Enhanced dynamic nuclear polarization via swept microwave frequency combs.

Dynamic nuclear polarization (DNP) has enabled enormous gains in magnetic resonance signals and led to vastly accelerated NMR/MRI imaging and spectroscopy. Unlike conventional cw-techniques, DNP methods that exploit the full electron spectrum are appealing since they allow direct participation of all electrons in the hyperpolarization process. Such methods typically entail sweeps of microwave radiation over the broad electron linewidth to excite DNP but are often inefficient because the sweeps, constrained by adiabaticity requirements, are slow. In this paper, we develop a technique to overcome the DNP bottlenecks set by the slow sweeps, using a swept microwave frequency comb that increases the effective number of polarization transfer events while respecting adiabaticity constraints. This allows a multiplicative gain in DNP enhancement, scaling with the number of comb frequencies and limited only by the hyperfine-mediated electron linewidth. We demonstrate the technique for the optical hyperpolarization of 13C nuclei in powdered microdiamonds at low fields, increasing the DNP enhancement from 30 to 100 measured with respect to the thermal signal at 7T. For low concentrations of broad linewidth electron radicals [e.g., TEMPO ((2,2,6,6-tetramethylpiperidin-1-yl)oxyl)], these multiplicative gains could exceed an order of magnitude.

A novel method for quantitative measurements of gene expression in single living cells.

Gene expression is at the heart of virtually any biological process, and its deregulation is at the source of numerous pathological conditions. While impressive progress has been made in genome-wide measurements of mRNA and protein expression levels, it is still challenging to obtain highly quantitative measurements in single living cells. Here we describe a novel approach based on internal tagging of endogenous proteins with a reporter allowing luminescence and fluorescence time-lapse microscopy. Using luminescence microscopy, fluctuations of protein expression levels can be monitored in single living cells with high sensitivity and temporal resolution over extended time periods. The integrated protein decay reporter allows measuring protein degradation rates in the absence of protein synthesis inhibitors, and in combination with absolute protein levels allows determining absolute amounts of proteins synthesized over the cell cycle. Finally, the internal tag can be excised by inducible expression of Cre recombinase, which enables to estimate endogenous mRNA half-lives. Our method thus opens new avenues in quantitative analysis of gene expression in single living cells.

Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets.

Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has transformed our understanding of differentiation during development, regeneration, and disease. However, lineage tracing is technically demanding, often restricted in time-resolution, and most scRNA-seq datasets are devoid of lineage information. Here we introduce Gene Expression Memory-based Lineage Inference (GEMLI), a computational tool allowing to robustly identify small to medium-sized cell lineages solely from scRNA-seq datasets. GEMLI allows to study heritable gene expression, to discriminate symmetric and asymmetric cell fate decisions and to reconstruct individual multicellular structures from pooled scRNA-seq datasets. In human breast cancer biopsies, GEMLI reveals previously unknown gene expression changes at the onset of cancer invasiveness. The universal applicability of GEMLI allows studying the role of small cell lineages in a wide range of physiological and pathological contexts, notably in vivo. GEMLI is available as an R package on GitHub ( https://github.com/UPSUTER/GEMLI ).

Single-molecule force spectroscopy of the Aplysia cell adhesion molecule reveals two homophilic bonds.

Aplysia californica neurons comprise a powerful model system for quantitative analysis of cellular and biophysical properties that are essential for neuronal development and function. The Aplysia cell adhesion molecule (apCAM), a member of the immunoglobulin superfamily of cell adhesion molecules, is present in the growth cone plasma membrane and involved in neurite growth, synapse formation, and synaptic plasticity. apCAM has been considered to be the Aplysia homolog of the vertebrate neural cell adhesion molecule (NCAM); however, whether apCAM exhibits similar binding properties and neuronal functions has not been fully established because of the lack of detailed binding data for the extracellular portion of apCAM. In this work, we used the atomic force microscope to perform single-molecule force spectroscopy of the extracellular region of apCAM and show for the first time (to our knowledge) that apCAM, like NCAM, is indeed a homophilic cell adhesion molecule. Furthermore, like NCAM, apCAM exhibits two distinct bonds in the trans configuration, although the kinetic and structural parameters of the apCAM bonds are quite different from those of NCAM. In summary, these single-molecule analyses further indicate that apCAM and NCAM are species homologs likely performing similar functions.

