Measurement report: Summertime fluorescence characteristics of atmospheric water-soluble organic carbon in the marine boundary layer of the western Arctic Ocean

Accelerated warming and a decline in sea ice coverage in the summertime Arctic Ocean can significantly affect the emissions of marine organic aerosols and biogenic volatile organic compounds. However, how these changes affect the characteristics of atmospheric water-soluble organic carbon (WSOC), which plays an important role in the climate system, remains unclear. Thus, to improve our understanding of WSOC characteristics in the rapidly changing Arctic Ocean, including its summertime fluorescence characteristics, we simultaneously measured atmospheric concentrations of ionic species and WSOC, a fluorescence excitation–emission matrix coupled with parallel factor (EEM-PARAFAC) analysis of WSOC, and marine biological parameters in surface seawaters of the western Arctic Ocean during the summer of 2016. WSOC was predominantly present as fine-mode aerosols (diameter &lt;2.5 µm, median =92 %), with the mean concentration being higher in the coastal water areas (462±130 ngC m−3) than in the sea-ice-covered areas (242±88.4 ngC m−3). Moreover, the WSOC in the fine-mode aerosols was positively correlated with the methanesulfonic acid in the fine-mode aerosol samples collected over the sea-ice-covered areas (r=0.88, p&lt;0.01, n=10), suggesting high rates of sea–air gas exchange and emissions of aerosol precursor gases due to sea ice retreat and increasingly available solar radiation during the Arctic summer. Two fluorescent components, humic-like C1 and protein-like C2, were identified by the PARAFAC modeling of fine-mode atmospheric WSOC. The two components varied regionally between coastal and sea-ice-covered areas, with low and high fluorescence intensities observed over the coastal areas and the sea-ice-covered areas, respectively. Further, the humification index of WSOC was correlated with the fluorescence intensity ratio of the humic-like C1 / protein-like C2 (r=0.89, p&lt;0.01) and the WSOC concentration in the fine-mode aerosols (r=0.66, p&lt;0.05), with the highest values observed in the coastal areas. Additionally, the WSOC concentration in the fine-mode aerosols was positively correlated with the fluorescence intensity ratio of the humic-like C1 / protein-like C2 (r = 0.77, p&lt;0.01) but was negatively correlated with the biological index (r=-0.69, p&lt;0.01). Overall, these results suggested that the WSOC in the fine-mode aerosols in the coastal areas showed a higher degree of polycondensation and higher aromaticity compared to that in the sea-ice-covered areas, where WSOC in the fine-mode aerosols was associated with relatively new, less oxygenated, and biologically derived secondary organic components. These findings can improve our understanding of the chemical and biological linkages of WSOC at the ocean–sea-ice–atmosphere interface.</p

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education

The acrylic vessel for JSNS2^{2}-II neutrino target

The JSNS$^{2}$ (J-PARC Sterile Neutrino Search at J-PARC Spallation Neutron Source) is an experiment designed for the search for sterile neutrinos. The experiment is currently at the stage of the second phase named JSNS$^{2}$-II with two detectors at near and far locations from the neutrino source. One of the key components of the experiment is an acrylic vessel, that is used for the target volume for the detection of the anti-neutrinos. The specifications, design, and measured properties of the acrylic vessel are described

Characterization of the correlated background for a sterile neutrino search using the first dataset of the JSNS2^2 experiment

JSNS$^2$ (J-PARC Sterile Neutrino Search at J-PARC Spallation Neutron Source) is an experiment that is searching for sterile neutrinos via the observation of $\bar{\nu}_{\mu} \to \bar{\nu}_{e}$ appearance oscillations using muon decay-at-rest neutrinos. Before dedicated data taking in the first-half of 2021, we performed a commissioning run for 10 days in June 2020. Using the data obtained in this commissioning run, in this paper, we present an estimate of the correlated background which imitates the $\bar{\nu}_{e}$ signal in a sterile neutrino search. In addition, in order to demonstrate future prospects of the JSNS$^2$ experiment, possible pulse shape discrimination improvements towards reducing cosmic ray induced fast neutron background are described.Comment: 7 pages, 3 figure

CFGP: a web-based, comparative fungal genomics platform

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the ‘fill-in-the-form-and-press-SUBMIT’ user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI

Myotis rufoniger genome sequence and analyses: M-rufoniger&apos;s genomic feature and the decreasing effective population size of Myotis bats

Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66x fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10x coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger&apos;s red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has batspecific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat&apos;s reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since similar to 30k years ago. M. rufoniger&apos;s effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity

The overmethylated genes in Helicobacter pylori-infected gastric mucosa are demethylated in gastric cancers

<p>Abstract</p> <p>Background</p> <p>The transitional-CpG sites between weakly methylated genes and densely methylated retroelements are overmethylated in the gastric mucosa infected with <it>Helicobacter pylori </it>(<it>H. pylori</it>) and they are undermethylated in the gastric cancers depending on the level of loss of heterozygosity (LOH) events. This study delineated the transitional-CpG methylation patterns of CpG-island-containing and -lacking genes in view of the retroelements.</p> <p>Methods</p> <p>The transitional-CpG sites of eight CpG-island-containing genes and six CpG-island-lacking genes were semi-quantitatively examined by performing radioisotope-labelling methylation-specific PCR under stringent conditions. The level of LOH in the gastric cancers was estimated using the 40 microsatellite markers on eight cancer-associated chromosomes. Each gene was scored as overmethylated or undermethylated based on an intermediate level of transitional-CpG methylation common in the <it>H. pylori</it>-negative gastric mucosa.</p> <p>Results</p> <p>The eight CpG-island genes examined were overmethylated depending on the proximity to the nearest retroelement in the <it>H. pylori</it>-positive gastric mucosa. The six CpG-island-lacking genes were similarly methylated in the <it>H. pylori</it>-positive and -negative gastric mucosa. In the gastric cancers, long transitional-CpG segments of the CpG-island genes distant from the retroelements remained overmethylated, whereas the overmethylation of short transitional-CpG segments close to the retroelements was not significant. Both the CpG-island-containing and -lacking genes tended to be decreasingly methylated in a LOH-level-dependent manner.</p> <p>Conclusions</p> <p>The overmethylated genes under the influence of retroelement methylation in the <it>H. pylori</it>-infected stomach are demethylated in the gastric cancers influenced by LOH.</p