Fiber-connectorized ultrafast-laser-inscribed K-band integrated optics beam combiner for the CHARA telescope array.

A fiber-connectorized K-band integrated-optics two-telescope beam combiner was developed for long-baseline interferometry at the CHARA telescope array utilizing the ultrafast laser inscription (ULI) technique. Single-mode waveguide insertion losses were measured to be ∼1.1d B over the 2-2.3 µm window. The development of asymmetric directional couplers enabled the construction of a beam combiner that includes a 50:50 coupler for interferometric combination and two ∼75:25 couplers for photometric calibration. The visibility of the bare beam combiner was measured at 87% and then at 82% after fiber-connectorization by optimizing the input polarization. These results indicate that ULI technique can fabricate efficient fiber-connectorized K-band beam combiners for astronomical purposes.

Six-telescope integrated optics beam combiner fabricated using ultrafast laser inscription for J- and H-band astronomy.

We have built and characterized, to our knowledge, the first six-telescope discrete beam combiner (DBC) for stellar interferometry in the astronomical J-band. It is the DBC with the largest number of beam combinations and was manufactured using ultrafast laser inscription in borosilicate glass, with a throughput of ≈56%. For calibration of the visibility-to-pixel matrix, we use a two-input Michelson interferometer and extract the complex visibility. A visibility amplitude of 1.05 and relative precision of 2.9% and 3.8% are extracted for 1328 nm and 1380 nm, respectively. Broadband (≤40n m) characterization is affected by dispersion but shows similar performance.

N-Heterocyclization in Gliotoxin Biosynthesis is Catalyzed by a Distinct Cytochrome P450 Monooxygenase.

Gliotoxin and related epidithiodiketopiperazines (ETP) from diverse fungi feature highly functionalized hydroindole scaffolds with an array of medicinally and ecologically relevant activities. Mutation analysis, heterologous reconstitution, and biotransformation experiments revealed that a cytochrome P450 monooxygenase (GliF) from the human-pathogenic fungus Aspergillus fumigatus plays a key role in the formation of the complex heterocycle. In vitro assays using a biosynthetic precursor from a blocked mutant showed that GliF is specific to ETPs and catalyzes an unprecedented heterocyclization reaction that cannot be emulated with current synthetic methods. In silico analyses indicate that this rare biotransformation takes place in related ETP biosynthetic pathways.

Design, simulation and characterization of integrated photonic spectrographs for astronomy: generation-I AWG devices based on canonical layouts.

We present an experimental study on our first generation of custom-developed arrayed waveguide gratings (AWG) on a silica platform for spectroscopic applications in near-infrared astronomy. We provide a comprehensive description of the design, numerical simulation and characterization of several AWG devices aimed at spectral resolving powers of 15,000-60,000 in the astronomical H-band. We evaluate the spectral characteristics of the fabricated devices in terms of insertion loss and estimated spectral resolving power and compare the results with numerical simulations. We estimate resolving powers of up to 18,900 from the output channel 3-dB transmission bandwidth. Based on the first characterization results, we select two candidate AWGs for further processing by removal of the output waveguide array and polishing the output facet to optical quality with the goal of integration as the primary diffractive element in a cross-dispersed spectrograph. We further study the imaging properties of the processed AWGs with regards to spectral resolution in direct imaging mode, geometry-related defocus aberration, and polarization sensitivity of the spectral image. We identify phase error control, birefringence control, and aberration suppression as the three key areas of future research and development in the field of high-resolution AWG-based spectroscopy in astronomy.

Design, simulation and characterization of integrated photonic spectrographs for astronomy II: low-aberration Generation-II AWG devices with three stigmatic points.

In the second part of our series on integrated photonic spectrographs for astronomy, we present theoretical and experimental results on the design, simulation and characterization of custom-manufactured silica-on-silicon arrayed waveguide gratings (AWGs) constructed using the three-stigmatic-point method. We derive several mid-to-high resolution field-flattened AWG designs, targeting resolving powers of 11,000 - 35,000 in the astronomical H-band, by iterative computation of differential coefficients of the optical path function. We use numerical simulations to study the imaging properties of the designs in a wide wavelength range between 1500 nm and 1680 nm. We theoretically discuss the design-specific degradation of spectral resolving power at far-off-centre wavelengths and suggest possible solutions. In the experimental section, we provide characterization results of seven manufactured AWG devices of varying free spectral range and resolution. We obtain estimates on spectral resolving powers of up to 27,600 for polarized input at 1550 nm from measurements of the channel transmission bandwidth. Furthermore, we numerically predict expected resolving powers of up to 36,000 in the polarized mode and up to 24,000 in the unpolarized mode for direct continuous imaging of the spectrum.