Fermentation of six different forages in the semi-continuous fermentation technique Caesitec.

The aim of the present study was to compare carbohydrate degradation of forages which store carbohydrates either predominantly as fructan or starch, in horses' hindgut. The effects of an abrupt change from hay-based feeding to green fodder-based feeding on the caecal flora were tested with the in vitro hindgut simulation technique 'Caesitec'. Six trials with different forages (English ryegrass, tall fescue, grass mixture-horses, grass mixture-cows, lucerne, white clover) were conducted. During a 4-day stabilisation period, samples were taken once a day before loading the fermenters with hay. After diet-change to forage-based feeding, samples were taken four times a day. Ammonia and pH-value were measured before and 1, 2 and 6 h after loading the 'Caesitec'. Gas formation was measured daily. Bacterial numbers, lactate and short chain fatty acids were detected at four time-points of each trial. The grass mixtures contained the highest amounts of fructan. The pH-values were in the physiological range from pH 6 up to 7 (6.58-6.83) by feeding all forages. Gas formation, anaerobic and aerobic bacterial numbers increased after diet change from hay to any forage. The maximum amount of fructan (3.75 g/kg) in swiss pasture did not cause a permanent pathological change in the hindgut-flora.

Visualization of spin dynamics in single nanosized magnetic elements.

The design of future spintronic devices requires a quantitative understanding of the microscopic linear and nonlinear spin relaxation processes governing the magnetization reversal in nanometer-scale ferromagnetic systems. Ferromagnetic resonance is the method of choice for a quantitative analysis of relaxation rates, magnetic anisotropy and susceptibility in a single experiment. The approach offers the possibility of coherent control and manipulation of nanoscaled structures by microwave irradiation. Here, we analyze the different excitation modes in a single nanometer-sized ferromagnetic stripe. Measurements are performed using a microresonator set-up which offers a sensitivity to quantitatively analyze the dynamic and static magnetic properties of single nanomagnets with volumes of (100 nm)(3). Uniform as well as non-uniform volume modes of the spin wave excitation spectrum are identified and found to be in excellent agreement with the results of micromagnetic simulations which allow the visualization of the spatial distribution of these modes in the nanostructures.

Electron paramagnetic resonance investigation of the electron-doped manganite La(1-x)Te(x)MnO3 (0.1 ≤ x ≤ 0.2).

The electron paramagnetic resonance (EPR) properties of the electron-doped manganite La(1-x)Te(x)MnO(3) (0.1 ≤ x ≤ 0.2) are investigated based on the data of EPR spectra, resistivity, and magnetic susceptibility. With decreasing temperature from 400 K, the EPR linewidth ΔH(PP) decreases and passes through a minimum at T(min), then substantially increases with further decreasing temperature. The broadening of the EPR linewidth above T(min) can be understood in terms of the increase in the relaxation rate of spin of e(g) polarons to the lattice with increasing temperature due to the similarity between the temperature dependence of the linewidth ΔH(pp)(T) and the conductivity σ(T). For the samples with x = 0.1 and 0.15, the conductivity activation energy E(σ) is comparable with the activation energy E(a) deduced from the linewidth. Whereas for the x = 0.2 sample, there is a large difference between E(σ) (0.2206 eV) and E(a) (0.0874 eV).

Optimal control pulses for subspectral editing in low field NMR.

