Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small,natural river

Limnology - In recent years, biodiversity loss has become one of the most serious environmental issues worldwide, especially in aquatic ecosystems. To avoid diversity loss, it is necessary to...     

Effects of large-scale forest fire followed by illegal logging on the regeneration of boreal forests in Mongolia

Landscape and Ecological Engineering - We aimed to test the hypothesis that large-scale forest fire followed by illegal logging inhibits the regeneration of boreal forests in Mongolia. For this...     

The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing

Numerous microbes inhabit the mammalian intestinal track and strongly impact host physiology; however, our understanding of this ecosystem remains limited owing to the high complexity of the microbial community and the presence of numerous non-culturable microbes. Segmented filamentous bacteria (SFBs), which are clostridia-related Gram-positive bacteria, are among such non-culturable populations and are well known for their unique morphology and tight attachment to intestinal epithelial cells. Recent studies have revealed that SFBs play crucial roles in the post-natal maturation of gut immune function, especially the induction of Th17 lymphocytes. Here, we report the complete genome sequence of mouse SFBs. The genome, which comprises a single circular chromosome of 1 620 005 bp, lacks genes for the biosynthesis of almost all amino acids, vitamins/cofactors and nucleotides, but contains a full set of genes for sporulation/germination and, unexpectedly, for chemotaxis/flagella-based motility. These findings suggest a triphasic lifestyle of the SFB, which comprises two types of vegetative (swimming and epicellular parasitic) phases and a dormant (spore) phase. Furthermore, SFBs encode four types of flagellin, three of which are recognized by Toll-like receptor 5 and could elicit the innate immune response. Our results reveal the non-culturability, lifestyle and immunostimulation mechanisms of SFBs and provide a genetic basis for the future development of the SFB cultivation and gene-manipulation techniques.     

Assessing the impact of land use and climate change on the evergreen broad-leaved species of <Emphasis Type="Italic">Quercus acuta</Emphasis> in Japan

To assess the impact of Quercus acuta, a dominant species in the evergreen broad-leaved forests of Japan, and its habitat shifts as a result of climate change, we predicted the potential habitats under the current climate and two climate change scenarios using a random forest (RF). The presence/absence records of Q. acuta were extracted from the Phytosociological Relevè Data Base as response variables, and four climatic variables (warmth index, WI; minimum temperature of the coldest month, TMC; summer precipitation, PRS; and winter precipitation, PRW) were used as predictor variables. The mean decrease in the Gini criterion revealed that WI was the most influential factor followed by TMC. The RF revealed a considerable increase in potential habitats (PHs) under the climate change scenarios for 2081–2100 (RCM20, 180,141 km²; MIROC, 175,635 km²) relative to the current climate (150,542 km²). The land use variables were used for masking PH. The PH masked by land use (PHLU) was approximately half of the PH under the current conditions (74,567 km²). Under the climate change scenarios and 1 km migration options, the PHLU were not increased relative to its value under the current conditions. The distribution of Q. acuta was restricted by the northward shift in northern Honshu, but expanded as a result of the upward shift into the mountain areas of Western Japan. Habitat fragmentation reduced the ability of migration to respond to climate change in the lowland areas of Japan.     

Composition of aquatic invertebrates associated with macrophytes in Lake Tonle Sap,Cambodia

Faunal composition of aquatic invertebrate communities associated with submerged parts of several species of macrophytes were studied in different areas in littoral Lake Tonle Sap in Cambodia, with special reference to those in root systems (interrhizon) of a free-floating water hyacinth (Eichhornia crassipes). Nine phyla of invertebrates were collected, of which oligochaetes, shrimps and Limnoperna mussels were abundant along with meiobenthic crustaceans. The macrophyte-associated invertebrates in Lake Tonle Sap might be unique in having abundant sessile animals, such as sponges, bryozoans and Limnoperna mussels. The Limnoperna mussels attached to macrophytes were more abundant in offshore and inundated forest than in secluded vegetational stands toward the shoreline. It suggests that water movement can be an important factor determining the distribution and abundance of the sessile animals by controlling larval dispersions and might be associated with the hydrological characteristic of the lake, i.e., the lake opens to the large Mekong River with drastic seasonal changes in water level.     

Dynamics of intracellular information decoding

A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.     

Aberrant splicing of the hRasGRP4 transcript and decreased levels of this signaling protein in the peripheral blood mononuclear cells in a subset of patients with rheumatoid arthritis

Introduction  

An unidentified population of peripheral blood mononuclear cells (PBMCs) express Ras guanine nucleotide releasing protein 4 (RasGRP4). The aim of our study was to identify the cells in human blood that express hRasGRP4, and then to determine if hRasGRP4 was altered in any patient with rheumatoid arthritis (RA).     

Impaired insulin signaling in endothelial cells reduces insulin-induced glucose uptake by skeletal muscle

In obese patients with type 2 diabetes, insulin delivery to and insulin-dependent glucose uptake by skeletal muscle are delayed and impaired. The mechanisms underlying the delay and impairment are unclear. We demonstrate that impaired insulin signaling in endothelial cells, due to reduced Irs2 expression and insulin-induced eNOS phosphorylation, causes attenuation of insulin-induced capillary recruitment and insulin delivery, which in turn reduces glucose uptake by skeletal muscle. Moreover, restoration of insulin-induced eNOS phosphorylation in endothelial cells completely reverses the reduction in capillary recruitment and insulin delivery in tissue-specific knockout mice lacking Irs2 in endothelial cells and fed a high-fat diet. As a result, glucose uptake by skeletal muscle is restored in these mice. Taken together, our results show that insulin signaling in endothelial cells plays a pivotal role in the regulation of glucose uptake by skeletal muscle. Furthermore, improving endothelial insulin signaling may serve as a therapeutic strategy for ameliorating skeletal muscle insulin resistance.