Long non-coding RNA fine-tunes bone homeostasis and repair by orchestrating cellular crosstalk and β-catenin-OPG/Jagged1 pathway.

The IncRNA was initially believed to be dispensable for physiology due to the lack of observable phenotypes in knockout (KO) mice. However, our study challenges this conclusion. We found that both KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis.

Long non-coding RNA Malat1 fine-tunes bone homeostasis and repair by orchestrating cellular crosstalk and the β-catenin-OPG/Jagged1 pathway.

The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis.

Perspective: sustainability challenges, opportunities and solutions for long-term ecosystem observations.

As interest in natural capital grows and society increasingly recognizes the value of biodiversity, we must discuss how ecosystem observations to detect changes in biodiversity can be sustained through collaboration across regions and sectors. However, there are many barriers to establishing and sustaining large-scale, fine-resolution ecosystem observations. First, comprehensive monitoring data on both biodiversity and possible anthropogenic factors are lacking.

A Fast and Easy Method to Co-extract DNA and RNA from an Environmental Microbial Sample.

We herein propose a fast and easy DNA and RNA co-extraction method for environmental microbial samples. It combines bead beating and phenol-chloroform phase separation followed by the separation and purification of DNA and RNA using the Qiagen AllPrep DNA/RNA mini kit. With a handling time of ~3 h, our method simultaneously extracted high-quality DNA (peak size >10-15‍ ‍kb) and RNA (RNA integrity number >6) from lake bacterioplankton filtered samples.

Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.

Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively.

The crucial influence of trophic status on the relative requirement of nitrogen to phosphorus for phytoplankton growth.

Clarifying the pattern of relative nitrogen (N)-to-phosphorus (P) requirements for phytoplankton growth is of great significance for eutrophication mitigation and aquatic system management. The relative N-to-P requirement for phytoplankton growth is considered an essential trait determining species dominance within ecosystems and explaining phytoplankton response to nutrient availability. These requirements vary with environmental trophic status, though this variation remains unclear.

Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.

Background: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored.

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing.

Background: Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.

A freshwater radiation of diplonemids.

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown.

Distribution of the Harmful Bloom-Forming Cyanobacterium, Microcystis aeruginosa, in 88 Freshwater Environments across Japan.

Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3‍ ‍weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays.

Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes.

Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers.

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake.

Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.

Osteoclastic microRNAs and their translational potential in skeletal diseases.

Skeleton undergoes constant remodeling process to maintain healthy bone mass. However, in pathological conditions, bone remodeling is deregulated, resulting in unbalanced bone resorption and formation. Abnormal osteoclast formation and activation play a key role in osteolysis, such as in rheumatoid arthritis and osteoporosis.

G-protein Gα functions as a cytoskeletal and mitochondrial regulator to restrain osteoclast function.

Excessive osteoclastic bone erosion disrupts normal bone remodeling and leads to bone loss in many skeletal diseases, including inflammatory arthritis, such as rheumatoid arthritis (RA) and psoriatic arthritis, periodontitis and peri-prosthetic loosening. Functional control of osteoclasts is critical for the maintenance of bone homeostasis. However, the mechanisms that restrain osteoclast resorptive function are not fully understood.

Trophic niche breadth of pond zooplankton species using stable isotope analysis and the relationship with the abiotic and biotic factors.

Zooplankton species have different feeding habits, but the diversity of their food resources and the factors governing them are still largely unknown. We here estimated the differences in the trophic niche breadths of dominant zooplankton species in ponds, using stable isotopes. To understand the differences in trophic niches of different zooplankton species, we measured the carbon and nitrogen stable isotope ratios and calculated the nearest-neighbour distance (NND), and standard deviation of NND (SDNND) of the bi-plot space of stable carbon and nitrogen isotopes in pond zooplankton.

Characteristics of anxiety and the factors associated with presence or absence of each anxiety among radiation decontamination workers in Fukushima.

The aims of the present study were to investigate what kind of anxiety radiation decontamination workers have, and to analyze what factors are associated to presence or absence of their anxieties. A self-administered questionnaire was conducted, which included 10 anxiety items. A logistic regression model was then used to determine what factors were related to increased anxiety.