Simulations of mode-selective photonic lanterns for efficient coupling of starlight into the single-mode regime.

In ground-based astronomy, starlight distorted by the atmosphere couples poorly into single-mode waveguides, but a correction by adaptive optics, even if only partial, can boost coupling into the few-mode regime, allowing the use of photonic lanterns to convert into multiple single-mode beams. Corrected wavefronts result in focal patterns that couple mostly with circularly symmetric waveguide modes. A mode-selective photonic lantern is hence proposed to convert multimode light into a subset of single-mode waveguides of the standard photonic lantern, thereby reducing the required number of outputs. We ran simulations to show that only two out of the six waveguides of a 1×6 photonic lantern carry >95% of the coupled light to the outputs at D/r0<10 if the wavefront is partially corrected and the photonic lantern is made mode selective.

Seeking celestial positronium with an OH-suppressed diffraction-limited spectrograph.

Celestially, positronium (Ps) has been observed only through gamma-ray emission produced by its annihilation. However, in its triplet state, a Ps atom has a mean lifetime long enough for electronic transitions to occur between quantum states. This produces a recombination spectrum observable in principle at near IR wavelengths, where angular resolution greatly exceeding that of the gamma-ray observations is possible. However, the background in the near IR is dominated by extremely bright atmospheric hydroxyl (OH) emission lines. In this paper, we present the design of a diffraction-limited spectroscopic system using novel photonic components-a photonic lantern, OH fiber Bragg grating filters, and a photonic TIGER 2D pseudo-slit-to observe the Ps Balmer alpha line at 1.3122 µm for the first time, to our knowledge.

First stellar photons for an integrated optics discrete beam combiner at the William Herschel Telescope.

We present the first on-sky results of a four-telescope integrated optics discrete beam combiner (DBC) tested at the 4.2 m William Herschel Telescope. The device consists of a four-input pupil remapper followed by a DBC and a 23-output reformatter. The whole device was written monolithically in a single alumino-borosilicate substrate using ultrafast laser inscription. The device was operated at astronomical H-band (1.6 µm), and a deformable mirror along with a microlens array was used to inject stellar photons into the device. We report the measured visibility amplitudes and closure phases obtained on Vega and Altair that are retrieved using the calibrated transfer matrix of the device. While the coherence function can be reconstructed, the on-sky results show significant dispersion from the expected values. Based on the analysis of comparable simulations, we find that such dispersion is largely caused by the limited signal-to-noise ratio of our observations. This constitutes a first step toward an improved validation of the DBC as a possible beam combination scheme for long-baseline interferometry.

Metabolic engineering of Amycolatopsis japonicum for optimized production of [S,S]-EDDS, a biodegradable chelator.

The actinomycete Amycolatopsis japonicum is the producer of the chelating compound [S,S]-ethylenediamine-disuccinc acid (EDDS). [S,S]-EDDS is an isomer of ethylenediamine-tetraacetic acid (EDTA), an economically important chelating compound that suffers from an extremely poor degradability. Frequent use of the persistent EDTA in various industrial and domestic applications has caused an accumulation of EDTA in soil as well as in aqueous environments. As a consequence, EDTA is the highest concentrated anthropogenic compound present in water reservoirs. The [S,S]-form of EDDS has chelating properties similar to EDTA, however, in contrast to EDTA it is readily biodegradable. In order to compete with the cost-effective chemical synthesis of EDTA, we aimed to optimize the biotechnological production of [S,S]-EDDS in A. japonicum by using metabolic engineering approaches. Firstly, we integrated several copies of the [S,S]-EDDS biosynthetic genes into the chromosome of A. japonicum and replaced the native zinc responsive promoter with the strong synthetic constitutive promoter SP44*. Secondly, we increased the supply of O-phospho-serine, the direct precursor of [S,S]-EDDS. The combination of these approaches together with the optimized fermentation process led to a significant improvement in [S,S]-EDDS up to 9.8 g/L with a production rate of 4.3 mg/h/g DCW.

