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Summary Whole-genome sequencing (WGS), a powerful tool for detecting novel coding and non-coding disease-causing variants, has largely been applied to clinical diagnosis of inherited disorders. Here we leveraged WGS data in up to 62,653 ethnically diverse participants from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and assessed statistical association of variants with seven red blood cell (RBC) quantitative traits. We discovered 14 single variant-RBC trait associations at 12 genomic loci, which have not been reported previously. Several of the RBC trait-variant associations (RPN1, ELL2, MIDN, HBB, HBA1, PIEZO1, and G6PD) were replicated in independent GWAS datasets imputed to the TOPMed reference panel. Most of these discovered variants are rare/low frequency, and several are observed disproportionately among non-European Ancestry (African, Hispanic/Latino, or East Asian) populations. We identified a 3 bp indel p.Lys2169del (g.88717175_88717177TCT[4]) (common only in the Ashkenazi Jewish population) of PIEZO1, a gene responsible for the Mendelian red cell disorder hereditary xerocytosis (MIM: 194380 ), associated with higher mean corpuscular hemoglobin concentration (MCHC). In stepwise conditional analysis and in gene-based rare variant aggregated association analysis, we identified several of the variants in HBB, HBA1, TMPRSS6, and G6PD that represent the carrier state for known coding, promoter, or splice site loss-of-function variants that cause inherited RBC disorders. Finally, we applied base and nuclease editing to demonstrate that the sentinel variant rs112097551 (nearest gene RPN1) acts through a cis-regulatory element that exerts long-range control of the gene RUVBL1 which is essential for hematopoiesis. Together, these results demonstrate the utility of WGS in ethnically diverse population-based samples and gene editing for expanding knowledge of the genetic architecture of quantitative hematologic traits and suggest a continuum between complex trait and Mendelian red cell disorders.

Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.

Polyurethane, as a rubber material, can relieve the load on the ground and provide seismic design for the venue, which is of great significance for sports venues. In order to improve the seismic resistance and abrasion resistance of materials for sports fields and reduce accidents in sports, this article has carried out research on the polyurethane elastomer layered nanocomposites for sports fields and their preparation. Today’s world is a challenging era of science and technology. The fields of biotechnology, information, medicine, energy, environment, and national defense and security are closely related to the development of high tech, and the requirements for materials are becoming increasingly diversified. Polymer nanocomposite coating has the dual characteristics of organic and inorganic components. It not only retains the advantages of a polymer but also endows it with versatility. It meets the current application needs. It is a hot spot in today’s research. Among them, there are two major problems in the composite process of nanomaterials and polymers: dispersion and compatibility. How to improve the dispersion of nanoparticles and enhance the compatibility between nanoparticles and polymers is an urgent problem to be solved. In the method part, this article introduces a small amount of polyurethane and polyurethane elastomers formed after polyurethane modification and introduces layered compounds and nanocomposites and introduces several models involved in nanomaterials in terms of algorithms. In the analysis part, this paper conducts a comprehensive analysis of the hard segment mass fraction, mechanical properties, thermal decomposition behavior, degradation mechanism, and dynamic mechanical properties. With the increase of GO content, the tensile strength increases significantly and the elongation at break becomes smaller and smaller. When the GO content increases from 0% to 2%, the tensile properties of the WPU film increase from 2.6 MPa to 7.9 MPa and the fracture of the elongation decreased from 201.7% to 62.8%. This shows that the increase in GO content will make the composite material harder and brittle. It can be seen from the experimental results that the preparation of the polyurethane elastomer layered nanocomposite material designed in this paper has a good application effect on sports venues.

During the 29th Chinese National Antarctic Research Expedition, spatial variations in nitrogen isotopic composition of particulate nitrogen (δ15NPN) and their controlling factors were examined in detail with regard to nitrate drawdown by phytoplankton and particulate nitrogen (PN) remineralization in the Prydz Bay and its adjacent areas. To better constrain the nitrogen transformations, the physical and chemical parameters, including temperature, salinity, nutrients, PN and δ15NPN in seawater column were measured from surface to bottom. In addition, the nitrogen isotopic fractionation factor of nitrate assimilation by phytoplankton in the mixed layer, and the nitrogen isotopic fractionation factor of PN remineralization below the mixed layer were estimated using Rayleigh model and Steady State model, respectively. Our results showed that suspended particles had its lowest δ15NPN in the surface layer, which was due to the preferential assimilation of 14N in nitrate by phytoplankton. The δ15NPN in the mixed layer of the Prydz Bay and its adjacent areas decreased from the inner shelf to the outer basin, ascribing to the effect of isotope fractionation during phytoplankton assimilation. In mixed layer, the spatial distribution of δ15NPN associated with particulate organic matter (POM) production can be well interpreted according to Rayleigh model and Steady State model. The nitrogen isotope fractionation factor during phytoplankton assimilating nitrate was estimated as 10.0%o by Steady State model, which was more reasonable than that calculated by Rayleigh model. These results validate the previous reports of fractionation factor during nitrate assimilation by phytoplankton. Increasing δ15NPN with depth below the euphotic zone correlated with the decreasing PN contents, and it was attributed to preferential remineralization of 14N in PN by bacteria. In subsurface and deep layer, the δ15NPN distributions also conformed to Rayleigh model and Steady State model during PN remineralization, with a fractionation factor of about 3.6% and 3.2%, respectively. It is the first time to estimate the fractionation factor during POM production and remineralization in the Prydz Bay and its adjacent areas. Such fractionation may provide a useful tool for the follow-up study of the nitrogen dynamics in the Southern Ocean.

