Biology subjects

Goto, M.

Publications and source records attributed to Goto, M..

At least 19 recordsLinked to original sources

bioRxiv2026

WRN deficiency generates oncogenic rearrangements at TA-rich tandem repeats

Werner syndrome, a premature-aging disorder caused by inherited loss of the WRN helicase, predisposes to a narrow set of cancers, including melanoma and sarcoma, through mechanisms that have been unclear. WRN resolves the secondary structures that TA-dinucleotide repeats form, a role established for the expanded repeats of mismatch-repair-deficient cancers. We show that WRN loss also destabilizes native, unexpanded TA-rich tandem repeats, which become fragile sites where chromosomes break and rearrange. In melanoma these rearrangements recurrently produce an identical 15.7Mb-long deletion that transcriptionally activates TERT, the earliest driver of these tumors, and separately disrupt tumor suppressors such as CDKN2A/B and NF1. The same class of rearrangement occurs in WRN-deficient cancers of other types. WRN deficiency is thus a source of instability at TA-rich tandem repeats that generates oncogenic rearrangements.

cancer biology↗

bioRxiv2026

The automated eukaryotic pangenome pipeline EukPan reveals accessory genome differentiation beyond core-gene phylogeny in Aspergillus oryzae

Pangenome analysis reveals recurrent gene-content variation beyond a single reference genome, but its application to eukaryotes is constrained by inconsistent gene annotation. ANNEVO predicts gene models from genome FASTA assemblies without RNA-seq data. We developed EukPan, an automated post-annotation pipeline that standardizes GFF/GTF files, selects representative isoforms, constructs proteomes, infers orthogroups, builds a concatenated single-copy core-protein alignment, and summarizes shared accessory orthogroups while excluding orthogroups detected in only one genome. Applied with ANNEVO to 123 Aspergillus oryzae genomes, EukPan identified 11,245 core and 4,407 shared accessory orthogroups. The core-protein phylogeny broadly recovered the reported A-H classification, whereas accessory-genome analyses clearly separated the 33 group-A strains from the other 90 strains. Directional analysis identified 62 group-A-associated and 158 group-A-depleted orthogroups, with major facilitator superfamily (MFS) transporter and fungal Zn2Cys6 transcription-factor domains prominent in the depleted set. Among 93 orthogroups present in all non-A strains and absent from all group-A strains, 59 mapped to 10 segments of RIB40, the standard A. oryzae reference genome and a non-A (group-F) strain. EukPan therefore enables reproducible, coordinated core- and accessory-pangenome analysis from eukaryotic genome assemblies.

genomics↗

bioRxiv2026

Selective depletion of AMH-expressing granulosa cells in vivo impairs follicular development and fertility in female mice

In mammals, ovarian follicle development is a highly coordinated process that underlies female fertility. Granulosa cells expressing anti-Mullerian hormone (AMH) are widely used as a marker of growing follicles. However, the in vivo roles of granulosa cells in follicular development and female fertility remain unclear. Here, we analyzed AMH-toxin receptor-mediated cell knockout (AMH-TRECK) transgenic (Tg) mice on a NOG background, in which AMH-expressing granulosa cells are specifically depleted by diphtheria toxin (DT). We first found that, after a single DT injection into postnatal AMH-TRECK Tg females, AMH-expressing granulosa cells in primary and secondary follicles exhibited cleaved caspase-3 signals 1 day later and were depleted 4 days later. Second, after repeated DT injections weekly from 1 to 7 weeks of age in AMH-TRECK Tg females, antral follicles and corpora lutea were rarely observed, and the numbers of primordial, primary, and secondary follicles were decreased. Following PMSG and hCG stimulation, repeated DT-injected Tg females exhibited a reduced number of ovulated oocytes with a low proportion of mature oocytes, resulting in reduced IVF rates and fertility. Further, after a cessation of repeated DT treatment, ovarian weight and follicular development recovered: the numbers of primary, secondary, and antral follicles were recovered, whereas the primordial follicle pool remains reduced. We conclude that selective depletion of AMH-expressing granulosa cells in vivo impairs follicular development and fertility. Our model enables assessment of the in vivo effects of granulosa cell depletion and may provide a useful platform for future transplantation-based studies to understand complex follicular dynamics.

developmental biology↗

bioRxiv2026

Animal model of leprous neuritis using transfer of sensitized lymphocytes into M. leprae-inoculated nude mice

BackgroundLeprosy is curable with multidrug therapy, but preventing peripheral neuropathy remains challenging. In leprosy, reversal reactions (Type 1 reactions) are characterized by sudden enhanced cell-mediated immunity against Mycobacterium leprae (M. leprae), leading to acute neuritis that may cause irreversible nerve damage, paralysis, sensory impairment, and muscle atrophy. Armadillo and nude mouse models are used to study M. leprae infection, but detailed neuropathological models for immune-mediated reactions in leprosy are lacking. This study aimed to establish a reproducible animal model to analyze leprous neuritis pathogenesis. Methodology/Principal FindingsBALB/c nude mice were inoculated with M. leprae and six months later received transfers of naive CD4+ cells, sensitized CD4+ cells, or sensitized whole spleen cells from BALB/c mice. Histological and quantitative analyses were performed four weeks post-transfer. Mice that received transfer of sensitized CD4+ cells or sensitized spleen cells exhibited footpad swelling up to 88% greater than in animals with no cell transfer. Mice that received the sensitized cells also had massive inflammatory cell infiltration into nerve fascicles. Quantitative imaging confirmed a significant reduction in the percentage of myelinated area in mice that received transfer of sensitized CD4+ (p < 0.05) or whole spleen cells (p < 0.01) compared to control mice with no transfer. Furthermore, bacterial fragmentation within the endoneurium coincided with myelinated axon destruction, indicating that the immune response targeted bacilli but simultaneously damaged nerve structures. Conclusions/SignificanceThis study successfully reproduced leprous peripheral neuritis that resembles the reversal reaction in humans. The findings indicate that CD4+ cells are primary drivers of inflammation, whereas interactions between multiple immune cell populations in whole spleen cell transfers further exacerbate disease pathology. This model confirms that host immune responses are crucial for nerve injury progression. This model provides a valuable tool for investigating neuroprotective therapies to prevent permanent disability in patients with leprosy. Author SummaryAlthough leprosy can be treated as an infectious disease, many patients still suffer from permanent peripheral nerve damage, known as leprous neuritis. A particularly dangerous condition called the "reversal reaction" occurs when the immune system of an infected individual suddenly overreacts, causing severe acute inflammation in the nerves. Without prompt treatment, this inflammatory response can result in irreversible nerve damage, paralysis, and muscle atrophy. In this study, we developed a new animal model using "nude mice", which lack their own T-cells, to understand how this damage happens. We infected these mice with leprosy bacteria and then transferred specific immune cells, specifically sensitized CD4+ T cells, isolated from M. leprae-immunized mice. The results showed that this transfer triggered significant footpad swelling and caused inflammatory cells to invade the nerve fascicles. Most importantly, we observed a significant reduction in myelin, the protective coating that promotes nerve signaling. These findings confirm that nerve damage is largely driven by the hosts own immune response attempting to clear the bacteria. By successfully recreating this reaction, our research provides a vital tool for developing new therapies aimed at preventing permanent disability and protecting the physical functions of patients.

immunology↗

bioRxiv2026

A lethal mouse model of Oz virus infection reveals hepatic involvement and enables evaluation of antiviral and vaccine efficacy

Oz virus (OZV), a member of the genus Thogotovirus in the family Orthomyxoviridae, is an emerging tick-borne virus reported in Japan. A fatal human case and seroepidemiological evidence of widespread exposure among wild animals and humans suggest its potential public health significance. However, no animal models suitable for pathogenic studies or evaluation of countermeasures are available for OZV. Here, we have established a lethal mouse model of OZV infection using cell-adapted virus and mice lacking type I interferon signaling (B6 Ifnar1 KO mice). OZV infection resulted in 100% mortality and was characterized by robust viral replication in the liver and spleen, severe hepatitis, and acute liver injury. Using this model, we also demonstrated that oral administration of T-705, an antiviral drug widely used against RNA viruses, as well as immunization with an inactivated whole virus particle vaccine, protected B6 Ifnar1 KO mice from lethal OZV infection by mitigating the acute hepatitis. The present study provides critical insights into OZV pathogenesis and establishes a practical in vivo platform for the development of countermeasures against OZV infection. Significance statementEmerging tick-borne viruses pose a growing public health concern, yet progress in understanding their pathogenesis and in developing countermeasures is often limited by the lack of relevant animal models. Oz virus (OZV), a recently identified thogotovirus associated with a fatal human case, exemplifies this challenge. Here, we establish a lethal mouse model of OZV infection that reveals pronounced hepatic involvement as a central pathological feature. Using this model, we demonstrate effective protection by both an antiviral drug and an inactivated vaccine against lethal OZV challenge. This study provides a practical in vivo platform for investigating OZV pathogenesis and for accelerating the development of medical countermeasures against this emerging tick-borne virus.

microbiology↗

bioRxiv2025

Higher trophic status leads to more diverse and divergent microeukaryote communities over time in urban lakes from the Greater Paris (France)

Effects of trophic status on lake microeukaryote community dynamics remain underexplored. Spanning oligotrophic to hypereutrophic conditions, peri-urban lakes located in the Greater Paris region (France) offer unique opportunities to compare these dynamics along a eutrophication gradient. Here, community composition was characterized using 18S rRNA gene metabarcoding, and analyzed in the context of environmental parameters and chlorophyll a-derived trophic status throughout an 18-month sampling period. Microeukaryote assemblages were dominated by Cryptophyceae, Spirotrichea, Chrysophyceae, and Chlorophyceae, with mixotrophic and heterotrophic taxa dominating across all lakes. Taxa richness peaked at intermediate trophic levels, consistent with the intermediate disturbance hypothesis. Beta-diversity and network analyses revealed increasing community modularity, reduced connectivity, and enhanced temporal variability with higher trophic status. In lakes reaching the hypereutrophic status, communities diverged progressively over time, suggesting the onset of regime shifts. Conversely, oligo-to mesotrophic lakes maintained more connected and stable assemblages. These findings demonstrate that eutrophication fosters more diverse and increasingly divergent microeukaryote communities, underscoring its role as a central driver of microbial community restructuring in urban freshwater systems.

microbiology↗

bioRxiv2025

Effects of Oxytocin and p-Cresol on BDNF Expression in Pancreatic Cancer Cells

This study demonstrates for the first time how p-cresol and oxytocin influence BDNF expression in pancreatic cancer cells. Specifically, it was found that while treated with p-cresol, an organic compound produced by gastrointestinal bacteria, BDNF expression in pancreatic cancer cells increases. However, while co-treated with oxytocin, a peptide hormone, BDNF expression decreases in these cells.

cancer biology↗

bioRxiv2025

Dynamics of Fanconi anemia protein D2 in association with nuclear lipid droplet formation

Fanconi anemia (FA) is a rare genetic disease caused by the loss of function of one of the 22 associated genes and is characterized by bone marrow failure, cancer predisposition, and developmental defects. The proteins encoded by these genes (FA proteins) mainly function in DNA damage response and repair. Although FA deficiency has multiple effects on the regulation of lipid metabolism, the molecular function of FA proteins in the context of FA pathology remains unclear. In the present study, we demonstrated that FANCD2, a key component of FA proteins, interacts with lipid metabolism-related factors and that FANCD2 deficiency downregulates the cellular levels of fatty acids. Moreover, a portion of FANCD2 is localized to nuclear lipid droplets in response to oleic acid treatment. These subcellular dynamics are independent of FANCD2 monoubiquitination, which is essential for the DNA damage response. Collectively, these findings demonstrate that FANCD2 responds to not only DNA damage but also oleic acid exposure, providing insights into the pathogenesis of lipid dysregulation in FA.

