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Kume, T.

Publications and source records attributed to Kume, T..

12 recordsLinked to original sources

Microscale nonrandomness revisited: An overlooked predictor of ecological change

Abrupt ecological transitions have driven the development of early warning signal metrics that track how ecological systems respond as external conditions gradually change and systems approach transitions between states. However, their generality and applicability remain uncertain, particularly for short-term ecological dynamics that can occur without directional external change. To address this gap, we propose a general framework based on the hypothesis that microscale nonrandomness, quantified from frequency distributions or spatial patterns, predicts subsequent short-term rates of change in populations and interactions, as well as current macroscale ecosystem states. We applied the framework to four datasets: time series from an incubation experiment of phytoplankton-parasitic chytrid interactions; spatiotemporal field observations of leaf beetles on willow trees and aphids in a crop system; and spatial snapshot data linking soil surface characteristics with aboveground and soil ecosystem properties in a forest vegetations-soil system. We quantified microscale nonrandomness using Morisita I_{delta} from frequency distributions and Moran's I and SADIE from spatial patterns. Across all systems, models incorporating microscale nonrandomness metrics consistently showed greater cross-validated predictive performance than those based on macroscale variables or spatial averages alone. Although their relative performance varied among systems, frequency-based metrics performed as well as or better than spatially explicit metrics in some cases. The consistent improvement across contrasting systems supports the broad applicability of this framework, including under limited data conditions. This framework broadens ecological forecasting to short-term, continuous dynamics beyond those associated with directional environmental change.

ecology↗

Degradation of net ecosystem carbon balance in cool-temperate forests by sika deer-induced stand structure alterations and subsequent soil erosion

Although natural forests sequester carbon, this function may decline under chronic herbivory by abundant ungulates (hereafter overbrowsing). Specifically, overbrowsing alters stand structure, potentially impair carbon exchanges related to the vegetation. Further, overbrowsing may also accelerate soil erosion, especially in heavy-rainfall regions like Monsoon Asia. We quantified these impacts by estimating net ecosystem carbon balance (NECB; g C m-2 yr-1) by subtracting heterotrophic respiration (Rh) and lateral carbon export via erosion (Se) from net primary production (Pn) in southern Kyushu, Japan. Here, about 40-years of overbrowsing by sika deer (Cervus nippon) altered mixed broadleaf-conifer stands with presence of understory (PU) into stands with no understory (NU), then further altered into stands dominated by unpalatable shrublands (SR) or stands with canopy gaps (CG). The PU maintained a positive NECB (plot mean = 307.0 g C m-2 yr-1) because high Pn (721.9) exceeded the sum of Rh (175.4) and Se (239.5). Alteration from PU into NU converted NECB to negative (-98.2 g C m-2 yr-1). This was because the suppressed Pn (400.2 g C m-2 yr-1) could not offset the sum of Rh (170.6) and Se (327.7). Further degradation into CG caused a profound negative NECB (-894.4 g C m-2 yr-1), where Pn (71.9) offset only 7% of the sum of surging Rh (464.8) and Se (501.5). Alteration into SR showed a partially recovered NECB (97.3 g C m-2 yr-1), driven by shrub growth (Pn; 554.5, Rh; 175.4, Se; 239.5). However, this recovery is still limited given that lowered shrub biomass and prior topsoil loss via erosion. Our results validate previous findings that stand alteration from PU to SR or CG through NU leads to up to a 49% loss of ecosystem carbon stocks. Preventing stand alteration and soil erosion are key countermeasures against chronic overbrowsing and subsequent erosion. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/719128v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@167aef0org.highwire.dtl.DTLVardef@e45a6org.highwire.dtl.DTLVardef@fec89borg.highwire.dtl.DTLVardef@1246bea_HPS_FORMAT_FIGEXP M_FIG C_FIG We reported that over 40 years of sika deer overbrowsing and subsequent soil erosion severely degraded the net ecosystem carbon balance (NECB) of mountain forests in Japan. The loss of understory vegetation drove the transition of intact stands into degraded states (no-understory, shrub-dominated, or canopy gaps). Based on field measurements, we quantified that this structural alteration suppressed net primary production (Pn) while increased both heterotrophic respiration (Rh) and lateral carbon loss via soil erosion (Se). Consequently, the forest shifted from a net carbon sink (+307 g C m-{superscript 2} yr-{superscript 1}) to a source (up to -894 g C m-{superscript 2} yr-{superscript 1}). These findings provide compelling empirical evidence that increasing ungulate populations, compounded by the rising frequency of heavy rainfall, may severely undermine the carbon sequestration functions traditionally expected of natural forests.

