phyloBARCODER: A web tool for phylogenetic classification of eukaryote metabarcodes using custom reference databases.

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (1) species or classification of query sequences and (2) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of non-mitochondrial genes, e.g., ITS or rbcL.

Effects of flusulfamide on spore germination of Plasmodiophora brassicae.

Flusulfamide inhibits germination of Plasmodiophora brassicae resting spores to suppress clubroot disease, but its mechanism of action on the germination of P. brassicae resting spores remains unclear. In this study, P. brassicae resting spores were treated with flusulfamide and visualized using transmission electron microscopy (TEM). The gene expression of P. brassicae resting spores was analyzed using RT-PCR, followed by immunoblotting analysis. TEM results revealed that flusulfamide suppressed the primary zoosporogenesis of P. brassicae resting spores during the early phase, and RT-PCR results revealed that flusulfamide affected the gene expression during the germination of the resting spores. Immunoblot and RT-qPCR analyses revealed that PbCyp3, an immunophilin (peptidyl-prolyl-isomerase) gene, was highly expressed, resulting in the unusual accumulation of PbCYP3 protein in P. brassicae resting spores immediately after treatment with flusulfamide. This suggests that flusulfamide may cause aberrant folding of proteins involved in primary zoosporogenesis, thereby inhibiting germination.

[Successful treatment with tucidinostat in a patient with relapsed adult T-cell leukemia/lymphoma following allogeneic hematopoietic stem cell transplantation].

Aggressive types of adult T-cell leukemia-lymphoma (ATL), namely, the acute type, lymphoma type, and chronic type with poor prognostic factors, have a poor prognosis. Although allogeneic hematopoietic stem cell transplantation (HSCT) may improve prognosis, relapse is common. In June 2021, tucidinostat was approved for relapsed or refractory ATL in Japan. We report a case of a 62-year-old man with relapsed ATL after allogeneic HSCT. In March 2017, he was diagnosed with ATL (acute type) and received two courses of mLSG-15 therapy. ATL cells reappeared in his peripheral blood, so he underwent allogeneic bone marrow transplantation in September 2017. In June 2021, his soluble interleukin-2 receptor (sIL-2R) level increased, and he began experiencing sensory abnormalities in his face and legs. In September, he developed respiratory failure and was diagnosed with relapse of ATL. He was again treated with mLSG-15. His sIL-2R normalized and the sensory abnormalities decreased, but sIL-2R rose again in February 2022. After tucidinostat treatment was initiated, sIL-2R normalized and the patient's general condition improved. Tucidinostat shows promise as an effective treatment for ATL that has relapsed after allogeneic HSCT.

Electrolytic Hydrogen Release from Hydrogen Boride Sheets.

Solid-state hydrogen storage materials are safe and lightweight hydrogen carriers. Among the various solid-state hydrogen carriers, hydrogen boride (HB) sheets possess a high gravimetric hydrogen capacity (8.5 wt%). However, heating at high temperatures and/or strong ultraviolet illumination is required to release hydrogen (H2 ) from HB sheets. In this study, the electrochemical H2 release from HB sheets using a dispersion system in an organic solvent without other proton sources is investigated. H2 molecules are released from the HB sheets under the application of a cathodic potential. The Faradaic efficiency for H2 release from HB sheets reached >90%, and the onset potential for H2 release is -0.445 V versus Ag/Ag+ , which is more positive than those from other proton sources, such as water or formic acid, under the same electrochemical conditions. The total electrochemically released H2 in a long-time experiment reached ≈100% of the hydrogen capacity of HB sheets. The H2 release from HB sheets is driven by a small bias; thus, they can be applied as safe and lightweight hydrogen carriers with economical hydrogen release properties.

Real-world clinical characteristics of post-essential thrombocythemia and post-polycythemia vera myelofibrosis.