Complex phase masks for OH suppression filters in astronomy: part I: design.

The design of a complex phase mask (CPM) for inscribing multi-notch fiber Bragg grating filters in optical fibers for OH suppression in astronomy is presented. We demonstrate the steps involved in the design of a complex mask with discrete phase steps, following a detailed analysis of fabrication constraints. The phase and amplitude of the complex grating is derived through inverse modelling from the desired aperiodic filter spectrum, following which the phase alone is encoded into the surface relief of a CPM. Compared to a complicated "running-light" Talbot interferometer based inscription setup where the phase of the inscribing beam is controlled by electro- or acousto-optic modulators and synchronized to a moving fiber translation stage, CPM offers the well-known convenience and reproducibility of the standard phase mask inscription technique. We have fabricated a CPM that can suppress 37 sky emission lines between 1508 nm to 1593 nm, with a potential of increasing to 99 channels for suppressing near-infrared (NIR) OH-emission lines generated in the upper atmosphere and improving the performance of ground-based astronomical telescopes.

Performance limits of astronomical arrayed waveguide gratings on a silica platform.

We present a numerical and experimental study of the impact of phase errors on the performance of large, high-resolution arrayed waveguide gratings (AWG) for applications in astronomy. We use a scalar diffraction model to study the transmission spectrum of an AWG under random variations of the optical waveguide lengths. We simulate phase error correction by numerically trimming the lengths of the optical waveguides to the nearest integer multiple of the central wavelength. The optical length error distribution of a custom-fabricated silica AWG is measured using frequency-domain interferometry and Monte-Carlo fitting of interferogram intensities. In the end, we give an estimate for the phase-error limited size of a waveguide array manufactured using state-of-the-art technology. We show that post-processing eliminates phase errors as a performance limiting factor for astronomical spectroscopy in the H-band.

Chromatic response of a four-telescope integrated-optics discrete beam combiner at the astronomical L band.

We show the results of simulation and experimental study of a 4-telescope zig-zag discrete beam combiner (DBC) for long-baseline stellar interferometry working at the astronomical L band (3 - 4 µm) under the influence of a narrow bandwidth light source. Following Saviauk et al. (2013), we used a quasi-monochromatic visibility-to-pixel matrix (V2PM) for retrieving the complex coherence functions from simulated and experimentally measured power at the output of the device. Simulation and coefficient of determination (R2) measurements show that we are able to retrieve the visibility amplitudes with >95 % accuracy of our chromatic model source up to a bandwidth of 100 nm centred at 3.5 µm. We characterized a DBC manufactured by 3D ultra-fast laser inscription (ULI) written on gallium lanthanum sulphate (GLS). Experimental results showed retrieval of visibility amplitude with an accuracy of 80-90 % at 69 nm bandwidth, validating our simulation. The standard deviation of experimental phase residuals are between 0.1-0.4 rad, which shows that the retrieval procedure is sufficient to get good quality images, where phase perturbations of less than 1 rad are expected under good seeing conditions for astronomical applications.

Monitoring and external control of pH in microfluidic droplets during microbial culturing.

BACKGROUND: Cell-based experimentation in microfluidic droplets is becoming increasingly popular among biotechnologists and microbiologists, since inherent characteristics of droplets allow high throughput at low cost and space investment. The range of applications for droplet assays is expanding from single cell analysis toward complex cell-cell incubation and interaction studies. As a result of cellular metabolism in these setups, relevant physicochemical alterations frequently occur before functional assays are conducted. However, to use droplets as truly miniaturized bioreactors, parameters like pH and oxygen availability should be controlled similar to large-scale fermentation to ensure reliable research. RESULTS: Here, we introduce a comprehensive strategy to monitor and control pH for large droplet populations during long-term incubation. We show the correlation of fluorescence intensity of 6-carboxyfluorescein and pH in single droplets and entire droplet populations. By taking advantage of inter-droplet transport of pH-mediating molecules, the average pH value of several million droplets is simultaneously adjusted in an a priori defined direction. To demonstrate the need of pH control in practice, we compared the fermentation profiles of two E. coli strains, a K12-strain and a B-strain, in unbuffered medium with 5 g/L glucose for standard 1 L bioreactors and 180 pL droplets. In both fermentation formats, the commonly used B-strain E. coli BL21 is able to consume glucose until depletion and prevent a pH drop, while the growth of the K12-strain E. coli MG1655 is soon inhibited by a low pH caused by its own high acetate production. By regulating the pH during fermentation in droplets with our suggested strategy, we were able to prevent the growth arrest of E. coli MG1655 and obtained an equally high biomass yield as with E. coli BL21. CONCLUSION: We demonstrated a comparable success of pH monitoring and regulation for fermentations in 1 L scale and 180 pL scale for two E. coli strains. This strategy has the potential to improve cell-based experiments for various microbial systems in microfluidic droplets and opens the possibility for new functional assay designs.

