Efficient Synthetic Access to Stable Isotope Labelled Pseudouridine Phosphoramidites for RNA NMR Spectroscopy.

Here we report the efficient synthetic access to 13C/15N-labelled pseudouridine phosphoramidites, which were incorporated into a binary H/ACA box guide RNA/product complex comprising 77 nucleotides (nts) in total and into a 75 nt E. coli tRNAGly. The stable isotope (SI) labelled pseudouridines were produced via a highly efficient chemo-enzymatic synthesis. 13C/15N labelled uracils were produced via chemical synthesis and enzymatically converted to pseudouridine 5'-monophosphate (ΨMP) by using YeiN, a Ψ-5'-monophosphate C-glycosidase. Removal of the 5'-phosphate group yielded the desired pseudouridine nucleoside (Ψ), which was transformed into a phosphoramidite building suitable for RNA solid phase synthesis. A Ψ -building block carrying both a 13C and a 15N label was incorporated into a product RNA and the complex formation with a 63 nt H/ACA box RNA could be observed via NMR. Furthermore, the SI labelled pseudouridine building block was used to determine imino proton bulk water exchange rates of a 75 nt E. coli tRNAGly CCmnm5U, identifying the TΨC-loop 5-methyluridine as a modifier of the exchange rates. The efficient synthetic access to SI-labelled Ψ building blocks will allow the solution and solid-state NMR spectroscopic studies of Ψ containing RNAs and will facilitate the mass spectrometric analysis of Ψ-modified nucleic acids.

An optical-frequency synthesizer using integrated photonics.

Optical-frequency synthesizers, which generate frequency-stable light from a single microwave-frequency reference, are revolutionizing ultrafast science and metrology, but their size, power requirement and cost need to be reduced if they are to be more widely used. Integrated-photonics microchips can be used in high-coherence applications, such as data transmission 1 , highly optimized physical sensors 2 and harnessing quantum states 3 , to lower cost and increase efficiency and portability. Here we describe a method for synthesizing the absolute frequency of a lightwave signal, using integrated photonics to create a phase-coherent microwave-to-optical link. We use a heterogeneously integrated III-V/silicon tunable laser, which is guided by nonlinear frequency combs fabricated on separate silicon chips and pumped by off-chip lasers. The laser frequency output of our optical-frequency synthesizer can be programmed by a microwave clock across 4 terahertz near 1,550 nanometres (the telecommunications C-band) with 1 hertz resolution. Our measurements verify that the output of the synthesizer is exceptionally stable across this region (synthesis error of 7.7 × 10-15 or below). Any application of an optical-frequency source could benefit from the high-precision optical synthesis presented here. Leveraging high-volume semiconductor processing built around advanced materials could allow such low-cost, low-power and compact integrated-photonics devices to be widely used.

Contributions towards variable temperature shielding for compact NMR instruments.

The application of compact NMR instruments to hot flowing samples or exothermically reacting mixtures is limited by the temperature sensitivity of permanent magnets. Typically, such temperature effects directly influence the achievable magnetic field homogeneity and hence measurement quality. The internal-temperature control loop of the magnet and instruments is not designed for such temperature compensation. Passive insulation is restricted by the small dimensions within the magnet borehole. Here, we present a design approach for active heat shielding with the aim of variable temperature control of NMR samples for benchtop NMR instruments using a compressed airstream which is variable in flow and temperature. Based on the system identification and surface temperature measurements through thermography, a model predictive control was set up to minimise any disturbance effect on the permanent magnet from the probe or sample temperature. This methodology will facilitate the application of variable-temperature shielding and, therefore, extend the application of compact NMR instruments to flowing sample temperatures that differ from the magnet temperature.

Mining and urbanization affect river chemical water quality and macroinvertebrate communities in the upper Selenga River basin, Mongolia (revised version).

