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Catechol O-methyltransferase (COMT) is an enzyme that transfers a methyl group to the catechol-derivative substrates using S-adenosyl-l-methionine (SAM) and Mg2+. We report the biochemical and structural analysis of COMT from Niastella koreensis (NkCOMT). NkCOMT showed the highest activity with Mg2+, although the enzyme also showed a significant level of activity with Cu2+ and Zn2+. NkCOMT structures complexed with SAH and Mg2+ elucidated how the enzyme stabilized the cosubstrate and the metal ion and revealed that the region near the SAM binding site undergoes conformational changes upon the binding of the cosubstrate and the metal ion. We also identified the catechol binding pocket of the enzyme and explained a broad substrate specificity of the bacterial enzyme and its ability to accommodate the catechol derivatives. In addition, we developed the NkCOMTE211R and NkCOMTE211K variants that showed both enhanced activities and regiospecificity for the production of the para-forms. Our study provides a structural basis for regiospecificity of NkCOMT, which is related with the conformational change upon binding of SAM and Mg2+.

Unlike other Cirsium in Korea, Cirsium nipponicum (Island thistle) is distributed only on Ulleung Island, a volcanic island off the east coast of the Korean Peninsula, and a unique thistle with none or very small thorns. Although many researchers have questioned the origin and evolution of C. nipponicum, there is not much genomic information to estimate it. We thus assembled the complete chloroplast of C. nipponicum and reconstructed the phylogenetic relationships within the genus Cirsium. The chloroplast genome was 152,586 bp, encoding 133 genes consisting of 8 rRNA genes, 37 tRNA genes, and 88 protein-coding genes. We found 833 polymorphic sites and eight highly variable regions in chloroplast genomes of six Cirsium species by calculating nucleotide diversity, as well as 18 specific variable regions distinguished C. nipponicum from other Cirsium. As a result of phylogenetic analysis, C. nipponicum was closer to C. arvense and C. vulgare than native Cirsium in Korea: C. rhinoceros and C. japonicum. These results indicate that C. nipponicum is likely introduced through the north Eurasian root, not the mainland, and evolved independently in Ulleung Island. This study contributes to further understanding the evolutionary process and the biodiversity conservation of C. nipponicum on Ulleung Island.

Cysteine is a semiessential amino acid and plays an important role in metabolism and protein structure and has also been applied in various industrial fields, such as pharmaceutical, food, cosmetic, and animal feed industries. Metabolic engineering studies have been conducted for the cysteine production through bacterial fermentation, but studies on the cysteine biosynthetic pathway in microorganisms are limited. We report the biochemical characteristics of cystathionine γ-lyase from Bacillus cereus ATCC 14579 (BcCGL). We also determined the crystal structure of BcCGL in complex with the PLP cofactor and identified the substrate binding mode. We observed that the replacement of the conserved Glu321 residue to alanine showed increased activity by providing wider active site entrance and hydrophobic interaction for the substrate. We suggest that the structural differences of the α13-α14 region in CGL enzymes might determine the active site conformation.

BackgroundPlazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology.FindingsIn total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration.ConclusionThis first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.

Background Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. Results The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. Conclusions Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.

Filters with various bandwidths at low intermediate frequency (IF) have been demonstrated using aluminum nitride (AlN) microresonator technology. Specifically, at 13 MHz, 6 kHz, and 25 kHz bandwidth filters were implemented using a single resonator topology, and 250 kHz and 500 kHz bandwidth filters were constructed via the parallel lattice topology using four sub-resonators and L-matching networks. The bandwidths of these filters are from 0.046% to 3.8%, and particularly the 500 kHz bandwidth filter at 13 MHz is wider than that of the resonator kt2 limit (40 kHz). The 100x variations in filter percent bandwidth were realized in a 1700 nm-thick aluminum nitride film on the same wafer through CMOS-compatible fabrication processes. Changes in the filter termination for proper filter matching were implemented in the Agilent Genesys RF and microwave design simulation software using actual measured filter responses with 50 Ω termination. The great flexibility in filter bandwidths and resonant frequencies, as well as other benefits such as size, manufacturing cost, isolation, and insertion loss provided by AlN microresonators will enable next generation multi-band, multi-waveform, and cognitive radios for defense and consumer wireless applications.