Low field NMR is an inexpensive and low footprint technique to obtain physical, chemical, electronic and structural information on small molecules, but suffers from poor spectral dispersion, especially when applied to the analysis of mixtures. Subspectral editing employing optimal control pulses is a suitable approach to cope with the severe signal superpositions in complex mixture spectra at low field. In this contribution, the use of optimal control pulses is demonstrated to be feasible at a field strength as low as 0.5 T. The optimal control pulse shapes were calculated using the Krotov algorithm. Downsizing the complexity of the algorithm from exponential to polynomial is shown to be possible by using a system approach with each system corresponding to a (small) molecule. In this way compound selective excitation pulses can be calculated. The signals of substructures of the cyclopentenone molecule were excited using optimal control pulses calculated by the Krotov algorithm demonstrating the feasibility of subspectral editing. Likewise, for a mixture of benzoic acid and alanine, editing of the signals of either benzoic acid or alanine employing optimal control pulses was shown to be possible. The obtained results are very promising and can be extended to the targeted analysis of complex mixtures such as biofluids or metabolic samples at low field strengths opening access for benchtop NMR to point of care settings.

Adaptation to metabolic acidosis and its recovery are associated with changes in anion exchanger distribution and expression in the cortical collecting duct.

It is well known that acid/base disturbances modulate proton/bicarbonate transport in the cortical collecting duct. To study the adaptation further we measured the effect of three days of acidosis followed by the rapid recovery from this acidosis on the number and type of intercalated cells in the rabbit cortical collecting duct. Immunofluorescence was used to determine the expression of apical pendrin in ß-intercalated cells and the basolateral anion exchanger (AE1) in α-intercalated cells. Acidosis resulted in decreased bicarbonate and increased proton secretion, which correlated with reduced pendrin expression and the number of pendrin-positive cells, as well as decreased pendrin mRNA and protein abundance in this nephron segment. There was a concomitant increase of basolateral AE1 and α-cell number. Intercalated cell proliferation did not seem to play a role in the adaptation to acidosis. Alkali loading for 6-20 h after acidosis doubled the bicarbonate secretory flux and reduced proton secretion. Pendrin and AE1 expression patterns returned to control levels, demonstrating that adaptive changes by intercalated cells are rapidly reversible. Thus, regulation of intercalated cell anion exchanger expression and distribution plays a key role in adaptation of the cortical collecting duct to perturbations of acid/base.

Invasive pneumococcal disease in children prior to implementation of the conjugate vaccine in the Zurich region, Switzerland.

OBJECTIVE: To describe symptoms, disease manifestations and outcome of invasive pneumococcal disease in children prior to implementation of the pneumococcal vaccine. PATIENTS AND METHODS: Analysis of children younger than 16 years of age with invasive pneumococcal disease (IPD; n = 119). Children with culture-confirmed IPD, without underlying illness at risk for invasive disease, were included. RESULTS: IPD in 90 children (age: median 2, mean 3.2 years) included 15 with meningitis, 16 with septicaemia, 14 with bacteraemia, 24 with pneumonia and 21 with skin, bone and joint infections. Symptoms of IPD most often described were fever and gastrointestinal symptoms (abdominal pain, vomiting, or diarrhoea), and coughing. More than 90% of children with pneumonia were coughing. Most importantly, clinical signs significantly predictive for severe IPD included tachycardia for sepsis, tachypnea for pneumonia, and meningeal signs for meningitis. Leukocyte, neutrophil and platelet counts were lower and C-reactive protein concentrations were higher on admission in children with complicated than in children with uncomplicated IPD but, due to wide overlap of these numbers, the difference was not of prognostic help to predict clinical course and outcome. Overall, 40% of children with IPD manifested complications and IPD showed a mortality rate of 6.6%. CONCLUSIONS: IPD is a serious disease with a high complication rate and mortality. The clinical signs tachycardia, tachypnea, and meningism were highly predictive for severe IPD. The initial clinical presentation and laboratory evaluation were mostly unpredictable with respect to complications and outcome in contrast to the clinical signs.

