Screening of Genes Co-Associated with Sudden Infant Death Syndrome and Infectious Sudden Death in Infancy and Bioinformatics Analysis of Their Regulatory Networks.

OBJECTIVES: The common differentially expressed mRNAs in brain, heart and liver tissues of deceased sudden infant death syndrome (SIDS) and infectious sudden death in infancy (ISDI) confirmed by autopsy was screened by bioinformatics to explore the common molecular markers and pathogenesis of SIDS and ISDI. METHODS: The datasets of GSE70422 and GSE136992 were downloaded, the limma of R software was used to screen differentially expressed mRNA in different tissue samples of SIDS and ISDI decedents for overlapping analysis. The clusterProfiler of R software was used to conduct gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The protein-protein interaction (PPI) network was constructed by STRING database, while the hub gene was screened by cytoHubba plug-in. RESULTS: Compared with the control group, there were 19 significant differentially expressed genes in the tissue samples of SIDS and ISDI decedents, among which 16 in the heart tissue and 3 in the liver tissue, and the astrotactin 1 (ASTN1) gene expression difference in the heart tissue was most significant. The PPI network identified Ras homolog family member A (RHOA), integrin subunit alpha 1 (ITGA1), and H2B clustered histone 5 (H2BC5) were hub genes. The analysis of GO and KEGG showed that differentially expressed genes were enriched in the molecular pathways of actin cytoskeleton regulation, focal adhesion and response to mycophenolic acid. CONCLUSIONS: ASTN1, RHOA and ITGA1 may participate in the development of SIDS and ISDI. The enrichment of differentially expressed genes in immune and inflammatory pathways suggests a common molecular regulatory mechanism between SIDS and ISDI. These findings are expected to provide new biomarkers for molecular anatomy and forensic identification of SIDS and ISDI.

Efficient genetic engineering of murine cochlear organoids.

Organoid culture is a popular model to study gene function as the easy manipulating and time saving compared with in vivo experiments. This is widely used in auditory system for studying supporting cells (SCs) or hair cells (HCs) as only very few SCs or HCs can be harvested in both human and murine cochlea. However, the use of organoids is still a challenge due to the low efficiency in genetic modification. Here we took Lin28b as an example and compared Lin28b gain-of-function (GOF) and loss-of-function (LOF) with different genetic engineering methods and found that TetOn induced GOF or LOF was more efficient compared with lipofection or lentiviral transduction in the experimental conditions we used. Cell apoptosis in TetOn induction system was lowest compared with the other methods in this study. Our study is the first to compare the efficiency of different genetic engineering techniques in cochlear organoid culture, which may also apply to organoids established with other tissues.

Responses to soil pH gradients of inorganic phosphate solubilizing bacteria community.

Soil pH is commonly considered a dominant factor affecting the function of microbiota. Few studies, however, have focused on communities of bacteria able to solubilize inorganic phosphate (iPSB), which are important for the mobilization of soil phosphorus (P), because finding an effective method to assess the abundance and diversity of iPSB communities is difficult. We used a newly reported method of database alignment and quantified the gene pqqC to analyze the compositions of iPSB communities from five soils with pH gradients ranging from 4 to 8. The iPSB community structure differed significantly between these soil types. Among iPSB community, Bacillus was the dominant genus, followed by Arthrobacter and Streptomyces. A redundancy analysis indicated that soil pH was the most important of 15 soil factors and their pairwise interactions, accounting for 5.12% of the variance. The abundance of the iPSB communities increased with pH within the gradients which was confirmed by experimental adjustment of pH, suggesting that the defect P status in high pH soil was speculated as the driving force of iPSB community population. Our study demonstrated the dominant role of soil pH on the iPSB community, which may contribute to the understanding the possible mechanism of microbial P mobilization for better improvement of P use-efficiency.

Massilia phosphatilytica sp. nov., a phosphate solubilizing bacteria isolated from a long-term fertilized soil.

A Gram-stain-negative and rod-shaped bacterial strain, 12-OD1T, with rock phosphate solubilizing ability was isolated from agricultural soil in Hailun, Heilongjiang, PR China. The isolate was affiliated to the genus Massilia, based on 16S rRNA gene sequence alignments, having the highest similarities with Massilia putida6 NM-7T (98.67 %), Massilia kyonggiensis TSA1T (98.28 %), and Massilia norwichensis NS9T (98.07 %), respectively. The DNA G+C content was 67.72 mol% and DNA-DNA hybridization showed low relatedness values (less than 47 %) between strain 12-OD1T and other phylogenetically related species of the genus Massilia. The predominant isoprenoid quinone was Q-8 and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C17 : 0 cyclo (25.4 %), C16 : 0 (23.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1 ω6c) (22.5 %), which differentiates it from close relatives within the genus Massilia. Combined genetic, physiological and biochemical properties indicate that strain 12-OD1T is a novel species of the genus Massilia, for which the name Massilia phosphatilytica sp. nov., is proposed, with the type strain 12-OD1T (=CCTCC AB 2016251T=LMG 29956T=KCTC 52513T).

Long-term nitrogen fertilization decreased the abundance of inorganic phosphate solubilizing bacteria in an alkaline soil.

Inorganic phosphate solubilizing bacteria (iPSB) are essential to facilitate phosphorus (P) mobilization in alkaline soil, however, the phylogenetic structure of iPSB communities remains poorly characterized. Thus, we use a reference iPSB database to analyze the distribution of iPSB communities based on 16S rRNA gene illumina sequencing. Additionally, a noval pqqC primer was developed to quantify iPSB abundance. In our study, an alkaline soil with 27-year fertilization treatment was selected. The percentage of iPSB was 1.10~2.87% per sample, and the dominant iPSB genera were closely related to Arthrobacter, Bacillus, Brevibacterium and Streptomyces. Long-term P fertilization had no significant effect on the abundance of iPSB communities. Rather than P and potassium (K) additions, long-term nitrogen (N) fertilization decreased the iPSB abundance, which was validated by reduced relative abundance of pqqC gene (pqqC/16S). The decreased iPSB abundance was strongly related to pH decline and total N increase, revealing that the long-term N additions may cause pH decline and subsequent P releases relatively decreasing the demands of the iPSB community. The methodology and understanding obtained here provides insights into the ecology of inorganic P solubilizers and how to manipulate for better P use efficiency.

A polyoxometalate-encapsulating cationic metal-organic framework as a heterogeneous catalyst for desulfurization.

A new cationic triazole-based metal-organic framework encapsulating Keggin-type polyoxometalates, with the molecular formula [Co(BBPTZ)3][HPMo12O40]⋅24 H2O [compound 1; BBPTZ = 4,4'-bis(1,2,4-triazol-1-ylmethyl)biphenyl] is hydrothermally synthesized and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and single-crystal X-ray diffraction. The structure of compound 1 contains a non-interpenetrated 3D CdSO4 (cds)-type framework with two types of channels that are interconnected with each other; straight channels that are occupied by the Keggin-type POM anions, and wavelike channels that contain lattice water molecules. The catalytic activity of compound 1 in the oxidative desulfurization reaction indicates that it is not only an effective and size-selective heterogeneous catalyst, but it also exhibits distinct structural stability in the catalytic reaction system.

Polyoxometalate-based entangled coordination networks induced by an extended bis(triazole) ligand.

The introduction of an extended bridging bis(triazole) ligand, that is, 4,4'-bis(1,2,4-triazol-1-ylmethyl)biphenyl (BBPTZ), into the hydrothermal reaction system containing transition metal ions and Keggin-type polyoxometalates (POMs) led to the isolation of three new organic-inorganic hybrid entangled coordination networks, [Cu(I)2Cu(II)(BBPTZ)6][SiW12O40]⋅12H2O (1), [Ni(BBPTZ)2(H2O)][H2SiW12O40]⋅11H2O (2), and [Ni2(BBPTZ)4(H2O)2][SiW12O40]⋅3H2O (3). All three compounds were characterized by elemental analysis, IR spectroscopy, TG analysis, powder X-ray diffraction, and single-crystal X-ray diffraction. Compound 1 contains a 2-D POM-based metal-organic layer entangled with 1-D ladder-like metal-organic chains. The adjacent 2-D networks are parallel to each other, further stacking into a 3-D supramolecular framework with 1-D channels. Compound 2 exhibits a 1-D cantilever-type loop-containing chain. The Keggin-type POMs act as the cantilever groups, leading to the adjacent catilever-type chains interwaving together to form a 3-D supramolecular open framework with two types of channels. Compound 3 possesses a 3-D open framework based on 2-D metal-organic undulated layer and Keggin-type POM clusters. Three sets of such frameworks further interpenetrate with each other to form an interesting three-fold interpenetrating framework. The photocatalytic activities of compounds 1-3 for the decomposition of methylene blue (MB) under UV light have been investigated.

New entangled coordination networks based on charge-tunable keggin-type polyoxometalates.

Investigation into a hydrothermal reaction system with transition-metal (TM) ions, 1,4-bis(1,2,4-triazol-1-lmethyl)benzene (BBTZ) and various charge-tunable Keggin-type polyoxometalates (POMs) led to the preparation of four new entangled coordination networks, [Co(II) (HBBTZ)(BBTZ)2.5 ][PMo12 O40 ] (1), [Cu(I) (BBTZ)]5 [BW12 O40 ]⋅H2 O (2), [Cu(II) (BBTZ)]3 [AsW(V) 3 W(VI) 9 O40 ]⋅10 H2 O (3), and [Cu(II) 5 (BBTZ)7 (H2 O)6 ][P2 W22 Cu2 O77 (OH)2 ]⋅6 H2 O (4). All compounds were characterized by using elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction, and single-crystal X-ray diffraction. The mixed valence of W centers in compound 3 was further confirmed by using XPS spectroscopy and bond-valence sum calculations. In the structural analysis, the entangled networks of 1-4 demonstrate zipper-closing packing, 3D polythreading, 3D polycatenation, and 3D self-penetration, respectively. Moreover, with the enhancement of POM negative charges and the use of different TM types, the number of nodes in the coordination networks of 1-4 increased and the basic metal-organic building motifs changed from a 1D zipper-type chain (in 1) to a 2D pseudorotaxane layer (in 2) to a 3D diamond-like framework (in 3) and finally to a 3D self-penetrating framework (in 4). The photocatalytic properties of compounds 1-4 for the degradation of methylene blue under UV light were also investigated; all compounds showed good catalytic activity and the photocatalytic activity order of Keggin-type species was initially found to be {XMo12 O40 }>{XW12 O40 }>{XW12-n TMn O40 }.

Polyoxometalate-templated lanthanide-organic hybrid layers based on 6(3)-honeycomb-like 2D nets.

The reaction of a double-betaine-containing ligand with LnPMo(12)O(40)·nH(2)O (Ln = Dy, Tb and Er) led to the isolation of new polyoxometalate-templated lanthanide-organic hybrid layers with the molecular formula [Ln(L)(1.5)(H(2)O)(5)][PMo(12)O(40)]·1.5CH(3)CN·2H(2)O (Ln = Dy (1), Tb (2) and Er (3); L = 1,4-bis(pyridinil-4-carboxylato)-l,4-dimethylbenzene). All compounds were characterized by elemental analyses, TG analyses, IR and the single-crystal X-ray diffraction. Compounds 1-3 are isostructural and possess a 2D undulating cationic network [Ln(L)(1.5)(H(2)O)(5)](n)(3n+) with the honeycomb-like cavities. Interestingly, the interval 2D networks are further connected by the H-bonds to form a 3D supramolecular framework. Moreover, two of such identical supramolecular frameworks are 2-fold interpenetrated with each other and encapsulate the α-Keggin-type [PMo(12)O(40)](3-) anionic templates and the solvent molecules. These composite compounds display both luminescent properties (induced by organic ligands and/or lanthanide ions) and electrocatalytic activities towards the reduction of nitrite.

Determination of dextran sulfate sodium with crystal violet by triple-wavelength overlapping resonance Rayleigh scattering.

A triple-wavelength overlapping resonance Rayleigh scattering (TWO-RRS) method was developed to detect dextran sulfate sodium (DSS) with crystal violet (CV). At pH 10.0 Britton Robinson buffer solution medium, the interaction of CV with DSS occurred which greatly enhanced the RRS intensity with the new RRS peaks appearing at 340, 501 and 671 nm and all these three peaks enhanced with the increase of DSS concentration in the range of 0.04-2.5 microg ml(-1) and the detection limit for the three single peaks was 0.024, 0.027, and 0.027 microg ml(-1), respectively, whereas that of the TWO-RRS method was 0.013 microg ml(-1). The TWO-RRS method was found to have much better flexibility and high sensitivity than the single-wavelength method. In this paper, the interaction conditions were optimized. The affecting factors and characteristics of RRS for the interaction of DSS with CV were investigated and a sensitive method for the determination of trace amounts of DSS using the TWO-RRS method was developed.