Using graph-based model to identify cell specific synthetic lethal effects.

Synthetic lethal (SL) pairs are pairs of genes whose simultaneous loss-of-function results in cell death, while a damaging mutation of either gene alone does not affect the cell's survival. This makes SL pairs attractive targets for precision cancer therapies, as targeting the unimpaired gene of the SL pair can selectively kill cancer cells that already harbor the impaired gene. Limited by the difficulty of finding true SL pairs, especially on specific cell types, current computational approaches provide only limited insights because of overlooking the crucial aspects of cellular context dependency and mechanistic understanding of SL pairs.

Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures.

Metastatic propagation is the leading cause of death for most cancers. Prediction and elucidation of metastatic process is crucial for the treatment of cancer. Even though somatic mutations have been linked to tumorigenesis and metastasis, it is less explored whether metastatic events can be identified through genomic mutational signatures, which are concise descriptions of the mutational processes.

Novel strategy for copper precipitation from cupric complexes wastewater: Catalytic oxidation or reduction self-decomplexation?

Cupric (Cu(II)) complexes in industrial wastewater are responsible for the failure of conventional alkaline precipitation, but the properties of cuprous (Cu(I)) complexes at alkaline circumstance have not been focused. This report proposed a novel strategy for the remediation of Cu(II)-complexed wastewater by coupling alkaline precipitation with green benign reductant, namely, hydroxylamine hydrochloride (HA). This remediation process (HA-OH) exhibits superior Cu removal efficiency that cannot be achieved with the same dosage of oxidants (3 mM).

Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells.

Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts.

Assembly of UiO-66 onto Co-doped FeO nanoparticles to activate peroxymonosulfate for efficient degradation of fenitrothion and simultaneous in-situ adsorption of released phosphate.

Although sulfate radical-based advanced oxidation processes (SR-AOPs) have shown great potential for the efficient degradation of various organic contaminants, there is few research on the removal of organophosphorus pesticides (OPPs) through SR-AOPs. In this work, Co-doped FeO magnetic particles encapsulated by zirconium-based metal-organic frameworks (Co-FeO@UiO-66) were prepared and employed to activate peroxymonosulfate (PMS) for the elimination of fenitrothion (FNT) and the simultaneous in-situ adsorption of produced phosphate. The catalyst exhibited efficient catalytic performance, achieving above 90.

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos.

Trophoblast stem cells (TSCs) are critical to mammalian embryogenesis by providing the cell source of the placenta. TSCs can be derived from trophoblast cells. However, the efficiency of TSC derivation from somatic cell nuclear transfer (NT) blastocysts is low.

Facile synthesis of core-shell phase-transited lysozyme coated magnetic nanoparticle as a novel adsorbent for Hg(II) removal in aqueous solutions.

Adsorption using nanomaterials is considered an effective method for controlling the levels of toxic heavy metal in wastewater. Herein, a novel adsorbent, core-shell phase-transited lysozyme film-coated magnetic nanoparticles (FeO@SiO@PTL) for Hg(II) ions removal from aqueous solutions was explored via facile and fast phase transformation and self-assembly process of lysozyme. The physiochemical properties of FeO@SiO@PTL were investigated using various characterization techniques.

Surface molecular imprinting on polystyrene resin for selective adsorption of 4-hydroxybenzoic acid.

Using chloromethylated polystyrene resin, N,N-diethylaminoethyl methacrylate, and ethylene glycol dimethacrylate as support, functional monomer and cross-linker, respectively, the molecularly imprinted resin (MIR) and non-imprinted resin (NIR) were fabricated by the combination of atom transfer radical polymerization and surface imprinting technique for the selective adsorption of 4-hydroxybenzoic acid (4-HB) from aqueous solutions. The prepared adsorbents were characterized by N adsorption/desorption isotherms, Fourier-transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The adsorption processes of the 4-HB with MIR and NIR followed pseudo-second-order kinetics, and the adsorption isotherms were appreciably described by the Langmuir model.

Polyethylenimine-functionalized polyacrylonitrile anion exchange fiber as a novel adsorbent for rapid removal of nitrate from wastewater.

