Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster.

The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.

Organosulfur Materials for Rechargeable Batteries: Structure, Mechanism, and Application.

Lithium-ion batteries have received significant attention over the last decades due to the wide application of portable electronics and increasing deployment of electric vehicles. In order to further enhance the performance of the batteries and overcome the capacity limitations of inorganic electrode materials, it is imperative to explore new cathode and functional materials for rechargeable lithium batteries. Organosulfur materials containing sulfur-sulfur bonds as a kind of promising organic electrode materials have the advantages of high capacities, abundant resources, tunable structures, and environmental benignity. In addition, organosulfur materials have been widely used in almost every aspect of rechargeable batteries because of their multiple functionalities. This review aims to provide a comprehensive overview on the development of organosulfur materials including the synthesis and application as cathode materials, electrolyte additives, electrolytes, binders, active materials in lithium redox flow batteries, and other metal battery systems. We also give an in-depth analysis of structure-property-performance relationship of organosulfur materials, and guidance for the future development of organosulfur materials for next generation rechargeable lithium batteries and beyond.

Metabolomics efficiently discriminates monozygotic twins in peripheral blood.

Monozygotic (MZ) twins cannot be distinguished using conventional forensic STR typing because they present identical STR genotypings. However, MZ twins do not always live in the same environment and often have different dietary and other lifestyle habits. Metabolic profiles are deyermined by individual characteristics and are also influenced by the environment in which they live. Therefore, they are potential markers capable of identifying MZ twins. Moreover, the production of proteins varies from organism to organism and is influenced by both the physiological state of the body and the external environment. Hence, we used metabolomics and proteomics to identify metabolites and proteins in peripheral blood to discriminate MZ twins. We identified 1749 known metabolites and 622 proteins in proteomic analysis. The metabolic profiles of four pairs of MZ twins revealed minor differences in intra-MZ twins and major differences in inter-MZ twins. Each pair of MZ twins exhibited distinct characteristics, and four metabolites-methyl picolinate, acesulfame, paraxanthine, and phenylbenzimidazole sulfonic acid-were observed in all four MZ twin pairs. These four differential exogenous metabolites conincidently show that the different external environments and life styles can be well distinguished by metabolites, considering that twins do not all have the same eating habits and living environments. Moreover, MZ twins showed different protein profiles in serum but not in whole blood. Thus, our results indicate that differential metabolites provide potential biomarkers for the personal identification of MZ twins in forensic medicine.

Synchronously Improved Multiple Afterglow and Phosphorescence Efficiencies in 0D Hybrid Zinc Halides with Ultrahigh Anti-Water Stabilities.

Zero-dimensional (0D) hybrid metal halides have been emerged as room-temperature phosphorescence (RTP) materials, but synchronous optimization of multiple phosphorescence performance in one structural platform remains less resolved, and stable RTP activity in aqueous medium is also unrealized due to serious instability toward water and oxygen. Herein, we demonstrated a photophysical tuning strategy in a new 0D hybrid zinc halide family of (BTPP)2ZnX4 (BTPP = benzyltriphenylphosphonium, X = Cl and Br). Infrequently, the delicate combination of organic and inorganic species enables this family to display multiple ultralong green afterglow and efficient self-trapped exciton (STE) associated cyan phosphorescence. Compared with inert luminescence of [BTPP]+ cation, incorporation of anionic [ZnX4]2- effectively enhance the spin-orbit coupling effect, which significantly boosts the photoluminescence quantum yield (PLQY) up to 30.66% and 54.62% for afterglow and phosphorescence, respectively. Synchronously, the corresponding luminescence lifetime extend to 143.94 ms and 0.308 µs surpassing the indiscernible phosphorescence of [BTPP]X salt. More importantly, this halide family presents robust RTP emission with nearly unattenuated PLQY in water and harsh condition (acid and basic aqueous solution) over half a year. The highly efficient integrated afterglow and STE phosphorescence as well as ultrahigh aqueous state RTP realize multiple anti-counterfeiting applications in wide chemical environments.

Infliximab Inhibits Colitis Associated Cancer in Model Mice by Downregulating Genes Associated with Mast Cells and Decreasing Their Accumulation.

