Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation.

Transcriptional enhanced associate domain (TEAD) proteins bind to YAP/TAZ and mediate YAP/TAZ-induced gene expression. TEADs are not only the key transcription factors and final effector of the Hippo signaling pathway, but also the proteins that regulate cell proliferation and apoptosis. Disorders of Hippo signaling pathway occur in liver cancer, breast cancer, colon cancer and other cancers. S-palmitylation can stabilize the structure of TEADs and is also a necessary condition for the binding of TEADs to YAP/TAZ. The absence of TEAD palmitoylation prevents TEADs from binding to chromatin, thereby inhibiting the transcription and expression of downstream target genes in the Hippo pathway through a dominant-negative mechanism. Therefore, disrupting the S-palmitylation of TEADs has become an attractive and very feasible method in cancer treatment. The palmitate binding pockets of TEADs are conservative, and the crystal structures of TEAD2-palmitoylation inhibitor complexes and the potential TEAD2 inhibitors are more than other TEADs, TEAD2 can be selected to be the target receptor. In this study, structure-based and ligand-based virtual screening, molecular dynamics simulations, Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) calculations, residue decomposition binding energy calculations, and ADME predictions have been performed to discover 11 potential TEAD2 S-palmitylation inhibitors. ChEBML196567 and ZINC000013942794 are the most recommended, because they formed strong binding energies and stable hydrogen bonds with TEAD2 and have good drugbility and high human oral absorption. We found that it was easier to find the targeting small molecules using a combination of structure-based and ligand-based virtual screening methods. Besides, a new core structure has been found in the selected small molecules. In addition, we analyzed the binding modes of these small molecules to TEAD2, and confirmed the hot spot residues Cys380, Ser345, Tyr426, Phe428, Ile408, and Met379. AVAILABILITY OF DATA AND MATERIAL: Supplementary materials are available online.

Triangulation supports agricultural spread of the Transeurasian languages.

The origin and early dispersal of speakers of Transeurasian languages-that is, Japanese, Korean, Tungusic, Mongolic and Turkic-is among the most disputed issues of Eurasian population history1-3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by 'triangulating' genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic-Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional 'pastoralist hypothesis'6-8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.

The genomic origins of the Bronze Age Tarim Basin mummies.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road.

Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.

Removal of U(VI) from aqueous and polluted water solutions using magnetic Arachis hypogaea leaves powder impregnated into chitosan macromolecule.

In this study m-AHLPICS (magnetic Arachis hypogaea leaves powder impregnated into chitosan) was prepared and utilized as an adsorbent to remove U(VI) from aqueous and real polluted wastewater samples. m-AHLPICS was characterized by using the BET, XRD, FTIR, SEM with elemental mapping and magnetization measurements. Different experimental effects such as pH, dose, contact time, and temperature were considered broadly. Chitosan modified magnetic leaf powder (m-AHLPICS) exhibits an excellent adsorption capacity (232.4 ± 5.59 mg/g) towards U(VI) ions at pH 5. Different kinetic models such as pseudo-first-order, and pseudo-second-order models were used to know the kinetic data. Langmuir, Freundlich and D-R isotherms were implemented to know the adsorption behavior. Isothermal information fitted well with Langmuir isotherm. Kinetic data followed by the pseudo-second-order kinetics (with high R2 values, i.e., 0.9954, 0.9985 and 0.9971) and the thermodynamic data demonstrate that U(VI) removal using m-AHLPICS was feasible, and endothermic in nature.

RNA Expression Profile and Alternative Splicing Signatures of Genistein-Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis.

Little information has been available about the influence of dietary genistein (GEN) on hepatic transcriptome of laying broiler breeder (LBB) hens. The study is aimed at broadening the understanding of RNA expression profiles and alternative splicing (AS) signatures of GEN-treated breeder hens and thereby improving laying performance and immune function of hens during the late egg-laying period. 720 LBB hens were randomly allocated into three groups with supplemental dietary GEN doses (0, 40 mg/kg, and 400 mg/kg). Each treatment has 8 replicates of 30 birds. Dietary GEN enhanced the antioxidative capability of livers, along with the increased activities of glutathione peroxidase and catalase. Furthermore, it improved lipid metabolic status and apoptotic process in the liver of hens. 40 mg/kg dietary GEN had the better effects on improving immune function and laying performance. However, transcriptome data indicated that 400 mg/kg dietary GEN did negative regulation of hormone biosynthetic process. Also, it upregulated the expressions of EDA2R and CYR61 by the Cis regulation of neighbouring genes (lncRNA_XLOC_018890 and XLOC_024242), which might activate NF-κB and immune-related signaling pathway. Furthermore, dietary GEN induced AS events in the liver, which also enriched into immune and metabolic process. Therefore, the application of 40 mg/kg GEN in the diet of breeder hens during the late egg-laying period can improve lipid metabolism and immune function. We need to pay attention to the side-effects of high-dose GEN on the immune function.

Ellagic acid promotes browning of white adipose tissues in high-fat diet-induced obesity in rats through suppressing white adipocyte maintaining genes.