Wide Field Spectral Imaging with Shifted Excitation Raman Difference Spectroscopy Using the Nod and Shuffle Technique.

Wide field Raman imaging using the integral field spectroscopy approach was used as a fast, one shot imaging method for the simultaneous collection of all spectra composing a Raman image. For the suppression of autofluorescence and background signals such as room light, shifted excitation Raman difference spectroscopy (SERDS) was applied to remove background artifacts in Raman spectra. To reduce acquisition times in wide field SERDS imaging, we adapted the nod and shuffle technique from astrophysics and implemented it into a wide field SERDS imaging setup. In our adapted version, the nod corresponds to the change in excitation wavelength, whereas the shuffle corresponds to the shifting of charges up and down on a Charge-Coupled Device (CCD) chip synchronous to the change in excitation wavelength. We coupled this improved wide field SERDS imaging setup to diode lasers with 784.4/785.5 and 457.7/458.9 nm excitation and applied it to samples such as paracetamol and aspirin tablets, polystyrene and polymethyl methacrylate beads, as well as pork meat using multiple accumulations with acquisition times in the range of 50 to 200 ms. The results tackle two main challenges of SERDS imaging: gradual photobleaching changes the autofluorescence background, and multiple readouts of CCD detector prolong the acquisition time.

One Sensor for Multiple Colors: Fluorescence Analysis of Microdroplets in Microbiological Screenings by Frequency-Division Multiplexing.

High-speed multiwavelength fluorescence measurements are of paramount importance in microfluidic analytics. However, multicolor detection requires an intricate arrangement of multiple detectors and meticulously aligned filters and dichroic beamsplitters that counteract the simplicity, versatility, and low cost of microfluidic approaches. To break free from the restrictions of optical setup complexity, we introduce a simpler single-sensor setup based on laser-frequency modulation and frequency-division multiplexing (FDM). We modulate lasers to excite the sample with four non-overlapping frequency signals. A single photomultiplier tube detects all the modulated emitted light collected by an optical fiber in the microfluidic chip. Signal demodulation is performed with a lock-in amplifier separating the emitted light into four color channels in real time. This approach not only reduces complexity and provides setup flexibility but also results in improved signal quality and, thus, higher signal-to-noise ratios that translate into increased sensitivity. To validate the setup for high-throughput biological applications, we measured multiple signals from different microorganisms and fluorescently encoded droplet populations for exploring beneficial or antagonistic roles in microbial cocultivation systems, as is the case for antibiotic screening assays.

Coding of Experimental Conditions in Microfluidic Droplet Assays Using Colored Beads and Machine Learning Supported Image Analysis.

To efficiently exploit the potential of several millions of droplets that can be considered as individual bioreactors in microfluidic experiments, methods to encode different experimental conditions in droplets are needed. The approach presented here is based on coencapsulation of colored polystyrene beads with biological samples. The decoding of the droplets, as well as content quantification, are performed by automated analysis of triggered images of individual droplets in-flow using bright-field microscopy. The decoding strategy combines bead classification using a random forest classifier and Bayesian inference to identify different codes and thus experimental conditions. Antibiotic susceptibility testing of nine different antibiotics and the determination of the minimal inhibitory concentration of a specific antibiotic against a laboratory strain of Escherichia coli are presented as a proof-of-principle. It is demonstrated that this method allows successful encoding and decoding of 20 different experimental conditions within a large droplet population of more than 105 droplets per condition. The decoding strategy correctly assigns 99.6% of droplets to the correct condition and a method for the determination of minimal inhibitory concentration using droplet microfluidics is established. The current encoding and decoding pipeline can readily be extended to more codes by adding more bead colors or color combinations.