ecology↗

TDP-43 controls RNA structure through high affinity lattice interactions

TDP-43 is an RNA binding protein implicated in neurodegenerative disease. TDP-43 binds to GU dinucleotide repeats, which are highly abundant sequences in human RNA. Here we show TDP- 43 has one of the highest affinities and specificities measured for an RNA binding protein. Binding prevents formation of the pUG fold, an intramolecular quadruplex, and conversely pUG fold formation prevents TDP-43 binding. A rapid on-rate allows TDP-43 to capture single stranded RNA prior to folding. The protein recognizes the RNA as a 1D lattice, in which overlapping binding sites produce efficient initial binding events that interfere with subsequent interactions. This effect is partially overcome by RNA facilitated protein-protein interactions, which serve to increase the on-rate of a second TDP-43 molecule. In conjunction with all atom models, these data reveal how TDP-43 recognizes RNA repeat sequences and identify an interplay between RNA folding and protein recognition that may be relevant to human disease.

biochemistry↗

Sequence and ionic requirements of pUG fold quadruplexes

Poly(UG) or "pUG" repeat RNA can fold into a left-handed parallel quadruplex, the pUG fold. The pUG fold directs the amplification of RNAi in C. elegans, and pUG sequences are abundant in eukaryotic transcriptomes. Here, we report the sequence and ionic requirements for pUG folding. The pUG fold requires 12 guanosines but has an otherwise flexible sequence requirement. The uridines can be substituted with other nucleotides, with some sequence variants folding better than pUG RNA. The GA repeat sequence (GA)12 also forms a pUG-like fold, albeit with lower thermodynamic stability than (GU)12. The pUG fold can tolerate multiple deoxyribose substitutions but does not fold when the backbone is entirely deoxyribose. It has a high affinity and specificity for potassium ions (K1/2 = 6 mM) and does not fold in sodium or ammonium ions. Addition of 2 mM Mg2+ does not further stabilize the pUG fold, and the polyamines spermine and spermidine slightly decrease its stability. Finally, the pUG fold is sensitive to surrounding sequence context and complementary flanking sequences can stabilize pUG folds, while other sequences can interfere with folding. These data expand our understanding of RNA folding and provide a basis for understanding and predicting pUG folds.

biochemistry↗

Machine-learning-based automated Schlemms canal volumetric segmentation for optical coherence tomography

Volumetric segmentation of Schlemms Canal (SC) in optical coherence tomography (OCT) is time-consuming, creating a barrier to experiments studying glaucoma and the anatomy of the trabecular outflow pathways in vivo. To this end, we developed an automated segmentation tool, Schlemms Canal-Localization and Semantic Segmentation (SC-LSS), for the volumetric segmentation of SC in in vivo mice eyes from visible-light OCT (vis-OCT). SC-LSS first localizes the boundaries of SC and subsequently determines the boundaries of SC within the localized region. We used 324 B-scans from 16 mouse eyes for training, validation, and testing the model, and 203 additional B-scans from 16 mouse eyes to evaluate the models accuracy. We found that the Dice coefficient between segmentations generated by SC-LSS and manual expert graders was 0.70 {+/-} 0.20 and that the Dice coefficient between two expert graders was 0.73 {+/-} 0.18 (p = 0.10). Furthermore, SC-LSS captured decreases in SC size with increasing intraocular pressure, yielding a 51.5% decrease in SC size at 20 mmHg compared to 5 mmHg. SC-LSS also identified a 20.1% increase in SC size following the administration of pilocarpine. We anticipate that SC-LSS will accelerate studies on factors regulating the trabecular outflow pathways and their role in glaucoma development and management.

bioengineering↗

FOXC1 and FOXC2 maintain mitral valve endothelial cell junctions, extracellular matrix, and lymphatic vessels to prevent myxomatous degeneration

BackgroundMitral valve (MV) disease including myxomatous degeneration is the most common form of valvular heart disease with an age-dependent frequency. Genetic evidence indicates mutations of the transcription factor FOXC1 are associated with MV defects, including mitral valve regurgitation. In this study, we sought to determine whether murine Foxc1 and its closely related factor, Foxc2, are required in valvular endothelial cells (VECs) for the maintenance of MV leaflets, including VEC junctions and the stratified trilaminar extracellular matrix (ECM). MethodsAdult mice carrying tamoxifen-inducible, endothelial cell (EC)-specific, compound Foxc1;Foxc2 mutations (i.e., EC-Foxc-DKO mice) were used to study the function of Foxc1 and Foxc2 in the maintenance of mitral valves. The EC-mutations of Foxc1/c2 were induced at 7 - 8 weeks of age by tamoxifen treatment, and abnormalities in the MVs of EC-Foxc-DKO mice were assessed via whole-mount immunostaining, immunohistochemistry, and Movat pentachrome/Massons Trichrome staining. ResultsEC-deletions of Foxc1 and Foxc2 in mice resulted in abnormally extended and thicker mitral valves by causing defects in regulation of ECM organization with increased proteoglycan and decreased collagen. Notably, reticular adherens junctions were found in VECs of control MV leaflets, and these reticular structures were severely disrupted in EC-Foxc1/c2 mutant mice. PROX1, a key regulator in a subset of VECs on the fibrosa side of MVs, was downregulated in EC-Foxc1/c2 mutant VECs. Furthermore, we determined the precise location of lymphatic vessels in murine MVs, and these lymphatic vessels were aberrantly expanded in EC-Foxc1/c2 mutant mitral valves. ConclusionsOur results indicate that Foxc1 and Foxc2 are required for maintaining the integrity of the MV, including VEC junctions, ECM organization, and lymphatic vessels to prevent myxomatous mitral valve degeneration.

cell biology↗

Foxc1 and Foxc2 function in osteochondral progenitors for the progression through chondrocyte hypertrophy and mineralization of the primary ossification center.

The forkhead box transcription factor genes Foxc1 and Foxc2 are expressed in the condensing mesenchyme of the developing skeleton prior to the onset of chondrocyte differentiation. To determine the roles of these transcription factors in limb development we deleted both Foxc1 and Foxc2 in lateral plate mesoderm using the Prx1-cre mouse line. Resulting compound homozygous mice died shortly after birth with exencephaly, and malformations to this sternum and limb skeleton. Notably distal limb structures were preferentially affected, with the autopods displaying reduced or absent mineralization. The radius and tibia bowed and the ulna and fibula were reduced to an unmineralized rudimentary structure. Molecular analysis revealed reduced expression of Ihh leading to reduced proliferation and delayed chondrocyte hypertrophy at E14.5. At later ages, Prx1-cre;Foxc1{Delta}/ {Delta};Foxc2 {Delta} / {Delta} embryos exhibited restored Ihh expression and an expanded COLX-positive hypertrophic chondrocyte region, indicating a delayed exit and impaired remodeling of the hypertrophic chondrocytes. Osteoblast differentiation and mineralization were disrupted at the osteochondral junction and in the primary ossification center (POC). Levels of OSTEOPONTIN were elevated in the POC of compound homozygous mutants, while expression of Phex was reduced, indicating that impaired OPN processing by PHEX may underlie the mineralization defect we observe. Together our findings suggest that Foxc1 and Foxc2 act at different stages of endochondral ossification. Initially these genes act during the onset of chondrogenesis leading to the formation of hypertrophic chondrocytes. At later stages Foxc1 and Foxc2 are required for remodeling of HC and for Phex expression required for mineralization of the POC.