Promoting brown adipose tissue (BAT) formation and function reduces obesity. Ellagic Acid (EA), located abundantly in plant extracts and fruits, has been shown to modulate formation and differentiation of adipocytes, although its role in the process of browning of white adipose tissue (WAT) has not been elucidated. In this study, fifty-six five-week old SD rats were randomly assigned to receive normal diet (ND, 10% lipids) or high-fat diet (HFD, 60% lipid) with or without various dosages of EA for 24 weeks. Our results showed that high fat diet intake triggered overweight, glucose intolerance and white adipocyte hypertrophy, the effects of which were mitigated by EA treatment. Meanwhile, EA supplementation reduced serum resistin levels, improved hepatic steatosis and serum lipid profile in DIO (high fat diet induced obesity) rats. Moreover, EA supplementation significantly decreased mRNA expression of Zfp423 and Aldh1a1, the key determinants of WAT plasticity. EA also increased mRNA expression of brown adipocyte markers including UCP1, PRDM16, Cidea, PGC1α, Ppar-α; beige markers including CD137and TMEM26; mitochondrial biogenesis markers including TFAM in inguinal WAT (iWAT) when compared to their counterparts. EA treatment significantly improved mitochondrial function, as measured by citrate synthase activity. More importantly, EA markedly elevated the expression of UCP1 in iWAT, which is a specific protein of brown adipocyte. In conclusion, our results provided evidence that EA improved obesity-induced dyslipidemia and hepatic steatosis in DIO rats via browning of iWAT through suppressing white adipocyte maintaining genes and promoting expression of key thermogenic genes. These findings suggest that EA could be a promising therapeutic avenue to treat metabolic diseases.

Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.

Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.

Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d.

Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.

Dietary genistein supplementation in laying broiler breeder hens alters the development and metabolism of offspring embryos as revealed by hepatic transcriptome analysis.

Genistein (GEN) is a type of isoflavone mainly derived from soy products. In this experiment, we added 40 and 400 mg/kg GEN to the diet of laying broiler breeder hens to clarify the maternal effects of GEN on the development and metabolism of chick embryos. GEN treatment at 40 mg/kg increased embryonic length, weight, and liver index, as well as the width of the proliferative zone in the tibial growth plate of chick embryos. Gene ontology (GO) cluster analysis of the hepatic transcriptome showed that GEN treatment promoted embryonic development and cell proliferation. Low-dose GEN treatment increased insulin growth factor-binding protein (IGFBP)3 mRNA expression in the embryonic liver, whereas high-dose GEN treatment increased IGFBP5 expression and activated the apoptosis and protein tyrosine kinase signaling pathways. Furthermore, adding supplemental GEN to the diet of hens promoted the glycolysis process in the embryonic liver through the insulin-signaling pathway, upregulated target genes (phosphoglucomutase-2, hexokinase 1, dihydroxyacetone phosphate by aldolase, phosphofructokinase, platelet, and enolase 2), and enhanced the transport of carboxylic acids and cholesterol and the synthesis of unsaturated fatty acid (arachidonic acid) in the embryonic liver through upregulation of liver X receptor, sterol regulatory element-binding protein 1, and patatin-like phospholipase A. Additionally, GEN treatment increased fatty acid ß-oxidation and Na+/K+-ATPase activity in the embryonic liver through activation of peroxisome proliferator-activated receptors (PPARs; PPARα and PPARδ) and the AMPK signaling pathway, which could provide energy for embryonic development. In addition, GEN treatment in hens increased superoxide dismutase activity and metallothionein expression in the chick embryonic liver and promoted lymphocyte proliferation through upregulation of mRNA expression of CDKN1A, IL12RB1, Sox11, PRKAR1A, PRKCQ, and TCF3. The improved immunity and antioxidant capacity, as a result of maternal GEN effects, was conducive to embryonic development. In summary, the addition of GEN to the diet of laying broiler breeder hens significantly promoted the development and metabolism of chick embryos.-Lv, Z., Fan, H., Zhang, B., Ning, C., Xing, K., Guo, Y. Dietary genistein supplementation in laying broiler breeder hens alters the development and metabolism of offspring embryos as revealed by hepatic transcriptome analysis.

[Enzymatic production of oral nutritional liquid from oyster].

OBJECTIVE: To prepare an oral nutritional liquid for protecting liver and antialcoholic from defatted oyster powder. METHODS: The orthogonal design was used to determine the optimal enzymatic hydrolytic condition and the enzymolysis liquid from oyster was deodorized and seasoned. RESULTS: The optimum hydrolytic conditions were determined as follows: defatted oyster powder added concentration of 2%, ratio of enzyme to base material 10%, enzymatic hydrolytic time 90 min, temperature 50 degrees C, pH 6.2. The content of glycogen, crude protein and amino acids in the oral nutritional liquid were 461 mg/100 mL, 381 mg/100 mL and 294.5 mg/100 mL, respectively. CONCLUSIONS: The processing conditions are stable and reliable and can be used to provide reference for further pilot scale production.