Environmentally dependent interactions shape patterns in gene content across natural microbiomes.

Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions.

Functional regimes define the response of the soil microbiome to environmental change.

The metabolic activity of soil microbiomes plays a central role in carbon and nitrogen cycling. Given the changing climate, it is important to understand how the metabolism of natural communities responds to environmental change. However, the ecological, spatial, and chemical complexity of soils makes understanding the mechanisms governing the response of these communities to perturbations challenging.

The potato rhizosphere microbiota correlated to the yield of three different regions in Korea.

We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield.

High-quality genome resource of a basidiomycetous yeast, isolate RS1, isolated from rice seed.

(anamorph: ) is a basidiomycetous yeast in the Ustilaginaceae family and is a core member of the rice seed microbiome. RS1 was isolated from surface-sterilized rice seeds. This 18.

Global patterns in gene content of soil microbiomes emerge from microbial interactions.

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits.

Dysbiotic but nonpathogenic shift in the fecal mycobiota of patients with rheumatoid arthritis.

Rheumatoid arthritis (RA) is closely associated with the oral and gut microbiomes. Fungal cell wall components initiate inflammatory arthritis in mouse models. However, little is known regarding the role of the fungal community in the pathogenesis of RA.

Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations.

Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation.

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil.

The soil environment determines plants' health and performance during their life cycle. Therefore, ecological understanding on variations in soil environments, including physical, chemical, and biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive and extensive blueprint of the bacterial, archaeal, and fungal communities in rice paddy soils with differing soil types and chemical properties.

The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.

The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In , genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems.

The Role of DNA Methylation in Transcriptional Regulation of Pro-Nociceptive Genes in Rat Trigeminal Ganglia.

Epigenetic modulation by DNA methylation is associated with aberrant gene expression in sensory neurons, which consequently leads to pathological pain responses. In this study, we sought to investigate whether peripheral inflammation alters global DNA methylation in trigeminal ganglia (TG) and results in abnormal expression of pro-nociceptive genes. Our results show that peripheral inflammation remotely reduced the level of global DNA methylation in rat TG with a concurrent reduction in and expression.

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed.

Background: Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood.

Results: We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures.

Modification of mean wake flow behind a very slender axisymmetric body of revolution by imposed nonlinear unstable helical modes.

For a sufficiently slender axially symmetric body placed in a uniform stream, only convectively unstable modes are found in previous experiments. This work imposes theoretically and computationally a pair of most unstable helical modes, symmetrically and asymmetrically. The Reynolds stress modification of the developing laminar mean wake flow is modified into an elliptic-like cross section for symmetrical forcing; the consequences of unequal upstream amplitudes are also explored.

Development of a novel approach to the assessment of eye-hand coordination.

Background: Current methods to measure eye-hand coordination (EHC) have been widely applied in research and practical fields. However, some aspects of the methods, such as subjectivity, high price, portability, and high appraisal contribute to difficulties in EHC testing.

New Methods: The test was developed on an Apple iPad(®) and involves tracing up to 13 shapes with a stylus pen.

Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA.

Originally the novel protein Blom7α was identified as novel pre-mRNA splicing factor that interacts with SNEV(Prp19/Pso4), an essential protein involved in extension of human endothelial cell life span, DNA damage repair, the ubiquitin-proteasome system, and pre-mRNA splicing. Blom7α belongs to the heteronuclear ribonucleoprotein K homology (KH) protein family, displaying 2 KH domains, a well conserved and widespread RNA-binding motif. In order to identify specific sequence binding motifs, we here used Systematic Evolution of Ligands by Exponential Enrichment (SELEX) with a synthetic RNA library.

Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4.

The removal of introns from pre-mRNA is performed by the spliceosome that stepwise assembles on the pre-mRNA before performing two catalytic steps. The spliceosome-associated CDC5L-SNEV(Prp19-Pso4) complex is implicated in activation of the second catalytic step of pre-mRNA splicing, and one of its members, SNEV(Prp19-Pso4), is also implicated in spliceosome assembly. To identify interaction partners of SNEVPrp19-Pso4, we have performed yeast two-hybrid screenings.

Detection of hypothetical proteins in 10 individual human tumor cell lines.

The search for new structures in tumors by genomics and proteomics methods is a major goal in tumor biology and may lead to the detection of markers or antigens for the generation of tumor vaccines. The aim of this study was to identify proteins that have been predicted so far based upon their nucleic acid sequence only or show poor identity to known proteins in tumor cell lines. Cell lines of neuroblastoma, colorectal, cervix carcinoma, adenocarcinoma of the ovary, lung and breast cancer, promyelocytic leukaemia, rhabdomyosarcoma, osteosarcoma and malignant melanoma were used.

The role of the sympathetic nervous system in moxibustion-induced immunomodulation in rats.

The effects of chemical sympathectomy on moxibustion-induced changes in splenic natural killer (NK) cell cytotoxicity, T and B cell proliferation were studied. Direct moxibustion was applied to the unilateral Zusanli region. NK cell cytotoxicity was suppressed by moxibustion in both vehicle-treated rats and sympathectomized rats.