There are few prospective studies on patients with post-essential thrombocythemia myelofibrosis (PET-MF) and post-polycythemia vera myelofibrosis (PPV-MF). Therefore, we conducted a nationwide longitudinal prospective survey to clarify the clinical characteristics of these diseases. A total of 197 PET-MF and 117 PPV-MF patients diagnosed between 2012 and 2021 were analyzed. The median age at diagnosis was 70.0 years for both diseases. The time from diagnosis of ET or PV to that of MF was 9.6 and 10.4 years, respectively, with no significant difference. Patients with PPV-MF had higher hemoglobin levels and white blood cell counts than those with PET-MF, whereas those with PET-MF had higher platelet counts than those with PPV-MF. Although splenomegaly was more frequent in patients with PPV-MF at diagnosis, there was no difference in the frequency of constitutional symptoms. Ruxolitinib was the most common treatment administered to 74.6% and 83.8% of patients with PET-MF and PPV-MF, respectively. Patients with PET-MF and PPV-MF had similar prognoses, with 3-year overall survival (OS) of 0.742 in PET-MF and 0.768 in PPV-MF patients. In both diseases, leukemic transformation was the leading cause of death, followed by infection. The 3-year OS for patients with PET/PPV-MF and primary MF diagnosed during the same period was 0.754 and 0.626, respectively, with no significant difference. This survey provides real-world clinical features and prognostic data on secondary myelofibrosis in the ruxolitinib era.

Pathogenicity chromosome of Fusarium oxysporum f. sp. cepae.

Fusarium oxysporum f. sp. cepae (Foc) is the causative agent of Fusarium basal rot disease in onions, which leads to catastrophic global crop production losses. Therefore, the interaction of Foc with its host has been actively investigated, and the pathogen-specific (PS) regions of the British strain Foc_FUS2 have been identified. However, it has not been experimentally determined whether the identified PS region plays a role in pathogenicity. To identify the pathogenicity chromosome in the Japanese strain Foc_TA, we initially screened effector candidates, defined as small proteins with a signal peptide that contain two or more cysteines, from genome sequence data. Twenty-one candidate effectors were identified, five of which were expressed during infection. Of the expressed effector candidates, four were located on the 4-Mb-sized chromosome in Foc_TA. To clarify the relationship between pathogenicity and the 4-Mb-sized chromosome in Foc_TA, nine putative 4-Mb-sized chromosome loss strains were generated by treatment with benomyl (a mitotic inhibitor drug). A pathogenicity test with putative 4-Mb-sized chromosome loss strains showed that these strains were impaired in their pathogenicity toward onions. Genome analysis of three putative 4-Mb-sized chromosome loss strains revealed that two strains lost a 4-Mb-sized chromosome in common, and another strain maintained a 0.9-Mb region of the 4-Mb-sized chromosome. Our findings show that the 4-Mb-sized chromosome is the pathogenicity chromosome in Foc_TA, and the 3.1-Mb region within the 4-Mb-sized chromosome is required for full pathogenicity toward onion.

The SIX5 Protein in Fusarium oxysporum f. sp. cepae Acts as an Avirulence Effector toward Shallot (Allium cepa L. Aggregatum Group).

Fusarium oxysporum f. sp. cepae (Foc) causes basal rot disease in Allium species, including onions (Allium cepa L.) and shallots (A. cepa L. Aggregatum group). Among Allium species, shallots can be crossbred with onions and are relatively more resistant to Foc than onions. Thus, shallots are considered a potential disease-resistant resource for onions. However, the mechanisms underlying the molecular interactions between shallots and Foc remain unclear. This study demonstrated that SIX5, an effector derived from Foc (FocSIX5), acts as an avirulence effector in shallots. We achieved this by generating a FocSIX5 gene knockout mutant in Foc, for which experiments which revealed that it caused more severe wilt symptoms in Foc-resistant shallots than the wild-type Foc and FocSIX5 gene complementation mutants. Moreover, we demonstrated that a single amino acid substitution (R67K) in FocSIX5 was insufficient to overcome shallot resistance to Foc.

COVID­19 antibody production by vaccination in chemotherapy with CD20 antibody for B­cell lymphoma.

Most hematologic diseases are immunosuppressed, either by the disease itself or by treatment. As such, the implementation of vaccination is largely at the discretion of the attending physician. In this context, an objective measure is needed, therefore the index of vaccination against coronavirus disease 2019 (COVID-19) in B-cell lymphomas treated with antibody therapy against CD20 (including after the completion of therapy) was examined. A total of 40 patients with B-cell lymphoma during or after antibody therapy against CD20 were vaccinated twice with the BNT162b2 messenger RNA (mRNA) COVID-19 vaccine (Pfizer, Inc. and BioNTech SE.) at 3-week intervals and then again six months later with the same vaccine or mRNA-1273 (Moderna, Inc.). Antibody testing was conducted ~1 month after the third vaccination. Analysis was performed using the antibody titers to the anti-spike immunoglobulin assay, with a titer of 0.8 U/ml or higher (considered positive) and a titer of 264 U/ml or higher (considered the value at which the efficacy of the vaccine can be fully expected). Significant factors of antibody acquisition were identified when i) antibody titers were 0.8 U/ml or higher (CD4 ≥400/µl), ii) no anti-CD20 antibody maintenance therapy was undertaken (CD19 ≥100/µl), iii) patients were not on treatment (CD4 ≥400/µl), or 4) at least six months had passed since treatment ended (CD19 ≥100/µl). When antibody titers were 264 U/ml or higher, the treatment method, the stage of the primary disease and other factors related to the condition treatment method of the patient were relevant. When these were analyzed by multivariate analysis, the significant factor when antibody titers were set to 0.8 U/ml was CD19 ≥100/µl. In contrast, when setting them to 264 U/ml or higher, CD4 ≥400/µl was not significant, but there was a tendency for it to be related. The findings of the present study on vaccine-induced antibody acquisition in patients with B-cell lymphoma indicated that it is desirable to have a CD19 titer of at least 100/µl and a CD4 titer of at least 400/µl (both conditions should be met), and that no maintenance therapy with anti-CD20 antibody should be administered for at least six months after the last treatment or completion of the treatment. Interestingly, when the criteria for antibody titers were compared between 0.8 U/ml, where antibody titer is detected, and 264 U/ml, where vaccine efficacy is expected, several key factors were different. It is possible that these key factors may change depending on the antibody titer used as a criterion.

Hepatitis C Virus (HCV)-Ribonucleic Acid (RNA) As a Biomarker for Lymphoid Malignancy with HCV Infection.

The hepatitis C virus (HCV) is potentially associated with liver cancer, and advances in various drugs have led to progress in the treatment of hepatitis C and attempts to prevent its transition to liver cancer. Furthermore, reactivation of HCV has been observed in the treatment of lymphoma, during which the immortalization and proliferation of lymphocytes occur, which leads to the possibility of further stimulating cytokines and the like and possibly to the development of lymphoid malignancy. There are also cases in which the disappearance of lymphoid malignancy has been observed by treating HCV and suppressing HCV-Ribonucleic acid (RNA), as well as cases of recurrence with an increase in HCV-RNA. While HCV-associated lymphoma has a poor prognosis, improving the prognosis with Direct Acting Antivirals (DAA) has recently been reported. The reduction and eradication of HCV-RNA by means of DAA is thus important for the treatment of lymphoid malignancy associated with HCV infection, and HCV-RNA can presumably play a role as a biomarker. This review provides an overview of what is currently known about HCV-associated lymphoma, its epidemiology, the mechanisms underlying the progression to lymphoma, its treatment, the potential and limits of HCV-RNA as a therapeutic biomarker, and biomarkers that are expected now that DAA therapy has been developed.

Effective treatment of hydrogen boride sheets for long-term stabilization.

Two-dimensional hydrogen boride (HB) sheets prepared via the ion-exchange reaction from magnesium diboride (MgB2) are known to possess several intriguing properties for a wide range of applications; however, previous reports have shown that the sheets prepared using this method contain small amounts of reactive components, making them unsuitable for certain applications. Therefore, developing a method for preparing HB sheets that exhibit long-term stability and do not contain reactive species is essential. In this study, we developed an effective treatment method for achieving long-term stabilization of HB sheets. We found that by pre-treating the HB sheets with water and then filtering the dried product from an acetonitrile dispersion, we could achieve excellent long-term stability over nine months. This stability was maintained even outside of a glovebox, with no H2 released by the decomposition and/or reaction. X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) absorption spectroscopy measurements revealed that the sample exhibited pure HB characteristics with negatively charged boron and B-H-B and terminal B-H bonds, even after nine months of storage. Furthermore, based on thermal desorption spectroscopy (TDS) measurements, the presence of reactive species in the as-prepared HB sheets is attributed to fluctuating B-H bonds with relatively weak binding energies that can be removed using the method developed in this study.