The development of an adsorbent with high adsorption ability and favorable cyclic regeneration performance for the removal of nitrate residues from wastewater is a task of vital importance. To this end, polyacrylonitrile fiber (PANF) was modified with polyethyleneimine (PEI), and alkyl groups were then introduced around the active amine groups to prepare three polymer-based anion exchange fibers (PAN-PEI-3C, PAN-PEI-5C, and PAN-PEI-8C). The novel fibers were characterized using techniques such as scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and thermogravimetric analysis (TGA).

Curcumin micelles suppress gastric tumor cell growth by upregulating ROS generation, disrupting redox equilibrium and affecting mitochondrial bioenergetics.

Gastric cancer is the fourth most common cancer and the second most frequent cause of cancer death worldwide. Chemotherapy is an important treatment. However, traditional chemotherapy drugs have low bioavailability and targeting ability.

Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma.

As a transcription factor, MYCN regulates myriad target genes including the histone chaperone FACT. Moreover, FACT and MYCN expression form a forward feedback loop in neuroblastoma. It is unclear whether MYCN is involved in chromatin remodeling in neuroblastoma through regulation of its target genes.

Ferroptosis is governed by differential regulation of transcription in liver cancer.

Ferroptosis is an outcome of metabolic disorders and closely linked to liver cancer. However, the mechanism underlying the fine regulation of ferroptosis in liver cancer remains unclear. Here, we have identified two categories of genes: ferroptosis up-regulated factors (FUF) and ferroptosis down-regulated factors (FDF), which stimulate and suppress ferroptosis by affecting the synthesis of GSH.

circRNA_104075 stimulates YAP-dependent tumorigenesis through the regulation of HNF4a and may serve as a diagnostic marker in hepatocellular carcinoma.

Some types of circular RNA (circRNA) are aberrantly expressed in human diseases including hepatocellular carcinoma (HCC). However, its regulation mechanism and diagnostic roles are largely unknown. Here, we identified that circRNA_104075 (circ_104075) was highly expressed in HCC tissues, cell lines and serum.

Reduced Self-Diploidization and Improved Survival of Semi-cloned Mice Produced from Androgenetic Haploid Embryonic Stem Cells through Overexpression of Dnmt3b.

Androgenetic haploid embryonic stem cells (AG-haESCs) hold great promise for exploring gene functions and generating gene-edited semi-cloned (SC) mice. However, the high incidence of self-diploidization and low efficiency of SC mouse production are major obstacles preventing widespread use of these cells. Moreover, although SC mice generation could be greatly improved by knocking out the differentially methylated regions of two imprinted genes, 50% of the SC mice did not survive into adulthood.

Adsorption performance of polydopamine-modified attapulgite granular adsorbent for methylene blue.

Polydopamine-modified granule organo-attapulgite adsorbent (PDA-GOAT) was facilely prepared via a dip-coating approach. The samples were characterized by scanning electron microscopy, X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. Surface area and pore size were calculated from the Brunauer-Emmett-Teller method by N adsorption-desorption isotherm.

TFCP2 Is Required for YAP-Dependent Transcription to Stimulate Liver Malignancy.

Although YAP-dependent transcription is closely associated with liver tumorigenesis, the mechanism by which YAP maintains its function is poorly understood. Here, we show that TFCP2 is required for YAP-dependent transcription and liver malignancy. Mechanistically, YAP function is stimulated by TFCP2 via a WW-PSY interaction.

Global MicroRNA Expression Profiling of Mouse Livers following Ischemia-Reperfusion Injury at Different Stages.

Hepatic ischemia-reperfusion injury is a dynamic process consisting of two stages: ischemia and reperfusion, and triggers a cascade of physiological and biochemical events. Given the important role of microRNAs in regulating gene expression, we analyzed gene expression changes in mouse livers at sham control, ischemia stage, and reperfusion stage. We generated global expression profiles of microRNA and mRNA genes in mouse livers subjected to ischemia-reperfusion injury at the three stages, respectively.

Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming.

The core pluripotency factor Oct4 plays key roles in somatic cell reprogramming through transcriptional control. Here, we profile Oct4 occupancy, epigenetic changes, and gene expression in reprogramming. We find that Oct4 binds in a hierarchical manner to target sites with primed epigenetic modifications.

Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers.

Background: Nucleosome organization determines the chromatin state, which in turn controls gene expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it is still unclear to what degree the re-established nucleosome organization of induced pluripotent stem cells (iPSCs) resembles embryonic stem cells (ESCs), and whether the iPSCs inherit some residual gene expression from the parental fibroblast cells.

Results: We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system.

Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals.