Biology subjects

Mori, A.

Publications and source records attributed to Mori, A..

6 recordsLinked to original sources

bioRxiv2026

Forest biodiversity benefits from warmer microclimate, but only in colder regions

The diversity of many forest-dwelling organisms depends on forest structure, but it remains unknown to which degree this is mediated by microclimatic temperature, and whether microclimatic buffering is universally beneficial for forest biodiversity. In 234 broad-leaved forest plots across nine climatically differing regions in Germany, we measured micro- and macroclimatic temperatures, canopy cover, and deadwood volume after experimental manipulations of forest structure through thinning operations and gap cuts. We surveyed 21 taxonomic groups, representing plants, bacteria, fungi, and animals, to assess how their diversity depended on the predictors. Multi-taxon diversity, and diversity of ten separate taxonomic groups, increased from closed to open canopies. Only necrophagous beetles were more diverse in closed stands. These effects of canopy cover on diversity were partly mediated by microclimatic temperatures. Thereby, diversity responses to microclimatic temperature depended on the macroclimatic context. In regions with colder summers, locally warmer microclimates in canopy gaps had strong positive effects on biodiversity, while these effects were not found in regions with warmer summers. Consequently, management strategies aimed at multi-taxon forest diversity conservation should be chosen based on the regional climate, favoring canopy gaps primarily in colder regions, and taking future climate warming into consideration.

ecology↗

bioRxiv2025

Enhancing structural heterogeneity in managed forest landscapes promotes gamma but not beta diversity in understorey plant communities

O_LIAlthough habitat heterogeneity is known to enhance local species diversity, the effects of management-driven structural heterogeneity on understorey plant communities across spatial scales remain poorly understood, despite their crucial role for forest biodiversity and ecosystem functioning. C_LIO_LITo analyse how forest understorey plant communities respond to an enhancement of structural heterogeneity in managed forests, we established 11 experimental sites consisting of two paired forest landscapes, an untreated homogenous control and a treatment district (ESBC). In treatment districts, structural heterogeneity was enhanced through different combinations of local patch-scale manipulations of light and deadwood features, leading to greater between-patch heterogeneity at the landscape scale. We performed a meta-analysis across these 11 sites using a Hill-Chao number and sample coverage standardisation framework. C_LIO_LIGamma diversity increased across taxonomic, functional and phylogenetic facets in structurally heterogeneous forests (ESBC districts) via higher alpha diversity. This effect was positively associated with heterogeneity in light availability between forest patches, but not with their mean light availability. In contrast, we found no support that species turnover among patches (i.e., beta diversity) significantly contributes on average to the observed increase in gamma diversity. However, both the direction and magnitude of beta diversity responses varied substantially among landscapes. C_LIO_LIOn average, structurally heterogeneous forests supported higher species richness for both open and closed forest habitat species. C_LIO_LISynthesis and applications: Our findings highlight the benefits of enhancing structural heterogeneity for understorey plant diversity in managed forest landscapes. Specifically, management strategies that create a spatial mosaic of interventions, such as combining single-tree removal with group felling, can increase the variety of light niches among forest patches, thereby supporting the conservation of a wide range of understorey plant species, including forest specialists. C_LI

ecology↗

bioRxiv2025

Enhancing experimentally the structural heterogeneity of forests increase soil fungal diversity but functional lifestyles in contrasting ways

Fungal communities in soils are highly diverse both in species and functions forming a major backbone of forest ecosystems. Recent observational high-throughput-sequencing studies have shown that fungal diversity is correlated with resource availability and climate across different spatial scales. However, the underlying mechanisms remain poorly understood. Across Germany, we experimentally manipulated 11 typically homogeneous, broadleaf production forests to increase their between-patch-heterogeneity (ESBC) and compared them with a control forest. In specific, we enhanced light availability via canopy openness and deadwood resources in the ESBC treatments. Fungal communities were determined by metabarcoding at 234 patches and analysed using a novel meta-analytical approach for pairwise comparisons of taxonomic and phylogenetic diversity along Hill numbers. We hypothesized that {gamma}-diversity is primarily driven by {beta}-diversity increasing with canopy mediated microclimate variability and secondarily by -diversity increasing with resource availability. Furthermore, we expected an increase in {gamma}-diversity by unique phylogenetic lineages supporting the insurance hypothesis. Our results showed a significant increase in {gamma}-diversity in ESBC forests, first by - and second by {beta}-diversity, both of which were influenced mainly by microclimate and not resource availability. The increase of phylogenetic diversity with ESBC was weak indicating functional similarity of species. Analysis of symbiotic, saprotrophic and parasitic fungal assemblages revealed contrasting effects of resource availability and microclimate across the scales. As in the UN Decade of Ecosystem Restoration many forest managers aim to increase the heterogeneity of forests and are simultaneously face rising tree mortality, our study provides first robust empirical evidence for the varying effects of forest gaps and deadwood on fungal diversity across -, {beta}-, {gamma}-scales for this major kingdom.