Frequency tuning of aluminum nitride (AlN) microresonators has been demonstrated via localized heating (ovenization) of the resonator. Specifically, piezoelectrically driven ~ 100 MHz microresonators were heated by embedded joule heaters in vacuum. Three different designs with three different film stacks were tested, and among the tested devices, thermal resistances as large as 92 K/mW have been demonstrated, which corresponds to 1-mW power consumption to yield a temperature increase of 92°C. To minimize heat loss, the devices were suspended from the substrate by high thermal isolation beam-type supports. The beams exhibit very high thermal resistance not only due to their high length to cross-sectional area ratio but also because they are made of thin-film-deposited polycrystalline aluminum nitride. Film-deposited AlN has been shown to have thermal conductivity much lower than that measured in bulk materials. Thermal time constants for these devices were measured ranging from submilliseconds to 10 ms depending on the design and film stacks, and frequency tunability was measured as high as 2548 parts per million/mW. The availability of a power-efficient frequency tuning method, coupled with all other performance benefits, makes AlN microresonators a promising candidate for the next-generation timing devices and tunable filters for multiband communication systems.

Microsystem technologies have the potential to significantly improve the performance, reduce the cost, and extend the capabilities of solar power systems. These benefits are possible due to a number of significant beneficial scaling effects within solar cells, modules, and systems that are manifested as the size of solar cells decrease to the sub-millimeter range. To exploit these benefits, we are using advanced fabrication techniques to create solar cells from a variety of compound semiconductors and silicon that have lateral dimensions of 250 - 1000 µm and are 1 - 20 µm thick. These fabrication techniques come out of relatively mature microsystem technologies such as integrated circuits (IC) and microelectromechanical systems (MEMS) which provide added supply chain and scale-up benefits compared to even incumbent PV technologies.

Electrostatic tuning of the frequency in micromachined Si-SiO2 composite resonators for temperature compensation is demonstrated and analyzed. Electrostatic tuning exploits the bias voltage dependence of frequency for the compensation. Si-SiO2 composite resonators have intrinsically small frequency variation over temperature, thus being appropriate for electrostatic tuning. We developed a tuning procedure and applied it to a flexural-mode composite resonator. Experimental results show ±2.5-ppm stability over a 90°C-wide temperature range.

This paper proposes the use of ac polarization for resonant electrostatic microelectromechanical systems that eliminates the frequency drift caused by dielectric charging and charge screening. It is mathematically and experimentally shown that an ac-polarized resonator can sustain stable oscillations when used in a positive feedback oscillator circuit. We also demonstrate an oscillator topology that generates a drift-free reference frequency tone with this technique in spite of using a resonator that exhibits large frequency drifts under dc polarization. Long-term data are presented for these drift-susceptible devices, showing a significant improvement in frequency stability.

This paper investigates the effects of dielectric charge on resonant frequency in thermally oxidized silicon resonators hermetically encapsulated using ?epi-seal.? SiO2 coatings are effective for passive temperature compensation of resonators but make the devices more susceptible to charging-related issues. We present a theoretical model for the electromechanical effects of charge trapped in the dielectrics within the transduction gap of a resonator. Observations of resonance frequency against varying resonator bias voltage are fitted to this model in order to obtain estimates for the magnitude of the trapped oxide charge. Statistics collected from wet- and dry-oxidized devices show that lower fixed oxide charge can be expected upon dry oxidation. In addition, observations of time-varying resonator frequency indicate the presence of mobile oxide charge in a series of voltage biasing and temperature experiments.