Room temperature "optical nanodiamond hyperpolarizer": Physics, design, and operation.

Dynamic Nuclear Polarization (DNP) is a powerful suite of techniques that deliver multifold signal enhancements in nuclear magnetic resonance (NMR) and MRI. The generated athermal spin states can also be exploited for quantum sensing and as probes for many-body physics. Typical DNP methods require the use of cryogens, large magnetic fields, and high power microwave excitation, which are expensive and unwieldy. Nanodiamond particles, rich in Nitrogen-Vacancy (NV) centers, have attracted attention as alternative DNP agents because they can potentially be optically hyperpolarized at room temperature. Here, unraveling new physics underlying an optical DNP mechanism first introduced by Ajoy et al. [Sci. Adv. 4, eaar5492 (2018)], we report the realization of a miniature "optical nanodiamond hyperpolarizer," where 13C nuclei within the diamond particles are hyperpolarized via the NV centers. The device occupies a compact footprint and operates at room temperature. Instrumental requirements are very modest: low polarizing fields, low optical and microwave irradiation powers, and convenient frequency ranges that enable miniaturization. We obtain the best reported optical 13C hyperpolarization in diamond particles exceeding 720 times of the thermal 7 T value (0.86% bulk polarization), corresponding to a ten-million-fold gain in averaging time to detect them by NMR. In addition, the hyperpolarization signal can be background-suppressed by over two-orders of magnitude, retained for multiple-minute long periods at low fields, and deployed efficiently even to 13C enriched particles. Besides applications in quantum sensing and bright-contrast MRI imaging, this work opens possibilities for low-cost room-temperature DNP platforms that relay the 13C polarization to liquids in contact with the high surface-area particles.

Transmission of growth cone traction force through apCAM-cytoskeletal linkages is regulated by Src family tyrosine kinase activity.

Tyrosine kinase activity is known to be important in neuronal growth cone guidance. However, underlying cellular mechanisms are largely unclear. Here, we report how Src family tyrosine kinase activity controls apCAM-mediated growth cone steering by regulating the transmission of traction forces through receptor-cytoskeletal linkages. Increased levels of tyrosine phosphorylation were detected at sites where beads coated with apCAM ligands were physically restrained to induce growth cone steering, but not at unrestrained bead binding sites. Interestingly, the rate and level of phosphotyrosine buildup near restrained beads were decreased by the myosin inhibitor 2,3-butanedione-2-monoxime, suggesting that tension promotes tyrosine kinase activation. While not affecting retrograde F-actin flow rates, genistein and the Src family selective tyrosine kinase inhibitors PP1 and PP2 strongly reduced the growth cone's ability to apply traction forces through apCAM-cytoskeletal linkages, assessed using the restrained bead interaction assay. Furthermore, increased levels of an activated Src family kinase were detected at restrained bead sites during growth cone steering events. Our results suggest a mechanism by which growth cones select pathways by sampling both the molecular nature of the substrate and its ability to withstand the application of traction forces.

The Ig superfamily cell adhesion molecule, apCAM, mediates growth cone steering by substrate-cytoskeletal coupling.