Fiber Vector Bend Sensor Based on Multimode Interference and Image Tapping.

A grating-less fiber vector bend sensor is demonstrated using a standard single mode fiber spliced to a multimode fiber as a multimode interference device. The ring-shaped light intensity distribution at the end of the multimode fiber is subject to a vector transition in response to the fiber bend. Instead of comprehensive imaging processing for the analysis, the image can be tapped out by a seven-core fiber spliced to the other end of the multimode fiber. The seven-core fiber is further guided to seven single mode fibers via a commercial fan-out device. By comparing the relative light intensities received at the seven outputs, both the bend radius and its direction can be determined. Experiment has shown that a slight bend displacement of 10 µm over a 1.2-cm-long multimode fiber in the X direction (bend angle of 0.382°) causes a distinctive power imbalance of 4.6 dB between two chosen outputs (numbered C4 and C7). For the same displacement in the Y direction, the power ratio between the previous two outputs C4 and C7 remains constant, while the imbalance between another pair (C3 and C4) rises significantly to 7.0 dB.

Genomics-Driven Discovery of a Symbiont-Specific Cyclopeptide from Bacteria Residing in the Rice Seedling Blight Fungus.

The rice seedling blight fungus Rhizopus microsporus harbors endosymbiotic bacteria (Burkholderia rhizoxinica) that produce the virulence factor rhizoxin and control host development. Genome mining indicated a massive inventory of cryptic nonribosomal peptide synthetase (NRPS) genes, which have not yet been linked to any natural products. The discovery and full characterization of a novel cyclopeptide from endofungal bacteria is reported. In silico analysis of an orphan, symbiont-specific NRPS predicted the structure of a nonribosomal peptide, which was targeted by LC-MS/MS profiling of wild-type and engineered null mutants. NMR spectroscopy and chemical derivatization elucidated the structure of the bacterial cyclopeptide. Phylogenetic analyses revealed the relationship of starter C domains for rare N-acetyl-capped peptides. Heptarhizin is produced under symbiotic conditions in geographically constrained strains from the Pacific clade; this indicates a potential ecological role of the peptide.

An integrated chip-mass spectrometry and epifluorescence approach for online monitoring of bioactive metabolites from incubated Actinobacteria in picoliter droplets.

We present a lab-on-a-chip approach for the analysis of secondary metabolites produced in microfluidic droplets by simultaneous epifluorescence microscopy and electrospray ionization mass spectrometry (ESI-MS). The approach includes encapsulation and long-term off-chip incubation of microbes in surfactant-stabilized droplets followed by a transfer of droplets into a microfluidic chip for subsequent analysis. Before the reinjected droplets are spaced and electrosprayed from an integrated emitter into a mass spectrometer, the presence of fluorescent marker molecules is monitored nearly simultaneously with a custom-made portable epifluorescence microscope. This combined fluorescence and MS-detection setup allows the analysis of metabolites and fluorescent labels in a complex biological matrix at a single droplet level. Using hyphae of Streptomyces griseus, encapsulated in microfluidic droplets of ~ 200 picoliter as a model system, we show the detection of in situ produced streptomycin by ESI-MS and the feasibility of detecting fluorophores inside droplets shortly before they are electrosprayed. The presented method expands the analytical toolbox for the discovery of bioactive metabolites such as novel antibiotics, produced by microorganisms.

Divide and conquer: an efficient solution to highly multimoded photonic lanterns from multicore fibres.

Photonic lanterns typically allow for single-mode action in a multimode fibre. Since their invention over a decade ago for applications in astrophotonics, they have found important uses in diverse fields of applied science. To date, large aperture highly-mulitmoded to single-mode lanterns have been difficult as fabrication techniques are not practical for mass replication. Here as a proof of concept, we demonstrate three different devices based on multicore fibre photonic lanterns with: 100µm core diameters; NAs = 0.16 and 0.15; and requiring 259 single-mode core system, specifically 7 multicore fibres each with 37 cores, instead of 259 individual single-mode fibres. The average insertion loss excluding coupling efficiencies is only 0.4dB (>91% transmission). This concept has numerous advantages, in particular, (i) it is a direct scaleable solution, (ii) eases imprinting of photonic functions, e.g. fibre Bragg gratings; and (iii) new approach for large-area optical fibre slicers for future large-aperture telescopes.