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.

DNA methylation plays important roles in prokaryotes, and their genomic landscapes-prokaryotic epigenomes-have recently begun to be disclosed. However, our knowledge of prokaryotic methylation systems is focused on those of culturable microbes, which are rare in nature. Here, we used single-molecule real-time and circular consensus sequencing techniques to reveal the 'metaepigenomes' of a microbial community in the largest lake in Japan, Lake Biwa.

The Broad Habitat Spectrum of the CL500-11 Lineage (Phylum Chloroflexi), a Dominant Bacterioplankton in Oxygenated Hypolimnia of Deep Freshwater Lakes.

CL500-11 (phylum ) is one of the most ubiquitous and abundant bacterioplankton lineages in deep freshwater lakes inhabiting the oxygenated hypolimnion. While metagenomics predicted possible eco-physiological characteristics of this uncultured lineage, no consensus on their ecology has so far been reached, partly because their niche is not clearly understood due to a limited number of quantitative field observations. This study investigated the abundance and distribution of CL500-11 in seven deep perialpine lakes using catalyzed reporter deposition-fluorescence hybridization (CARD-FISH).

Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi.

Background: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.

Results: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition.

Life in company dormitories and a career change are associated with anxiety over lack of privacy among radiation decontamination workers in Fukushima Prefecture, Japan.

Objectives: The purpose of the present study was to obtain knowledge for improvement of the housing and life among radiation decontamination workers by examining the effect of housing type on anxiety over lack of privacy.

Methods: This cross-sectional study comprised 544 male radiation decontamination workers in Fukushima Prefecture who anonymously answered self-administered questionnaires in 2013, including measurement of privacy anxiety, housing type, career change, social support, and sociodemographics. Chi-square tests and binary logistic regression analysis were used to evaluate the associations between these factors and anxiety over lack of privacy.

Differential Responses of Two Ecologically Similar Case-Bearing Caddisfly Species to a Fish Chemical Cue: Implications for a Coexistence Mechanism.

The mechanisms for the coexistence of multiple species occupying the same ecological niche are often puzzling. Predator effects on competitively superior species is one possible mechanism. In this study, we tested whether the presence of size-selective predators (fishes) acts as a mechanism for the coexistence of two species of case-bearing caddisfly larvae, Perissoneura paradoxa and Psilotreta kisoensis (Odontoceridae, Trichoptera).

Preventive measures and lifestyle habits against exertional heat illness in radiation decontamination workers.

Objectives: The aim of this study was to reveal the current state of preventive measures and lifestyle habits against heat illness in radiation decontamination workers and to examine whether young radiation decontamination workers take less preventive measures and have worse lifestyle habits than the elder workers.

Methods: This was a cross-sectional study. Self-administered questionnaires were sent to 1,505 radiation decontamination workers in Fukushima, Japan.

Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated hypolimnion of deep freshwater lakes.

The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance.

Def6 Restrains Osteoclastogenesis and Inflammatory Bone Resorption.

Inflammatory bone resorption mediated by osteoclasts is a major cause of morbidity and disability in many inflammatory disorders, including rheumatoid arthritis (RA). The mechanisms that regulate osteoclastogenesis and bone resorption in inflammatory settings are complex and have not been well elucidated. In this study, we identify the immunoregulator differentially expressed in FDCP 6 homolog (Def6) as a novel inhibitor of osteoclastogenesis in physiological and inflammatory conditions.

Roles of chondroitin sulfate proteoglycan 4 in fibrogenic/adipogenic differentiation in skeletal muscle tissues.

Intramuscular adipose tissue and fibrous tissue are observed in some skeletal muscle pathologies such as Duchenne muscular dystrophy and sarcopenia, and affect muscle strength and myogenesis. They originate from common fibrogenic/adipogenic cells in the skeletal muscle. Thus, elucidating the regulatory mechanisms underlying fibrogenic/adipogenic cell differentiation is an important step toward the mediation of these disorders.