Genome-wide association studies (GWAS) have identified multiple genomic loci linked to blood cell traits, however understanding the biological relevance of these genetic loci has proven to be challenging. Here, we performed a transcriptome-wide association study (TWAS) integrating gene expression and splice junction usage in neutrophils (N = 196) with a neutrophil count GWAS (N = 173,480 individuals). We identified a total of 174 TWAS-significant genes enriched in target genes of master transcription factors governing neutrophil specification. Knockout of a TWAS candidate at chromosome 5q13.2, TAF9, in CD34+ hematopoietic and progenitor cells (HSPCs) using CRISPR/Cas9 technology showed a significant effect on neutrophil production in vitro. In addition, we identified 89 unique genes significant only for splice junction usage, thus emphasizing the importance of alternative splicing beyond gene expression underlying granulopoiesis. Our results highlight the advantages of TWAS, followed by gene editing, to determine the functions of GWAS loci implicated in hematopoiesis., Yao Yao et al. perform transcriptome-wide association analysis through integration of gene expression data and results of a previously-published genome-wide association study for neutrophil count. They find 34 independent genomic regions associated with expression changes and show that knockout of one candidate gene, TAF9, in CD34+ progenitor cells increases neutrophil maturation in vitro.

Microbe-assisted phytoremediation provides an eco-friendly and cost-effective approach to reclaim Cd- and Pb-contaminated soils. In this work, incubation and pot experiments were established to investigate the effect of Streptomyces pactum (Act12) combined with compost on soil physicochemical properties, enzymatic activities, and thereby acted on phytoextraction of Cd and Pb by using potherb mustard (Brassica juncea Coss.). The addition of Act12 and compost increased EC (7.2%), available phosphorus (P) (14.9%), available potassium (K) (17.0 folds), DOC (37.7%), OM (2.8 folds), urease (49.8%), dehydrogenase (2.2 folds), and alkaline phosphatase (23.0 folds) of soil, while reduced pH (7.7%) compared with control. Significant decrease of available Cd and Pb uptake was observed after adding compost and Act12 by 29.1% and 32.2%. Presence of compost and Act12 enhanced the biomass by 3.98 folds and 1.83 folds in shoots and roots of plant. Results showed the assimilation of Cd and Pb in shoots was increased by 103.8% and 48.7% due to the increased of biomass. Meanwhile, the rhizosphere effect of soil microorganisms increased the uptake of Cd (60.4%) and Pb (19.2%) in roots. These findings suggested that Act12 joined with compost-strengthened potherb mustard phytoremediation of Cd- and Pb-polluted soils, which may provide new insights into the clean-up of mining-contaminated soils in field practice.

Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to permanently remedy blood disorders, although its application in engrafting hematopoietic stem cells (HSCs) remains unexplored. In this study, we purified A3A (N57Q)-BE3 base editor for ribonucleoprotein (RNP) electroporation of human-peripheral-blood-mobilized CD34+ hematopoietic stem and progenitor cells (HSPCs). We observed frequent on-target cytosine base edits at the BCL11A erythroid enhancer at +58 with few indels. Fetal hemoglobin (HbF) induction in erythroid progeny after base editing or nuclease editing was similar. A single therapeutic base edit of the BCL11A enhancer prevented sickling and ameliorated globin chain imbalance in erythroid progeny from sickle cell disease and β-thalassemia patient-derived HSPCs, respectively. Moreover, efficient multiplex editing could be achieved with combined disruption of the BCL11A erythroid enhancer and correction of the HBB −28A>G promoter mutation. Finally, base edits could be produced in multilineage-repopulating self-renewing human HSCs with high frequency as assayed in primary and secondary recipient animals resulting in potent HbF induction in vivo. Together, these results demonstrate the potential of RNP base editing of human HSPCs as a feasible alternative to nuclease editing for HSC-targeted therapeutic genome modification. A single therapeutic base edit of the BCL11A enhancer in human HSPCs can ameliorate cellular defects associated with sickle cell disease and β-thalassemia in vitro and efficiently induce fetal hemoglobin expression upon engraftment in mice in vivo.

Significance STAT3 (signal transducer and activator of transcription 3) is a master transcription factor that organizes cellular responses to cytokines and growth factors and is implicated in inflammatory disorders. STAT3 is a well-recognized therapeutic target for human cancer and inflammatory disorders, but how its function is regulated in a cell type–specific manner has been a major outstanding question. We discovered that Stat3 imposes self-directed regulation through controlling transcription of its own regulator homeodomain-interacting protein kinase 2 ( Hipk2 ) in a T helper 17 (Th17) cell–specific manner. Our validation of the functional importance of the Stat3–Hipk2 axis in Th17 cell development in the pathogenesis of T cell–induced colitis in mice suggests an approach to therapeutically treat inflammatory bowel diseases that currently lack a safe and effective therapy.