Inflammatory bowel diseases (IBDs), such as Crohn's disease or ulcerative colitis, can be treated with anti TNF-alpha (TNF-α) antibodies (Abs), but they also put patients with IBDs at risk of cancer. We aimed to determine whether the anti TNF-α Ab induces colon cancer development in vitro and in vivo, and to identify the genes involved in colitis-associated cancer. We found that TNF-α (50 ng/mL) inhibited the proliferation, migration, and invasion of HCT8 and COLO205 colon cancer cell lines and that anti TNF-α Ab neutralized TNF-α inhibition in vitro. The effects of anti TNF-α Ab, infliximab (10 mg/kg) were investigated in mouse models of colitis-associated cancer induced by intraperitoneally injected azoxymethane (AOM: 10 mg/kg)/orally administered dextran sodium sulfate (DSS: 2.5%) (AOM/DSS) in vivo. Infliximab significantly attenuated the development of colon cancer in these mice. Microarray analyses and RT-qPCR revealed that mast cell protease 1, mast cell protease 2, and chymase 1 were up-regulated in cancer tissue of AOM/DSS mice; however, those mast cell related genes were downregulated in cancer tissue of AOM/DSS mice with infliximab. These results suggested that mast cells play a pivotal role in the development of cancer associated with colitis in AOM/DSS mice.

Nuclear DNA replicates during zygote development in Arabidopsis and Torenia fournieri.

The progression of the cell cycle is continuous in most cells, but gametes (sperm and egg cells) exhibit an arrest of the cell cycle to await fertilization to form a zygote, which then continues through the subsequent phases to complete cell division. The phase in which gametes of flowering plants arrest has been a matter of debate, since different phases have been reported for the gametes of different species. In this study, we reassessed the phase of cell-cycle arrest in the gametes of two species, Arabidopsis (Arabidopsis thaliana) and Torenia fournieri. We first showed that 4', 6-diamidino-2-phenylindole staining was not feasible to detect changes in gametic nuclear DNA in T. fournieri. Next, using 5-ethynyl-2'-deoxyuridine (EdU) staining that detects DNA replication by labeling the EdU absorbed by deoxyribonucleic acid, we found that the replication of nuclear DNA did not occur during gamete development but during zygote development, revealing that the gametes of these species have a haploid nuclear DNA content before fertilization. We thus propose that gametes in the G1 phase participate in the fertilization event in Arabidopsis and T. fournieri.

A competitive PCR-based method to detect a single copy of T-DNA insertion in transformants.

Gene function studies benefit from the availability of mutants. In plants, Agrobacterium-mediated genetic transformation is widely used to create mutants. These mutants, also called transformants, contain one or several transfer-DNA (T-DNA) copies in the host genome. Quantifying the copy number of T-DNA in transformants is beneficial to assess the number of mutated genes. Here, we developed a competitive polymerase chain reaction (PCR)-based method to detect a single copy of a T-DNA insertion in transformants. The competitor line BHK- -1 that contains a single copy of competitor BHK- (BHK, Basta, Hygromycin, Kanamycin-resistant genes) was crossed with test transformants and the genomic DNA of F1 plants was subjected to competitive PCR. By analyzing the gray ratio between two PCR products, we were able to determine whether or not the test transformants contained a single copy of T-DNA insertion. We also generated the control lines BHK±1:1 and BHK±2:1 , which contain the target (BHK+ ) and competitor (BHK- ) in a ratio of 1:1 and 2:1, respectively. The ratios of their PCR products are useful references for quantitative analysis. Overall, this method is reliable and simple in experimental manipulations and can be used as a substitute for Southern-blot analysis to identify a single copy of T-DNA insertion in transformants.

SAGD: a comprehensive sex-associated gene database from transcriptomes.

Many animal species present sex differences. Sex-associated genes (SAGs), which have female-biased or male-biased expression, have major influences on the remarkable sex differences in important traits such as growth, reproduction, disease resistance and behaviors. However, the SAGs resulting in the vast majority of phenotypic sex differences are still unknown. To provide a useful resource for the functional study of SAGs, we manually curated public RNA-seq datasets with paired female and male biological replicates from the same condition and systematically re-analyzed the datasets using standardized methods. We identified 27,793 female-biased SAGs and 64,043 male-biased SAGs from 2,828 samples of 21 species, including human, chimpanzee, macaque, mouse, rat, cow, horse, chicken, zebrafish, seven fly species and five worm species. All these data were cataloged into SAGD, a user-friendly database of SAGs (http://bioinfo.life.hust.edu.cn/SAGD) where users can browse SAGs by gene, species, drug and dataset. In SAGD, the expression, annotation, targeting drugs, homologs, ontology and related RNA-seq datasets of SAGs are provided to help researchers to explore their functions and potential applications in agriculture and human health.

Organosulfides: An Emerging Class of Cathode Materials for Rechargeable Lithium Batteries.

Lithium-ion batteries have received significant attention over the last decades due to the wide application of portable electronics and increasing deployment of electric vehicles. In order to further increase the energy density of batteries and overcome the capacity limitations (<250 mAh g-1) of inorganic cathode materials, it is imperative to explore new cathode materials for rechargeable lithium batteries. Organic compounds including organic carbonyl, radicals, and organosulfides are promising as they have advantages of high capacities, abundant resources, and tunable structures. In the 1980s, a few organosulfides, in particular organodisulfides, as cathode materials were studied to a certain extent in rechargeable lithium batteries. However, they showed low capacities and poor cycling performance, which made them unappealing then in comparison to transition metal oxide cathode materials. As a result, organosulfides have not been extensively studied like other cathode materials including organic carbonyls and radicals. In recent years, organosulfides with long sulfur chains (e.g., trisulfide, tetrasulfide, pentasulfide, etc.) in the structures have been receiving more attention in conjunction with the development of lithium-sulfur batteries. As a major class of sulfur derivatives, they have versatile structures and unique properties in comparison with elemental sulfur. In this Account, we first generalize the working principles of organosulfides in lithium batteries. We then discuss organosulfide molecules, which have precise lithiation sites and tunable capacities. The organic functional groups can provide additional benefits, such as discharge voltage and energy efficiency enhancement by phenyl groups and cycling stability improvement by N-heterocycles. Furthermore, replacing sulfur by selenium in these compounds can improve their electrochemical properties due to the high electronic conductivity and low bond energy associated with selenium. We list organosulfide polymers consisting of phenyl rings, N-heterocycles, or aliphatic segments. Organosulfides as electrolyte additives or components for forming a solid-electrolyte interphase layer on lithium metal anode are also presented. Carbon materials such as carbon nanotubes and reduced graphene oxide can enhance the battery performance of organosulfide cathodes. We discuss the synthesis methods for polysulfide molecules and polymers. Finally, we show the advantages of organosulfides over sulfur as cathode materials in lithium batteries. This Account provides a summary of recent development, in-depth analysis of structure-performance relationship, and guidance for future development of organosulfides as promising cathode materials for next generation rechargeable lithium batteries.

Tin(ii)-catalyzed dehydrative cross-coupling of 2H-chromene hemiacetals with ketones.

A dehydrative cross-coupling of 2H-chromene hemiacetals with ketones is described. Without the derivatization of 2H-chromene hemiacetals to 2H-chromene acetals, the direct C-OH/C-H coupling reaction has been accomplished with water as the only by-product. With the use of Sn(OTf)2 as the promoter, the reaction goes smoothly under mild conditions.

The TRiC/CCT Chaperonin and Its Role in Uncontrolled Proliferation.

The cell cycle is a sophisticated space-time regulated mechanism where a wide variety of protein modules and complexes associate functioning in a concerted manner to regulate and transfer the genetic material to daughter cells. CCT (chaperonin containing TCP-1, also known as TRiC) is a molecular machine that forms a high molecular weight complex (1000 KDa). CCT is emerging as a key molecule during mitosis due to its essential role in the folding of many important proteins involved in cell division (Cdh1, Plk1, p27, Cdc20, PP2a regulatory subunits, tubulin or actin) suggesting its involvement in uncontrolled proliferation. The assembly is formed by eight different subunits called CCTα, ß, γ, δ, ε, ζ, η and θ in mammals corresponding to CCT1-8 in yeast. CCT/TRiC is organized in a unique intra- and inter-ring arrangement. The chaperonin monomers share a common domain structure including an equatorial domain, which contains all the inter-ring contacts, most of the intra-ring contacts and the ATP binding site, whose binding and hydrolysis triggers the conformational changes that take place during the functional cycle. All chaperonins display an open substrate-receptive conformation, where the unfolded protein is recognized and trapped, and a closed conformation where the substrate is isolated from the bulk of the intracellular environment. In this chapter we discuss the complex set of intra- and inter-ring allosteric signals during chaperonin function.

Worldwide tendency and perspectives in traumatic dental injuries: A bibliometric analysis over two decades (1999-2018).