Mongolia is a country with a quickly growing economy mainly based on the mining of gold, copper, coal, and other minerals. Mining, urbanization, and agriculture impact the water quality in the upper Selenga River basin in northern Mongolia, which is the center of the Mongolian economy. Previous measurements of pollution loads were alarming, but restricted to chemical measurements. Here, for the first time, we combine freshwater biomonitoring and laboratory water quality data across a broad gradient of water quality and land use intensity. We track the effects of different types of pollution on aquatic invertebrates and test their use as bioindicators. We collected water samples, environmental parameters, and macroinvertebrates at 36 sampling sites at the rivers of Tuul, Kharaa, and Orkhon and their tributaries Sugnugur, Boroo, Sharyn Gol, Gatsuurt, and Yeröö. PCA of catchment water quality distinguished three groups of pollutants prevalent at the sites, (1) nutrients, (2) salt ions (Cl-, Na+, Mg2+, So42-, Ca2+) and mining by-products (B, Sr, U, Mo), and (3) (heavy) metals, which often exceeded regulatory standards. We recorded a total of 59 macroinvertebrate taxa belonging to 31 families in seven insect orders plus Amphipoda and Gastropoda. Species diversity declined with higher impact. Five environmental factors structured macroinvertebrate community composition in RDA: elevation of sample location, site total nitrogen, dissolved oxygen, electrical conductivity, and water chemistry. We conclude that macroinvertebrate communities are an appropriate and inexpensive tool for monitoring water quality in Mongolia and suggest government action to establish a long-term monitoring program.

Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.

The flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free-living and symbiotic bacteria have developed, alongside hydrolysis, a non-hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase-catalyzed reactions. Here, based on study of enzymes from the phytopathogen Agrobacterium tumefaciens, we reveal a conserved Mn2+ metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3-keto-glucosides and water addition to the resulting 2-hydroxy-3-keto-glycal product, yielding 3-keto-glucose. Extending our search of GUL-encoded putative lyases to the human gut commensal Bacteroides thetaiotaomicron, we discover a Ca2+ metallocenter active site in a putative glycoside hydrolase-like protein and demonstrate its catalytic function in the eliminative cleavage of 3-keto-glucosides of opposite (α) anomeric configuration as preferred by the A. tumefaciens enzyme (ß). Structural and biochemical comparisons reveal the molecular-mechanistic origin of 3-keto-glucoside lyase stereo-complementarity. Our findings identify a basic set of GUL-encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in the bacterial domain of life.

Power-Law Density of States in Organic Solar Cells Revealed by the Open-Circuit Voltage Dependence of the Ideality Factor.

The density of states (DOS) is fundamentally important for understanding physical processes in organic disordered semiconductors, yet hard to determine experimentally. We evaluated the DOS by considering recombination via tail states and using the temperature and open-circuit voltage (V_{oc}) dependence of the ideality factor. By performing Suns-V_{oc} measurements, we find that the energetic disorder increases deeper into the band gap, which is not expected for a Gaussian or exponential DOS. The linear dependence of the disorder on energy reveals the power-law DOS in organic solar cells.

Microresonator-based solitons for massively parallel coherent optical communications.

Solitons are waveforms that preserve their shape while propagating, as a result of a balance of dispersion and nonlinearity. Soliton-based data transmission schemes were investigated in the 1980s and showed promise as a way of overcoming the limitations imposed by dispersion of optical fibres. However, these approaches were later abandoned in favour of wavelength-division multiplexing schemes, which are easier to implement and offer improved scalability to higher data rates. Here we show that solitons could make a comeback in optical communications, not as a competitor but as a key element of massively parallel wavelength-division multiplexing. Instead of encoding data on the soliton pulse train itself, we use continuous-wave tones of the associated frequency comb as carriers for communication. Dissipative Kerr solitons (DKSs) (solitons that rely on a double balance of parametric gain and cavity loss, as well as dispersion and nonlinearity) are generated as continuously circulating pulses in an integrated silicon nitride microresonator via four-photon interactions mediated by the Kerr nonlinearity, leading to low-noise, spectrally smooth, broadband optical frequency combs. We use two interleaved DKS frequency combs to transmit a data stream of more than 50 terabits per second on 179 individual optical carriers that span the entire telecommunication C and L bands (centred around infrared telecommunication wavelengths of 1.55 micrometres). We also demonstrate coherent detection of a wavelength-division multiplexing data stream by using a pair of DKS frequency combs-one as a multi-wavelength light source at the transmitter and the other as the corresponding local oscillator at the receiver. This approach exploits the scalability of microresonator-based DKS frequency comb sources for massively parallel optical communications at both the transmitter and the receiver. Our results demonstrate the potential of these sources to replace the arrays of continuous-wave lasers that are currently used in high-speed communications. In combination with advanced spatial multiplexing schemes and highly integrated silicon photonic circuits, DKS frequency combs could bring chip-scale petabit-per-second transceivers into reach.

Two Novel Iboga-Type and an Oxindole Glucuronide Alkaloid from Tabernaemontana peduncularis Disclose Related Biosynthetic Pathways to Tabernaemontana divaricata.