cell biology↗

bioRxiv2024

A summer in the Greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lakes within a relatively restricted area. Here, a four-month time-series was carried out during summertime to monitor planktonic microbial communities of nine lakes located within a [~]70 km radius around Paris (Ile-de-France, France) of comparable morphologies, yet distinct trophic statuses (mesotrophic to hypereutrophic). The contribution of the trophic status and intra-summer variations were investigated on prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). Sampled lakes harbored highly distinct and diverse prokaryotic communities. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. The trophic status appears as the main driver of both community structure and functional potential. When focusing on function involved in biogeochemical cycles, responses to phosphorus limitation (mostly polyphosphate-related processes) were highlighted between trophic statuses. Hypereutrophic lakes communities displayed the highest contrast and heterogeneity over time, suggesting a regime shift compared to lakes of lower trophic status. This study explores the influence of eutrophication on lakes microbiome ecology, by comparing for the first time the planktonic microbial communities and their functional potential of lakes of distinct trophic status in close vicinity over a summer season.

microbiology↗

bioRxiv2024

Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

The 5-3 exoribonuclease Rat1 (or Xrn2) plays a pivotal role in termination of mRNA transcription by eukaryotic RNA polymerase II (RNAPII). Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a "torpedo" to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of a Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast Komagataella phaffii. The Rat1-Rai1-Rtt103 complex structure revealed that Rat1 and Rai1 form a heterotetramer, with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and directly binds to the RNA exit site of transcribing RNAPII to extract RNA into the Rat1 nuclease active site. This interaction changes the RNA path in favor of termination (the "pre-termination" state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the "post-termination" states. These structures shed light on the mechanism of eukaryotic mRNA transcription termination.

biochemistry↗

bioRxiv2024

Exploring the molecular structure of lipids in the design of artificial lipidated antifungal proteins

Fungal infections have been a concern for decades, yet effective and approved antifungal agents are limited. We recently developed a potential method to enhance the antifungal activity of a small chitin-binding domain (LysM) from Pteris ryukyuensis chitinase A (PrChiA) by the site-specific introduction of a palmitoyl (C16) group catalyzed by microbial transglutaminase (MTG). Herein, we attempted the conjugation of a series of lipid-peptide substrates with LysM genetically fused with a C-terminal MTG-reactive Q-tag (LysM-Q) to yield LysM-lipid conjugates (LysM-lipids) with different lengths (LysM-C12, -C14, and -C16) and different numbers of alkyl chains [LysM-(C12)2, - (C14)2, and -(C16)2]. The enzymatic conjugation proceeded smoothly for all LysM-lipids, except for LysM-(C16)2 because of the low aqueous dispersibility of the hydrophobic (C16)2 lipid-peptide substrate. The combination of amphotericin B (AmB) with LysM-C14 or LysM-C16 exhibited the highest antifungal performance against Trichoderma viride whereas alterations in the number of alkyl chains were not effective in enhancing the antifungal activity of the LysM-lipids. Fluorescent microscopic analysis showed that the fungal cell wall was stained with C14- and C16-modified LysM-muGFP fusion proteins when combined with AmB, suggesting a synergistic action of AmB and LysM-lipids with a suitable lipid length. All LysM-lipids showed minimum cytotoxicity toward mammalian cells, suggesting that LysM-lipids could be a safe additive in the development of new antifungal formulations.