ecology↗

bioRxiv2023

Comprehensive IsomiR sequencing profile of human pancreatic islets and EndoC-βH1 beta-cells

Aims/HypothesisMiRNAs play a crucial role in regulating the islet transcriptome, influencing beta cell functions and pathways. Emerging evidence suggests that during biogenesis a single miRNA locus can generate various sequences, known as isomiRNAs (isomiRs). However, a comprehensive profiling analysis of isomiRs in human pancreatic islets and beta cells is still lacking. This study aims to unveil the isomiRs expression profile in Laser Capture Microdissected (LCM) human pancreatic islets (HI) from non-diabetic donors and in the human beta cell line EndoC-{beta}H1, in order to shed light on novel molecular mechanisms governing beta cell function. MethodsRNA was extracted from LCM HI deriving from n=19 non-diabetic donors and from EndoC-{beta}H1 beta cells. Small RNA-seq was performed. Data were processed with the sRNAbench online pipeline for miRNAs/isomiRs quantification. Results were further validated using an external miRNA-seq database (isomiRdb). ResultsIn both HI and EndoC-{beta}H1, isomiRs accounted for a substantial proportion of total miRNA reads (HI: 59.4+/-1.9%; EndoC-{beta}H1: 43.8+/-0.6%). Among isomiRs, the most prevalent types were 3-end modifications, including trimming (HI=71.8+/-2.8%; EndoC-{beta}H1=55.8+/-1.0%) and extension (HI: 12.1+/-1.9%; EndoC-{beta}H1: 17.4+/-0.9%), followed by non-templated addition (HI: 9.8+/-0.9%; EndoC-{beta}H1: 14.0+/-1.2%). The analysis of the composition of the n=10 most expressed miRNAs highlighted a significant contribution of reads assigned to isomiRs. For instance, the most abundant miRNA, miR-375-3p, resulted from 59.7+/-2.4% of canonical and 40.3+/-2.4% of isomiRs in EndoC-{beta}H1 and from 45.3+/-2.0% of canonical and 54.7+/-2.0% of isomiR reads in HI. Interestingly, miR-7-5p, a beta cell-specific miRNA, was predominantly expressed as an isomiR both in EndoC-{beta}H1 (65.3+/-2.7%) and in HI (82.4+/-1.4%). To identify a reliable beta cell isomiR signature, common sequences detected in HI and EndoC-{beta}H1 were filtered based on their contribution to total miRNA expression, ultimately resulting in a set of 46 isomiRs. The expression of the isomiR signature in beta cells was further evaluated using an external database, isomiRdb, which contains small-RNA sequencing data from 99 different human cell types. This analysis revealed a significant enrichment of 11 out of the 46 isomiRs in beta cells compared to other cell types. The signature was functionally characterized through regression analysis with clinical and metabolic parameters related to beta cell function in non-diabetic individuals, demonstrating a significant negative correlation between basal insulin secretion and isomiR-411-5p, but not with its corresponding canonical miRNA. Conclusion/InterpretationThis study provides a comprehensive profile of isomiR expression in pancreatic islets and beta cells, highlighting the potential significance of isomiRs as novel regulators of beta cell function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/566223v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@145f36borg.highwire.dtl.DTLVardef@1701433org.highwire.dtl.DTLVardef@13e5866org.highwire.dtl.DTLVardef@1dbe50_HPS_FORMAT_FIGEXP M_FIG C_FIG Research in ContextO_ST_ABSWhat is already know about this subject?C_ST_ABS- isomiRs are sequence variants of microRNAs (miRNAs) and may have distinct functional role respect to the canonical sequence. - isomiRs show cell/tissue specificity and are involved in multiple disease contexts. What is the key question?- What is the profile of isomiRs in human pancreatic islets (HI) and in beta cells? - Do isomiRs have a functional role in beta cells? What are the new findings?- IsomiRs represent a relevant fraction of total miRNAs in HI and beta cells. - 3end miRNA sequence modifications are the major fraction of isomiRs in beta cells. - A set of n=11 isomiRs, more expressed than their canonical miRNAs, are enriched in beta cells compared to the other human cell types. - Specific isomiRs are associated with beta cell glucose sensitivity and basal insulin secretion. How might this impact on clinical practice in the foreseeable future?- A comprehensive profile of isomiRs in beta cells may improve our understanding of molecular mechanisms driving beta cell function and dysfunction. - A highly detailed and granular view of miRNAs sequence variants and their expression levels may help in the design of novel therapeutic RNA-based strategies.