developmental biology↗

Endothelial FOXC1 and FOXC2 promote intestinal regeneration after ischemia-reperfusion injury

Intestinal ischemia induces mucosal damage while simultaneously activating intestinal stem cells (ISCs), which subsequently regenerate the damaged intestinal epithelium. However, whether paracrine factors secreted from vascular endothelial cells (ECs) - blood and lymphatic ECs (BECs and LECs, respectively) - regulate ISC-mediated regeneration have yet to be elucidated. Here, we identify FOXC1 and FOXC2 as essential regulators of paracrine signaling in regeneration of the small intestine after ischemia-reperfusion (I/R) injury. EC- and LEC-specific deletions of Foxc1, Foxc2, or both in mice augment I/R-induced intestinal damage by causing defects in vascular regrowth, expression of the chemokine CXCL12 and the Wnt activator R- spondin 3 in BECs and LECs, respectively, and activation of Wnt signaling in ISCs. Treatment with CXCL12 and R-spondin 3 rescues the I/R-induced intestinal damage in EC- and LEC-Foxc mutant mice, respectively. This study provides evidence that FOXC1 and FOXC2 are required for intestinal regeneration by stimulating paracrine CXCL12 and Wnt signaling.

molecular biology↗

Differential roles of neural crest- and endothelial-derived FOXC2 in trabecular meshwork and Schlemms Canal in glaucomatous pathology

Impaired development and maintenance of the Schlemms Canal (SC) is associated with perturbed aqueous humor outflow regulation and glaucoma progression. Key molecular mechanisms, such as ANGPT/TIE2, PROX1, and VEGF-C/VEGFR-3 regulate SC development and maintenance, but mechanisms of paracrine signaling from neighboring tissues, including the trabecular meshwork (TM) are poorly understood. Here, we show Foxc2 is critical within the neural crest (NC)-derived TM and SC endothelium for development of the aqueous humor outflow pathway. In mice, NC- specific deletion of Foxc2 results in abnormal anterior eye segment development, including impaired SC morphogenesis and functional maintenance, loss of SC identity, and impaired maintenance of intraocular pressure (IOP). Visible light optical coherence tomography angiography analysis also demonstrated functional impairment of the SC in response to changes in IOP in NC-Foxc2-/- mice, suggesting increased TM stiffness. Utilization of single-cell RNA-sequencing (scRNA-seq) analysis then identified that this phenotype is predominately characterized by transcriptional changes associated with extracellular matrix organization and stiffness in TM-associated cell clusters, including increased matrix metalloproteinase (MMP) expression, which can generate soluble TIE2 that acts as an ANGPT trap. As FOXC2 is also critically involved in development of the lymphatic vasculature in other tissues, we also show that endothelial-specific deletion of Foxc2 resulted in impaired SC morphogenesis due to loss of TIE2 expression, which was rescued by deletion of the TIE2 phosphatase VE-PTP. Thus, NC-Foxc2 is critical for development of the TM, and both NC- and endothelial-Foxc2 are key for maintenance of SC identity and its morphogenesis.

developmental biology↗

Loss of Foxc1 and Foxc2 function in chondroprogenitor cells disrupts endochondral ossification.

Endochondral ossification forms and grows the majority of the mammalian skeleton and is tightly controlled through gene regulatory networks. The forkhead box transcription factors Foxc1 and Foxc2 have been demonstrated to regulate aspects of osteoblast function in the formation of the skeleton but their roles in chondrocytes to control endochondral ossification are less clear. We demonstrate that Foxc1 expression is directly regulated by SOX9 activity, one of the earliest transcription factors to specify the chondrocyte lineages. Moreover we demonstrate that elevelated expression of Foxc1 promotes chondrocyte differentiation in mouse embryonic stem cells and loss of Foxc1 function inhibits chondrogenesis in vitro. Using chondrocyte-targeted deletion of Foxc1 and Foxc2 in mice, we reveal a role for these factors in chondrocyte differentiation in vivo. Loss of both Foxc1 and Foxc2 caused a general skeletal dysplasia predominantly affecting the vertebral column. The long bones of the limb were smaller and mineralization was reduced and organization of the growth plate was disrupted. In particular, the stacked columnar organization of the proliferative chondrocyte layer was reduced in size and cell proliferation in growth plate chondrocytes was reduced. Differential gene expression analysis indicated disrupted expression patterns in chondrogenesis and ossification genes throughout the entire process of endochondral ossification in Col2-cre;Foxc1{Delta}/{Delta};Foxc2{Delta}/{Delta} embryos. Our results suggest that Foxc1 and Foxc2 are required for correct chondrocyte differentiation and function. Loss of both genes results in disorganization of the growth plate, reduced chondrocyte proliferation and delays in chondrocyte hypertrophy that prevents correct ossification of the endochondral skeleton.

developmental biology↗

Pleiotropy in FOXC1-attributable phenotypes involves altered ciliation and cilia-dependent signaling

Alterations to cilia are responsible for a wide range of severe disease; however, understanding of the transcriptional control of ciliogenesis remains incomplete. We evaluated whether ciliary dysfunction contributed to the pleiotropic phenotypes caused by the Forkhead transcription factor FOXC1. Here, we show that patients with FOXC1-attributable Axenfeld-Rieger Syndrome (ARS) have a prevalence of ciliopathy-associated phenotypes comparable to syndromic ciliopathies. We demonstrate that altering the level of Foxc1, via shRNA mediated inhibition and mRNA overexpression, modifies cilia length in vitro. These structural changes were associated with substantially perturbed cilia-dependent signaling [Hedgehog (Hh) and PDGFR] and the altered ciliary compartmentalization of a major Hh pathway transcription factor, Gli2. Analyses of two Foxc1 murine mutant strains demonstrated altered axonemal length in the choroid plexus with the increased expression of an essential regulator of multi-ciliation, Foxj1. The novel complexity revealed in ciliation of the choroid plexus indicates a partitioning of function between these Forkhead transcription factors. Collectively, these results support a contribution from ciliary dysfunction to some FOXC1-induced phenotypes.

genetics↗

Dynamic and synergistic influences of air temperature and rainfall on general flowering in a Bornean lowland tropical forest

Supra-annually synchronized flowering events occurring in tropical forests in Southeast Asia, known as general flowering (GF), are \"spectacular and mysterious\" forest events. Recently, studies that combined novel molecular techniques and model-based theoretical approaches suggested that cool temperature and drought synergistically drove GF. Although the novel approaches advanced our understanding of GF, it is usually difficult to know whether the mathematical formulation reasonably well represents the complex and dynamic processes involved in GF. In the present study, we collected a 17-year set of community-wide phenology data during 1993 to 2011 from Lambir Hills National Park in Borneo, Malaysia, and analyzed it using a model-free approach, empirical dynamic modeling (EDM), that does not rely on specific assumptions about the underlying mechanisms, to overcome and complement the previous limitations. By using EDM, we found that GF in the forest in Lambir Hills National Park is synergistically driven by cool air temperature and drought, which is consistent with the previous studies. Also, we found that cumulative meteorological variables, rather than instantaneous values, drive GF with delayed effects, which is also consistent with the previous studies. Interestingly, the present study showed that effects of cumulative meteorological variables on GF changed through time, which implies that the relationship between GF and meteorological variables may be influenced by other factors such as plant/soil nutrient resource dynamics. Future studies integrating novel mathematical/statistical frameworks, long-term and large spatial scale ecosystem monitoring and molecular phenology data are promising for better understanding and fore-casting of GF events in tropical forests in Southeast Asia.

ecology↗