Phytochemical investigation of the two Tabernaemontana species (Apocynaceae) T. peduncularis Wall. and T. divaricata (L.) R.Br. ex Roem. & Schult. indicated closely related biosynthetic pathways leading to lipophilic and hydrophilic alkaloids. In total, 18 specialized metabolites comprising indole-derived alkaloid aglycones, three oxindole-derived alkaloid glycosides, and two iridoid glucosides could be identified in the studied species. Among the alkaloids, the two Iboga-type alkaloids 3,7-coronaridine isoindolenine, coronaridine 3,4-iminium and a javaniside derivative bearing a glucuronic acid, named javanuronic acid, could be described by spectroscopic and spectrometric methods for the first time. A docking experiment using alpha-fold was performed to generate a protein model of the enzyme 7-deoxyloganetic acid glucosyl transferase. Performed bioassays exhibited a growth reduction of neonate Spodoptera littoralis larvae and reduced cell viability of HepG2 cells of the extracts containing Iboga alkaloids, whilst the javaniside derivatives containing hydrophilic fraction did not show any effects. These findings indicate a high flexibility in the formation of bioactive indole alkaloid aglycones by Tabernaemontana species and also evidence similar accumulation trends in both species as well as indicate that biosynthetic routes leading to oxindole alkaloids like javanisides are more widespread than reported. Furthermore, the incorporation of the three novel compounds into potential biosynthetic pathways is discussed.

Mining and urbanization affect river chemical water quality and macroinvertebrate communities in the upper Selenga River Basin, Mongolia.

Mongolia is a country with a quickly growing economy mainly based on mining of gold, copper, coal, and other minerals. Mining, urbanization, and agriculture impact the water quality in the upper Selenga River Basin in northern Mongolia, which is the center of the Mongolian economy. Previous measurements of pollution loads were alarming, but restricted to chemical measurements. Here, for the first time, we combine freshwater biomonitoring and laboratory water quality data across a broad gradient of water quality and land use intensity. We track the effects of different types of pollution on aquatic invertebrates and test their use as bioindicators. We collected water samples, environmental parameters, and macroinvertebrates at 36 sampling sites at the rivers of Tuul, Kharaa, and Orkhon and their tributaries Sugnugur, Boroo, Sharyn Gol, Gatsuurt, and Yeröö. PCA of catchment water quality distinguished three groups of pollutants prevalent at the sites: (1) nutrients, (2) saline components (Cl-, Na +, Mg2+, SO42-, Ca2+) and mining by-products (B, Sr, U, Mo), and (3) (heavy) metals, which often exceeded regulatory standards. We recorded a total of 59 macroinvertebrate taxa belonging to 32 families in seven insect orders plus Amphipoda and Gastropoda. Species diversity declined with higher impact. Five environmental factors structured macroinvertebrate community composition in RDA: elevation of sample location, site total nitrogen, dissolved oxygen, electrical conductivity, and water chemistry. We conclude that macroinvertebrate communities are an appropriate and inexpensive tool for monitoring water quality in Mongolia and suggest government action to establish a long-term monitoring program.

Continuous process technology for glucoside production from sucrose using a whole cell-derived solid catalyst of sucrose phosphorylase.

Advanced biotransformation processes typically involve the upstream processing part performed continuously and interlinked tightly with the product isolation. Key in their development is a catalyst that is highly active, operationally robust, conveniently produced, and recyclable. A promising strategy to obtain such catalyst is to encapsulate enzymes as permeabilized whole cells in porous polymer materials. Here, we show immobilization of the sucrose phosphorylase from Bifidobacterium adolescentis (P134Q-variant) by encapsulating the corresponding E. coli cells into polyacrylamide. Applying the solid catalyst, we demonstrate continuous production of the commercial extremolyte 2-α-D-glucosyl-glycerol (2-GG) from sucrose and glycerol. The solid catalyst exhibited similar activity (≥70%) as the cell-free extract (~800 U g-1 cell wet weight) and showed excellent in-operando stability (40 °C) over 6 weeks in a packed-bed reactor. Systematic study of immobilization parameters related to catalyst activity led to the identification of cell loading and catalyst particle size as important factors of process optimization. Using glycerol in excess (1.8 M), we analyzed sucrose conversion dependent on space velocity (0.075-0.750 h-1) and revealed conditions for full conversion of up to 900 mM sucrose. The maximum 2-GG space-time yield reached was 45 g L-1 h-1 for a product concentration of 120 g L-1. Collectively, our study establishes a step-economic route towards a practical whole cell-derived solid catalyst of sucrose phosphorylase, enabling continuous production of glucosides from sucrose. This strengthens the current biomanufacturing of 2-GG, but also has significant replication potential for other sucrose-derived glucosides, promoting their industrial scale production using sucrose phosphorylase. KEY POINTS: • Cells of sucrose phosphorylase fixed in polyacrylamide were highly active and stable. • Solid catalyst was integrated with continuous flow to reach high process efficiency. • Generic process technology to efficiently produce glucosides from sucrose is shown.

