Search

Abstract Background Recent advances in high-resolution mass spectrometry have now enabled the study of proteomes at the single-cell level, offering the potential to unveil novel aspects of cellular processes. Remarkably, there has been no prior attempt to investigate single-plant cell proteomes. In this study, we aimed to explore the feasibility of conducting a proteomic analysis on individual protoplasts. Findings As a result, our analysis identified 978 proteins from the 180 protoplasts, aligning with well-known biological processes in plant leaves, such as photosynthetic electron transport in photosystem II. Employing the SCP package in the SCoPE2 workflow revealed a notable batch effect and extensive missing values in the data. Following correction, we observed the heterogeneity in single-protoplast proteome expression. Comparing the results of single-protoplast proteomics with those of bulk leaf proteomics, we noted that only a small fraction of bulk data was detected in the single-protoplast proteomics data, highlighting a technical limitation of the current single-cell proteomics method. Conclusions In summary, we demonstrated the feasibility of conducting a single-protoplast proteomic experiment, revealing heterogeneity in plant cellular proteome expression. This underscores the importance of analyzing a substantial number of plant cells to discern statistically significant changes in plant cell proteomes upon perturbation such as abscisic acid treatment in future studies. We anticipate that our study will contribute to advancing single-protoplast proteomics in the near future.

Abstract There is a growing demand for adsorption technologies for recovering and recycling precious metals (PMs) in various industries. Unfortunately, amine-functionalized polymers widely used as metal adsorbents are ineffective at recovering PMs owing to their unsatisfactory PM adsorption performance. Herein, a star-shaped, hydrazide-functionalized polymer (S-PAcH) is proposed as a readily recoverable standalone adsorbent with high PM adsorption performance. The compact chain structure of S-PAcH containing numerous hydrazide groups with strong reducibility promotes PM adsorption by enhancing PM reduction while forming large, collectable precipitates. Compared with previously reported PM adsorbents, commercial amine polymers, and reducing agents, S-PAcH exhibited significantly higher adsorption capacity, selectivity, and kinetics toward three PMs (gold, palladium, and platinum) with model, simulated, and real-world feed solutions. The superior PM recovery performance of S-PAcH was attributed to its strong reduction capability combined with its chemisorption mechanism. Moreover, PM-adsorbed S-PAcH could be refined into high-purity PMs via calcination, directly utilized (upcycled) as catalysts for dye reduction, or regenerated for reuse, demonstrating its high practical feasibility. Our proposed PM adsorbents would have a tremendous impact on various industrial sectors from the perspectives of environmental protection and sustainable development.

AbstractQuercus turbinella (section Quercus; Fagaceae) is an evergreen shrub characteristic in central Arizona and it concerns one of the most abundant and economically important genera of Quercus in the Northern Hemisphere. Here, we have sequenced the complete chloroplast genome to provide insight into the phylogenetic relationship of Q. turbinella. The whole genome is 161,208 bp in length with two inverted repeat regions of 25,827 bp each, which separate a large single-copy region of 90,552 bp and a small single-copy region of 19,002 bp. A total of 136 genes were annotated, including 88 protein-coding genes, eight ribosomal RNAs, and 40 transfer RNAs. The result of the maximum-likelihood phylogenetic analysis strongly suggested that Quercus turbinella had a close relationship to Quercus macrocarpa with strong bootstrap support.

Korea consists of 63% forested land, more than twice the global average (31%). Despite ongoing reforestation efforts since the initiation of erosion contron and greening project in 1973, many of the species planted during that plan were nonnative, such as Pinus rigida and Robinia pseudoacacia. The study area, Sejong City, is undergoing various development activities. Given the anticipated influx of nonnative species and the reduction of plant biodiversity, accurate survey and analysis are essential for the conservation of Sejong City. In recent years, remote sensing techniques have been utilized as an alternative to traditional vegetation surveys. Remote sensing employs hyperspectral imagery, and LiDAR, allowing for faster and more accurate data collection and analysis without direct on-site access. This study utilized remote sensing technologies, including hyperspectral imagery and LiDAR, to collect forest resource information in Mt. Geumbyeong, Sejong City. The area around Mt. Geumbyeong, is characterized by Quercus acutissima, Robinia pseudoacacia, and Pinus rigida. In total, there are 19 species, with 43,657 individual trees, an average height of 16.91 m, an average breast height diameter of 38.85 cm, and an average age of 68.99 years. The aim is to provide fundamental data for forest management, urban forestry, and restoration efforts amid various disturbances, such as development activities, in the area. Subsequent and ongoing data collection through additional surveys and environmental assessments in the vicinity would enable the analysis of species-specific growth rates, the impact of disturbance factors, forest management, and health assessments over multiple years.

Fibroblast growth factor 2 (FGF2) is an attractive biomaterial for pharmaceuticals and functional cosmetics. To improve the thermo-stability of FGF2, we designed two mutants harboring four-point mutations: FGF2-M1 (D28E/C78L/C96I/S137P) and FGF2-M2 (D28E/C78I/C96I/S137P) through bioinformatics, molecular thermodynamics, and molecular modeling. The D28E mutation reduced fragmentation of the FGF2 wild type during preparation, and the substitution of a whale-specific amino acid, S137P, enhanced the thermal stability of FGF2. Surface-exposed cysteines that participate in oligomerization through intermolecular disulfide bond formation were substituted with hydrophobic residues (C78L/C78I and C96I) using the in silico method. High-resolution crystal structures revealed at the atomic level that the introduction of mutations stabilizes each local region by forming more favorable interactions with neighboring residues. In particular, P137 forms CH-π interactions with the side chain indole ring of W123, which seems to stabilize a β-hairpin structure, containing a heparin-binding site of FGF2. Compared to the wild type, both FGF2-M1 and FGF2-M2 maintained greater solubility after a week at 45 °C, with their Tm values rising by ~ 5 °C. Furthermore, the duration for FGF2-M1 and FGF2-M2 to reach 50% residual activity at 45 °C extended to 8.8- and 8.2-fold longer, respectively, than that of the wild type. Interestingly, the hydrophobic substitution of surface-exposed cysteine in both FGF2 mutants makes them more resistant to proteolytic cleavage by trypsin, subtilisin, proteinase K, and actinase than the wild type and the Cys → Ser substitution. The hydrophobic replacements can influence protease resistance as well as oligomerization and thermal stability. It is notable that hydrophobic substitutions of surface-exposed cysteines, as well as D28E and S137P of the FGF2 mutants, were designed through various approaches with structural implications. Therefore, the engineering strategies and structural insights adopted in this study could be applied to improve the stability of other proteins.

Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h−1) and 200 mM formate (0.34 h−1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.

Dracocephalum rupestre (tribe Mentheae; Lamiaceae) is a perennial herb from Korea and China with high ornamental and medicinal value. Here, we report its complete chloroplast genome to provide insight into the phylogenetic relationships of Dracocephalum. The genome is 151,230 bp long, with two inverted repeat regions (25,643 bp each) that separate a large single-copy region (82,536 bp) and a small single-copy region (17,408 bp). It contains 133 genes that encode 88 proteins, eight rRNAs, and 37 tRNAs. The maximum-likelihood phylogenetic analysis strongly supported Dracocephalum monophyly, showing that the genus forms a sister group with the subtribe Menthinae in the tribe Mentheae.

Abstract Fibroblast growth factor 21 (FGF21) has pharmaceutical potential against obesity-related metabolic disorders, including non-alcoholic fatty liver disease. Since thermal stability is a desirable factor for therapeutic proteins, we investigated the thermal behavior of human FGF21. FGF21 remained soluble after heating; thus, we examined its temperature-induced structural changes using circular dichroism (CD). FGF21 showed inter-convertible temperature-specific CD spectra. The CD spectrum at 100 °C returned to that at 20 °C when the heated FGF21 solution was cooled. Through loop swapping, the connecting loop between β10 and β12 in FGF21 was revealed to be associated with the unique thermal behavior of FGF21. According to surface plasmon resonance (SPR) experiments, in vitro cell-based assays, and model high-fat diet (HFD)-induced obesity studies, heated FGF21 maintained biological activities that were comparable to those of non-heated and commercial FGF21s. Based on sequence comparison and structural analysis, five point-mutations were introduced into FGF21. Compared with the wild type, the heated FGF21 variant displayed improved therapeutic potential in terms of body weight loss, the levels of hepatic triglycerides and lipids, and the degree of vacuolization of liver in HFD-fed mice.

Abstract Imaging of parotid gland tumors is challenging due to the wide variety of differential diagnoses. Malignant parotid tumors can have very similar features to benign ones, such as slow growth and displacement instead of infiltration of neighboring structures. Malignant and benign tumors may therefore not be clinically distinguishable. Correct characterization of parotid tumors (i.e., benign or malignant) determines preoperative treatment planning and is important in optimizing the individualized surgical plan. Magnetic resonance imaging (MRI) is the imaging modality of choice for evaluation of suspected parotid gland lesions and differentiation between benign and malignant lesions. Certain conventional MRI features can suggest whether a mass is more likely to be a benign or low-grade malignancy or a high-grade malignancy and adding diffusion-weighted imaging or advanced MRI techniques like perfusion can aid in this distinction. Morphological features seen on MRI, such as low signal on T2-w, infiltrative changes or ill-defined margins, change over time and diffusion restriction can point to the malignant nature of the lesion. MRI is useful for detection and localization of the lesion(s), and associated findings like perineural spread of tumor, lymph node involvement and infiltrative changes of the surrounding tissues. In this pictorial essay, we present selected images of a variety of benign and malignant parotid tumors and emphasize the MRI features that may be useful in their characterization.

Abstract Similar to the global phenomenon, many plant species endemic to Korean limestone karst forests are at risk of extinction due to human intervention. Zabelia tyaihyonii is a familiar shrub, called “Hardy abelia” and “Fragrant abelia” growing in the karst forests of Korea, where it is one of the most threatened species. We investigated the genetic structure and demographic history of Z. tyaihyonii, which allow us to develop appropriate conservation and management strategies. The genetic structure was evaluated using a total of 187 samples from 14 populations, covering the entire distribution of Z. tyaihyonii in South Korea. We utilized 254 and 1753 SNP loci obtained via MIG‐seq (Multiplexed ISSR Genotyping by sequencing) for structure and demographic analyses, respectively. The population demographic modeling was performed with site frequency spectrum. To gain further historical insights, we also employed ENM (Ecological Niche Modeling). We found two distinct clusters (CLI and CLII) of ancient origin (ca. 490 ka). Despite CLII experiencing a more severe bottleneck, both clusters showed similar levels of genetic diversity, indicating mutual historical gene flow. Their historical distribution range seems to have changed very little. We proposed a historical distribution scenario for Z. tyaihyonii, taking into account its intrinsic factors, and emphasized a more complex response to Quaternary climate change beyond simple allopatric speciation models. These findings provide valuable insights for conservation and management strategies for Z. tyaihyonii.

Summary: Opposing effects of interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) on SARS-CoV-2 infection have been reported. The reasons for this are unclear and the role of IFITMs in infection of other human coronaviruses (hCoVs) remains poorly understood. Here, we demonstrate that endogenous expression of IFITM2 and/or IFITM3 is critical for efficient replication of SARS-CoV-1, SARS-CoV-2 and hCoV-OC43 but has little effect on MERS-, NL63-and 229E-hCoVs. In contrast, overexpression of IFITMs inhibits all these hCoVs, and the corresponding spike-containing pseudo-particles, except OC43, which is enhanced by IFITM3. We further demonstrate that overexpression of IFITMs impairs cell surface expression of ACE2 representing the entry receptor of SARS-CoVs and hCoV-NL63 but not hCoV-OC43. Our results explain the inhibitory effects of artificial IFITM overexpression on ACE2-tropic SARS-CoVs and show that three hCoVs, including major causative agents of severe respiratory disease, hijack IFITMs for efficient infection of human cells.

The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D. genkwa) to 174,773 bp (D. championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D. championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D. championii and D. genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.

Indoor organic photovoltaics (OPVs) show immense potential as a reliable energy harvester for powering emerging Internet of Things devices because of their unique optoelectrical properties. The extremely low number of charge carriers under indoor lighting conditions in comparison to 1-sun conditions necessitates different techniques to optimize the performance of indoor OPVs. In this study, an indium tin oxide (ITO) surface was modified using a water-soluble β-cyclodextrin–polyacryloyl hydrazide (CD–PAH). The abundant amine functional groups on the polyacryloyl hydrazide arms induce a vacuum-level shift owing to their excellent electron-withdrawing ability. Consequently, the work function (WF) of ITO decreased from 4.5 to 4.1 eV, providing a suitable energy-level alignment between ITO and the photoactive layer. The photovoltaic performance of inverted poly(3-hexylthiophene):indene-C60 bisadduct-based OPVs with the surface-treated ITO was evaluated under various lighting conditions. The average power conversion efficiency of the optimized OPV increased substantially from 1.2 ± 0.1% to 3.5 ± 0.1% under 1 sun illumination and 2.4 ± 0.2% to 8.1 ± 0.4% under light-emitting diode illumination. This remarkable performance improvement can be attributed to the excellent transmittance, smooth surface morphology, and suitable WF of the surface-modified ITO.

In this study, we sequenced the complete plastid genome (plastome) of Neolitsea aciculata, an evergreen broad-leaved tree endemic to East Asia, a woody component of East Asian warm-temperate and subtropical forests across China, Korea, and Japan. The plastome of N. aciculata is assembled as a single contig (152,722 bp). A large and a small single copy (93,785 and 18,795 bp, respectively) of the genome are separated by a pair of inverted repeats (20,071 bp). The genome consists of 126 genes, including 80 protein-coding, eight ribosomal RNA, and 36 transfer RNA genes. Two genes in the IR region (ycf1 and ycf2) are pseudogenized. Our phylogenetic analysis revealed the phylogenetic position of N. aciculata in a highly supported clade of the genus Neolitsea along with other two congeners, N. pallens and N. sericea.

We here sequenced the complete plastid genome (plastome) of Vaccinium japonicum (Ericaceae), a deciduous broad-leaved shrub endemic to East Asia. This species has considerable practical economic value. The plastome of V. japonicum is assembled as a single contig (187,213 bp). A large single copy (104,637 bp) and a small single copy (3,000 bp) of the genome are separated by a pair of inverted repeats (39,788 bp). The genome consists of 135 genes, which include 88 protein coding, eight ribosomal RNA, and 39 transfer RNA genes. The plastome of V. japonicum is similar to that of Vaccinium macrocarpon in gene content and order. Our phylogenetic analysis revealed the phylogenetic position of V. japonicum in a highly supported clade of the genus Vaccinium together with other four congeners, V. bracteatum, V. vitis-idaea, V. uliginosum and V. macrocarpon.

Abstract The high genetic diversity of rear‐edge refugia populations is predicted to have resulted from species repeatedly migrating to low latitudes during glacial periods over the course of Quaternary climate change. However, several recent empirical studies of cold‐tolerant plants revealed the opposite pattern. We investigated whether current habitats of the cold‐adapted and range‐restricted Bupleurum euphorbioides in the Baekdudaegan, South Korea, and North Korea could be interglacial refugia, and documented how their rear‐edge populations differ genetically from those of typical temperate species. Phylogeographic analysis and ecological niche modeling (ENM) were used. The genetic structure was analyzed using microsatellite markers and chloroplast DNA sequences. The congener B. longiradiatum was included as a typical temperate plant species. Despite having almost identical life history traits, these congeneric species exhibited contrasting patterns of genetic diversity. ENM revealed an apparent maximum range contraction during the last interglacial. In contrast, its range expanded northward to the Russian Far East (Primorsky) during the Last Glacial Maximum. Thus, we hypothesize that B. euphorbioides retreated to its current refugia during interglacial periods. Unlike populations in the central region, the rear‐edge populations were genetically impoverished and uniform, both within populations and in pooled regional populations. The rear‐edge B. euphorbioides survived at least one past interglacial, contributing to the species’ genetic diversity. We believe that such genetic variation in the cold‐adapted B. euphorbioides gives the species the necessary adaptations to survive an upcoming favorable environment (the next glacial), unless there is artificial environmental change.

Summary: Background: Plasma extracellular vesicles (pEV) can harbor a diverse array of factors including active proteases and the amyloid-precursor-protein (APP) cleavage product Aβ, involved in plaque formation in Alzheimer`s diseases (AD). A potential role of such vesicles in AD pathology is unexplored. Methods: In a case-control study of randomly selected patients with AD and other neurological diseases (n = 14), and healthy controls (n = 7), we systematically analyzed the content of pEV, using different assay systems. In addition, we determined their entry path into brain tissue, employing animal (mice) injection experiments with ex vivo generated EV that were similar to AD-pEV, followed by multi antigen analysis (MAA) of brain tissue (n = 4 per condition). The results were compared with an IHC staining of human brain tissue in a small cohort of AD patients (n = 3) and controls with no neurodegenerative diseases (n = 3). Findings: We show that pEV levels are considerably upregulated in AD patients. Besides numerous inflammatory effectors, AD-pEV contained α-, β- and γ-secretases, able to cleave APP in in target cells. In vitro generated EV with similar characteristics as AD-pEV accumulated in the choroid plexus (CP) of injected animals and reached primarily hippocampal neurons. Corroborating findings were made in human brain samples. An inhibitor of hyaluronic-acid-synthetase (HAS) blocked uploading of proteases and Hyaluronan onto EV in vitro and abolished CP targeting in animal injection experiments. Interpretation: We conclude that protease-containing pEV could be part of a communication axis between the periphery and the brain that could be become detrimental depending on pEV concentration and duration of target cell impact.

Little is known about the community structure and metabolic potential of microbial communities in hydrothermal fields in the Central Indian Ridge (CIR). In this study, a metagenomic sequencing approach was conducted to explore the microbial diversity in three sediment samples collected during the 2019 expedition from two recently discovered hydrothermal vent fields; Invent E and Onnuri Vent Field (OVF). Analysis of unassembled metagenomic reads using the Metagenomic analysis server (MG-RAST) revealed that microbial communities of the two sampling sites were very similar, showing the dominance of Bacteria over Archaea. Proteobacteria, Firmicutes, Bacteroidetes, as well as Euryarchaeota were dominant in all samples. Functional annotation based on KEGG categories shows that the microbial populations in these vent fields possess metabolic capabilities for aerobic respiration, carbon fixation through the Calvin–Bassham–Benson (CBB) cycle, the reverse tricarboxylic acid (rTCA) cycle, and reductive acetyl-CoA pathway as well as sulfur and nitrogen metabolisms. Comparative metagenome analysis with different datasets obtained from different ocean ridges showed that microbial communities at low activity or hydrothermally influenced area differ from highly active hydrothermal communities. This study provides insights into the genetic diversity and functional capability of the microbial communities of slow to intermediate spreading hydrothermal systems.

Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.

Since the Anthropocene, biodiversity loss owing to human activity and climate change has worsened. Quercus gilva is an evergreen oak species native to China, Japan, and South Korea and is threatened by a long history of human impact. The purpose of this study was to (1) reassess the threatened category of Q. gilva based on a detailed survey, and (2) identify the genetic structure and diversity of Q. gilva based on genomic data. First, we conducted a detailed survey of the populations in China. Second, we collated all the literature and information. Finally, genome-wide genetic variation was analyzed based on 65 individuals from 22 populations. We found that Q. gilva has suffered rapid population decline, and at present, most populations are very small. The evolutionary path of Q. gilva was from the southwest to east of China and then to Japan and South Korea. Quercus gilva showed no distinct genetic structure and had a relatively low genetic diversity. Among the 22 populations, most populations in southwestern China, South Korea, and Japan had high genetic diversity. The populations in Jingning (Zhejiang province; ZJN), Wuyuan (Jinaxi province; JWY), and Zherong (Fujian province; FZR) suffered a strong bottleneck. In conclusion, Q. gilva is an endangered species native to East Asia. Because of the very low genetic diversity of Q. gilva and most populations are small, we need to (1) strengthen the protection of this species, (2) conduct conservation actions with in-situ reinforcement populations, and (3) select populations with high genetic diversity as provenances for afforestation efforts. Finally, we suggest that in the future, genetic diversity should be considered as the sixth criterion for IUCN to evaluate the threatened category.

In research on membranes, the addition of co-solvents to the polymer dope solution is a common method for tuning the morphology and separation performance. For organic solvent nanofiltration (OSN) applications, we synthesized polybenzimidazole (PBI) membranes with high separation properties and stability by adding acetonitrile (MeCN) to the dope solution, followed by crosslinking with dibromo-p-xylene. Accordingly, changes in the membrane structure and separation properties were investigated when MeCN was added. PBI/MeCN membranes with a dense and thick active layer and narrow finger-like macrovoids exhibited superior rejection properties in the ethanol solution compared with the pristine PBI membrane. After crosslinking, they displayed superior rejection properties (96.56% rejection of 366-g/mol polypropylene glycol). In addition, the membranes demonstrated stable permeances for various organic solvents, including acetone, methanol, ethanol, toluene, and isopropyl alcohol. Furthermore, to evaluate the feasibility of the modified PBI OSN membranes, ecamsule, a chemical product in the fine chemical industry, was recovered. Correspondingly, the efficient recovery of ecamsule from a toluene/methanol solution using the OSN process with PBI/MeCN membranes demonstrated their applicability in many fine chemical industries.

We are reporting the complete plastid genome (plastome) of Quercus acuta, an evergreen broad-leaved oak endemic to East Asia. This species is important for maintaining the warm-temperate evergreen forest biome in East Asia. The Q. acuta plastome is 160,522 base pairs (bp) long, with two inverted repeat (IR) regions (25,839 bp each) that separate a large single copy (LSC) region (90,199 bp) and a small single copy (SSC) region (18,645 bp). The phylogenetic tree shows that Quercus acuta is closely related to Quercus sichourensis with strong bootstrap support.

Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (GIS that was close to or even below zero in all populations), and a high level of genetic differentiation (FST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.

In this paper, the potential of a Maillard reaction-based time–temperature indicator (TTI) as a device for the visualization of shelf life was evaluated by comparing the quality variations of cold-stored strawberries and the color changes of Maillard reaction solutions. The color variations of the Maillard reaction solutions stored in the same storage environment as the cold-stored strawberries showed suitable characteristics for the visualization of shelf life, such as pronounced color changes, a wide-ranging color variation rate, and activation energy. In particular, the concentrations of the reaction solutions with the combinations of 3.0 M D-xylose, 1.5 M glycine, and 0.3 M Na2HPO4; 2.0 M D-xylose, 1.5 M glycine, and 0.3 M Na2HPO4; and 4.0 M D-xylose, 1.0 M glycine, and 0.3 M Na2HPO4 were suitable for the visualization of the weight loss variation, color difference variation, and appearance damage. These concentrations showed similar color variations and Arrhenius activation energies to the variation of the quality characteristics, such as weight loss and color difference. Additionally, a Maillard reaction-based time–temperature indicator (TTI) has a wide applicability to other agricultural products using the wide range of the color change rate and the activation energy.

Abstract Background Gas-fermenting acetogens have received a great deal of attention for their ability to grow on various syngas and waste gas containing carbon monoxide (CO), producing acetate as the primary metabolite. Among them, some Clostridium species, such as C. ljungdahlii and C. autoethanogenum, are of particular interest as they produce fuel alcohols as well. Despite recent efforts, alcohol production by these species is still unsatisfactory due to their low productivity and acetate accumulation, necessitating the isolation of strains with better phenotypes. Results In this study, a novel alcohol-producing acetogen (Clostridium sp. AWRP) was isolated, and its complete genome was sequenced. This bacterium belongs the same phylogenetic group as C. ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii based on 16S rRNA homology; however, the levels of genome-wide average nucleotide identity (gANI) for strain AWRP compared with these strains range between 95 and 96%, suggesting that this strain can be classified as a novel species. In addition, strain AWRP produced a substantial amount of ethanol (70–90 mM) from syngas in batch serum bottle cultures, which was comparable to or even exceeded the typical values obtained using its close relatives cultivated under similar conditions. In a batch bioreactor, strain AWRP produced 119 and 12 mM of ethanol and 2,3-butanediol, respectively, while yielding only 1.4 mM of residual acetate. Interestingly, the alcohologenesis of this strain was strongly affected by oxidoreduction potential (ORP), which has not been reported with other gas-fermenting clostridia. Conclusion Considering its ethanol production under low oxidoreduction potential (ORP) conditions, Clostridium sp. AWRP will be an interesting host for biochemical studies to understand the physiology of alcohol-producing acetogens, which will contribute to metabolic engineering of those strains for the production of alcohols and other value-added compounds from syngas.

Fibroblast growth factor 11 (FGF11) is a member of the intracellular fibroblast growth factor superfamily. Here, we identified FGF11 as a novel mediator of adipogenesis. During 3T3‐L1 adipocyte differentiation, the expression of FGF11 decreased at the mitotic clonal expansion stage and increased at the terminal differentiation stage. FGF11 knockdown reduced the expression of peroxisome proliferator‐activated receptor gamma (PPARγ), a master regulator of adipogenesis, resulting in the inhibition of adipocyte differentiation. Treatment with the PPARγ agonist rosiglitazone restored the inhibition of adipogenesis caused by FGF11 knockdown. We also report that the expression of the PPARγ regulators CCAAT/enhancer‐binding protein α, sterol regulatory element‐binding protein 1, KLF9, KLF2, GATA binding factor 2, and GATA binding factor 3 was influenced by FGF11. These results suggest that FGF11 indirectly controls the expression of PPARγ through modifying the expression of multiple PPARγ regulators, thereby mediating adipogenesis.

Abstract Background Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura’s jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. Results We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura’s jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). Conclusions Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

ABSTRACTResistance to β-lactams is one of the most serious problems associated with Gram-negative infections. β-Lactamases are able to hydrolyze β-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-β-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.

(1) Background: We studied how the generation position of air anions in a closed-type plant factory affects the growth characteristics of lettuce and identified the optimal position. (2) Methods: We used LEDs (red/green/blue = 8:1:1) as a light source and set the temperature and RH of the plant factory to 20 ± 2 ℃ and 50% ± 5%, respectively. We grew lettuce under three air anion conditions—sideward, upward, and downward—and compared the growth characteristics to those of a control grown without air anions. We measured the growth characteristics of the lettuce at 3 and 4 weeks after sowing, and the measurement items were shoot fresh weight (FW) and dry weight (DW); leaf area (LA), length (LL), and width (LW); SPAD; antioxidant capacity; and total phenol content. (3) Results: At 4 weeks, FW in the downward treatment condition was 25.3% higher than in the control, and DW showed a similar difference. LA was about 1943.94 cm²/plant in the downward treatment condition, which was about 15.5% higher than in the control. (4) Conclusions: We conclude that air anion generation has a positive effect on lettuce growth, and the optimal generation position for air anions is downward.