Recurrent spontaneous abortion (RSA) is a gestational disease with complex pathogenesis, and trophoblast cells are closely involved in the pathogenesis of RSA. This study aimed to explore the regulatory effects and mechanisms of SNHG6 on trophoblast cells. The expression of SNHG6, miR-101-3p, and OTUD3 were detected in villous tissues from patients with unexplained RSA and normal pregnant women with induced abortion by qRT-PCR. The target relationships between miR-101-3p and SNHG6/OTUD3 were confirmed by dual-luciferase reporter assay. The viability, migration, and apoptosis of trophoblast cells were measured by MTT, wound healing, and flow cytometry assays, respectively. Western blot was performed to detect the protein expression of OTUD3, Ki-67, Bax, and Bcl-2. The results showed that SNHG6 and OTUD3 were up-regulated, and miR-101-3p was down-regulated in RSA patients. MiR-101-3p was a target of SNHG6, and OTUD3 was a target of miR-101-3p. There were negative correlations between the expression of miR-101-3p and OTUD3/SNHG6 in RSA patients. In addition, both SNHG6 silencing and miR-101-3p overexpression could increase cell viability and migration, decrease cell apoptosis, up-regulate Ki-67 and Bcl-2, and down-regulate Bax in HTR-8/SVneo cells. The effects of SNHG6 silencing on HTR-8/SVneo cells were reversed by miR-101-3p silencing or OTUD3 overexpression. To sum up, silencing of SNHG6 enhanced the viability and migration, and inhibited the apoptosis of trophoblast cells through regulating miR-101-3p/OTUD3. SNHG6/miR-101-3p/OTUD3 may be potential targets for the prevention of unexplained RSA.

Soil potentially toxic metals (PTMs) pollution caused by anthropogenic activities has become serious concern with respect to the crop safety production. In this study, an emerging biochar derived from kiwi pruning branches waste was employed as amendment aiming to evaluate its remediation potential on smelter- and mining-contaminated soils. The effect of biochar on the soil physicochemical properties, leachability, and chemical fractions acted on stabilization practice of PTMs in soil was investigated. The results showed that the addition of biochar increased the soil pH, cation exchange capacity, organic matter, and enzymatic activities (dehydrogenase, urease, and sucrase) but reduced the extraction toxicity of PTMs in both smelter (Fengxian, FX) and mining (Tongguan, TG) soils. The fraction analysis showed that the maximum reduction of exchangeable fraction of Cd, Zn, and Pb in the 4% biochar amended soils decreased by 11.1, 13.3, and 24.7% in FX soil and 7.67, 22.8, and 7.89% in TG soil, respectively, in comparison with to control (no biochar added). Additionally, the residual fraction of Cd, Zn, and Pb increased by 55.9, 7.14, and 11.0% in FX soil and 23.7, 5.86, and 10.0% in TG soil, respectively. The further greenhouse experiment showed that the Indian mustard (Brassica juncea) production increased with the increasing application dosages of biochar, while the PTMs uptakes in plant notably decreased after amendments. Conversion of kiwi pruning branches waste into emerging biochar benefits the agricultural waste recycling utilization and enhances PTMs-contaminated soil remediation in practice. Graphical abstract.

Photocatalytic hydrogen evolution from water is a valid method to face the challenge of energy shortage. TiO2, as the most well-known and investigated semiconductor photocatalyst, has been extensively applied in this field. However, the hydrogen evolution performance of TiO2 suffer from low efficiency due to the high combination of photo-induced carries and the narrow light utilization range resulting from wide band gap. In this work, we use the commercial TiO2 (P25) and fullerene (C60) as precursors to construct an efficient photocatalyst via a mild mixed method. The introduction of C60 not only effectively broaden light absorption, but also suppressed the recombination of photo-generated carriers on TiO2. The photocatalytic water splitting property of the optimum sample achieve 597.2 μmol g−1 h−1, which is 31 times higher than pure P25.

The conversion of the normal cellular prion protein (PrPC) to the misfolded pathogenic scrapie prion protein (PrPSc) is the biochemical hallmark of prion replication. So far, various chemical compounds that inhibit this conformational conversion have been identified. Here, we report the novel anti-prion activity of SGI-1027 and its meta/meta analogue (M/M), previously known only as potent inhibitors of DNA methyltransferases (DNMTs). These compounds effectively decreased the level of PrPSc in cultured cells with permanent prion infection, without affecting PrPC at the transcriptional or translational levels. Furthermore, SGI-1027 prevented effective prion infection of the cells. In a PrP aggregation assay, both SGI-1027 and M/M blocked the formation of misfolded PrP aggregates, implying that binding of these compounds hinders the PrP conversion process. A series of binding and docking analyses demonstrated that both SGI-1027 and M/M directly interacted with the C-terminal globular domain of PrPC, but only SGI-1027 bound to a specific region of PrPC with high affinity, which correlates with its potent anti-prion efficacy. Therefore, we report SGI-1027 and related compounds as a novel class of potential anti-prion agents that preferentially function through direct interaction with PrPC., Graphical abstract A novel activity of DNMT inhibitor SGI-1027 was discovered to suppress the pathogenic process of prion. The direct binding of SGI-1027 to prion protein with a normal conformation was discovered to suppress the formation of misfolded prion proteins.Image 1

