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BackgroundSubstance use occurs at a high rate in persons with a psychiatric disorder. Genetically informative studies have the potential to elucidate the etiology of these phenomena. Recent developments in genome-wide association studies (GWAS) allow new avenues of investigation.MethodUsing results of GWAS meta-analyses, we performed a factor analysis of the genetic correlation structure, a genome-wide search of shared loci, and causally informative tests for six substance use phenotypes (four smoking, one alcohol, and one cannabis use) and five psychiatric disorders (ADHD, anorexia, depression, bipolar disorder, and schizophrenia).ResultsTwo correlated externalizing and internalizing/psychosis factor were found, although model fit was beneath conventional standards. Of 458 loci reported in previous univariate GWAS of substance use and psychiatric disorders, about 50% (230 loci) were pleiotropic with additional 111 pleiotropic loci not reported from past GWAS. Of the 341 pleiotropic loci, 152 were associated with both substance use and psychiatric disorders, implicating neurodevelopment, cell morphogenesis, biological adhesion pathways, and enrichment in 13 different brain tissues. Seventy-five and 114 pleiotropic loci were specific to either psychiatric disorders or substance use phenotypes, implicating neuronal signaling pathway and clathrin-binding functions/structures, respectively. No consistent evidence for phenotypic causation was found across different Mendelian randomization methods.ConclusionsGenetic etiology of substance use and psychiatric disorders is highly pleiotropic and involves shared neurodevelopmental path, neurotransmission, and intracellular trafficking. In aggregate, the patterns are not consistent with vertical pleiotropy, more likely reflecting horizontal pleiotropy or more complex forms of phenotypic causation.

Elevated levels of atmospheric CO2 (eCO2) promote rice growth and increase methane (CH4) emissions from rice paddies, because increased input of plant photosynthate to soil stimulates methanogenic archae. However, temporal trends in the effects of eCO2 on rice growth and CH4 emissions are still unclear. To investigate changes in the effects of eCO2 over time, we conducted a two-season pot experiment in a walk-in growth chamber. Positive effects of eCO2 on rice leaf photosynthetic rate, biomass, and grain yield were similar between growing seasons. However, the effects of eCO2 on CH4 emissions decreased over time. Elevated CO2 increased CH4 emissions by 48%–101% in the first growing season, but only by 28%–30% in the second growing season. We also identified the microbial process underlying the acclimation of CH4 emissions to atmospheric CO2 enrichment: eCO2 stimulated the abundance of methanotrophs more strongly in soils that had been previously exposed to eCO2 than in soils that had not been. These results emphasize the need for long-term eCO2 experiments for accurate predictions of terrestrial feedbacks.

Cattle temperament is an interesting trait due to its correlation with production efficiency, labor safety, and animal welfare. To date, however, its genetic basis is not clearly understood. Here, we performed a genome-wide association study for a series of temperament traits in cattle, assessed with via open field and novel object tests, using autosomal single nucleotide polymorphisms (SNPs) derived from the whole-genome sequence. We identified 37 and 29 genome-wide significant loci in the open field and novel object tests, respectively. Gene set analysis revealed the most significant pathway was the neuroactive ligand-receptor interaction pathway, which may be essential for emotional control in cattle. Analysis of the expression levels of 18 tissue-specific genes based on transcriptomic data showed enrichment in the brain, with some candidate genes involved in psychiatric and neurodegenerative diseases in humans. Based on principal component analysis, the first principal component explained the largest variance in the open field and novel object test data, and the most significant loci were assigned to牛性情是一个非常有意思的性状，它与生产效率、役用安全、动物福利等紧密相关，但其遗传机制尚不清楚。该研究通过旷场测试及新物体测试分别获得了15和14个与性情相关的性状数据，结合30头婆罗门牛及128头云岭牛的常染色体基因组序列单核苷酸多态性(SNPs)进行全基因组关联分析（GWAS）。结果显示在旷场测试和新物体测试中分别鉴定出37 和29个显著位点。基因注释发现多个旷场测试性状的显著位点位于参与突触抑制和恐惧消退神经元受体基因

Acinetobacter baumannii has become a major healthcare threat that causes nosocomial infections, especially in critically ill patients. The spread of carbapenem-resistant A. baumannii (CRAB) strains has long been a clinical concern. It is important to study the epidemiology and virulence characteristics of different CRAB isolates in order to tailor infection prevention and antibiotic prescribing. In this study, a total of 71 CRAB isolates were collected in the hospital, and clinical characteristics of infections were analyzed. The genomic characteristics and phylogenetic relationships were elucidated based on genome sequencing and analysis. The isolates were assigned to three sequence types (STs, Pasteur) and nine capsular polysaccharide (KL) types, among which ST2/KL22 was the most prevalent CRAB in the hospital. Even though all the ST2/KL22 isolates contained the same reported virulence genes, one specific clade of ST2/KL22 showed more pathogenic in mouse infection model. Complete genomic analysis revealed differences at the oprD locus between the low- and high-virulent isolates. More specifically, a premature stop codon in the low-virulence strains resulted in truncated OprD expression. By evaluating pathogenicity in C57BL/6 J mice, knock-out of oprD in high-virulent isolate resulted in virulence attenuation, and complementing the avirulent strain with full-length oprD from high-virulent isolate enhanced virulence of the former. The oprD gene may be associated with the enhanced virulence of the specific ST2/KL22 clone, which provides a potential molecular marker for screening the hypervirulent A. baumannii strains.

Straw incorporation is a global common practice to improve soil fertility and rice yield. However, the effect of straw incorporation on rice yield stability is still unknown, especially under high fertilization level conditions. Here, we reported the effect of straw returning on rice yield and yield stability under high fertilization levels in the rice–wheat system over nine years. The results showed that straw incorporation did not significantly affect the average rice yield of nine years. Straw incorporation reduced the coefficient of variation of rice yield by 25.8% and increased the sustainable yield index by 8.2%. The rice yield positively correlated with mean photosynthetically active radiation (PAR) of rice growth season and the effects of straw incorporation on rice yield depended on the PAR. Straw incorporation increased the rice yield by 5.4% in the low PAR years, whereas it did not affect the rice yield in the high PAR years. Long-term straw incorporation lowered soil bulk density but improved the soil organic matter, total N, available N, available P, and available K more strongly than straw removal. Our findings suggest that straw incorporation can increase rice yield stability through improving the resistance of rice plant growth to low PAR.

Background Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds. Results Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip. Conclusions The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.

