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There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based single-cell whole-genome sequencing (scWGS) method named SMOOTH-seq (single-molecule real-time sequencing of long fragments amplified through transposon insertion). We evaluate the method for detecting CNVs, SVs, and SNVs in human cancer cell lines and a colorectal cancer sample and show that SMOOTH-seq reliably and effectively detects SVs and ecDNAs in individual cells, but shows relatively limited accuracy in detection of CNVs and SNVs. SMOOTH-seq opens a new chapter in scWGS as it generates high fidelity reads of kilobases long. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02406-y.

Background Pituitary neuroendocrine tumors (PitNETs) are the second most common intracranial tumor. We lacked a comprehensive understanding of the pathogenesis and heterogeneity of these tumors. Methods We performed high-precision single-cell RNA sequencing for 2679 individual cells obtained from 23 surgically resected samples of the major subtypes of PitNETs from 21 patients. We also performed single-cell multi-omics sequencing for 238 cells from 5 patients. Results Unsupervised clustering analysis distinguished all tumor subtypes, which was in accordance with the classification based on immunohistochemistry and provided additional information. We identified 3 normal endocrine cell types: somatotrophs, lactotrophs, and gonadotrophs. Comparisons of tumor and matched normal cells showed that differentially expressed genes of gonadotroph tumors were predominantly downregulated, while those of somatotroph and lactotroph tumors were mainly upregulated. We identified novel tumor-related genes, such as AMIGO2, ZFP36, BTG1, and DLG5. Tumors expressing multiple hormone genes showed little transcriptomic heterogeneity. Furthermore, single-cell multi-omics analysis demonstrated that the tumor had a relatively uniform pattern of genome with slight heterogeneity in copy number variations. Conclusions Our single-cell transcriptome and single-cell multi-omics analyses provide novel insights into the characteristics and heterogeneity of these complex neoplasms for the identification of biomarkers and therapeutic targets.

This study describes the synthesis of a coumarin-based reversible fluorescent probe BuCAC for the detection of Cu2+ and S2− in CH3CN : PBS (v/v = 8 : 2, pH = 7.4) solution. The resulting BuCAC exhibited high sensitivity (detection limit = 3.03 × 10−7 M) and selectivity towards Cu2+ through a 2 : 1 binding mode. In the presence of S2−, the BuCAC–Cu2+ recovered to BuCAC and CuS, which in turn perform the function of a sensitive probe with a lower detection limit of about 1.7 × 10−7 M. This “on–off–on” process can easily occur in 1 min with a repetition of at least 5 times. The sensing mechanism was confirmed by Job's plot analysis, MS, and density theory calculation. Besides, fluorescence imaging in zebrafish, HeLa cells, and soybean root tissue revealed that the probe BuCAC could serve as a valuable tool for monitoring and tracking intracellular Cu2+ and S2− while benefiting from its excellent fluorescence performance and lower cytotoxicity.

A novel quinoline fluorescent probe QNP ((E)-N′-(5-chloro-2-hydroxybenzylidene) quinoline-2-carbohydrazide) for detection of Al3+ ion was designed, synthesized and characterized. QNP displayed a high fluorescence enhancement in the presence of Al3+ ion in DMF:PBS (99:1, v/v) solution and the detection limit was as low as 1.25 μM with high selectivity and excellent sensitivity from 0 to 3 μM. The sensing ability of QNP towards Al3+ ion is attributed to the synergistic effect of PET and ICT. Furthermore, the binding stoichiometry between QNP and Al3+ ion is of 1:1 by Job’s plot and mass spectrum, and the calculated binding constant is 4.29 × 108 M−1. The detection of Al3+ ion in water samples illustrates that QNP could be applied to the detection of practical samples in the environment. Bioimaging experiments on Hela cells, zebrafish and soybean root tissues demonstrate that it has potential application to investigate biological processes involving Al3+ ion within living cells. A quinoline-based turn-on fluorescence probe for the detection of Al3+ and its bioimaging in living cells, plant, and zebrafish.

The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Corticotropes exhibit an early intermediate state prior to full differentiation. Three cell types of the PIT-1 lineage (somatotropes, lactotropes and thyrotropes) segregate from a common progenitor coexpressing lineage-specific transcription factors of different sublineages. Gonadotropes experience two multistep developmental trajectories. Furthermore, we identify a fetal gonadotrope cell subtype expressing the primate-specific hormone chorionic gonadotropin. We also characterize the cellular heterogeneity of pituitary stem cells and identify a hybrid epithelial/mesenchymal state and an early-to-late state transition. Here, our results provide insights into the transcriptional landscape of human pituitary development, defining distinct cell substates and subtypes and illustrating transcription factor dynamics during cell fate commitment., Editor’s summary_NCOMMS-19-41732B The anterior pituitary gland controls body growth and reproduction but how early development is dynamically regulated is unclear. Here, the authors use scRNA-seq of human fetal pituitaries to identify different developmental routes and state transitions of five hormone-producing cell lineages, and a hybrid epithelial/mesenchymal state of pituitary stem cells.

Proper development of fetal germ cells (FGCs) is vital for the precise transmission of genetic and epigenetic information through generations. The transcriptional landscapes of human FGC development have been revealed; however, the epigenetic reprogramming process of FGCs remains elusive. Here, we profiled the genome-wide DNA methylation and chromatin accessibility of human FGCs at different phases as well as gonadal niche cells at single-cell resolution. First, we found that DNA methylation levels of FGCs changed in a temporal manner, whereas FGCs at different phases in the same embryo exhibited comparable DNA methylation levels and patterns. Second, we revealed the phase-specific chromatin accessibility signatures at the promoter regions of a large set of critical transcription factors and signaling pathway genes. We also identified potential distal regulatory elements including enhancers in FGCs. Third, compared with other hominid-specific retrotransposons, SVA_D might have a broad spectrum of binding capacity for transcription factors, including SOX15 and SOX17. Finally, using an in vitro culture system of human FGCs, we showed that the BMP signaling pathway promoted the cell proliferation of FGCs, and regulated the WNT signaling pathway by orchestrating the chromatin accessibility of its ligand genes. Our single-cell epigenomic atlas and functional assays provide valuable insights for understanding the strongly heterogeneous, unsynchronized, yet highly robust nature of human germ cell development.

Several bioactive dehydroabietylamine Schiff-bases (L1−L4), amides (L5−L11) and complex CuL3(NO3)2, Cu(L5)3, Co(L6)2Cl2 had been synthesized successfully for developing more efficient but lower toxic antiproliferative compounds. Their antiproliferative activities to Hela (cervix), HepG2 (liver), MCF-7 (breast), A549 (lung) and HUVEC (umbilical vein, normal cell) were investigated in vitro. The toxicity of all compounds was less than dehydroabietylamine (L0). For HepG2 cells, L1, L2 and L3 had higher anti-HepG2 activity, especially L1 (0.52 µM) had highest anti-HepG2 activity but low toxicity. For MCF-7 cells, L1, L2, L3 and L4 had higher anti-MCF-7 activity, especially L3(0.49 µM) had highest anti-MCF-7 activity but low toxicity. For A549 cells, L2 and L3 had higher anti-A549 activity. Furthermore, L1 and L3 may be the great promise antiproliferative drugs with nontoxic side effects, due to the high anti-HepG2 and anti-MCF-7 inhibition rate in vivo, 65% and 61%, respectively. L1, L2 and L3 could induce apoptosis through intercalating into DNA.

Hematopoietic stem cells (HSCs) in adults are believed to be born from hemogenic endothelial cells (HECs) in mid-gestational embryos. Due to the rare and transient nature, the HSC-competent HECs have never been stringently identified and accurately captured, let alone their genuine vascular precursors. Here, we first used high-precision single-cell transcriptomics to unbiasedly examine the relevant EC populations at continuous developmental stages with intervals of 0.5 days from embryonic day (E) 9.5 to E11.0. As a consequence, we transcriptomically identified two molecularly different arterial EC populations and putative HSC-primed HECs, whose number peaked at E10.0 and sharply decreased thereafter, in the dorsal aorta of the aorta-gonad-mesonephros (AGM) region. Combining computational prediction and in vivo functional validation, we precisely captured HSC-competent HECs by the newly constructed Neurl3-EGFP reporter mouse model, and realized the enrichment further by a combination of surface markers (Procr+Kit+CD44+, PK44). Surprisingly, the endothelial-hematopoietic dual potential was rarely but reliably witnessed in the cultures of single HECs. Noteworthy, primitive vascular ECs from E8.0 experienced two-step fate choices to become HSC-primed HECs, namely an initial arterial fate choice followed by a hemogenic fate conversion. This finding resolves several previously observed contradictions. Taken together, comprehensive understanding of endothelial evolutions and molecular programs underlying HSC-primed HEC specification in vivo will facilitate future investigations directing HSC production in vitro.

The medial prefrontal cortex (mPFC), a key part of the brain networks that are closely related to the regulation of behavior, acts as a key regulator in emotion, social cognition, and decision making. Astrocytes are the majority cell type of glial cells, which play a significant role in a number of processes and establish a suitable environment for the functioning of neurons, including the brain energy metabolism. Astrocyte’s dysfunction in the mPFC has been implicated in various neuropsychiatric disorders. Glucose is a major energy source in the brain. In glucose metabolism, part of glucose is used to convert UDP-GlcNAc as a donor molecule for O-GlcNAcylation, which is controlled by a group of enzymes, O-GlcNAc transferase enzyme (OGT), and O-GlcNAcase (OGA). However, the role of O-GlcNAcylation in astrocytes is almost completely unknown. Our research showed that astrocytic OGT could influence the expression of proteins in the mPFC. Most of these altered proteins participate in metabolic processes, transferase activity, and biosynthetic processes. GFAP, an astrocyte maker, was increased after OGT deletion. These results provide a framework for further study on the role of astrocytic OGT/O-GlcNAcylation in the mPFC.

Germline cells are the beginning of new individuals in multicellular animals, including humans. Our understanding of these cell types is limited by the difficulty of analyzing the precious and heterogeneous germline tissue samples. The rapid development of single-cell sequencing technologies provides a chance for comprehensive profiling of the omics dynamics of human germline development. In this review, we discuss progress in analyzing the development of human germline cells, including preimplantation and implantation embryos, fetal germ cells (FGCs), and adult spermatogenesis by single-cell transcriptome and epigenome sequencing technologies.

Implantation is a milestone event during mammalian embryogenesis. Implantation failure is a considerable cause of early pregnancy loss in humans1. Owing to the difficulty of obtaining human embryos early after implantation in vivo, it remains unclear how the gene regulatory network and epigenetic mechanisms control the implantation process. Here, by combining an in vitro culture system for the development human embryos after implantation and single-cell multi-omics sequencing technologies, more than 8,000 individual cells from 65 human peri-implantation embryos were systematically analysed. Unsupervised dimensionality reduction and clustering algorithms of the transcriptome data show stepwise implantation routes for the epiblast, primitive endoderm and trophectoderm lineages, suggesting robust preparation for the proper establishment of a mother-to-offspring connection during implantation. Female embryos showed initiation of random X chromosome inactivation based on analysis of parental allele-specific expression of X-chromosome-linked genes during implantation. Notably, using single-cell triple omics sequencing analysis, the re-methylation of the genome in cells from the primitive endoderm lineage was shown to be much slower than in cells of both epiblast and trophectoderm lineages during the implantation process, which indicates that there are distinct re-establishment features in the DNA methylome of the epiblast and primitive endoderm—even though both lineages are derived from the inner cell mass. Collectively, our work provides insights into the complex molecular mechanisms that regulate the implantation of human embryos, and helps to advance future efforts to understanding early embryonic development and reproductive medicine. Transcriptomics and DNA methylomics are used to study the implantation process of human embryos at single-cell resolution.

This study aimed to determine the cold hardiness of Phauda flammans (Lepidoptera: Zygaenidae) larvae. Supercooling points of the 1st–6th instar larvae of P. flammans ranged from –7.7 to –13.0 °C. The lethal temperatures were –8 °C for 1st, –5 °C for 2nd, and –7 °C for 3rd–6th instars. Lethal times at the instar-specific lethal temperatures were 12 h for 1st, 14 h for 2nd, 15 h for 3rd, 17 h for 4th, and 18 h for 5th–6th instars. The times required for all larvae to die in an incubator at 5 °C were 30 d for 1st, 3rd, 4th, and 5th instars, and 25 d for 2nd and 6th instars. The findings suggest that P. flammans is a chill-intolerant species, and larvae will die if the air temperature decreases to –5 to –8 °C for 12–18 h or to 5 °C for 25–30 d. Such conditions are, however, unlikely to occur in southern China.

Background Data focusing on the synergistic effect of programmed cell death 1 (PD-1) inhibitors and brain radiotherapy for brain metastases (BMs) in lung cancer is scarce. Methods A total of 60 lung cancer patients receiving PD-1 inhibitors with or without brain radiotherapy were identified in this retrospective study. The primary endpoints were intracranial progression-free survival (iPFS), extracranial progression-free survival (PFS), and overall survival (OS) among three groups. Results Twenty-one patients received PD-1 inhibitors and concurrent brain radiotherapy, 20 patients were treated with PD-1 inhibitors and non-concurrent brain radiotherapy, and the other 19 patients were treated with PD-1 inhibitors alone. Patients in the concurrent group achieved a higher intracranial objective response rate (iORR, 61.1% vs. 29.4% vs. 25.0%) and a higher intracranial disease control rate (iDCR, 83.3% vs. 58.8% vs. 56.3%) compared with those in the non-concurrent group and PD-1 inhibitors alone group. The median iPFS was significantly longer in the concurrent group than the non-concurrent group and the PD-1 inhibitors alone group (9.8, 5.7, and 4.8 months, P=0.039, respectively). The median PFS were 9.2, 5.7 and 4.6 months (P=0.347) in the concurrent group, non-concurrent group and PD-1 inhibitors alone group. And the median OS were not reached, 12.1 and 6.9 months (P=0.206), respectively. Multivariate analysis revealed that the lack of concurrent brain radiotherapy was independently associated with a shorter iPFS. Conclusions PD-1 inhibitors with concurrent brain radiotherapy achieved a higher iORR, iDCR, and iPFS in lung cancer patients with treated or newly diagnosed BMs.

The discovery of embryonic cell-free DNA (cfDNA) in spent embryo culture media (SECM) has brought hope for noninvasive preimplantation genetic testing. However, the cellular origins of SECM cfDNA are not sufficiently understood, and methods for determining maternal DNA contamination are limited. Here, we performed whole-genome DNA methylation sequencing for SECM cfDNA. Our results demonstrated that SECM cfDNA was derived from blastocysts, cumulus cells, and polar bodies. We identified the cumulus-specific differentially methylated regions (DMRs) and oocyte/polar body-specific DMRs, and established an algorithm for deducing the cumulus, polar body, and net maternal DNA contamination ratios in SECM. We showed that DNA methylation sequencing accurately detected chromosome aneuploidy in SECM and distinguished SECM samples with low and high false negative rates and gender discordance rates, after integrating the origin analysis. Our work provides insights into the characterization of embryonic DNA in SECM and provides a perspective for noninvasive preimplantation genetic testing in reproductive medicine.

Gonadal somatic cells are the main players in gonad development and are important for sex determination and germ cell development. Here, using a time-series scRNA-seq strategy, we analyzed the fetal germ cells (FGCs) and gonadal somatic cells in human embryos and fetuses. Clustering analysis of testes and ovaries revealed several novel cell subsets, including POU5F1+SPARC+ FGCs and KRT19+ somatic cells. Furthermore, our data indicated that DLK1+ cells may be the progenitors of steroidogenic cell lineages in both sexes and that TAC1+ cells may be the progenitors of granulosa cells in females. Intriguingly, the testosterone synthesis function transitioned from fetal Sertoli cells to adult Leydig cells in a step-wise manner. Moreover, interactions between gonadal somatic cells were systematically explored and verified in our study. In detail, we observed that Sertoli cells interacted with Leydig cells through DHH-PTCH1 and PDGFA-PDGFRA/PDGFRB ligand-receptor gene pairs. More importantly, we identified cell type-specific developmental defects of both FGCs and gonadal somatic cells in a Turner syndrome embryo (45, XO). Our work provides a blueprint of the complex yet highly ordered development and interactions of human FGCs and gonadal microenvironment cells.

A single-cell survey of developing human CC was performed with comprehensive temporal and spatial information., Neurogenesis processes differ in different areas of the cortex in many species, including humans. Here, we performed single-cell transcriptome profiling of the four cortical lobes and pons during human embryonic and fetal development. We identified distinct subtypes of neural progenitor cells (NPCs) and their molecular signatures, including a group of previously unidentified transient NPCs. We specified the neurogenesis path and molecular regulations of the human deep-layer, upper-layer, and mature neurons. Neurons showed clear spatial and temporal distinctions, while glial cells of different origins showed development patterns similar to those of mice, and we captured the developmental trajectory of oligodendrocyte lineage cells until the human mid-fetal stage. Additionally, we verified region-specific characteristics of neurons in the cortex, including their distinct electrophysiological features. With systematic single-cell analysis, we decoded human neuronal development in temporal and spatial dimensions from GW7 to GW28, offering deeper insights into the molecular regulations underlying human neurogenesis and cortical development.

Ten coumarin-3-formamido derivatives, N-benzyl-coumarin-3-carboxamide (2), N-fluorobenzyl-coumarin-3-carboxamide (3-5), N-methoxybenzyl-coumarin-3-carboxamide (6-8), N-((1-methyl-1H-imidazol-5-yl)methyl)-coumarin-3-carboxamide (9), N-(thiophen-2-ylmethyl)-coumarin-3-carboxamide (10), and N-(furan-2-ylmethyl)-coumarin-3-carboxamide (11), were synthesized and characterized. Compound 5 crystallizes in a monoclinic system P21 /c space group with four chemical formulas in a unit cell; molecules of compound 5 are self-assembled into a two-dimensional supramolecular structure by intermolecular hydrogen bonds and C⋯C π stacking. The potential anticancer effects of these compounds on HeLa (cervical carcinoma), MCF-7 (breast), A549 (lung), HepG2 (liver), and human umbilical vein (HUVEC) cells were examined. Compared with compounds 1-8 and 10-11, compound 9 exhibits potent in vitro cytotoxicity against HeLa cells and lower cytotoxicity against normal cells. Therefore, further in-depth investigations of compound 9 were performed. Absorption titration experiments and fluorescence spectroscopy studies suggested that compound 9 binds to DNA through the intercalation mode.

Rapid and accurate diagnosis of multidrug-resistant tuberculosis (MDR-TB) is important for timely and appropriate therapy. In this study, a rapid and easy-to-perform molecular test that integrated polymerase chain reaction (PCR) amplification and a specific 96-well microplate hybridization assay, called PCR-ELISA (enzyme-linked immunosorbent assay), were developed for detection of mutations in rpoB, katG, and inhA genes responsible for rifampin (RIF) and isoniazid (INH) resistance and prediction of drug susceptibility in Mycobacterium tuberculosis clinical isolates. We evaluated the utility of this method by using 32 multidrug-resistent (MDR) isolates and 22 susceptible isolates; subsequently, we compared the results with data obtained by conventional drug susceptibility testing and DNA sequencing. The sensitivity and specificity of the PCR-ELISA test were 93.7% and 100% for detecting RIF resistance, and 87.5% and 100% for detecting INH resistance, respectively. These results were comparable to those yielded by commercially available molecular tests such as the GenoType MTBDRplus assay. Based on the aforementioned results, we conclude that the PCR-ELISA microplate hybridization assay is a rapid, inexpensive, convenient, and reliable test that will be useful for rapid diagnosis of MDR-TB, for improved clinical care.

EGFR-TKIs are confronted with big challenge of everlasting activated EGFR mutations which lack effective binding sites; this barrier is the dark side that largely limits the outcome of NSCLC patients in the clinic. Combination strategies show impressive anti-tumor efficacy that compared with EGFR-TKI mono-treatment, especially targeting both stem cells and non-stem cells. SHP2 (Src homology 2-containing phosphotyrosine phosphatase 2) plays an important role in regulating various malignant biology through hyper-activating intracellular pathways due to either overexpression or catalytical mutation. Some pathways, in which SHP2 was involved, were overlapped with EGFR downstream, and others were not subject to EGFR. Interestingly, SHP2 suppression was reported to destroy the stemness of cancer. Therefore, we hypothesize that SHP2 inhibitor might be a promising drug that could synergistically enhance or sensitize the anti-tumor efficacy of EGFR-TKIs in EGFR mutated NSCLC patients. Here, we summarized the mechanisms of SHP2 in regulating EGFR mutated NSCLC patients, and attempted to reveal the potential synergistic file://localhost/C/:Program%20Files%20(x86):Youdao:Dict:7.5.2.0:resultui:dict:%3Fkeyword=effects of SHP2 inhibitor combined with EGFR-TKIs.

To what extent stromal cells in the tumor microenvironment (TME) are transformed by colorectal cancer (CRC) cells is unexplored. To dissect alterations in these non-malignant cells, we performed single-cell multiomics sequencing of 21 patients with microsatellite-stable CRCs and 6 cancer-free, elderly individuals. Surprisingly, somatic copy number alterations (SCNAs) are prevalent in immune cells, fibroblasts, and endothelial cells in both the TME and the normal tissues of each individual. Moreover, the proportions of fibroblasts with SCNAs in tumors (11.1%-47.7%) are much higher than those in adjacent normal tissues (1.1%-10.6%), with gain of chromosome 7 strongly enriched in the TME, clearly indicating clonal expansion. Furthermore, five genes (BGN, RCN3, TAGLN, MYL9, and TPM2) are identified as fibroblast-specific biomarkers of poorer prognosis of CRC. Our study provides evidence and functional relevance of pervasive genomic alterations in the stromal cells of TME in CRC.

Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multiomics sequencing together with multiregional sampling of the primary tumor and lymphatic and distant metastases, we developed insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sublineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 patients whose DNA we sequenced. The cancer cells’ DNA demethylation degrees clearly correlated with the densities of the heterochromatin-associated histone modification H3K9me3 of normal tissue and those of repetitive element long interspersed nuclear element 1. Our work demonstrates the feasibility of reconstructing genetic lineages and tracing their epigenomic and transcriptomic dynamics with single-cell multiomics sequencing.

DNA methylation, chromatin states and their interrelationships represent critical epigenetic information, but these are largely unknown in human early embryos. Here, we apply single-cell chromatin overall omic-scale landscape sequencing (scCOOL-seq) to generate a genome-wide map of DNA methylation and chromatin accessibility at single-cell resolution during human preimplantation development. Unlike in mice, the chromatin of the paternal genome is already more open than that of the maternal genome at the mid-zygote stage in humans, and this state is maintained until the 4-cell stage. After fertilization, genes with high variations in DNA methylation, and those with high variations in chromatin accessibility, tend to be two different sets. Furthermore, 1,797 out of 5,155 (35%) widely open chromatin regions in promoters closed when transcription activity was inhibited, indicating a feedback mechanism between transcription and open chromatin maintenance. Our work paves the way for dissecting the complex, yet highly coordinated, epigenetic reprogramming during human preimplantation development.

Background Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic, and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed. Conclusions We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis. Electronic supplementary material The online version of this article (10.1186/s13059-018-1416-2) contains supplementary material, which is available to authorized users.

To seek more efficient and lower toxicity anticancer compounds, several imidazole combining dehydroabietylamine derivatives including organic salts (L(1)–L(2)) and amides (L(3)–L(5)) were synthesized. Their antineoplastic activity against HeLa (cervix), MCF-7 (breast), A549 (lung) and HepG2 (liver) cells and HUVECs (umbilical vein, normal cells) in vitro were evaluated by MTT assay. The results unequivocally showed that nearly all compounds had better antineoplastic activity and lower toxicity than dehydroabietylamine (L(0)). For MCF-7 cells, L(2) (0.75 μM) and L(5) (2.17 μM) had higher anti-MCF-7 activity than L(0) and DOX. For A549 cells, L(1) (1.85 μM) and L(2) (4.37 μM) had higher anti-A549 activity than L(0); in particular, the IC(50) value of L(1) was much lower than that of DOX. Among these investigated compounds, L(2) and L(5) had lower IC(50) values (0.75 μM and 2.17 μM) against MCF-7 cells and lower toxicity, which suggested that they may be potential future anticancer drugs. In addition, L(1) and L(2) could suppress cancer cell proliferation by inducing apoptosis. L(1)–L(5) could bind with DNA through intercalation.

DNA methylation is a crucial layer of epigenetic regulation during mammalian embryonic development 1–3 . Although the DNA methylome of early human embryos has been analyzed 4–6 , some of the key features have not been addressed thus far. Here we performed single-cell DNA methylome sequencing for human preimplantation embryos and found that tens of thousands of genomic loci exhibited de novo DNA methylation. This finding indicates that genome-wide DNA methylation reprogramming during preimplantation development is a dynamic balance between strong global demethylation and drastic focused remethylation. Furthermore, demethylation of the paternal genome is much faster and thorough than that of the maternal genome. From the two-cell to the postimplantation stage, methylation of the paternal genome is consistently lower than that of the maternal genome. We also show that the genetic lineage of early blastomeres can be traced by DNA methylation analysis. Our work paves the way for deciphering the secrets of DNA methylation reprogramming in early human embryos.

The inflammatory response of sepsis induced by lipopolysaccharide (LPS) may result in irreversible cardiac dysfunction. Glutamine (GLN) has a multitude of pharmacological effects, including anti-inflammatory abilities. Previous studies have reported that GLN attenuated LPS-induced acute lung injury and intestinal mucosal injury. The present study investigated whether GLN exerts potential protective effects on LPS-induced cardiac dysfunction. Male Sprague-Dawley rats were divided into three groups (15 rats per group), including the control (saline-treated), LPS and LPS+GLN groups. Pretreatment with 1 g/kg GLN was provided via gavage for 5 days in the LPS+GLN group, while the control and LPS groups received the same volume of normal saline. On day 6, a cardiac dysfunction model was induced by administration of LPS (10 mg/kg). After 24 h, the cardiac functions of the rats that survived were detected by echocardiography and catheter-based measurements. The serum levels of tumor necrosis factor α (TNF-α), interleukin (IL)-1β and IL-6 were detected by enzyme-linked immunosorbent assay, while the mRNA levels of toll-like receptor (TLR)4, TNF-α, IL-1β and IL-6 were examined by reverse transcription-quantitative polymerase chain reaction. The protein expression of TLR4, mitogen-activated protein kinase (MAPK) and nuclear factor-κB (NF-κB) were also determined by western blot analysis. The results of echocardiography and catheter-based measurements revealed that GLN treatment attenuated cardiac dysfunction. GLN treatment also attenuated the serum and mRNA levels of the pro-inflammatory cytokines. In addition, the protein levels of TLR4, phosphorylated (p-)extracellular signal-regulated kinase, p-c-Jun N-terminal kinase and p-P38 were reduced upon GLN pretreatment. Furthermore, GLN pretreatment resulted in decreased activation of the NF-κB signaling pathway. In conclusion, GLN has a potential therapeutic effect in the protection against cardiac dysfunction mediated by sepsis through regulating the TLR4/MAPK/NF-κB signaling pathway.

A new hexanedioic acid analogue, (2S,5R)-2-ethyl-5-methylhexanedioic acid (1), along with two known compounds, thymine (2) and cerevisterol (3), were isolated from Penicillium sp. OC-4, an endophytic fungus associated with Orchidantha chinensis, which has been used in folk medicine for the treatment of fever and cough. The structure of compound 1 was unequivocally elucidated on the basis of one- and two-dimensional NMR spectroscopic (1H NMR, 13C NMR, COSY, HSQC, HMBC), HR-ESI-MS, optical rotation data, and IR spectrum. The antibacterial and antioxidant activities of compound 1 were investigated. The compound displayed strong antioxidant activity with EC50 value of 1.08 mg/mL on superoxide anion racdicals.

The circadian clock refers to the inherent biological rhythm of an organism, which, is accurately regulated by numerous clock genes. Studies in recent years have reported that the abnormal expression of clock genes is ubiquitous in common abdominal malignant tumors, including liver, colorectal, gastric and pancreatic cancer. In addition, the abnormal expression of certain clock genes is closely associated with clinical tumor parameters or patient prognosis. Studies in clock genes may expand the knowledge about the mechanism of occurrence and development of tumors, and may provide a new approach for tumor therapy. The present study summarizes the research progress in this field.

Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos. We found that within < 12 h of fertilization, each individual cell undergoes global genome demethylation together with the rapid and global reprogramming of both maternal and paternal genomes to a highly opened chromatin state. This was followed by decreased openness after the late zygote stage. Furthermore, from the late zygote to the 4-cell stage, the residual DNA methylation is preferentially preserved on intergenic regions of the paternal alleles and intragenic regions of maternal alleles in each individual blastomere. However, chromatin accessibility is similar between paternal and maternal alleles in each individual cell from the late zygote to the blastocyst stage. The binding motifs of several pluripotency regulators are enriched at distal nucleosome depleted regions from as early as the 2-cell stage. This indicates that the cis-regulatory elements of such target genes have been primed to an open state from the 2-cell stage onward, long before pluripotency is eventually established in the ICM of the blastocyst. Genes may be classified into homogeneously open, homogeneously closed and divergent states based on the chromatin accessibility of their promoter regions among individual cells. This can be traced to step-wise transitions during preimplantation development. Our study offers the first single-cell and parental allele-specific analysis of the genome-scale chromatin state and DNA methylation dynamics at single-base resolution in early mouse embryos and provides new insights into the heterogeneous yet highly ordered features of epigenomic reprogramming during this process.

Objective : This study aimed to determine if gastric cardia adenocarcinoma (GCA) risk was associated with the lys (A or *2) allele at the rs671 (glu504lys) polymorphism within the aldehyde dehydrogenase 2 (ALDH2) gene in a Chinese Han population. We also aimed to investigate ALDH2 genotypic distributions between subjects from high- and low-incidence areas for both GCA and esophageal squamous cell carcinoma (ESCC).Methods : We designed a case-control study including 2,686 patients with GCA and 3,675 control subjects from high- and low-incidence areas for both GCA and ESCC in China. TaqMan allele discrimination assay was used to genotype the rs671 polymorphism. χ2 test and binary logistic regression analysis were used to estimate the odds ratios for the development of GCA, and multivariate ordinal logistic regression was used to analyze ALDH2 genotypic distributions among different groups.Results : Compared with ALDH2*1/*1 homozygotes, ALDH2*1/*2 and ALDH2*2/*2 carriers did not increase the risk for GCA in the Chinese Han population (P>0.05). Interestingly, the ratio of homozygous or heterozygous ALDH2 *2 carriers in high-incidence areas for both GCA and ESCC was lower than that in low-incidence areas (PConclusions : Genotypes of rs671 at ALDH2 may not increase GCA susceptibility in Chinese Han populations. In addition, the ALDH2 genotypic distribution differs between Chinese Han populations from high- and low-incidence areas for both GCA and ESCC. Our findings may shed light on the possible genetic mechanism for the dramatic geographic differences of GCA occurrence in China.

We described a novel single-cell RNA-seq technique called MR-seq (measure a single-cell transcriptome repeatedly), which permits statistically assessing the technical variation and identifying the differentially expressed genes between just two single cells by measuring each single cell twice. We demonstrated that MR-seq gave sensitivity and reproducibility similar to the standard single-cell RNA-seq and increased the positive predicate value. Application of MR-seq to early mouse embryos identified hundreds of candidate intra-embryonic heterogeneous genes among mouse 2-, 4- and 8-cell stage embryos. MR-seq should be useful for detecting differentially expressed genes among a small number of cells.

Background From December 2019 to February 2020, 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a serious outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. Related clinical features are needed. Methods We reviewed 69 patients who were hospitalized in Union hospital in Wuhan between 16 January and 29 January 2020. All patients were confirmed to be infected with SARS-CoV-2, and the final date of follow-up was 4 February 2020. Results The median age of 69 enrolled patients was 42.0 years (interquartile range 35.0–62.0), and 32 patients (46%) were men. The most common symptoms were fever (60 [87%]), cough (38 [55%]), and fatigue (29 [42%]). Most patients received antiviral therapy (66 [98.5%] of 67 patients) and antibiotic therapy (66 [98.5%] of 67 patients). As of 4 February 2020, 18 (26.9%) of 67 patients had been discharged, and 5 patients had died, with a mortality rate of 7.5%. According to the lowest SpO2 during admission, cases were divided into the SpO2 ≥ 90% group (n = 55) and the SpO2 < 90% group (n = 14). All 5 deaths occurred in the SpO2 < 90% group. Compared with SpO2 ≥ 90% group, patients of the SpO2 < 90% group were older and showed more comorbidities and higher plasma levels of interleukin (IL) 6, IL10, lactate dehydrogenase, and C reactive protein. Arbidol treatment showed tendency to improve the discharging rate and decrease the mortality rate. Conclusions COVID-19 appears to show frequent fever, dry cough, and increase of inflammatory cytokines, and induced a mortality rate of 7.5%. Older patients or those with underlying comorbidities are at higher risk of death.

Epigenetic dynamics, such as DNA methylation and chromatin accessibility, have been extensively explored in human preimplantation embryos. However, the active demethylation process during this crucial period remains largely unexplored. In this study, we use single-cell chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to quantify the DNA 5-formylcytosine (5fC) levels of human preimplantation embryos. We find that 5-formylcytosine phosphate guanine (5fCpG) exhibits genomic element-specific distribution features and is enriched in L1 and endogenous retrovirus-K (ERVK), the subfamilies of repeat elements long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs), respectively. Unlike in mice, paired pronuclei in the same zygote present variable difference of 5fCpG levels, although the male pronuclei experience stronger global demethylation. The nucleosome-occupied regions show a higher 5fCpG level compared with nucleosome-depleted ones, suggesting the role of 5fC in organizing nucleosome position. Collectively, our work offers a valuable resource for ten-eleven translocation protein family (TET)-dependent active demethylation-related study during human early embryonic development., The use of CLEVER-seq to delineate the 5-formylcytosine landscape of human early embryos at single-cell resolution enhances our understanding of TET-dependent active demethylation processes during human preimplantation embryo development.

Cardiac arrest (CA) yields poor neurological outcomes. Salubrinal (Sal), an endoplasmic reticulum (ER) stress inhibitor, has been shown to have neuroprotective effects in both in vivo and in vitro brain injury models. This study investigated the neuroprotective mechanisms of Sal in postresuscitation brain damage in a rodent model of CA. In the present study, rats were subjected to 6 min of CA and then successfully resuscitated. Either Sal (1 mg/kg) or vehicle (DMSO) was injected blindly 30 min before the induction of CA. Neurological status was assessed 24 h after CA, and the cortex was collected for analysis. As a result, we observed that, compared with the vehicle-treated animals, the rats pretreated with Sal exhibited markedly improved neurological performance and cortical mitochondrial morphology 24 h after CA. Moreover, Sal pretreatment was associated with the following: (1) upregulation of superoxide dismutase activity and a reduction in maleic dialdehyde content; (2) preserved mitochondrial membrane potential; (3) amelioration of the abnormal distribution of cytochrome C; and (4) an increased Bcl-2/Bax ratio, decreased cleaved caspase 3 upregulation, and enhanced HIF-1α expression. Our findings suggested that Sal treatment improved neurological dysfunction 24 h after CPR (cardiopulmonary resuscitation), possibly through mitochondrial preservation and stabilizing the structure of HIF-1α.

Diachasmimoorpha longicaudata (Ashmead, D. longicaudata) (Hymenoptera: Braconidae) is a solitary species of parasitoid wasp and widely used in integrated pest management (IPM) programs as a biological control agent in order to suppress tephritid fruit flies of economic importance. Although many studies have investigated the behaviors in the detection of their hosts, little is known of the molecular information of their chemosensory system. We assembled the first transcriptome of D. longgicaudata using transcriptome sequencing and identified 162,621 unigenes for the Ashmead insects in response to fruit flies fed with different fruits (guava, mango, and carambola). We annotated these transcripts on both the gene and protein levels by aligning them to databases (e.g., NR, NT, KEGG, GO, PFAM, UniProt/SwissProt) and prediction software (e.g., SignalP, RNAMMER, TMHMM Sever). CPC2 and MIREAP were used to predict the potential noncoding RNAs and microRNAs, respectively. Based on these annotations, we found 43, 69, 60, 689, 26 and 14 transcripts encoding odorant-binding protein (OBP), chemosensory proteins (CSPs), gustatory receptor (GR), odorant receptor (OR), odorant ionotropic receptor (IR), and sensory neuron membrane protein (SNMP), respectively. Sequence analysis identified the conserved six Cys in OBP sequences and phylogenetic analysis further supported the identification of OBPs and CSPs. Furthermore, 9 OBPs, 13 CSPs, 3 GRs, 4IRs, 25 ORs, and 4 SNMPs were differentially expressed in the insects in response to fruit flies with different scents. These results support that the olfactory genes of the parasitoid wasps were specifically expressed in response to their hosts with different scents. Our findings improve our understanding of the behaviors of insects in the detection of their hosts on the molecular level. More importantly, it provides a valuable resource for D. longicaudata research and will benefit the IPM programs and other researchers in this filed.

Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development, including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.

ObjectiveFamilial adenomatous polyposis (FAP) is characterised by the development of hundreds to thousands of adenomas at different evolutionary stages in the colon and rectum that will inevitably progress to adenocarcinomas if left untreated. Here, we investigated the genetic alterations and transcriptomic transitions from precancerous adenoma to carcinoma.DesignWhole-exome sequencing, whole-genome sequencing and single-cell RNA sequencing were performed on matched adjacent normal tissues, multiregionally sampled adenomas at different stages and carcinomas from six patients with FAP and one patient with MUTYH-associated polyposis (n=56 exomes, n=56 genomes and n=8,757 single cells). Genomic alterations (including copy number alterations and somatic mutations), clonal architectures and transcriptome dynamics during adenocarcinoma carcinogenesis were comprehensively investigated.ResultsGenomic evolutionary analysis showed that adjacent lesions from the same patient with FAP can originate from the same cancer-primed cell. In addition, the tricarboxylic acid cycle pathway was strongly repressed in adenomas and was then slightly alleviated in carcinomas. Cells from the ‘normal’ colon epithelium of patients with FAP already showed metabolic reprogramming compared with cells from the normal colon epithelium of patients with sporadic colorectal cancer.ConclusionsThe process described in the previously reported field cancerisation model also occurs in patients with FAP and can contribute to the formation of adjacent lesions in patients with FAP. Reprogramming of carbohydrate metabolism has already occurred at the precancerous adenoma stage. Our study provides an accurate picture of the genomic and transcriptomic landscapes during the initiation and progression of carcinogenesis, especially during the transition from adenoma to carcinoma.

Background Comprehensive analysis of the tissue of origin of plasma cell-free DNA (cfDNA) remains insufficient. A genome-scale DNA methylation method for this analysis is of both biological and clinical interest. Methods We used the methylated CpG tandem amplification and sequencing (MCTA-Seq), which is a genome-scale DNA methylation method, for analyzing cfDNA. We performed MCTA-Seq to pair plasma cfDNA and white blood cell genomic DNA from 14 healthy individuals for comparative analysis, with eight tissues being analyzed for identifying tissue-specific markers. The relative contributions of multiple tissues to cfDNA were calculated for plasma cfDNA obtained from healthy adults (n = 25), cholelithiasis patients (n = 13), liver cirrhosis patients (n = 17), hepatocellular carcinoma patients (n = 30), and acute pancreatitis patients (n = 8). Results We identified a total of 146 tissue-specific hypermethylation markers. Simulation analysis showed that MCTA-Seq can accurately measure DNA fractions contributed by multiple tissues to cfDNA. We demonstrated that the liver is the major non-hematopoietic tissue contributing to plasma cfDNA in healthy adults. The method also detected increases in the liver-derived DNA in the blood from patients with liver diseases, which correlate with an increase in the liver enzyme level. Furthermore, the results indicated that blood cells make a major contribution to the elevation of cfDNA levels in acute pancreatitis, liver cirrhosis, and hepatocellular carcinoma patients. Finally, we characterized a novel set of tissue-specific hypermethylation markers for cfDNA detection, which are located within the intragenic regions of tissue-specific highly expressed genes. Conclusions We have used MCTA-Seq for simultaneously measuring cfDNA fractions contributed by multiple tissues. Applying this approach to healthy adults and liver and pancreas disease patients revealed the tissue of origin of cfDNA. The approach and the identified markers should facilitate assessing the cfDNA dynamics in a variety of human diseases. Electronic supplementary material The online version of this article (10.1186/s13148-019-0689-y) contains supplementary material, which is available to authorized users.

e16037 Background: Apatinib, a highly selective VEGFR2 inhibitor, has shown a clinical benefit as third-line or further-line treatment in patients with gastric cancer in a randomized phase III study with the initial dose of 850mg. However, the study was conducted in a small scale (n = 267) under standardized conditions. Here, we assessed exposure and effectiveness of apatinib at different doses using data collected from a post-marketing phase IV study that included a broader patient population with a larger sample size. Methods: Patients with advanced or metastatic advanced gastric cancer or gastroesophageal junction adenocarcinoma who were aged 18-75 with ECOG performance status of 0-2 and failed at least two lines of chemotherapy were enrolled. Apatinib was recommended with an initial dose of 850 mg q.d orally, while the initial dose was determined at the discretion of the investigators. Administration of apatinib regarding the initial dose, duration of treatment, dose modification, average daily exposure dose (ADED) and its effect on progression-free survival (PFS) and overall survival (OS) were analyzed. Results: A total of 2004 patients were included in the intention-to-treat population. The median age was 59 (range, 19-85) years, 71.8% of patients were male, 84.2% had ECOG performance status of 0-1; 96.4% had stage IV disease, and 98.8% had metastases, among which 34.2% with more than 2 metastases. Five patients did not receive therapy. Compared to 5.5% of patients with the initial dose > 500mg, 94.1% was given at the initial dose≤500mg; 8.6% had ADED > 500mg and 91.1% had ADED ≤500mg. The median duration of treatment was 56 days. Treatment interruption and discontinuation, and dose reduction occurred in 34.4%, 24.5%, and 13.7% of patients due to adverse events, respectively. Survival analyses in the initial dose ≤500mg/ > 500mg subgroups showed median PFS of 2.6 months (95%CI 2.20-2.79) vs 2.7 months (95% CI 1.91-3.32), median OS of 5.6 months (95% CI 5.26-5.95) vs 5.9 months (95% CI 4.40-6.87). In the ADED ≤500mg/ > 500mg subgroups, the median PFS was 2.6 months (95% CI 2.14-2.76) vs 3.0 months (95% CI 2.27-3.61), and median OS was 5.7 months (95% CI 5.32-6.08) vs 6.1 months (95% CI 5.36-7.72). Conclusions: In conclusion, more than 90% of the patients received a lower dose regimen, which indicate dosage of 500mg or lower is a tolerated exposure. Furthermore, dose at 500mg or lower produced similar efficacy to that more than 500mg. Clinical trial information: NCT02426034.

DNA methylation, chromatin accessibility, and gene expression represent different levels information in biological process, but a comprehensive multiomics analysis of the mammalian heart is lacking. Here, we applied nucleosome occupancy and methylome sequencing, which detected DNA methylation and chromatin accessibility simultaneously, as well as RNA-seq, for multiomics analysis of the 4 chambers of adult and fetal human hearts, and adult mouse hearts. Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. Novel long noncoding RNAs were identified in the human heart, and the gene expression profiles of major cardiovascular diseases associated genes were displayed. Furthermore, cross-species comparisons revealed human-specific and mouse-specific differentially expressed genes between the atria and ventricles. We also reported the relationship among multiomics and found there was a bell-shaped relationship between gene-body methylation and expression in the human heart. In general, our study provided comprehensive spatiotemporal and evolutionary insights into the regulation of gene expression in the heart., Multi-omic analyses of the four chambers of the human and mouse heart, including transcriptome, DNA methylation and chromatin accessibility, reveals characteristic patterns of gene regulation at the level of heart regions.

We previously tested HER2-targeted antibody drug conjugates (ADC) in immunocompromised (SCID) mice, precluding evaluation of host immunity, impact on cancer stem cells (CSCs), and potential benefit when combined with PD-L1 blockade. In this study, we tested HER2-targeted ADC in two immunocompetent mouse tumor models. HER2-targeted ADC specifically inhibited the growth of HER2-expressing tumors, prolonged animal survival, and reduced HER2(+) and PD-L1(+) cells. ADC plus anti-PD-L1 antibody augmented therapeutic efficacy, modulated immune gene signatures, increased the number and function of CD3(+) and CD19(+) tumor-infiltrating lymphocytes (TILs), induced tumor antigen specific immunological memory, stimulated B cell activation, differentiation, and IgG1 production both systemically and in the tumor microenvironment. In addition, ADC therapy modulated T cell subsets and their activation in TILs. Furthermore, HER2-targeted ADC reduced the number and tumorigenicity of ALDH(hi) CSCs. This study demonstrates that HER2-targeted ADC effectively targets ALDH(hi) CSCs and this effect is augmented by co-administration of anti-PD-L1 antibody.

The heterogeneity and molecular characteristics of progenitor cells, especially glial progenitors, in the developing human cerebral cortex remain elusive. Here, we find that EGFR expression begins to sharply increase after gestational week (GW) 20, which corresponds to the beginning stages of human gliogenesis. In addition, EGFR+ cells are mainly distributed in the germinal zone and frequently colocalize with the stemness marker SOX2 during this period. Then, by performing single-cell RNA sequencing on these EGFR+ cells, we successfully enriched and characterized various glial- and neuronal-lineage progenitor cells and validated their phenotypes in fixed slices. Notably, we identified two subgroups with molecular characteristics similar to those of astrocytes, and the immunostaining results show that these cells are mainly distributed in the outer subventricular zone and might originate from the outer radial glial cells. In short, the EGFR-sorting strategy and molecular signatures in the diverse lineages provide insights into human glial development.

In normal physiological and healthy conditions, red blood cells (RBCs) deform readily as they pass through the microcapillaries and the spleen, however, upon invasion by the malaria parasite, the host RBC membrane begins to lose their deformability. In spite of the progress in understanding malaria pathogenesis, the primary mechanism responsible for the loss of deformability remains unclear. In this paper, we examine the effects of Plasmodium falciparum infection and maturation on the deformability of parasitized or infected red blood cells (iRBCs) by means of a three-dimensional (3D) multiscale red blood cell (RBC) framework. This multiscale framework is developed based on the Cauchy–Born rule and the meshfree IMLS-Ritz method. The atomistic scale strain energy density function of the RBC membrane was computed using a selected representative cell based on the membrane spectrin network. The results obtained from our numerical simulations affirm that the presence of malaria infection significantly increases the rigidity of RBC membrane. It was observed that in the trophozoite and schizont infection stages, biconcave cell geometry leads to better prediction than nearly spherical geometry in comparison with experimental studies. Furthermore, we confirm that increase in temperature also results to increased stiffening of the cell membrane. Lastly, the observed decrease in the deformability of iRBC membrane may be primarily due to the structural remodeling and changes in the microstructure of the membrane rather than the change in cell shape.

Mirabilis jalapa L is the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa L is limited. Using fluorescent differential display (FDD) screening, we report the identification of a novel Ty1-copia -like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66 based on its sequence homology to the GAG protein from Ty1-copia retrotransposon. Using degenerate primers based on the DNA sequence of REC66 , a total of fourteen different variants in reverse transcriptase (RT) sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copia retrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copia retrotransposons and plant genome evolution in the genus Mirabilis or family Nyctaginaceae. https://doi.org/10.2298/ABS160326103J Received: March 26, 2016; Revised: May 30, 2016; Accepted: July 11, 2016; Published online: November 4, 2016 How to cite this article: Shunri J, JoshuaLG, Haiyan F, Dan L, ShesterB, Liang Y, Wen L, Suzhi Z, Yi Y, Peng L. Identification and characterization of REC66 , a Ty1-copia- like retrotransposon in the genome of red flower of Mirabilis jalapa L.. Arch Biol Sci. 2017;69(2):315-22.

Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo. Our work offers a comprehensive and high-resolution roadmap for dissecting chromatin state transition dynamics during the epigenomic reprogramming of human and mouse FGCs.

Hypoxia-inducible factor-1 alpha (HIF-1α) plays a vital role in the initiation, evaluation and prognosis in lung cancer. The prognostic value of HIF-1α reported in diverse study remains disputable. Accordingly, a meta-analysis was implemented to further understand the prognostic role of HIF-1α in lung cancer. The relationship between HIF-1α and the clinicopathological characteristics and prognosis of lung cancer were investigated by a meta-analysis. PubMed and Embase were searched from their inception to January 2015 for observational studies. Fixed-effects or random-effects meta-analyses were used to calculate odds ratios and 95% confidence intervals of different comparisons. A total of 20 studies met the criteria. The results showed that HIF-1α expression in lung cancer tissues was significantly higher than that in normal lung tissues. Expression of HIF-1α in patients with squamous cell carcinoma was significantly higher than that of patients with adenocarcinomas. Similarly, non-small cell lung cancer (NSCLC) patients had higher HIF-1α expression than small cell lung cancer (SCLC) patients. Moreover, lymph node metastasized tissues had higher HIF-1α expression than non-lymph node metastasized tissues. A high level HIF-1α expression was well correlated with the expression of vascular endothelial growth factor and epidermal growth factor receptor in the NSCLC. Notably, NSCLC or SCLC patients with positive HIF-1α expression in tumor tissues had lower overall survival rate than patients with negative HIF-1α expression. It was suggested that HIF-1α expression may be a prognostic biomarker and a potential therapeutic target for lung cancer.

Lu Wen,1 Pei Zeng,1 Liping Zhang,1 Wenli Huang,1 Hui Wang,2 Gang Chen1 1Department of Pharmaceutics, School of Pharmacy, 2School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s RepublicofChina Abstract: In this study, silver nanoparticles (AgNPs) were synthesized for the first time using an antibacterial endophytic fungus of Chinese medicinal herb Orchidantha chinensis, which has anti-inflammatory and antimicrobial activities. The AgNPs were analyzed by various characterization techniques to reveal their morphology, chemical composition, and stability. Also, the relationship between Chinese medicinal herbs, endophytic fungi, and the property ofAgNPs was investigated for the first time. Interestingly, an experiment performed in this study revealed the proteins produced by the endophytic fungus to be capped on the nanoparticles, which led to an increase in the stability of spherical and polydispersed AgNPs with low aggregation for over 6months. More importantly, further study demonstrated that the AgNPs possessed superior antibacterial activity and effectively promoted wound healing. Altogether, the biosynthesis of active AgNPs using the endophytic fungus from Chinese medicinal herb based on the symbiosis theory is simple, eco-friendly, and promising. Keywords: silver nanoparticles, Orchidantha chinensis, endophytic fungi, symbiosis theory, wound healing

The development of next generation sequencing (NGS) platform-based single-cell RNA sequencing (scRNA-seq) techniques has tremendously changed biological researches, while there are still many questions that cannot be addressed by them due to their short read lengths. We developed a novel scRNA-seq technology based on third-generation sequencing (TGS) platform (single-cell amplification and sequencing of full-length RNAs by Nanopore platform, SCAN-seq). SCAN-seq exhibited high sensitivity and accuracy comparable to NGS platform-based scRNA-seq methods. Moreover, we captured thousands of unannotated transcripts of diverse types, with high verification rate by reverse transcription PCR (RT-PCR)–coupled Sanger sequencing in mouse embryonic stem cells (mESCs). Then, we used SCAN-seq to analyze the mouse preimplantation embryos. We could clearly distinguish cells at different developmental stages, and a total of 27,250 unannotated transcripts from 9,338 genes were identified, with many of which showed developmental stage-specific expression patterns. Finally, we showed that SCAN-seq exhibited high accuracy on determining allele-specific gene expression patterns within an individual cell. SCAN-seq makes a major breakthrough for single-cell transcriptome analysis field., This study describes a novel single-cell RNA-seq technology called SCAN-seq which can capture the full-length transcripts in single cells based on the third-generation Nanopore sequencing platform, and demonstrates its performance on mouse preimplantation embryos.