bioengineering↗

bioRxiv2023

Engineered Active Zymogen of Microbial Transglutaminase

Microbial transglutaminase (MTG) has shown to be a powerful biocatalytic glue for site-specific crosslinking of a range of biomolecules and synthetic molecules, those handled with an MTG-reactive moiety. The preparation of active recombinant MTG requires the posttranslational proteolytic digestion of propeptide working as an intramolecular chaperon to assist the correct folding of MTG zymogen (MTGz) in the biosynthesis. Herein, we propose an engineered active zymogen of MTG (EzMTG) that is expressed as soluble form in the host E. coli cytosol and exhibits the cross-linking activity without limited proteolysis. Based on the 3D structure of MTGz and serendipitous findings, saturated mutagenesis of K10 or Y12 in propeptide domain leads to generate several active MTGz mutants. In particular, K10D/Y12G mutant exhibited the catalytic activity comparable with a mature form. However, the expression level was low possibly due to the reduction of chaperone activity and/or the promiscuous substrate specificity of MTG, which is potentially harmful to the host cells. By contrast, soluble K10R/Y12A mutant is expressed in the cytosol of host E. coli and exhibited unique substrate-dependent reactivity toward peptidyl substrates. The quantitative analysis of the binding affinity of mutated propeptide to the active site suggested the trade-off relationship of EzMTGs between the binding affinity and the catalytic activity. Our proof-of-concept study provides insights into the design of a new biocatalyst by using the zymogen as a scaffold and will convey a potential route to the high-throughput screening of MTG mutants for bioconjugation applications.

biochemistry↗

bioRxiv2023

Multi-omics analyses from a single sample: Prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types

Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Non-targeted metabolomics are a suitable tool to bridge this gap, yet extractions protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA sequencing after direct DNA extraction, or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on non-axenic cultures of cyanobacteria, lake water column, biofilm, gut of wild and lab-reared fish, indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.

microbiology↗

bioRxiv2022

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase

Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the ATP-dependent RNA translocase/helicase Rho, which causes the dissociation of RNA/DNA from RNAP elongation complex (EC). However, structural basis of the interplay between Rho and RNAP remains obscure. Here we report the cryo-electron microscopy structure of the Rho-engaged EC. The Rho hexamer binds RNAP through the C-terminal domains, which surround the RNA-exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to the Rho central channel. The {beta}-flap tip at the RNA exit is critical to the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho-binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation. TeaserCryo-EM captures the structure of an RNA polymerase elongation complex engaged with the termination factor Rho.

biochemistry↗

bioRxiv2022

Strategy for selective acquisition of transgenic marmosets using the piggyBac transposon system

Transgenic (Tg) nonhuman primates (NHPs) are excellent potential models due to their physiological similarities with humans. In NHPs, the lentiviral vector is the only available transgenesis method, but transgene sizes are limited. The piggyBac (PB) transposon system is a DNA element sandwiched between two terminal inverted repeats (TRs) that allows transposases to introduce larger genes than lentiviral vectors. However, embryos with integrated transgenes are difficult to distinguish using this system. To address this issue, we placed the Enhanced Green Fluorescent Protein (EGFP) gene inside the TRs and the humanized kusabira orange 1 (hKO1) fluorescent protein gene with the proteolysis-promoting sequence d2PEST outside the TRs to create an indicator for gene integration using fluorescent protein expression. In HEK293T cells, hKO1 and EGFP co-expression after transfection gradually changed to decay of hKO1 expression and enhancement of EGFP expression by transposase within five days. In mouse and marmoset embryos, hKO1 expression was attenuated, while only EGFP expression was observed at the blastocyst stage. All offspring obtained through embryo transfer of EGFP-expressing embryos were Tg; thus, we established a new PB system capable of determining Tg embryos and successfully produced Tg marmosets, for the first time, in NHPs.

molecular biology↗

bioRxiv2021

Bcr4 is a Chaperone for the Inner Rod Protein in the Bordetella Type III Secretion System

Bordetella bronchiseptica injects virulence proteins called effectors into host cells via a type III secretion system (T3SS) conserved among many Gram-negative bacteria. Small proteins called chaperones are required for stabilizing some T3SS components or localizing them to the T3SS machinery. In a previous study, we identified a chaperone-like protein named Bcr4 that regulates T3SS activity in B. bronchiseptica. Bcr4 does not show strong sequence similarity to well-studied T3SS proteins of other bacteria, and its function remains to be elucidated. Here, we investigated the mechanism by which Bcr4 controls T3SS activity. A pull-down assay revealed that Bcr4 interacts with BscI, based on its homology to other bacterial proteins, to be an inner rod protein of the T3SS machinery. An additional pull-down assay using truncated Bcr4 derivatives and secretion profiles of B. bronchiseptica producing truncated Bcr4 derivatives showed that the Bcr4 C-terminal region is necessary for the interaction with BscI and activation of the T3SS. Moreover, the deletion of BscI abolished the secretion of type III secreted proteins from B. bronchiseptica and the translocation of a cytotoxic effector into cultured mammalian cells. Finally, we showed that BscI is unstable in the absence of Bcr4. These results suggest that Bcr4 supports the construction of the T3SS machinery by stabilizing BscI. This is the first demonstration of a chaperone for the T3SS inner rod protein among the virulence bacteria possessing the T3SS. ImportanceThe type III secretion system (T3SS) is a needle-like complex that projects outward from bacterial cells. Bordetella bronchiseptica uses the T3SS to inject virulence proteins into host cells. Our previous study reported that a protein named Bcr4 is essential for the secretion of virulence proteins from B. bronchiseptica bacterial cells and delivery through the T3SS. Because other bacteria lack a Bcr4 homologue, the function of Bcr4 has not been elucidated. In this study, we discovered that Bcr4 interacts with BscI, a component of the T3SS machinery. We showed that a B. bronchiseptica BscI-deficient strain was unable to secrete type III secreted proteins. Furthermore, in a B. bronchiseptica strain that overproduces T3SS component proteins, Bcr4 is required to maintain BscI in bacterial cells. These results suggest that Bcr4 stabilizes BscI to allow construction of the T3SS in B. bronchiseptica.

microbiology↗

bioRxiv2021

Overexpression of the RNA-binding protein NrdA affects global gene expression and secondary metabolism in Aspergillus species

RNA-binding protein Nrd1 plays a role in RNA polymerase II transcription termination. In this study, we showed that the orthologous NrdA is important in global mRNA expression and secondary metabolism in Aspergillus species. We constructed an nrdA conditional expression strain using the Tet-On system in Aspergillus luchuenesis mut. kawachii. Downregulation of nrdA caused a severe growth defect, indicating that NrdA is essential for the proliferation of A. kawachii. Parallel RNA-sequencing and RNA immunoprecipitation-sequencing analysis identified potential NrdA-interacting transcripts, corresponding to 32% of the predicted protein coding genes of A. kawachii. Subsequent gene ontology analysis suggested that overexpression of NrdA affects the production of secondary metabolites. To clarify this, we constructed NrdA-overexpressing strains of Aspergillus nidulans, Aspergillus fumigatus, and Aspergillus oryzae. Overexpression of NrdA reduced the production of sterigmatocystin and penicillin in A. nidulans, as well as that of helvolic acid and pyripyropene A in A. fumigatus. Moreover, it increased the production of kojic acid and reduced production of penicillin in A. oryzae. These effects were accompanied by almost consistent transcriptional changes in the relevant genes. Collectively, these results suggest that NrdA is the essential RNA-binding protein, which plays a significant role in global gene expression and secondary metabolism in Aspergillus species. IMPORTANCENrd1, a component of the Nrd1-Nab3-Sen1 complex, is an essential RNA-binding protein involved in transcriptional termination in yeast. However, its role in filamentous fungi has not been studied. In this study, we characterized an orthologous NrdA in the Aspergillus species, identified potential NrdA-interacting mRNA, and investigated the effect of overexpression of NrdA on mRNA expression in Aspergillus luchuensis mut. kawachii. The results indicated that NrdA controls global gene expression involved in versatile metabolic pathways, including the secondary metabolic process. We demonstrated that NrdA overexpression significantly affected the production of secondary metabolites in Aspergillus nidulans, Aspergillus oryzae, and Aspergillus fumigatus. Our findings are of importance to the fungal research community because the secondary metabolism is an industrially and clinically important aspect for the Aspergillus species.

microbiology↗

bioRxiv2020

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

ecology↗