Germplasm preservation of livestock or endangered animals and expansion of germline stem cells are important. The purpose of this study is to investigate whether supplementation of trehalose to the freezing medium (FM) reduces tissular damage and improves the quality of testicular cells in the cryopreserved bovine testicular tissues. We herein established an optimized protocol for the cryopreservation of bovine testicular tissues, and the isolation as well as culture of bovine germ cells containing spermatogonial stem cells (SSCs) from these tissues. The results showed that FM containing 10% dimethyl sulfoxide (Me2SO/DMSO), 10% knockout serum replacement (KSR) and 20% trehalose (FM5) combined with the uncontrolled slow freezing (USF) procedures has the optimized cryoprotective effect on bovine testicular tissues. The FM5 + USF protocol reduced the cell apoptosis, maintained high cell viability, supported the structural integrity and seminiferous epithelial cohesion similar to that in the fresh tissues. Viable germ cells containing SSCs were effectively isolated from these tissues and they maintained germline marker expressions in the co-testicular cells and co-mouse embryonic fibroblasts (MEF) feeder culture systems respectively, during the short-term culture. Additionally, upregulated transcriptions of spermatogenic differentiation marker C-KIT and meiotic marker SYCP3 were detected in these cells after retinoic acid-induced differentiation. Together, FM5 + USF is suitable for the cryopreservation of bovine testicular tissues, with benefits of reducing the apoptosis, maintaining the cell viability, supporting the testicular structure integrity, and sustaining the survival and differentiation potential of bovine germ cells containing SSCs.

Melatonin mediates multiple physiological processes in plants and is involved in many reactions related to the protection of plants from abiotic stress. In this paper, the effect of melatonin on the antioxidant capacity of rice under salt stress was studied. Melatonin alleviated the inhibition of salt stress on the growth of rice seedlings, mainly by increasing the dry weight and fresh weight of shoots and roots. Melatonin alleviated the membrane damage caused by salt stress, which was mainly manifested by the decrease of TBARS content and the decrease of leaf and root damage. During the whole salt stress period, rice after melatonin pretreatment showed lower ROS (H2O2, O2•−,OH−) accumulation. In the early stage (1–3 d) of stress, the rice after melatonin pretreatment showed a strong increase in antioxidant enzyme activity, while in the later stage (5,7 d), it showed a strong increase in antioxidant content. During the whole period of salt stress, melatonin had a weak regulatory effect on AsA-GSH cycle. Through the above regulation process, the decreasing effect of melatonin on ROS content of rice under salt stress did not decrease with prolonged stress time in a short time (1-7 d). In conclusion, melatonin improved the antioxidant capacity of rice under continuous salt stress, and rice showed variable antioxidant strategies after melatonin pretreatment.

In this study, Illumina MiSeq sequencing of the 16 S rRNA gene was used to describe the bacterial communities in the South China Sea (SCS) during the southwest monsoon period. We targeted different regions in the SCS and showed that bacterial community was driven by the effects of the river, upwelling, and mesoscale eddy through changing the environmental factors (salinity, temperature, and nutrients). Distinct bacterial communities were observed among different chemical conditions, especially between the estuary and the open sea. The abundance of Burkholderiales, Frankiales, Flavobacteriales, and Rhodobacterales dominated the estuary and its adjacent waters. Bacteria in cyclonic eddy were dominated by Methylophilales and Pseudomonadales, whereas Prochlorococcus, SAR11 clade, and Oceanospirillales had relatively high abundance in the anticyclonic eddy. Overall, the abundance of specific phylotypes significantly varied among samples with different chemical conditions. Chemical conditions probably act as a driver that shapes and controls the diversity of bacteria in the SCS. This study suggests that the interaction between microbial and environmental conditions needs to be further considered to fully understand the diversity and function of marine microbes.

Emerging evidence has suggested a pivotal role of circular RNAs (circRNAs) in the progression of asthma. In this paper, we explored the mechanisms underlying the modulation of circRNA homeodomain interacting protein kinase 3 (circHIPK3, circ_0000284) in airway smooth muscle cell (AMSC) migration and proliferation induced by platelet-derived growth factor (PDGF). The stability of circHIPK3 was gauged by Ribonuclease R (RNase R) and Actinomycin D assays. Relative expression levels of circHIPK3, microRNA (miR)-375 and matrix metallopeptidase 16 (MMP-16) were measured by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. Cell proliferation, invasion, and apoptosis were evaluated by Cell Counting Kit-8 (CCK-8) assay, transwell assay, and flow cytometry, respectively. Cell migration was detected by wound-healing and transwell assays. Direct relationship between miR-375 and circHIPK3 or MMP-16 was verified by dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Our results indicated that PDGF induced the expression of circHIPK3 in human AMSCs (HAMSCs). CircHIPK3 silencing impeded proliferation, migration, invasion and promoted apoptosis of PDGF-treated HAMSCs. Mechanistically, circHIPK3 targeted miR-375 by directly binding to miR-375. MiR-375 was a downstream effector of circHIPK3 in controlling PDGF-induced proliferation, invasion and migration. MMP-16 was directly targeted and inhibited by miR-375, and circHIPK3 functioned as a post-transcriptional modulator of MMP-16 expression through miR-375. Moreover, miR-375-mediated inhibition of MMP-16 impacted HAMSC proliferation, invasion and migration induced by PDGF. Our findings identified the miR-375/MMP-16 axis as a novel mechanism for the modulation of circHIPK3 in PDGF-induced migration and proliferation in HASMCs.

A new neolignan, (-)-(7S, 8R)-3‑methoxy-4', 7-epoxy-8, 5'-neolignane-5, 9, 3', 9′-tetraol (1) and a new biphenylpropanoid, 1, 2-epoxy-1-(3', 4'-dihydroxyphenyl-)-3-(2'', 3'', 5''-trihydroxyphenyl-) propane (2), together with eight known compounds (3-10), were isolated from the 95% EtOH extract of the leaves of Cupressus funebris Endl. Their structures were determined by spectroscopic methods including NMR, circular dichroism (CD) spectra and comparison of the NMR data with reported in references. The antioxidant activities of all compounds were evaluated by DPPH, ABTS, and FRAP methods. Compounds 2 (IC50: 33.98 ± 0.11 μM), 3 (IC50: 32.97 ± 0.63 μM), 8 (IC50: 32.07 ± 1.57 μM), and 9 (IC50: 33.30 ± 2.29 μM) showed stronger DPPH free radical scavenging activity than l -ascorbic acid (IC50: 64.31 ± 1.32 μM). Except for 4, the other compounds showed ABTS radical scavenging abilities comparable to l -ascorbic acid (54.91 ± 1.18 μM) with the IC50 ranged from 24.42 ± 1.78 μM to 138.70 ± 13.58 μM. Compound 3 (0.72 ± 0.02 mmol/g) showed the same ferric reducing antioxidant power (FRAP) as l -ascorbic acid (0.83±0.02 mmol/g).

In this study, the effect of coelomic fluid isolates (CFIs) from sea cucumbers (Stichopus japonicus) on autolysis of minced muscle tissue of S. japonicus was investigated. The coelomic fluid of S. japonicus at the concentration of 90% showed suppression effects on activities of papain and trypsin with inhibitory rate of 26.6% and 40.4%, respectively. Moreover, the effect of CFIs on autolysis of minced muscle tissue from S. japonicus was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and trichloroacetic acid (TCA)-soluble oligopeptide assay. CFIs exhibited significantly inhibitory effect on autolytic muscle mince samples with inhibitory rate at 56.2–87.2%. Both heat and proteinase treatments did not influence the inhibitory effect of CFIs on autolysis of minced muscle tissue from S. japonicus. These results suggest that the non-protein and thermally stable substances contribute to the inhibitory effect of CFIs, which can be used to improve sea cucumber quality.

Circular RNA (circRNAs) functions vital in the pathogenesis and progression of hepatocellular carcinoma (HCC). However, the expressions and functions of certain circRNAs on metastasis and proliferation of that cancer is still unclear. Bioinformation analysis and qRT-PCR indicated that CircC16orf62 was prominent upregulated in HCC of which the expression level was positively associated to cancer’s malignant progression. Gain or loss-of-function studies indicated that the reduction of CircC16orf62 expression promotes the proliferation, invasion, and glycolysis of HCC in vitro and in vivo. The bioinformatic analysis found that miR-138-5p and PTK2 were the downstream target of CircC16or62. Then, the FISH(Fluorescence immunoin situ hybridization) and cell nucleoplasmic separation determined that CircC16orf62 located in the cell cytoplasm. Plasmid vectors or siRNAs were used to change the expression of CircC16orf62, miR-138-5p, and PTK2 in PC cell lines. CircC16orf62 functioned as a molecular sponge for miR-138-5p, and a competitive endogenous RNA for PTK2, promoting AKT/mTOR pathway activation. Our observations lead us to conclude that CircC16orf62 functions as an oncogene in HCC progression, behaving as a competitive endogenous RNA for miR-138-5p binding, thus activating the AKT/mTOR pathway. In conclusion, CircC16orf62 is an oncogene through the miR-138-5p/PTK2/Akt axis in HCC cells, indicating CircC16orf62 can be a therapeutic target with potentiality for liver cancer and a predictive marker for people with HCC.

Directed evolution and targeted genome editing have been deployed to create genetic variants with usefully altered phenotypes. However, these methods are limited to high-throughput screening methods or serial manipulation of single genes. In this study, we implemented multicopy chromosomal integration using CRISPR-associated transposases (MUCICAT) to simultaneously target up to 11 sites on the

Galeaspida is an endemic clade of jawless stem-gnathostomes (‘ostracoderms’), known exclusively from the Silurian and Devonian of China and Vietnam. Among galeaspids, the family Sanqiaspidae is of particular interest for providing the first information on the galeaspid trunk and caudal fin; however, the cranial morphology of sanqiaspids remains poorly known. Here we report the first occurrence of Sanqiaspis in the Xujiachong Formation of Qujing, East Yunnan, and describe new material of Sanqiaspis from two other sites in South China. The new data corroborate the presence of the two median transverse canals in Sanqiaspis as a possible synapomorphy of the Sanqiaspidae. As a key member of the Xujiachong Assemblage, Sanqiaspis is known from the Xujiachong, Guanshanpo, Posongchong, and Si Ka formations. Stratigraphic correlation of eight Early Devonian sections in South China and North Vietnam indicates that the Sanqiaspis-bearing layers can be correlated with the transitional beds between the Lianhuashan and Nahkaoling formations in Liujing, Guangxi. Therefore, the middle-upper part of the Si Ka Formation in northern Vietnam and the upper part of the Lianhuashan Formation in Guangxi should be dated as Pragian, rather than Lochkovian. The fish assemblage from the Pragian of the South China Block documents the diversification of galeaspids, notably Huananaspidiformes, and exhibits much the same endemic pattern as that of early vascular plants and brachiopods. This endemism might be linked with the semi-closed epicontinental nature of the South China Sea during the Early Devonian, which formed a biodiversity hotspot as in the modern Red Sea.

The transcription factor nuclear factor erythroid-derived 2-like 2 (NRF2) participates in the activation of the antioxidant cytoprotective pathway and other important physiological processes to maintain cellular homeostasis. The dysregulation of NRF2 activity plays a role in various diseases, such as cardiovascular diseases, neurodegenerative diseases, and cancer. Thus, NRF2 activity is tightly regulated through multiple mechanisms, among which phosphorylation by kinases is critical in the posttranslational regulation of NRF2. For instance, PKC, casein kinase 2, and AMP-activated kinase positively, while GSK-3 negatively regulates NRF2 activity through phosphorylation of different sites. Here, we provide an overview of the phosphorylation regulation pattern of NRF2 and discuss the therapeutic potential of interventions targeting NRF2 phosphorylation.

Hepatocellular carcinoma (HCC) is a common malignancy, and the hepatitis B virus (HBV) is its major pathogenic factor. Over the past decades, it has been confirmed that HBV infection could promote disease progression through a variety of mechanisms, ultimately leading to the malignant transformation of liver cells. Many factors have been identified in the pathogenesis of HBV-associated HCC (HBV-HCC), including HBV gene integration, genomic instability caused by mutation, and activation of cancer-promoting signaling pathways. As research in the progression of HBV-HCC progresses, the role of many new mechanisms, such as epigenetics, exosomes, autophagy, metabolic regulation, and immune suppression, is also being continuously explored. The occurrence of HBV-HCC is a complex process caused by interactions across multiple genes and multiple steps, where the synergistic effects of various cancer-promoting mechanisms accelerate the process of disease evolution from inflammation to tumorigenesis. In this review, we aim to provide a brief overview of the mechanisms involved in the occurrence and development of HBV-HCC, which may contribute to a better understanding of the role of HBV in the occurrence and development of HCC.

The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.

This study evaluated the gel and microstructure properties of scallop (Patinopecten yessoensis) male gonads hydrolysates (SMGHs) combined with xanthan gum (XG). SMGHs/XG hydrogel matrix properties and structures were elucidated via different analysis tools such as rheometry, LF-NMR, FTIR, AFM, and Cryo-SEM. The addition of XG significantly improved the rheological properties of SMGHs, as indicated by 3.1-fold G' and 1.3-fold melting temperature with increasing the XG dose to 5.6 mg/ml. The corresponding decrease in the T23 relaxation time from 450.3 to 365.6 ms also signified the strong binding between SMGHs and XG. SMGHs/XG also had a higher proton density (T1 and T2 weighted images) due to the higher bound and free water content of the hybrid gel systems, respectively. Additionally, the blueshift in the amide I and II bands in SMGHs/XG further indicated stronger electrostatic interactions between SMGHs and XG. Such scenarios resulted in a well-distributed and compact network with a rougher surface of SMGHs/XG in comparison to pure SMGHs and XG, as assessed by AFM and SEM. These results suggest that SMGHs/XG gel could be a potential hybrid gel applied in the food industry. PRACTICAL APPLICATION: Scallop (Patinopecten yessoensis) male gonads are edible, but are usually discarded during processing of scallop adductor. Because of its rich nutrition and gelation properties, scallop male gonads have a potential role in developing marine source-protein as a functional food base. The SMGHs/XG binary gel would be potentially applied in delivery system in food and biological fields. Further study is undergoing to apply SMGHs/XG binary gel to embed bioactive compounds, such as curcumin and β-carotene.

Magnesium protoporphyrin IX methyltransferase (ChlM) plays an important role in the regulation of chlorophyll biosynthesis and chloroplast development. In the present study, we isolated a ChlM gene, designated ClChlM, from Cymbidium [Cymbidium longibracteatum (Wu & Chen) Chen & Liu]. The open reading frame (ORF) sequence of ClChlM was 945 bp and encoded a putative protein of 314 amino acids. The deduced ClChlM contained the conserved SAM/SAH binding pocket and substrate binding sites. Subcellular localization analysis of ClChlM revealed that the protein was localized in the chloroplast. Ectopic overexpression of ClChlM in tobacco (Nicotiana benthamiana Domin) increased ALA-synthesizing capacity and chlorophyll content and widely upregulated the expression level of photosynthesis-related genes, such as ClHemA, ClGSA, ClLhcb, ClCHLI, and ClCHLH. In conclusion, these results demonstrate that ClChlM plays a crucial role in the regulation of chlorophyll biosynthesis in C. longibracteatum and will help in breeding for leaf colour variance in the future. © 2021 Friends Science Publishers

Background Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats. Results The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process. Conclusions The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.

Urate transporter 1 (URAT1) and glucose transporter 9 (GLUT9) are important targets for the development of uric acid-lowering drugs. We previously showed that the flexible linkers of URAT1 inhibitors could enhance their potency. In this study we designed and synthesized CDER167, a novel RDEA3710 analogue, by introducing a linker (methylene) between the naphthalene and pyridine rings to increase flexibility, and characterized its pharmacological and pharmacokinetics properties in vitro and in vivo. We showed that CDER167 exerted dual-target inhibitory effects on both URAT1 and GLUT9: CDER167 concentration-dependently inhibited the uptake of [(14)C]-uric acid in URAT1-expressing HEK293 cells with an IC(50) value of 2.08 ± 0.31 μM, which was similar to that of RDEA3170 (its IC(50) value was 1.47 ± 0.23 μM). Using site-directed mutagenesis, we demonstrated that CDER167 might interact with URAT1 at S35 and F365. In GLUT9-expressing HEK293T cells, CDER167 concentration-dependently inhibited GLUT9 with an IC(50) value of 91.55 ± 15.28 μM, whereas RDEA3170 at 100 μM had no effect on GLUT9. In potassium oxonate-induced hyperuricemic mice, oral administration of CDER167 (10 mg·kg(−1) · d(−1)) for 7 days was more effective in lowering uric acid in blood and significantly promoted uric acid excretion in urine as compared with RDEA3170 (20 mg·kg(−1) · d(−1)) administered. The animal experiment proved the safety of CDER167. In addition, CDER167 displayed better bioavailability than RDEA3170, better metabolic stability and no hERG toxicity at 100 μM. These results suggest that CDER167 deserves further investigation as a candidate antihyperuricemic drug targeting URAT1 and GLUT9.

Dysregulations in transcription factors (TFs) and their genetic products play important roles in tumorigenesis, tumor progression and metastasis. However, prognostic value of the transcriptional regulatory networks in different cancers has not been investigated in depth. The purpose of our study was to identify and validate a potential predictive signature that combines TFs and their regulatory products in eight solid tumors. We used bioinformatics analysis to identify MET Transcriptional Regulator (MACC1) and Serine Peptidase Inhibitor Kunitz Type 1 (SPINT1) as candidate TFs with the respective downstream regulatory proteins for patient prognosis in pan‐cancer. Subsequent molecular analysis of clinical gastric cancer tissue samples further verified the negative correlation between MACC1 and SPINT1. Further, we showed that mechanistically, MACC1/SPINT1 mediated the pro‐HGF proteolysis and c‐Met phosphorylation in HGF/c‐MET signaling pathway. Kaplan‐Meier plots and receiver operating characteristics analysis revealed that the two‐gene signature combining MACC1 with SPINT1 was effective in predicting survival in all eight cancer cohorts tested. In conclusion, our study clarified the regulatory relationship between MACC1 and SPINT1 in the context of the HGF/c‐MET signaling pathway and determined MACC1/SPINT1 panel as a valuable signature for the prediction of prognosis in patients for multiple solid cancer types., The manuscript addressed on the regulatory relationship and tumor prognostic value of transcription factors (TFs) MACC1 and transmembrane protein SPINT1. Through bioinformatics analysis and molecular experiments, we verified the transcriptional regulatory relationship and biological functions of MACC1 and SPINT1 in HGF/c‐Met signaling axis. Besides, MACC1/SPINT1 panel was established to effectively predict survival in eight cancers.

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (Cas9)-based genome editing tool pCas/pTargetF system that we established previously has been widely used in Escherichia coli MG1655. However, this system failed to manipulate the genome of E. coli BL21(DE3), owing to the potential higher leaky transcription of the gRNA-pMB1 specific to pTargetF in this strain. In this study, we modified the pCas/pTargetF system by replacing the promoter of gRNA-pMB1 with a tightly regulated promoter PrhaB, changing the replicon of pCas to a nontemperature-sensitive replicon, adding the sacB gene into pCas, and replacing the original N20-specific sequence of pTargetF with ccdB gene. We call this updated system as pEcCas/pEcgRNA. We found that gRNA-pMB1 indeed showed a slightly higher leaky expression in the pCas/pTargetF system compared with pEcCas/pEcgRNA. We also confirmed that genome editing can successfully be performed in BL21(DE3) by pEcCas/pEcgRNA with high efficiency. The application of pEcCas/pEcgRNA was then expanded to the E. coli B strain BL21 StarTM (DE3), K-12 strains MG1655, DH5α, CGMCC3705, Nissle1917, W strain ATCC9637, and also another species of Enterobacteriaceae, Tatumella citrea DSM13699, without any specific modifications. Finally, the plasmid curing process was optimized to shorten the time from $\sim$60 h to $\sim$32 h. The entire protocol (including plasmid construction, editing, electroporation and mutant verification, and plasmid elimination) took only $\sim$5.5 days per round in the pEcCas/pEcgRNA system, whereas it took $\sim$7.5 days in the pCas/pTargetF system. This study established a faster-acting genome editing tool that can be used in a wider range of E. coli strains and will also be useful for other Enterobacteriaceae species.

A new genus and species of the Galeaspida Qushiaspis elaia gen. et sp. nov. is described from the Lower Devonian Xujiachong Formation of Qujing, Yunnan Province, southwestern China. The new genus d...