Dynamic cytoskeletal rearrangements are involved in neuronal growth cone motility and guidance. To investigate how cell surface receptors translate guidance cue recognition into these cytoskeletal changes, we developed a novel in vitro assay where beads, coated with antibodies to the immunoglobulin superfamily cell adhesion molecule apCAM or with purified native apCAM, replaced cellular substrates. These beads associated with retrograde F-actin flow, but in contrast to previous studies, were then physically restrained with a microneedle to simulate interactions with noncompliant cellular substrates. After a latency period of approximately 10 min, we observed an abrupt increase in bead-restraining tension accompanied by direct extension of the microtubule-rich central domain toward sites of apCAM bead binding. Most importantly, we found that retrograde F-actin flow was attenuated only after restraining tension had increased and only in the bead interaction axis where preferential microtubule extension occurred. These cytoskeletal and structural changes are very similar to those reported for growth cone interactions with physiological targets. Immunolocalization using an antibody against the cytoplasmic domain of apCAM revealed accumulation of the transmembrane isoform of apCAM around bead-binding sites. Our results provide direct evidence for a mechanical continuum from apCAM bead substrates through the peripheral domain to the central cytoplasmic domain. By modulating functional linkage to the underlying actin cytoskeleton, cell surface receptors such as apCAM appear to enable the application of tensioning forces to extracellular substrates, providing a mechanism for transducing retrograde flow into guided growth cone movement.

Binding between the neural cell adhesion molecules axonin-1 and Nr-CAM/Bravo is involved in neuron-glia interaction.

Neural cell adhesion molecules of the immunoglobulin superfamily mediate cellular interactions via homophilic binding to identical molecules and heterophilic binding to other family members or structurally unrelated cell-surface glycoproteins. Here we report on an interaction between axonin-1 and Nr-CAM/Bravo. In search for novel ligands of axonin-1, fluorescent polystyrene microspheres conjugated with axonin-1 were found to bind to peripheral glial cells from dorsal root ganglia. By antibody blockage experiments an axonin-1 receptor on the glial cells was identified as Nr-CAM. The specificity of the interaction was confirmed with binding studies using purified axonin-1 and Nr-CAM. In cultures of dissociated dorsal root ganglia antibodies against axonin-1 and Nr-CAM perturbed the formation of contacts between neurites and peripheral glial cells. Together, these results implicate a binding between axonin-1 of the neuritic and Nr-CAM of the glial cell membrane in the early phase of axon ensheathment in the peripheral nervous system.

A direct interaction of axonin-1 with NgCAM-related cell adhesion molecule (NrCAM) results in guidance, but not growth of commissural axons.

An interaction of growth cone axonin-1 with the floor-plate NgCAM-related cell adhesion molecule (NrCAM) was shown to play a crucial role in commissural axon guidance across the midline of the spinal cord. We now provide evidence that axonin-1 mediates a guidance signal without promoting axon elongation. In an in vitro assay, commissural axons grew preferentially on stripes coated with a mixture of NrCAM and NgCAM. This preference was abolished in the presence of anti-axonin-1 antibodies without a decrease in neurite length. Consistent with these findings, commissural axons in vivo only fail to extend along the longitudinal axis when both NrCAM and NgCAM interactions, but not when axonin-1 and NrCAM or axonin-1 and NgCAM interactions, are perturbed. Thus, we conclude that axonin-1 is involved in guidance of commissural axons without promoting their growth.

Hyperpolarized relaxometry based nuclear T1 noise spectroscopy in diamond.

The origins of spin lifetimes in quantum systems is a matter of importance in several areas of quantum information. Spectrally mapping spin relaxation processes provides insight into their origin and motivates methods to mitigate them. In this paper, we map nuclear relaxation in a prototypical system of [Formula: see text] nuclei in diamond coupled to Nitrogen Vacancy (NV) centers over a wide field range (1 mT-7 T). Nuclear hyperpolarization through optically pumped NV electrons allows signal measurement savings exceeding million-fold over conventional methods. Through a systematic study with varying substitutional electron (P1 center) and [Formula: see text] concentrations, we identify the operational relaxation channels for the nuclei at different fields as well as the dominant role played by [Formula: see text] coupling to the interacting P1 electronic spin bath. These results motivate quantum control techniques for dissipation engineering to boost spin lifetimes in diamond, with applications including engineered quantum memories and hyperpolarized [Formula: see text] imaging.

Plant enemy-derived elicitors increase the foliar tannin concentration of Onobrychis viciifolia without a trade-off to growth.