Packaging of microelectromechanical systems (MEMS) is a critical step in the transition from development to commercialized product. This paper presents a thin-film encapsulation process that allows varying trench widths suitable for MEMS devices with lateral deflections as large as 20 ?m. The process involves the deposition and planarization of a sacrificial-oxide layer of up to 23 ?m thick, the deposition of a 20 ?m epitaxial-silicon sealing cap, the release of structures using hydrofluoric acid (HF) vapor, and the sealing of the structure at low pressure. Devices produced using this encapsulation method are capable of surviving standard backend processes such as wafer singulation and wire bonding. Among the numerous types of devices encapsulated, two different types of silicon MEMS resonators were fabricated. These functioning resonators demonstrate the ability of the process to successfully encapsulate devices, taking advantage of both large and small trench widths. Such a generalized fabrication platform greatly expands the possibilities of the wafer-scale encapsulation to numerous MEMS devices and retains the robustness necessary for backend processing.

Utilizing silicon and silicon dioxide's opposing temperature coefficients of Young's modulus, composite resonators with zero linear temperature coefficient of frequency are fabricated and characterized. The resulting resonators have a quadratic temperature coefficient of frequency of approximately -20 ppb/degC2 and a tunable turnover temperature in the -55degC to 125degC range. Reduction of the temperature dependence of frequency is shown in flexural-mode resonators (700 kHz-1.3 MHz) and extensional-mode ring resonators (20 MHz). The linear temperature coefficient of Young's modulus of silicon dioxide is extracted from measurements to be +179 ppm/degC. The composite resonators are fabricated and packaged in a CMOS-compatible wafer-scale hermetic encapsulation process. The long-term stability of the resonators is monitored for longer than six months. Although most devices exhibit less than 2 ppm frequency drift, there is evidence of dielectric charging in the silicon dioxide.

The temperature dependence of the quality factor of microelectromechanical system (MEMS) resonators is analyzed and measured. For silicon MEMS resonators, there are several energy loss mechanisms that determine the quality factor. These include air-damping, thermoelastic dissipation, and anchor and surface losses. For resonators operating at a low pressure in hermetic wafer-scale encapsulation, the effect of each energy loss mechanism is discussed. The temperature dependence of each mechanism and their contribution to the total quality factor is investigated. MEMS resonators can be designed to have either strong or weak dependence of on temperature, which is if the effects of the temperature on the dominant loss mechanisms are well understood. The sensitivity of up to 1% changes in quality factor per degree Celsius change of temperature was demonstrated by experiment. By using as the thermometer for temperature compensation, a preliminary experiment demonstrated less than 4-ppm resonant frequency variation over the 0 -70 temperature range. This indicates that the quality factor can be used as an absolute intrinsic thermometer for temperature compensation in the MEMS resonators.

This paper presents an in-chip thermal-isolation technique for a micro-ovenized microelectromechanical-system resonator. Resonators with a microoven can be used for high-precision feedback control of temperature to compensate for the temperature dependence of resonator frequency over a wide temperature range. However, ovenization requires power consumption for heating, and the thermal time constant must be minimized for effective temperature control. This paper demonstrates an efficient local-thermal-isolation mechanism, which can reduce the power requirement to a few milliwatts and the thermal time constant to a few milliseconds. In this method, the mechanical suspension of the resonator is modified to provide thermal isolation and include an integrated resistive heater. This combination provides mechanical suspension, electrical heating, and thermal isolation in a compact structure that requires low heating power and has a small thermal time constant. A power consumption of approximately 12 mW for a 125degC temperature rise and a thermal time constant ranging from 7 to 10 ms is reported in this paper, which is orders of magnitude lower than that of commercially available ovenized quartz resonators. A CMOS-compatible wafer-scale encapsulation process is used to fabricate this device, and the thermal-isolation design is achieved without any modification to the existing resonator fabrication process.

This paper presents a capacitive X/Y and Z-axis accelerometer, pressure sensor, and resonant thermometer, co-fabricated in a single die using an ultra-clean, high-temperature, wafer-scale, production-compatible encapsulation process. This process is free of bond rings and getter areas, thereby reducing overall die size to a minimum. Utilizing a process that allows for nitride and silicon etch stops, we show that it is possible to design high-sensitivity pressure sensors and accelerometers with very little cross-sensitivity. In addition, remaining sensitivities to environmental effects, such as temperature, can be compensated to reveal a suite of on-chip high-performance sensors that is accurate over temperature. All of this is accomplished in a process similar to current high-volume production processes in industry.