We assessed the efficacy of Ca-bentonite (CB) alone and combined with Ca-hydroxide (CH), tobacco biochar (TB), and zeolite (ZL) aiming to immobilize Cu and Pb and decrease their bioavailability and uptake by pak choi followed by maize in a mining contaminated soil. The CB alone was able to decrease the availability and uptake of Cu and Pb by pak choi and maize. The mono- and multi-combination of CH, TB, and ZL with CB showed contradictory impact on the availability and uptake of Cu and Pb as compared to the mono-application of CB. The combination of CB with ZL and CH + ZL reduced the uptake of Pb by pak choi and maize, while the combination of CB with TB and ZL reduced the uptake of Cu by pak choi and maize as compared to the mono-application of CB. The co-application of CB with CH increased the phytoextraction of Cu by maize and Pb by pak choi shoots as compared to the mono-application of CB. We conclude that modified clays such as CB alone or combined with ZL, TB, and/or CH might be suitable candidates for phytomanagement of Cu and Pb contaminated soils.

Thermal conversion of phytoremediation plant waste into biochar was performed as a safe approach for organic waste management. In this work, a promising phytoremediation plant―Silphium perfoliatum L. was pyrolyzed for biochar production at 350, 550 and 750 °C. The long-term leaching risk of potentially toxic metals (PTMs) in the derived biochars and the oxidation resistance of the biochars were investigated. The results showed that PTMs in the biochar could transform into more stable and less toxic forms with the elevated pyrolysis temperature. PTMs leaching behavior in the 350 °C biochar was considerably sensitive to the leaching while that in the 750 °C biochar was not affected. The biochar produced at a higher temperature possessed a greater oxidation resistance with little amount of C loss, and the stronger oxidation resistance would prevent the release of metals bound to the organic matter. The findings of this study demonstrated that high-temperature pyrolysis was able to reduce the potential risk of PTMs and ensure carbon stability.

Due to the remoteness and difficulty of sampling, the 210Po and 210Pb data are scarce in the Southern Ocean. Here, the activity concentrations of 210Po and 210Pb around Prydz Bay in austral summer were determined to understand their spatial variation and evaluate the dynamics of particle organic matter (POM). The activity concentrations of dissolved 210Po (D210Po) and 210Pb (D210Pb) range from 0.47 to 3.20 Bq⋅m–3 and from 1.15 to 2.97 Bq⋅m–3, respectively, with the lower values in the shelf. The particulate 210Po (P210Po) and 210Pb (P210Pb) are lower in the open ocean and increase to the coastal waters, among which the circumpolar deep water (CDW) is the lowest. The activity concentration of total 210Pb (T210Pb) ranges from 1.26 Bq⋅m–3 to 3.16 Bq⋅m–3, with a higher value in CDW, which is ascribed to radiogenic production from 226Ra and subsequent lateral transport. Occasionally a high value of T210Po occurs in deep water (>3.00 Bq⋅m–3), which may be caused by the remineralization of POM. The disequilibria between T210Po and T210Pb appears throughout the water column at most stations. The average T210Po/T210Pb)A.R. in the euphotic zone is 0.66, reflecting the effect of strong particle scavenging. There is a good positive correlation between the solid-liquid ratio of 210Po and POC, while 210Pb does not, indicating that particulate organic matter regulates the biogeochemical cycle of 210Po around Prydz Bay. Based on the 210Po/210Pb disequilibria, the export flux of POC in the water column is estimated to be 0.8–31.9 mmol m–2 d–1, with the higher values in the shelf.

Chemoresistance is a common problem in cancer treatment, and circular RNA (circRNA) has been found to be associated with the progression of chemoresistance in cancer. However, the role and mechanism of circRNA centrosomal protein 128 (circ-CEP128) in the chemoresistance of cervical cancer (CC) are still unclear. The expression of circ-CEP128, microRNA (miR)-432-5p, and myeloid cell leukemia-1 (MCL1) was measured by quantitative real-time PCR. The paclitaxel resistance of cells was assessed using MTT assay. Cell proliferation, apoptosis, migration, and invasion were determined using MTT assay, colony formation assay, flow cytometry, and transwell assay. The protein levels of metastasis markers and MCL1 were examined using western blot analysis. Mice xenograft models were constructed to assess the effect of circ-CEP128 silencing on CC tumor growth and paclitaxel sensitivity. The interaction between miR-432-5p and circ-CEP128 or MCL1 was confirmed by dual-luciferase reporter assay and RIP assay. Circ-CEP128 had highly expression in CC tumor tissues and cells. Silencing of circ-CEP128 could enhance the paclitaxel sensitivity of CC cells by decreasing cell growth, migration, and invasion. Also, knockdown of circ-CEP123 reduced CC tumor growth and promoted the paclitaxel sensitivity of CC tumors. MiR-432-5p was found to be sponged by circ-CEP128, and its inhibitor could reverse the promoting function of circ-CEP128 silencing on the paclitaxel sensitivity of CC cells. Additionally, MCL1 was a target of miR-432-5p, and circ-CEP128 could sponge miR-432-5p to regulate MCL1. Besides, overexpressed MCL1 also could reverse the enhancing effect of miR-432-5p on the paclitaxel sensitivity of CC cells. In conclusion, the present study showed that circ-CEP128 silencing could increase the paclitaxel sensitivity of CC by regulating the miR-432-5p/MCL1 axis.

