Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency.

Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.

The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation.

Endogenous retroviruses (ERVs) are repetitive sequences in the genome, belonging to the retrotransposon family. During the course of life, ERVs are associated with multiple aspects of chromatin and transcriptional regulation in development and pathological conditions. In mammalian embryos, ERVs are extensively activated in early embryo development, but with a highly restricted spatial-temporal pattern; and they are drastically silenced during differentiation with exceptions in extraembryonic tissue and germlines. The dynamic activation pattern of ERVs raises questions about how ERVs are regulated in the life cycle and whether they are functionally important to cell fate decision during early embryo and somatic cell development. Therefore, in this review, we focus on the pieces of evidence demonstrating regulations and functions of ERVs during stem cell differentiation, which suggests that ERV activation is not a passive result of cell fate transition but the active epigenetic and transcriptional regulation during mammalian development and stem cell differentiation.

Pyridinium porphyrins and AuNPs mediated bionetworks as SPR signal amplification tags for the ultrasensitive assay of brain natriuretic peptide.

Extension of the self-assembled bionanonetworks into surface plasmon resonance (SPR) assay investigation provides an effective signal amplification approach. We fabricated a bionetwork by nucleic acids, organic compounds, and supramolecular gold nanoparticles for ultrasensitive SPR detection of B-type natriuretic peptide (BNP). The SPR method was developed by a sandwich-type format of aptamer-target-antibody, and the aptamer-modified bionanonetworks induced localized SPR and large refractive index for different concentrations of the target BNP. The linear concentration range and limit of detection were 1-10,000 pg/mL (R2 = 0.9852) and 0.3 pg/mL respectively. The detection recovery was in the range 92.13 to 108.69%. The approach embraces the following main advantages: (1) Cooperative double recognition was realized by calix[4]arenes for amino aptamers and pyridinium porphyrins. (2) The approach provided the specificity for supramolecular-based nanomaterials and a simple synthesis process via the ordered self-assembly under mild conditions. (3) The bionanonetworks endowed the SPR assay with signal amplification and stable determination for trace proteins. Therefore, it is expected that this study may offer a new SPR signal-amplified platform of organic-inorganic bionanonetworks to achieve sensitive, stable, and real-time determination. Graphical abstract Schematic of bionanonetwork based on porphyrin-mediated functionalized gold nanoparticles for SPR signal amplification to quantitatively detect BNP.

Pueribacillus theae gen. nov., sp. nov., isolated from Pu'er tea.

A novel bacterial strain, designated T8T, isolated from ripened Pu'er tea, was investigated by using a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, sporogenous and rod-shaped with flagella. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Bacillaceae in the class Bacilli and represented an independent taxon separated from other genera. Strain T8T shared low levels of 16S rRNA gene sequence similarity (<94 %) to members of other genera in the family Bacillaceae and was most closely related to Bacillus composti SgZ-9T (93.3 % sequence similarity). The DNA G+C content of strain T8T was 40 mol%. The major fatty acids (>10 %) of strain T8T were iso-C15 : 0 and iso-C16 : 0. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. MK-7 (62 %), MK-6 (31 %) and MK-8 (7 %) were detected as the isoprenoid quinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine and six unidentified phospholipids. On the basis of the polyphasic evidence presented, strain T8T is considered to represent a novel genus and species in the family Bacillaceae, for which we propose the name Pueribacillus theae gen. nov., sp. nov. The type strain is T8T (=CGMCC 1.15924T=KCTC 333888T).

Bacillus camelliae sp. nov., isolated from Pu'er tea.

A novel aerobic, Gram-stain-positive, sporogenous, rod-shaped bacterial strain, 7578-1T, was isolated from ripened Pu'er tea. Based on 16S rRNA gene sequence similarity comparisons, strain 7578-1T was grouped into the genus Bacillus and appeared to be closely related to the type strains Bacillus shackletoniiLMG 18435T (98.4 %), Bacillus acidicolaDSM 14745T (97.6 %), Bacillus paralicheniformis KACC 18426T (97.2 %) and Bacillus ginsengihumi KCTC 13944T (96.7 %). The fatty acid profile containing the major fatty acids, iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0 supported the allocation of strain 7578-1T to the genus Bacillus. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major menaquinone was MK-7 (95 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified phospholipid and one unidentified lipid. The average nucleotide identity values between strain 7578-1T and its most closely related species were 67.8-82.4 % by OrthoANIu analysis. The DNA-DNA relatedness value between strain 7578-1T and the type strains of closely related species were 17-39 %, again indicating that strain 7578-1T represented a novel species in the genus Bacillus. The DNA G+C content of strain 7578-1T was 36.0 mol%. On the basis of the presented polyphasic evidence, strain 7578-1T is considered to represent a novel species of the genus Bacillus, for which we propose the name Bacillus camelliae sp. nov. The type strain is 7578-1T (=CGMCC 1.15374T=KCTC 33845T).