Background: Estrogen receptor alpha (ER/ESR1) mutations are found in 20-40% of endocrine resistant ER+ metastatic breast cancers, and they are associated with worse outcome. Preclinical studies have shown that they cause ligand-independent growth, resistance to endocrine therapy, and there is growing evidence for a role in metastasis. It is not known how ESR1 mutant cancer cells cause metastases and whether such a mechanism may indicate novel therapeutic options. Methods: ddPCR was used to detect hotspot ESR1 mutations. Transcriptome data were derived from cell line models and clinical samples. For in vitro phenotypic characterization, Y537S and D538G genome-edited MCF7 and T47D cell models from four different labs were used. Cell-cell adhesive properties were assessed using calcein-labelled adhesion, spontaneous cell aggregation and microfluidic aggregation assays. Altered expression of cell-cell adhesion genes detected in RNA seq data was validated via qRT-PCR, immunoblot and immune staining. Functional contributions of desmosome and gap junctions were tested by blocking peptide and carbenoxolone respectively. Mutant ER cistromes were profiled using ChIP-sequencing. Tail vein injection was performed on nude mice to evaluate metastasis in vivo. Mouse lung micro-metastatic foci were quantified using human-specific CK19 staining. Circulating tumor cells (CTCs) clustering propensity in vivo was assessed via intracardiac injection of ESR1 WT and mutant cells into nude mice following CTC microfilter capture. CTCs enumeration from breast cancer patients’ blood samples was performed using CellSearchTM system. Results: We identified a significant enrichment of ESR1 mutations in distant (12/48) vs local (0/27) recurrences, confirming the strong association of mutant ER with metastasis. Transcriptomic analysis revealed altered cell-to-cell interaction pathways in ESR1 mutant tumors compared to ESR1 WT tumors, suggesting a previously undescribed role of ESR1 mutations in reprogramming cell-cell adhesome. ESR1 mutant cells grown in suspension culture revealed more compact multicellular spheroids compared to WT cells. This observation was confirmed under both static and microfluidic conditions, indicative of increased cell-cell interactions. The effect was more pronounced in MCF7 compared to T47D cells, and it correlated with increased expression of multiple desmosome and gap junction pathway genes, which were also significantly enriched in ESR1 mutant tumors. Pharmacological blockade of desmosome and gap junctions significantly rescued enhanced cell-cell adhesion in ESR1 mutant cells. Mechanistically, our ER ChIP-seq did not identify any gained mutant ER binding sites in proximity to cell-cell adhesion gene loci, indicating indirect regulation by mutant ER. Consistent with this, expression of Connexin 43, one of the top upregulated gap junction components, was induced by cFOS found to be highly upregulated in ESR1 mutant cells. Tail vein injection of ESR1-mutant cells derived more distant macro- (MCF7) and micro- (T47D) metastases. Given increasing evidence for role of cell-cell attachment in CTC phenotypes, we tested CTC formation for ESR1 WT and mutant cells. In vivo studies showed MCF7 Y537S ESR1 mutant cells formed larger multi-cellular CTC clusters with increased compactness compared to WT CTCs. These preclinical data translated to clinical observation, where we observed an enrichment of CTC clusters in patients with ESR1 mutant-metastatic breast cancers. Conclusion: Hotspot ESR1 mutations induce expression of multiple desmosome and gap junction genes and confer increased cell-cell adhesion, which facilitate breast cancer metastasis via increased CTCs clustering propensity. These findings might guide approaches to test potential repurpose of drugs targeting gap junction in ER mutant tumors. Citation Format: Zheqi Li, Yang Wu, Amir Bahreini, Jian Chen, Ye Qin, Kevin M. Levine, Nilgun Tasdemir, Nolan Priedigkeit, Li Zhu, George C. Tseng, Yu Jiang, Benjamin Troness, Laki Buluwela, Simak Ali, Spencer Arnesen, Jason Gertz, Ben H. Park, Qiang Zhang, Lorenzo Gerratana, Andrew Davis, Jennifer M. Atkinson, Dorraya El-Ashry, Massimo Cristofanilli, Adrian V. Lee, Steffi Oesterreich. Hotspot ESR1 mutations rewire cell-cell adhesome to facilitate breast cancer metastasis [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr GS1-05.

The adenosine monophosphate (AMP)-activated protein kinase (Ampk) is a central regulator of metabolic pathways, and increasing Ampk activity has been considered to be an attractive therapeutic target. Here, we have identified an orphan ubiquitin E3 ligase subunit protein, Fbxo48, that targets the active, phosphorylated Ampkα (pAmpkα) for polyubiquitylation and proteasomal degradation. We have generated a novel Fbxo48 inhibitory compound, BC1618, whose potency in stimulating Ampk-dependent signaling greatly exceeds 5-aminoimidazole-4-carboxamide-1-β-ribofuranoside (AICAR) or metformin. This compound increases the biological activity of Ampk not by stimulating the activation of Ampk, but rather by preventing activated pAmpkα from Fbxo48-mediated degradation. We demonstrate that, consistent with augmenting Ampk activity, BC1618 promotes mitochondrial fission, facilitates autophagy and improves hepatic insulin sensitivity in high-fat-diet-induced obese mice. Hence, we provide a unique bioactive compound that inhibits pAmpkα disposal. Together, these results define a new pathway regulating Ampk biological activity and demonstrate the potential utility of modulating this pathway for therapeutic benefit.

Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P

In this paper, some cationic dipeptides from scallop (Patinopecten yessoensis) male gonads (SMGs), which can synergistically gel with ι-carrageenan (ι-C), were screened by the in silico approach. Fourteen protein sequences of SMGs were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and nano liquid chromatography-mass spectrometry/mass spectrometry (nanoLC-MS/MS) analysis and were then hydrolyzed via in silico simulation. A total of 414 sequences were obtained with 56 duplicates, half of which were positively charged at pH 7. Among the cation sequences, 171 had good water solubility, including two amino acids (Lys and Arg). The molecular weight analysis of the cationic water-soluble sequences showed that 0.2–0.3 kDa accounted for the highest proportion. Based on the obvious synergistic effect of Lys and ι-C, 11 Lys-containing dipeptides, including Ser-Lys (SK), Thr-Lys (TK), Trp-Lys (WK), Ala-Lys (AK), Leu-Lys (LK), Gly-Lys (GK), Val-Lys (VK), Cys-Lys (CK), Asn-Lys (NK), Phe-Lys (FK), and Met-Lys (MK), were finally screened out to study gelation with ι-C. It was found that the dipeptides/ι-C formed firm gels except WK/ι-C. The values of the storage modulus (G′) of 11 dipeptides/ι-C were investigated by a rheometer. The G′ of 8 dipeptides/ι-C was higher than 1000 Pa. These results indicated that the in silico-screened dipeptides from SMGs can form composite gels with ι-C, which can be used for the design and development of functional hydrogels.

Ovarian cancer is the first leading cause of death in gynecological cancers. The continuous survival and metastasis of cancer cells are the main causes of death and poor prognosis in patients with ovarian cancer. Berberine is an effective component extracted from the rhizomes of coptis chinensis and phellodendron chinensis. In our study, we aim to explore the molecular mechanism underlying the regulation of proliferation, migration and invasion by berberine in ovarian cancer cells. CCK8 assay was used for detection of proliferative capacity of SKOV3 and 3AO cells. Wound healing assay was used to estimate cell migration and transwell assay was used to assess cell invasion. The mRNA expression of miR-145 and MMP16 were examined by quantitative real-time polymerase chain reaction (qRT-PCR). The protein level of MMP16 was detected by western blot analysis. In addition, luciferase reporter assays were used to demonstrate MMP16 was a target of miR-145. The results demonstrated berberine inhibited proliferation, migration and invasion, promoted miR-145 expression, and decreased MMP16 expression in SKOV3 and 3AO cells. MMP16 was a target of miR-145. Moreover, downregulation of MMP16 contributed to the inhibition of proliferation, migration and invasion by berberine. Together, our results revealed that berberine inhibited proliferation, migration and invasion through miR-145/MMP16 in SKOV3 and 3AO cells, highlighting the potentiality of berberine to be used as a therapeutic agent for ovarian cancer.

Abstract N-butanol is an important chemical and can be naturally synthesized by Clostridium species; however, the poor n-butanol tolerance of Clostridium impedes the further improvement in titer. In this study, Lactobacillus brevis, which possesses a higher butanol tolerance, was selected as host for heterologous butanol production. The Clostridium acetobutylicum genes thl, hbd, and crt which encode thiolase, β-hydroxybutyryl-CoA dehydrogenase, and crotonase, and the Treponema denticola gene ter, which encodes trans-enoyl-CoA reductase were cloned into a single plasmid to express the butanol synthesis pathway in L. brevis. A titer of 40 mg/L n-butanol was initially achieved with plasmid pLY15-opt, in which all pathway genes are codon-optimized. A titer of 450 mg/L of n-butanol was then synthesized when ter was further overexpressed in this pathway. The role of metabolic flux was reinforced with pLY15, in which only the ter gene was codon-optimized, which greatly increased the n-butanol titer to 817 mg/L. Our strategy significantly improved n-butanol synthesis in L. brevis and the final titer is the highest achieved amongst butanol-tolerant lactic acid bacteria. Graphic abstract

OBJECTIVE: To investigate the differences of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and galectin-3 concentrations in lobar pneumonia and bronchopneumonia induced by mycoplasma pneumoniae (MP) in children and to explore these related factors predicting the severity of MP. METHODS: A total of 148 children with mycoplasma pneumoniae pneumonia (MPP) and 32 healthy controls were analyzed from March 2017 to August 2018 in our province. Clinical information was collected from the hospitalized MP patients. The 148 patients with MPP were divided into two groups: lobar pneumonia group and bronchial pneumonia group. The 32 healthy children were considered the control group. The concentrations of TNF-α, IL-6 and Gal-3 were examined in the serum of 148 children patients with MPP and 32 healthy children by double-antibody sandwich enzyme-linked immunosorbent assay (ELISA). RESULTS: The TNF-α, IL-6 and Gal-3 levels were obviously higher in both the lobar pneumonia and bronchial pneumonia groups, compared to those in the control group. Furthermore, these levels were significantly higher in the lobar pneumonia group, compared to the bronchial pneumonia group. After treatment, the levels of TNF-α, IL-6 and Gal-3 totally descended during the recovery period. CONCLUSION: There are differences in serum TNF-α, IL-6 and Gal-3 concentrations in lobar pneumonia and bronchial pneumonia caused by MP in children. In general, the TNF-α, IL-6 and Gal-3 levels were significantly higher in the lobar pneumonia group, when compared to the bronchial pneumonia group. This was because most lobar pneumonia cases are much more serious than bronchial pneumonia. Moreover, it has been proven that TNF-α, IL-6 and Gal-3 may play an important role in the pathogenesis development of MPP. At the same time, these are important issues in diagnosing MPP.

Microsporidia are a group of obligate intracellular parasites causing significant disease in human beings and economically important animals. Though a few spore wall proteins (SWPs) have now been identified in these intriguing species, the information on SWPs remains too little to elucidate the spore wall formation mechanisms of microsporidia. It has been well described that numerous proteins with tandem repeats tend to be localized on the cell wall of fungi and parasites. Previously, by scanning the proteins with tandem repeats in microsporidian Nosema bombycis, we obtained 83 candidate SWPs based on whether those proteins possess a signal peptide and/or transmembrane domain. Here, we further characterized a candidate protein (EOB13250) with three tandem repeats in the N-terminal region and a transmembrane domain in C-terminus of N. bombycis. Sequence analysis showed that the tandem repeat domain of EOB13250 was species-specific for this parasite. RT-PCR indicated that the expression of the gene encoding this protein started on the fourth day postinfection. After cloned and expressed in Escherichia coli, a polyclone antibody against the recombinant EOB13250 protein was prepared. Western blotting demonstrated this protein exist in N. bombycis. Immunofluorescence analysis (IFA) and immunoelectron microscopy analysis (IEM) further provided evidence that EOB13250 was an endospore wall protein. These results together suggested that EOB13250 was a novel spore wall protein of N. bombycis. This study provides a further enrichment of the number of identified spore wall proteins in microsporidia and advances our understanding of the spore wall formation mechanism in these obligate unicellular parasites.

This paper presents a simple strategy to adjust bacterial cellulose (BC) nanofiber distribution on the biomimetic 3D scaffolds by in situ bacteria culture on the protein scaffolds which were prepared by selecting gelatin (Gel) with positive charge and silk fibroin (SF) with negative charge. The protein scaffolds with different structures and properties were obtained by adjusting the proportion of Gel and SF. Due to the electrical attraction and repulsion of bacteria and protein, the density and distribution of bacteria on the protein scaffolds is obviously different. Thus, after in situ culture, protein/BC scaffolds with different nanofibers density and distribution from basically adhering to the pore wall to distributing in the middle pore were obtained, which make different cell shape and distribution. It is can be easily realized by adjusting the properties of scaffold materials to guide the growth of bacteria which provides a simple idea for the design of tissue engineering scaffolds applied in medical implants, cell supports and other tissue regeneration.

Modulation of protein fate decision and protein homeostasis plays a significant role in altering the protein level, which acts as an orientation to develop drugs with new mechanisms. The molecular chaperones exert significant biological functions on modulation of protein fate decision and protein homeostasis under constantly changing environmental conditions through extensive protein–protein interactions (PPIs) with their client proteins. With the help of molecular chaperone machinery, the processes of protein folding, trafficking, quality control and degradation of client proteins could be arranged properly. The core members of molecular chaperones, including heat shock proteins (HSPs) family and their co-chaperones, are emerging as potential drug targets since they are involved in numerous disease conditions. Development of small molecule modulators targeting not only chaperones themselves but also the PPIs among chaperones, co-chaperones and clients is attracting more and more attention. These modulators are widely used as chemical tools to study chaperone networks as well as potential drug candidates for a broader set of diseases. Here, we reviewed the key checkpoints of molecular chaperone machinery HSPs as well as their co-chaperones to discuss the small molecules targeting on them for modulation of protein fate decision., Graphical abstract This review summarizes the current states on modulation of molecular chaperone by small molecules, focusing on the protein fate decision by comprehensive strategies and different mechanisms.Image 1

B-cell lymphoma-2 (Bcl-2) family proteins, comprising proapoptotic proteins (Bax and Bak), antiapoptotic proteins (Bcl-2, Bcl-XL, Bcl-w, Mcl-1, and A1) and BCL-2 homology domain 3 (BH3)-only proteins (Bid, Noxa, and Puma), have long been identified as pivotal apoptosis regulators. As an antiapoptotic member, myeloid cell leukemin-1 (Mcl-1) can bind with proapoptotic proteins and inhibit apoptosis. Mcl-1 is frequently overexpressed and closely associated with oncogenesis and poor prognosis in several cancers, posing a tremendous obstacle for cancer therapy. Recently, an increasing number of Mcl-1-selective small-molecule inhibitors have entered preclinical studies and advanced into clinical trials. In this review, we briefly introduce the role of Mcl-1 in apoptosis and highlight the recent development of Mcl-1 small-molecule inhibitors.

