A single-cell analysis of the molecular lineage of chordate embryogenesis

Progressive unfolding of gene expression cascades underlies diverse embryonic lineage development. Here, we report a single-cell RNA sequencing analysis of the complete and invariant embryonic cell lineage of the tunicate Ciona savignyi from fertilization to the onset of gastrulation. We reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type embryo and identified eight fate transformations upon fibroblast growth factor (FGF) inhibition. For most FGF-dependent asymmetric cell divisions, the bipotent mother cell displays the gene signature of the default daughter fate. In convergent differentiation of the two notochord lineages, we identified additional gene pathways parallel to the master regulator T/Brachyury. Last, we showed that the defined Ciona cell types can be matched to E6.5-E8.5 stage mouse cell types and display conserved expression of limited number of transcription factors. This study provides a high-resolution single-cell dataset to understand chordate early embryogenesis and cell lineage differentiation

CASK Silence Overcomes Sorafenib Resistance of Hepatocellular Carcinoma Through Activating Apoptosis and Autophagic Cell Death

Hepatocellular carcinoma (HCC) patients usually fail to be treated because of drug resistance, including sorafenib. In this study, the effects of CASK in HCC were investigated using gain- or loss-of-function strategies by performing cell counting kit-8 assay, colony formation assay, flow cytometry, transmission electron microscopy, immunofluorescent confocal laser microscopy, tumor xenograft experiment and immunohistochemistry staining. The current results suggested that CASK expression was positively associated with sorafenib resistance and poor prognosis of HCC. Moreover, inhibition of CASK increased the role of sorafenib partially by promoting apoptosis and autophagy, while CASK overexpression presented the opposite effects. Besides, when treatment with sorafenib, inhibition of apoptosis using the pan-caspase inhibitor Z-VAD-FMK and inhibition of autophagy using autophagy inhibitor 3-Methyladenine (3-MA) or small interfering RNA (siRNA) of LC3B all significantly reversed CASK knockout-induced effects, suggesting that both apoptosis and autophagy were involved in CASK-mediated above functions and autophagy played a pro-death role in this research. Intriguingly, similar results were observed in vivo. In molecular level, CASK knockout activated the c-Jun N-terminal kinase (JNK) pathway, and treatment with JNK inhibitor SP600125 or transiently transfected with siRNA targeting JNK significantly attenuated CASK knockout-mediated autophagic cell death. Collectively, all these results together indicated that CASK might be a promising biomarker and a potential therapeutic target for HCC patients

A Macromolecular Approach to Eradicate Multidrug Resistant Bacterial Infections while Mitigating Drug Resistance Onset

Polymyxins remain the last line treatment for multidrug-resistant (MDR) infections. As polymyxins resistance emerges, there is an urgent need to develop effective antimicrobial agents capable of mitigating MDR. Here, we report biodegradable guanidinium-functionalized polycarbonates with a distinctive mechanism that does not induce drug resistance. Unlike conventional antibiotics, repeated use of the polymers does not lead to drug resistance. Transcriptomic analysis of bacteria further supports development of resistance to antibiotics but not to the macromolecules after 30 treatments. Importantly, high in vivo treatment efficacy of the macromolecules is achieved in MDR A. baumannii-, E. coli-, K. pneumoniae-, methicillin-resistant S. aureus-, cecal ligation and puncture-induced polymicrobial peritonitis, and P. aeruginosa lung infection mouse models while remaining non-toxic (e.g., therapeutic index—ED50/LD50: 1473 for A. baumannii infection). These biodegradable synthetic macromolecules have been demonstrated to have broad spectrum in vivo antimicrobial activity, and have excellent potential as systemic antimicrobials against MDR infections

Modeling Ice-shelf Ocean Interaction at Petermann Glacier, Greenland

Petermann Glacier drains about 4% of the Greenland ice sheet area, with at least 80% of its mass loss through basal melting of the floating ice shelf. Utilizing a high-resolution coupled ice-shelf-ocean model, we aim at understanding the ocean circulation in Nares Strait and the mechanism of oceanic heat supply below the ice shelf as well as quantifying the basal mass loss. The numerical model is based on the Finite-Volume Community Ocean Model (FVCOM), taking advantage of its flexible spatial resolution that can follow the topography. A regional model domain has been set up, which spans the greater Nares Strait region and covers Petermann Fjord with 200-m horizontal resolution and includes the Petermann Glacier geometry. As a first step, we focus on the role of tides for transporting ocean water into the ice-shelf cavity. Tidal simulations are validated with available observations, demonstrating the capability of FVCOM in reproducing the tidal current pattern in Nares Strait. Lagrangian particle trajectories are computed to explore the water exchange in Petermann Fjord. It is found that tidal oscillations in Nares Strait lead to a residual circulation in the fjord and inside the ice-shelf cavity. These results suggest that tidal dynamics plays an important role in modulating regional circulation in Petermann Fjord and heat transport to Petermann Ice Shelf

