Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons.

Synechococcus is an important photosynthetic picoplankton in the temperate to tropical oceans. As a photosynthetic bacterium, Synechococcus has an efficient mechanism to adapt to the changes in salinity and light intensity. The analysis of the distributions and functions of such microorganisms in the ever changing river mouth environment, where freshwater and seawater mix, should help better understand their roles in the ecosystem. Toward this objective, we have collected and sequenced the ocean microbiome in the river mouth of Kwangyang Bay, Korea, as a function of salinity and temperature. In conjunction with comparative genomics approaches using the sequenced genomes of a wide phylogeny of Synechococcus, the ocean microbiome was analyzed in terms of their composition and clade-specific functions. The results showed significant differences in the compositions of Synechococcus sampled in different seasons. The photosynthetic functions in such enhanced Synechococcus strains were also observed in the microbiomes in summer, which is significantly different from those in other seasons.

Pan-genome analysis of Bacillus for microbiome profiling.

Recent advances in high-throughput sequencing technology allow for in-depth studies on microbial genomes and their communities. While multiple strains of the same species could display genomic variations with different gene contents in diverse habitats and hosts, the essential functions for a specific species are conserved as core genes that are shared among strains. We have comprehensively analyzed 238 strains of five different Bacillus species to identify the properties of core and strain-specific genes. Core and strain-specific genes in each Bacillus species show significant differences in their functions and genomic signatures. Using the core genes defined in this study, we have precisely identified the Bacillus species that exist in food microbiomes. Without resorting to culture-based whole genome sequencing, an unexpectedly large portion of the core genes, 98.22% of core genes in B. amyloliquefaciens and 97.77% of B. subtilis, were reconstructed from the microbiome. We have performed a pan-genome analysis on the core gene data of multiple Bacillus species to investigate the Bacillus species in food microbiome. Our findings provide a comprehensive genetic landscape of the Bacillus species, which is also consistent with previous studies on a limited number of strains and species. Analysis based on comprehensive core genes should thus serve as a powerful profiling tool to better understand major constituents in fermented food microbiomes.

Chemically Homogeneous and Thermally Robust Ni1-xPtxSi Film Formed Under a Non-Equilibrium Melting/Quenching Condition.

To synthesize a thermally robust Ni1-xPtxSi film suitable for ultrashallow junctions in advanced metal-oxide-semiconductor field-effect transistors, we used a continuous laser beam to carry out millisecond annealing (MSA) on a preformed Ni-rich silicide film at a local surface temperature above 1000 °C while heating the substrate to initiate a phase transition. The melting and quenching process by this unique high-temperature MSA process formed a Ni1-xPtxSi film with homogeneous Pt distribution across the entire film thickness. After additional substantial thermal treatment up to 800 °C, the noble Ni1-xPtxSi film maintained a low-resistive phase without agglomeration and even exhibited interface flattening with the underlying Si substrate.

Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches.

The human microbiome is one of the key factors affecting the host immune system and metabolic functions that are not encoded in the human genome. Culture-independent analysis of the human microbiome using metagenomics approach allows us to investigate the compositions and functions of the human microbiome. Computational methods analyze the microbial community by using specific marker genes or by using shotgun sequencing of the entire microbial community. Taxonomy profiling is conducted by using the reference sequences or by de novo clustering of the specific region of sequences. Functional profiling, which is mainly based on the sequence similarity, is more challenging since about half of ORFs predicted in the metagenomic data could not find homology with known protein families. This review examines computational methods that are valuable for the analysis of human microbiome, and highlights the results of several large-scale human microbiome studies. It is becoming increasingly evident that dysbiosis of the gut microbiome is strongly associated with the development of immune disorder and metabolic dysfunction.

Demonstration of a Ge/GeSn/Ge quantum-well microdisk resonator on silicon: enabling high-quality Ge(Sn) materials for micro- and nanophotonics.

We theoretically study and experimentally demonstrate a pseudomorphic Ge/Ge0.92Sn0.08/Ge quantum-well microdisk resonator on Ge/Si (001) as a route toward a compact GeSn-based laser on silicon. The structure theoretically exhibits many electronic and optical advantages in laser design, and microdisk resonators using these structures can be precisely fabricated away from highly defective regions in the Ge buffer using a novel etch-stop process. Photoluminescence measurements on 2.7 µm diameter microdisks reveal sharp whispering-gallery-mode resonances (Q > 340) with strong luminescence.

Highly selective dry etching of germanium over germanium-tin (Ge(1-x)Sn(x)): a novel route for Ge(1-x)Sn(x) nanostructure fabrication.

We present a new etch chemistry that enables highly selective dry etching of germanium over its alloy with tin (Ge(1-x)Sn(x)). We address the challenges in synthesis of high-quality, defect-free Ge(1-x)Sn(x) thin films by using Ge virtual substrates as a template for Ge(1-x)Sn(x) epitaxy. The etch process is applied to selectively remove the stress-inducing Ge virtual substrate and achieve strain-free, direct band gap Ge0.92Sn0.08. The semiconductor processing technology presented in this work provides a robust method for fabrication of innovative Ge(1-x)Sn(x) nanostructures whose realization can prove to be challenging, if not impossible, otherwise.