molecular biology↗

bioRxiv2023

Development of digital Hi-C assay

Abstracts Enhancers are genomic elements and contain all necessary cis-regulatory contexts. Such enhancers are convened to the appropriate promoter of target genes for gene regulations even though the enhancers and the promoters are apart a few mega-base pairs away from each other. In addition to physical distance, nucleotide mutations in enhancers influence a partial group of the target genes. Those make it more complicated to reveal the paired relationship between enhancer and promoter of target genes. Recently, advanced computational approaches are employed to predict such interactions. One approach requires a large number of different high-throughput datasets to predict such interactions; however, in practical aspects, all datasets for tissues and conditions of interest are not available. Whereas the alternative approach requires only genome sequences for particular predictions, their predictions are insufficient for practical applications. We address those issues by developing the digital Hi-C assay with a transformer-algorithm basis. This assay allows us to create models from simple/small/limited sequence-based datasets only. We apply the trained models to be able to identify long-distance interactions of genomic loci and three-dimensional (3D) genomic architectures in any other tissue/cell datasets; additionally, we demonstrated the predictions of genomic contexts by analysing the prediction patterns around the target locus in the three following genomic-context problems: enhancer-promoter interactions (i.e., promoter-capture Hi-C), the CTCF-enriched regions, and TAD-boundary regions. Because our approach adopted a sequence-based approach, we can predict the long-distance interactions of genomic loci by using the genomic sequences of the users interest (e.g., input sequences from high-throughput assay datasets such as ATAC-seq and ChIP-seq assays). Consequently, we provide an opportunity to predict interactions of genomic loci from a minimum dataset.

bioinformatics↗

bioRxiv2022

The role of rice SOG1 and SOG1-like in DNA damage response

Higher plants are constantly exposed to environmental stresses, and therefore complicated defense systems, including DNA damage response (DDR) and DNA repair systems, have developed to protect plant cells. In Arabidopsis, the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) has been reported to play a key role in DDR. Here, we focus on DDR in rice--thought to be a simpler system compared with Arabidopsis due to lack of induction of endocycle even under DNA damage stress. Rice SOG1 (OsSOG1) and SOG1-like (OsSGL) were identified as putative AtSOG1 orthologs with complete or partial conservation of the serine-glutamine (SQ) motifs involved in activation via phosphorylation. In addition to OsSOG1- or OsSGL-knockout mutants, OsSOG1 non-phosphorylatable mutants (OsSOG1-7A) were generated by homologous recombination-mediated gene targeting. Based on DNA damage susceptibility and transcriptome analysis using these mutants, we demonstrated that OsSOG1, but not OsSGL, plays a central role in the DDR and DNA repair. OsSOG1 regulated target genes via CTT (N)7 AAG motifs reported previously as AtSOG1 recognition sites. The loss of transcription activities and DNA damage tolerance of OsSOG1-7A was not complete compared with OsSOG1-knockout mutants, raising the possibility that another phosphorylation site might be involved in the activation of OsSOG1. Furthermore, our findings have highlighted differences in SOG1-mediated DDR between rice and Arabidopsis, especially regarding induction of cell-cycle arrest and endocycle arrest, revealing rice-specific DDR mechanisms. One sentence summaryRice transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 controls DNA damage response and DNA repair through activation via phosphorylation and the direct regulation of expression of numerous genes.

plant biology↗