Microbiome and lipidomic analysis reveal the interplay between skin bacteria and lipids in a cohort study.

Human skin acts as a protective barrier between the body and the external environment. Skin microbiome and intercellular lipids in the stratum corneum (SC) are essential for maintaining skin barrier function. However, the interplay between skin bacteria and the lipids is not fully understood.

Agonist-Induced Ca Signaling in HEK-293-Derived Cells Expressing a Single IP Receptor Isoform.

In mammals, three genes encode IP receptors (IPRs), which are involved in agonist-induced Ca signaling in cells of apparently all types. Using the CRISPR/Cas9 approach for disruption of two out of three IPR genes in HEK-293 cells, we generated three monoclonal cell lines, IP3R1-HEK, IP3R2-HEK, and IP3R3-HEK, with the single functional isoform, IPR1, IPR2, and IPR3, respectively. All engineered cells responded to ACh with Ca transients in an "all-or-nothing" manner, suggesting that each IPR isotype was capable of mediating CICR.

Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome.

Introduction: Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome.

Methods: Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks.

Proliferation, migration, and resistance to oxidative and thermal stresses of HT1080 cells with knocked out genes encoding Hsp90α and Hsp90β.

Heat shock protein 90 (Hsp90) fulfils essential housekeeping functions in the cell associated with the folding, stabilization, and turnover of various proteins. In mammals, there exist two Hsp90 isoforms, stress-inducible Hsp90α and constitutively expressed Hsp90β. In an attempt to identify cellular processes dependent on Hsp90α and Hsp90β, we generated a panel of clones of human fibrosarcoma HT1080 cells with the knocked out HSP90AA1 or HSP90AB1 genes encoding, respectively, Hsp90α and Hsp90β.

EVC001 Is Well-Tolerated and Improves Human Milk Oligosaccharide Utilization in Preterm Infants in the Neonatal Intensive Care Unit.

Not all infants carry specialized gut microbes, meaning they cannot digest human milk oligosaccharides and therefore do not receive complete benefits from human milk. EVC001 is equipped to convert the full array of complex oligosaccharides into compounds usable by the infant, making it an ideal candidate to stabilize gut function and improve nutrition in preterm infants. A prospective, open-label study design was used to evaluate the tolerability of EVC001 and its effects on the fecal microbiota in preterm infants in a Neonatal Intensive Care Unit.

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.

Microbiome analyses of blood and tissues suggest cancer diagnostic approach.

Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia-IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins.

On Global Attraction to Stationary States for Wave Equations with Concentrated Nonlinearities.

The global to stationary states is established for solutions to 3D wave equations with concentrated nonlinearities: each finite energy solution converges as to stationary states. The attraction is caused by nonlinear energy radiation.

A communal catalogue reveals Earth's multiscale microbial diversity.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project.

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns.

High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms.

Ferromagnetic Coupling in the Heterospin Bis-Catecholato-Manganese(IV) Complex with Pyridine Substituted by Nitronyl-nitroxide.

A new bis(3,6-di-tert-butyl-catecholato)manganese complex with two 4-NIT-Py ligands was synthesized and characterized [4-NIT-Py = pyridine substituted at position 4 with nitronyl-nitroxide radical, 2-(pyridin-4-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl]. X-ray diffraction indicated an octahedral environment of the manganese atom with a trans arrangement of ligands. Bonds lengths in the inner coordination core of the metal and in the chelate cycles that are representative of the charge distribution between the metal and ligands displayed a Mn(IV)(Cat) charge distribution.

Origin of microbial biomineralization and magnetotaxis during the Archean.

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the and This phylogenetic divergence occurred well before the Great Oxygenation Event.

Open-Source Sequence Clustering Methods Improve the State Of the Art.

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs.

On the Linear Stability of Crystals in the Schrödinger-Poisson Model.

We consider the Schrödinger-Poisson-Newton equations for crystals with one ion per cell. We linearize this dynamics at the periodic minimizers of energy per cell and introduce a novel class of the ion charge densities that ensures the stability of the linearized dynamics. Our main result is the for the Bloch generators of the linearized dynamics under a Wiener-type condition on the ion charge density.

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

[This corrects the article DOI: 10.1186/s40168-015-0081-x.].

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

Background: The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses.

Results: Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered.

Deciphering metatranscriptomic data.

Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms within a sample, and the second is to taxonomically classify the organisms and determine their individual functional roles within a community.

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

Motivation: The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species.

Results: We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data.

[Medical gels for ultrasonographic diagnosis, therapy and electrocardiography].

The All-Russian Research Institute of Medical Polymers has designed the medical gels REPAC, DIAGEL, for ultrasound diagnosis, REPAC-T for ultrasound therapy, ELCON and ELCARD for electrocardiography. REPAC, DIAGEL, and REPAC-T have the least sound damping factor (approximately 10(-3) dB/cm) as compared to other similar gels. REPAC and DIAGEL showed a good performance when they were applied in clinical practice during a year.

[Clinico-morphologic characteristics of X-linked pseudohypertrophic myopathy].

A clinical, genealogical, EMG and morphological study of the development of pseudohypertrophic myopathy linked with X-chromosome allowed one to distinguish 2 variants: 1) the malignant (Duchenne form) and 2) benign (Baker form). Although both forms have similar clinical symptoms, the Baker form has a later onset, a more favourable development and more preserved motor functions. The activity of fructosodiphosphataldolase and creatinphosphokinase in the blood serum of these patients was significantly lower than in Duchenne' myopathy.