BACKGROUND/AIMS: Traumatic dental injuries (TDIs) are considered to be a public dental health problem worldwide. The aim of the current study was to provide the worldwide tendency and perspectives in TDIs in the last two decades via bibliometric analysis. METHODS: ''Tooth injuries'' was searched as the Medical Subject Headings term within PubMed with the date range from 1999 to 2018. Two investigators perused information in the articles according to the inclusion and exclusion criteria. The articles were independently categorized according to the following aspects: (a) annual scholarly output; (b) leading countries or regions; (c) leading journals; (d) productive authors; (e) citations; (f) study design; (f) distribution of topics; and (g) the type of dentition and TDIs. VOSviewer 1.6.7 and Citespace 5.2 were used for analyzing and visualizing bibliometric networks. RESULTS: A total of 2627 articles about traumatic dental injuries were published and indexed in PubMed during the two decades, and the number of publications on traumatic dental injuries was rising in general. The research outputs were mainly concentrated in developed countries and affiliated hospitals of universities. Brazil was the most productive country. The journal Dental Traumatology had the most contributions to the scientific research of traumatic dental injuries. "Case report" was the most frequent type of article (36.50%), followed by cross-sectional studies (19.57%) and case-control studies (13.67%). Most studies focused on the treatment of TDIs (38.94%), especially for avulsion (21.01%), crown fracture (9.71%), and intrusion (5.25%). Permanent teeth (66%) were the dominant dentition. CONCLUSION: There is a lack of high-quality well-designed studies such as cohort studies. The number of publications on prevention and the primary dentition is disproportionate in relation to their significance.

Changes in mitochondrial DNA levels during early embryogenesis in Torenia fournieri and Arabidopsis thaliana.

Changes in the amount of mitochondrial DNA (mtDNA) have never been investigated in plant zygotes or early plant embryos due to the difficulty in isolating these cells, although such changes have been investigated in mammalian embryos. Using the single-cell quantitative real-time polymerase chain reaction (PCR) and laser confocal microscopy, we surveyed the changes in mtDNA levels during early embryogenesis in Torenia fournieri and Arabidopsis thaliana. In contrast with the amount of mtDNA in early mammalian embryos, which does not change, we found that mtDNA doubling occurred during zygotic development in T. fournieri and during two-cell proembryo development in A. thaliana. These findings reveal that mtDNA doubling occurs during early embryogenesis in T. fournieri and A. thaliana, indicating that the dynamics of mtDNA in early plant embryos differs from that in early mammalian embryos.

TADEA-PCR is a highly efficient method of amplifying unknown flanking fragments of T-DNA transformants.

Forward genetic analysis, widely used to find new gene functions, benefits from the availability of mutants. At present, based on Agrobacterium-mediated plant transformation technology, many transfer (T)-DNA transformants have been created. However, cloning their T-DNA insertion sites, which enables identification of the mutated genes, is still challenging. In this study, we improved adapter ligation-mediated polymerase chain reaction (A-PCR), which mainly utilizes the Thermal Asymmetric interlaced reaction and Degenerate sequence-recognizing restriction Endonucleases (TADE). Using the new method TADE-mediated A-PCR (TADEA-PCR), we successfully cloned 22 of all the 24 junction sites in 10 Arabidopsis thaliana L. transformants that contained 12 T-DNA insertions in total, giving a success rate of 91.7%. In most cases, the two junction sites resulting from a single T-DNA insertion were simultaneously cloned. In addition, TADEA-PCR was able to clone more than two junction sites present in one transformant containing several T-DNA insertions. Overall, TADEA-PCR is a powerful technique for cloning T-DNA insertion sites.

Maribacter marinus sp. nov. isolated from a deep-sea seamount.

A Gram-stain negative, rod-shaped, aerobic strain, designated YC973T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain YC973T is related to the genus Maribacter and has high 16S rRNA gene sequence similarity to Maribacter orientalis KMM 3947T (97.6%). The predominant cellular fatty acids were iso-C15:0, iso-C15:1 G and an unidentified fatty acid of equivalent chain-length 13.565. The polar lipid profile contained phosphatidylethanolamine and five unidentified lipids. The genomic DNA G+C content of strain YC973T was 36.1 mol%. On the basis of the evidence presented in this study, strain YC973T represents a novel species of the genus Maribacter, for which we propose the name Maribacter marinus sp. nov. (type strain YC973T = KACC 19025T = CGMCC 1.16328T).

Mesoflavibacter profundi sp. nov. Isolated from a Deep-Sea Seamount.

The Gram-stain-negative, rod-shaped, aerobic strain, designated YC1039T, was isolated from a seamount northern Mariana Trench in the tropical western Pacific. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain YC1039T was related to the genus Mesoflavibacter and had highest 16S rRNA gene sequence similarities to Mesoflavibacter sabulilitoris GJMS-9T (98.3%) and Mesoflavibacter zeaxanthinifaciens TD-ZX30T (98.2%). The predominant cellular fatty acids were iso-C15:1 G and iso-C15:0. The polar lipid profile contained phosphatidylethanolamine, two unidentified phospholipids, and 13 unidentified lipids. The respiratory quinone was MK-6. The genomic DNA G+C content of strain YC1039T was 29.8 mol%. On the basis of the evidence presented in this study, strain YC1039T represents a novel species of the genus Mesoflavibacter, for which we propose the name Mesoflavibacter profundi sp. nov. (type strain YC1039T = KACC 19026T = CGMCC 1.16329T).