Standardization and Control of Grignard Reactions in a Universal Chemical Synthesis Machine using online NMR.

A big problem with the chemistry literature is that it is not standardized with respect to precise operational parameters, and real time corrections are hard to make without expert knowledge. This lack of context means difficult reproducibility because many steps are ambiguous, and hence depend on tacit knowledge. Here we present the integration of online NMR into an automated chemical synthesis machine (CSM aka. "Chemputer" which is capable of small-molecule synthesis using a universal programming language) to allow automated analysis and adjustment of reactions on the fly. The system was validated and benchmarked by using Grignard reactions which were chosen due to their importance in synthesis. The system was monitored in real time using online-NMR, and spectra were measured continuously during the reactions. This shows that the synthesis being done in the Chemputer can be dynamically controlled in response to feedback optimizing the reaction conditions according to the user requirements.

Kramers-Kronig detection of four 20 Gbaud 16-QAM channels using Kerr combs for a shared phase estimation.

We experimentally demonstrate Kramers-Kronig detection of four 20 Gbaud 16-quadrature-amplitude-modulated (QAM) channels after 50 km fiber transmission using two soliton Kerr combs as signal sources and local oscillators. The estimated carrier phase at the receiver for each of the channels is relatively similar due to the coherence between the frequency comb lines. The standard deviation of the estimated carrier phase difference of the channels is less than 0.08 rad after 50 km single-mode fiber (SMF) transmission. This enables the carrier phase recovery derived from one channel to be shared among multiple channels. In the back-to-back scenario, the bit error rate (BER) performance for shared carrier phase recovery shows an optical signal-to-noise ratio penalty of ${\sim}{0.5}\;{\rm dB}$∼0.5dB compared to the BER performance for carrier phase recovery when derived for each channel independently. BERs below the forward error correction threshold are achieved after 50 km SMF transmission with both independent and shared carrier phase recovery for four 20-Gbaud 16-QAM signals.

Artificial neural networks for quantitative online NMR spectroscopy.

Industry 4.0 is all about interconnectivity, sensor-enhanced process control, and data-driven systems. Process analytical technology (PAT) such as online nuclear magnetic resonance (NMR) spectroscopy is gaining in importance, as it increasingly contributes to automation and digitalization in production. In many cases up to now, however, a classical evaluation of process data and their transformation into knowledge is not possible or not economical due to the insufficiently large datasets available. When developing an automated method applicable in process control, sometimes only the basic data of a limited number of batch tests from typical product and process development campaigns are available. However, these datasets are not large enough for training machine-supported procedures. In this work, to overcome this limitation, a new procedure was developed, which allows physically motivated multiplication of the available reference data in order to obtain a sufficiently large dataset for training machine learning algorithms. The underlying example chemical synthesis was measured and analyzed with both application-relevant low-field NMR and high-field NMR spectroscopy as reference method. Artificial neural networks (ANNs) have the potential to infer valuable process information already from relatively limited input data. However, in order to predict the concentration at complex conditions (many reactants and wide concentration ranges), larger ANNs and, therefore, a larger training dataset are required. We demonstrate that a moderately complex problem with four reactants can be addressed using ANNs in combination with the presented PAT method (low-field NMR) and with the proposed approach to generate meaningful training data. Graphical abstract.

Second- and third-order nonlinear wavelength conversion in an all-optically poled Si3N4 waveguide.

Silicon nitride (Si3N4) is commonly employed to integrate third-order nonlinear optical processes on a chip. Its amorphous state, however, inhibits significant second-order nonlinear response. Recently, second-harmonic generation enhancement has been observed in Si3N4 waveguides after an all-optical poling (AOP) method. Here we demonstrate that, after AOP of a Si3N4 waveguide, for up to 2 W of coupled pump power, the same telecom-band signal undergoes larger interband wavelength conversion efficiency, based on sum-frequency generation (SFG), than intraband wavelength conversion, based on four-wave mixing. We also confirm the appearance of a phase-matching condition after AOP by measuring the conversion bandwidth and efficiency of SFG at different pump wavelengths.

Orthogonally polarized frequency comb generation from a Kerr comb via cross-phase modulation.