We have developed a single-wafer vacuum encapsulation for microelectromechanical systems (MEMS), using a thick (20-mum) polysilicon encapsulation to package micromechanical resonators in a pressure 600 cycles of -50 to 80degC, and no measurable change in cavity pressure was seen. We have also performed accelerated leakage tests by driving hydrogen gas in and out of the encapsulation at elevated temperature. Two results have come from these hydrogen diffusion tests. First, hydrogen diffusion rates through the encapsulation at temperatures 300-400degC have been determined. Second, the package was shown to withstand multiple temperature cycles between room and 300-400degC without showing any adverse affects. The high robustness and stability of the encapsulation can be attributed to the clean, high-temperature environment during the sealing process

Thermoelastic dissipation (TED) is analyzed for complex geometries of micromechanical resonators, demonstrating the impact of resonator design (i.e., slots machined into flexural beams) on TED-limited quality factor. Zener first described TED for simple beams in 1937. This work extends beyond simple beams into arbitrary geometries, verifying simulations that completely capture the coupled physics that occur. Novel geometries of slots engineered at specific locations within the flexural resonator beams are utilized. These slots drastically affect the thermal-mechanical coupling and have an impact on the quality factor, providing resonators with quality factors higher than those predicted by simple Zener theory. The ideal location for maximum impact of slots is determined to be in regions of high strain. We have demonstrated the ability to predict and control the quality factor of micromechanical resonators limited by thermoelastic dissipation. This enables tuning of the quality factor by structure design without the need to scale its size, thus allowing for enhanced design optimization

The dispersive properties of phononic crystals can be utilized to manipulate the phononic impedance of a material and to engineer the frequency-delay response of time domain signal processing circuits. In this paper we study, in both the frequency and time domains, the dispersive properties of phononic crystals formed in thin suspended plates of aluminum nitride.

We report on a demonstration prototype module created to explore the viability of using microscale solar cells combined with microlens array concentrators to create a thin, flat-plate concentrator module with a relatively large acceptance angle for use with coarse two-axis tracking systems designed for flat-plate, one-sun modules. The demonstration module was comprised of an array of 216 cell/microlens units and was manufactured using standard tools common to the integrated circuit, microelectromechanical system (MEMS), and electronics assembly industries. The module demonstrated an acceptance angle of ±4°, an optical concentration level of 36X, and a focal depth of 13.3 mm. The acceptance angle and focal depth of the system successfully demonstrated adequate performance for integration into a system using a coarse two-axis tracker for flat-plate modules. To fully take advantage of this system approach, significant future work is required to reduce optical losses, increase cell and module efficiency, reduce the focal length to approximately 5 mm, and increase the concentration level to greater than 100X while maintaining an acceptance angle of at least ±2°.

We report on the modeling, fabrication and characterization of a new serpentine geometry for platinum bolometers realized with plasma-enhanced atomic layer deposition (PEALD). The measured responsivity of 7.5 · 107 VW-1 A-1 of the proposed structure is almost four times higher than that of previously published PEALD deposited platinum bolometers with a traditional square absorber design [1]. This improvement was achieved without increasing the sensor's footprint or fabrication complexity.

As the radio frequency (RF) spectrum has become more crowded, the need for adaptable RF components, especially filters, has grown. Recently, aluminum nitride (AlN) microresonator filters have been reported. These filters/resonators are small ( 1000) desired for steep filter roll-off, can achieve many filters covering a very wide frequency span (kHz to GHz) on a single chip and can be monolithically integrated with CMOS transistors for reconfiguring the filter array. Using AlN microresonator on CMOS technology, miniature, adaptable RF filters based on banks of switched filters have recently been reported.