Elevation of Pollen Mitochondrial DNA Copy Number by WHIRLY2: Altered Respiration and Pollen Tube Growth in Arabidopsis.

In plants, the copy number of the mitochondrial DNA (mtDNA) can be much lower than the number of mitochondria. The biological significance and regulatory mechanisms of this phenomenon remain poorly understood. Here, using the pollen vegetative cell, we examined the role of the Arabidopsis (Arabidopsis thaliana) mtDNA-binding protein WHIRLY2 (AtWHY2). AtWHY2 decreases during pollen development, in parallel with the rapid degradation of mtDNA; to examine the importance of this decrease, we used the pollen vegetative cell-specific promoter Lat52 to express AtWHY2. The transgenic plants (LWHY2) had very high mtDNA levels in pollen, more than 10 times more than in the wild type (ecotype Columbia-0). LWHY2 plants were fertile, morphologically normal, and set seeds; however, reciprocal crosses with heterozygous plants showed reduced transmission of LWHY2-1 through the male and slower growth of LWHY2-1 pollen tubes. We found that LWHY2-1 pollen had significantly more reactive oxygen species and less ATP compared with the wild type, indicating an effect on mitochondrial respiration. These findings reveal that AtWHY2 affects mtDNA copy number in pollen and suggest that low mtDNA copy numbers might be the normal means by which plant cells maintain mitochondrial genetic information.

Synthesis, crystal structures, and antibacterial evaluation of metal complexes based on functionalized 2-phenylquinoline derivatives.

A series of dinuclear paddle-wheel like transition metal complexes based on 2-phenylquinoline-4-carboxylic derivative L have been synthesized and characterized by IR, elemental analysis, and X-ray diffraction single crystal analysis. The biological activities of L and its complexes were evaluated as assayed antibacterial activities, including Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. The results indicated that these complexes showed better antibacterial activities than the free ligand or metal salts alone. Among them, the Zn(II) and Cd(II) complexes with IC50 of 0.57 µg/mL and 0.51 µg/mL, respectively, showed excellent antibacterial activity against Staphylococcus aureus.

Dexamethasone-Loaded Lipid Calcium Phosphate Nanoparticles Treat Experimental Colitis by Regulating Macrophage Polarization in Inflammatory Sites.

Background: The M1/M2 polarization of intestinal macrophages exerts an essential function in the pathogenesis of ulcerative colitis (UC), which can be adjusted to alleviate the UC symptoms. Purpose: A kind of pH-sensitive lipid calcium phosphate core-shell nanoparticles (NPs), co-loading with dexamethasone (Dex) and its water-soluble salts, dexamethasone sodium phosphate (Dsp), was constructed to comprehensively regulate macrophages in different states towards the M2 phenotype to promote anti-inflammatory effects. Methods: Dex and Dsp were loaded in the outer lipid shell and inner lipid calcium phosphate (Cap) core of the LdCaPd NPs, respectively. Then, the morphology of NPs and methods for determining drug concentration were investigated, followed by in vitro protein adsorption, stability, and release tests. Cell experiments evaluated the cytotoxicity, cellular uptake, and macrophage polarization induction ability of NPs. The in vivo distribution and anti-inflammatory effect of NPs were evaluated through a 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced BALB/c mice ulcerative colitis model. Results: The LdCaPd NPs showed a particle size of about 200 nm and achieved considerable loading amounts of Dex and Dsp. The in vitro and in vivo studies revealed that in the acidic UC microenvironment, the cationic lipid shell of LdCaPd underwent protonated dissociation to release Dex first for creating a microenvironment conducive to M2 polarization. Then, the exposed CaP core was further engulfed by M1 macrophages to release Dsp to restrict the pro-inflammatory cytokines production by inhibiting the activation and function of the nuclear factor kappa-B (NF-κB) through activating the GC receptor and the NF kappa B inhibitor α (I-κBα), respectively, ultimately reversing the M1 polarization to promote the anti-inflammatory therapy. Conclusion: The LdCaPd NPs accomplished the sequential release of Dex and Dsp to the UC site and the inflammatory M1 macrophages at this site, promoting the regulation of macrophage polarization to accelerate the remission of UC symptoms.