BACKGROUND AND AIMS: Molecular experiments suggest that the regulation of the biosynthesis of condensed tannin (CT) is sensitive to the presence of plant enemies. The enemy-specific response of CT concentrations to simulated attacks by pathogenic fungi, bacteria or herbivores was studied in Onobrychis viciifolia grown at four levels of nutrient availability. It was hypothesized that CT concentrations increase in response to an attack, and that constitutive and induced levels of CT are higher at low than at high nutrient availability. Investment in CT was also predicted to be negatively related to plant growth. METHODS: Recently discovered substances by which plants recognize their opponents (i.e. elicitors) were used to simulate attacks to Onobrychis viciifolia grown at 0.0027, 0.075, 0.67 or 2 mm phosphorus in the nutrient solution. KEY RESULTS: Relative growth rate and final biomass (P < 0.001) were highest at 0.67 mm of phosphorus. CT concentrations decreased with increasing phosphorus availability, from 94.9 to 69.0 mg g(-1) leaf dry weight (P < 0.001). Compared with unscathed plants, sterile mere mechanical wounding reduced tannin concentrations from 83.8 to 69.3 mg g(-1) leaf dry weight (P < 0.01). Local CT concentrations were higher when wounded leaves were additionally treated with fungal (+15.9 %), bacterial (+19.6 %) or insect (+31.0 %) elicitors (each elicitor; P < 0.05); however, only the insect elicitor (saliva of the lepidopteron Spodoptera littoralis) induced CT concentrations higher than those of unscathed leaves. CONCLUSIONS: CT concentrations were inducible in the vicinity of the wound but the level of induction was unrelated to the nutrient status of the plant. There was no evidence of a growth-defence trade-off. The inverse relationship between CT concentrations and nutrient availability appears to reflect passive growth dilution at high nutrient availability, rather than surplus CT production at low nutrient availability.

Antimicrobial resistance of Yersinia enterocolitica strains from human patients, pigs and retail pork in Switzerland.

To obtain basic data for future resistance monitoring programs, 386 Yersinia enterocolitica strains from human patients, raw retail pork and pig feces were tested for their susceptibilities to 16 antimicrobial agents and two antimicrobial growth promoters (carbadox and olaquindox). No strains were resistant to ceftriaxone, cefuroxime, ciprofloxacine, gentamicin, kanamycin, neomycin or polymyxin. Although in Switzerland carbadox and olaquindox were used as growth promoters for pigs for over 25 years, all strains were susceptible to them. In contrast, there were high levels of resistance to ampicillin, cefalothin and amoxicillin/clavulanic acid. Less than 10% of clinical isolates and strains from pig feces were resistant to streptomycin, sulfonamide, trimethoprim/sulfamethoxazole, tetracyclin, trimethoprim and chloramphenicol, but strains from retail pork were all susceptible to these antimicrobial agents. This finding suggested that pork is probably not a major source of Y. enterocolitica that cause human infections in Switzerland. A difference between clinical isolates and strains from pork was also shown by serotyping. Clinical isolates frequently belonged to the O3 and O9 groups whereas these two serotypes were not found in strains from pork. Resistance to multiple antimicrobial agents was rare. When examined by pulsed field gel electrophoresis (PFGE), two strains of fecal origin with an identical pattern of resistance to six antimicrobial agents were shown to be unrelated. Of four clinical isolates with resistances to five antimicrobial agents, two were of the same pulsotype. Retrospectively, it was found that these strains came from two members of the same household and thus represented a mini-outbreak.

An emerging link between cytoskeletal dynamics and cell adhesion molecules in growth cone guidance.

It has become increasingly evident that growth cone guidance depends on the concerted actions of cytoskeletal proteins, molecular motors and cell adhesion molecules. Recent studies suggest that modulation of coupling between extracellular substrates and intracellular cytoskeletal networks via cell surface receptors is an important mechanism for regulating directed neuronal growth.