospitalization among urban (95% CI: - 0.059, - 0.044) and rural (95% CI: - 0.10, - 0.08) dual eligibles, respectively. Among dual eligibles with CHF, the relationship was even stronger with decreases of 0.09 percentage points (95% CI: - 0.10, - 0.08) and 0.15 percentage points (95% CI: - 0.17, - 0.13) among urban and rural residents, respectively. CONCLUSIONS: Increased primary care use is associated with lower rates of preventable hospitalizations for dual eligibles age 65 and older, especially for dual eligibles with diabetes and congestive heart failure. In turn, efforts to reduce preventable hospitalizations for this dual-eligible population should consider how to increase access to and use of primary care.

The Rhesus Macaque Serves As a Model for Human Lateral Branch Nephrogenesis.

BACKGROUND: Most nephrons are added in late gestation. Truncated extrauterine nephrogenesis in premature infants results in fewer nephrons and significantly increased risk for CKD in adulthood. To overcome the ethical and technical difficulties associated with studies of late-gestation human fetal kidney development, third-trimester rhesus macaques served as a model to understand lateral branch nephrogenesis (LBN) at the molecular level. METHODS: Immunostaining and 3D rendering assessed morphology. Single-cell (sc) and single-nucleus (sn) RNA-Seq were performed on four cortically enriched fetal rhesus kidneys of 129-131 days gestational age (GA). An integrative bioinformatics strategy was applied across single-cell modalities, species, and time. RNAScope validation studies were performed on human archival tissue. RESULTS: Third-trimester rhesus kidney undergoes human-like LBN. scRNA-Seq of 23,608 cells revealed 37 transcriptionally distinct cell populations, including naïve nephron progenitor cells (NPCs), with the prior noted marker genes CITED1, MEOX1, and EYA1 (c25). These same populations and markers were reflected in snRNA-Seq of 5972 nuclei. Late-gestation rhesus NPC markers resembled late-gestation murine NPC, whereas early second-trimester human NPC markers aligned to midgestation murine NPCs. New, age-specific rhesus NPCs (SHISA8) and ureteric buds (POU3F4 and TWIST) predicted markers were verified in late-gestation human archival samples. CONCLUSIONS: Rhesus macaque is the first model of bona fide LBN, enabling molecular studies of late gestation, human-like nephrogenesis. These molecular findings support the hypothesis that aging nephron progenitors have a distinct molecular signature and align to their earlier human counterparts, with unique markers highlighting LBN-specific progenitor maturation.

Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients.

BACKGROUND: Single-cell transcriptomes from dissociated tissues provide insights into cell types and their gene expression and may harbor additional information on spatial position and the local microenvironment. The kidney's cells are embedded into a gradient of increasing tissue osmolality from the cortex to the medulla, which may alter their transcriptomes and provide cues for spatial reconstruction. METHODS: Single-cell or single-nuclei mRNA sequencing of dissociated mouse kidneys and of dissected cortex, outer, and inner medulla, to represent the corticomedullary axis, was performed. Computational approaches predicted the spatial ordering of cells along the corticomedullary axis and quantitated expression levels of osmo-responsive genes. In situ hybridization validated computational predictions of spatial gene-expression patterns. The strategy was used to compare single-cell transcriptomes from wild-type mice to those of mice with a collecting duct-specific knockout of the transcription factor grainyhead-like 2 (Grhl2CD-/-), which display reduced renal medullary osmolality. RESULTS: Single-cell transcriptomics from dissociated kidneys provided sufficient information to approximately reconstruct the spatial position of kidney tubule cells and to predict corticomedullary gene expression. Spatial gene expression in the kidney changes gradually and osmo-responsive genes follow the physiologic corticomedullary gradient of tissue osmolality. Single-nuclei transcriptomes from Grhl2CD-/- mice indicated a flattened expression gradient of osmo-responsive genes compared with control mice, consistent with their physiologic phenotype. CONCLUSIONS: Single-cell transcriptomics from dissociated kidneys facilitated the prediction of spatial gene expression along the corticomedullary axis and quantitation of osmotically regulated genes, allowing the prediction of a physiologic phenotype.

Repeated Oral Vaccination of Cattle with Shiga Toxin-Negative Escherichia coli O157:H7 Reduces Carriage of Wild-Type E. coli O157:H7 after Challenge.