Background: Before and after surgery melanoma patients harbor elevated levels of extracellular vesicles in plasma (pEV), suppressing tumor cell activity. However, due to technical reasons and lack of cell-specific biomarkers, their cellular origin remains obscure. Methods: We mimicked the interaction of tumor cells with liver cells and PBMC in vitro, and compared newly secreted EV-associated miRNAs and protein factors with those detected in melanoma patient`s pEV. Findings: Our results suggest that pEV from melanoma patients are secreted in part by residual or relapsing tumor cells, but also by liver and peripheral blood mononuclear cells (PBMC). Our approach identified factors that were seemingly associated either with tumor cell activity, or the counteracting immune system, including liver cells. Notably, the presence/absence of these factors correlated with the clinical stage and tumor relapse. Interpretation: Our study may provide new insights into the innate immune defense against tumor cells and implies that residual tumor cells could be more active than previously thought. In addition we provide some preliminary evidence that pEV marker patterns could be used to predict cancer relapse.

For ethylene/ethane separation, a CMS (carbon molecular sieve) membrane was developed with a PAN (polyacrylonitrile) polymer precursor on an alumina support. To provide an excellent thermal property to PAN precursor prior to the pyrolysis, the stabilization as a pre-treatment process was carried out. Tuning the stabilization condition was very important to successfully preparing the CMS membrane derived from the PAN precursor. The stabilization and pyrolysis processes for the PAN precursor were finely tuned, and optimized in terms of stabilization temperature and time, as well as pyrolysis temperature, heating rate, and soaking time. The PAN stabilized at >250 °C showed improved thermal stability and carbon yield. The CMS membrane derived from stabilized PAN showed reasonable separation performance for ethylene permeance (0.71 GPU) and ethylene/ethane selectivity (7.62), respectively. Increasing the pyrolysis temperature and soaking time gave rise to an increase in the gas permeance, and a reduction in the membrane selectivity. This trend was opposite to that for the CMS membranes derived from other polymer precursors. The optimized separation performance (ethylene permeance of 2.97 GPU and ethylene/ethane selectivity of 7.25) could be achieved at the pyrolysis temperature of 650 °C with a soaking time of 1 h. The separation performance of the CMS membrane derived from the PAN precursor was comparable to that of other polymer precursors, and surpassed them regarding the upper bound trade off.

Ultrathin and smooth polyamide (PA) reverse osmosis (RO) membranes have attracted significant interest due to their potential advantages of high permeance and low fouling propensity. Although a layered interfacial polymerization (LIP) technique aided by the insertion of a polyelectrolyte interlayer has proven effective in fabricating ultrathin and uniform membranes, the RO performance and pH stability of the fabricated LIP membrane remain inadequate. In this study, a poly(piperazineamide) (PIPA) layer prepared via interfacial polymerization (IP) was employed as an interlayer to overcome the limitations of the prototype LIP method. Similar to the control polyelectrolyte-interlayered LIP membrane, the PIPA-interlayered LIP (pLIP) membrane had a much thinner (~20 nm) and smoother selective layer than the membrane fabricated via conventional IP due to the highly surface-confined and uniform LIP reaction. The pLIP membrane also exhibited RO performance exceeding that of the control LIP and conventional IP-assembled membranes, by enabling denser monomer deposition and a more confined interfacial reaction. Importantly, the chemically crosslinked PIPA interlayer endowed the pLIP membrane with higher pH stability than the control polyelectrolyte interlayer. The proposed strategy enables the fabrication of high-performance and pH-stable PA membranes using hydrophilic supports, which can be applied to other separation processes, including osmosis-driven separation and organic solvent filtration.

The identification of a loose sleeper is important for the operation and safety of a railway system because the excessive movement of a loose railway sleeper can cause derailment and passenger discomfort. There are available methods on how to detect a loose sleeper, such as: 1) a method using a conventional approach based on human judgement and experience, which is not advisable if the researcher is a beginner; 2) Fixed Post method, wherein a fixed post with displacement sensor is installed in a ballast, which is not reliable because vibration of a sleeper during train passage might affect the results from this test; and 3) Non-Destructive Testing (NDT) methods, which include the use of Light Falling Weight Deflectometer (LFWD) and line scan camera, both of which are, however, expensive to use for a routine testing technique. In this paper, Finite Element Analysis (FEA) was performed to set the criteria for the loose sleepers. Impulse Response (IR) Method was used on an actual site. The spectral velocity of flexural waves and mobility function from the impulse response test were proposed to investigate the quality of a railway sleeper.

Chaperonins (CPNs) are ATP-dependent protein-folding machines. Here the authors present the open and closed crystal structures of a Group III CPN from the thermophilic bacterium Carboxydothermus hydrogenoformans, discuss its mechanism and structurally compare it with Group I and II CPNs.

Previously, we developed a one-step sequence- and ligation-independent cloning (SLIC) method that is simple, fast, and cost-effective. However, although one-step SLIC generally works well, its cloning efficiency is occasionally poor, potentially due to formation of stable secondary structures within the single-stranded DNA (ssDNA) region generated by T4 DNA polymerase during the 2.5 min treatment at room temperature. To overcome this problem, we developed a modified thermo-regulated one-step SLIC approach by testing shorter T4 DNA polymerase treatment durations (5 s–2.5 min) over a wide range of temperatures (25–75°C). The highest cloning efficiency resulted when inserts with homology lengths

Abstract Previously, we reported that the hyperthermophilic archaeon Thermococcus onnurineus NA1 could grow on formate and produce H2. Formate conversion to hydrogen was mediated by a formate-hydrogen lyase complex and was indeed a part of chemiosmotic coupling to ATP generation. In this study, we employed an adaptation approach to enhance the cell growth on formate and investigated molecular changes. As serial transfer continued on formate-containing medium at the serum vial, cell growth, H2 production and formate consumption increased remarkably. The 156 times transferred-strain, WTF-156T, was demonstrated to enhance H2 production using formate in a bioreactor. The whole-genome sequencing of the WTF-156T strain revealed eleven mutations. While no mutation was found among the genes encoding formate hydrogen lyase, a point mutation (G154A) was identified in a formate transporter (TON_1573). The TON_1573 (A52T) mutation, when introduced into the parent strain, conferred increase in formate consumption and H2 production. Another adaptive passage, carried out by culturing repeatedly in a bioreactor, resulted in a strain, which has a mutation in TON_1573 (C155A) causing amino acid change, A52E. These results implicate that substitution of A52 residue of a formate transporter might be a critical factor to ensure the increase in formate uptake and cell growth.

Taxillus yadoriki (Loranthaceae) is a hemiparasitic evergreen shrub distributed in Korea and Japan. We report the complete chloroplast genome of T. yadoriki to provide insight into the phylogenetic relationship of Loranthaceae. This genome is 122,192 bp long, with two IR regions (22,756 bp each) that separate a large single-copy (LSC) region (70,628 bp) and a small single-copy (SSC) region (6052 bp). It contains 109 genes that encode 68 proteins, 8 rRNAs, and 33 tRNAs. All of ndh genes have been lost and the SSC region consists of only four genes similar to other Taxillus species. In ML phylogenetic, monophyly of Taxillus was strongly supported with high bootstrap value and formed a sister group with Scurrula.

We here report the complete chloroplast genome of Pedicularis verticillata and the reconstructed chloroplast genome of Pedicularis cheilanthifolia, the first such genome reported for this genus. The P. verticillata genome is 142,733 bp, including a 24,984-bp inverted repeat (IR) region, 89,723-bp large single-copy (LSC) region, and 12,042-bp small single copy (SSC) region, and the P. cheilanthifolia genome is 147,807 bp (IRs: 24,916 bp; LSC: 82,718 bp; SSC: 15,257 bp). The chloroplast genome of P. verticillata contains 116 genes, including 71 coding genes, 8 rRNAs, and 37 tRNAs. In the genomes of both species, 10 ndh genes are lost and ndhB was identified in the IR region. Additionally, rps16 is also lost in P. verticillata but not in P. cheilanthifolia. The maximum-likelihood phylogenetic tree showed that Pedicularis is a monophyletic and sister group to other hemi-parasitic species in Orobanchaceae.

Joining technology of silicon semiconductors devices to direct bond copper (DBC) substrates in high-temperature power electronics packages is of utmost importance today. In this study, Sn–Cu solder was prepared by electroplating on a direct bonded copper (DBC) substrate. The electroplated DBC system thus prepared was TLP bonded with Si chip at 250 °C for 10 min under a vacuum atmosphere. The effect of electrical charge used for plating Sn–Cu solder, void fraction in the joint, Sn–Cu solder composition on the joining characteristics, and shear strength of the Si-DBC system were analyzed. The experimental results showed that the plating thickness increased almost linearly with plating time and electrical charge. A sound Sn–Cu solder plating thickness was obtained at 40 mA cm ^−2 , 11 C cm ^−2 , 20 min with 20 at% Cu in the deposit. Furthermore, the plated Sn–Cu solder layer transformed to Cu _6 Sn _5 and Cu _3 Sn after joining at 250 °C for 10 min. The shear bonding strength of the Si/DBC joint increased with Cu content in the Sn–Cu solder until 20 at% in the Sn–Cu interlayer.

Tumor necrosis factor (TNF) is a key cytokine in HIV replication and pathogenesis. For reasons that are not entirely clear, the cytokine remains upregulated despite anti-retroviral therapy (ART). Here we demonstrate that HIV Nef induces an alternative TNF secretion mechanism that remains active in chronic infection. Ingestion of Nef-containing plasma extracellular vesicles (pEV) from ART patients by primary immune cells, but also Nef expression, induced intracellular proTNF cleavage and secretion of vesicular TNF endosomes. Key event was the Nef-mediated routing of the TNF-converting enzyme ADAM17 into Rab4+ early endosomes and the Rab27+ secretory pathway. Analysis of lymph-node tissue by multi-epitope-ligand-cartography (MELC) confirmed a vesicular TNF secretion phenotype that co-localized with persistent Nef expression, and implicated Notch1 as an essential co-factor. Surprisingly Notch1 had no transcriptional effect but was required for the endosomal trafficking of ADAM17. We conclude that Nef expression and Nef-containing pEV mobilize TNF from endosomal compartments in acute and chronic infection.

Background: The National Health Insurance Service (NHIS) conducted a screening test to detect chronic diseases such as hypertension and diabetes in Korea. This study evaluated the effects of health screening for DM on pharmacological treatment. Methods: The data from qualification and the General Health Screening in 2012, the insurance claims of medical institutions from Jan 2009 to Dec 2014, and the diabetic case management program extracted from the NHIS administrative system were used. Total 16068 subjects were included. Visiting rate to medical institution, medication possession ratio and the rate of medication adherence of study subjects were used as the indices. Results: The visiting rates to medical institutions were 39.7%. The percentage who received a prescription for a diabetes mellitus medication from a doctor was 80.9%, the medication possession ratio was 70.8%, and the rate of medication adherence was 57.8%. Conclusion: The visiting rate, medication possession ratio and rate of medication adherence for DM medication were not high. In order to increase the visiting rate, medication possession ratio and rate of medication adherence, NHIS should support environment in which medical institutions and DM patients can do the role of each part.

We present a simple smartphone-based measurement system consisting of a smartphone, a holder, and a lateral flow immune strip. The smartphone camera and light source were used to read the colorimetric signal from the lateral flow assay. A smartphone application was written and installed onto the smartphone. Various concentrations of cortisol were successfully measured using the images captured by the smartphone. Measurement of human salivary cortisol was then demonstrated using the lateral flow assay and the quantitative analysis was validated with the smartphone. The system was further evaluated using human saliva, demonstrating an accurate and reproducible platform for rapid and point-of-care quantification of cortisol using a smartphone-based measurement system.

We have obtained the complete chloroplast (cp) genome sequence for Sarcandra glabra. This genome is 158,881 bp long, with 39.2% GC content. It includes a large single copy region of 88,169 bp that is separated from the 18,446-bp small single copy region by two inverted repeat regions (26,133 bp each). This genome contains 130 genes, i.e. 85 protein-coding genes, 37 tRNA, and eight tRNA. Maximum likelihood analysis, based on 13 complete cp genomes, showed that S. glabra is closely related to two other family members, Chloranthus spicatus and C. japonicus.

We determined the complete chloroplast genome of Pedicularis hallaisanensis (Orobanchaceae), a hemi-parasitic perennial herb. This genome is 143,469 bp long and features a large single-copy region (81,664 bp) and a small single-copy region (12,203 bp), separated by two inverted-repeat regions (24,801 bp each). It contains 115 genes – 70 for coding, eight for rRNA, and 37 for tRNA. However, 11 ndh genes have been pseudogenized, truncated, or deleted. Our phylogenetic tree showed that these hemi-parasitic plants are sister to holo-parasitic genera within Orobanchaceae.

The wax-leafed Viburnum japonicum (Adoxaceae) is an evergreen shrub distributed in Japan, Korea, and Taiwan. We sequenced its complete chloroplast (cp) genome to examine its phylogenetic relationship within Dipsacales. This genome is 158,614 bp long and features a large single-copy region (87,059 bp) and a small single-copy region (18,523 bp), separated by two inverted-repeat regions (26,516 bp each). It contains 128 genes, including 84 coding genes, eight rRNAs, and 36 tRNAs. The overall GC content is 38.1%. Our phylogenetic tree showed that V. japonicum is closely related to V. utile and is clustered together with four species in the family Adoxaceae.

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4–chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.

The limited durability of resin-dentin bonds severely compromises the longevity of composite resin restorations. Resin-dentin bond degradation might occur via degradation of water-rich and resin sparse collagen matrices by host-derived matrix metalloproteinases (MMPs). This review article provides overview of current knowledge of the role of MMPs in dentin matrix degradation and four experimental strategies for extending the longevity of resin-dentin bonds. They include: (1) the use of broad-spectrum inhibitors of MMPs, (2) the use of cross-linking agents for silencing the activities of MMPs, (3) ethanol wet-bonding with hydrophobic resin, (4) biomimetic remineralization of water-filled collagen matrix. A combination of these strategies will be able to overcome the limitations in resin-dentin adhesion.

Dimethyl sulfide (DMS) is a climatically active gas released into the atmosphere from oceans. It is produced mainly by bacterial enzymatic cleavage of dimethylsulfoniopropionate (DMSP), and six DMSP lyases have been identified to date. To determine the biogeographical distribution of bacteria relevant to DMS production, we investigated the diversity of dddP—the most abundant DMS-producing gene—in the northwestern Pacific Ocean using newly developed primers and the pyrosequencing method. Consistent with previous studies, the major dddP-containing bacteria in coastal areas were those belonging to the Roseobacter clade. However, genotypes closely related to the SAR116 group were found to represent a large portion of dddP-containing bacteria in the surface waters of the oligotrophic ocean. The addition of DMSP to a culture of the SAR116 strain Candidatus Puniceispirillum marinum IMCC1322 resulted in the production of DMS and upregulated expression of the dddP gene. Considering the large area of oligotrophic water and the wide distribution of the SAR116 group in oceans worldwide, we propose that these bacteria may play an important role in oceanic DMS production and biogeochemical sulfur cycles, especially via bacteria-mediated DMSP degradation.

Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA.

It is believed that the inherent differentiation program of melanocytes during embryogenesis predisposes melanoma cells to high frequency of metastasis. Sox10, a transcription factor expressed in neural crest stem cells and a subset of progeny lineages, plays a key role in the development of melanocytes. We show that B16F10 melanoma cells transfected with siRNAs specific for Sox10 display reduced migratory activity which in turn indicated that a subset of transcriptional regulatory target genes of Sox10 is likely to be involved in migration and metastasis of melanoma cells. We carried out a microarray-based gene expression profiling using a Sox10-specific siRNA to identify relevant regulatory targets and found that multiple genes including melanocortin-1 receptor (Mc1r) partake in the regulation of migration. We provide evidences that the effect of Sox10 on migration is mediated in large part by Mitf, a transcription factor downstream to Sox10. Among the mouse melanoma cell lines examined, however, only B16F10 showed robust down-regulation of Sox10 and inhibition of cell migration indicating that further dissection of dosage effects and/or cell line-specific regulatory networks is necessary. The involvement of Mc1r in migration was studied in detail in vivo using a murine metastasis model. Specifically, B16F10 melanoma cells treated with a specific siRNA showed reduced tendency in metastasizing to and colonizing the lung after being injected in the tail vein. These data reveal a cadre of novel regulators and mediators involved in migration and metastasis of melanoma cells that represents potential targets of therapeutic intervention.