We experimentally demonstrate that a single microresonator can emit two orthogonally polarized individually coherent combs: (i) a strong polarized soliton comb and (ii) an orthogonally polarized continuous wave seeded weaker comb, generated from the first one via cross-phase modulation, sharing the repetition rate of the soliton comb. Experimental results show that the power of the transverse electric-polarized seed can be well below the threshold of comb generation (e.g., 0.1 mW). In addition, simulations show that a dark pulse could be generated in the anomalous dispersion regime by a bright soliton when the two orthogonally polarized modes have the same group velocity in the microresonator.

Reconfigurable optical generation of nine Nyquist WDM channels with sinc-shaped temporal pulse trains using a single microresonator-based Kerr frequency comb.

Sinc-shaped temporal pulse trains have a spectrally efficient, rectangular Nyquist spectrum. We demonstrate the simultaneous and reconfigurable optical generation of multiple Nyquist-shaped wavelength-division-multiplexed (WDM) channels having temporal sinc-shaped pulse trains as data carriers. The channels are generated through the insertion of coherent lines using cascaded continuous-wave amplitude modulation around the spectral lines of a microresonator-based Kerr optical frequency comb. For each of nine Kerr frequency comb lines, we insert sub-groups of uniform and coherent lines to generate nine WDM channels. The deviations from ideal Nyquist pulses for the nine channels at repetition rates of 6 and 2 GHz are between 4.2%-6.1% and 2%-4.5%, respectively. Each WDM channel is modulated with on-off keying (OOK) at 6 Gbit/s. In addition, we show the reconfigurability of this method by varying the number of WDM channels, the generated sinc-shaped pulse train repetition rates, the duration, and the number of zero-crossings.

Influence of Surface Wettability on Discharges from Water Drops in Electric Fields.

It is known that electrified droplets deform and may become unstable when the electric field they are exposed to reaches a certain critical value. These instabilities are accompanied by electric discharges due to the local enhancement of the electric field caused by the deformed droplets. Here we report and highlight an interesting aspect of the behavior of unstable water droplets and discharge generation: by implementing wettability engineering, we can manipulate these discharges. We demonstrate that wettability strongly influences the shape of a droplet that is exposed to an electric field. The difference in shape is directly related to differences in the critical value of the applied electric field at which inception of discharge occurs. Using theoretical models, we can predict and sufficiently support our observations. Thus, by tailoring the wettability of the surface, we can control droplet's behavior from expediting the discharge inception to completely restricting it.

Dominance-diversity relationships in ant communities differ with invasion.

The relationship between levels of dominance and species richness is highly contentious, especially in ant communities. The dominance-impoverishment rule states that high levels of dominance only occur in species-poor communities, but there appear to be many cases of high levels of dominance in highly diverse communities. The extent to which dominant species limit local richness through competitive exclusion remains unclear, but such exclusion appears more apparent for non-native rather than native dominant species. Here we perform the first global analysis of the relationship between behavioral dominance and species richness. We used data from 1,293 local assemblages of ground-dwelling ants distributed across five continents to document the generality of the dominance-impoverishment rule, and to identify the biotic and abiotic conditions under which it does and does not apply. We found that the behavioral dominance-diversity relationship varies greatly, and depends on whether dominant species are native or non-native, whether dominance is considered as occurrence or relative abundance, and on variation in mean annual temperature. There were declines in diversity with increasing dominance in invaded communities, but diversity increased with increasing dominance in native communities. These patterns occur along the global temperature gradient. However, positive and negative relationships are strongest in the hottest sites. We also found that climate regulates the degree of behavioral dominance, but differently from how it shapes species richness. Our findings imply that, despite strong competitive interactions among ants, competitive exclusion is not a major driver of local richness in native ant communities. Although the dominance-impoverishment rule applies to invaded communities, we propose an alternative dominance-diversification rule for native communities.

Double inverse nanotapers for efficient light coupling to integrated photonic devices.

Efficient light coupling to integrated photonic devices is of key importance to a wide variety of applications. "Inverse nanotapers" are widely used, in which the waveguide width is reduced to match an incident mode. Here, we demonstrate novel "double inverse" tapers, in which we reduce both the waveguide height and width. We demonstrate >45% chip-through coupling efficiency for both the transverse electric and transverse magnetic polarizations in Si3N4 tapers of >500 nm width, in comparison to regular inverse tapers that necessitate <100 nm width. The double inverse tapers show polarization-independent coupling and allow the fabrication using photolithography, relevant for applications at near-infrared and visible wavelengths, e.g., supercontinuum and soliton microcomb generation.