Subcutaneous vaccination of cattle for enterohemorrhagic Escherichia coli O157:H7 reduces the magnitude and duration of fecal shedding, but the often-required, repeated cattle restraint can increase costs, deterring adoption by producers. In contrast, live oral vaccines may be repeatedly administered in feed, without animal restraint. We investigated whether oral immunization with live stx-negative LEE+E. coli O157:H7 reduced rectoanal junction (RAJ) colonization by wild-type (WT) E. coli O157:H7 strains after challenge. Two groups of cattle were orally dosed twice weekly for 6 weeks with 3 × 109 CFU of a pool of three stx-negative LEE+E. coli O157:H7 strains (vaccine group) or three stx-negative LEE- non-O157:H7 E. coli strains (control group). Three weeks following the final oral dose, animals in both groups were orally challenged with a cocktail of four stx+ LEE+E. coli O157:H7 WT strains. Subsequently, WT strains at the RAJ were enumerated weekly for 4 weeks. Serum antibodies against type III secretion protein (TTSP), the translocated intimin receptor (Tir), and EspA were determined by enzyme-linked immunosorbent assay (ELISA) at day 0 (preimmunization), day 61 (postimmunization, prechallenge), and day 89 (postchallenge). Vaccine group cattle had lower numbers of WT strains at the RAJ than control group cattle on postchallenge days 3 and 7 (P ≤ 0.05). Also, vaccine group cattle shed WT strains for a shorter duration than control group cattle. All cattle seroconverted to TTSP, Tir, and EspA, either following immunization (vaccine group) or following challenge (control group). Increased antibody titers against Tir and TTSP postimmunization were associated with decreased numbers of WT E. coli O157:H7 organisms at the RAJ.IMPORTANCE The bacterium E. coli O157:H7 causes foodborne disease in humans that can lead to bloody diarrhea, kidney failure, vascular damage, and death. Healthy cattle are the main source of this human pathogen. Reducing E. coli O157:H7 in cattle will reduce human disease. Using a randomized comparison, a bovine vaccine to reduce carriage of the human pathogen was tested. A detoxified E. coli O157:H7 strain, missing genes that cause disease, was fed to cattle as an oral vaccine to reduce carriage of pathogenic E. coli O157:H7. After vaccination, the cattle were challenged with disease-causing E. coli O157:H7. The vaccinated cattle had decreased E. coli O157:H7 during the first 7 days postchallenge and shed the bacteria for a shorter duration than the nonvaccinated control cattle. The results support optimization of the approach to cattle vaccination that would reduce human disease.

Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell.

Rationale: Lymphangioleiomyomatosis (LAM) is a metastatic neoplasm of reproductive-age women associated with mutations in tuberous sclerosis complex genes. LAM causes cystic remodeling of the lung and progressive respiratory failure. The sources and cellular characteristics of LAM cells underlying disease pathogenesis remain elusive.Objectives: Identification and characterization of LAM cells in human lung and uterus using a single-cell approach.Methods: Single-cell and single-nuclei RNA sequencing on LAM (n = 4) and control (n = 7) lungs, immunofluorescence confocal microscopy, ELISA, and aptamer proteomics were used to identify and validate LAMCORE cells and secreted biomarkers, predict cellular origins, and define molecular and cellular networks in LAM.Measurements and Main Results: A unique cell type termed LAMCORE was identified, which was distinct from, but closely related to, lung mesenchymal cells. LAMCORE cells expressing signature genes included known LAM markers such as PMEL, FIGF, CTSK, and MLANA and novel biomarkers validated by aptamer screening, ELISA, and immunofluorescence microscopy. LAM cells in lung and uterus are morphologically indistinguishable and share similar gene expression profiles and biallelic TSC2 mutations, supporting a potential uterine origin for the LAMCORE cell. Effects of LAM on resident pulmonary cell types indicated recruitment and activation of lymphatic endothelial cells.Conclusions: A unique population of LAMCORE cells was identified in lung and uterus of patients with LAM, sharing close transcriptomic identity. LAM cell selective markers, secreted biomarkers, and the predicted cellular molecular features provide new insights into the signaling and transcriptional programs that may serve as diagnostic markers and therapeutic targets to influence the pathogenesis of LAM.

Single-Cell Profiling of AKI in a Murine Model Reveals Novel Transcriptional Signatures, Profibrotic Phenotype, and Epithelial-to-Stromal Crosstalk.

BACKGROUND: Current management of AKI, a potentially fatal disorder that can also initiate or exacerbate CKD, is merely supportive. Therefore, deeper understanding of the molecular pathways perturbed in AKI is needed to identify targets with potential to lead to improved treatment. METHODS: We performed single-cell RNA sequencing (scRNA-seq) with the clinically relevant unilateral ischemia-reperfusion murine model of AKI at days 1, 2, 4, 7, 11, and 14 after AKI onset. Using real-time quantitative PCR, immunofluorescence, Western blotting, and both chromogenic and single-molecule in situ hybridizations, we validated AKI signatures in multiple experiments. RESULTS: Our findings show the time course of changing gene expression patterns for multiple AKI stages and all renal cell types. We observed elevated expression of crucial injury response factors-including kidney injury molecule-1 (Kim1), lipocalin 2 (Lcn2), and keratin 8 (Krt8)-and of several novel genes (Ahnak, Sh3bgrl3, and Col18a1) not previously examined in kidney pathologies. AKI induced proximal tubule dedifferentiation, with a pronounced nephrogenic signature represented by Sox4 and Cd24a. Moreover, AKI caused the formation of "mixed-identity cells" (expressing markers of different renal cell types) that are normally seen only during early kidney development. The injured tubules acquired a proinflammatory and profibrotic phenotype; moreover, AKI dramatically modified ligand-receptor crosstalk, with potential pathologic epithelial-to-stromal interactions. Advancing age in AKI onset was associated with maladaptive response and kidney fibrosis. CONCLUSIONS: The scRNA-seq, comprehensive, cell-specific profiles provide a valuable resource for examining molecular pathways that are perturbed in AKI. The results fully define AKI-associated dedifferentiation programs, potential pathologic ligand-receptor crosstalk, novel genes, and the improved injury response in younger mice, and highlight potential targets of kidney injury.

Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development.

Single-cell RNA-seq is a powerful technique. Nevertheless, there are important limitations, including the technical challenges of breaking down an organ or tissue into a single-cell suspension. Invariably, this has required enzymatic incubation at 37°C, which can be expected to result in artifactual changes in gene expression patterns. Here, we describe a dissociation method that uses a protease with high activity in the cold, purified from a psychrophilic microorganism. The entire procedure is carried out at 6°C or colder, at which temperature mammalian transcriptional machinery is largely inactive, thereby effectively 'freezing in' the in vivo gene expression patterns. To test this method, we carried out RNA-seq on 20,424 single cells from postnatal day 1 mouse kidneys, comparing the results of the psychrophilic protease method with procedures using 37°C incubation. We show that the cold protease method provides a great reduction in gene expression artifacts. In addition, the results produce a single-cell resolution gene expression atlas of the newborn mouse kidney, an interesting time in development when mature nephrons are present yet nephrogenesis remains extremely active.

Quantum Hall Network Models as Floquet Topological Insulators.

Network models for equilibrium integer quantum Hall (IQH) transitions are described by unitary scattering matrices that can also be viewed as representing nonequilibrium Floquet systems. The resulting Floquet bands have zero Chern number, and are instead characterized by a chiral Floquet winding number. This begs the question, How can a model without Chern number describe IQH systems? We resolve this puzzle by showing that nonzero Chern number is recovered from the network model via the energy dependence of network model scattering parameters. This relationship shows that, despite their topologically distinct origins, IQH and chiral Floquet topology-changing transitions share identical universal scaling properties.

Baseline analysis of Mycoplasma mycoides subsp. mycoides antigens as targets for a DIVA assay for use with a subunit vaccine for contagious bovine pleuropneumonia.

BACKGROUND: Mycoplasma mycoides subsp. mycoides (Mmm) is the causative agent of contagious bovine pleuropneumonia in cattle. A prototype subunit vaccine is being developed, however, there is currently no diagnostic test that can differentiate between infected cattle and those vaccinated with the prototype subunit vaccine. This study characterized Mmm proteins to identify potential antigens for use in differentiating infected from vaccinated animals. RESULTS: Ten Mmm antigens expressed as recombinant proteins were tested in an indirect ELISA using experimental sera from control groups, infected, and vaccinated animals. Data were imported into R software for analysis and drawing of the box and scatter plots while Cohen's Kappa assessed the level of agreement between the Mmm antigens. Two vaccine antigens (MSC_0499 and MSC_0776) were superior in detecting antibodies in sera of animals vaccinated with the subunit vaccines while two non-vaccine antigens (MSC_0636 and LppB) detected antibodies in sera of infected animals showing all clinical stages of the disease. Sensitivity and specificity of above 87.5% were achieved when the MSC_0499 and MSC_0636 antigens were tested on sera from vaccinated and infected animals. CONCLUSIONS: The MSC_0499 and MSC_0776 antigens were the most promising for detecting vaccinated animals, while MSC_0636 and LppB were the best targets to identify infected animals. Further testing of sera from vaccinated and infected animals collected at different time intervals in the field should help establish how useful a diagnostic test based on a cocktail of these proteins would be.

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf.

The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages.