Biology subjects

Kawakami, H.

Publications and source records attributed to Kawakami, H..

4 recordsLinked to original sources

bioRxiv2026

Detecting terrestrial insects from naturally exuding tree sap using environmental DNA: a pilot study

Terrestrial environmental DNA (eDNA) approaches are rapidly expanding, yet robust, field-ready substrates for detecting insect DNA remain limited in forest ecosystems. Tree sap is a localized microhabitat that attracts diverse insects and may provide a useful substrate for surface eDNA sampling, but its potential for insect monitoring has rarely been evaluated. Here, we present a pilot proof-of-concept study testing naturally exuding tree sap and sap-mimicking traps as terrestrial eDNA substrates. We collected swab samples from sap and trap surfaces at two forest sites in Japan (Fujisawa and Minamisanriku) and performed metabarcoding using COI and an arthropod-focused 16S marker (gInsect). Reads were processed into amplicon sequence variants and assigned by BLAST top hits against NCBI nt, with high-confidence detections defined at identity [≥]98%. Across sites, sap and trap swabs yielded multiple high-confidence insect detections spanning several orders, including sap-associated stag beetles (Dorcus spp.). Overlap with contemporaneous conventional monitoring was limited, suggesting that sap-surface eDNA and conventional surveys capture partly different components of sap-associated insect assemblages. In a targeted 2024 spot survey, actively fermenting sap yielded multiple insect eDNA detections, whereas inactive, non-fermented sap yielded no high-confidence insect detections. Although limited by small sample size and the absence of dedicated process controls, these findings support the feasibility of tree sap as a localized terrestrial eDNA substrate and provide a basis for future replicated studies of sap-associated insect monitoring.

ecology↗

bioRxiv2023

Optineurin deficiency impairs autophagy to cause interferon beta overproduction and increased survival of mice following viral infection

BackgroundOptineurin (OPTN) is associated with several human diseases, including amyotrophic lateral sclerosis (ALS), and is involved in various cellular processes, including autophagy. Optineurin regulates the expression of interferon beta (IFN{beta}), which plays a central role in the innate immune response to viral infection. However, the role of optineurin in response to viral infection has not been fully clarified. It is known that optineurin-deficient cells produce more IFN{beta} than wild-type cells following viral infection. In this study, we investigate the reasons for, and effects of, IFN{beta} overproduction during optineurin deficiency both in vitro and in vivo. MethodsTo investigate the mechanism of IFN{beta} overproduction, viral nucleic acids in infected cells were quantified by RT-qPCR and the autophagic activity of optineurin-deficient cells was determined to understand the basis for the intracellular accumulation of viral nucleic acids. Moreover, lethal viral infection experiments using optineurin-disrupted (Optn-KO) animals were performed. ResultsIFN{beta} overproduction following viral infection was observed not only in several types of optineurin-deficient cell lines but also in Optn-KO mice and human ALS patient cells carrying mutations in OPTN. IFN{beta} overproduction in Optn-KO cells was revealed to be caused by excessive accumulation of viral nucleic acids, which was a consequence of reduced autophagic activity caused by the loss of optineurin. Additionally, IFN{beta} overproduction in Optn-KO mice suppressed viral proliferation, resulting in increased mouse survival following lethal viral challenge. ConclusionOur findings indicate that the combination of optineurin deficiency and viral infection leads to IFN{beta} overproduction in vitro and in vivo. The effects of optineurin deficiency are elicited by viral infection, therefore, viral infection may be implicated in the development of optineurin-related diseases.

immunology↗

bioRxiv2022

Structural insights into AT-rich DNA recognition by SALL family proteins

Spalt-like 4 (SALL4) plays an essential role in controlling the pluripotent property of embryonic stem cells (ESCs) via binding to AT-rich regions of genomic DNA. Here we present crystal structures of the the zinc finger cluster 4 (ZFC4) domain of SALL4 (SALL4ZFC4) bound with different double stranded DNAs containing a conserved AT-rich motif. In the structures, two zinc fingers of SALL4ZFC4 coordinatively recognize an AATA tetranucleotide. We also solved the DNA-bound structures of SALL3ZFC4 and SALL4ZFC1. These structures illuminate a common recognition mode for AT-rich DNA by the SALL family proteins. The DNA binding activity is essential for SALL4 function as DNA-binding defective mutants of mouse Sall4 failed to repress aberrant gene expression in Sall4-/- mESCs. Thus, these analyses provide new insights into the mechanisms of action underlying SALL family in controlling cell fate via preferentially targeted to AT-rich sites within genomic DNAs during cell differentiation.

biochemistry↗

bioRxiv2019

Aggressive periodontitis with neutropenia caused by MMD2 mutation

Aggressive periodontitis causes rapid periodontal tissue destruction and is a disease that occurs at a young age and runs in the patients family. Here, we revealed a heterozygous A116V missense mutation in the gene encoding monocyte to macrophage differentiation associated 2 (MMD2) protein in a Japanese family with aggressive periodontitis and neutropenia. Analyses of patients peripheral blood revealed a low number of neutrophils but abundant quantity of CD34+ hematopoietic stem and progenitor cells (HSPCs). Moreover, mutant Mmd2 mice showed severe alveolar bone loss and neutropenia. In patients and mutant Mmd2 mice, differentiation of HSPCs into granulocytes was also impeded, and their granulocytes were functionally impaired. Taken together, A116V mutation in MMD2 gene induced mild neutropenia and slightly limited the immune defense response. Our studies suggested that aggressive periodontitis in association with A116V MMD2 mutation constitutes a new immune system defect that belongs to the same spectrum of severe congenital neutropenia.

genomics↗