Aim: To explore the biological functions and clinical significance of CAVIN2 in lung cancer. Materials & methods: Methylation-specific PCR was used to measure promoter methylation of CAVIN2. The function of CAVIN2 was tested by Cell Counting Kit-8, colony formation, Transwell, flow cytometric analysis, acridine orange/ethidium bromide, chemosensitivity assay and xenograft assay. Results: CAVIN2 is significantly downregulated by promoter methylation in lung cancer. CAVIN2 overexpression inhibits lung cancer cell migration and invasion. Furthermore, ectopic expression of CAVIN2 inhibits cell proliferation in vivo and in vitro by inducing G2/M cell cycle arrest, which sensitizes the chemosensitivity of lung cancer cells to paclitaxel and 5-fluorouracil, but not cisplatin. Conclusion: CAVIN2 is a tumor suppressor in non-small-cell lung cancer and can sensitize lung cancer cells to paclitaxel and 5-fluorouracil.

Having great medicinal values, Dendrobium species of “Fengdou” (DSFs) are a taxonomically complex group in Dendrobium genus including many closely related and recently diverged species. Traditionally used DNA markers have been proved to be insufficient in authenticating many species of this group. Here, we investigated 101 complete plastomes from 23 DSFs, comprising 72 newly sequenced and 29 documented, which all exhibited well-conserved genomic organization and gene order. Plastome-wide comparison showed the co-occurrence of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), which can be explained by both the repeat-associated and indel-associated mutation hypotheses. Moreover, guanine-cytosine (GC) content was found to be negatively correlated with the three divergence variables (SNPs, indels and repeats), indicating that GC content may reflect the level of the local sequence divergence. Our species authentication analyses revealed that the relaxed filtering strategies of sequence alignment had no negative impact on species identification. By assessing the maximum likelihood (ML) trees inferred from different datasets, we found that the complete plastome and large single-copy (LSC) datasets both successfully identified all 23 DSFs with the maximum bootstrap values. However, owing to the high efficiency of LSC in species identification, we recommend using LSC for accurate authentication of DSFs., Graphical abstract Compared with other datasets, the large single-copy (LSC) and complete plastome datasets both exhibited the highest discriminatory power of 100% for Dendrobium species of “Fengdou” (DSFs). Considering the potential advantages of LSC in the efficiency and cost of authentication, we recommend using the LSC for accurate authentication of DSFs.Image 1

The Y chromosome plays key roles in male fertility and reflects the evolutionary history of paternal lineages. Here, we present a de novo genome assembly of the Hu sheep with the first draft assembly of ovine Y chromosome (oMSY), using nanopore sequencing and Hi-C technologies. The oMSY that we generated spans 10.6 Mb from which 775 Y-SNPs were identified by applying a large panel of whole genome sequences from worldwide sheep and wild Iranian mouflons. Three major paternal lineages (HY1a, HY1b and HY2) were defined across domestic sheep, of which HY2 was newly detected. Surprisingly, HY2 forms a monophyletic clade with the Iranian mouflons and is highly divergent from both HY1a and HY1b. Demographic analysis of Y chromosomes, mitochondrial and nuclear genomes confirmed that HY2 and the maternal counterpart of lineage C represented a distinct wild mouflon population in Iran that diverge from the direct ancestor of domestic sheep, the wild mouflons in Southeastern Anatolia. Our results suggest that wild Iranian mouflons had introgressed into domestic sheep and thereby introduced this Iranian mouflon specific lineage carrying HY2 to both East Asian and Africa sheep populations.

Background Peroxiredoxin 1 (PRDX1) has been identified as a dual regulator of tumorigenesis. However, its expression, clinical significance, and biological function in nasopharyngeal carcinoma (NPC) remain unknown. This study aimed to explore the role and underlying mechanisms of PRDX1 in NPC. Materials and methods The expression of PRDX1 in NPC tissues was evaluated by immunohistochemistry, and the relationships between the expression of PRDX1 and clinical features and prognosis of NPC patients were analyzed. The effects of PRDX1 on NPC cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition (EMT) were examined. A tumor-bearing model of nude mouse was established to verify the function of PRDX1 in vivo. Results PRDX1 expression level was negatively associated with recurrence and metastasis of NPC. PRDX1 knockdown promoted NPC cell proliferation, migration, invasion and EMT in vitro, and enhanced tumor growth in vivo, while PRDX1 overexpression had opposite effects. Furthermore, transcriptome analysis showed that PRDX1 inhibited the activation of PI3K/AKT/TRAF1 signaling in NPC cells. Conclusion PRDX1 inhibits NPC by inhibiting the activation of PI3K/AKT/TRAF1 signaling. PRDX1 is a tumor suppressor in human NPC and may be a prognostic biomarker for NPC patients.

Somatic cell nuclear transfer (SCNT) has been successfully used for cloning in a variety of mammalian species. However, SCNT reprogramming efficiency is relatively low, in part, due to incomplete DNA methylation reprogramming of donor cell nuclei. We previously showed that ten-eleven translocation 3 (TET3) is responsible for active DNA demethylation during preimplantation embryonic development in bovines. In this study, we constructed TET3-overexpressing cell lines in vitro and observed that the use of these fibroblasts as donor cells increased the blastocyst rate by approximately 18 percentage points compared to SCNT. The overexpression of TET3 in bovine SCNT embryos caused a decrease in the global DNA methylation level of the pluripotency genes Nanog and Oct-4, ultimately resulting in an increase in the transcriptional activity of these pluripotency genes. Moreover, the quality of bovine TET3-NT embryos at the blastocyst stage was significantly improved, and bovine TET3-NT blastocysts possessed more total number of cells and fewer apoptotic cells than the SCNT blastocysts, similar to in vitro fertilization (IVF) embryos. Nevertheless, DNA methylation of the imprinting control region (ICR) for the imprinted genes H19-IGF2 in SCNT embryos remained unaffected by TET3 overexpression, maintaining parent-specific activity for further development. Thus, the results of our study provide a promising approach to rectify incomplete epigenetic reprogramming and achieve higher cloning efficiency.

The present study aimed to explore the possible functions of radial oxygen loss (ROL) on mangrove nutrition. A field survey was conducted to explore the relations among ROL, root anatomy and leaf N in different mangrove species along a continuous tidal gradient. Three mangroves with different ROL (Avicennia marina [A. marina], Kandelia obovata and Rhizophora stylosa) were then selected to further explore the dynamics of N at the root-soil interface. The results showed that seaward pioneer mangrove species such as A. marina appeared to exhibit higher leaf N despite growing under poorer nutrient conditions. Greater leaf N in pioneer mangroves coincided with their special root structure (e.g., high porosity together with a thin lignified/suberized exodermis) and powerful ROL. An interesting positive relation was observed between ROL and leaf N in mangroves. Moreover, rhizo-box data further showed that soil nitrification was also strongly correlated with ROL. A. marina, which had the highest ROL among the three mangrove species studied, consistently possessed the highest levels of NO3−, nitrification and ammonia-oxidizing bacteria and archaea gene copies in the rhizosphere. Besides, both NO3− and NH4+ influxes were found to be higher in the roots of A. marina when compared to those of K. obovata and R. stylosa. In summary, greater N acquisition by pioneer mangroves such as A. marina was strongly correlated with ROL which would regulate N transformation and translocation at the root-soil interface. The implications of this study may be significant in mangrove nutrition and the mechanisms involved in mangrove zonation.