Genome-Wide Characterization of Effector Protein-Encoding Genes in Sclerospora graminicola and Its Validation in Response to Pearl Millet Downy Mildew Disease Stress.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is the essential food crop for over ninety million people living in drier parts of India and South Africa. Pearl millet crop production is harshly hindered by numerous biotic stresses. Sclerospora graminicola causes downy mildew disease in pearl millet. Effectors are the proteins secreted by several fungi and bacteria that manipulate the host cell structure and function. This current study aims to identify genes encoding effector proteins from the S. graminicola genome and validate them through molecular techniques. In silico analyses were employed for candidate effector prediction. A total of 845 secretory transmembrane proteins were predicted, out of which 35 proteins carrying LxLFLAK (Leucine-any amino acid-Phenylalanine-Leucine-Alanine-Lysine) motif were crinkler, 52 RxLR (Arginine, any amino acid, Leucine, Arginine), and 17 RxLR-dEER putative effector proteins. Gene validation analysis of 17 RxLR-dEER effector protein-producing genes was carried out, of which 5genes were amplified on the gel. These novel gene sequences were submitted to NCBI. This study is the first report on the identification and characterization of effector genes in Sclerospora graminicola. This dataset will aid in the integration of effector classes that act independently, paving the way to investigate how pearl millet responds to effector protein interactions. These results will assist in identifying functional effector proteins involving the omic approach using newer bioinformatics tools to protect pearl millet plants against downy mildew stress. Considered together, the identified effector protein-encoding functional genes can be utilized in screening oomycetes downy mildew diseases in other crops across the globe.

Dismantling of Reinforced Concrete Using Steam Pressure Cracking System: Drilling and Crack Propagation.

This study investigated a new dismantling system for concrete structures using a steam pressure cracking agent. We improved the mechanical systems such that it can drill through reinforcing steel bars. Therefore, the control method of the system and shape of the drill tip were improved. When the drill tip is stuck with chips and stopped, it is automatically pulled out and reinserted to recover the rotation. By changing the tip angle of the drill bit from 75° to 90°, it became possible to cut reinforcing bars, which were difficult to cut previously. In addition, we designed a crawler-type mechanical system and improved it such that it can be moved to the appropriate position and operated at any angle. This study revealed that the energy required for the drilling process accounts for more than 90% of the total dismantling energy. Through experiments using an impact hammer drill and observations of fracture surfaces using a three-dimensional scanner, we analysed the characteristics of reinforced concrete. In addition, the feasibility of the design for dismantling reinforced concrete was confirmed based on the determined energy associated with crack propagation.

Molecular Analysis of MgO Nanoparticle-Induced Immunity against Fusarium Wilt in Tomato.

Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (FOL), is a devastating soilborne disease in tomatoes. Magnesium oxide nanoparticles (MgO NPs) induce strong immunity against Fusarium wilt in tomatoes. However, the mechanisms underlying this immunity remain poorly understood. Comparative transcriptome analysis and microscopy of tomato roots were performed to determine the mechanism of MgO NP-induced immunity against FOL. Eight transcriptomes were prepared from tomato roots treated under eight different conditions. Differentially expressed genes were compared among the transcriptomes. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that in tomato roots pretreated with MgO NPs, Rcr3 encoding apoplastic protease and RbohD encoding NADPH oxidase were upregulated when challenge-inoculated with FOL. The gene encoding glycine-rich protein 4 (SlGRP4) was chosen for further analysis. SlGRP4 was rapidly transcribed in roots pretreated with MgO NPs and inoculated with FOL. Immunomicroscopy analysis showed that SlGRP4 accumulated in the cell walls of epidermal and vascular vessel cells of roots pretreated with MgO NPs, but upon FOL inoculation, SlGRP4 further accumulated in the cell walls of cortical tissues within 48 h. The results provide new insights into the probable mechanisms of MgO NP-induced tomato immunity against Fusarium wilt.

Highly Dispersed Ni Nanoclusters Spontaneously Formed on Hydrogen Boride Sheets.

Hydrogen boride (HB) sheets are two-dimensional materials comprising a negatively charged hexagonal boron network and positively charged hydrogen atoms with a stoichiometric ratio of 1:1. Herein, we report the spontaneous formation of highly dispersed Ni nanoclusters on HB sheets. The spontaneous reduction reaction of Ni ions by the HB sheets was monitored by in-situ measurements with an ultraviolet-visible spectrometer. Acetonitrile solutions of Ni complexes and acetonitrile dispersions of the HB sheets were mixed in several molar ratios (the HB:Ni molar ratio was varied from 100:0.5 to 100:20), and the changes in the absorbance were measured over time. In all cases, the results suggest that Ni metal clusters grow on the HB sheets, considering the increase in absorbance with time. The absorbance peak position shifts to the higher wavelength as the Ni ion concentration increases. Transmission electron microscopy images of the post-reaction products indicate the formation of Ni nanoclusters, with sizes of a few nanometers, on the HB sheets, regardless of the preparation conditions. These highly dispersed Ni nanoclusters supported on HB sheets will be used for catalytic and plasmonic applications and as hydrogen storage materials.

FoMC69 Gene in Fusarium oxysporum f. sp. radicis-lycopersici Is Essential for Pathogenicity by Involving Normal Function of Chlamydospores.

Fusarium oxysporum f. sp. radicis-lycopersici (Forl) causes crown and root rot disease in tomato, effecting severe economic losses. However, research on the pathogenicity genes and infection strategy of Forl is limited compared to that on F. oxysporum f. sp. lycopersici (Fol). In this study, we characterized FoMC69 gene in Forl as a homolog of MC69 required for pathogenicity in rice blast pathogen-Magnaporthe oryzae. Gene expression analysis revealed that FoMC69 expressionin Forl is higher than that in Folin planta. FoMC69-knockout mutant of Forl had significantly reduced root rot symptoms compared to the wild-type strain, and full pathogenicity was restored by complementation. By contrast, ΔFoMC69 mutant of Fol presented the same symptoms as the wild type, suggesting that FoMC69 of Forl, but not of Fol, was essential for full virulence in tomato plants. Morphological differences between the Forl and ΔFoMC69 in the roots were observed by fluorescent labeling using WGA-FITC. Chlamydospores of the ΔFoMC69 mutant of Forlcontinuously increased during infection and were three times higher than that of the wild type at 21 days post-inoculation. These observations suggest that FoMC69 of Forl is required for virulence to tomato plants by involving the normal development and germination of chlamydospores.

Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA.

Environmental DNA (eDNA) is increasingly used to noninvasively monitor aquatic animals in freshwater and coastal areas. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean. Small pelagic fish have a large biomass and are widely distributed in the open ocean. We tested the performance of two OceanDNA analysis methods-species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers-to determine the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure. The results from OceanDNA methods were compared to those of net sampling to test for consistency. Then, we compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method; the reason is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, the combined usage of the two methods to monitor quantitative distribution of small pelagic fish species with information of fish community structures was recommended.

Cutting of Diamond Substrate Using Fixed Diamond Grain Saw Wire.

This study demonstrates that a single-crystal diamond substrate can be cut along designed lines using the diamond-saw-wire cutting method. We developed an original saw-wire fixed diamond-grain using a bronze solder with a high melting temperature. We created a unique product machine system with a high vacuum furnace and a bronze solder that contains a metallic compound. The diamond cutting mechanism employed in this study is based on the mild wear phenomenon, owing to the friction between the diamond surfaces. A linear relationship between the cutting length and wire feed distance was observed. The relationship can be approximated as y = 0.3622x, where y (µm) is the cutting depth and x (km) is the wire feed distance. The life of the saw-wire was longer than that of the 6000 km wire feed distance and was tested by reciprocating an 8-m short wire at a speed, tension, and cutting force of 150 m/min, 1 N, and 0.2 N, respectively. A single crystal diamond substrate could be cut along the designed line, which was more than 2 mm long. The cutting speed was maintained constant at 0.36 µm/km.

Convulsive Seizure Due to Hypomagnesemia Caused by Short-term Vonoprazan Intake.

A 71-year-old woman was admitted for the treatment of diffuse large B-cell lymphoma of the ileum. She had been taking lansoprazole but was switched to vonoprazan due to epigastric discomfort. Three weeks after starting vonoprazan intake, she had a convulsive seizure, and a blood test showed hypomagnesiemia. The cause of hypomagnesemia was considered to be malabsorption of magnesium from the intestinal tract associated with vonoprazan. After discontinuation of vonoprazan, the magnesium level quickly recovered, and the seizures did not relapse. It is important to consider the risk of hypomagnesemia in patients taking vonoprazan, even for a short period of time.