Immune Infiltration Landscape in Lung Squamous Cell Carcinoma Implications

Intrinsic cancer cells and the tumor-infiltrating immune cells (TIICs) recruited to the immune microenvironment define the malignant phenotype of lung squamous cell carcinoma (LUSC). Understanding more about the immune microenvironment of LUSC enables the selection of high-risk patients who would derive benefit from immunotherapy. Based on large public LUSC cohorts obtained from TCGA and GEO datasets, 22 types of infiltrating immune cell subgroups were evaluated by CIBERSORT. Meta-analysis, principal component analysis (PCA), single-sample gene set enrichment analysis (ssGSEA), and hierarchical clustering analysis were used to evaluate specific immune responses of LUSC. The distribution of TIICs of LUSC was entirely different from normal. TIIC subpopulations were also found to be closely associated with clinical features and molecular subtypes. Unsupervised clustering analysis revealed that three distinct TIIC subgroups existed with different survival patterns. TIICs are extensively implicated in the pathogenesis and development of LUSC. Characterizing the composition of TIICs influences the metabolism, pathological stage, and survival of tumor patients. It is hoped that this immune landscape could provide a more accurate understanding of the development and immunotherapy of LUSC

A nested high-resolution unstructured grid 3-D ocean-sea ice-ice shelf setup for numerical investigations of the Petermann ice shelf and fjord

Three-dimensional numerical simulation of circulation in fjords hosting marine-terminating ice shelves is challenging because of the complexity of processes involved in such environments. This often requires a comprehensive model setup. The following elements are needed: bathymetry (usually unknown beneath the glacier tongue), ice shelf draft (impacting water column thickness), oceanographic state (including tidal elevation, salinity, temperature and velocity of the water masses), sea ice and atmospheric forcing. Moreover, a high spatial resolution is needed, at least locally, which may be augmented with a coarser and computationally cheaper (nested) model that provides sufficiently realistic conditions at the boundaries. Here, we describe procedures to systematically create such a setup that uses the Finite Volume Community Ocean Model (FVCOM) for the Petermann Fjord, Northwest Greenland. The first simulations are validated against temperature and salinity observations from the Petermann Fjord in September 2019. We provide • Complete bathymetry, ice-draft and water column thickness datasets of the Petermann Fjord, with an improved representation of the topography underneath the glacier tongue. • Boundary conditions for ocean, atmosphere and sea ice derived from a suite of high-resolution regional models that can be used to initialize and run the regional ocean model with realistic geophysical settings

A Comparative Study of Intensive Litopenaeus vannamei Culture on Four Bottom Substrates Without Water Change

National Science and Technology Supporting Program of the Twelfth Five-Year Plan of China [2011BAD13B10]; Special Fund for Agro-scientific Research in the Public Interest, China [201103034]The effect of four bottom substrates, oyster shell powder (OP), sugarcane bagasse (SB), a mixture of OP and SB (OS) and fresh soil (FS), on the water quality and bacterial and zooplankton density of intensive shrimp (Litopenaeus vannamei) culture tanks without water change and the growth performance of cultured shrimp were compared in this study. At the end of a 110 days culturing trial, the total ammonium-N (TAN) of the water on SB and the nitrite nitrogen (NO2-N) on OS was significantly lower than that on the other substrates (P<0.05), which coincided with the high density of ammonium-and nitrite-oxidizing bacteria in the water on SB and OS, respectively. The concentration of chlorophyll a (Chl a) increased slowly on OP, SB and OS but remained low on FS. The density of total bacteria on OP, SB and OS was one order of magnitude higher than that on FS, and the density of zooplankton on SB and OS was significantly higher than that on FS or OP (P<0.05). The improved water quality and increased density of bacteria and zooplankton on SB and OS may have had a synergistic effect on shrimp culture, improving its growth performance (high survival rate and yield and low feed conversion rate). SB and OS were more effective for improving the growth performance of intensively cultured L. vannamei without water change than OP and FS. To our knowledge, this study presents the first evidence regarding the effect of different bottom substrates on intensive shrimp culture