Biology subjects

Nishino, M.

Publications and source records attributed to Nishino, M..

5 recordsLinked to original sources

bioRxiv2023

Histone methyltransferase SUV39H1 regulates the Golgi complex via the nuclear envelope-spanning LINC complex

Cell motility is related to the higher-order structure of chromatin. Stimuli that induce cell migration change chromatin organization; such stimuli include elevated histone H3 lysine 9 trimethylation (H3K9me3). We previously showed that depletion of histone H3 lysine 9 methyltransferase, SUV39H1, suppresses directional cell migration. However, the molecular mechanism underlying this association between chromatin and cell migration remains elusive. The Golgi apparatus is a cell organelle essential for cell motility. In this study, we show that loss of H3K9 methyltransferase SUV39H1 but not SETDB1 or SETDB2 causes dispersion of the Golgi apparatus throughout the cytoplasm. The Golgi dispersion triggered by SUV39H1 depletion is independent of transcription, centrosomes, and microtubule organization, but is suppressed by depletion of any of the following three proteins: LINC complex components SUN2, nesprin-2, or microtubule plus-end-directed kinesin-like protein KIF20A. In addition, SUN2 is closely localized to H3K9me3, and SUV39H1 affects the mobility of SUN2 in the nuclear envelope. Further, inhibition of cell motility caused by SUV39H1 depletion is restored by suppression of SUN2, nesprin-2, or KIF20A. In summary, these results show the functional association between chromatin organization and cell motility via the Golgi organization regulated by the LINC complex.

cell biology↗

bioRxiv2022

Genetic differentiation of water penny beetles may be associated with the formation process of the ancient Lake Biwa.

BackgroundWater flow is one of several factors that determine the habitats of aquatic insects. The conversions of stagnant (lentic) and running (lotic) water are physiologically and ecologically constrained. In general, aquatic insect species only occur in one of these environments. Though Eubrianax ramicornis (Coleoptera: Psephenidae) usually resides in rivers, however, it is also known to occur near the shores of Lake Biwa in Japan. Here, we investigated the genetic differences between the two Eubrianax species of Lake Biwa and its inflowing rivers, and other regions of Japan for the first time. Lake Biwa is an ancient lake and about four million years old. Though over 60 endemic species were described from Lake Biwa, they are mostly fish and molluscs, with only two species of aquatic insects. There are few reports of endemic aquatic insects in other ancient lakes, too. Discussion of the endemism of Eubrianax and its promoting factors is expected to provide insights into the evolution of aquatic insects in ancient lakes. MethodsWe surveyed and morphologically identified psephenid larvae in Lake Biwa and its inflowing rivers during the summers of 2017 and 2018 (Hayashi, 2009: Hayashi & Sota, 2009). We conducted phylogenetic analyses of two regions of COI and estimated the ages of population divergence based on fossil records of Eubrianax beetles in Lake Biwa as well as those of previously reported populations in other regions. We also analyzed two COI regions of the E. ramicornis haplotypes in Lake Biwa. ResultsFour psephenid species were identified among the samples collected in Lake Biwa and its inflowing rivers. Of these, E. ramicornis was collected only at the Lake Biwa shore whereas its congeneric E. granicollis was collected only from the rivers inflowing the lake. The phylogenetic analyses showed that E. ramicornis of Lake Biwa were clearly differentiated from those in previously reported regions and this divergence was estimated to have occurred 1.40 MYA. At that time, there was no lake at the location of present-day Lake Biwa. It is thought that rivers and their dammed flood plains to the east, with gravel and sand supplied by the rising Suzuka Mountains further to the east. Such an environments is preferable for E. ramicornis and they were thought to have become isolated from the surrounding rivers during the formation of Lake Biwa. On the contrary, there was no genetic differentiation between the E. granicollis population at the Lake Biwa inflow rivers and those elsewhere. Hence, E. granicollis might have migrated to the Lake Biwa watershed later than E. ramicornis and maintained gene flow over a wide area. The genetic differentiation of E. ramicornis reported here for the first time suggests that a species with a wide distribution may rather be evolving endemic to Lake Biwa. Reports on the endemism of aquatic insects in ancient lakes are scarce. This study is expected to bring new perspectives to the study of insect evolution in ancient lakes.

ecology↗

bioRxiv2022

Machine learning improves global models of plant diversity

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, neural networks) and conventional statistical methods (generalised linear models, generalised additive models) to model species richness and phylogenetic richness of vascular plants worldwide based on 830 regional plant inventories including c. 300,000 species and predictors of past and present environmental conditions. Machine learning showed an outstanding performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modelling techniques (ensemble predictions) to reveal global patterns and centres of plant diversity at multiple resolutions down to 7,774 km2. Our predictive maps provide the most accurate estimates of global plant diversity available to date at grain sizes relevant for conservation and macroecology.

ecology↗

bioRxiv2022

A dataset of 5 million city trees: species clustering and climate effects in urban forests

Sustainable cities depend on urban forests. City trees improve our health, clean the air, store CO2, and cool local temperatures. Comparatively less is known about urban forests as ecosystems, particularly their spatial composition, nativity statuses, biodiversity, and tree health. Here, we assembled and standardized a new dataset of N=5,132,890 trees from 63 of the largest US cities with detailed information on location, health, nativity status, and species. We further designed new tools to analyze the ecosystem structure of urban forests, including spatial clustering and abundance of native trees, and validate these tools in comparison to past methods. We show that city trees are significantly clustered by species in 93% of cities, potentially increasing pest vulnerability (even in cities with biodiverse urban forests). Further, non-native species significantly homogenize urban forests across cities, while native trees comprise 0.44%-85.6% (median=45.6%) of city tree populations. Native trees are less frequent in drier cities, and indeed climate significantly shapes both nativity and biodiversity in urban forests. Parks are more biodiverse than urban settings. Compared to past work which focused primarily on canopy cover and species richness, we show the importance of analyzing spatial composition and nativity statuses in urban forests (and we created new datasets and tools to do so). This dataset could be analyzed in combination with citizen-science datasets on bird, insect, or plant biodiversity; social and demographic data; or data on the physical environment. Urban forests offer a rare opportunity to intentionally design biodiverse, heterogenous, rich ecosystems.

ecology↗

bioRxiv2020

Tongue thickness measured by ultrasonography is associated with tongue pressure in the Japanese elderly

The term "oral frailty" reflects the fact that oral health is associated with physical frailty and mortality. Tongue thickness measurement is one of the evaluations for swallowing function. The aim of this study was to investigate the relationship between tongue thickness and tongue pressure in the Japanese elderly. We evaluated 254 elderly patients; all the participants underwent tongue ultrasonography and tongue pressure measurement. To determine tongue thickness, we measured the vertical distance from the surface of the mylohyoid muscle to the tongue dorsum using ultrasonography. Result analyses revealed that tongue thickness was linearly associated with tongue pressure in both sexes. In male participants, dyslipidemia, lower leg circumference, and tongue pressure were independently significantly associated with tongue thickness. In female participants, body mass index and tongue pressure were independently significantly associated with tongue thickness. Tongue thickness was significantly decreased by age for both men and women. The optimal cutoff for tongue thickness to predict the tongue pressure of < 20 kPa was 41.3 mm in males, and 39.3 mm in females. In the Japanese elderly, tongue thickness using ultrasonography is associated with tongue pressure. Tongue thickness and tongue pressure, which are sensitive markers for oral frailty, decrease in aging. The tongue ultrasonography provides a less invasive technique for determining tongue thickness and related aspiration risks for elderly patients.

neuroscience↗