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Photoconductive arrays on insulating substrates for high-field terahertz generation
Get PDFWe report on the design, fabrication and characterisation of large-area photoconductive THz array structures, consisting of a thin LT-GaAs active region transferred to an insulating substrate using a wafer-scale bonding process. The electrically insulating, transparent substrate reduces the parasitic currents in the devices, allowing peak THz-fields as high as 120 kV cm−1 to be generated over a bandwidth >5 THz. These results are achieved using lower pulse energies than demanded by conventional photoconductive arrays and other popular methods of generating high-field THz radiation. Two device sizes are fully characterised and the emission properties are compared to generation by optical rectification in ZnTe. The device can be operated in an optically saturated regime in order to suppress laser noise.journal articl
Spatially resolved hydration shells and dynamics of different sulfur species in water from first-principle molecular dynamics simulations
Get PDFA comprehensive ab initio molecular dynamics (AIMD) simulation study is performed on the waterborne S-IV and S-VI species for different oxidation states and characterized for their spatial hydration nature, hydrogen bonding (H-bonding) and spectroscopic aspects. The vibrational modes of the power spectra and the influence of H-bonding for each species in the condensed phases are characterized by comparing with the normal modes of the species in the gas phase. In particular, it has been found that the H-bonds formed by S–IV species are more in number than those of S–VI species per oxygen site and are at least 2 times more durable than those for the latter. It has been predicted that such characteristics of H-bonds will significantly change the transport characteristics of the species.journal articl
Identification, cloning and heterologous expression of biosynthetic gene cluster for desertomycin
Get PDFFrom our in-house microbial genome database of secondary metabolite producers, we identified a candidate biosynthetic gene cluster for desertomycin from Streptomyces nobilis JCM4274. We report herein the cloning of the 127-kb entire gene cluster for desertomycin biosynthesis using bacterial artificial chromosome vector. The entire biosynthetic gene cluster for desertomycin was introduced in the heterologous host, Streptomyces lividans TK23, with an average yield of more than 130 mg l(-1).journal articl
On-Surface Synthesis of Unsaturated Carbon Nanostructures with Regularly Fused Pentagon–Heptagon Pairs
Get PDFMultiple fused pentagon–heptagon pairs are frequently found as defects at the grain boundaries of the hexagonal graphene lattice and are suggested to have a fundamental influence on graphene-related materials. However, the construction of sp2-carbon skeletons with multiple regularly fused pentagon–heptagon pairs is challenging. In this work, we found that the pentagon–heptagon skeleton of azulene was rearranged during the thermal reaction of an azulene-incorporated organometallic polymer on Au(111). The resulting sp2-carbon frameworks were characterized by high-resolution scanning probe microscopy techniques and feature novel polycyclic architectures composed of multiple regularly fused pentagon–heptagon pairs. Moreover, the calculated analysis of its aromaticity revealed a peculiar polar electronic structure.journal articl
Comparative genomics of four strains of the edible brown alga, Cladosiphon okamuranus
Get PDFBACKGROUND: The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is one of the most important edible seaweeds, and it is cultivated for market primarily in Okinawa, Japan. Four strains, denominated S, K, O, and C, with distinctively different morphologies, have been cultivated commercially since the early 2000s. We previously reported a draft genome of the S-strain. To facilitate studies of seaweed biology for future aquaculture, we here decoded and analyzed genomes of the other three strains (K, O, and C).
RESULTS: Here we improved the genome of the S-strain (ver. 2, 130 Mbp, 12,999 genes), and decoded the K-strain (135 Mbp, 12,511 genes), the O-strain (140 Mbp, 12,548 genes), and the C-strain (143 Mbp, 12,182 genes). Molecular phylogenies, using mitochondrial and nuclear genes, showed that the S-strain diverged first, followed by the K-strain, and most recently the C- and O-strains. Comparisons of genome architecture among the four strains document the frequent occurrence of inversions. In addition to gene acquisitions and losses, the S-, K-, O-, and C-strains possess 457, 344, 367, and 262 gene families unique to each strain, respectively. Comprehensive Blast searches showed that most genes have no sequence similarity to any entries in the non-redundant protein sequence database, although GO annotation suggested that they likely function in relation to molecular and biological processes and cellular components.
CONCLUSIONS: Our study compares the genomes of four strains of C. okamuranus and examines their phylogenetic relationships. Due to global environmental changes, including temperature increases, acidification, and pollution, brown algal aquaculture is facing critical challenges. Genomic and phylogenetic information reported by the present research provides useful tools for isolation of novel strains.journal articl
Spectral analysis for gene communities in cancer cells
Get PDFWe investigate gene interaction networks in various cancer cells by spectral analysis of the adjacency matrices. We observe the localization of the networks on hub genes, which have an extraordinary number of links. The eigenvector centralities take finite values only on special nodes when the hub degree exceeds the critical value dc≃40. The degree correlation function shows the disassortative behaviour in the large degrees, and the nodes whose degrees are d≳40 have a tendency to link to small degree nodes. The communities of the gene networks centred at the hub genes are extracted based on the amount of node degree discrepancies between linked nodes. We verify the Wigner–Dyson distribution of the nearest neighbour eigenvalues spacing distribution P(s) in the small degree discrepancy communities (the assortative communities), and the Poisson P(s) in the communities of large degree discrepancies (the disassortative communities) including the hubs.journal articl
Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue
Get PDFIn December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)emerged, causing the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV, the agent responsible for the 2003 SARS outbreak, utilises angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) host molecules for viral entry. ACE2 and TMPRSS2 have recently been implicated in SARS-CoV-2 viral infection. Additional host molecules including ADAM17, cathepsin L, CD147 and GRP78 may also function as receptors for SARS-CoV-2.To determine the expression and in situ localisation of candidate SARS-CoV-2 receptors in the respiratory mucosa, we analysed gene expression datasets from airway epithelial cells of 515 healthy subjects, gene promoter activity analysis using the FANTOM5 dataset containing 120 distinct sample types, single cell RNA sequencing (scRNAseq) of 10 healthy subjects, proteomic datasets, immunoblots on multiple airway epithelial cell types, and immunohistochemistry on 98 human lung samples.We demonstrate absent to lowACE2promoter activity in a variety of lung epithelial cell samples andlowACE2gene expression in both microarray and scRNAseq datasets of epithelial cell populations.Consistent with gene expression, rare ACE2 protein expression was observed in the airway epithelium and alveoli of human lung, confirmed with proteomics. We present confirmatory evidence for the presence ofTMPRSS2, CD147 and GRP78 protein in vitro in airway epithelial cells and confirm broad in situ protein expression of CD147 and GRP78 in the respiratory mucosa. Collectively, our data suggest the presence of a mechanism dynamically regulating ACE2 expression inhuman lung, perhaps in periods of SARS-CoV-2 infection, and also suggest that alternative receptors forSARS-CoV-2 exist to facilitate initial host cell infection.journal articl
The Ants (Hymenoptera, Formicidae) of Sri Lanka: a taxonomic research summary and updated checklist
Get PDFAn updated checklist of the ants (Hymenoptera: Formicidae) of Sri Lanka is presented. These include representatives of eleven of the 17 known extant subfamilies with 341 valid ant species in 79 genera. Lioponera longitarsus Mayr, 1879 is reported as a new species country record for Sri Lanka. Notes about type localities, depositories, and relevant references to each species record are given. Accounts of the dubious and some undetermined species from Sri Lanka are also provided. 82 species (24%) are endemic whereas 18 species that are non-native to Sri Lanka are recorded. The list provides a synthesis of the regional taxonomical work carried out to date and will serve as a baseline for future studies on the ant fauna of this biodiversity hotspot.journal articl
Metabolomics of human fasting: new insights about old questions
Get PDFSince ancient days, human fasting has been performed for religious or political reasons. More recently, fasting has been employed as an effective therapy for weight reduction by obese people, and numerous studies have investigated the physiology of fasting by obese subjects. Well-established fasting markers (butyrates, BCAAs and carnitines) were considered essential energy substitutes after glycogen storage depletion. However, a recently developed metabolomic approach has unravelled previously unappreciated aspects of fasting. Surprisingly, one-third (44) of 120 metabolites investigated increase during 58 h of fasting, including antioxidative metabolites (carnosine, ophthalmic acid, ergothioneine and urates) and metabolites of entire pathways, such as the pentose phosphate pathway. Signalling metabolites (3-hydroxybutyrate and 2-oxoglutarate) and purines/pyrimidines may also serve as transcriptional modulators. Thus, prolonged fasting activates both global catabolism and anabolism, reprogramming metabolic homeostasis.journal articl
Strong Plasmon–Exciton Coupling in Ag Nanoparticle—Conjugated Polymer Core-Shell Hybrid Nanostructures
Get PDFStrong plasmon-exciton coupling between tightly-bound excitons in organic molecular semiconductors and surface plasmons in metal nanostructures has been studied extensively for a number of technical applications, including low-threshold lasing and room-temperature Bose-Einstein condensates. Typically, excitons with narrow resonances, such as J-aggregates, are employed to achieve strong plasmon-exciton coupling. However, J-aggregates have limited applications for optoelectronic devices compared with organic conjugated polymers. Here, using numerical and analytical calculations, we demonstrate that strong plasmon-exciton coupling can be achieved for Ag-conjugated polymer core-shell nanostructures, despite the broad spectral linewidth of conjugated polymers. We show that strong plasmon-exciton coupling can be achieved through the use of thick shells, large oscillator strengths, and multiple vibronic resonances characteristic of typical conjugated polymers, and that Rabi splitting energies of over 1000 meV can be obtained using realistic material dispersive relative permittivity parameters. The results presented herein give insight into the mechanisms of plasmon-exciton coupling when broadband excitonic materials featuring strong vibrational-electronic coupling are employed and are relevant to organic optoelectronic devices and hybrid metal-organic photonic nanostructures.journal articl