Drug-resistant bacterial infections have stolen the spotlight in recent years as stubborn diseases intimidating public health, thus urgently requiring the development of innovative treatment strategies with high antibacterial efficiency and low bacterial resistance. Here, a polymeric antimicrobial with synergistic chemo-photodynamic therapy function is fabricated to combat drug-resistant bacterial infections. In this strategy, polymeric micelles based on amphiphilic poly(aspartic acid)-block-poly(e-caprolactone) (PAsp-b-PCL) are used as nanocarriers to encapsulate a photosensitizer protoporphyrin IX (PpIX) in the micellar core, which then undergo silver nanoparticle decoration on the micellar shell through an in situ reduction method. Compared with mono-therapy, the combination of silver nanoparticle decoration and light-activatable PpIX enables the resulting polymeric antimicrobial to exert chemo-photodynamic activity to kill drug-resistant bacteria more potently in vitro. Furthermore, the prepared polymeric antimicrobials with synergistic antibacterial activity show robust eradication efficacy against subcutaneous infections induced by drug-resistant Staphylococcus aureus in a murine model. Therefore, our study provides a simple and potent strategy to realize combination therapy for eradicating drug-resistant bacterial infections.

Major effectors of adult-stage fetal globin silencing include the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to the γ-globin genes but rather its chromatin occupancy is solely concentrated at CHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for ZNF410’s effects on γ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. These studies identify a new rational target for HbF induction for the β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex.

Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE that interfere with neutrophil maturation. We conducted a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) that correlated ELANE mutations with neutrophil maturation potential. Highly efficient gene editing of early exons elicited nonsense-mediated decay (NMD), overcame neutrophil maturation arrest in HSPCs from ELANE-mutant SCN patients, and produced normal hematopoietic engraftment function. Conversely, terminal exon frameshift alleles that mimic SCN-associated mutations escaped NMD, recapitulated neutrophil maturation arrest, and established an animal model of ELANE-mutant SCN. Surprisingly, only -1 frame insertions or deletions (indels) impeded neutrophil maturation, whereas -2 frame late exon indels repressed translation and supported neutrophil maturation. Gene editing of primary HSPCs allowed faithful identification of variant pathogenicity to clarify molecular mechanisms of disease and encourage a universal therapeutic approach to ELANE-mutant neutropenia, returning normal neutrophil production and preserving HSPC function.

Background: Phage-host interaction is one of the essential questions in microbial environments. These interactions not only are appealing systems to study coevolution but also have been increasingly emphasized due to their roles in human health, diseases, and novel therapeutic development. Meanwhile, molecular and ecological co-evolutionary processes of phages and microbe leave signals in their genomic sequences, defined as phage-host interaction signals (PHISs) in this study, which allow us to predict microbe-phage interactions in silico . Results: We developed PHISDetector, which utilizes sophisticated bioinformatics methods to detect comprehensive in silico PHISs, including sequence composition, CRISPR targeting, prophage, and protein-protein interaction signals, further systematically integrates various categories of PHISs, and carries out machine-learning modeling to predict phage-host interactions. PHISDetector captures phage-host associations in a data-driven manner and reflects various phage-microbe interaction patterns or mechanisms so that users can easily compare the results from different approaches to better understand phage-microbe coevolution. We present it as a software pipeline for phage-host interaction identification, annotation and analysis in a comprehensive and user-friendly manner. PHISDetector can be run either as a web-server (http://www.microbiome-bigdata.com/PHISDetector/) or as a stand-alone version especially designed for virome studies.Conclusions: PHISDetector is a unique tool capable of incorporating all five categories of PHISs for comprehensive prediction of global phage-host interactions. PHISDetector outperforms currently available tools which are limited by accuracy, effective detection range, types of interacting signals, and the capability to apply for high-throughput virome studies.

The friend leukemia integration 1 (Fli-1) gene is involved in the expression control of key genes in multiple pathogenic/physiological processes, including cell growth, differentiation, and apoptosis, this implies that Fli-1 is a strong candidate for drug development. In our previous study, a 3′,5′-diprenylated chalcone, (E)-1-(2-hydroxy-4-methoxy-3,5-diprenyl) phenyl-3-(3-pyridinyl)-propene-1-one (C10), was identified as a novel anti-prostate cancer (PCa) agent. Here, we investigated the molecular mechanisms underlying the anti-cancer effects of C10 on the growth, metastasis, and invasion of PC3 cells in vitro. Our results show that C10 exhibited a strong inhibitory effect on proliferation and metastasis of PC3 cells via several cellular and flow cytometric analyses. Further mechanism studies revealed that C10 likely serves as an Fli-1 agonist for regulating the expression of Fli-1 target genes including phosphatidylinositol 3-kinase (P110), murine double minute2 (MDM2), B-cell lymphoma-2 (Bcl-2), Src homology-2 domain-containing inositol 5-phosphatase 1 (SHIP-1), and globin transcription factor-1 (Gata-1) as well as the phosphorylation of extracellular-regulated protein kinases 1 (ERK1). Further, we confirmed that C10 can regulate the expressions of vascular endothelial growth factor 1 (VEGF-1), transforming growth factor-β2 (TGF-β2), intercellular cell adhesion molecule-1 (ICAM-1), p53, and matrix metalloproteinase 1 (MMP-1) genes associated with tumor apoptosis, migration, and invasion. Thus, C10 exhibits stronger anticancer activity with novel molecular targets and regulatory molecular mechanisms, indicating its great potency for development as a novel targeted anticancer drug.

A series of NaY(WO 4 ) 2 :Sm 3+ phosphors were prepared by high temperature solid state reaction. When excited by ultraviolet and blue light, their emission spectra cover entirely visible light region, due to intrinsic luminescence of WO 4 2- group as well as Sm 3+ 4f-4f transitions. White light emission was obtained from NaY 0.99 Sm 0.01 (WO 4 ) 2 phosphor under radiation of 265 nm UV light, and intense yellow and red emission from 6 H J(J=5/2, 7/2, 9/2) transitions were observed when pumped Sm 3+ 4 G 5/2 by 405 nm blue light. With incorporation of Sm 3+ into NaY(WO 4 ) 2 host, higher-level emission from Sm 3+ at 650 nm was generated by energy transfer from WO 4 2- to Sm 3+ under excitation of 265 nm. The corresponding energy transfer mechanism was demonstrated to be a dipole-dipole interaction. In addition, tunable emission from blue to white and, finally, to red was realized by increasing Sm 3+ doping concentration. The band gap of NaY(WO 4 ) 2 calculated from diffuse reflection spectra indicates a semiconducting character. All these results show that NaY 1−x Sm x (WO 4 ) 2 phosphor provides promising application for conversion of frequencies emitted by UV or blue LEDs.

Phage-microbe interactions not only are appealing systems to study coevolution but also have been increasingly emphasized due to their roles in human health, diseases, and novel therapeutic development. Meanwhile, their interactions leave diverse signals in bacterial and phage genomic sequences, defined as phage-host interaction signals (PHISs), such as sequence composition, CRISPR targeting, prophage, and protein-protein interaction signals. We infer that proper detection and integration of these diverse PHISs will allow us to predict phage-host interactions. Here, we developed PHISDetector, a novel tool to predict phage-host interactions by detecting and integrating diverse in silico PHISs and scoring the probability of phage-host interactions using machine-learning models based on PHIS features. PHISDetector is available as a one-stop web service version for general users to study individual inputs. A stand-alone software version is also provided to process massive phage contigs from virome studies. PHISDetector is freely available at http://www.microbiome-bigdata.com/PHISDetector/ and https://github.com/HIT-ImmunologyLab/PHISDector.

The effect of manure compost alone and combined with Streptomyces pactum (Act12) applied in the smelter-contaminated soil was investigated. The soil fertility, enzymatic activities, potentially toxic metals (PTMs) solubility, and phytoremediation efficiency of potherb mustard (Brassica juncea, Coss.) were assessed. Results showed that the application of compost reduced the soil pH, while significantly increased the soil electrical conductivity (EC) (7.0 folds), available phosphorus (AP) (10.8 folds), available potassium (AK) (2.81 folds), dissolved organic carbon (DOC) (5.22 folds), organic matter (OM) (4.93 folds), together with soil enzymatic activities viz. urease (UR) (4.39 folds), dehydrogenase (DEH) (45.0 folds) and alkaline phosphatase (ALP) (123.9 folds) in comparison with control. The inoculation of Act12 increased AP, AK, DOC, OM and UR values, but reduced EC, DEH and ALP values compared to corresponding lone compost amendment. Additionally, Act12 solubilized PTMs (Cd and Zn) in the soil, and accordingly enhanced the PTMs uptake in the plant. The phytoextraction indices viz. biological concentration factor (BCF), translocation factor (TF) and metal extraction amount (MEA) indicated that compost and Act12 had a synergistic role in enhancing the phytoremediation efficiency, among which MEA values of Cd and Zn maximally increased by 9.64 and 11.4 folds, respectively, compared to control. Redundancy analysis (RDA) indicated that phytoextraction indices correlated well with soil parameters. Our results suggested that manure compost associated with Act12 is a potential strengthening strategy in phytoremediation of PTMs contaminated soil.