The production of acetone-butanol-ethanol by solventogenic Clostridium using lignocellulosic biomass can be a potential alternative to petroleum-based butanol. However, previous studies on nondetoxified lignocellulose hydrolysate could not provide better results when compared to those in synthetic medium. In this study, we engineered the pentose pathway of Clostridium beijerinckii NCIMB 8052, which was then subjected to adaptive laboratory evolution in the gradient mixture of synthetic medium and pretreated corn stover enzymatic hydrolysate (CSH) prepared according to the National Renewable Energy Laboratory (NREL) standard. The final resultant strain CIBTS1274A produced 20.7 g/L of total solvents in NREL CSH diluted to 6% initial total sugars, supplemented with ammonium acetate. This performance was comparable with that of corn-based butanol. In addition, this strain was successfully used in the scale-up operation using nondetoxified corn stover and corncob hydrolysate at Lignicell Refining Biotechnologies Ltd., which once was the only commercial biobutanol industry in the world.

Increasing organic fertilizer application can improve the sustainability of soil productivity, but the effects of increased organic fertilizer application with reduced chemical fertilizer application over different time periods on chemical properties and bacterial community of grape rhizosphere soil in an arid region are not clear. In this study, three years of fixed-point field tests were used to compare the effects of various fertilization treatments on the soil properties and bacterial community in the grape rhizosphere. The results showed that (1) T1 and T2 significantly increased SOM, AN, AP and AK contents in grape rhizosphere soil. TN, TP and TK contents in grape leaves of T2 were the highest of those in five fertilization treatments. (2) The abundances of Proteobacteria and Bacteroidetes phyla and especially of Arthrobacter, Pseudomonas, Nitrosopira and Bacillus genera were higher in T2 than in the other samples. (3) SOM, AP and AN contents in soil were the main factors affecting soil bacterial community and mineral element contents in grape leaves and roots according to an RDA analysis. In summary, the application of organic fertilizer with reduced chemical fertilizer for two years had the greatest impact on the soil properties and bacterial community of the grape rhizosphere soil.

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar .

Although induced pluripotent stem cells (iPSCs) had been generated from several somatic cell types in cattle, their pluripotency and differentiation capacities after freezing/thawing, and the dysregulated transcripts involved in pathways critical for reprogramming were not investigated. Additionally, selection of proper source cells is critical for iPSC derivation because the residual influence of the somatic origin may variegate their differentiation propensity. Sertoli cells (SCs) have special properties suitable for iPSCs derivation. Herein bovine SCs were enriched from the cryopreserved testicular tissues and reprogrammed into iPSCs using lentivirus carrying yamanaka factors (OSKM). These iPSCs have typical morphology resembling human iPSCs and remain normal karyotypes. They can express alkaline phosphatase activity and common pluripotency markers with a low methylation in the promoter region of Nanog. They can also form embryoid bodies and teratomas that give rise to cells/tissues from three embryonic germ layers. Transcriptome profiling showed that the exogenous OSKM were silenced and 8009 dysregulated mRNAs were identified. The pluripotency, methyldioxygenase and anti-apoptosis genes were all upregulated but the apoptotic gene downregulated in these iPSCs. Bunch of pathways related to the reprogramming, inflammation and viral infection pathways were upregulated, while pathways associated with the differentiation, senescence, metabolism and apoptosis were downregulated in these cells. After cryopreservation/thawing, the recovered iPSCs remain strong pluripotency and differentiation capabilities. Together, iPSCs were derived from the bovine SCs isolated from the cryopreserved neonatal bull testis, pluripotency and differentiation capacities verified, iPSCs cryopreserved, cultured and again reverified for pluripotency and differentiation capacities.

Background Following acute ischemic stroke (AIS), approximately half of patients do not achieve recanalization after intravenous administration of tissue plasminogen activator (rt-PA). Thrombolysis resistance is a possible reason for recanalization failure. Thrombolysis resistance is likely related to the ultrastructure and composition of the thrombus. However, there is a paucity of published information on the relationship between thrombus ultrastructure and thrombolysis resistance. Case presentation Two patients who underwent mechanical thrombectomy were observed within 4.5 h after stroke onset. One patient failed to respond to rt-PA (defined as thrombolysis resistant), and the other patient did not receive rt-PA treatment (non-rtPA). In each patient, the occluded artery was the internal carotid artery or middle cerebral artery. According to the Trial of ORG 10172 in Acute Stroke Treatment classification, both patients had large atherosclerotic cerebral infarction. By scanning electron microscopy (SEM) and transmission electron microscopy (TEM), we found that the thrombus structure was significantly different between the two patients. Conclusion Grid-like dense fibrin, compressed polyhedral erythrocytes, and large accumulation of neutrophils may be characteristics of thrombolysis resistant thrombi.

Twenty-one β-dihydroagarofuran-type sesquiterpenes compounds were isolated from the dry roots of Tripterygium wilfordii, including eight new β-dihydroagarofuran-type sesquiterpenes nature products (2, 6, 8-13) and thirteen known compounds, the structure of these compounds were elucidated by extensive NMR spectroscopic and mass spectrometric analysis. Among all isolated compound 10 exhibited cytotoxicity toward five carcinoma cells, including A549, HOS, MCF-7, MDA-MB-231 and MCF7/TAMR cells, with half-maximal inhibition of cell proliferation values ranging from 13.77 to 25.19 μM.

Objective The effects of the Apolipoprotein E (ApoE) genotype on peripheral amyloid beta (Aβ) and Aβ transporter levels are still unclear. Soluble low-density lipoprotein receptor-related protein-1 (sLRP1) and soluble receptor of advanced glycation end products (sRAGE) are the major transporter for Aβ, which can prevent plasma Aβ from flowing into brain. The aim of this study was to investigate the relationships between the ApoE genotype and plasma Aβ, sLRP1, sRAGE levels. Design Cross-sectional study. Setting The committee office of the village. Participants Residents lived in the village for more than 3 years, aged 40–85 years (n = 1,119, 63.5% women). Measurements Plasma biomarkers include ApoE genotype, Aβ, sLRP1, sRAGE, fasting blood-glucose, and blood lipids. General information, medical history, living habits, and cognitive status (cognitive impairment or not) were also collected. Results After controlling for all possible covariates, multiple linear regression analysis showed that the plasma level of Aβ42 was higher and log-transformed sLRP1 was lower in ApoE e4 carriers than that in noncarriers (βAβ42 = 1.214, 95% confidence interval: 0.105–2.316, pAβ42 = 0.031; βsLRP1 = −0.075, 95% confidence interval: −0.129 to −0.021, psLRP1 = 0.006, respectively). Partial correlation analysis showed that plasma Aβ40 was positively correlated with log-transformed sLRP1 and log-transformed sRAGE (rsLRP1 = 0.116, psLRP1 Conclusion ApoE e4 carriers had higher plasma Aβ42 levels and lower sLRP1 levels. These data indicated that the ApoE e4 allele may also contribute to the pathogenesis of Alzheimer's disease through its effects on peripheral Aβ42 and sLRP1 levels, but it needs to be further elucidated.