Hydrogen iodide (HI) neutral beam etching characteristics of InGaN and GaN for micro-LED fabrication.

We investigated the etching characteristics of hydrogen iodide (HI) neutral beam etching (NBE) of GaN and InGaN and compared with Cl2NBE. We showed the advantages of HI NBE versus Cl2NBE, namely: higher InGaN etch rate, better surface smoothness, and significantly reduced etching residues. Moreover, HI NBE was suppressed of yellow luminescence compared with Cl2plasma. InClxis a product of Cl2NBE. It does not evaporate and remains on the surface as a residue, resulting in a low InGaN etching rate. We found that HI NBE has a higher reactivity with In resulting in InGaN etch rates up to 6.3 nm min-1, and low activation energy for InGaN of approximately 0.015 eV, and a thinner reaction layer than Cl2NBE due to high volatility of In-I compounds. HI NBE resulted in smoother etching surface with a root mean square average (rms) of 2.9 nm of HI NBE than Cl2NBE (rms: 4.3 nm) with controlled etching residue. Moreover, the defect generation was suppressed in HI NBE compared to Cl2plasma, as indicated by lower yellow luminescence intensity increase after etching. Therefore, HI NBE is potentially useful for high throughput fabrication ofµLEDs.

Evidence of One-Dimensional Channels in Hydrogen-Bonded Organic Porous Thin Films Fabricated at the Air/Liquid Interface.

Visualization of periodically aligned pores in organic frameworks is a key to the understanding of their structural control. Comparing to monolayer-thick self-assembled molecular networks, real-space nanoscale characterization of thicker films, especially obtaining information on the stacking manner of molecules is challenging. Here, we report an atomic force microscopy study of hydrogen-bonded thin films fabricated at the air/liquid interface. The presence of one-dimensional channels is evidenced by resolving honeycomb structures over the films with the thickness variation of more than several nanometers. We also demonstrate that the film thickness can be controlled by the ratio of mixed solvent rather than the surface pressure during the fabrication at the air/liquid interface.

Characterization of iron-sulfur clusters in flavin-containing opine dehydrogenase.

Flavin-containing opine dehydrogenase from Bradyrhizobium japonicum forms a heterooligomeric α4ß4γ4 enzyme complex. An electron paramagnetic resonance spectroscopy analysis using wild-type and site-directed mutants revealed that [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the γ- and α-subunits, respectively. The latter was found to be important for structural folding and enzyme catalysis.

Catalytic [2+2+1] Synthesis of Fused Thiophenes Using Thiocarbonyls as Sulfur Donors.

The use of N-(p-chlorophenyl)methylbenzoxazole-2-thione as a sulfur-atom donor enables the catalytic [2+2+1] cycloaddition of diynes in wet DMF at 80 °C when open to air, thus affording diverse fused thiophenes with good yields and wide functional-group compatibility. A plausible mechanism, involving a cationic ruthenacycle intermediate, was also proposed on the basis of several control experiments.

A combined experimental and computational study on the cycloisomerization of 2-ethynylbiaryls catalyzed by dicationic arene ruthenium complexes.

Ruthenium-catalyzed cycloisomerization of 2-ethynylbiaryls was investigated to identify an optimal ruthenium catalyst system. A combination of [η(6) -(p-cymene)RuCl2 (PR3 )] and two equivalents of AgPF6 effectively converted 2-ethynylbiphenyls into phenanthrenes in chlorobenzene at 120 °C over 20 h. Moreover, 2-ethynylheterobiaryls were found to be favorable substrates for this ruthenium catalysis, thus achieving the cycloisomerization of previously unused heterocyclic substrates. Moreover, several control experiments and DFT calculations of model complexes were performed to propose a plausible reaction mechanism.

Exoproteome profiles of Clostridium cellulovorans grown on various carbon sources.

The cellulosome is a complex of cellulosomal proteins bound to scaffolding proteins. This complex is considered the most efficient system for cellulose degradation. Clostridium cellulovorans, which is known to produce cellulosomes, changes the composition of its cellulosomes depending on the growth substrates. However, studies have investigated only cellulosomal proteins; profile changes in noncellulosomal proteins have rarely been examined. In this study, we performed a quantitative proteome analysis of the whole exoproteome of C. cellulovorans, including cellulosomal and noncellulosomal proteins, to illustrate how various substrates are efficiently degraded. C. cellulovorans was cultured with cellobiose, xylan, pectin, or phosphoric acid-swollen cellulose (PASC) as the sole carbon source. PASC was used as a cellulose substrate for more accurate quantitative analysis. Using an isobaric tag method and a liquid chromatography mass spectrometer equipped with a long monolithic silica capillary column, 639 proteins were identified and quantified in all 4 samples. Among these, 79 proteins were involved in saccharification, including 35 cellulosomal and 44 noncellulosomal proteins. We compared protein abundance by spectral count and found that cellulosomal proteins were more abundant than noncellulosomal proteins. Next, we focused on the fold change of the proteins depending on the growth substrates. Drastic changes were observed mainly among the noncellulosomal proteins. These results indicate that cellulosomal proteins were primarily produced to efficiently degrade any substrate and that noncellulosomal proteins were specifically produced to optimize the degradation of a particular substrate. This study highlights the importance of noncellulosomal proteins as well as cellulosomes for the efficient degradation of various substrates.

Insights Into the Regulation of Offspring Growth by Maternally Derived Ghrelin.

The regulation of fetal development by bioactive substances such as hormones and neuropeptides derived from the gestational mother is considered to be essential for the development of the fetus. On the other hand, it has been suggested that changes in the physiological state of the pregnant mother due to various factors may alter the secretion of these bioactive substances and induce metabolic changes in the offspring, such as obesity, overeating, and inflammation, thereby affecting postnatal growth and health. However, our knowledge of how gestational maternal bioactive substances modulate offspring physiology remains fragmented and lacks a systematic understanding. In this mini-review, we focus on ghrelin, which regulates growth and energy metabolism, to advance our understanding of the mechanisms by which maternally derived ghrelin regulates the growth and health of the offspring. Understanding the regulation of offspring growth by maternally-derived ghrelin is expected to clarify the fetal onset of metabolic abnormalities and lead to a better understanding of lifelong health in the next generation of offspring.

Low-frequency noise induced by cation exchange fluctuation on the wall of silicon nitride nanopore.

Nanopore-based biosensors have attracted attention as highly sensitive microscopes for detecting single molecules in aqueous solutions. However, the ionic current noise through a nanopore degrades the measurement accuracy. In this study, the magnitude of the low-frequency noise in the ionic current through a silicon nitride nanopore was found to change depending on the metal ion species in the aqueous solution. The order of the low-frequency noise magnitudes of the alkali metal ionic current was consistent with the order of the adsorption affinities of the metal ions for the silanol surface of the nanopore (Li

Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides.

Nanopore DNA sequencing with a solid-state nanopore requires deceleration of the ultrafast translocation speed of single-stranded DNA (ssDNA). We report an unexpected phenomenon: controlled dielectric breakdown (CBD) with a divalent metal cation, especially Ca2+, provides a silicon nitride nanopore with the ability to decelerate ssDNA speed to 100 µs per base even after solution replacement. This speed is two orders of magnitude slower than that for CBD with a conventional monovalent metal cation. Temperature dependence experiments revealed that the enthalpic barrier for a nanopore created via CBD with Ca2+ is 25-30kBT, comparable to that of a biological nanopore. The slowing effect originates from the strong interaction between ssDNA and divalent cations, which were coated on the sidewall of the nanopore during the CBD process. In addition, we found that the nanopore created via CBD with Ca2+ can decelerate the speed of even single-nucleotide monomers, dNMPs, to 0.1-10 ms per base. The four single nucleotides could be statistically identified according to their blockade currents. Our approach is simple and practical because it simultaneously allows nanopore fabrication, ssDNA deceleration and the identification of nucleotide monomers.

Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution.

DNA sequencing via solid-state nanopores is a promising technique with the potential to surpass the performance of conventional sequencers. However, the identification of all four nucleotide homopolymers with a typical SiN nanopore is yet to be clearly demonstrated because a guanine homopolymer rapidly forms a G-quadruplex in a typical KCl aqueous solution. To address this issue, we introduced an alkaline CsCl aqueous solution, which denatures the G-quadruplex into a single-stranded structure by disrupting the hydrogen-bonding network between the guanines and preventing the binding of the K+ ion to G-quartets. Using this alkaline CsCl solution, we provided a proof-of-principle that single-stranded DNA homopolymers of all four nucleotides could be statistically identified according to their blockade currents with the same single nanopore. We also confirmed that a triblock DNA copolymer of three nucleotides exhibited a trimodal Gaussian distribution whose peaks correspond to those of the DNA homopolymers. Our findings contribute to the development of practical DNA sequencing with a solid-state nanopore.

Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction.

The practical use of solid-state nanopores for DNA sequencing requires easy fabrication of the nanopores, reduction of the DNA movement speed and reduction of the ionic current noise. Here, we report an integrated nanopore platform with a nanobead structure that decelerates DNA movement and an insulating polyimide layer that reduces noise. To enable rapid nanopore fabrication, we introduced a controlled dielectric breakdown (CDB) process into our system. DNA translocation experiments revealed that single nanopores were created by the CDB process without sacrificing performance in reducing DNA movement speed by up to 10 µs/base or reducing noise up to 600 pArms at 1 MHz. Our platform provides the essential components for proceeding to the next step in the process of DNA sequencing.

Prevention of Dielectric Breakdown of Nanopore Membranes by Charge Neutralization.

To achieve DNA sequencing using a solid-state nanopore, it is necessary to reduce the electric noise current. The noise current can be decreased by reducing the capacitance (C) of the nanopore device. However, we found that an electric-charge difference (ΔQ) between the electrolyte in one chamber and the electrolyte in another chamber occurred. For low capacitance devices, this electric-charge imbalance can lead to unexpectedly high voltage (ΔV = ΔQ/C) which disrupted the membrane when the two electrolytes were independently poured into the chambers. We elucidated the mechanism for the generation of initial defects and established new procedures for preventing the generation of defects by connecting an electric bypass between the chambers.

Tandem ruthenium-catalyzed transfer-hydrogenative cyclization/intramolecular Diels-Alder reaction of enediynes affording dihydrocoumarin-fused polycycles.

A tandem transfer-hydrogenative cyclization/intramolecular Diels-Alder reaction of enediyne substrates, containing 1,6-diyne, acrylate dienophile, and phenol tether moieties, was successfully accomplished using the combination of a cationic ruthenium complex, [CpRu(AN)3]PF6 (1b, Cp = η(5)-C5H5, AN = MeCN), as the catalyst and a Hantzsch ester as the H2 surrogate to afford interesting dihydrocoumarin-fused polycyclic products as single diastereomers.

Elucidation of potentially virulent factors of Candida albicans during serum adaptation by using quantitative time-course proteomics.

Candida albicans is an opportunistic pathogen that causes fatal disease if the host immunity is compromised. The mortality rate of systemic candidiasis is very high; hence, there is a ceaseless demand for novel pharmaceuticals. In this study, quantitative time-course proteomics of C. albicans during adaptation to fetal bovine serum (FBS) is described. Survival in blood is essential for virulence of C. albicans, and a detailed analysis is required. We cultivated C. albicans in FBS for 0-180min, and determined quantitative time-course variations of 1024 proteins in the cultured cells by using a LC-MS/MS system with a long monolithic silica capillary column. Clustering analysis identified FBS-induced proteins associated with detoxification of oxidative species, high-affinity glucose transport, citrate cycle, oxidative phosphorylation, and iron acquisition. Furthermore, we identified possible virulence factors such as orf19.4914.1 (named Blood-induced peptide 1, Blp1). Heterologous expression of BLP1 in Saccharomyces cerevisiae shortened the lag phase and resulted in a pleiotropic stress-tolerance phenotype, indicating a possible role for quick adaptation to a stressful environment. While further experiments are necessary to prove virulence of the identified factors, systematic identification of candidate virulence proteins in this study will lead to profound understanding of virulence of C. albicans. BIOLOGICAL SIGNIFICANCE: This paper describes time-course proteomics of C. albicans during adaptation to serum, which is an essential process for fatal systemic candidiasis. Using a LC-MS/MS system with a monolithic silica capillary column, we have successfully characterized time-course variations of 1024 proteins. Among them, orf19.4914.1 (Blp1) was identified as a novel pleiotropic stress-tolerance peptide, which could have an important role for virulence of C. albicans.

Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources.

We performed a focused proteome analysis of cellulosomal proteins predicted by a genome analysis of Clostridium cellulovorans [Tamaru, Y., et al.. 2010. J. Bacteriol. 192:901-902]. Our system employed a long monolithic column (300 cm), which provides better performance and higher resolution than conventional systems. Twenty-three cellulosomal proteins were, without purification, identified by direct analysis of the culture medium. Proteome analysis of the C. cellulovorans cellulosome after culture in various carbon sources demonstrated the production of carbon source-adapted cellulosome components.