The effect of acid concentration in nitrocellulose (NC) on thermal stability of NC for civil use was studied using differential scanning calorimeter (DSC). The thermal explosion temperature (Tb) and kinetic parameters of NC thermal decomposition were calculated using different methods based on the thermal decomposition behaviors of NC in high pressure-gold plated stainless steel crucible at different heating rates. The results show that acid content in NC reduces the stability of NC remarkably, including reducing the characteristic decomposition temperature such as peak temperature (Tp), onset temperature (Tonset), initial temperature (T0) and critical temperature of thermal explosion (Tb). The big difference between NC with different acid content is that the relative quantity of activation energy and the change trend of activation energy. The most interesting thing is that NC with more acid content has the lower characteristic temperature but higher calculated activation energy.

The present reaction provides a simple and convenient synthetic strategy to construct β-iodovinyl sulfones through molecular iodine and DTBP (di-tert-butyl peroxide) promoted difunctionalization of alkynes with sodium benzenesulfinates under mild and environmentally-benign conditions. A series of substituted (E)-β-iodovinyl sulfones were synthesized with excellent stereo- and regio-selectivities.

// Fan Zhang 1, * , Chunyan Ren 2, * , Hengqiang Zhao 1 , Lei Yang 1 , Fei Su 1 , Ming-Ming Zhou 2 , Junwei Han 1 , Eric A. Sobie 2 , Martin J. Walsh 2 1 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, PR China 2 Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA * These authors have contributed equally to this work Correspondence to: Martin J. Walsh, email: martin.walsh@mssm.edu Eric A. Sobie, email: eric.sobie@mssm.edu Junwei Han, email: hanjunwei1981@163.com Keywords: triple-negative breast cancer, landmark for cancer prognosis, GTPase, ubiquitination, oxidative damage Received: July 27, 2016 Accepted: September 22, 2016 Published: September 27, 2016 ABSTRACT Triple negative breast cancers (TNBCs) are highly heterogeneous and aggressive without targeted treatment. Here, we aim to systematically dissect TNBCs from a prognosis point of view by building a subnetwork atlas for TNBC prognosis through integrating multi-dimensional cancer genomics data from The Cancer Genome Atlas (TCGA) project and the interactome data from three different interaction networks. The subnetworks are represented as the protein-protein interaction modules perturbed by multiple genetic and epigenetic interacting mechanisms contributing to patient survival. Predictive power of these subnetwork-derived prognostic models is evaluated using Monte Carlo cross-validation and the concordance index (C-index). We uncover subnetwork biomarkers of low oncogenic GTPase activity, low ubiquitin/proteasome degradation, effective protection from oxidative damage, and tightly immune response are linked to better prognosis. Such a systematic approach to integrate massive amount of cancer genomics data into clinical practice for TNBC prognosis can effectively dissect the molecular mechanisms underlying TNBC patient outcomes and provide potential opportunities to optimize treatment and develop therapeutics.

Shark liver oil (SLO) has been widely used as a food supplement to boost human immunity. The extraction method of shark liver oil is immature. In this study, four different extraction methods of shark liver oil were tried, the effect of the solid-liquid ratio, quality of the enzyme, reaction pH and temperature on SLO extraction rate have been discussed. Infrared spectroscopy, gas chromatography and high performance liquid chromatography was used to detect the main composition of SLO, and U14 tumor bearing mice were used to explore anti-tumor effect of SLO. Our results show that alkaline protease extraction method was the best with an extraction rate of 30.15%, and the solid-liquid ratio, quality of the enzyme, reaction pH and temperature was 1:2, 2% of the liver quality, 9, 3.5 h, 48°C respectively. Characteristic peak of alkoxy glycerol, squalene and vitamin A was presented in the IR spectra of SLO, the proportion of alkoxy glycerol, squalene content and vitamin was 35.3, 40.4 and 7.8% determined by gas chromatography (GC) and high performance liquid chromatography (HPLC). The inhibition rate was 54.56. Key words: Shark liver oil, extraction, characterization, gas chromatography, high performance liquid chromatography (HPLC).

Ethnopharmacological relevance Colla Corii Asini is a widely used traditional Chinese medicine to treat anemia with a long history due to its stimulating effect in hematopoiesis, but the components contributing to this effect are still unknown. In this study, we aimed to establish a methodology to isolate the bioactive components and provide pharmacological basis for its usage in treating anemia. Methods 5-FU and γ-ray radiation induced anemic mice models were generated by treating with 5-FU at 150 mg/kg body weight and γ-rays by a 4 MV linear accelerator by total body irradiation using female ICR mice respectively. Oral administration of fraction A was performed by gastric lavage at 1 g/kg and 2 g/kg body weight for 12 days and 25 days and peripheral blood sample was collected from ocular sinus red blood cell (RBC) and white blood cell (WBC) counts every 3 days and 5 days for 5-FU and radiation induced models, respectively. Next, fraction A was separated to A1 and A2 using cation exchange chromatography (IEC) based on ionic strength. Fraction A1 was further separated using reverse phase chromatography (RPC) based on the hydrophobicity first with 0–10% linear gradient, then 20%, 30%, 50% constant gradient of 60% acetonitrile in neutral Na 2 HPO 4 buffer. Peak fractions were pooled, evaporatively dried, and dissolved in ultrapure water. Finally, fraction A11 was analyzed combining tandem mass spectrometry and proteomic tools and two peptides (peptide 11 and 16) were identified. The hematopoietic effects of multiple fractions and the two peptides were measured using colony-forming units-erythroid (CFU-E), an indication of late erythroid progenitor cells and colony-forming units granulocyte-monocyte (CFU-GM), an indication of granulocyte and monocyte progenitor cells respectively on hematopoietic progenitor cells prepared from bone marrow ( Till and Mcculloch 1961 ). Results Fraction A at 1 g/kg and 2 g/kg could increase RBC and WBC counts in 5-FU and radiation induced anemic mice models. Fraction A1 at 0.1 mg/ml and 0.5 mg/ml, exhibited stronger hematopoietic activity than fraction A2, both of which were subfractions from fraction A using IEX, by elevated CFU-E and CFU-GM of mouse bone marrow cells. Furthermore, fraction A11 at 0.1 mg/ml showed stronger CFU-E and CFU-GM than fractions A12 to A14 from RPC separation. Finally, peptide 11 and peptide 16 were identified from tandem mass spectrometry and peptide 11 increased CFU-E and CFU-GM in a dose dependent manner. Conclusions We combined multiple approaches including chromatography, mass spectrometry, cell-based assays, as well as animal studies to identify and demonstrate that the hematopoietic effect of Colla Corii Asini is at least in part from the peptidic components identified using our methodology. This is the first time to isolate peptidic components from Colla Corii Asini , and to provide molecular basis for its usage in treating anemia, which may particularly have the potential to benefit cancer patients suffering from myelosuppression due to radiotherapy or chemotherapy.

Several major effectors of adult-stage fetal globin silencing have been identified, including the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening of 1591 transcription factors, we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to the γ-globin genes but rather its chromatin occupancy is solely concentrated at CHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements, one at its promoter and the other at an enhancer 6 kb upstream, with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. Peaks at these clusters display up to 57- and 77-fold enrichment respectively for ZNF410 binding compared to controls. Footprint analysis shows that the ZNF410 motifs are protected from nuclease cleavage. No other bona fide peaks could be detected across the genome in HUDEP-2 cells or primary CD34+ HSPC-derived erythroid precursors. We demonstrate that the ZNF410-bound elements at CHD4 completely account for ZNF410's effects on γ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios (6 homozygous Zfp410Gt/Gt gene-trap allele mice out of 20 live births) with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. Engrafting human erythrocytes induce HbF from ~2.5% in controls to ~17% in ZNF410 edited recipients, by hemoglobin HPLC. These studies identify a new rational target for HbF induction for the β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex. FIGURE LEGEND: ZNF410 chromatin occupancy is restricted to CHD4. (A) Dense mutagenesis of ZNF410 shows its five C2H2 zinc-finger domains (red rectangles) are especially critical for HbF repression. (B) Genome-wide ZNF410 binding was identified by CUT&RUN in HUDEP-2 cells. Enrichment for ZNF410 binding was concentrated at just two sites in the genome - at the promoter and at an enhancer ~6 kb upstream of CHD4. (C) Genome-wide ZNF410 motif occurrences (JASPAR motif shown in center) were mapped using a 3 kb sliding window. Clusters of ZNF410 motifs were found only at three locations in the genome, including the CHD4 promoter and CHD4 -6 kb enhancer. (D) CHD4 locus showing ZNF410 binding (red peaks) at the CHD4 promoter and CHD4 -6 kb enhancer regions with anti-HA antibody recognizing epitope-tagged ZNF410 and anti-ZNF410 antibody recognizing endogenous ZNF410 in both HUDEP-2 cells and CD34+ HSPC derived erythroid precursors. CUT&RUN footprints demonstrate ZNF410 motif protection, ATAC-seq chromatin accessibility and phyloP DNA sequence conservation. Disclosures Bauer: Pfizer: Consultancy; Syros Pharmaceuticals: Consultancy; Fulcrum Therapeutics: Consultancy; Sanofi: Research Funding.

The present work was done to explore the joint effect of Streptomyces pactum (Act12) and plant nutrients on phytoremediation of smelter-contaminated soils. The physiological indicators and phytoextraction indices of potherb mustard (Brassica juncea, Coss) grown in Act12 inoculated soil with or without Hoagland’s solution (H), humic acid (HA) and peat (PS) were evaluated. The results indicated that H, HA and PS acted synergistically with Act12, notably increasing chlorophyll and soluble protein contents and thereby promoting plant growth. Soil nutrient treatments reduced the antioxidant activities (PPO, CAT and POD) by 28.2–41.4%, 22.3–90.1% and 15.2–59.4% compared to control, respectively. Act12 and H treatments markedly facilitated plant to accumulate more cadmium (Cd) and zinc (Zn), but it was observed decreases when applied with HA and PS. Metal uptake (MU) values further indicated the differences in phytoextraction efficiency, i.e., H > PS > Control > HA. Taken together, Act12 combined with plant nutrients contributed to alleviating metal toxicity symptoms of plant. Hoagland’s solution and peat were highlighted in the present phytoextraction trial, and recommended as soil additives.